Mgy377H1: Microbiology I

Front 1

What is the main difference between a bacteria and a virus?

Back 1

Bacteria: Cellular organisms (single/clusters of cells), living

Viruses: Not cellular, not "living"

Front 2

What are viruses?

Back 2

Essentially nucleic acid (DNA or RNA) wrapped in a protein lipid coat

Do not have a "metabolism"

Require help of cells to replicate their genome and make progeny

Front 3

Do bacteria exhibit social and multi-cellular characteristics?

Back 3

Vast majority do

Front 4

Very briefly, describe a bacteria's metabolism:

Back 4

Bacteria take up chemicals from environment and convert them into biomass or energy

They excrete waste and products

Bacterial cells contain lipids, proteins, sugars and nucleic acids (RNA and DNA)

Front 5

How do bacteria reproduce?

Back 5

Autonomously

Front 6

How do bacteria reproduce autonomously?

Back 6

Bacteria take simple chemicals from the environment to generate more complex ones

These are used to create new cells under the direction of genetic information contained within the pre-existing cells

Front 7

Can bacteria differentiate?

Back 7

Yes they can but they do not always do so

Front 8

What does it mean by "bacteria can differentiate"?

Back 8

Many bacteria can generate new cells that are strikingly different than the parental cells

They don't look the same during different stages of growth

Front 9

How do bacteria communicate and coordinate with one another?

Back 9

By means of chemical signaling

Sensing and adapting to their environment

Front 10

How do bacteria move?

Back 10

Autonomously

Front 11

What does it mean by "bacteria can move autonomously"?

Back 11

Many bacteria possess flagella or other cell structures to help them move

Front 12

How do bacteria responding when they are sensing their environment?

Back 12

Either directly or by changing the genes they are expressing

Front 13

Do bacteria evolve?

Back 13

Yes

Bacteria change over time to both gain new properties and lose old ones

Their genomes are highly plastic

Front 14

Briefly, what is the life cycle of Myxococcus xanthus?

Back 14

A) Spherical structure that contains ~1*10^5 cells that contains stress-resistant spores. Very tightly packed

B-D) Fruiting body receives nutrients, individual spores germinate and cells emerge together as an "instant" swarm

E-F) Whey prey/nutrient available, swarm becomes predatory collective that moves and feed cooperatively, pooling extracellular enzymes to lyse and consume prey bacteria

G) Wave formation

H) Aggregates and mound building

Front 15

What can Staphylococcus aureus cause in humans?

Back 15

Nausea

Vomiting

Abdominal cramping

Explosive diarrhea

Front 16

What did Yersinia pestis cause?

Back 16

It caused the bubonic plague

Lethal (killed 1/3 of the population of Europe and Asia during the bubonic plague)

Front 17

What is unique about Trichonympha?

Back 17

It is an anaerobic eukaryotic protist that has the ability to break down wood as a food souce

Front 18

What is cellulose?

Back 18

A polymer of glucose very similar to starch except for the presence of a beta(1-4) linkage between every other sugar molecule

This enables very tight packing adjacent glycan chains making it hard for enzymes to access easil

Front 19

Describe the Trichonympha's coat:

Back 19

Trichonympha carries a coat of bacteria that are essential for it to survive on wood as a primary energy source

These bacteria provide organic nitrogen in the form of urea or amino acids that themselves fix from atmospheric nitrogen

Front 20

What does ectosymbionts mean?

Back 20

Symbionent relationships where lives on the outside of the bacterial cell

Front 21

What are enveloped viruses?

Back 21

Surrounded by lipids

Uses host cell machinery to replicate

Front 22

In taxonomy, what is classification?

Back 22

Arrangement of organisms into groups (taxa)

Front 23

In taxonomy, what is nomenclature?

Back 23

Assignment of names

Front 24

In taxonomy, what is identification?

Back 24

Determining to which recognized taxon any given bacterial isolate belongs

Front 25

In taxonomy, what is phylogeny analysis?

Back 25

Classification based on evolutionary relationships

Front 26

What is the significance of taxonomy?

Back 26

Allows to organize huge amounts of knowledge about organisms because all members of a particular group share many characteristics

Allow to make predictions for further research based on knowledge of similar organisms

Allow to communicate efficiently in the scientific community

Essential for accurate identification of microorganisms

Front 27

What is the ranks/hierarchy of taxnomy?

Back 27

1) Domains/Kingdoms

2) Phylum

3) Class

4) Order

5) Family

6) Genus

7) Species (subseven: strains)

Front 28

In taxonomy, what is a genus?

Back 28

Collection of species

Front 29

In taxonomy, what is a species?

Back 29

A collection of strains that share many stable properties and different significantly from other groups of strains

Front 30

What is a bacterial strain?

Back 30

Population of organisms that descended from a single organism or a pure culture isolate that differ form other members of the species in a small way

Front 31

How are strains different from another? How are there strain variation?

Back 31

In strains, they will have subtle variations, changes and properties where one can cause disease and the other does not where vast majroity of genes in the genomes, they are most (99%) likely the same

Front 32

What is significant about the E. coli strain O1578:H7?

Back 32

Gets you very sick when you eat it in meat

Front 33

What is reproductive isolation?

Back 33

Method to see if you can you reproduce with another thing and produce a viable offspring where the cells can reproduce

If can be achieved, you are of the same species

Front 34

What is phenetic classification?

Back 34

Classification based on phenotypic characteristics may reveal possible evolutionary relationships

They can be:

1) Morphological characteristics

2) Physiological and metabolic characteristics

3) Molecular characteristics (DNA GC-content, lipids, capsule types, etc...)

Front 35

What type of bacteria morphology is this?

Back 35

Straight rod or bacillus

Front 36

Give an example of a straight rod/bacillus bacteria?

Back 36

Escherichia

Front 37

What type of bacteria morphology is this?

Back 37

Club-shaped rod

Front 38

What type of bacteria morphology is this?

Back 38

Branching rod

Front 39

What type of bacteria morphology is this?

Back 39

Comma form

Front 40

What type of bacteria morphology is this?

Back 40

Spore forming rod

Front 41

What type of bacteria morphology is this?

Back 41

Spiral form

Front 42

What type of bacteria morphology is this?

Back 42

Spherical/Cocci

Front 43

If bacteria grows like this, what type of cell arrangement is it?

Back 43

Diplococci (one division plane)

Front 44

If bacteria grows like this, what type of cell arrangement is it?

Back 44

Chain (one division plane)

Front 45

If bacteria grows like this, what type of cell arrangement is it?

Back 45

Tetrad (two division planes)

Front 46

If bacteria grows like this, what type of cell arrangement is it?

Back 46

Cluster (three division planes)

Front 47

What did Hans Christian Gram do?

Back 47

Develop a staining procedure that gained wide-spread use as a primary diagnostic test to identify bacteria species

Front 48

If a bacteria is purple/pink after gram staining, what type of gram bacteria are they?

Back 48

Gram-negative

Front 49

If a bacteria is dark blue after gram staining, what type of gram bacteria are they?

Back 49

Gram-positive

Front 50

Does antibiotic perceptibly widely differ depending on bacteria's gram?

Back 50

Yes

Front 51

What is the gram stain procedure?

Back 51

1) Flood heat-fixed smear with crystal violet for 1 min (all cells turn purple)

2) Add iodine solution for 3 min

3) Decolorize with alcohol briefly for about 20 sec (gram positive purple/blue, gram negative cell colourless)

4) Counterstrain with safranin for 1-2 minutes (positive blue/purple, negative pink/red)

Front 52

Why would you add iodine solution in a gram stain procedure?

Back 52

Interacts with crystal violet and makes insoluble rocks with the dye

Front 53

What does the alcohol in gram staining do in the gram staining procedure?

Back 53

Removes crystal violet iodine from the gram negative cells and the slide background

Front 54

Why in gram stain procedure would you use the counterstrain safranin?

Back 54

To help make the gram negative bacteria more visible

Front 55

Why are there differences in gram staining between gram positive and negative?

Back 55

Differences in cell wall structure of gram-positive and gram-negative cells

Front 56

What makes gram-positive cells different from gram-negative cells?

Back 56

90% of their cell wall consists of peptidoglycan layers

This thick peptidoglycan of gram-positive bacteria traps crystal violet/iodine complexes that form during the gram stain procedure

They are more susceptible to antibiotics

Front 57

Why are gram-positive cells more susceptible to antibiotics?

Back 57

Because drugs have an easy time getting past peptidoglycan layer as it has a lot of pores in it

Front 58

What makes gram-negative cells different from gram-positive cells?

Back 58

Only 10% of the cell wall is peptidoglycan (they only have one layer)

Their thin peptidoglycan that fails to trap the crystal violet/iodine during de-staining procedure with alcohol is main different in staining

Their outer layer is highly impermeable (lipid bilayer) to a lot of compounds that are bigger than a dissaccharide

Front 59

What does nosocomial infections mean?

Back 59

Hospital infections

Front 60

When it comes to treatments, which is more deadly, gram negative or gram positive?

Back 60

Gram negative

Front 61

List one possible bacteria that this microscope image shows:

Back 61

Staphylococcus

Front 62

List one possible bacteria that the gram negative rods could be:

Back 62

E. coli

Front 63

What type of morphology does Escherichia have?

Back 63

Straight rod/bacillus

Front 64

What type of morphology does Corynebacterium have?

Back 64

Club-shaped rod

Front 65

What type of morphology doe Actinomyces have?

Back 65

Branching rod

Front 66

What type of morphology does Vibrio have?

Back 66

Comma form

Front 67

What type of morphology does Bacillus have?

Back 67

Spore forming rod

Front 68

What type of morphology does Spirochaeta have?

Back 68

Spiral form

Front 69

What type of morphology does Staphylococcus have?

Back 69

Spherical/Cocci

Front 70

What type of growth cell arrangement does Neisseria have?

Back 70

Diplococci

Front 71

What type of growth cell arrangement does Streptococcus have?

Back 71

Chain

Front 72

What type of growth cell arrangement does Sarcina have?

Back 72

Tetrad

Front 73

What type of growth cell arragement does Staphylcoccus have?

Back 73

Cluster

Front 74

Is Staphlycoccus gram positive or negative?

Back 74

Gram positive

Front 75

Is Listeria gram positive or negative?

Back 75

Gram positive

Front 76

Is Clostridia (C. diff) gram positive or negative?

Back 76

Gram positive

Front 77

Is Mycobacterium tuberculosis gram positive or negative?

Back 77

Gram positive

Front 78

Is Neisseria gram positive or negative?

Back 78

Gram negative

Front 79

What is the morphology of Neisseria?

Back 79

Spherical/Cocci

Front 80

What can Neisseria cause in humans?

Back 80

Gonorrhea

Front 81

Is Haemophillus gram positive or negative?

Back 81

Gram negative

Front 82

What is the morphology of Haemophillus?

Back 82

Spherical/cocci

Front 83

What can Haemophillus cause in humans?

Back 83

Pneumoniae

Front 84

Is E. coli gram positive or negative?

Back 84

Gram negative

Front 85

Is Salmonella gram positive or negative?

Back 85

Gram negative

Front 86

Is Yersinia gram positive or negative?

Back 86

Gram negative

Front 87

Is Vibrio cholerae gram positive or negative?

Back 87

Gram negative

Front 88

What are the criteria for evolutionary chronometers?

Back 88

Molecule (DNA or protein) should be universally distributed in all organisms studied

They must be functionally equivalent in each organism

Must be able to align the sequence properly in order to identify regions of sequence of homology and sequence heterogeneity

The sequence changes of these molecules must reflect the evolutionary distance

Front 89

Which rRNA's make up majority of the ribosomal small subunit?

Back 89

16s rRNA of bacteria

18s rRNA of eukaryotes

Front 90

What are Archaea?

Back 90

Hybrid ancestors of eukaryotes

Front 91

What are the three fundamental groups of life-forms or domains?

Back 91

Bacteria

Arhcaea

Eukarya

Front 92

The top of the red line is positive, everything below is gram negative.

Why?

Back 92

They are evolutionary distant as they have to make huge radical change to their surface where they kind of became a whole new 'animal'

Front 93

What is genomics?

Back 93

A branch of science/technology that specializes in the systematic study of genomes

Front 94

What were the first two viruse genomes completely sequenced?

Back 94

1976 - MS2 phage

1977 - PhiX174 phage

Front 95

What is the Sanger Method?

Back 95

Have stand you want to be sequence with a primer that is complimentary

Prepare four reaction mixtures in test tubes, each including dNTPs which you use those nucleotides to expand as well as small amounts of dideoxynucleotides with A, C, T, G which terminate growth of the chain

Replicate products and separate produce by gel electrophoresis

Read sequences as complement of bands containing labeled strands

Front 96

What is the Sanger Method based on?

Back 96

It is based on DNA polymerase-dependent synthesis of a complementary DNA strain in presence of natural 2'-deoxynucleotides (dNTPs) and 2',3'-dideoxynucleotides (ddNTPs) that server as nonreversible synthesis terminators

The DNA synthesis reaction is randomly terminated whenever a ddNTP is added to growing oligonucleotide chain, resulting in truncated products of varying length with appropriate ddNTP at their 3' terminus

Front 97

What role does the ddNTPs serve in the Sanger Method?

Back 97

Nonreversible synthesis terminators

They randomly terminate DNA synthesis reaction when added to a growing olgonucleotide chain resulting in a truncated products of varying length with an appropriate ddNTP at their 3' terminus

Front 98

What is the Shotgun-cloning method?

Back 98

1) DNA is randomly sheared into small fragments that are then ligated into plasmids

2) Thousands of plasmids are generated, each of which has some random fragment of the genome you want to sequence

3) "Library" of plasmids are put into E. coli so that each may be purified in amounts sufficient for cloning so when grown, each colony of E. coli has a different plasmid

4) Plasmids are isolated from thousands of E. coli clones each harboring a plasmid with different random segment of the genome you are trying to sequence

5) Determine 500-1000bp sequence from each end of cloned piece of DNA (done by using primers complmentary to plasmid area flanking either end of insert)

6) After sequencing 1000s of plasmids this way the sequence can be stitched together by a computer to assemble the full genome

Front 99

Why would you not want to use sonification in DNA sheering for shotgun-cloning?

Back 99

If used sonification, you would need to repair ends and make sure size of fragment is 3kbp

Front 100

What are the limitations to whole genome shotgun-cloning method?

Back 100

Cloning bias - Some gene segments toxic to E. coli and cannot be cloned resulting in"gaps" in assembled sequence that must be filled

Project maintenance issues - Must maintain A LOT of different E. coli isolates

Slow and expensive

Front 101

What is Illumina/Solexa sequencing?

Back 101

Next-generation sequencing platforms and very commonly used

It uses a Sanger-like sequencing reaction using dye-labeled reversible terminator nucleotides and it amplifies the DNA fragment on surface of a slide or a "flow cell"

Building sequencing with dye-labeled nucleotides and treated with certain wavelength/chemicals where the dye will block the next nucleotide and then remove the dye and do the next step then zap with chemical/wavelength removing the dye and do the next one… etc… etc. … etc…

Front 102

What are the steps to Illumina/Solexe sequencing?

Back 102

1) Prepare genome DNA samples

2) Attach DNA to surface

3) Bridge amplification

4) Fragments become double stranded

5) Denature the double-stranded molecules

6) Complete amplification

7) Determine first base

8) Image first base

9) Determine second base

10) Image second chemistry cycle

11) Sequence reads over multiple chemistry cycles

12) Align data

Front 103

In Illumina/Solexe sequencing, what is happening during the first step "Prepare genome DNA sample"?

Back 103

Random fragment and sheer it RE or sonification and ligated adapted (ligationis covalently linking known pieces of DNA onto unknown DNA where you can put your primer onto)

Front 104

In Illumina/Solexe sequencing, what is happening during the second step "Attach DNA to surface"?

Back 104

Theseare coded and can capture the piece of DNA and do it at such a dilution wherethe DNAs on the slide will fall apart far from one another and bound the DNA tothe surface

Front 105

In Illumina/Solexe sequencing, what is happening during the third step "Bridge amplification"?

Back 105

Do PCR amplification on the (the n's) slide using the primers that are attached to the surface of the slide

Front 106

In Illumina/Solexe sequencing, what is happening during the fourth step "Fragments become double stranded"?

Back 106

Enzyme incorporates nucleotide to build double-stranded bridges on the solid phase substrate

Front 107

In Illumina/Solexe sequencing, what is the happening during the 5th step "Denature the double-stranded molecules"?

Back 107

Denaturation leaves single-stranded templates anchored to the substrate

Front 108

In Illumina/Solexe sequencing, what is happening during the 6th step "Complete amplification"?

Back 108

Several million dense clusters of double-stranded DNA are generated in such channel of the flow cell

Unique piece of DNA which amplified to create its own unique piece of DNA which are different from other clusters

Front 109

In Illumina/Solexe sequencing what is happening during the 7th step "Determine the first base"?

Back 109

First chemistry cycle to initiate the first sequencing cycle, add all four labeled reversible terminators, primers and DNA polymerase enzyme to the flow cell

Front 110

In Illumina/Solexe sequencing what is happening during the 8th step "Image first base"?

Back 110

Do oneround of synthesize where above the slide, there is a camera that looks downonto the DNA where depending on what colour the DNA changes, that is thenucleotide it is

It allows you to look at millions of sot where each spot lining up differently

This allows the build of millions of sequencing simultaneously

Front 111

In Illumina/Solexe sequencing, what is happening during the 9th step "Determine second base"?

Back 111

Second chemistry cycle to initiate the next sequencing cycle, add all four labeled reversible terminators and enzyme to the flow cell

Front 112

In Illumina/Solexe sequencing, what is happening during the 10th step "Image second chemistry cycle"?

Back 112

After laser excitation, collect the image data as before. Record the identity of the second base of each cluster

Front 113

In Illumina/Solexe sequencing, what is happening during the 11th step "Sequence reads over multiple chemistry cycles"?

Back 113

Repeat cycles of sequencing to determine the sequence of base in a given fragment in single base at a time

Front 114

In Illumina/Solexe sequencing, what is happening during the final step "Align data"?

Back 114

Blew apart the DNA (shot gun) with millions and reading and begin to stitch together the entire sequence based on the reads

Front 115

How are the genomes sequenced by Illumina/Solexe or other methods assembled?

Back 115

By "stitch" together millions of individual "reads"

Looking for overlap between sequences that fill gaps, match other sequences or extend sequences

Front 116

In genome sequence alignment, what do the blue squares mean?

Back 116

They are errors where there is mismatch from the rest of them

One of the two:

1) Mutation

2) Mistake by sequencing and/or primer/polymerize

Front 117

What are open reading frames?

Back 117

Stretches of DNA that code for a protein

Front 118

What does annotating a DNA sequence mean?

Back 118

Basically understanding what the sequence means

Requires computers to look for patterns and largely automated which can lead to errors

Front 119

What is metagenomics?

Back 119

Going to an environment, taking whatever is there and sequencing it

Formicrobes this is a huge deal as many microbes are uncultivable and no way ofstudying (95%) of them as we did not know how to culture (and did not even knewthey existed)

Front 120

What are the two strategies for metagenomics?

Back 120

1) SEQUENCE EVERYTHING!!!!!

2) Sequence 16S genes in population

Front 121

What is the metagenomics strategy "Sequence everything"?

Back 121

Take the total DNA and sequence everything that is there

What you get is protein coding genes, ribosome genes and a whole bunch of a lot of things

It is very hard for the computer to do because there are many genomes and it would be hard for the computer to figure out what and where to overlap

Front 122

What is the metagenomics strategy "Sequence 16S genes in population"?

Back 122

If you want to know who is there, you can sequence the 16S rRNA DNA

With these you can see how the gut microbiome changes when there is a change in diet

You have to PCR the 16S rRNA DNA

There are current databases of different microbes and what their different 16S rRNA looks like

If you do this procedure properly, you can get good ratios and tell that an specific population increases and/or decreases

Do this by counting the number of E. coli/species rRNA reads are on the slide

Front 123

What does 16S rRNA sequencing require?

Back 123

PCR of 16S rRNA requires that you use primers against the highly conserved regions of the molecule

These primers will amplify about 900 bases of sequences containing enough variability to tell you what you are looking at

Front 124

What is significant about these two pictures?

Back 124

These two pictures are stained with nucleic acid dye

Nucleotide basically fills up the entire cytoplasm on bacteria while in eukaryotes, the DNA is contained in a membrane enclosed nucleus

Eukaryotes is all about enclosing compartments in membranes while during mitosis/mitosis, membrane breaks down but during regular gap phases, its DNA is usually kept separate from cytoplasm

Front 125

Compare Eukaryotic vs Bacteria/Archaeal DNA:

Back 125

Eukaryotes have linear chromosomes - Bacterial tend to be circular

Eukaryotes have problems with replicating ends (solved by capping with telomeres) - Bacteria have no problem

Front 126

What is a possible explanation for why Protopterus aethiopicus (marbled lungfish) has such a large genome of ~130 billion bp?

Back 126

Probablythis because of transpose got in and made a lot of copies/junk DNA

Front 127

At what size do bacterial genomes usually max out at?

Back 127

~12 million

Front 128

What is the chromosomes like for bacteria?

Back 128

Bacteria usually have one major chromosome that contains all housekeeping functions (not always case)

Some has two chromosome

Some has three chromosome which may actually be two chromosomes and mega plasmid

Front 129

Why is it significant that the %GC content differ between bacteria?

Back 129

GCcontent differ a quite bit between bacteria, usually E. coli land in the 50%

Looking at codon table, most AA are coded by first two nucleotides, third base in triplet is the wobble position that gives variability (chooses G or C at third position of triplet w/o effecting protein sequence)

Front 130

Is there a correlation among total number of ORFs in the genome noncoding DNA and genome size for prokaryotic genomes?

Back 130

Consistently observe that bacterial genomes encode about 1 open reading frame for every 1000 base pairs of DNA regardless of size

Most bacterial genomes don't have a lot of "junk" DNA, that they are very streamlined

Front 131

What does it mean by "Bacterias are masters of efficiency"?

Back 131

As soon as one protein sequence one ends, another begins

Typically, a stop codon leads into a start codon

Front 132

Eukaryotic genomes tend to be loaded with what?

Back 132

Junk DNA

Silence transposable elements that tend to replicate itself

Front 133

Why is soil a unique niche for bacteria?

Back 133

Soil isrich with different microbes and different temperatures and will need manydifferent genes for many different functions and they have different types food

They have highly dynamic environments

Bacteria can go into arms race and kill each other

They need genes to fight against phages, amibos, microbes, bacteria, eating complex carbohydrates, etc...

Front 134

What is the %GC content of Burkholderia vietnamiensis?

Back 134

65.7%

Front 135

What is the niche for Burkholderia vietnamiensis?

Back 135

Soil bacterium

Front 136

What is the %GC content for Mycobacterium marinum?

Back 136

65.7%

Front 137

What is niche for Mycobacterium marinum?

Back 137

Free living water bacterium

Front 138

What is the %GC content for Pseudomonas aeruginosa?

Back 138

%66.6

Front 139

What is the niche for Pseudomonas aeruginosa?

Back 139

Soil bacterium

Front 140

What are plasmids in bacteria?

Back 140

Plasmids are small circles

Plasmids carries accessory function (i.e. antibiotic resistance) whereas chromosomes carries essential functions for cell

Plasmids are dispensable, chromosomes are not

Bacterial chromosomes are not shaped the same way as eukaryotic genome

Front 141

How does amino acid codon create biases in bacteria genomes?

Back 141

Little diversity mechanism to protect them from foreign invaders which allows to distinguish self from non-self

Basically it's like if a bacteria's genome has a lot of "A" and "T" bases, but then it encounters a gene that has a lot of "G" and "C" bases, then they'd be like oh this isn't my gene, it's probably foreign then (for example, a bacteriophage trying to inject its genome into a bacterial cell)

Front 142

What is a mutation of an existing gene?

Back 142

A gene in the genome is altered by recombination or through a mutagenic process to yield a gene with altered function

Front 143

What is a gene duplication?

Back 143

A gene is duplicated into two copies

One copy keeps the ancestral function

The other copy is free to change by mutation

Front 144

What is horizontal (lateral) gene transfer?

Back 144

Just steal what you need from another bacteria

Bacterial exclusive

Front 145

What plays a major role in prokaryotic evolution?

Back 145

Horizontal (lateral) gene transfer

Front 146

What are genomic or pathogenicity islands?

Back 146

Large blocks of newly acquired genes are called genomic islands but if they are involved in disease, they are pathogenicity islands

Front 147

Salmonella typhimurium encodes 5 major pathogenicity islands called what?

Back 147

SPI-1 through -5

Front 148

What does the pathogenicity islands of Salmonella typhimurium do?

Back 148

Help the bacteria survive and cause inflammation in the host

Front 149

What does Salmonella typhimurium SPI-1 do?

Back 149

Encodes a type-III secretion system necessary for invasion into animal cells

Invasion

Front 150

What does Salmonella typhimurium SPI-2 do?

Back 150

Encodes a type-III secretion system necessary for survival in macrophages

Macrophage survival

Front 151

What does Salmonella typhimurium SPI-3 do?

Back 151

Genes here work with SPI-2 to ensure survival in macrophages

Macrophage survival

Front 152

What does Salmonella typhimurium SPI-4 do?

Back 152

Encodes an adhesin and works with SPI-1 to help invasion

Epithelial interaction

Front 153

What does Salmonella typhimurium SPI-5 do?

Back 153

Necessary for survival in macrophages

Inflammation

Front 154

How can you identify genes acquired by horizontal gene transfer?

Back 154

Compare region to several other closely related species

Look at GC-content difference (different bacteria prefer to use different codon to code for the same amino acid where if it doesn't make the strain/species, you can guess that it was obtained lately and from whom)

Encoded on phage or transposon

Front 155

What do the red lines mean?

Back 155

Red lines connect genes that from the top genome to their identical counterpart in the bottom genome

Front 156

What does the gap (the arrow is pointing to) mean?

Back 156

A genomic island

Strain 1 has a gene that strain 2 does not have which could be indication of horizontal acquired islands

Front 157

What factor helps distinguish the Salmonella typhimurium SPI's from rest of genome?

Back 157

The SPI's are more AT-rich than rest of genome

Front 158

Where does Mycobacterium tuberculosis live?

Back 158

Lives almost exclusively in human long

Not well adapted for outside life

Front 159

What is Mycobacterium leprae niche?

Back 159

Lives exclusively in human host and cannot survive on its own

Front 160

What does Mycobacterium leprae cause?

Back 160

Leprosy

Front 161

What is the niche of Candidatus carsonella?

Back 161

Endosymbiont

Front 162

What does endosymbionts mean?

Back 162

Bacterial cells that reside permanently inside another cell

Front 163

True of False:

Mitochondria is an ancient endosymbiont

Back 163

TRUE

Front 164

Where are majority of the proteins found in the mitochondria from?

Back 164

Not encoded by mtDNA but instead encoded in nucleus of host cell

Such proteins have to be transported to mitochondria after synthesis in cell cytoplasm

Front 165

What is a reducing agent?

Back 165

Takes a compound and takes electrons out to oxidize it

Front 166

What is an oxidizing agent?

Back 166

Adds an electron to reduce a compound

Front 167

When "A" is being oxidized, is it gaining or losing electrons?

Back 167

Losing

Front 168

When "B" is being reduced, is it gaining or losing electrons?

Back 168

Gaining

Front 169

Why are redox reactions important?

Back 169

Oxidation-reduction (redox) reactions are important because they are the principal sources of energy on this planet

Both neutral, or biological and artifical

Front 170

What does oxidation of molecules usually do (in respects to energy)?

Back 170

Oxidation of molecules by removal of hydrogen or combination with oxygen normally liberates large quantities of energy

Front 171

When something is going from reduced state to oxidized state, what is happening to the energy?

Back 171

Diminishing availability of energy from oxidative processes

Front 172

What is the oxidized form of K?

Back 172

Front 173

What is the oxidized form of Mg?

Back 173

Front 174

What is the oxidized form of H2?

Back 174

Front 175

What are electron donors?

Back 175

In catabolism, electron donor referred to as an energy source

Amount of energy released depends on energy donor and acceptor

Front 176

Briefly, what is the electron transport chain?

Back 176

Consistsof a series of enzyme that are anchored in a membrane together which carriesout oxidation

Front 177

Where does the ETC take place?

Back 177

On the mitochondrial membrane in eukaryotes

On cell membrane in bacteria

Front 178

Is ETC an oxidizing or reducing reaction?

Back 178

Oxidizing

Front 179

Briefly explain the ETC of bacteria:

Back 179

1) Usually starts with NADH converted to NAD+, releasing an electron into NDH-1

2) Two electrons go through NHD-1 pushing 4 protons (H+) from inside to outside of cell where the electrons then with 2 more protons join the Quinone pool

3) Quinone releases 2 electrons and protons to Cyt bo which pushes 2 protons out and water

4) Protons go through ATP synthase to convert protons as an motive force to generate ATP from ADP

Front 180

How many protons have been used moving electrons from NHD-1 to quinone pool?

Back 180

6 H+

Front 181

What does ETC usually start with in bacteria?

Back 181

NADH

Front 182

What are ATP synthase of bacteria?

Back 182

Present on cytoplasmic membrane

Generate ATP form ADP using proton motive force

Multi-subunit motor consisting of two parts, F0 (proton-conducting channel in membrane, C units rotate) and F1 (headpiece in cytoplasm, transmits energy to create ATP)

Front 183

Where are ATP synthase found in bacteria?

Back 183

Cytoplasmic membrane

Front 184

What do ATP synthase of bacteria use to generate ATP?

Back 184

Using proton motive force (PMF) to generate ATP from ADP

Front 185

What is the multi-subunit motor F0 of the ATP synthase in bacteria?

Back 185

Proton-conducting channel in membrane

C units rotate

Front 186

What is the multi-subunit motor F1 of ATP synthase in bacteria?

Back 186

Headpiece in cytoplasm

Transmits energy to create ATP

Front 187

Briefly, label the steps of the citric acid cycle:

Back 187

1) Pyruvate converts NAD+ + CoA into NADH releasing CO2 becoming Acetyl-CoA

2) Citrate synthase converts Acetyl-CoA into Citrate(3-) releasing CoA

3) Citrate(3-) converted into Aconitate(3-)

4) Aconitate(3-) converted into Isocitrate(3-)

5) With isocitrate(3-), converts NAD(P)+ into CO2 and NAD(P)H and itself into alpha-Ketoglutarate(2-)

6) CoA + NAD+ converted into NADH and CO2 with alpha-Ketoglutrarate(2-) into Succinyl-CoA

7) Using Succinyl-CoA, GDP + Pi into GTP and CoA and Succinate(2-)

8) Succinate(2-) converted into Fumarate(2-) with FADH into FAD

9) Fumarate(2-) into Malate(2-)

10) With Malate(2-), NAD+ into NADH and Oxalacetate(2-)

11) Begin cycle again at step 2)

Front 188

What are the product of the citric acid cycle?

Back 188

NAD(P)H and NADH and FADH

Front 189

From glycolysis, how many electrons are carried to ETS (ETC of bacteria) and via what?

Back 189

4 electrons carried via 2 NADH + 2H+

Front 190

What are the beginning and ending products of glycolysis?

Back 190

Glucose into 2 Pyruvate

Front 191

How many ATPs are generated from Glycolysis?

Back 191

2 ATP

Front 192

From the conversion of 2 pyruvate to 2 Acetyl-CoA, how many electrons are carried to ETS and via what?

Back 192

4 Electrons carried via 2 NADH + 2 H+

Front 193

From the TCA cycle, how many electrons are carried to the ETS and via what?

Back 193

16 electrons carried via 6 NADH + 6 H+ and 2 FADH2

Front 194

How many ATP's are generated from the TCA cycle?

Back 194

2 ATP

Front 195

How many ATPs are generated from ETS?

Back 195

34 ATP

Front 196

How many ATPs are generated from the complete oxidation of glucose?

Back 196

38 ATP

Front 197

What is heterotrophic nutrition?

Back 197

Relying on organic compounds for energy

Front 198

What are chemolithotrophs?

Back 198

Organism that is able to use inorganic reduced compounds as a source of energy

Most are autotrophic, obtain carbon from CO2

Their reducing power for biosynthesis comes from directly from inorganic compounds (sufficiently low E0') and reverse electron flow

Front 199

How much free energy of a energy-rich phosphate bond of ATP has?

Back 199

-31.8 kJ/mol

Front 200

Do anaerobes that use alternate electron acceptors have oxygen as final oxidizer?

Back 200

It can but not all which is why they do not need O2 to live

Front 201

What are sulfur oxidizing bacteria?

Back 201

Take in such compounds as sulfur compounds or pure sulfur and turn into energy

Final product is H+ and sulphuric acid

Front 202

What are sulfur granules in sulfur oxidizing bacteria?

Back 202

Storage system for intermediates in their metabolism

Sulfur can be found in here

Front 203

What do sulfur oxidizing bacteria do with hydrogen sulfide?

Back 203

Convert it into sulfur which gets converted into sulfate

Front 204

What are the two ways sulfite can be oxidized?

Back 204

1) Sulfite oxidase pathway

2) Adenosine phosphosulfate (APS) reductase

Front 205

What reductant can be generated by reverse electron flow?

Back 205

NADH

Front 206

What is the ETC like in sulfur oxidizing bacteria?

Back 206

Usually have different starting enzyme compared to other bacteria

HS- gets oxidized by FP which goes into either ETC or Reverse electron flow

ETC:

1) Electron from oxidized HS- to Quinone pumping out H+

2) Quinone to Cyt B to Cyt C which takes of S2O3(2-) or S(0)

3) Pushes electron to Cya aa3 which converts 1/2 O2 into H2O and pushes more H+ out

4) H+ gradient creates ATP

Front 207

What is the reverse electron flow like in sulfur oxidizing bacteria?

Back 207

Usually have different starting enzyme compared to other bacteria

HS- gets converted into FP which goes into either ETC or Reverse electron flow

Reverse electron flow:

1) FP causes NAD+ to be converted into NADH

2) With CO2 + ATP, NADH goes into Calvin cycle

Front 208

What is unique about the tubeworm (Rfitia pachyptila) relating to sulfur?

Back 208

These bacteria take hydrogen sulfide and produce energy and organic molecules

Convert inorganic substances into organic compounds which tubeworm uses to grow

They live next to underwater vents which pump out hydrothermal fluid which contain H2S

Front 209

Ferrous iron is insoluble at what pH? What happens to it at that pH?

Back 209

Neutral pH

Spontaneously oxidizes and precipitates as ferric hydroxide Fe(OH)3

Front 210

Where can iron oxidizing bacteria be found?

Back 210

Acid, iron-rich environments

Front 211

What type of energy consuming bacteria is Thiobacillus ferroxidans?

Back 211

Iron oxidizing bacteria

Front 212

What type of energy consuming bacteria is Leptospirrillum ferroxidans?

Back 212

Iron oxidizing bacteria

Front 213

What are iron oxidizing bacteria?

Back 213

Uses iron (ferrous into ferric) for their energy source and have a very short route of electron transport to oxygen

Must oxidize large amounts of iron in order to grow

Front 214

What is Rusticyanin?

Back 214

Enzyme that mediates the oxidation of ferrous iron

Copper-containing protein in periplasm

Mediates oxidation of Fe2+ and passes electrons to Cytochrome C

Also passes electrons to Cytochrome A which oxidizes oxygen and pumps H+ out

Front 215

What are the electron donors of inorganic compounds?

Back 215

Phosphite

Hydrogen

Sulfide

Sulfur

Ammonium

Nitrate

Ferrous iron

Front 216

What is the ETC of iron oxidizing bacteria?

Back 216

1) Rusticyanin oxidizes Fe2+ into Fe3+, forcing an electron inside membrane to Cyt C

2) Cyt C electron goes to Cyt A pushing protons outside

3) With 2e-, converts 1/2 O2 into H2O and, releasing 2 H+

4) Proton gradient creates ATP

Front 217

What is the reverse electron flow of iron oxidizing bacteria?

Back 217

1) Rusticyanin oxidizes Fe2+ into Fe3+, forcing an electron inside membrane to Cyt C

2) Cyt C electron causes NAD+ converted into NADH in pH 6 environment

3) With CO2 + ATP, NADH goes into Calvin cycle

Front 218

Where does the Rusticyanin sit on iron oxidizing bacteria?

Back 218

On the outside of the outer membrane

Front 219

What is the ETC of H2 oxidizing bacteria?

Back 219

1) H2 oxidized by H2ase pushing electron to Quinone

2) Quinone pushes protons out of cell and electron to Cyt B

3) To Cyt C

4) To Cyt A

5) Cyt A forces protons out and converts 1/2 O2 to H2O

6) Proton gradient creates ATM

Front 220

What is the reverse electron flow of H2 oxidizing bacteria?

Back 220

1) H2ase oxidizes H2

2) Reduces NAD+ with H+ to NADH

3) With CO2 + ATP, NADH goes into calvin cycle

Front 221

What is Nitrite Oxidoreductase?

Back 221

Oxidize nitrite into nitrate

Oxygen is the primal acceptor

Front 222

What is anaerobic respiration?

Back 222

Terminal electron acceptor other than oxygen

Involves electron transport chain

Front 223

What is assimilative reduction?

Back 223

Inorganic compounds reduced for use as nutrient source

Only enough reduced for growth needs

Front 224

What is dissimilative reduction?

Back 224

Reduced for energy production

Large amount of inorganic compound is reduced

Products of reduction are excreted

Front 225

What is the most common electron acceptor for anaerobics?

Back 225

Nitrate

Front 226

Can methane be used as an energy source?

Back 226

Yes

Front 227

What is the source of energy and electron of iron bacteria (iron oxidizing bacteria)?

Back 227

Ferrous iron into ferric iron

Fe2+ -> Fe3+

Front 228

What is the source of energy and electrons of nitrosifying bacteria?

Back 228

Ammonia into nitrite

NH3 -> NO2-

Front 229

What is the source of energy and electrons of nitrifying bacteria?

Back 229

Nitrite into nitrate

NO2- -> NO3-

Front 230

What is the source of energy and electrons of purple sulfur bacteria?

Back 230

Sulfide into sulfur

S2- -> S0

Front 231

What is the source of energy and electrons of sulfur-oxidizing bacteria?

Back 231

Sulfur into sulfate

S0 -> SO4(2-)

Front 232

What is the source of energy and electrons of aerobic hydrogen bacteria?

Back 232

Hydrogen into water

H2 -> H2O

Front 233

What is the source of energy and electrons of anammox bacteria?

Back 233

Ammonia into nitrogen

NH3 -> N2

Front 234

What is the source of energy and electrons of carboxydotrophoic bacteria?

Back 234

Carbon monoxide into carbon dioxide

CO -> CO2

Front 235

What is autotrophic CO2 fixation?

Back 235

Need to incorporate carbon from CO2 for biosynthesis

Front 236

What are some pathways for atutotrophic CO2 fixation?

Back 236

Calvic cycle

Reverse citric acid cycle

Hydroxypropionate cycle

Front 237

What are required for calvin cycle?

Back 237

NADPH and ATP

Front 238

What is RubisCO?

Back 238

Ribulose biphosphate carboxylase (a key enzyme in the calvin cycle)

It is a rate limiting step for CO2 fixation in the Calvin cycle

Most abundant protein on earth and source of energy for all heterotrophs

Attaches CO2 to a sugar (Ribulose biphosphate) and convert it into Phosphoglyceric acid (PGA)

Front 239

What does RubisCO convert?

Back 239

CO2 + ribulose biphosphate -> Phosphoglyceric acid (PGA)

Front 240

What are carboxysomes?

Back 240

Usually have RubisCO and carbonic anhydrase inside in close interaction which increases efficiency of reaction

Sugars like bicarbonates enter carboxysomes

Front 241

Briefly, what are the steps in the Calvin cycle?

Back 241

1) Ribulose 1,5-bis-phosphate converted using 3 CO2 and 3 H2O into 3-Phosphate-Glycerate by RubisCO

2) Using 6 ATPs, 6 NADPHs and 6 H+, 3-Phosphate-Glycerate is reduced to Glyceraldhyde-3-Phosphate

3) After 6 Glyceraldehyde-3-Phosphate produces, 1 enters biosynthesis of glucose, 5 gets phosphorylated into Ribulose-5-Phosphate

4) Ribulose-5-Phosphate undergoes phosphorylation using 3 ATP and restarts cycle

Front 242

How much energy is required for the Calvin cycle?

Back 242

9 ATP

Front 243

What is a difference between reverse citric acid cycle and citric acid cycle?

Back 243

Most enzymes are the same except working backwards

Only enzyme difference is citrate synthase replaced with citrate lyase

Front 244

What are the two ferredoxin-linked reactions in reverse citric acid cycle?

Back 244

1) Carboxylation of succinyl-CoA to alpha-ketoglutarate

2) Carboxylation of acetyl-CoA to pyruvate

Front 245

What is the net reaction of Reverse citric acid cycle?

Back 245

3 CO2 + 12 H+ + 5 ATP into Triose-Phosphate

Front 246

Briefly, what happens in the reverse citric acid cycle?

Back 246

1) Oxalacetate with 2H+ gets converted into Malate

2) Gets converted into Fumarate

3) Gets converted into Succinate with 2H+

4) Gets converted into Succinyl-CoA using ATP

5) Using Ferredoxin red and CO2, gets converted into alpha-Ketoglutarate

6) Using 2H+ and CO2, gets converted into Isocitrate

7) Gets converted into Citrate

8) Using Citrate lyase either gets converted into Oxalacetate and restarts cycle OR using ATP, gets converted into Acetyl-CoA

9) Using Ferredoxin red and CO2, gets converted into Pyruvate

10) Gets converted into Phosphoenolpyruvate using ATP

11) Using ATP and 2 H+, gets converted into Triose-Phosphate

12) Gets converted into Hexose-Phosphate

13) Used for cell amterial

Front 247

What happens if you take our Ferredoxin red out of the Reverse citric acid cycle?

Back 247

It will stop production/conversion of alpha-ketoglutarate and/or pyruvate

Front 248

From Oxalacetate to Triose-Phosphate, how much ATP is used in the reverse citric acid cycle?

Back 248

4 ATP

Front 249

What is the hydroxypropionate cycle?

Back 249

Present only in green nonsulfer phototroph Chloroflexus

Two CO2 is reduced to glyoxylate (Acetyl-CoA is carboxylated twice and yields methylmalonyl-CoA rearranged to acetyl-CoA and glyoxylate which is converted to other compounds by serine or glycine intermediate)

Front 250

Briefly, what happens during the hydroxypropionate cycle?

Back 250

1) Acetyl-CoA converted into Hydroxypropionyl-CoA using 2 ATPs, 4 H+ and a CO2

2) Gets converted into Propionyl-CoA using 2 H+

3) Gets converted in Methylmalonyl-CoA using ATP and CO2

4) Releases 2 H+ and either gets converted to Acetyl-CoA and restarts cycle OR Glyoxylate which is used for cell material

Front 251

What is the net reaction for the hydroxypropinate cycle?

Back 251

2 CO2 + 4 H+ + 3 ATP -> Glyoxylate

Front 252

Is the Hydroxypropionate cycle found in Eukaryotes?

Back 252

No (or at least none are known)

Front 253

Is the Reductive acetyl-CoA pathway found in Eukaryotes?

Back 253

No (or at least none are known)

Front 254

Is the Reverse (reductive) TCA cycle found in Eukaryotes?

Back 254

Yes, anaplerotic reactions fix CO2 to regenerate TCA

Front 255

What happens during Glycolysis?

Back 255

1) Glucose converted into Glucose-6-P using Hexokinases and ATP

2) Using Isomerase, converted into Fructose-6-P

3) Using ATP with Phosphofructokinase, converted into Fructose-6-1,6-P

4) Using Aidolase, converted to 2 Glyceraldehyde-3-P

5) Using a inorganic phosphate and Glyceraldehyde-3-P dehydrogenase while releasing an electron to reduce 2 NAD+ into 2 NADH, converted into 2 1,3-Biphosphoglycerate-P (non-reversible redox reaction)

6) Using Phosphoglycerckinase, converted into 2 3-Phosphoglycerate-P, producing 2 ATP

7) Converted into 2 2-Phosphoglycerate-P

8) Using Enolase, converted into 2 Phosphoenoipyruvate-P

9) Using Pyruvate kinase, converted into 2 Pyruvate, producing 2 ATP

Front 256

How many ATPs are produced during glycolysis?

Back 256

4 ATP

Front 257

What is another name for Glycolyss?

Back 257

Embden-Meyerhof pathway

Front 258

Does glycolysis occur in the presence or absence of O2?

Back 258

Both

Front 259

In glycolysis, 4 ATP are produced, but only 2 can be used, why?

Back 259

2 ATP are used during glycolysis early steps

Front 260

In glycolysis, how many NADH are produced per glucose?

Back 260

2 NADH

Front 261

What is phototraphy?

Back 261

Use of light as energy source by photosynthesis (conversion of light energy to chemical energy)

Front 262

What are photosystems?

Back 262

Systems of proteins and membranes that are found in bacteria and plants that allow energy derived from sunlight (light energy, packages of photons) into chemical energy (excited electrons, like making ATP)

Act like electron transport chains by generating protein gradient across photosynthetic membrane

Front 263

What are photosynthetic vesicles?

Back 263

Membrane invaginations where these photosynthetic complexes are set up

Can be found in purple bacteria

Front 264

What are purple bacteria?

Back 264

Produce intracytoplasmic membranes into which pigments are inserted

Originated from invaginations of cytoplasmic membrane

Allow purple bacteria to increase the amount of pigment and better utilize light

Front 265

What are green bacteria?

Back 265

Another type of photosynthetic bacteria

They have chlorosomes, looks like organelles along plasma membrane (this where photosynthesis happens)

Front 266

What are Antenna pigments?

Back 266

Funnel light energy to reaction center

Very important at low light intensity

Front 267

What is located on top of a reaction center of phototrophic bacteria?

Back 267

A cytochrome that transfer electron in

Front 268

What is the purpose of the cytochrome on top of a reaction center of phototrophic bacteria?

Back 268

To transfer electrons in

Front 269

Is there chlorophyll in a reaction center of phototrophic bacteria? If so, where?

Back 269

In the middle of the special pair with pigments going around it to the side

Front 270

What are the point to pigments in the reaction center of phototrophic bacteria?

Back 270

To hold the pigments

Front 271

What is the "Special pair" of bacteriochlorophyll for a reaction center of phototrophic bacteria?

Back 271

Called special pair because there are two cholorphylls together in a special orientation at 7A away which allows them to absorb light

Front 272

What differs bacteriopheophytin from bacteriochlorophyll?

Back 272

Bacteriopheophytin is Bacteriochlorophyll without Mg2+

Front 273

Why is Chlorophyll very good at light absorbence?

Back 273

Due to its structure and the Mg2+ ion in the middle of it

Front 274

Briefly, what are the steps of the reaction center of phototrophic bacteria when light interact with it?

Back 274

1) Excited electron located in special pair is transferred to bacteriochlorophyll where electron is then quickly transferred to a bacteriopheophytin

2) Electron is then transferred to QA (quinone, when this happens, it becomes ubiquinol)

3) Electron is then slowly transferred to QB via nonheme ferrous iron

4) The electron hole in the special pair is filled by an electron from the heme of the cytochrome c

5) Second exciton is transferred via the same route to the semiquinone to form ubiquinol which is free to diffuse within the membrane

Front 275

What does the Antenna complex that surrounds the reaction center do?

Back 275

Featured in all photosynthetic center and also absorb light at wavelengths that are distinct from chlorophyll which helps get light funnel into reaction center but they cannot make excited electrons but transfer light by excitation transfer (transfer without transfer radiation)

Front 276

What is exciton transfer?

Back 276

Excitation energy transferred by a radiationless process to a neighbouring molecule

No electron transfer

Front 277

What are carotenoids?

Back 277

Accessory pigments allow more energy capture

Associated with light harvesting pigment which can transfer energy to reaction center

Serve protection role to absorb light in blue (high energy) region and quench toxic oxygen species

Front 278

What is the electron flow and ATP synthesis in purple bacteria like?

Back 278

Electron to ubiquinol to cytochrome c2 which donated its electron to reduce radical cation of the special pair

For every two electrons transferred to ubiquinol to cytochrome c2, four H+ are released into the periplasmic space, generating a proton gradient

This is an infinite cycle

Front 279

Briefly, what are the steps of electron flow in purple bacteria?

Back 279

1) Red or infrared light hits the P870

2) P870 goes from +0.5V to -1.0V

3) Electron goes from P870 to Bph

4) Then to QA then QB then Q/pool where there will be a H+ transport across photosyntethic membra

5) Electron then go to Cyt c2 then P870

Front 280

What is a problem with purple bacteria and generating reducing power and its solution?

Back 280

Quinone is more positive than NAD -> NADH (NADH more energetic)

Solution: Organism must undergo reverse electron flow which require ATP

Front 281

What is reverse electron flow in purple bacteria?

Back 281

1) Red or infrared light hits the P870

2) P870 goes from +0.5V to -1.0V

3) Electron goes from P870 to Bph

4) Then to QA then QB then Q/pool where reverse electron flow begins

5) Using proton gradient, causes NAD(P)+ to be reduced to NAD(P)H using ATP

When continuing the electron flow, there is an external electron donor for the Cyt c2 step

In reverse electron flow, electrons move from inorganic electron donor to NADP (passed from donor to cytochrome 2on outside, quinone to NAD(P) on inside)

Front 282

Why does the reverse electron flow in purple bacteria begin at the quinone pool step?

Back 282

The first table electron accept is the quinone as it has more positive E0' than NADH

Front 283

When does reverse electron flow begin for green sulfur bacterium and Helicobacterium?

Back 283

Their first stable electron acceptor is FeS as it has more negative E0' than NADH

NOTE: These bacterium do not actually have a reverse electron flow as FeS is in an energy state higher than NADH so you can directly to it

Front 284

What is anoxygenic photosynthesis?

Back 284

Photosynethsis without oxygen production

Involves only one photosystem

Electron transport through a series of electron carries

Carriers organized in photosynthetic membranes in series from negative to positive reduction potentials

No net input or consumption of electrons

Front 285

What do photosynthesis of cyanobacteria produce?

Back 285

O2

Front 286

What are thylakoids?

Back 286

These are membranes

This is where photosynthesis is taken place

Can be found in cyanobacteria

Front 287

What do chloroplast in plants and algae do?

Back 287

Mediates photosynthesis in plants and algae

Chloroplast is cyanobacteria that got swallowed by an ancient eukaryote (similar to mitochondria)

Front 288

What O2 levels in the atmosphere rose and atmospheric CH4 levels reduced, what happened to the earth?

Back 288

Loss of this greenhouse gas led to a prolonged ice age (300-400 million years where ice at equator was ~1600 meters thick)

Front 289

What are stromatolites?

Back 289

Bacterial fossils with iron oxide trapped in them

Front 290

What is ferrodoxin?

Back 290

They are iron-sulfur proteins that mediate electron transfer in a range of metabolic reactions

Generated by separate photosystem in cyanobacteria

Reduced from light energy

Used for CO2 fixation or to generated NADH or NADPH

Front 291

What are quinone?

Back 291

Mobile, lipid-soluble carriers that shuttle electrons (and protons) between large, relatively immobile macromolecular complexes embedded in the membrane

Front 292

In the Z pathway of oxygenic photosynethesis, what is photosystem 1?

Back 292

What is like in purple bacteria

Uses light energy to generate reduced ferredoxin, a powerful reductant

Front 293

In the Z pathway of oxygenic photosynthesis, what is photosytem 2?

Back 293

Oxygenic photosynthesis

When sunlight hits it, it becomes a strong oxidizing agent it strips oxygen off from water generating O2 and protons that can go into electron transport chain

Front 294

What can plastocyanin (PC) do?

Back 294

Cantake electron, pass it to photosystem 1 to generate the reducing compoundneeded to fix carbon

Front 295

Briefly, what happens in the Z pathway reaction complexes and ATP synthesis?

Back 295

Water gets excited, releasing O2, producing protons used for proton motive force and transferring electron to ETC Passing electron to ferrodoxin, then pass it to Fd reductase to make NADPH from NADP

Front 296

What is Oxygenic photosynthesis?

Back 296

Two photosystems (P700 and P680) that are connected by an electron transport chain

Front 297

Why do oxygenic photosynthesis not need reverse transport flow?

Back 297

Electron that is passed onto Fd (from FeS) is higher energy state than NADH and thus it can make NADH without consuming energy for reverse transport and doesn't require an electron donor

Front 298

What does oxygenic photosynthesis consume?

Back 298

Water

Front 299

How is ferredoxin reduced from light energy?

Back 299

1) Light photoexcites bacteriochloroophyll

2) Drives splitting (photolysis) of 2H+ from electron donors (sulphides and organic molecules)

3) Electrons flow to phylloquinone then ferredoxin

Front 300

How can ferredoxin be used to generated NADPH?

Back 300

Via Ferredoxin NADH Oxidoreducatase (FNR)

Front 301

What are the most efficient nitrogen fixing bacteria?

Back 301

Symbiotic living bacteria

Front 302

Why does fixing N2 take a lot of energy?

Back 302

It requires breaking three bonds in N2

Front 303

What are the steps for root hairs of plants host symbiotic relationship with bacteria?

Back 303

1) Recognition and attachment (rhicadhesin-mediated)

2) Excretion of nod factors by bacterium causing root hair curling

3) Invasion where Rhizobia penetrate root hair and multiply within an "infection thread"

4) Bacteria in infection thread grow toward root cell

5) Formation of bacteroid state within plant cell

6) Continued plant and bacterial cell division

Front 304

For symbiotic relationships, bacteria species tend to be quite specific to certain plants, why?

Back 304

Because the plant and bacteria are "talking" (chemical signals) to each other and if they don't understand each other, they do not make good nodules

Plants will only grow root hairs for bacteria if "talking" well

Front 305

What is an infection thread?

Back 305

Bacterial material to allow it to attract more bacteria into the root

All done by signaling between bacteria and plant

Front 306

After the bacteria has successfully invaded the plant cells and formation of bacteroid state within plant cell is done, what enzyme do the bacteria start producing?

Back 306

Nitrogenase

Front 307

After the bacteria has successfully invaded the plant cells and formation of bacteroid state within plant cell is done, what does the bacteria start doing?

Back 307

Start fixing nitrogen while the plant will start sending organic carbon to supply energy for the bacteria

Front 308

After the bacteria has successfully invaded the plant cells and formation of bacteroid state within plant cell is done, what does the plant start doing for the bacteria?

Back 308

Send organic carbon to supply energy for the bacteria to start fixing nitrogen

Front 309

What do the nodules do for the bacteria in a plant?

Back 309

Protect the bacteria from O2 exposure

Front 310

In nitrogen fixation, for one molecule of nitrogen, how many ATPs do you need?

Back 310

16 ATP

Front 311

In nitrogen fixation from N2 into 2 NH4+, is the flavodoxin being oxidized or reduced?

Back 311

Oxidized

Front 312

What enzyme is used in nitrogen fixation from N2 to 2 NH4+?

Back 312

Nitrogenase

Front 313

How does nitrogenase work?

Back 313

There are actually two enzymes in nitrogenase

Nitrogenase ONE reduces ferrodoxin

Nitrogenase TWO oxidizes MoFe

This process uses 2 ATP

The reduced form of MoFe converts N2 + 8H into NH4 + H2

Front 314

Do all organisms that fix nitrogen have some version of Nitrogenase?

Back 314

Yes

Front 315

What is Nitrogenase reductase?

Back 315

A 60kD homodimer with a single 4Fe-4S cluster that keeps the nitrogenase in a reduced state

Very oxygen-sensitive

Binds MgATP where 4 ATP required per pair of electron transfer

Causes reduction of N2 to 2 NH3 + H2 which requires 4 pairs of electrons (16 ATP per N2)

Front 316

What is nitrogenase?

Back 316

A 220 kD heterotetramer

Each molecule of enzyme contains 2 Molybdenum (Mo), 32 Fe, 30 equivalents of acid-labile sulfide (FeS clusters)

It is slow, uses only three molecules of N2 per second

Highly O2 sensitive

Front 317

What is Leghaemoglobin?

Back 317

Made by plants and exported into nodule to bind to excess O2

Bacteria and plant must be present for production of this molecule and only found in nodule

Front 318

Why would a plant produce Leghaemoglobin?

Back 318

Nitrogenase (enzyme used by symbiotic bacteria Rhizobia in nodule) is a highly oxygen sensitive enzyme

Leghaemoglobin will bind to any excess oxygen in the nodule

Front 319

What are the two principal pathways for ammonium assimilation?

Back 319

Principal route: GDH/GS in organisms rich in N

Secondary route: GS/GOGAT in organisms confronting N limitation

Front 320

What is GOGAT?

Back 320

Glutamate synthase (or Glutamate: oxo-glutarate aminotransferase)

Converts alpha-ketoglutarate + glutamine into glutamate

Front 321

What happens during pathway 1 (secondary route) of ammonia assimilatory cycle?

Back 321

1) NH4+ + Glutamate + ATP will be converted into Glutamine + ADP + Pi

2) If enough Nitrogen around, Glutamine converted into amino acids, proteins, purines and pyrimidines. If not enough Nitrogen around:

Glutamine + alpha-ketoglutarate into Glutamate by GOGAT

Front 322

What happens during pathway 2 (principal route) of ammonia assimilatory cycle?

Back 322

1) NH4+ + alpha-ketoglutarate gets convereted into Glutamate by Glutamate Dehydrogenase (GDH)

2) Glutamate gets converted into amino acids and proteins

Front 323

During the secondary route of ammonia assimilatory cycle, what happens if there is not enough nitrogen?

Back 323

Glutamine gets converted back into glutamate by addition of alpha-ketoglutarate by GOGAT

Front 324

What is denitrification?

Back 324

Denitrification converts nitrate (NO3) in the soil to atmospheric nitrogen (N2)

Denitrifying bacteria live deep in soil and in aquatic sediments where conditions make it difficult for them to get oxygen (using nitrate as an electron acceptor)

Denitrifying bacteria use nitrate as an alternative to oxygen, leaving free nitrogen gas as a byproduct

Front 325

What enzymes can be found in denitrification?

Back 325

Nitrate reductase

Nitrous oxide reductase

Front 326

What are the two types of nitrogen fixers recognized?

Back 326

1) Free-living (non-symbiotic)

2) Mutualistic (symbiotic)

Front 327

What happens during the sulfur cycle?

Back 327

Front 328

Why would most bacteria live in communities compared to living on their own?

Back 328

Communities allows them to take up products made by other organisms and consume those

Front 329

In Li-Hung Lin, et. al. research "Long-Term Sustainability of a High-Energy, Low-Diversity Crustal Biome", they found alkaline saline ground water at 2.8 kilometers depth in Archaean metabasalt microbial biome dominated by a single phlyotype.

How were the sulfate reducers sustained?

Back 329

Sulfate reducers were sustained by geological produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years

Front 330

What do most Mycobacterium have in common?

Back 330

Gram positive

Waxy coat on surface

Front 331

What is Mycobacterium marinum?

Back 331

Free living bacterium

Lives in water

Double the genome size of Mycobacterium leprae

Front 332

What is Mycobacterium tuberculosis?

Back 332

Grows in humans and gets into lungs but can cultivate on a petri dish

Most of the time, it undergoes latent state where people can live with TB infection without knowing it

An immunosuppressent can activate TB which can cause really bad pulmonary infection

Front 333

What is Mycobacterium leprae?

Back 333

Genome size ~3.27 million bp

GC rich genome

Causes leprosy

Very slow growing bacteria

Can only live within humans and cannot cultivate on lab media (only animals)

Front 334

What are pseudogenes?

Back 334

Genes that should look like genes and should code for proteins but are inactivated

Front 335

What is Candidatus Carsonella?

Back 335

Endosymbionts

Symbiotic relationship by living inside another cell

Smallest genome size

Front 336

What is symbiosis characterized by?

Back 336

1) Bacteria are restricted to a single inset cell type - "mycetocyte" or "bacteriocyte" - where they are not spread out throughout the body but rather contained within a specialized cell (mutalistic relationship)

2) Bacteria are maternally transmitted

3) Association between the bacteria and the host is required by both partners (host may die if bacteria is taken out)

Front 337

Endosymbiotic bacteria reside in what type of cells?

Back 337

Specialized cells called "bacteriocytes" or "mycetocytes"

Front 338

The relationship between the whiteflies, devastating agricultural parasites, and their endosymbionts goes back ~180 million years. Why?

Back 338

These bacteria can help capture and recycle nitrogen from uric acid, preventing it from being lost from the insects

These insects eat diets that are high in carbon but low in nitrogen

Front 339

Is inheritance of endosymbionts usually vertical, horizontal, maternal, etc...?

Back 339

Vertical and maternal

Front 340

Can a male with an endosymbionts give inheritances to that endosymbiont?

Back 340

No, inherit only directly from mothers

Front 341

What are the ways that a mother can give inheritance of their endosymbiont?

Back 341

Trans-ovarial

Smearing of endosymbionts on shell of deposited egg (when egg shell breaks, insect will pick up endosymbionts)

Transmission through feed (mother have specialized "sacs" to secrete bacteria into young during feeding)

Front 342

What happens when an Wolbachia infects an insect such as a worm (filarial nematode)?

Back 342

Engage in reproductive parasitism where they affect how the insect reproduce so they can spread

Once infects one female insect, it ensures its sreadp to all progeny, often means getting rid of the males

Front 343

What is cytoplasmic incompatibility of reproductive parasitism?

Back 343

Most common reproductive manipulation caused by Wolbachia endosymbionts

Embryos derived when infected males mate with uninfected females are inviable

Infected females can mate with both infected and uninfected males (population rapidly acquires more and more infected members)

Front 344

With cytoplasmic incompatibility of reproductive parasitism, what happens when a infected male mates with an uninfected female?

Back 344

Eggs will die because there are factors in the sperm that is incompatible with the cytoplasm of the uninfected female

Front 345

When an insect infected with a reproductive parasitism like Wolbachia, what happens during ferminization?

Back 345

During development process, genetic male has genetic material to make a male

But Wolbachia endosymbiont suppresses those hormones and female structures are made instead, making functional female (they will reproduce like females)

Front 346

When an insect infected with a reproductive parasitism like Wolbachia, what is male killing?

Back 346

In some insects, Wolbachia infected male embryos fail to develop properly, leading to entire brood of infected females

This helps spread Wolbachia in highly resource-limited environments where competition between siblings for resource is fiere

Front 347

What an insect infected with a reproductive parasitism like Wolbachia, what is parthenogensis (virgin birth)?

Back 347

Some insects (notably wasps) have a sex-determination system where unfertilized (haploid) embyros are male and fertilized embryos (diploids) are female

Wolbachia infected haploid embryos undergo a second round of RNA replication to become diploid and hence develop into females even though no fertilization occured

Front 348

Are endosymbiont genomes AT or GC rich?

Back 348

Very AT-rich

Front 349

What is the endosymbiotic theory or "symbiogenesis"?

Back 349

States the new forms of life can arise form the merging of two separate cells into a single functioning entity

Front 350

Who is Lynn Margulis?

Back 350

Developed and proposed the Endosymbiotic theory

Front 351

TRUE or FALSE:

Mitochondria and chloroplast (plastids) are ancient endosymbionts

Back 351

TRUE

Front 352

What evidence for the endsymbiotic origins of mitochondria and plastids (chloroplast) do we have?

Back 352

They have their own DNA that appears bacterial in origin

They encode ribosomes similar to bacterial ribosomes

Mitochondria have their own double membrane and includes lipids (cardiolipin) that are similar to bacteria

They multiply and divide using binary fission

They use N-formylmethionine as the intiating amino acid in protein synthesis

Some eukaryotes have chloroplast that have cell walls

Front 353

The mitochondria have their own what that the cell also has?

Back 353

Ribosome

tRNA genes

NADH dehydrogenase

ATP synthase

Cytochrome oxidase subunits

Front 354

What is a serious problem with antibiotics that block bacterial protein synthesis (aminoglycosides and tetracyclines)?

Back 354

Mitochondrial ribosomes are similar enough to bacterial ribosomes that the antibiotics block protein synthesis of the mitochondria

Front 355

How are mitochondria inherited?

Back 355

Maternally

Front 356

When did King Richard III die and what did it signify?

Back 356

King Richard III of England was killed August 22, 1485 by the army of Henry VII at the Battle of Bosworth Field

His death marked the end of the Plantegenet dynasty which had ruled for over 300 years

Front 357

What is a cell envelope?

Back 357

Shell of membranes and peptidoglycan that surround the bacterial cytoplasm

Generic term for what surrounds the cytoplasm, regardless what is in it

Front 358

Do gram-positive cells have a peptidoglycan? If so where?

Back 358

Yes on the outside

Front 359

How many membranes do gram-negative bacteria have?

Back 359

2, outer and cytoplasmic/inner

Front 360

Is this a gram positive or negative cell? Label its components

Back 360

Positive

Front 361

Is this a gram positive or negative cell? Label its components

Back 361

Negative

Front 362

Do gram negative bacteria have a thick or thin peptidoglycan layer?

Back 362

Thin

Front 363

Do gram positive bacteria have a thick or thin peptidoglycan layer?

Back 363

Thick

Front 364

Do gram negative or positive bacteria have a outer membrane?

Back 364

Negative

Front 365

Do gram negative or positive bacteria have a periplasm?

Back 365

Negative

Front 366

In one sentence, describe what a periplasm is:

Back 366

Concentrated gel-like matrix in space between inner cytoplasm membrane and bacterial order membrane

Front 367

Do gram negative or positive bacteria have lipopolysaccharides (LPS)?

Back 367

Negative

Front 368

Why do gram negative bacteria have LPS and not gram positive?

Back 368

The LPS is part is the phospholipid bilayer which extends outwards towards the outside of the cell

Due to gram negative bacteria having an outer membrane (and positive only have a peptidoglycan layer on the outside), only gram negative bacteria will have LPS

Front 369

Do gram negative or positive bacteria have lipoteichoic acid?

Back 369

Positive

Front 370

What is lipoteichoic acid?

Back 370

Surface-assocaited adhesion amphiphile

Regulator of autolytic wall enzymes

Released from bacterial cells mainly after bacteriolysis induced by lysozyme, cationic peptides from leucocytes or beta-lactam antibiotics

Front 371

Why are lipoteichoic acids only found on gram positive bacteria?

Back 371

They are only found on the peptidoglycan layer to interact with the outside environment

Due to gram positive bacteria have peptidogycan layer as their outermost layer and negative as middle layer, only positive can have lipoteichoic acid

Front 372

Do gram positive or negative bacteria have teichoic acid?

Back 372

Positive

Front 373

How are lipid content different between gram positive and negative bacteria?

Back 373

Negative has high lipid content, positive is low

Front 374

Why do gram negative bacteria have high lipid content compared to gram positive?

Back 374

They have high lipid content because they have an extra membrane

Front 375

What is a phospholipid mainly composed?

Back 375

A glycerol derivative (of three C's) that are attached to two hydrophobic fatty acids on the non-polar side and a phosphoryl head group attached to another group on the polar/hydrophillic side

Front 376

True or False?

Lipid bilayers spontaneously organize in aqueous environments

Back 376

True

Front 377

What is cardiolipin?

Back 377

AKA diphosphatidylglycerol

Phosphate group of the lipid attaches onto another phosphate group of another lipid by a glycerol bridge

Found in bacteria (like E. coli) and in the mitochondria

Front 378

Where can you find cardiolipin?

Back 378

In bacteria like E. coli and in mitochondria membrane

Front 379

What functions do bacteria membranes serve?

Back 379

Permeability barrier

Anchor for surface proteins

Energy capture and storage

Front 380

How does the membrane of the bacteria function as a permeability barrier?

Back 380

Prevents leakage and functions as a gateway for transport of nutrients into and out of the cell

Front 381

How does the membrane of bacteria function as an energy capture and storage?

Back 381

Generation and maintenance of ion gradients (e.g. proton motive force)

Use proteins on membrane to capture charges on outside of cell and bring them in

Front 382

What happens to rate of permeability across a bacterial membrane if you add three carbons?

Back 382

A reduction of a thousand fold reduction of getting through the lipid bilayer membrane's permeability spontaneously

Front 383

Where is the periplamic space located?

Back 383

In the space between outer membrane and cytoplasmic membrane and includes spaces between strands of peptidolycan (cell wall) of gram negative bacteria

Front 384

What does it mean that the periplasm is iso-osmotic with the cytoplasm?

Back 384

Both periplasm and cytoplasm have same number of molecules and ions per unit volume

Keeping same osmotic pressure and concentration of particles on outside and inside

Front 385

True of False:

Periplasm is not a dynamic changeable matrix of material

Back 385

FALSE

Periplasm is a dynamic changeable matrix of material

Front 386

Describe the outer membrane of a gram-negative bacteria?

Back 386

A asymmetric lipid bilayer consists of phospholipids (inner leaflet), and lipopolysacharides (LPS, in outer leaflet) and protein

~8nm thick

Strong permeability barrier to hydrophobic compounds and large hydrophilic agents and is responsible for resistance to various antibiotics and chemotherapeutic agents

Front 387

Approximately how thick generally is the outer membrane of a gram-negative bacteria?

Back 387

~8nm

Front 388

Does the outer membrane of gram-negative bacteria play a role in resistance to various antibiotics and chemotherapeutic agents?

Back 388

Yes

Front 389

Can LPS be found in humans?

Back 389

No, exclusive to bacteria

Front 390

What does a human body do when an LPS is found in its blood stream?

Back 390

Our immune system has specific receptors to recognize LPS and distinguish self-cells from non-self-cells

Front 391

Is LPS an antigen?

Back 391

It is a potent antigen

Front 392

What is a main cause/symptom of an immune response to an LPS?

Back 392

Sepsis or septic shock

Front 393

What are serotypes and serotyping?

Back 393

Serotypes are groups within a single species of microorganism which share distinctive surface structures (like O and H antigens)

Serotyping is using serotypes as pathogenic diagnostics methods

Front 394

What are LPS composed of?

Back 394

Proximal, hydrophobic lipid A region

Distal (sticks towards environment), hydrophilic "O-antigen" polysaccharide

Core oligosaccharide region that connects the two

Front 395

What are O-antigens?

Back 395

Multiple repeats of short olgiosaccharide

Highly variable between species and even strains within a species

These sugars repeat over and over and over again, attached to one another

Front 396

What are core olgiosaccharides?

Back 396

Short olgiosaccharide that links O-antigen to lipid A anchor

Front 397

What is Lipid A?

Back 397

Forms the outer leaflet (or face) of the outer membrane

Inner leaflet or face of the outer membrane is composed of phospholipids

The unsaturated fatty acids which are linked to two sugars which have been modified with phosphates and is one thing the human immune system reacts to

This region is hydrophobic

Front 398

What part of the LPS is lipid A?

Back 398

The hydrophobic, membrane-anchoring region

Attached to the core oligosaccharide through KDO (2-keto-3-deoxyoctonic acid) which is negative charged and only found in bacteria

Front 399

What does Lipid A consist of?

Back 399

Phosphorylated N-acetylglucosamine (NAG) dimer with 4 to 7 saturated fatty acids attached

Front 400

What connects Lipid A and the core olgiosaccharide in LPS?

Back 400

KDO (2-keto-3-deoxyotonic acid)

Front 401

Can variation happen with Lipid A of LPS?

Back 401

Yes

Front 402

Why does variation happen with Lipid A of LPS?

Back 402

Bacteria can modify their lipid to avoid some antibiotics

Bacteriophages (viruses) will bind to LPS, inject their viruses and by scrambling up their LPS, bacteria can avoid these viruses

Variation can cause it to be harder for the human immune system to recognize

Front 403

Do core olgiosaccharides of LPS have variation?

Back 403

They do but are more conserved between species so less variations

Front 404

What do core olgiosaccharides consist of?

Back 404

Short chain of sugars

Front 405

What are the two unusual sugars present in core olgiosaccharides of LPS?

Back 405

Heptose and 2-keto-3-deoxyoctonoic (KDO)

Front 406

What is KDO?

Back 406

2-keto-3-deoxyoctonoic acid

A unique and invariably present in LPS and an indicator in assays for LPS

Connects Lipid A to core olgiosaccharides in LPS

Front 407

What is the o-polysaccharide of the LPS?

Back 407

AKA O-antigen

Consists of repeating olgiosaccharide subunits made up of 3-5 sugars where length ranging up to 40 repeat units (much longer than core polysaccharide) and maintains hydrophilic domains of LPS molecules

Variation in sugar content contribute to wide variety of antigen types in gram-negative species

Front 408

Can bacteria produce their own specified and exclusive sugars?

Back 408

Yes

Front 409

Where can you find divalent cations in the LPS?

Back 409

Proximal part of core containing KDO and lipid A backbone

It binds to the negative charges

Front 410

What happens when you phosphorylate KDO?

Back 410

You make it more negative which attracts divalent cations

Front 411

Many gram-negative bacteria are naturally resistant to what?

Back 411

Hydrophobic antibiotics

Detergents

Hydrophobic dyes

Front 412

Which is more resistant to chemotherapeutic agents, gram negative or positive?

Back 412

Negative

Front 413

What is a function of divalent cations in LPS?

Back 413

Can neutralize negative charges on membrane lipids

This assists in tight packing

Front 414

What is a chelator?

Back 414

Chemicals that "grab" ions like Mg2+ and/or Ca2+

Front 415

What are the effects of chelators?

Back 415

Brief treatment of E. coli with EDTA released about half of the LPS from cells owing to the removal of divalent cations such as Mg2+ and Ca2+

EDTA-treated cells become hypersusceptible to a wide range of hydrophobic antibiotics, dyes and detergents

The increase in permeability is likely due to filling in of the space, formerly occupied by LPS, by phospholipid molecules, thereby creating phospholipid bilayer domain

Front 416

What happens to a bacterial cell when you treat it with EDTA?

Back 416

Becomes hypersusceptible to wide range of hydrophobic antibiotics, dyes and detergents

Front 417

What causes the increased permeability when treating bacterial cells with chelators?

Back 417

Likely due to filling in of space which was formerly occupied by LPS by phospholipid molecules

Front 418

Kauffmann-White O-serogrouping system for E. coli uses what as its basis?

Back 418

Differences in O-antigens

Front 419

When an animal generates an antibody against one type of O-antigen, will it react with another type of O-antigen?

Back 419

No, once created they are specific for that type of O-antigen

Front 420

Of serological classification, what is the O-antigen?

Back 420

Outermost portion of bacteria's surface covering

O-antigen of the LPS

Front 421

Of serological classification, what is the H-antigen?

Back 421

Slender threadlike structures

Ex) Flagella

Front 422

Of E. coli strain O157:H7, what do the numbers and letters mean?

Back 422

The O means O-antigen, the 157 is the 157th identified O-structure and the 7th type of flagella (H) antigen

Front 423

What is another name for LPS?

Back 423

Endotoxin

Front 424

When infecting purified LPS or Lipid A into animals, what does it cause?

Back 424

Wide spectrum of nonspecific pathophysiological reactions such as:

Fever

Changes in white blood cell count

Disseminated intravascular coagulation

Tumor necrosis

Hypotension

Shock

Death

Front 425

When infecting purified LPS or Lipid A into animals, what causes wide spectrum of nonspecific pathophysiological reactions?

Back 425

A hyperactive immune response that can lead to septic shock

Front 426

What is septic shock?

Back 426

Serious condition that occurs when a body-wide infection leads to a dangerously low blood pressure

Front 427

What does Hydrophilic O poly-saccharides do for Lipid A?

Back 427

Act as a water-solubilizing carrier for toxic Lipid A

Front 428

What is peptidolycan?

Back 428

AKA PG or murein

Chemically unique, rigid structural component of cell wall found in bacteria

Human immune system has receptors for these

Provide shape of cells and preserve integrity of cytoplasmic membrane from rupture in medium or low osmolarity

Contains compounds unique to the microbial world like D-amino acids, diaminopimelic acid (DAP) and N-acetyl muramic acid (NAM)

Front 429

What gives bacterial cells their shape and help preserve integrity of cytoplasmic membrane from rupture in medium or low osmolarity?

Back 429

The peptidoglycan

Front 430

Will you find DAP or NAM in humans?

Back 430

No, exclusive to microbes

Front 431

What happens to a bacteria cell when you have a lysozyme digest its walls in a low solute solution?

Back 431

Water will enter the cell, causing lysis (cell bursting)

Front 432

What happens to a bacteria cell when you have lysozyme digest its walls in an isotonic solute solution?

Back 432

The internal components (its membrane and everything in it) will be a protoplast outside of the lysised cell wall

Front 433

In peptidoglycan, what is the wall glycan made up of?

Back 433

NAG (N-acetyl-glucosamine)

NAM (N-acetyl-muramic acid)

Front 434

In peptidoglycan, what is the wall peptide made up of?

Back 434

5 amino acid peptides

L-alanine

D-isoglutamate or Di-isoglutamine

Lysine or mDAP (not produced in human bodies)

D-alanine

And another D-alanine

Front 435

Will you find NAG in humans?

Back 435

NAG is found in mammals (yes)

Front 436

Will you find NAM in humans?

Back 436

No

NAM is a derivative of NAG that has an extra carboxyl group that can link it to the N-terminus (amino group) of wall peptide, unique to bacteria

Front 437

NAM is a derivative of what and what makes it different from that?

Back 437

Derivative of NAG

Has extra carboxyl group that can link it to the N-terminus of the wall peptide

Front 438

What chirality will you most likely find in human amino acids and bacteria peptidoglycan amino acids?

Back 438

L- in humans, D- in bacteria peptidoglycan

Front 439

Where will you find D-isoglutamate in bacteria?

Back 439

In the peptidoglycan of gram negative bacteria

Front 440

Where will you find D-isoglutamine in bacteria?

Back 440

In peptidoglycan of gram positive bacteria

Front 441

What is transglycoslyation?

Back 441

Polymerization of peptidoglycan subunits via their sugars leads to formation of long glycan strands that alternate between NAG and NAM by glycosidic bonds

Front 442

What is the third amino acid in a wall peptide of peptidoglycan?

Back 442

A lysine or mDAP (meso-diaminopimelic acid) which has a free amino group on them

Front 443

What is the purpose of the free amino group of the third amino acid in a wall peptide of a peptidoglycan?

Back 443

To form a peptide bond with an amino group attached to a carboxyl group found at the C-terminus of a wall peptide

Front 444

What happens during a transpeptidation reaction?

Back 444

C-terminal D-alanine of one subunit is removed by a transpeptidase enzyme

Then links free amino group of neighbouring wall peptide to newly liberated C-terminus of first wall peptide

Front 445

Can peptidoglycan vary from species to species?

Back 445

Yes

Front 446

What is a difference between typical gram negative and positive peptidoglycans?

Back 446

Negative:

D-isoGlu

mDAP

Positive:

D-isoGln

L-Lys

Front 447

Why do bacteria peptidoglycans have D amino acids instead of the typical chirality of L?

Back 447

Bacteria secrete proteases which recognize L shaped amino acids and degrade them/breaking the peptide-linkage bonds

Having D- amino acid instead of L, this allows the protease not to eat its own bacterial cell wall

Front 448

Do gram-negative bacteria always have cross-link wall peptides?

Back 448

Not always but usually

Front 449

How do gram-negative bacteria do cross-linking for wall peptides?

Back 449

They cross link wall peptides by linking amino groups on the side chain of a mDAP (or m-A2pm) to carboxy terminus of the D-Ala on position 4 of adjacent wall peptide

Front 450

How do gram-positive bacteria do cross-linking for wall peptides?

Back 450

Bacteria usually cross link wall peptides by linking amino group on the side chain of a lysine in position 3 to a chain of amino acids

The N-terminus of this "crossbridge" connects to the carboxy terminus of the D-Ala in position 4 of the adjacent wall peptide

Front 451

In a cross link wall peptide, what positions amino acids/molecules are connected?

Back 451

For gram negative and positive, its from position 3 to position 4's D-Ala

Front 452

Does gram negative or positive bacteria have extra peptides at the wall peptide connection?

Back 452

Gram positive

Front 453

Why would gram positive bacteria have extra peptides at their cross-bridge/interbridges?

Back 453

Bacteria are constantly fighting to each other and destroying one another where this variation can give one bacteria an advantage over another one

Bacteriophages pop bacteria cell wall to get out but with variation of peptidoglycan (such as 5 Gly) can make bacteria resistant to popping

Diversity of each bacteria's cell wall help avoid parasites mass extinction/an epidemic

Front 454

What position of the peptidoglycan wall peptide never (or ~99.999999%) never change?

Back 454

Position 4, D-Ala

Front 455

Describe briefly and broadly how cell wall synthesis (how wall peptides get synthesized attached to peptidoglycan) for S. aureus?

Back 455

Made in cytoplasm where NAG (or GlcNAc) will be attached to a nucleotide UTP

UDP-GlcNAc (UTP-NAG) enzymatically converted to UDP-NAM (MurNAc)

NAM-wall peptide transferred to a lipid which then modified further before being flipped by a "flipase" (MurJ protein) to outside of cell membrane for assembly into cell wall

Front 456

In cell wall synthesis for peptidoglycan, where are all the energy requiring steps taken place?

Back 456

In the cytoplasm

Front 457

What is the protein MurJ?

Back 457

A protein transfer complex (a flipase)

Transport peptidoglycan wall peptide brick from inner to outer leaflet of the inner membrane

Front 458

What does the enzyme transglycosylase do?

Back 458

Connects the NAG + NAM with other NAG + NAMs

Front 459

What does the enzyme transpeptidase do?

Back 459

Creates cross-bridges/interbridges between position 3 and 4 of wall peptide amino acids

Front 460

Where does LPS biosynthesis start in?

Back 460

In the cytoplasm with nucleotide linked sugars that get transferred to lipids

Front 461

Where is the O-antigen of LPS assembled?

Back 461

It is assembled on the same type of bactoprenol lipid as what peptidoglycan would bind to during synthesis

They are then transferred to periplasm by specialized membrane proteins (RfbX or MsbA-1 and 2) then ligated together

O-antigen subunits are polymerized onto the LPS core then the completed molecule is transferred to outer membrane

Front 462

What does LPS transport from inner to outer membrane require?

Back 462

It requires a whole multi-protein machinery to transport it

It is not spontaneous

Front 463

Why does LPS require a multi-protein machinery to transport it instead of being spontaneous?

Back 463

LPS is a lipid, it would never cross the aqueous periplasm by itself

It takes energy to extract LPS from inner membrane and get it to the outer membrane

This energy comes from ATP hydrolysis inside the cell which is carried out in the cytoplasm with proteins that carry this energy into exterior membrane

Front 464

For LPS transport from inner to outer membrane, where does this energy come from?

Back 464

ATP hydrolysis inside the cell (cytoplasm)

Front 465

Staphylococcus aureus has the ability to bind and do what to antibodies (immunoglobulins) of mammals?

Back 465

When they bind, this prevent bound antibodies from working properly by binding using "protein A"

Front 466

What is Protein A?

Back 466

Exquisitely high affinity for human antibodies and prevent them from working

It is a immunoglobulin-binding factor and displayed on surface of bacterial cell

Can be found in gram-positive bacteria

It consists of a C-terminal sorting signal that will be in the membrane while its N-terminus protrudes out

Front 467

What can be found in the C-terminal sorting signal of Protein A?

Back 467

Three parts

1) Highly conserved LPXTG sequence (X is any)

2) Stretch of mostly hydrophobic residues for about 20 amino acids long

3) Positively charged C-terminal tag of about 5 amino acids (rich in lysine or arginine amino acids)

Front 468

What part of Protein A causes it to get temporarily restrained into the membrane?

Back 468

The hydrophobic C-terminal domain

Front 469

What does the enzyme Sortase do?

Back 469

It sites on the surface of the cell and recognizes anything with a LPXTG motif (such as Protein A) and cleaves it between T and G residues

It will then transport that motif to a penta-Gly crossbridge of a peptidoglycan and attach it by transpeptidation and transglycosylation reaction

Front 470

What happens to the hydrophobic domain after the C-terminal sorting sequencing has been cleaved by Sortase?

Back 470

It is degraded

Front 471

Where does the enzyme Sortase cut?

Back 471

It sites on the surface of the cell and recognizes anything with a LPXTG motif (such as Protein A) and cleaves it between T and G residues

Front 472

What type of reaction does Sortase use to attach a Protein A LPXT to a peptidoglycan?

Back 472

Transpeptidation and transglycoslyation reaction

Front 473

What are the steps of incorporating Protein A into the peptidoglycan wall?

Back 473

1) Protein C go through membrane and hydrophobic domain stuck in membrane

2) Sortase cleaves between LPXTG

3) Transports it to a wall peptide

4) Tranpeptidation and transglycoslyation reaction adds it to the wall peptide

Front 474

What happens if every wall peptide of peptidoglycan had a protein A attached to it?

Back 474

If every brick was attached to a Protein A, it would not be able to create a net/mesh structure

Front 475

What is Murein (Braun's) lipoprotein?

Back 475

Holds outer membrane onto cell and attaches it to peptidoglycan

Most abundant protein in gram-negative cells

Amino-terminal cysteine residue is modified and carries a glycerol molecule to which two fatty acids are esterified where also linked to a fatty acid (N- to lipid, C- to cell wall)

Front 476

How are Murein (Braun's) lipoprotein's anchored onto the peptidoglycan?

Back 476

Fatty acyl residues are inserted in the outer membrane (inner leaflet) and epsilon amino group of a C-terminal lysine residue from the protein forms peptide bonds with free epsilon-carboxyl group of mDAP in peptidoglycan

Front 477

What happens if a gram-negative bacteria does not have Murein (Braun's) lipoprotein?

Back 477

The outer membrane would peel off

Front 478

To what position does Murein (Braun's) lipoprotein bind to?

Back 478

The side chain of the C-terminal lysine residues are attached to the peptidoglycan via free mDAP carboxyl group

Front 479

What are porins?

Back 479

Most abundant proteins in the outermembrane

They make pores in the membrane, spanning the outer membrane to form a narrow, water-filled "pore" or channel through the membrane

Front 480

What type of property do nutrients that go through porins usually have?

Back 480

Hydrophilic

Front 481

What are the major types of porins?

Back 481

Classical porins

Specific channels

Front 482

What are classical porins?

Back 482

Form nonspecific pores or channels for rapid passage of small hydrophilic molecules across outer membrane

Usually form trimer where each subunit was made by 16-beta strands traversing the membrane to form a beta barrel surrounding a large channel

Front 483

What is PhoE?

Back 483

It is a unique classical porin in that it is produced only under conditions of phosphate starvation by environmental conditions

Front 484

Classical porins form what type of structure that is made up of what?

Back 484

Form trimers that are made up of 16-beta strands traversing the membrane to form a beta barrel surrounding a large channel

Front 485

What is the diameters of classical porins and what they do allow through them?

Back 485

The diameter of classical porin channels are 1.1-1.2nm

They allow passage of hydrophilic molecules with molecular weight less than 600-700 Da

Front 486

Under adverse conditions/poor nutrition, what happens to OmpC?

Back 486

It is replaced by OmpF which form pores of larger diameter (1.2m), allow cells to take up larger molecules

Front 487

Does OmpF and OmpC prefer cations or anions?

Back 487

Cations slightly over anions

Front 488

Does PhoE prefer cations or anions?

Back 488

Anions

Front 489

What is the regulation of OmpF?

Back 489

Repressed under conditions of highly external osmolarity

Front 490

What is the regulation of OmpC?

Back 490

Expressed under conditions of high external osmolarity

Front 491

What is the regulation of OmpD?

Back 491

Expression depends on cAMP

Front 492

What is the regulation of PhoE?

Back 492

Repressed by external phosphate

Front 493

If you have high external osmolarity, which classical porins will be expressed and repressed?

Back 493

OmpF repressed

OmpC expressed

Front 494

Would you find OmpD in E. coli?

Back 494

No

Front 495

If a drug inhibits and eliminates cAMP, what happens to OmpD?

Back 495

It will not be expressed

Front 496

What does the structure of OmpF look like?

Back 496

Three beta barrels (made from beta sheets)

Front 497

What makes the eyelet of the beta barrel for OmpF?

Back 497

The eyelet is formed by two negative charged residues:

1) Glutamic acid at position E117

2) Aspartic acid at position D113

As well as four residues from the opposing barrel wall: a lysine at position 16 and arginines at position 42, 82 and 132

Front 498

What is OprF in Pseudomonas aeruginosa?

Back 498

Major porin of P. aeruginosa

Allows much slower diffusion of small solutes than other porins (50-100 times slower than OmpF of E. coli)

Front 499

What does Pseudomonas aeruginosa cause in humans?

Back 499

Cause serious lung infection in immunocompromised individuals and cystic fibrosis patients

Very difficult to treat due to notoriously impermeable outermembrane (because of OprF) where it can live in disinfectants and antibiotics because of this

Front 500

What are specific channels?

Back 500

They mediate the downhill (spontaneous) diffusion of specific classes of nutrients

Not as general and exclude most things because their shape will only let in a certain shape such as maltose or lactose

Front 501

What is LamB in E. coli?

Back 501

Favours passage of maltose and maltodextrins across the outer membrane

Porin-like trimeric protein and constructed as beta-barrel from 18 beta-strands

It is also a phage lamba receptor for E. coli

Does not require energy

Front 502

What happens if you have a mutant of LamB in E. coli?

Back 502

Mutants of this will not be affected by the virus its receptor is for

It also could not let in maltose and maltodextrins

Front 503

Does LamB require energy?

Back 503

No, LamB structure does not require energy

Front 504

What is Maltodextrin?

Back 504

A polysaccharide that is used as food additive

Produced from starch by partial hydrolysis

Front 505

Do specific channels require energy?

Back 505

No

Front 506

What is ScrY?

Back 506

Specific channel

Transporter for surcrose

Found in some strains of E. coli

Front 507

What is Tsx?

Back 507

Specific channel

Transports nucleosides

Receptor for phage T6

Found in some strains of E. coli and Salmonella

Front 508

How do bacteria capture iron from its environment?

Back 508

By secreting Siderophores

Front 509

What is Siderophores?

Back 509

A low molecular weight molecule that can form soluble complex with ferric iron

Too big to just pass through a porin channel

Front 510

Can vitamin B12 go through a porin?

Back 510

No, too big

Front 511

What are TonB dependent transporters?

Back 511

Outermembrane porin transport receptors that require TonB and energy from the cytoplasm

Can transport ferrichrome, vitamin B12 and iron siderophores across them

They are dependent on TonB because there is no energy in the periplasm so this would be energergized from the cytoplasm's proton motive force to energy the transporter

Front 512

What is ferrichrome?

Back 512

Cyclic hexa-peptide that forms a complex with iron

It is a siderophore (binds to Fe3+) composed of three Gly and three modified orinithine residues with hydroxamate groups

Front 513

What is FepA?

Back 513

Ferric enterobactin receptor

Beta-barrel structure

In the centre they have a plug domain that acts as a binding pocket (receptor) for their specific substrate

That substrate could be vitamin B12, heme molecule, a siderophore or something else larger and present at low concentration

Front 514

Will you find ATP in the periplasm?

Back 514

No

Front 515

What does TonB do to a TonB dependent transporter?

Back 515

TonB acts on the "cork" domain of the TBDT that blocks the OM receptor until it is engaged by its substrate (such as Vitamin B12)

Front 516

What is BtuF?

Back 516

A periplasmic binding protein that transports vitamin B12 to the inner membrane ABC transporter protein (BtuCD) or ATP-binding cassett after being added to the perplasm by the TBDT

Front 517

Which of these are least effective against Gram-negative bacteria?

Back 517

Vancomycin because too big

Front 518

How does Vancomycin inhibit cell synthesis?

Back 518

Binds to D-Ala and prevent it from being used as a substrate

Front 519

What does the antibiotic Chloramphenicol do?

Back 519

Inhibit protein synthesis

Front 520

What does the antibiotic Tetracycline do?

Back 520

Inhibit protein synthesis

Front 521

What does the antibiotic Rifamycin do?

Back 521

Inhibit RNA synthesis

Front 522

What does the antibiotic Penicillin G do?

Back 522

Inhibit cell wall synthesis

Front 523

What does the antibiotic Vancoymcin do?

Back 523

Inhibit cell wall synthesis by binding to D-Ala and prevent it from being used as a substrate

Front 524

What are the four basic mechanisms for antibiotic resistance?

Back 524

1) Bacteria can hibernate (go into static growth and not make new cell wall)

2) Bacteria can destroy antibiotics by enzymes

3) Bacteria can mutate target to no longer bind to antibiotic

4) Bacteria can keep antibiotic away from target by decreasing permeability or increasing efflux

Front 525

How do bacteria keep antibiotics away from the target?

Back 525

Decrease permeability by decreasing influx through expression of modified porins, fewer porins or change of membrane structure

Increase efflux by pumping the drugs out

Front 526

What is the AcrA/AcrB/TolC complex?

Back 526

Major contributor to antibiotic resistance

Strains that lack any of the three components have greatly increased susceptibility to several classes of antibiotics

Front 527

What does ArcB do in the ArcA/ArcB/TolC complex?

Back 527

Uses energy from proton gradient across the inner membrane to drive efflux of compounds at the periplasm-IM interface

Passes these compounds to TolC efflux channel for final export outside the cell

Front 528

What does TolC do in the ArcA/ArcB/TolC complex?

Back 528

It is an efflux channel for exporting compounds from ArcB to outside of the cell

Front 529

What is a lytic transglycosylase?

Back 529

Break bonds between NAG and NAM of peptidoglycan

Front 530

What is a amidases?

Back 530

Breaks the bond between NAM and wall peptide

Front 531

What is a endopeptidase?

Back 531

Breaks bonds between any two amino acids in wall peptide and crossbirdge peptides

Front 532

If a bacteria has D-iGln, is it gram positive or gram negative?

Back 532

Gram positive

Front 533

Where would lytic transglycosylase, amidase and endopeptidase cut between two wall peptide bricks?

Back 533

Front 534

What is the name for the lytic transglycosylase enzyme that cuts the NAG at its reducing end towards the NAM?

Back 534

A glucosaminidase

Front 535

What is the name of the lytic transglycosylase enzyme that cuts the NAM at its reducing end towards the NAM?

Back 535

Muramidase

Front 536

What is lysozyme?

Back 536

A muramidase that is produced by animals to destroy invading bacteria

Can be found in human tears as well as human immune cells make certain types of these to destroy bacterial cells

First enzyme to have is structure solved

Front 537

What is Lysostaphin?

Back 537

Endopeptidase produced by Staphylococcus simulans to kill Staphylococcus aureus by targeting and cleaving the unique pentaglycine crossbirdge found in its cell wall

Front 538

What are filementation temperature sensitive mutants in E. coli?

Back 538

Genetic mutants that have been isolated to form filaments when exposed to higher growth temperatures

Front 539

Why are temperature sensitive mutants significant?

Back 539

They enable us to study essential genes

Cells can be grown normally at one temperature and then switched to "non-permissive" temperature to study how loss of factor effects the cell

Front 540

What are conditional knockouts?

Back 540

Under one condition they work fine but when you change to set condition, it stops working

Front 541

What is the mreC mutant in E. coli?

Back 541

Instead of making long filaments, they start producing small circular cells

Front 542

What is side wall formation in bacteria?

Back 542

As the cells grow longer, new peptidoglycan is incorporated along the walls of the cell

Front 543

What is septum formation in bacteria?

Back 543

At the appropriate time, the rod-shaped cell switches to synthesize the division septum (forms two seperate cells)

Front 544

What does the MreC and MreD do?

Back 544

Code proteins for cell elongation

If you get rid of these guys, the bacteria cells begin to look like round dots (separate without elongation)

Front 545

What happens if you get rid of MreC and MreD from bacteria?

Back 545

Bacteria growth will cause them to look like round dots

Without MreC and MreD, the bacteria will separate without elongation

Front 546

What is PBP2 in the elongase complex?

Back 546

Penicillin binding protein 2 (when penicillin binds, it stops working)

It is a transpeptidase/transglycosylase

Front 547

What is MraY in the elongase complex?

Back 547

Makes "Lipid 1" (makes one of the bricks before getting flipped out)

Front 548

What is MurG in the elongase complex?

Back 548

Enzyme in synthesis of the "lipid 2" peptidoglycan precursors

Front 549

What is the MreB in the elongase complex?

Back 549

A bacterial actin homolog

Proposed to make filaments inside the cell

Front 550

What happens when you inhibit the elongase complex?

Back 550

Leads to round shaped cells

Front 551

How can inhibition of the elongase complex happen in bacteria?

Back 551

Can occur through mutations in any of the elongase proteins by use of certain chemical that interfere with the elongase

Front 552

What does the antibiotic Mercillinam do?

Back 552

Inhibit PBP2 thereby causing the formation of small round cells

Front 553

What happens when penicillin binds to PBP2?

Back 553

It prevents it from working (do any transpeptidase and/or transglycosylase)

Can cause formation of small round cells/inhibition of elongation

Front 554

What is the divisome in bacteria?

Back 554

A complex of enzymes and transmembrane proteins that synthesize the bacterial septum

Front 555

What happens if you block any of the Fts proteins in the divisome?

Back 555

It blocks septum formation forming long filament formations of the bacteria

Front 556

What happens if you block septum formation/synthesizing?

Back 556

The bacteria will grow long like a long filament formation

Front 557

What is the PBP3 and PBP1b of the divisome?

Back 557

It does transpeptidase and transglycosylase

Front 558

What is MurG of the divisome?

Back 558

Enzyme in synthesis of the lipid 2 peptidoglycan precursor

Front 559

What is the FtsZ of the divisome?

Back 559

Bacterial homolog of eukaryotic tubulin

Proposed to make filaments inside the cell that form a ring

This ring contracts to drive septum formation

Front 560

What happens when you inhibit divisome?

Back 560

Leads to filamentous cells

Front 561

How can you inhibit the divisome?

Back 561

Inhibition can occur through the use of certain chemicals that interfere with the divisome or through mutations in any of the divisome proteins

Front 562

What does sanguinarine do to B. subtilis cells?

Back 562

Inhibits FtsZ of divisome causing cell filamentation

Front 563

Can bacteria be viable while being a filamentous cell?

Back 563

They will be viable for a while but will die

Front 564

What is fluorescence microscopy?

Back 564

Process where you stimulate a molecule with one wavelength of light and it emits a longer wavelength of light

Front 565

In fluorescence microscopy, why are you only simulating the first wavelength of light in the reaction?

Back 565

Reason why is that first wavelength of light that you are stimulating reaction with, is absorbed by some atom or molecule orbital and kicked up to higher energy orbital state then within a few microseconds drop back down and emits a longer wavelength of light

Front 566

Explain the general steps in fluorescence micrscopy?

Back 566

1) Energy of UV photon is absorbed by electron

2) Electron is raised to orbital of higher energy

3) Electron loses some energy as heat and drops to slightly lower orbital

4) Fluorescence is emitted at longer wavelength

5) Electron returns to original level

Front 567

What is immunofluorescence micrscopy?

Back 567

In this technique, the protein you are looking for is labeled using antibodies (hence "immunofluorescence), typically two antibodies are used

Front 568

How do you label the protein inside of a cell in immunofluorescence microscopy?

Back 568

You must kill the cell (by fixation with formaldehyde) and permeabilize the cell (with detergent and lysozome)

You cannot use this technique on living cells unless the protein is exposed on the surface

Front 569

Can you use immunofluorescence micrscopy on living cells?

Back 569

No unless protein is exposed on the surface of the cell

Front 570

What are the general steps to immunofluorescence microscopy?

Back 570

1) Purify protein of interest

2) Round up an animal, inject animal with purified protein of interest

3) Come back a few weeks later, bleed it and get antibodies out of the animal

4) Hope the animal created antibodies

From here there are two options:

I) Put fluorescent tag on that antibody

II) Buy a antibody against that antibody commercially that is already fluorescently labelled

Front 571

What does fixation do during immunofluorescence microscopy?

Back 571

Lock all proteins in place using chemicals that crossing the protein so they do not move around while you are killing the cell

Front 572

What is fluorescence micrscopy?

Back 572

Using fusions to fluorescent proteins

The protein of interest is genetically engineered to be attached to a fluorescent protein like GFP or dsRed

Front 573

What is chimera or chimeric protein?

Back 573

When you add an extra domain to a protein

Front 574

Where do fluorescent protein usually attach to on the protein of interest in a microscopy?

Back 574

At the N- or C- terminus of the protein of interest

Front 575

Where can a problem arise with during fluorescence microscopy?

Back 575

Problems can arise if protein of interest is only made in very small quantities

Or if it doesn't work correctly when fluorescent protein is attached

Important not to overexpress chimeric protein since this can cause protein to go to locations in the cell it isn't suppose to

Front 576

Where was GFP originally isolated from?

Back 576

The jellyfish Aequorea victoria

Front 577

What is the chromophore in GFP?

Back 577

It is the fluorescent part of the protein

Made up by three amino acids (Glycine, tyrosine and theronine/serine) buried in the core of the molecular

Forms spontaneously

Front 578

How does a fluorescent microscope work?

Back 578

1) Bacterial cell illuminated with light at wavelength that excites GFP chromophore

2) GFP molecule emits light at longer wavelength (light scatters in all direction and microscope picks up some)

3) Dichroic mirror reflects only wavelength desired of the emitted light

4) Goes through camera to viewer

Front 579

What are the draw back of using standard (wide-field) fluorescent microscopes?

Back 579

You lose positional information in the Y-axis (lose visual depth)

High degrees of scattering and background fluorescence from molecules both above and below the focal plane bur the image

Front 580

What are the solutions to the draw backs/limitations of using a standard (wide-field) fluorescent microscope?

Back 580

1) Use a confocal microscopy

2) Use a TIRF microscopy

Front 581

What is a confocal microscopy?

Back 581

AKA Confocal laser scanning microscopy

Both excitation light and emitted light are focused together (lower the amount of light at specific spot)

Helps visualize cells in 3D by adjusting plane of focus at several intervals, merging the stack of images to build a 3D model

Allows observation of live microbes in real time

Front 582

What is TIRF microscopy?

Back 582

AKA Total Interal Reflection Fluorescence Micrscopy

Relies on phenomenon that occurs when light reflects inside of a prism

When angel of light hits prism wall is very small, 100% of light is reflected away

However, at point of impact, tiny electromagnetic wave called "evanescent wave" is produced

Unlike normal light, this wave decays rapidly (exponentially)

This wave can only penetrate into liquid above prism to a depth of 100 nanometers which reduced background fluorescence

Front 583

What is a limitation of TIRF microscopy?

Back 583

You can only look at the part of the cell closest to the coverslip

Front 584

TRUE or FALSE:

MreB and elongase complex make helical filaments

Back 584

FALSE

MreB and elongase complex do NOT make helical filaments

Front 585

What is AmiC in the divisome complex?

Back 585

A autolysin (self lysin)

A cell-wall lytic amidase (cleaves bond between glutamic acid and wall peptide)

Front 586

Why would the divisome include an enzyme that destroys cell walls like AmiC?

Back 586

Of the peptidoglycan wall, new bands are being built underneath and being attached to the wall where the amylase would come along and cut a bond and add in a new stand to the old peptidoglycan strand

This way, the wall will never be broken

Front 587

Is bacterial adaptive responses reversible?

Back 587

Yes, they go away some time after the stress goes away

Front 588

What is a gene?

Back 588

A stretch of DNA in a genome that encodes a discrete and individual protein or RNA

Front 589

Can bacterial do splicing?

Back 589

There are currently no found examples of "alternative splicing" or "spliceosomes" in bacteria

Front 590

What is an operon?

Back 590

A unit of genetic material that functions in a coordinated manner by means of an operator, a promoter and one or more structural genes

In an operon, genes can be overlapping, adjacent or have spaces between each gene

Front 591

What does it mean if a gene is monocistronic?

Back 591

The mRNA of gene contains a single RNA that codes for a single protein

Front 592

What does it mean if a gene is polycistronic?

Back 592

The mRNA of a gene contains a single RNA that codes for multiple proteins (like 3)

Front 593

What is a regulon?

Back 593

Operons around chromosome that share regulation

Example in image) The "pink" protein regulon consists of 5 genes, two monocistronic and a cluster of three polycystronic

Front 594

What is a promoter?

Back 594

Regions of DNA that control the transcription of adjacent genes by binding RNA polymerase to initiate transcription of an adjacent gene

Front 595

In a typical E. coli promoter, where will the Pribnow sequence (TATAAT box) be found?

Back 595

-10

Front 596

In a typical E. coli promoter, where will the UP element be found?

Back 596

Rich in AT-base pairs found approximately at -40 to -60 but can vary in position

Front 597

Which base pairs is the UP element rich in?

Back 597

AT-base pairs

Front 598

What are the consensus sequences of typical promoters from E. coli?

Back 598

-35 and -10 sequences

Front 599

Why is the recA promoter a strong promoter compared to other promoters?

Back 599

It largely adheres to the consensus sequence, lacking only a single base and having a slightly sub-optimal spacing between the -35 and -10 sequences

Front 600

How is the araBAD promoter a weak promoter?

Back 600

It does not adhere well to either the -10 or -35 consensus motifs and has sub-optimal spacing

The promoter has more mismatches than the natural/consensus

Front 601

What is the araBAD promoter controlling?

Back 601

The arabinose utilization operon

Front 602

If a researcher increases the space between the -35 and -10 of a bacterial promoter, would this make it a stronger or weaker promoter?

Back 602

Weaker

Front 603

If a promoter has many mismatches compared to the consensus promoter of bacteria, would it likely increase or decrease the strength/frequency of the promoter?

Back 603

Most likely make promoter weaker

Front 604

Why aren't all bacterial promoters optimal?

Back 604

Because you do not want to be transcribing all the time as well as some genes need to be transcribed a lot and some not so much as well as we want some genes to be off/on till some other factor come along

Front 605

What is the alpha subunit of bacterial RNAP (RNA Polymerase)?

Back 605

Two identical alpha subunits per holoenzyme with each alpha subunit have two distinct domains:

1) N-terminal domain (NTD) which interacts with RNAP via beta and beta prime subunits

2) C-terminal domain (CTD) which interacts with the up sequence on the promoter of DNA

Front 606

What is the NTD of the alpha subunit from bacterial RNAP?

Back 606

N-terminal domain which interacts with RNAP via beta and beta prime subunits

Front 607

What is the CTD of the alpha subunit from bacterial RNAP?

Back 607

C-terminal domain that interacts with the upstream sequence of the promoter of DNA

Front 608

What is the beta and beta prime subunits of bacterial RNAP?

Back 608

Largest distinct subunits

Carry out actual catalytic reaction, reading DNA into an RNA transcription

Front 609

What is the omega subunit of bacterial RNAP?

Back 609

Help complex subunits assembly, specifically beta prime

Little (if any) role in transcription

Front 610

What is the sigma subunit of the bacterial RNAP?

Back 610

Main recognition part for promoter sequences -35 and -10 regions

Responsible for correctly targeting RNAP to correct sequences on the chromosome

Front 611

What are the steps in bacterial transcription?

Back 611

1) Promoter recognition

2) Isomerization

3) Initiation

4) Promoter escape and elongation

Front 612

What happens during the first step of bacterial transcription: promoter recognition?

Back 612

RNAP binds to promoter to generate "closed complex" (driven by affinity of RNAP holoenzyme for its promoter sequence)

Transcription cannot occur from this point because DNA is still in double-stranded conformation

Front 613

What happens during the second step of bacterial transcription, isomerization?

Back 613

Promoter is unwound near the -10 sequence to expose a region of ssDNA from approximately -12 to +2

Facilitated by action of sigma factor

Goes from closed complex to an open complex

Front 614

What happens during the third step of bacterial transcription, initiation?

Back 614

Promoter is unwound near -10 sequence to expose a region of ssDNA

First few bases are transcribed

RNAP still trapped at promoter and "abortive" cycling of transcription can occur where small transcripts of less than 10 base pairs are made and RNAP never leaves the promoter

Front 615

What happens during the fourth step of bacterial transcription, promoter escape and elongation?

Back 615

Major conformational change can occur at this point

RNAP escapes the promoter and transcribes into adjacent gene

RNA leaves sigma factor behind

RNAP is now an "elongation" complex where it will transcribe the whole gene until it encounters specific termination signals downstream

Front 616

The rate at which forward progression through the pathway of RNAP transcription depend on what?

Back 616

How well the RNAP binds the promoter to form the initial closed complex

How easily the RNAP melts the DNA to form the open complex

How easily the RNAP can escape from the promoter and form the elongation complex

Front 617

Why would bacterial RNAP have different "alternative" sigma factors?

Back 617

Each sigma factor would have an optimal target for a unique promoter consensus sequence

This allows detection of different types of promoters

Front 618

What is sigma D/RpoD/sigma 70?

Back 618

The "housekeeping" sigma factor or also called as primary sigma factor

Transcribes most genes in growing cells

Front 619

What is sigma S/RpoS/sigma 38?

Back 619

Starvation/stationary phase sigma factor

To save energy

Front 620

What is sigma H/RpoH/sigma 32?

Back 620

Heat shock sigma factor

Turned on when exposed to heat to protect again the heat

Front 621

What is sigma 28/RpoF?

Back 621

The flagellar sigma factor

Front 622

What is sigma 24/RpoE?

Back 622

Extracytoplasmic/extreme heat stress sigma factor

Front 623

What is sigma 19/FecI?

Back 623

Ferric citrate sigma factor

Regulates the fec gene for iron transport

Front 624

What is sigma 54/RpoN?

Back 624

The nitrogen-limitation sigma factor

Is unrelated in sequence to other sigma factors and requires additional activating proteins to help initiate transcription

Front 625

Sequence specific DNA binding proteins typically target which groove?

Back 625

Typically target the major groove where there is a cavity wide enough to accommodate an alpha helix and where more DNA hydrogen bonds are exposed

Front 626

What is Class I activated promoters?

Back 626

DNA binding proteins target specific sequences upstream of the promoter and help recruit RNAP to a non-optimal promoter sequence by binding the C-terminal domain of the RNAP alpha subunit

(Green circles in image)

Front 627

What is Class II activated proteins?

Back 627

Activating protein binds a region just upstream of the -35 box where it can make contact with domain 4 of the sigma subunit

Front 628

How does protein-induced conformation change in DNA help activation of RNAP?

Back 628

Some promoters bind RNAP poorly because sequences not oriented or spaced properly

Activating proteins enhance transcription by bending DNA to improve ability of RNAP to bind these sub-optimal promoters

Front 629

What is simple repression of RNAP?

Back 629

Blocking RNAP from binding to its promoter, causing transcription to be repressed

Repressors bind "operator" sequences that lie within the promoter, blocking access of RNAP

Front 630

How does generating looped DNA cause simple repression of RNAP?

Back 630

Some repressors trap promoter DNA into a loop, preventing RNAP binding or traps RNAP into a complex that cannot escape the promoter

Front 631

If you have a depletion of nucleotides and ATP & energy, can you transcribe genes?

Back 631

No, those are what are required to do transcription

Front 632

What does the LacI gene do?

Back 632

Makes a repressor where if bound to a promoter for LacZYA, it shuts that gene off

Front 633

What does gene LacZ do?

Back 633

Produces beta-galactosidase

Front 634

What does the gene LacY do?

Back 634

Produce Lactose Permease

Front 635

How does lactose get into the bacterial cell?

Back 635

Lactose gets in by Lactose Permease

Front 636

What causes the repressor for LacZYA (LacI) to unbind to the DNA?

Back 636

Once lactose is in the cell, it will bind to LacI, causing conformational change, releasing to from the bound DNA

Front 637

What is the "Two-component" system?

Back 637

Most common way in which bacteria transmit signals from outside world to cytoplasm

Most abundant multi-step signaling pathways found in nature (over 70,000 two-component systems have been identified from genome sequences)

They have domains that can often be swapped to generate new signaling molecules

Front 638

In a broad, simple two-component system, what is a histidine kinase (HK)?

Back 638

Sensor of environmental signal

Transfer a phosphate from ATP to response regulator

Almost always found as a homo-dimer

Front 639

In a broad, simple two-component system, what is a response regulator (RR)?

Back 639

Molecule that controls the response output

Often the RR is a DNA binding protein that changes its affinity for DNA once it is phosphorylated on an aspartic acid by the HK

Front 640

Where would you find a histidine kinase sensor residue?

Back 640

You would find it on the inner membrane of bacteria

Front 641

What are the steps in environmental signals are transduced through phopshotransfer or phosphorelay?

Back 641

1) Signal detected by periplasmic domain of histidine/sensor kinase resulting in conformational change of protein complex

2) Newly activated kinase domain undergoes "autophosphorylation" where it transfer terminal phosphate from ATP to a conserved histidine residue in its catalytic domain (causing it to become activated)

3) Histidine kinase domain transfer phosphate from its conserved histidine residue to an aspartic acid residue in the response regulator, resulting in conformational change of the response regulator, altering its activity

4) Response regulator is now able to bind to DNA and active/repress transcription

5) Reverse. When environment change, some HKs can cat as phosphatase to remove phosphate from response regulator to shut down the system rapidly

Front 642

What are the least chemically stable phosphoryl-mediated signaling?

Back 642

Phosphohistidine & Phosphoasparate

Front 643

What are some very chemically stable phosphoryl-mediated signaling?

Back 643

Phosphoserine & Phosphothreonine & Phosphotyrosine

Front 644

What are phosphorelay systems?

Back 644

Systems that bounce phosphate between Histidine (H) and Aspartic Acid (D) residues

Allows more flexibility, allowing you to get modulated responses compared to two-component systems

Front 645

What are periplasmic sensing histidine kinases?

Back 645

Sense stimuli in the periplasm or outside world

Front 646

What are transmembrane sensing histidine kinase?

Back 646

Sense stimuli in the inner membrane

Front 647

What are cytoplasmic sensing histidine kinases?

Back 647

Sense cytoplasmic stimuli

Front 648

What is the ArcAB system?

Back 648

Uses phosphorelay to respond to oxygen levels and regulate gene expression

Repression of enzymes in aerobic metabolism, activation of enzymes in anaerobic metabolism

Front 649

ArcB protein is specifically sensitive to what?

Back 649

Redox-state of the quinone pool

Front 650

If there is a lot of electron flux going on, what will happen to the quinone pool for ArcB?

Back 650

Buildup of oxidized quinones

Front 651

When will the disulfide bonds be oxidized in ArcB protein?

Back 651

When there is a build up of oxidized quinones

Front 652

When will you find active ArcB protein?

Back 652

During anaerobic conditions when quinones are maximally reduced (no oxygen to give electrons to)

When disulfide bonds are reduced

Front 653

What is polymyxin B?

Back 653

Produced by a gram-positive bacteria

Can damage the outer membrane of gram-negative bacteria, killing them

Can poke holes in membrane (causing gradient dissolution) or go through it (binding to intercellular molecules)

The antimicrobial peptide interact with cell surface and have a preference for negatively charged membranes

Front 654

What is the basis for cross protection in bacteria?

Back 654

Generally cross protection occurs when protection against two apparently unrelated stresses utilize similar or identical defense systems

Front 655

The adaptive response in bacteria to polymyxin B is dependent on what?

Back 655

PhoP and PhoQ (still less than a 50% survival rate though)

Front 656

What bacterial treatments increase the survival rate of bacteria against polymyxin B?

Back 656

Wild type pretreated cells in low magnesium buffer 30 minutes before adding polymyxin

PhoP mutant pretreated cells in low magnesium buffer 30 minutes before adding polymyxin with PhoP added back onto the plasmid

Front 657

How does the PhoP/PhoQ system sense diverse causes of membrane stress?

Back 657

PhoQ has a patch of highly negatively charged amino acids (aspartic and glutamic acid)

Despite PhoQ should be repelled due to negative charged membrane, the domain is held in place by bridges formed by divalent cations (Mg2+ and Ca2+)

Loss of Mg or Ca (or antimicrobial peptides) disrupts the bridge

Front 658

How does low pH affect the PhoP/PhoQ system?

Back 658

Low pH affects aspartic acid and glutamates affecting their charge making them lose their negative charge (becoming neutral), causing conformation change of the PhoP/PhoQ

Front 659

When is the PhoP/PhoQ system in a repressed state?

Back 659

When there is Mg2+ or Ca2+ between them and the membrane

Front 660

When is PhoP/PhoQ system in an active state?

Back 660

Loss of Magnesium/Calcium

Antimicrobial peptides

Low pH causing amino acids becoming neutral charge

Front 661

What does the PhoP/PhoQ system do?

Back 661

They regulate a variety of genes that toughen up the outer membrane of bacteria

Front 662

What are Pags?

Back 662

PhoP-activated genes

Genes being produced when PhoP/PhoQ is active

Front 663

What are some Pags genes?

Back 663

Divalent metal transport

LPS modification

Outer membrane proteins

Superoxide dismutase

Front 664

What are Prgs?

Back 664

PhoP-repressed genes

Genes produced when PhoP/PhoQ is repressed

Front 665

What are some Prgs genes?

Back 665

Type-3 secretion system (SPI-1) involved in invading cells

Flagella

Front 666

How does an activated PhoP/PhoQ make changes to the LPS of the outer membrane?

Back 666

Adds an extra sugar to LPS (PmrAB/aminoarabinose modification)

Adds extra hydroxyl group (LpxO/addition of 2-hydroxy to myristate)

Palmitodylation of 3-hydroxyl group (PagP)

Front 667

Does turning on PhoP/PhoQ, making changes to the LPs of the outer membrane make it stronger or weaker?

Back 667

Stronger, more resistant to insult

Front 668

What does aminoarabinose/PmrAB do to LPS?

Back 668

Adds an extra sugar

Lessens negative charge on lipid A

Front 669

What does PagP mediated palmitolyation do to LPS?

Back 669

Palmitoylation of 3-hydroxyl group

Increases hydrophobicity

Front 670

What does hydroxymyristate/LpxO do to LPS?

Back 670

Addition of 2-hydroxy to myristate

Increases hydrogen bonding between adjacent lipid A units, enhancing the outer membrane's ability to resist penetration by organic ions

Front 671

Which system is required for Salmonella virulence?

Back 671

The PhoP/PhoQ system

Front 672

What is the SOD enzyme?

Back 672

Found in Salmonella, diverged from E. coli (horizontally transferred by Gifsy-2 phage)

An enzyme that can deactivate free radicals

Expressed in macrophages

Front 673

Why are phagocytic white blood cells dangerous to bacteria?

Back 673

Reactive oxygen species (peroxide, superoxide)

Reactive nitrogen (nitric oxide)

Antimicrobial proteins/peptides

Front 674

What is sodCI transcriptionally controlled by?

Back 674

The PhoP/PhoQ two-component regulatory systems

Front 675

What happens to sodCI when you have a PhoP-null mutation?

Back 675

Decrease in transcription of sodCI and loss of regulation

Front 676

What is sodCI horizontally transferred by?

Back 676

Gifsy-2 phage

Front 677

Are histidine sensor kinases highly modular?

Back 677

Yes

Front 678

Can domains be swapped to change the specificity of signaling?

Back 678

Yes, altering target (ex. magnesium sensor with sugar metabolism action)

Front 679

What is a condition for domain swapping in HK and RR molecules?

Back 679

Must have associating charges (negative and positive, hydrophobic and hydrophobic etc...)

Front 680

What is a bacterial adaptive response to alkylation damage of DNA?

Back 680

Agents that alkylate DNA, adds methyl group to various bases and backbones

Occurs spontaenously

Front 681

What is O6-meG?

Back 681

A damaged base that will mispair with wrong pair, causing mutations and possibly be lethal

Front 682

What four genes are required to repair alkylation damage?

Back 682

ada - alkB

alkA

aidB

Front 683

What does ada gene repair?

Back 683

MPT, O6-meG and O4-meT

Front 684

What does alkB gene repair?

Back 684

1meA and 3meC

Front 685

What does alkA gene repair?

Back 685

3meA, 3meG, O2-meT, O2-meC, 7-meG, 7-meA

Front 686

What does aidB gene repair?

Back 686

Currently unknown

Front 687

What is the ada gene & protein?

Back 687

Ada protein is a DNA repair protein and transcription factor

A sacrificial stoichiometric reagent DNA repair protein which takes a methyl group from a damaged methylated-DNA base or phosphate

Front 688

Can ada protein turn into a transcription factor? If so, when?

Back 688

When it has a methylated N-terminal domain in the presence of damage

Binds to a particular sequence at the promoter, allowing RNAP to bind more tightly (fairly weak promoter)

Front 689

When ada protein is acting as a transcription factor, what is N-Ada and C-Ada doing?

Back 689

N-Ada will be methylated, attaching to promoter

C-Ada will interact with alpha subunit of RNA polymerase

Front 690

What does the methylation of the N-terminal domain of Ada do to result in strong DNA-binding?

Back 690

Methylation reduces the size of a negatively charged patch in Ada

Front 691

Is DNA negatively or positively charged?

Back 691

Negatively

Front 692

What happens to proteins during heat shock?

Back 692

Hydrogen bonds and noncovalent bonds will be broken

Denaturation/unfolding causes exposure of hydrophobic regions

Front 693

What are chaperones?

Back 693

Proteins in E. coli used to combat against changes in temperature/heat shock

Have ability to bind to unfolded or aggregated proteins and use energy and allow them to fold properly

Front 694

What is the GroEL and GroES proteins?

Back 694

They form a chamber for folding proteins

They are able to enclose unfolded protein, use energy (by ATP-hydrolyses) to refold the protein using misfolds and then spit them out

They use hydrophobic surfaces, pulls apart the aggregated structure and allow them to fold back to original form

Front 695

Heat shock response is controlled by what alternative RNAP sigma subunit?

Back 695

Heat shock sigma factor AKA sigma H or sigma 32

Front 696

When there is a number in the sigma subunit for RNAP, what does that number mean?

Back 696

The kilodolton size/measurement/mass/molecular weight

Front 697

What factor increases the rate of sigma 32 translation?

Back 697

Increased upon heat treatment

Front 698

What does FtsH in bacteria do?

Back 698

It is a protease in the membrane of E. coli which eats/degrades sigma 32

Front 699

What do the chaperons DnaK and DnaJ do?

Back 699

Makes sigma 32 a better substrate for FtsH

Front 700

How can a whole field become infected with Anthrax?

Back 700

Doesn't spread across humans but rather through livestock like cows

Animals that are infected with Anthrax will be filled with bacteria that eat their nutrients and make spores causing the animals to die and decompose in the grass, releasing more spores

Front 701

Who discovered Anthrax?

Back 701

Robert Koch

Front 702

TRUE or FALSE:

Bacterial spore formation is a stress response

Back 702

TRUE

Front 703

Sporulation (endospore formation) occurs primarily in gram positive or negative bacteria?

Back 703

Typically in gram-positive

Rare in gram-negative

Front 704

In a laboratory, how can you induce sporulation?

Back 704

Sporulation can be induced by starvation for a carbon, nitrogen and/or phosphorus source

Sporulation begins immediately following exponential growth

Front 705

Is sporulation a reproductive process?

Back 705

No

When environmental conditions return to normal, one spore will transform into one vegetative cell which then undergoes cell division

Front 706

Are spores metabolically dormant?

Back 706

Yes

Front 707

What are spores highly resistant to?

Back 707

Variety of environmental insulds

UV and gamma radiation

Free radicals

High (120) and low temperature

Acid and alkali conditions

Hydrolytic enzymes

Organic solvents

Front 708

What allows spores to be seen with a light microscope?

Back 708

They can be seen with a light microscope due to high protein levels causing a high refractivity

Front 709

What is the cortex of a spore?

Back 709

Surrounds spore core and composed predominantly of peptidoglycan with different structure from that of vegetative cell wall

~50% of NAMare muramic acid lactam (MAL)

~25% of NAM carry single L-Ala therefore ~25% as many DAP residues available to participate cross-link formation in spore cortex

Important for maintenance of spore core dehydration which increases spore wet-heat resistance

Front 710

Do all spores have an exosporium?

Back 710

No, it is an optional feature/structure

Front 711

What is the spore coat?

Back 711

Outmost structure common to spores of all species

Consists of a species of one or more morphologically distinct layers that protect spore from variety of toxic molecules and from mechnical damage

Front 712

What is the core wall of a spore?

Back 712

Immediately underlying the cortex is a second layer of peptidoglycn with different structure, the germ cell wall

The core wall becomes the cell wall of newly growing vegetative cells

Front 713

Will you find teichoic acids in spores?

Back 713

No

Front 714

What is a spore core?

Back 714

Contains the cytoplasmic membrane, cytoplasm and nucleoid

Front 715

What is the core cytoplasm of the spore core?

Back 715

Highly dehydrated

Contains high concentration of dipicolinic acid (DPA) and calcium which forms calcium dipicolinic acid (this associated with low water content and heat resistance)

pH ~1 unit lower then growing cells

Front 716

Why is the core cytoplasm of spore cores highly dehydrated?

Back 716

Allows the cytoplasm to last for a long time

Less chance for reactions to occur

Front 717

What is the spore nucleoid like in the spore core?

Back 717

Highly condensed and bound by SASPs (small acid-soluble spore proteins) which protect DNA from potential damage from UV radiation, desiccation and dry heat

Front 718

Why are spore nucleoid high condensed and bound by SASPs?

Back 718

To protect DNA from potential damage from UV radiation, desiccation and dry heat

Front 719

What is the process of sporulation like?

Back 719

1) Vegetative cell goes through vegetative cycle for growth of medial division

2) Polar division for asymmetric cell division

3) Engulment of prespore

4) Cortex development

5) Spore coat development

6 & 7) Maturation and cell lysis (lyse mother cell to release spore)

8) Germination

9) Go to step 1

Front 720

What is Spo0A in sporulation?

Back 720

Master regulator that turns on genes for sporulation

Activates genes required for later events in sporulation

Represses genes involved in stationary-phase growth

A phosphorelay pathway produces Spo0A~P which initiates sporulation

Front 721

What initiates sporulation?

Back 721

Spo0A~P

Front 722

The switch from vegetative growth to sporulation involves a switch of what?

Back 722

Switch from sigma A to vegetative sigma factor H and F in forespore compartment of RNAP

Front 723

Bacteria motility is driven by what?

Back 723

Surface appendages

Front 724

What are the four type of bacteria movement/motility?

Back 724

Swim

Swarm

Twitch

Glide

Front 725

What is the flagella?

Back 725

Most common form of mobility in bacteria

Needed for both swimming and swarming

Movement in liquid media or moist surfaces

Helical, threat-like appendage

Front 726

What does the structure of flagella like?

Back 726

Front 727

What does the L Ring and P Ring do for the flagella?

Back 727

Anchor the flagella tail/filament to the membrane

Front 728

Which parts of the flagella help the flagella filament/tail spin?

Back 728

The ROTOR and STRATOR

Front 729

What does MotA/B do in flagella?

Back 729

Form proton channel

Front 730

Where does the energy for flagella movement come from?

Back 730

Proton movement or Proton motive force

Front 731

If flagella is rotating clockwise, is it going forwards or backwards?

Back 731

Backwards

Front 732

If flagella is rotating counter-clockwise, is it going forwards or backwards?

Back 732

Forwards

Front 733

How does flagella turn direction when it has a single flagella?

Back 733

Stops moving/rotating and reorients itself

Front 734

How does flagella turn direction when it has a bundled flagella?

Back 734

Tumbles by having flagella push apart

Front 735

What is bacterial swarming?

Back 735

Widespread flagella-based motility

Movement on solid surface with some fluid/moisture

Often form spearheaded raft along advancing front

Bacteria appear to be in a different state

Front 736

How do bacteria appear to be in a different state during swarming?

Back 736

Bacteria longer in length

Have more flagella (hyperflagellated) to overcome friction

Bacteria move as a group (swimming is independent)

Thought to be important in pathogenesis

Front 737

What is bacterial gliding?

Back 737

Movement on dry, solid surfaces without flagella or pili

Slower than flagella-based movement

~40 proteins spanning cytoplasm, inner membrane and periplasm (no clear mechanism)

Engerzied by proton motive force

Front 738

What is another name for bacterial gliding?

Back 738

Adventuours motility

Front 739

What is bacterial twitching?

Back 739

Movement on solid surfaces

Type 4 Pili acts as 'grappling hook' (extend, attach and retract)

Needed for biofilm formation and signal transduction on host cell surface

Tend to be rafts of cell moving outward

Front 740

What is Type 4 Pilus?

Back 740

Mostly found in gram positive bacteria

Main structure is made of a protein called Pili

Movement is through sequential pulling and attaching

Need ATPase to polyermize the pilli and another to retract

Front 741

What does PiliA of Type 4 Pilus do?

Back 741

Bind inanimate objects (plastic) and host cells glycolipids

Front 742

What does PilB of Type 4 Pilus do?

Back 742

Polymerizes PilA into growing pilus

Front 743

What does PilTU of Type 4 Pilus do?

Back 743

Retracts pilus

Front 744

What does PilD of Type 4 Pilus do?

Back 744

Prepillin peptidase processes PilA by removing leader sequence

Front 745

What is taxis?

Back 745

Bacteria direct movement based on environment

Front 746

What is chemotaxis?

Back 746

Directed motility

Towards/aways from chemicals

Receptors detect external attractant concentrations

Signals relayed to activate CheY which binds to motor switch

Front 747

What is phototaxis?

Back 747

Directed motility

Towards/away from light

Many photoreceptors but all seem to bind chromophore co-factors which absorb visible light

Electrochemical gradient and redox sensors seem involved but mechanisms unclear

Bacteria have dedicated photoreceptors

Front 748

What is aerotaxis?

Back 748

Directed motility

Towards/away from oxygen

Aer and Tsr receptors interact with electron transport chain

Sense redox changes

Similar to chemotaxis where activates CheY to control flagella motor switch

Front 749

What is magnetotaxis?

Back 749

Directed motility

Orientation in magnetic fields

Some bacteria can align themselves with Earth's magnetic field

Have organelles called magnetosomes containing magnetic crystals

Live in transition zones between high and low oxygen

Front 750

What is biased random walk of bacteria?

Back 750

Randomly transitions between 'runs' (CCW) and 'tumbles' to help find things to eat

When there is a gradient present, their runs become longer towards that attract

Front 751

How does a two-component system control chemotaxis?

Back 751

1) Membrane sensor for the chemical (this case repellent)

2) Protein CheW interacts with CheA

3) CheA is a kinase that will phosphoryalte CheY and CheB

4) CheY causes CW motion (default is CCW)

5) CheB demethylates sensor (CheR methylates it which increases activity)

Front 752

What does methylation of the two-component chemotaxis system do?

Back 752

Allows memory of the system which tells if it is moving towards or away from an attractant

Front 753

What is a magnetosome?

Back 753

Bacteria organelle for magnetotaxis

Contains magnetic crystal

Front 754

Do bacteria display ultraism and when?

Back 754

Yes during Myxococcal fruiting body where bacteria in the stems will not propagate so those on top would (they become stock cells)

Front 755

What is a biofilm?

Back 755

Bacteria that adhere to a surface (living, dead or abiotic) through various self-generated adhesions

Occur on most surfaces in nature and are the preferred mode of growth for majority of bacterial species (instead of the commonly laboratory planktonic growth)

Front 756

What is planktonic?

Back 756

"Without a plank"

Refers to bacteria free in solution, not attach to a surface

Opposite of a biofilm

Common laboratory bacterial growth method

Front 757

What happens to bacteria genes when they are in a biofilm?

Back 757

They begin to switch/change gene expression, changing their phsiological state

Front 758

Do bacteria have a choice whether they want to be biofilms or not?

Back 758

Yes, it is a choice

Kinda like a social behevaiour where they coordinate their behaviour in response to a stimulus

Front 759

Why are biofilms important?

Back 759

They are incredible hard to get rid of as they are resistant to antibiotics and disinfectants

They can invade pipes, industrial/marine systems, and medical devices

Front 760

How can we use biofilms for 'good'?

Back 760

Wastewater treatment and pollutant degradation (waste water gets passed over imbedded rocks and over microbes where it absorbs nutrients

Plant and animal growth promotion

Protection against pathogens by "normal flora" or "probiotic" biofilms

Front 761

What is normal flora?

Back 761

AKA Normal microbial flora

Relatively stable with specific general populating of various body regions during particular periods in individual's life

May aid or harm host or exist as commensals

Front 762

How would a normal flora aid a host?

Back 762

Competing for microenvironments more effectively than pathogens like Salmonella

Producing nutrients host can use

Block binding sites for pathogens

Production of anti-microbial compounds

Priming of immune response

Front 763

How may a normal flora harm the host?

Back 763

Causing dental caries, abscesses or other infectious disease

Front 764

What is Rhizosphere?

Back 764

Narrow region of soil that is directly influenced by root secretions and associated with soil microorganism

Front 765

Why would a plant want a biofilm on them such as red clover root hairs?

Back 765

Bacteria feed off dead cells, proteins and sugars released by roots

Bacteria fix nitrogen and make other nutrients for plants

Front 766

How do biofilms on humans help prevent infection?

Back 766

Block binding sites for pathogens by releasing soluble factors and competition for same receptors

Competition for nutrients

Production of anti-microbial compounds

Priming immune response

Front 767

Why is implant contamination a huge issue?

Back 767

Once a patient gets infected from a hip infection, the biofilm willconstantly grow and are very problematic

Even if cleared once, it can keep growing back

Front 768

What are the advantages for bacteria/biofilms sticking to a surface?

Back 768

Safety in numbers

Buffet benefits

Commerce

Front 769

In biofilms, how are there safety in numbers?

Back 769

Herd effect (predators might graze on your neighbour instead of you)

Protection from immune cells and molecules

Group detoxification of harmful substances

Front 770

In biofilms, what are buffet benefits?

Back 770

(An advantage for sticking to surfaces)

Food comes to you instead of going to food (reduce energy expenditure)

Neighbour may produce food for you from more complex substrates you cannot use

Front 771

In biofilms, what is commerce?

Back 771

(An advantage for sticking to surfaces)

Swapping of DNA fragments and replicons (plasmids, transposons, bacteriophages)

Stimulate further biofilm formation

Front 772

What are the disadvantages for bacteria to form a biofilm?

Back 772

Small town syndrome

Famine

Bad neighbourhoods

Front 773

For bacteria in biofilms, what is Small town syndrome?

Back 773

Progeny need to leave home and make their way in the world to acquire nutrients elsewhere

Disadvantage for bacteria to form biofilms

Front 774

For bacteria in biofilms, how can famine happen?

Back 774

Food stop going by certain bacteria which can cause the bacteria to eat its neighbours

Disadvantage for bacteria to form biofilms

Front 775

For bacteria in biofilms, how can there be bad neighbourhoods?

Back 775

Some bacteria might attract undesirable elements (such as immune cells) into a territory

Disadvantage for bacteria to form biofilms

Front 776

Are biofilms reproducible?

Back 776

Yes under a given set of conditions but it all depends on both genetic and environmental factors

Front 777

Are mushrooms and channels the only arrangements biofilms can form?

Back 777

No, other arrangements are possible

Front 778

Is it possible for a biofilms to contain more than one bacterial species?

Back 778

They often do

Front 779

Do biofilms have circulatory systems?

Back 779

Many biofilm structures contain water channels that permit convective flow of liquids through the biofilms

This shows there is an active exchange of nutrients from external environment

Front 780

TRUE or FALSE:

Biofilms are elastic

Back 780

TRUE

Clusters are quite elastic with intentional contraction and extension

Front 781

What is the substratum of biofilms?

Back 781

Underlying layer or substance beneath the surface

Front 782

How does the surface and the substratum of biofilms differ?

Back 782

Decreased oxygen and pH near substratum

Growth rate different in each area

Gene expression changes

Front 783

How does oxygen levels change in biofilms?

Back 783

It decreases near the substratum

Front 784

How does the pH change in biofilms?

Back 784

It decreased near the substratum

Front 785

How are growth rate different in each area of the biofilms?

Back 785

Often lower average growth rate or none at all in some areas

Front 786

What has a higher overall growth yield, planktonic or biofilm bacterial cultures?

Back 786

Biofilms

Reach a higher cell density/unit volume than planktonic

Front 787

What is going on in this biofilm?

Back 787

This image shows how gene expression changes in biofilms and is not uniform

Specifically what is going on is a two component regulatory system that recognizes phosphate where the active cell turns on alkaline phosphatase which can chop off phosphate from other molecules in the environment and use it for themselves (yellow ones expressing the substrate)

Front 788

What are some methods to study biofilms?

Back 788

Robbins device

Chemostats

Flow cells

Static systems

Front 789

What is the biofilm study technique, Robbins Device?

Back 789

Microbial culture flow through a tubular section made of glass, metal or clear plastic containing removable studs that permits study of various materials in same system

Front 790

What is the biofilm study technique, Flow cells?

Back 790

Spying on bacteria growing on a slide affixed to a chamber where fluid (sterial media) flow through

Front 791

How is Static Biofilm Assay done?

Back 791

1) Overnight broth culture

2) Remove broth and was unattached cells

3) Stain cells with crystal violet

4) Solubilize crystal violet (by alcohol or organic solvent) and read optical density

Front 792

Why would you remove broth and wash unattached cells in a Static Biofilm Assay?

Back 792

When washed out, the platonic bacteria gets washed out but the biofilm is stuck

Front 793

Here are the results of a static biofilm assay, what does these results show?

Back 793

The wild type as well as M3 and M4 can produce a biofilm

Front 794

How are biofilms commonly formed?

Back 794

1) Initial attachment

2) Firm attachment/microcolony

3) Initial encasement of microcolony by production of expolysaccharide (EPS) production

4) Maturation

5) Detachment and disperal under right conditions

Front 795

How bacteria attach to a surface depends on what?

Back 795

Properties of surface (made of, charge, hydrphobicity, etc...) and adhesions (flagella, pili, cell surface proteins, EPS)

Front 796

What are bacterial "conditioning film"?

Back 796

Surfaces typically have absorbed environmental components that change their properties

Front 797

What are the two steps of bacterial attachment?

Back 797

Dock (reversible) and Lock (irreversible)

Front 798

What happens if the bacteria of a biofilm have a pili mutant?

Back 798

Bacteria will accumulate on surface but will not organize themselves

Front 799

What happens if the bacteria of a biofilm have a flagellar mutant?

Back 799

The bacteria will barely stick to surface at all

Front 800

What happens if the bacteria of a biofilm can no longer do chemotaxis (or any taxis)?

Back 800

They will be confused

Make biofilm but cannot make chemotaxis (ability to swim towardsnutrient or away from repellent) so without this, you swim in a disorientatedway

Front 801

What happens if the bacteria of a biofilm no longer have motor function?

Back 801

They will be paralyzed as they cannot swim

Front 802

What aspect of the flagellum is necessary for biofilm formation?

Back 802

Presence of a functional flagellum

Front 803

What is bacterial FlhDC?

Back 803

Regulatory proteins that control flagella expression

These decrease in concentration as biofilm forms

Front 804

What is bacterial OmpR/EnvZ?

Back 804

Two-component regulatory proteins that control adhesin expression

They peak in concentration as biofilm forms irreversible (lock) attachment

Front 805

What is bacterial RcsCDB?

Back 805

Regulatory protein that control capsule production

Increases and peaks at irreversible attachment and decrease after biofilm formation

Front 806

What is the function of the exopolysaccharide?

Back 806

Cement/adherance to substratum

Structural/scaffold

Protection for desiccation by trapping water in

Protection from predation

Protection from biocides, antibiotics, antibodies and noxious substances

Nutrient storage and edible scaffold

Front 807

What are the three matrix proteins required in Vibrio cholerae biofilm formation?

Back 807

RbmA (produced first), RbmC (produced last) and Bap1 (produced second)

Front 808

What happens to Vibrio cholerae biofilm formation if the bacteria has an inability to produce VPS? (aka VPS- bacteria)

Back 808

VPS- prevents retention of daughter cells and stops accumulation of RbmA and RbmC that blocks biofilm formation

Front 809

What does the biofilm development of V. cholerae look like?

Back 809

1) Initial attachment occurs and RbmA accumulates on several sites on cell surface

2) Founder cell divides and RbmA continues to accumulate while Bap1 appears at cell surface interface at initial division site ensuring that daughter cell adhere to surface (lock)

3) Cells further divide and a cell cluster gradually forms, encased in a flexible envelope containing RbmC, Bap1 and VPS with the production and accumulation of RbmA

4) Mature biofilm forms as individual cell clusters expand and contact each other

5) Dissociation and dispersal

Front 810

What appears to be the responsibility of V. cholerae Bap1?

Back 810

Ensure that daughter cells of biofilm adhere to the surface

Front 811

TRUE or FALSE:

Biofilms can survive exposure to high levels of antimicrobials that kill planktonic cells of the same strain

Back 811

TRUE

Front 812

What does it mean that biofilms have antibiotic tolerance by Lack of Penetration/Diffusion?

Back 812

Of the antibiotic, the concentration takes a long time to hit anything relevant (they have a diffusion limitation)

Their protection is enhanced if the bacteria also have antibiotic resistance genes (ex. breakdown of antibiotic)

Front 813

What does it mean by biofilms have a diffusion limitation?

Back 813

Cells at the surface would be killed by high concentrations of antimicrobial compound while cells at bottom would be exposed to lower concentrations and survive

Front 814

What does it mean that biofilms have antibiotic tolerance by Slow Growth effects?

Back 814

The ones on the bottom are hibernating which means you are notmaking new cell wall, new proteins, or no transcription which means drugs thattarget cell wall, proteins and transcription will not work

Front 815

Why do the bacteria on the bottom of a biofilm have a slower growth rate than those higher up?

Back 815

They have reduced growth rate due to limiting oxygen and nutrients

Front 816

What does it mean that biofilms have antibiotic tolerance for Phenotypic tolerance?

Back 816

Changes in gene expression induced by growth in a biofilm that result in a tolerant subpopulation (not permanent mutations)

Includes many stress response genes

Front 817

How was the Pseudomonas aeruginosa PA14 gene 45E7 found?

Back 817

A experiment to find biofilm antibiotic resistant genes used a random library of 4000 strains with different mutations caused by a transposon randomly interrupt different genes

Then screen for mutants for loss of antibiotic resistant in biofilms where they found 45E7 which was more sensitive to several antibiotics while in biofilm

It had an insertion in the NdvB gene

Front 818

What is the Pseudomonas aeruginosa & B. japonicum NdvB gene?

Back 818

It encodes glucosyltransferase (links sugars to one another)

Makes cyclic-beta-(1,3)-glucans which is a circular polymer of glucose

The NdvB protein sits on the inner membrane

Front 819

What happens to a bacteria with a NdvB knockout?

Back 819

When gene is knocked out and cannot make NdvB protein, the bacteria becomes more susceptible to antibiotics

Without the NdvB gene, it does not make cyclic glucans

Front 820

What is the Tobramycin killing assay?

Back 820

Fractions eluted from columns preloaded with glucan/no glucan

Tobramycin will be trapped and released by 25% acetonitrile only when glucan is present

Front 821

Will bacteria that have the NdvB gene express that gene when in planktonic growth?

Back 821

No, only in biofilm growth

Front 822

How do the glucans produced by the NdvB gene produced antibiotic resistant to Tobramycin (Tb)?

Back 822

The diffusion of Tb into the cytoplasm may be slowed by the glucans produced by NdvB

The decreased diffusion of Tb may allow the biofilm cells additional time to adapt to and resist the action of the antibiotic

Front 823

What does it mean that biofilms have antibiotic tolerance by their Persister phenotype?

Back 823

The bacteria would go into long term deep hibernation

They undergo a deep unmetabolic state that makes them appear like spores and are highly resistant to different types of stress

Front 824

What happened to the city of Caffa in 1346 that caused the spread of the Black Death?

Back 824

Caffa was a trading post between Europe and Asia

At this time, there was a fight between the Italians and the Mongolians which caused the city to be put under siege

The Mongolians caught the Black Death and shot their corpses over the walls of Caffa, infecting the people inside who then traveled by sea to the rest of Europe

Front 825

What is the symptoms of the Black Death, AKA the Bubonic Plague?

Back 825

Severe malsia

Headache

Shaking chills

Fever

Pain and swelling

Adenopathy

Buboes (affected regional lymph nodes)

Gangrene

Front 826

What bacteria caused the Bubonic Plague?

Back 826

Yersinia pestis, a gram-negative rod closely related to Salmonella and E. coli

Front 827

How is Bubonic plague acquired?

Back 827

By flea bites through skin

Front 828

How is Pneumonic plague acquired?

Back 828

Caught through inhalation of air

Front 829

What is deadlier, bubonic plague or pneumonic plague?

Back 829

Pneumonic plague

Front 830

What is malaise?

Back 830

Feeling of general discomfort or uneasiness

Front 831

Where does Yersinia pestis live in fleas?

Back 831

In the flea's proventriculus, the valve-like organ between the esophagus and midgut

Front 832

How does the Yersinia pestis spread using its flea host?

Back 832

When bacteria gets into flea, builds up in esophagus and begins to starve so its bite more and more to feed itself

When they suck something up, it only goes half way and spits it back out, great for transmission

Front 833

Is the blockage of the flea's proventriculus necessary for bacterial infection?

Back 833

No, but it increases the rate of the flea's biting

Front 834

What is quorum sensing?

Back 834

Bacterial cell-to-cell communication using small freely disffusible small molecules called "autoinducers" where they would activate transcription

Also a way of telling how many bacteria and what type are present in the immediate environment

Front 835

What does quorum sensing do to gene expression?

Back 835

How the bacteria to switch between two distinct gene expression programs:

One that is favored at low-cell-density for individual, asocial behaviour

Another that is favored at high-cell-density for social, group behaviour and start producing goods called common groups

Front 836

What is luciferase?

Back 836

Produce bacterial luminescence

Involves oxidation of a long-chain aliphatic aldehyde and reduced flavin mononucleotide (FMNH2) with the liberation of excess free energy in the form of a blue-green light at 490nm

Front 837

Why does the Juvenile bobtail squid do bioluminescence?

Back 837

They are colonized in their light organ by Vibrio fisherii and specifically only this species and uses the light to blend in with the starry night sky (not expressed during day) to protect against predatory fish swimming underneath

Front 838

How does the Juvenile bobtail squid do bioluminescence?

Back 838

When squid under sun, bacteria turn off the gene that turns on light as it would be wasteful and in morning, the bacteria at its lowest count

Throughout the day, the bacteria are dividing in the light organ, fed by amino acids provided by the squid

At high concentrations of bacteria, enough autoinducers have accumulated in the light organ to trigger bacterial synthesis of luciferase/luciferin and this would produce a blue-green light out of the light organ shinning downwards

In the morning, approximately 95% of the bacteria culture will be expelled from the light organ and process begins again

Front 839

Which biological autoinducer has a Boron in it?

Back 839

An AI-2 autoinducer such as S-THMF-bacteria

Front 840

What is quorum sensing like in gram-negative bacteria that involve LuxI-like and LuxR-like enzymes?

Back 840

LuxI would secret an AI-1 molecule, a large hydrophobic and small molecule that is able to get across porins and inner membrane and can get into the cytoplasm

Once AI-1 in cytoplasm, it will bind to LuxR which is a DNA binding protein

The LuxR-AI-1 complex would activate or repress target gene expression

The LuxR-AI-1 complex would also lead to synthesis of more LuxI for more inducers

Front 841

In the LuxI and LuxR quorum sensing system, what is the purpose of the rapid amplification of autoinducers?

Back 841

To produce a quick change from very low to very high concentrations of autoinducers to ensure all cells nearby trigger at nearly the same time

Front 842

What is LuxI?

Back 842

An quorum sensing enzyme that produce AI-1

Front 843

What is LuxM?

Back 843

A quorum sensing enzyme that produce AI-1

Front 844

What is LuxS?

Back 844

A quorum sensing enzyme that produce AI-2

Front 845

What is CqsA?

Back 845

A quorum sensing enzyme that produce CAI-1

Front 846

How does the quorum sensing in V. harveyi work?

Back 846

They are complex, involving three different autoinducers (AI-1, AI-2 and CAI-1)

Front 847

What is the quorum sensing mechanism that is required in V. harveyi to inhibit LuxR?

Back 847

If there are no autoinducers being synthesized, LuxN, LuxP & Lux Q and CscQ with have phosphorylation, using ATP, its component regulatory system

Which will phosphorylate LuxU

Which will phosphorylate LuxO

Which will produce small RNAs

Which will inhibit LuxR

Which allows the secretion of Type 3 secretion

Front 848

What is the quorum sensing mechanism that is required in V. harveyi to produce Lux ABCDE genes?

Back 848

If there is AI-1 produced by LuxM, LuxN will not phosphorylate its complement system

If there is AI-2 produced by LuxS, LuxP & LuxQ will not phosphorylate its complement system

If there is CAI-1 produced by CqsA, CqsS will not phosphorylate its complement system

With LuxN, LuxP & LuxQ and CqsS systems inactivated, LuxU and LuxO will not get phosphorylated (inactivated)

This allows LuxR to inhibit Type 3 secretion and produce Lux ABCDE genes

Front 849

What is AHL?

Back 849

N-acyl homoserine lactone structures, an autoinducer-1 (AI-1)

Membrane permeant

Specific to each pathogen

Can be made by gram negative bacteria

Front 850

What is Furanosyl borate diester?

Back 850

An autoinducer-2 (AI-2)

Membrane impermeant

Conserved structure (except in Salmonella)

Only biological structure that has Boron origin in its structure

Made by gram negative and positive bacteria

Often made by LuxS enzyme and recognized by LuzQ surface receptor

Front 851

What molecule is needed for the formation of AHL and AI-2?

Back 851

SAM

Front 852

In Pseudomonas aeruginosa, what happens if you have a LasI mutant?

Back 852

It forms flat, undifferentiated biofilms that unlike wild-type biofilms, are sensitive to biocide sodium dodecyl sulfate

Front 853

What is the enzyme LasI?

Back 853

A quorum sensing enzyme that is a LuxI homlogue and produces AI-1

Front 854

What is this image showing?

Back 854

If you have a mutant is LasI, you will not get mushroom (or upward development) formation of bacteria but if you add a purified AI-1 (what LasI makes), the mushroom formation will somewhat return

Front 855

What is quorum interception in Salmonella?

Back 855

Salmonella lack LuxI gene and cannot make AHL but can detect multiple AHL's from other species using LuxR homologue, SdiA

They can also recognize modified AI-2 via a LuxP homologue, LsrB

Front 856

What is SdiA?

Back 856

A LuxR homlogue in Salmonella that detect other species AHL and actives several genes, one being rck (resistance to complement killing)

Becomes active during the transit of Salmonella enterica through gastrointestinal tract of turtles (other species too?)

Front 857

What is LsrB?

Back 857

A LuxP homologue in Salmonella that detect modified AI-2

Actives expression of AI-2 transporters and clear AI-2 from the medium

Front 858

How does a "typical" gram-positive bacteria do quorum sensing?

Back 858

Mature autoinducer peptide will be transcribed and translated

It will export by a membrane transporter and get detected by a histamine kinase on the inner membrane

Using ATP, it will active a response receptor by phosphorylation

This complex will activate or repress target genes

Front 859

What are some anti-QS strategies observed in bacteria?

Back 859

Metabolism of autoinducers by V. paradoxus

Degrade AHL using aiiA gene by B. subtilis

Autoinducing peptides active own virulence genes but inhibit those of other S. aureus groups in S. aureus

Front 860

How does the host cell (ex. human cells) respond to bacterial QS molecules?

Back 860

IL-8 production by lung epithelial cells

IFN(gamma) production by T cells

Cox-2 expression by fibroblasts

Acceleration of apoptosis by macrophages and neutrophils

Front 861

How does the upper airway epithelium do anti-QS?

Back 861

High degradation activity for C6 molecules and C4-HSL with very little diffusion

Front 862

Are bacteria QS degradation heat sensitive? How can this be shown?

Back 862

Yes

It can be shown by boiling cell lysate which inactivated QS degrading activity

Front 863

What is a glycan?

Back 863

Compound consisting of a large number of monosaccharides linked glycosidcally

Front 864

What enzyme is required to break down a glycan?

Back 864

Different enzymes are required to break down each bond

Front 865

Can humans create the proteins to break down the bonds of glycan?

Back 865

Our own genome only encodes enzymes with the capacity to break down only a few glycans including lactose, maltose, and sucrose as well as monosaccharides

We rely heavily on microbes to break down complex glycans

Front 866

What are Bacteroides thetaiotaomicron?

Back 866

Very successful glycophile and an abundant member of our microbiota and has the capacity for digesting (human) indigestible dietary polysaccharides

Can be found in the human gut and is anaerobic

Has 163 homologs of two TonB-dependent outer membrane proteins (SusC and SusD) that bind and import starch

Front 867

What are the purposes of TonB-dependent transporters and surface/perpiplasmic enzymes?

Back 867

These work to break large olgiosaccharides into simple sugars

TonB-dependent transporter SusC work in concert with starch binding lipoproteins, SusD, SusE, SusF and SusG which break down the olgiosaccharides into mono-/di-saccharides which then cross inner membrane through specific membrane transporters

Front 868

What is SusG?

Back 868

It is a surface enzyme that breaks large starch into smaller olgiosaccharides

Front 869

What are the steps of Bacteroides breakdown of olgiosacchardies into simple sugars?

Back 869

Starch binding initiated by SusD, SusE and SusF

Initial degradation carried out by SusG of large starch into smaller olgiosaccharides

Olgiosaccharides transporter into periplasm via SucC in concert with inner-membrane protein TonB

In periplasm, malto-oligosaccharides further degraded to glucose by SusA (AKA neopullulanse) and SusB (a alpha-glucosidase)

Simple sugars then imported across inner membrane by permease

Front 870

What is Arabinoxylan?

Back 870

A heteropolymer complex carbohydrate with multiple monosaccharides and glycosidic linkages

Each alpha/beta linkages must be broken by different enzymes

Front 871

Where is most of the glycan breakdown taken place in the human body?

Back 871

In the large intestine

Front 872

What has faster transit of materials; thin mucous layer or thick? Why?

Back 872

Thin

Thick has slower transit as it provides the bacteria time to digest the tough material

Front 873

How is the human gut like a fermenter?

Back 873

Our intestines are devoid of oxygen and the microbes that live in our gut are all capable of living anaerobically

Many of the gut bacterial species are strict anaerobes and will die in the presence of oxygen

Because we lack oxygen, the microbes lack the capacity to break down short fatty acids into anything smaller where the bacteria would then secret the byproducts of fermentation (which our tissues utilize)

Front 874

What is the small intestine like for nutrient digestion?

Back 874

Small intestine is where simple and easy to digest nutrients get absorbed into blood stream

Front 875

Where would you find colonocytes?

Back 875

The cells that line the intestine

Front 876

What is the primary energy source for colonocytes?

Back 876

Butyrate

Front 877

What happens if we allow oxygen into out gut?

Back 877

Some bacteria will die

Other bacteria will convert sugars, using the oxygen, into carbon dioxide which means they will use all the energy from fermentation for themselves and leave none for us

Front 878

What happens when you starve the bacteria in our gut and how would you starve them?

Back 878

Prolong periods of simple sugars and fat diets can cause the gut microbes to starve

When they starve, this can result in loss of diversity in the gut microbiota

Front 879

How is our microbiota established?

Back 879

Before birth, we are stile, protected by the amniotic sac

At birth, we first encounter bacteria as we pass through the vaginal canal which habors many types of commensal bacteria

As we eat complex food and grow, we develop a microbiota and stabilize our microbiota after the age of 3

Front 880

What does breast milk apparently do for a baby's microbiota?

Back 880

Break milk contain several polysaccharides that our bodies cannot break down

This suggests that breast milk is designed to help specific bacteria colonize the infant gut

Breast-fed have more total proteobacteria and bacteriodetes than formula fed which only have more firmicutes and no bacteriodetes

Front 881

Why are bacteriodetes important for the gut microbiota?

Back 881

They break down glycan

Front 882

What is the purpose of germ-free Gnotobiotic mice in relation to research into the microbiota?

Back 882

Take gut microbiota from people with different conditions, transfer them into mice and observe physiological effects the microbes produce

Front 883

Is there a link between obesity and the microbiome?

Back 883

Yes, an obesity-associated gut microbiome have increased capcity for energy harvest

Front 884

What happens if you put the microbiome of a lean mice into a cohouse obese mice?

Back 884

The cohouse mice will begin to lose weight (this suggests transferable property and changeable phenotype)

Front 885

TRUE or FALSE

The microbiota have no association with pathology

Back 885

FALSE

Changes in the microbiota can be associated with pathology

Front 886

What is Clostridium difficile?

Back 886

A gram-positive spore-forming anaerobe

Highly virulent toxin-producing strains that have emerged, causing debilitating and sometimes lethal intestinal infections

NOTE: There are other Clostridium in the human gut that are safe for us

Front 887

What is the number one risk-factor for C. difficile disease is what?

Back 887

Antibiotic use

Front 888

How is antibiotic use the number one risk factor for C. difficile disease?

Back 888

Antibiotics are wiping out protective microbes in our gut, enabling C. difficile to invade and establish a niche in our gut

Normally, the gut microbiota will be able to outcompete the C. difficle but due to the antibiotics, the C. difficile population can rapidly expand and produce a lot of toxins

Front 889

What appears to be wrong with this colon?

Back 889

It appears to have a C. difficile infection

Front 890

What is one method for treating C. difficile infections?

Back 890

Fecal transplantation

Front 891

What is fecal transplantation?

Back 891

Taking poop from a healthy individual and delivering it by mouth or anus route to the individual's infected with C. difficile

Front 892

How does the liver fight off C. difficile growth?

Back 892

The liver produces cholic acid which gets convereted into deoxycholic acid by Clostridium scindens

C. difficile are very sensitive and grows very poorly in the presence of deoxycholic acid which can end up stopping C. diff vegetative growth

Front 893

What are some common methods that bacteria acquire new genes naturally?

Back 893

Transformation/uptake of free DNA

Conjugation/mobile plasmids

Transduction/phages

Front 894

In bacterial conjugation, which bacteria is considered the "male" bacteria?

Back 894

The one that sends out the pilus to conjugate

Front 895

In the genetic exchange in prokaryotes, how does transformation occur?

Back 895

Donor bacterium will go through cell lysis

Competent recipient bacterium takes up DNA fragment

Recombination occurs

Front 896

In the gene exchange in prokaryotes, how does transduction occur?

Back 896

Donor bacterium will get infected by bacteriophage

New phages contain phage genetic bacterial and bacterial DNA

Bacterial DNA fragment injected into receipient bacterium by abnormal phage

Recombination occurs

Front 897

In the gene exchange in prokaryotes, how does conjugation occur?

Back 897

Donor bacterium + recipient bacterium will have a direct transfer of DNA by pilus

Seperating of the mating bacteria will then occur

Recombination

Front 898

What was Griffith's 1928 experiment?

Back 898

Inserted live S strain (capsuled bacteria) into mice, it died

Inserted Live R (no capsule) strain into mice, it lived

Inserted heat killed S strain into mice, it died

Inserted heat killed S strain with live R strain into mice, it lived

Showed the transformation principle

Front 899

Give a summary of Avery's transforming principle experiment?

Back 899

DNA alone changed R to S cells and this effect was lost when extract was treated with deoxyribonuclease

DNA carried the genetic information required for R to S conversion or transformation

Front 900

Can all bacteria take up DNA?

Back 900

No, only competent bacteria can (which can be natural or chemically modified to allow it)

Front 901

What is genetic transformation?

Back 901

A process by which free DNA is incorporated into a recipient cell and brings about genetic change

Front 902

What is a competent cell?

Back 902

A cell that is able to take up a molecule of DNA and be transformed

Front 903

What is natural competence?

Back 903

Genetically programmed physiological state permitting the efficient uptake of macromolecular DNA

Can be gram positive or negative

Front 904

What is artifically-induced competence?

Back 904

State of competence achived by chemical or physical treatment of the cell

Front 905

Are gram positive bacteria's competence regulated by something?

Back 905

Gram positive bacteria are regulated by growth phase to enter state of competence

They become competent later in their life cycle

Quorum sensing can help them be competent

Front 906

Why does quorum sensing have an impact on gram positive state of competence?

Back 906

The cells are growing well, they believe it would be good time to exchange DNA

A way to exchange DNA with their own species, because picking up DNA from different species can be dangerous whereas picking DNA from your own kind is safer

Can be wasteful if they exchange DNA in an environment where there's not enough bacteria around

Front 907

What is quorum sensing-based control of competence like in Streptococcus pneumoniae?

Back 907

Pheromone precursor (pre-CSP) is encoded by ComC and processed and secreted by action of ComAB proteins

This pheromone detected by histidine kinase ComD, leading to phosphorylation of ComE

Phosphorylated ComE drives transcription of ComeCDE and ComAB operons as well as ComX

ComX is minor sigma factor that appears to active transcription of late competence proteins which includes proteins involved in taking up DNA, RecA and negative regulatory protein that eventually turns off expression of Com operons

Front 908

In the quorum sensing-based control of competence in Streptococcus pneumoniae, what is the function of ComAB?

Back 908

Cleave the pre- off of pre-CSP and secrete CSP

Front 909

In the quorum sensing-based control of competence in Streptococcus pneumoniae, what is the function of ComD?

Back 909

A histidine kinase pheromone (CSP) detector that phosphorylates ComE when comes in contact with its pheromone

Front 910

In the quorum sensing-based control of competence in Streptococcus pneumoniae, what is the function of ComE?

Back 910

When phosphorylated by ComD, it drives transcription of ComCDE, ComAB and ComX operons

Front 911

In the quorum sensing-based control of competence in Streptococcus pneumoniae, what is the function of ComX?

Back 911

ComX is a minor sigma factor that appears to active the transcription of late competence proteins including proteins involved in taking up DNA, RecA and negative regulatory protein that eventually turns off expression of Com operons

Front 912

What is the gram-positive competence system composed of?

Back 912

A pseudopilus encoded by ComG operon that is related but not identical to Type-IV pilus (Type-2 secretion system)

A NucA nuclease

A ComEA DNA binding protein

A ComFA ATPase helicase/motor protein

A ComEC transmembrane pore

Front 913

How does DNA get into gram positive bacteria?

Back 913

DNA gains access to ComEA protein by pseudopilus

NucA nuclease introduces double stranded breaks, allowing free end to enter the cell

Enters cell through ComEC channel

ComFA protein is an ATPase that may act as a helicase to unwind DNA so DNA enters cell single stranded (entering by 3' end) where ssDNA bind to SSBP

5' end of incoming DNA chopped into nucleotides

RecA works a recombination protein, binding to ssDNA

Front 914

What is required on gram-negative bacteria for efficient transformation to occur?

Back 914

The incoming DNA to have a sequence called DUS (DNA-Uptake Sequences)

Front 915

Do bacteria have biases when picking up DNA?

Back 915

Gram positive no

Gram negative yes

Front 916

How does DNA get uptake into gram-negative bacteria?

Back 916

DNA containing DUS sequence is bound to known receptor on cell surface called DR

DNA passed through the PilQ-secretion complex

ComE, a periplasmic protein delivers DNA to ComA

DNA degraded to ssDNA before being passed through ComA channel

ssDNA binds to SSBP then RecA for recombination

Front 917

Does DNA uptake/import require energy?

Back 917

ATP yes as it generates significant force

(Bacteria like B. subtilis has an uptake rate of 80 +- 10 bp/s)

Front 918

What are two commons methods of artificially-induced competence?

Back 918

Calcium-induced competence

Electroporation

Front 919

What is calcium-induced competence?

Back 919

E. coli treated with high concentrations of calcium ions and then stored in the cold so become transformable at low efficiency

No specific DNA sequences required (although DNA methylation pattern will affect efficiency)

Simple reagents, no special equipment

Less than 10% of cells typically become competent

Front 920

What is electroporation?

Back 920

An artificially-induced competence method that uses pulsed electric fields to produce small, transient pores in lipid membranes

When DNA present outside the cell during electric pulse, they can enter through pores

Require sophisticated power supply which allows pulse current, duration and electrical resistance to be carefully controlled

Works with most species with ss- or ds-DNA

Approximately 95% of cells become competent but high death rate

Front 921

TRUE or FALSE and explain

DNA can be used as a nutrient by competence

Back 921

TRUE

Experiment done by Finkel and Kolter showed that when bacteria (wt that can do competence, and mutant that cannot) are put in a environment where DNA is their own food source, the wildtype will be able survive longer

Putting same bacteria in environment with no DNA, they both do not survive well

Front 922

What are these experimental results showing?

Back 922

Young biofilms are held together with DNA and will disperse if treated with DNase

Older biofilms are DNase resistant

Front 923

Why does ComGB mutant produce less/no biofilms?

Back 923

This is because it lost its competency due to the mutation of the pseudopilus involved in competence

Front 924

The fact that DNase treatment does not lower biofilms of ComGB mutants any further than their already lower levels, what does this suggest?

Back 924

DNA is not involved in the small amount of biofilm made by ComGB mutants

In other words, if you do not have a pseudopilus, it does not matter if DNase is there or not

Front 925

What does ComGB do?

Back 925

ComGB is a late competence protein required for DNA binding and uptake

Front 926

What are plasmids?

Back 926

Small, circular (usually), supercoiled DNA molecules

Present is more species but not all strains

May have ~1 to 1000 copies per cell

Uses replication machinery of the host

Have own replication origin and are autonomously replicated and stably inherited

Dispensable for growth under many conditions

NOTE: There are exceptions to all of the above

Front 927

What are some common strategies plasmids do to stably maintain themselves in the cell?

Back 927

Autonomous replication and copy number control (control their replication number where some plasmids can only be present in one copy in a cell)

Providing useful function for the cell such as drug resistance

Partition systems that actively segregate the plasmid to daughter cells

Addiction systems

Front 928

What is the function of the Col plasmids (ColE1, ColE2, ColE3)?

Back 928

They make toxins that kill other E. coli cells as well as an immunity protein so the toxin does not kill its own cell

Front 929

What is the function of the F plasmid?

Back 929

F-pilus and conjugation

Front 930

What is plasmid "Theta" replication?

Back 930

Using an origin of replication, having either uni- or bi-directional replication to form catenates and then individual plasmids

Front 931

What are plasmid catemers and how are the seperated?

Back 931

Catemers are products of plasmid replication where the leading and lagging strand form two rings looped into one another

Usually, these structures are resolved through action of Type 1 and 2 topoisomerase which transiently break the DNA backbone and one plasmid pass through the strands of the other plasmid

Front 932

Does plasmid replication always require an RNA primer to start replication?

Back 932

No, sometimes it can start with a nick in the DNA so that the replication can start in one direction from that nick (5' to 3')

Front 933

What is Rolling-circle replication?

Back 933

A plasmid replication method that goes in one direction where the branch goes in a circle

The displaced strand either goes into a single strand of the plasmid or replicate into a double stranded genome

Front 934

What is a stringent plasmid?

Back 934

Low copy number

Front 935

What is a relaxed plasmid?

Back 935

High copy number

Front 936

What is the ColE1-derived plasmid?

Back 936

Maintained at 10 to 20 copies per cell

Consists of three different components: RNA 1, RNA 2 and Rom/Rop

RNA 1 transcription is upstream of RNA 2 (and terminates at start of RNA 2) where it is ~100x higher in concentration than RNA 2 even though it is very unstable and degraded by RNase E

RNA 2 needs to fold into particular secondary structure in order to be processed by RNase H which allows it to prime DNA polymerase 1 (which the secondary structure can be inhibited by RNA 1)

Front 937

Is RNA 1 of ColE1 stable? What is it degraded by?

Back 937

It is very unstable and degraded by RNase E

Front 938

What can inhibit RNA 2 of ColE1?

Back 938

RNA 1

Front 939

If there is high concentration of RNA 2, will replication of ColE1 occur?

Back 939

Yes

Front 940

If there is high concentration of RNA 1, will replication of ColE1 occur?

Back 940

No

Front 941

What cleaves RNA 2 of ColE1?

Back 941

RNase H

Front 942

What is the function of Rom/Rop of ColE1?

Back 942

Stabilizes the RNA1 and RNA2 complex, turning off RNA 2

Front 943

When will there be an accumulation of RNA 1 and Rop?

Back 943

When there is high concentration of ColE1 plasmid

Front 944

What is the plasmid partitioning like for plasmids?

Back 944

ParR binds to ParC and pairs plasmid which form a nucleoprotein complex or partition complex

The partition complex serves as nucleation point for polymerization of ParM where ParM-ATP complex inserts at this point and push plasmids apart

The insertion leads to hydrolysis of ParM-ATP complex, leading to depolymerization of filament

At cell division, plasmids copies are at each cell extremity and will end up in future daughter cells

Front 945

What happens when ParM is bound to ATP?

Back 945

When bound, it contacts the partitioning complex

Starts hydrolyzing ATP to form filaments at the replication origin

Pushing plasmid apart so they appear on the two sides of the cell and division occurs

Front 946

Can two plasmids that use a common mechnaism for controlling plasmid replication, can they co-exist?

Back 946

No, they are incompatible

Front 947

Give an example of a plasmid that is incompatible with pBluescript (ColE1 origin)

Back 947

pUC (pMB1-derived origin)

Front 948

What are compatible plasmids?

Back 948

Two plasmids have different ways by which they control their copy number they do not interfere with each other

Front 949

What are incompatible plasmids?

Back 949

If two plasmids control their copy number using the same mechanism

The plasmids cannot be stably maintained in the cell with one another

Front 950

What is plasmid addiction?

Back 950

Some plasmids encode genes that will kill the host if the plasmid is lost after cell division

Typically they involve a stable toxin and an unstable anti-toxin that must continually be synthesized in order to suppress the activity of the toxin

Front 951

What happens is a bacteria gets rid of a plasmid they are "addicted" too?

Back 951

Without the plasmid, there will be no more anti-toxin being produced and the remaining anti-toxin are stable enough to stick around, the remaining toxin will begin to kill the cell

Front 952

What is the F plasmid "addiction"?

Back 952

Bacteria with the F plasmid will produce CcdA (inhibits CcdB and has short half-life) and CcdB (inhibits gyrase and long half-life)

The CcdB is a toxin that inhibits Gyrase, an enzyme necessary to maintain proper chromosome supercoiling

When F plasmid present, there is sufficient transcription of CcdA to keep CcdB from inhibiting Gyrase

When F plasmid is lost, the CcdA protein is longer being synthesized and begins to degrade allow the CcdB protein to become active and inhibit gyrase, killing the cell

Front 953

What was Lederberg and Tatum's 1946 experiment on bacteria?

Back 953

Their first experiment, they mixed two strains who couldn't grow on minimal media because couldn't make methionine or biotin, other threonine, leucine or thiamine and mixed them together and the mixed was able to grow which showed bacteria can exchange DNA

Their second experiment, they put the same bacteria on different ends of a tube with a fine filter that only let small molecules through and found no colonies grew, which meant that bacteria must touch each other to exchange DNA

Front 954

What does the F ("fertility") plasmid do?

Back 954

It is a large plasmid that causes plasmid addiction and has two origins of replication and an origin of transfer

Encodes all genes necessary for transfer and to repel transfer from similar plasmids (plasmid exclusion)

Encodes a transposon and some insertion sequences

Front 955

What is the F pilus?

Back 955

Encoded by the F-plasmid

They are receptor for some bacteriophages

Encodes a kind of Type 4 secretion system which transfers DNA instead of proteins

Front 956

What are the steps to conjugation?

Back 956

Contact between recipient cell and F+ cell (that has F- plasmid) is communicated to the plasmid to the origin of transfer by protein TraM

OriT is nicked on one strand by "relaxase"/helicase protein TraI

Cells brought into proximity by retraction of the pilus

Cells make tight contact with each other by a process called mating-pair stabilization (which is not essential for transfer but does occur in liquid environments)

Replication then occurs as a mechanism that is a modification of the rolling-circle replication

At same time, TraI-DNA complex is shot into the recipient cell by the T4SS (5' end first)

Synthesis of second strand begins in the recipient cell where the priming of the reaction may be catalyzed by TraI or by a host protein

Cell separate and conjugation is done

Front 957

What is plasmid surface exclusion?

Back 957

When a cell with one plasmid cannot make with a cell with the same plasmid

Front 958

What is the protein TraI?

Back 958

It is a helicase (or "relaxase") that is a monomer that is covalently attached to newly liberated 5' end of DNA

Front 959

Is the mating-pair stabilzation mandatory/essential for conjugation?

Back 959

It is not essential for transfer but does allow conjugation to occur in liquid environments

It is needed if the liquid/medium is moving

Front 960

What happens if you vortex a bacteria during conjugation?

Back 960

You will disrupt the stabialization process

Front 961

What is the TraT protein?

Back 961

Major outer membrane component of F+ bacteria

Inhibits formation of mating aggregates where the models include either competing with OmpA for binding to pilus tip or masking a region of OmpA

Front 962

What is the TraS protein?

Back 962

Inner membrane protein that prevents trigger of donor conjugal DNA metabolism

Thought to block transmission of mating signals

Front 963

What does the TraS and TraT proteins do?

Back 963

They are surface exclusion proteins by F+ bacteria, preventing mating of F+ bacterias

Front 964

What is the conjugation core complex structure?

Back 964

A conjugation system that spans both the outer and inner membrane that serve various functions such as including to act as a receptor for TraI-DNA complex

Includes the TraN, TraO and TraF in its core complex

Front 965

What is TraF?

Back 965

A subunit of the conjugation core complex structure that makes contact with lipids of the outer membrane with the lipids of the outer membrane

It is not a beta-barrel structure

Spans both the inner and outer membranes simultaneously

Front 966

What is Agrobacterium tumefaciens?

Back 966

A plant pathogen that is the cause of "crown gall disease"

If bacteria encounters a wound in a plant, it colonizes it

Front 967

What causes Crown Gall disease?

Back 967

When Agrobacterium tumefaciens enter a wound in a plant

The bacteria uses a conjugation apparatus encoded on a large conjugative plasmid (Ti) to deliver a segment of "T-DNA" into plant cells

This T-DNA is able to integrate into plant cell genome and from there, it directs the plant cell to divide (by producing hormones) to produce opines (a amino acid food for bacteria)

Front 968

How can the Ti plasmid be used for biotechnology?

Back 968

The Ti plasmid can be modified to deliver non-toxic genes to plant cells to make transgenic crops

Front 969

How can Ti plasmids be used to make transgenic crops?

Back 969

Gene of interest is inserted into DNA segment containing the delivery signals (oriT) of T-DNA

Non-virulent strain of Agrobacterium can transfer this DNA into a plant cell, enabling manipulation of what the plant produces

Front 970

TRUE or FALSE

Phages genomes can integrate itself into bacterial genome

Back 970

TRUE

Front 971

What are responsible for the abatement of 80% of prokaryotic heterotrophic production?

Back 971

Viral infections

Front 972

How do phages impact seasonal epidemics of cholera?

Back 972

Phages are inversely correlated with the prevenelance of environmental cholera phages

When phage levels are high, cholera bacteria levels are low

Front 973

What are three common lifestyles of phages?

Back 973

Virulent

Temperate

Filamentous

Front 974

What is the phage lifestyle virulent?

Back 974

Lytic

Viruses lyse or kill their host after infection

Front 975

What is the phage lifestyle temperate?

Back 975

Lysogenic

Viruses can achieve a state where their genome replicates along with the host genome without killing their host until an opportune time

In many cases these phage integrate into the host genome

Front 976

What is the phage lifestyle filamentous?

Back 976

Phage can replicate and direct the host to shed new phage particles without causing cell death

Population can keep growing after infection as it will not kill the host

These look like filaments

Front 977

What is the bacteriophage lytic cycle generally like?

Back 977

Bacteriophage attaches to the cell surface

Absorption will have, attaching the phage to the bacteria

Injection of the DNA from the head of the phage to the bacteria where no exposure of the DNA to extracellular environment

Transcription of the phage DNA will occur at multiple stages

Phage proteins are made of the phage DNA and conversion of bacterium to phage factor

The bacterium would work like a factory to produce phage structures

DNA get packed into new phages, assembling new phage particles

Proteins will be created like holin (disrupts cytoplasmic membrane) and lysozyme (degrades peptidoglycan) to lyse the cell, releasing the phage particles

Front 978

Can a bacteriophage release its phage particles without lysis of the cell?

Back 978

Yes, in the case of filamentous phages

Front 979

What does the protein Holin do?

Back 979

Disrupts the cytoplasmic membrane of bacteria

Front 980

What does the protein Lysozyme do?

Back 980

Degrade peptidoglycan of bacteria

Front 981

How do bacteriophages inject their genome into a bacteria?

Back 981

The bacteriophage would recognize the surface of a bacteria by using fibers that are on the tip of the tail

Begin attachment of phage to cell surface

Have tail contraction

Penetration and unplug

Inject the DNA

Front 982

TRUE or FALSE

Phages are very specific

Back 982

TRUE

Phages that infect E. coli will unlikely infect other species regardless of how related they are

Sometimes, they can even be strain specific

Front 983

Why are phages very specific?

Back 983

The phages recognize specific molecules on the surface like sugar, LPS, transporters or other proteins

Front 984

What type of virus is this?

Back 984

T4 virulent bacteriophage

Front 985

What is the T4 virulent bacteriophage?

Back 985

It is a mode for lytic phage growth

Its genome is a linear dsDNA

Front 986

How does the T4 phage inject their DNA (do infection)?

Back 986

There is a tube (needle) in the middle of the T4 that is going through the outermembrane of the bacteria

While injecting the DNA, it brings the outer and inner membrane together while making a hole in the peptidoglycan by lysomes

The DNA would leave the head and somehow go through the tube through the membranes

Front 987

How do you quantify plaque-forming units (PFU) by plaque assay?

Back 987

Dilute phage solution and mix with molten top agar and bacterial suspension

Pour mixture onto nutrient agar place

Where ever a phage landed, it will infect a few hundred other bacteria which will cause holes in the bacterial suspension

Can quantify suspension (holes/plaques)

Front 988

In a plaque assay (with viruses), why are you sandwiching the viruses between top agar and nutrient agar?

Back 988

Prevents the viruses from moving around

Front 989

Are the gram positive tail tips of bacteriophages the same for gram negative?

Back 989

No, they are different

Front 990

How is phage lamba head assembled?

Back 990

Begins with 12 gpB

Other proteins add on such as gpNu3, gpC, and 2 groE which will begin to form the head

A terminase with DNA and gpF1 gets added on to add the DNA into the empty head

A gpD protein will then stabalize the head

A gpW protein will plug the whole of the head

Then gpF2 which is required for attached the trail that is being assembled at the same time

Front 991

How is phage lambda tail assembled?

Back 991

The tail tip is formed using proteins gpJ, gpI, gpL, gpK, gpH, gpG and gpM

gbH is the tube/tape measuring protein

The tail tube formed with protein gpV which makes the rings around gbH

Then gpU (final ring) and gpZ will be added that will bind to gpF2 of the head complex, forming the phage particle

Front 992

In phage lambda, how many types of proteins make up the head of the phage particle?

Back 992

Only one type, gpE

Front 993

How is the empty phage head of lambda phage made?

Back 993

After gpB-containing-primer ring is formed, a conformational change will turn on proteases (gpC) that will cut off all scaffolds in head, letting it leave the head, making it empty

The gpNu3 protein is the scaffold which will bind to the capsule (gpE) protein and help assembly of the head shape

Front 994

How do most phages replicate?

Back 994

They replicate using the rolling circle replication, forming concatemers

Front 995

How are phage DNA packaged?

Back 995

The phage concatemers are cleaved into unit size by enzymes called terminases (green circles) that recognize specific packaging sequences

These are loaded into phage head by portal proteins (pink box) in an energy-dependent (ATP) process

Once head is full, the DNA will be cleaved by terminase protein

Front 996

What type of lifestyle does bacteriophage lambda life?

Back 996

A temperate phage (and a model for lysogeny)

Front 997

What is the usualy life cycle like for the temperate lambda phage?

Back 997

Begins lytic, infecting the bacteria by absoprtion and penetration

Phage DNA will then cyclize and then continue lytic, or become lysogenic

In lysogenic, it will integrate into DNA to form prophage and be replicated with the host

(still in lysogenic), the prophage can be induced by UV live to reform cyclic phage DNA and then continue lysogenic or become lytic

In lytic, it will replicate, assemble particles and lyse the cell

Front 998

What is lysogen?

Back 998

Bacterium containing a complete set of phage genes

Front 999

What is a prophage?

Back 999

Phage DNA in lysogens, whether integrated or not

Front 1000

What are the general properties of lysogen?

Back 1000

Lysogens are resistant to re-infection by a phage of the type that first lysogenized the cell (this resistance to superinfection is called immunity)

Even after many cell generations, a lysogen can initiate a lytic cycle (this is called induction where phage is excised as single DNA segment and lytic cycle begins)

Front 1001

How does a bacteriophage decide between lysis and lysogeny?

Back 1001

Lysis and lysogeny are controlled by the proteins encoded by cro and cI (AKA lambda repressors) genes

Lambda phage will remain in lysogenic state if cl proteins predominate, but will be transformed into the lytic cycle if cro proteins predominate

Front 1002

How does a bacteriophage re-enter the lytic mode?

Back 1002

When the host DNA is damaged (like UV irradiation), cl protein may be cleaved by protease activated by RecA protein

Cleaved cl protein cannot bind to operators

Thus, Cro proteins can be produced to transform the lambda phage into lytic cycle

Front 1003

How does the lambda phage chromosome insert itself into the bacterial chromosome?

Back 1003

Integrase is used to make staggered cuts and strand transfer which will insert the lambda into the bacterial chromosome

Front 1004

What protein is required for lambda phage chromosome excision from the bacterial chromosome?

Back 1004

Xis

Front 1005

What is the Lysis pathway for producing a cro repressor?

Back 1005

Synthesis of cro repressor from rightward transcription (PR) shuts off the cI promoter for repressor maintenance (PRM) but allows more PL and PR transcription

Front 1006

What is the purpose of lambda phage's protein, cIII?

Back 1006

It stabilizes cII from being degraded

Front 1007

How is the lysogeny pathway activates PRE?

Back 1007

At high multiplicity of infection, cII protein is made from rightward transcription

cIII is also made from leftward transcription

cIII prevents degradation of cII by FtsH proteases

cII accumulates and induces synthesis of cI repressor from PRE

Front 1008

How is the lysogeny pathway activates PRM?

Back 1008

cI binds

Activates promoter for cI maintenance and repressing transcription from PL and PR

Front 1009

What happens when a host bacteria, infected with phage lambda, has DNA damage?

Back 1009

It induces lysogen of the phage

Front 1010

How does DNA damage induce phage lambda lysogen?

Back 1010

When DNA is damaged, it turns on SOS response when ssDNA is exposed

When RecA becomes activated, the phage stimulates cI repressors to cleave itself causing N-term domain to bind to DNA and C-term domain to be a dimerization domain

When the cI interacts with RecA, it is cleaves and comes off the DNA, no longer having a repressor on the phage DNA

Phage is now in lysogen

Front 1011

Of the lambda phage, besides working as a repressor required for lytic growth, what other functions does cI have?

Back 1011

Makes cell immune to infection against other lambda phages

Front 1012

What does rexA and rexB in lambda prophage do?

Back 1012

Confer resistance to other phages

Front 1013

What does the lambda prophage gene bor do?

Back 1013

Increases survival of the E. coli in animal serum

Front 1014

TRUE or FALSE

Prophages can help assist a bacteria to become (more) pathogenic

Back 1014

TRUE

Front 1015

What genes make the E. coli O157 lethal?

Back 1015

A toxin gene called Shiga Toxin (these are also found in prophages)

Front 1016

In Carynebacterium diphtheriae, what is a commonly well known prophage-encoded toxin?

Back 1016

Diphtheria toxin

Front 1017

What are the evolutionary advantages to keep a huge percentage of phages in the bacterial genomes? (For the bacteria)

Back 1017

These phage genomes can help make their host more adaptive and fit to the environment which will increase the survival of the host

Front 1018

What are some mechanisms that phages can use for genetic mobilization?

Back 1018

Phage can randomly package wrong DNA at low frequency (generalized transduction)

Phage accidentally carry genes nearby their integration site on the host chromosome (specialized transduction)

Phage carry genes in their genomes that alter host physiology (ex. superoxide dismutase in prophage in Salmonella)

Phage can mobilize parasitic pathogenicity islands

Front 1019

What is transduction and how does it occur in nature?

Back 1019

Virus-mediated transfer of host DNA (chromosomal or plasmid) from one host cell (donor) to another (recipient)

In nature, this occurs (infrequently) due to error made during phage life cycle

Front 1020

What is generalized transduction occur by bacteriophages?

Back 1020

Occurs during lytic cycle of virulent or temperate phage and can transfer any part of bacterial genome

Random fragments of partially degraded bacterial DNA will be packaged by mistake

Generalized transducing particle contain no phage genes

Front 1021

How is an abnormal phage created for specialized transduction?

Back 1021

When the phage DNA excises from the bacterial genome, once in a while (rare), it will screw up and not use the proper recombination sites to excise

Instead it would excise some bacterial genome, forming a abnormal outlooping

This creates low frequency of phage particles

Front 1022

What is a SaPI?

Back 1022

S. aureus Pathogenicity Island

They contain genes for toxins such as the "super-Antigen" that causes Toxic Shock Syndrome

They encode some phage-like proteins but possess a few genes that are required to construc a phage particle

Front 1023

How do SaPI get from one cell to another?

Back 1023

The SaPI1 contain sequences that enable it to be packaged by phage 80alpha while excluding the 80alpha genome during packaging at high frequency

Front 1024

What happens when a 80alpha phage infects a Staphylococcus aureus with SaPI1?

Back 1024

The SaPI1 island directs its own packaging into the phage head while excluding the 80alpha genome during DNA packaging at high-frequency

Many phage particles would burst out of cell filled with SaPI1 DNA instead of 80alpha, spreading the islands to new strain

Front 1025

What toxin does SaPI encode for?

Back 1025

Toxis Shock Syndrome Toxin (TSST)

Front 1026

How does SaPI parasitize helper phages for their own life cycle?

Back 1026

SaPI is usually reperssed by Stl

When helper prophage gets induced and exists themselves from the genome to start expression genes, they will produce an enzyme called dUTPase that will inhibit Stl

This allows SaPI to become activated, excising itself from the host genome and begin to replicate and create proteins that allow it to hijack phage particles

This results in the particle having a normal tail but a small head

Front 1027

What is the point of the SaPI particle (or pathogenist island particle) having a small head?

Back 1027

The small particle head is not big enough to hold the original phage genome but now big enough to hold the SaPI genome

One way of hijacking the phage particle

Front 1028

What is TerS?

Back 1028

A enzyme produced by SaPI used to hijack the head of the phage by changing the terminase DNA binding specificity

It works with TerL

Front 1029

What causes cholera?

Back 1029

A gram negative bacteria called Vibrio cholerae that colonizes the small intestine

Cholera is caused by two virulence factors that was given to the bacteria by two phages: TCP and CTX

Front 1030

What is the virulence factor TCP?

Back 1030

Toxin co-regulated pilus operon

Encodes a self-binding Type-IV pilus that holds the Vibrio cells together

Also enodes a TcpF which is a secrete protein required for colonization

Front 1031

What is the virulence factor CTX?

Back 1031

Cholera toxin (this causes the symptoms of cholera)

A two-subunit toxin secreted from the bacteria that disrupts ion flow in epithelial cell of the intestine

Encoded by prophage CTX-phi

Front 1032

What is CTX-phi?

Back 1032

A filamentous phage that uses TCP as its receptor to enter the bacterial cell

Its prophage encodes CTX (Cholera toxin)

Front 1033

What are some common bacterial defense systems against phages?

Back 1033

Restriction-modification systems

Alterations to cell surface

Suicide systems

Xenogeneic silencing

Codon biases

CRISPR

Prophage encoded system

Front 1034

Briefly, how does altering the cell surface of a bacteria work as a defense against phages?

Back 1034

Phages are generally very specific to species and strains that they infect

Species specific diversity in LPS, peptidoglycan, etc... can change so it does not let the phage bind

Front 1035

Brielf, how does having a suicide system in bacteria work as a defense against phages?

Back 1035

Form of altruism where the bacteria kills itself to prevent the phage from replicating

Front 1036

Briefly, how is xenogeneic silencing in bacteria a defense against phages?

Back 1036

H-NS-like proteins silence foreign DNA

Front 1037

Briefly, how is codon biases in bacteria a defense against phages?

Back 1037

Bacteria use specific codons that are different from other bacteria which prevent translation of foreign DNA

Front 1038

Briefly, how is prophage encoded systems in bacteria a defense against other phages?

Back 1038

Protect against challenges with the same type of phage but sometimes phage encode secondary protection systems against other phages

Front 1039

How are restriction-modification systems a method of bacterial immunity against phages?

Back 1039

Restriction-modification systems cut DNA that come from a foreign source by recognizing specific sequences

They serve as powerful means of protection against phage and limit gene transfer between species

Front 1040

What is a Type 1 restriction enzyme?

Back 1040

Multisubunit enzyme that recognize a given sequence but cut far away from the recognition site

Front 1041

What is a Type 3 restriction enzyme?

Back 1041

Multisubunit enzyme that require two recognition sequences in opposite orientation on the same DNA molecule and cut outside the recognition sequence

Front 1042

What is a Type 2 restriction enzyme?

Back 1042

Enzyme that cut within or immediately adjacent to their cognate recognition site

Typically recognize a palindromic sequence

Front 1043

What is BamHI?

Back 1043

A type 2 restriction enzyme from Bacillus amyloliquefaciens strain H

Exists as dimer

Binds to GGATCC and cuts between first and second G residues on each side of palindrome

Front 1044

How does a bacterial protect its own DNA from the restriction-modification system?

Back 1044

By encoding second enzyme that selectively modifies the target sequence of restriction enzyme by methylating one of the bases in the recognition sequence

This modification enzyme is called methyltransferase

These enzyme genes usually adjacent to the restriction enzyme gene

Front 1045

What is CRISPR?

Back 1045

Clustered Regularly Interspaced Short Palindromic Repeats

It is a type of DNA repeat found in archaea prokaryotic genomes

The CRISPR regions that are commonly found in bacteria have spacer regions that match sequences of phage genomes

Bacteria adapt to phage infections by adding/modifying the spacer sequences similar to phage genome to prevent infection (phage resistance)

Front 1046

How is CRISPR used in bacteria for adaptation and resisting phage or foreign DNA?

Back 1046

When DNA comes into the cell that the bacteria has never seen before, it will chop up pieces of the phage DNA and incorporate them into the beginning locus/spacer sequences so it has memory of that phage infection and ready to fight against it again

Front 1047

Do phages have a defense/counter against the CRISPR system?

Back 1047

Yes, they have a mechanism that can inactive CRISPR

Front 1048

What is the Cas9 of the CRISPR system?

Back 1048

Cas9 CRISPR System can be used to edit any genome

It is a type 2 restriction enzyme and can be used to preciously edit a genome of an organism and cut at a specific 20 to 30 sequence

It is highly specific and can be a method to make mutations or repress genes

Front 1049

How does Cas9 function as a nickase? (nCas9)

Back 1049

Cas9 can function as a nickase (nCas9) when engineered to contain an inactivating mutation in either the HNH domain or RuvC domain active sites

When nCas9 is used with two sgRNAs that recognize offset target sites in DNA, a staggered double-stranded break is created

Front 1050

How does Cas9 function as an RNA-guided DNA binding protein?

Back 1050

Cas9 functions as a RNA-guided DNA binding protein when engineered to contain inactivating mutations in both of its active sites

This catalytically inactive or dead Cas9 (dCas9) can mediate transcriptional down-regulation or activation, particularly when fused to activator or repressor domains

Front 1051

Is there a way to visualize Cas9?

Back 1051

dCas9 can be fused to fluorescent domains such as GFP for live-cell imaging of chromosomal loci

Front 1052

What did Erwin Chargaff do?

Back 1052

He experimentally determined that the AT ratios and GC ratios are roughly the same in DNA

Front 1053

Briefly, what are some problems posed by horizontal gene transfer?

Back 1053

Disruption of essential genes

Regulatory disruption

Metabolic disruption

Disruption of chromosomal packaging

Front 1054

Briefly, what does it mean that horizontal gene transfer can cause regulatory disruption?

Back 1054

Results in fitness problems where genes that are supposed to be turn off are turn on (or vice versa)

Front 1055

Briefly, what does it mean that horizontal gene transfer can cause metabolic disruption?

Back 1055

Even if gene is useful to help metabolize, that gene might be turned on or off at the wrong time

Front 1056

What is the H-NS nucleoid-binding protein?

Back 1056

Acts almost exclusively to repress transcription

Binds DNA with relatively little sequence specificity preferring AT-rich DNA

The H-NS binding site is not highly sequence specific but does have a strong bias for AT rich DNA to generate extend footprints on DNA template

H-NS binds weakly to DNA

Front 1057

What do the blue lines/spikes mean?

Back 1057

When that gene is repressed by H-NS, the line would be longer and more negative

When that gene is not repressed, the line is shorter and more positive

When H-NS is removed, genes increase in expression

Front 1058

How can H-NS be used by the bacteria's horizontal gene transfer?

Back 1058

H-NS can regulate large number of genes obtained by the horizontal gene transfer

Specifically the can bind and regulate newly introduced AT-rich genes

Front 1059

What does the grey, blue and orange box mean?

Back 1059

Grey box is foreign pieces of DNA picked up horizontal gene transfer

The blue box known as pathogenicity islands

Orange box is prophages or lysogenic phages integrated into the chromosome

Front 1060

How do you do chromatin immunoprecipitation on microarray method?

Back 1060

Step 1) Crosslink protein to DNA with formaldehyde (which also kills the the cell)

Step 2) Sonicate (pop cell open with sonic waves) to sheer chromosomal DNA (protein of interest remains stuck onto piece of DNA due to treatment with formaldehyde)

Step 3) Incubate protein-DNA complex with antibodies against factor

Step 4) Precipitate with protein G beads and wash extensively (these beads will bind to antibodies and hold them down so you can wash away unwanted DNA)

Step 5) Incubate at 55 degrees for 5+ hours to break crosslink

Step 6) Clean, amplify and label co-precipiated fragments

Step 7) Hybridize to array to identify the bound fragments

Front 1061

If hp0226 is a newly inserted gene into a AT/GC-neutral sequence on Salmonella from H. pylori, what is this result showing?

Back 1061

Even if a gene is brand new and never seen before, the H-NS binding protein can still bind to newly introduced gene if that gene is AT-rich

Front 1062

Briefly, how can a DNA binding protein (like H-NS) tell AT-rich DNA from GC-rich or GC-neutral DNA?

Back 1062

New DNA comes in, if it is AT rich compared to the host genome that is 50% GC, they know it is not host DNA because it is too AT rich, thus H-NS will shut down the expression of the foreign DNA

Front 1063

What groove does the H-NS binding protein bind to?

Back 1063

The minor groove

Front 1064

What is the A-tract of DNA?

Back 1064

Were it has a lot of consecutive A or T residues

Front 1065

What base pairs can dramatically expand the minor groove?

Back 1065

TA steps (or adjacent pairs) can dramatically expand the minor groove and make it more flexible

Front 1066

What are GC-base pairs like in the minor groove?

Back 1066

They have an extra amino group pocking out that causes steric hindrance

Front 1067

What is the H-NS DNA binding protein's domain "QGR" or "RGR"?

Back 1067

A conserved peptide sequence motif

This is an AT-hook motif that nestles deeply into the minor groove of the AT-rich DNA, usually sections that have a TA step or two-flanked narrow regions

H-NS would be excluded from GC-rich DNA due to presence of extra amino group

Front 1068

Why is H-NS binding protein excluded from GC-rich DNA?

Back 1068

Due to the presence of an extra amino group in GC pairs in the minor groove

Front 1069

How does H-NS selectively target DNA sequences derived from a foreign source? How does it not target self DNA?

Back 1069

Weak binding of each individual H-NS subunit makes it like a velcro

Are whole series of weak interactions (strung together like a velcro), can make a strong overall interactions

A series of very weak interactions, when coupled together, it can make a stronger interaction

In other words, H-NS can discriminate on the basis of AT-content and length

Front 1070

How does the H-NS binding protein discriminate on the basis of AT-content and length?

Back 1070

Weak interaction by H-NS allows it to avoid interacting with DNA at accidental small patches of DNA that is AT rich

Instead, it focuses on long patch of AT-rich DNA within big blocks of foreign DNA

Front 1071

What is xenogenic silencing?

Back 1071

The silencing of foreign DNA in bacterial cells

Characteristic GC-content of the bacterial genome can be exploited to recognize the silence alien sequences

Explains how bacterial cells newly acquired genes are regulated by the bacterial cell without compromising its genomic and regulatory integrity

Has allowed bacteria to simultaneously acquire and protect themselves from foreign DNA

Requires minor-groove binding proteins that target structural features unique to AT-rich DNA

Front 1072

What is a mechanism that bacteria can use to counter or regulate H-NS binding proteins?

Back 1072

Certain transcription factors can displace H-NS off specific genes in appropriate context, time and place

These transcription factors are sequence specific to specific promoters

This can be activated by an external signal or membrane stress

Front 1073

The PhoP/PhoQ system is a response to what?

Back 1073

To membrane stressors that turn on a regulatory systems

Front 1074

What genes get activated by PhoP?

Back 1074

Divalent metal transport

LPS modifications (ugtL)

Outer membrane proteins

Superoxide dismutase

SlyA

Front 1075

What genes does PhoP repress?

Back 1075

SPI-1

Flagella

Front 1076

What is the outcome of the PhoP activation?

Back 1076

The outer membrane getting toughened up

Front 1077

What does the gene sodC do and what does it get activated by?

Back 1077

It fights superoxides

Gets activated by PhoP

Front 1078

What does the gene ugtL do and what does it get activated by?

Back 1078

Modifies outer membrane and protects against AMPs

Gets activated by PhoP

Front 1079

What happens if you cause mutants in the PhoP and SlyA genes?

Back 1079

When there are mutant genes in both of these components, it makes the bacteria more susceptible to killing by Polymyxin B

Front 1080

If you originally had mutants of PhoP and SlyA genes, what would happen to the susceptibility of bacteria by killing from Polymyxin B if you put back the SlyA gene?

Back 1080

You restore activity of the bacteria

Front 1081

What is needed for activation and transcription of ugtL?

Back 1081

Both PhoP and/or SlyA to be active

SlyA cannot increase ugtL transcription itself but required H-NS to be around to help

PhoP can stimulate transcription of ugtL unless H-NS is around but is low

Front 1082

How does transcription of ugtL happen?

Back 1082

Usually, there will be a H-NS that blocks PhoP binding for ugtL

SlyA is needed to bind to the DNA and bend it to release H-NS from ugtL

Then PhoP can bind and activate transcription of ugtL

Front 1083

The is Type 4 secretion system sec-dependent or sec-independent?

Back 1083

Sec-independent

Front 1084

What common features do all secretion systems have?

Back 1084

Each secretion system secretes their own cargo

They require energy

High structural homology to other structures like flagella and pili

Other require use of chaperones to keep the protein in the cargo unfolded and delivered to translocation machinery

Front 1085

When a sec secretion system is sec-dependent or sec-independent, what does the sec mean?

Back 1085

Sec is a transmembrane complex in the inner membrane

Found in both gram positive and negative bacteria

Front 1086

What is the Sec transmembrane complex like?

Back 1086

Conserved across all domains of life

Secretion is post-translation

Exports proteins across cytoplasmic membrane (this requires SecA and SecB)

Can insert proteins into cytoplasmic membrane (requires signal recognition particle (SRP))

Front 1087

What is Sec61?

Back 1087

Sec transmembrane complex in eukaryotes that is located on rough endoplasmic reticulum (ER)

Cotranslationally pumps proteins destined for secretion to ER lumen

Front 1088

How does Sec61 function?

Back 1088

It is found on the ER

Protein enters the ER where it is packaged in membrane vesicles

Transferred to Golgi

Vesicle goes to cytoplasmic membrane

Membrane fuses with cytoplasmic membrane and cargo is deposited outside

Front 1089

What does the cargo protein of a sec system's gene contain?

Back 1089

Signal peptide that consists of positively charged N-terminal domain, hydrophobic domain of ~20 AA and a polar C-terminal cleavage site

The its mature protein sequence

Front 1090

What is required to be conserved in the gene of proteins destined for Sec-secretion system?

Back 1090

A conserved N-terminal domain called a signal sequence or "signal/leader peptide"

Front 1091

How does the sec-secretion SRP-independent system work?

Back 1091

1) Signal/leader peptide is created by the ribosome and binds to the SecB chaperone

2) SecA will then bind to the SecB-signal peptide (the SecB chpaerone prevents premature/incorrect folding

3) The SecAB complex will bring the partially folded protein to secretion apparatus SecYEG channel

4) SecB will dissociate

5) This release triggers translocation

6) SecA initiates translocation by acting like a pump, hydrolyzing ATP and pushing 2.5kDa of protein into pore

7) Hydrophobic domain and the C terminal end will start going through the SecYEG channel, pumping the protein out through the pore while hydrpohobic domain remains at membrane

8) Signal peptidase cleaves the protein and leader peptide gets degraded

9) Protein is not outside gram positive (or in periplasm of gram negative)

Front 1092

How does sec-secretion SRP-dependent system work?

Back 1092

In this case, the leader peptide is typically more hydrophobic

1) Ribosome begins translating protein

2) A signal recognition particle (SRP) will bind, telling the ribosome it wants to dock

3) SRP docks onto FstY

4) GTP converted to GDP to release SRP from untranscribed protein and ribosome brings protein to translocation apparatus, SecYEG

5) Synthesize starts happening again of protein into the SecYEG channel

6) Hydrophobic domain slips into the membrane

Front 1093

What is one enzyme that cuts sec secreted proteins at the C-terminal end of the leader sequence?

Back 1093

Sortease at the G of LPXTG

Front 1094

For gram negative bacteria, there is a problem for transporting sec secretion proteins and that is there is no ATP in the periplasm. How do they overcome this problem?

Back 1094

They use autotransporters (Type 5 secretion)

Front 1095

How do type 5 secretion systems (autotransporters) work?

Back 1095

On the sec secretion protein at the C-terminal end, there would be a beta barrel domain, typically consisting of 14 beta strands

This would undergo spontaneous insertion into the outer membrane to create a channel through which central passenger domain gets secreted across

Front 1096

Where does the energy for autotransproters come from?

Back 1096

Comes from folding the protein from being unfolded

Front 1097

Is type 5 secretion sec dependent or independent? How come?

Back 1097

Sec dependent as it requires SecYEG first to get sec secretion protein from inner membrane to periplasm

Front 1098

What is the IgA protease autotransporter?

Back 1098

Degrades IgA on mucosal surfaces

Gets made and autotransported out of bacteria cells where its passenger domain encodes for proteases that are highly specific for IgA

Front 1099

Are type 5 secretion found on gram positive or negative bacteria?

Back 1099

Gram negative

Front 1100

What is chaperone/usher secretion?

Back 1100

Specific chaperons (like PapD) would bind to C-terminal motifs of the sec secretion protein

An 'Usher' protein (like PapC) would translocate proteins across membrane to make certain type of pilus with various subunits being brought to this translocation apparatus

Assembles bottom up

Front 1101

Is the chaperone/usher secretion system sec independent or dependent? How so?

Back 1101

Dependent as it uses SecYEG to get sec secretion protein to periplasm

Front 1102

Does the chaperone/usher secretion system require external energy?

Back 1102

No

Front 1103

What are Uropathogenic E. coli (UPEC)?

Back 1103

Causes urinary tract infections (UTI) that can progress to kidneys and are 10-20% recurrent infections in women

They have two types of pilus, Type 1 and Type P

Front 1104

What is UPEC Type 1 pili?

Back 1104

Infects bladder

Binds to mannosylated glycoproteins: uroplakin la and lb

Attachments to uroepithelial cells

Causes normal E. coli to get peed out

Front 1105

What is UPEC Type P pili?

Back 1105

Aka Pap Pili

Attaches to kidney cells

Binds glycophingolipids carrying Gal-alpha(1-4)Gal

Cause urinary tract infections

Front 1106

What is type 2 secretion (General Secretory Pathway)

Back 1106

Contains many different components to get cargo across the periplasm intermediate

1) Sec secretion protein gets into periplasm by SecYEG

2) PilD (stable 12-14 subunit pore, inserted on outermembrane by PulS) will process pseudopilin (PulGH) and recruit ATPase PulE on inner membrane

3) Minor pseudopilins (Pull-K) will self-assemble

4) Through using ATP (and PulC transmitting energy to outer membrane), molecules will make pseudopilin larger, pushing sec secretion protein through PilD

Front 1107

What type of secretion system is cholera toxin secreted from Vibrio cholerae using?

Back 1107

Type 2 secretion system

Front 1108

What is cholera toxin?

Back 1108

Secreted by Vibrio cholerae

Secreted by type 2 secretion system

Binds GM1 gangliosides on host surface and is endocytosed

Then secreted by ER to cytoplasm by Sec61

This causes efflux of chloride ions into intestinal lumen, trigger rapid fluid loss

You will die from dehydration from so much diarrhea

Front 1109

What are ATP binding cassettes?

Back 1109

Largest family of bacterial transporters as they import and export

Conserved across all life (example is Cystic fibrosis transmembrane receptors)

Transport variety of substrates

Secretion signal is structural

Secretion signal is not cleaved

Their ATPase has a unique ABC signature motif (LSGGQ)

Front 1110

How does Type 1 secretion (ABC transporters) export haemolysin?

Back 1110

The ABC transporter will consists of HlyB, HlyD and outer membrane porin Tol C

Haemolysin grabbed by HlyB (has ATPase function) and shuttles across inner membrane to HlyD (no periplasmic intermediate, contain in HlyD)

Transports across HlyD to TolC porin which goes through to outside of cell

Front 1111

How does Type 1 secretion (ABC transporters) import of D-Ala?

Back 1111

Dal-S binds to D-Ala (as a periplasmic protein) and brought to periplasmic transporter where D-Ala is imported through specific OM channels/porins

ABC transporter, using ATP, brings in the D-Ala, dissociating Dal-S

Front 1112

What is a haemolysin?

Back 1112

Generic term for a protein that when added to RBC, it can pop them

Front 1113

Is Type 1 (ABC transporter) sec dependent or independent?

Back 1113

Sec-independent

Front 1114

What is Type 3 secretion system?

Back 1114

Does direct delivery of protein (effectors) into host cell

They are contact dependent (channel stays closed until makes contact with host cell)

Energy-dependent secretion (ATP)

Large machine wiht 23 components

Structurally conserved

Front 1115

What is the basel body of a type 3 secretion like?

Back 1115

Has an InvG that is an outer membrane ring that spans periplasm, contacting the inner membrane ring

Has an inner rod (like PrgJ) that may control the needle length

Two inner membrane rings (PrgH outside, PrkG inside)

Front 1116

What is the "weapon" of the type 3 secretion?

Back 1116

3 proteins (2 hydrophobic and 1 hydrophilic) at the tip (SipB, SipC, and SipD) that forms a pore in other cell's plasma membrane

A needle of repeating PrgL stacks with central channel

Front 1117

Do type 3 secreted effectors have an N-terminal leader peptide?

Back 1117

Typically they do not but there will be a secretion signal at the N-terminal end

Front 1118

What bacteria causes Typhoid fever?

Back 1118

Salmonella enterica

Front 1119

Salmonella enterica has two type what secretion systems for causing Typhoid fever and what are they for? Do they have type "this" secretion system?

Back 1119

Two type 3 secretion systems needed for:

Invasion into host cell AND intracellular survival

They also do have more though

Front 1120

How is one of Salmonella enterica's type 3 secretion system used for invasion?

Back 1120

Encoded by SPI-1

Secretes across host place membrane

Causes formation of invasive ruffle where effectors cause actin rearrangements

Front 1121

How is one of Salmonella enterica's type 3 secretion system used for intracellular survival?

Back 1121

Encoded by SPI-2

Secretes across host vacuolar membrane

Causes formation of Salmonella induced filaments (Sifs) where the effectors manipulate endosome trafficking and fusion with SCV to form Sifs

Front 1122

Are all type 3 secretion systems bad (pathogenic)?

Back 1122

No, some can be used for endosymbiotic relationships

Front 1123

What are type 4 secretion systems?

Back 1123

They have many different functions (like conjugation, DNA uptake/release, effector translocation)

Effectors have C-terminal, non-cleavable secretion signals

Front 1124

What are type 4 secretion systems like?

Back 1124

They have outer membrane pore formed by secretin-like protein

Their periplasmic channel may require peptidoglycan hydrolase to be formed (to allow channel to go through)

Could house intact translocon chamber

ATPase energizes secretion

Could be staging area for pilus assembly

Front 1125

How does Helicobacter pylori make you sick and what does it cause?

Back 1125

Causes peptic ulcers and can lead to gastric cancer

Secretes CagA to alter host signal transduction, morphology and proliferation

Front 1126

What is Type 6 secretion system?

Back 1126

Present in ~25% of sequenced gram negative bacteria and common in free-living bacteria in "crowded" environments

It is a contractile injfection system similar to tailed bacteriophages (that can kill other bacteria)

Front 1127

How do Type 6 secretion systems work?

Back 1127

The tail tip is believed to be an effector (VgrG trimer) that is bound to Hcp which forms to hexameric rings

The TssM ATPase is needed to recruit Hcp and may trigger polymierization

It will recruit VipA/B

The dynamic polymierzation, contraction and disassembly will occur (essentially reloaded the secretion system)

Front 1128

What are the main roles of type 6 secretion system effectors?

Back 1128

Evolved VgrG proteins (effector domain fused to VgrG)

Classical toxins (secreted up Hcp channel)

Front 1129

Generalize: What are the purposes of type 6 secretion system effectors?

Back 1129

Antipathogenesis (preventing triggering diseases)

Pathogenesis

Intra- and inter-bacterial interactions

Front 1130

How do gram positive bacteria secrete effectors into host cells?

Back 1130

(By using cytolysins)

Typically it will bind very closely to host cell

The Sec secretion system is scattered all over the membrane, not found in one place

It will interact closely with the host cell and make a hymolysin to poke hole on the plasma membrane of the host cell and delivers the protein via Sec secretion system

They don't have OM to worry about

This mostly work to secrete some effectors into host cell

Front 1131

Is Sec sec-dependent?

Back 1131

Yes

Front 1132

Is Type 2 secretion system sec-dependent?

Back 1132

Yes

Front 1133

Is Chaperone/usher sec-dependent?

Back 1133

Yes

Front 1134

Is Type 5 secretion system sec-dependent?

Back 1134

Yes

Front 1135

Is Type 1 secretion system sec-dependent?

Back 1135

No

Front 1136

Which secretion systems are found in gram negative bacteria?

Back 1136

Type 5

Chaperone/Usher

Type 2

Type 1

Type 3

Type 4

Type 6

Front 1137

Is Type 4 secretion system sec-dependent?

Back 1137

No

Front 1138

Is Type 3 secretion system sec-dependent?

Back 1138

No

Front 1139

Is Type 6 secretion system sec-dependent?

Back 1139

No

Front 1140

Which secretion systems use ATP hydrolysis as an energy source?

Back 1140

Sec

Type 2

Type 1

Type 3

Type 4

Type 6

Front 1141

What are primary pathogens?

Back 1141

Cause disease in healthy hosts

Front 1142

What are opportunistic pathogens?

Back 1142

Cause disease only in immunocompromised patients

Front 1143

What is LD50?

Back 1143

Define as the amount of bacteria neccessary to kill half of the infected test animals

Can be affected by several independent factors including bacterial strain differences, differences between animals (mice vs hamster), conditions under which bacteria are grown and how they are administered

It is NOT a fixed numner and must be reported along with how experiment was performed

Front 1144

Is LD50 a fixed number?

Back 1144

No

When given in a report, experiment of how was performed will be found along with it

Front 1145

What is an infection cycle?

Back 1145

The route an organism takes from one individual to another

Front 1146

What is horizontal transmission?

Back 1146

From one member of a species to another (human to human)

Can occur through fomites (inanimate objects), vectors (mosquitoes), direct contact or air

Front 1147

What is vertical transmission?

Back 1147

From parent to child (usually mother to offspring)

Front 1148

What is accidental transmission?

Back 1148

A host who is not part of the normal infectious cycle accidentally encounters the pathogen and contracts disease

Front 1149

In a host-pathogen interaction, what is a reservoir?

Back 1149

Animal, bird or insect that normally harbors the pathogen

Front 1150

What is immunopathogenesis?

Back 1150

Occurs when the immune system's response to an infection damages host cells or tissues

Front 1151

What is a virulence factor?

Back 1151

A protein/gene that allows the pathogen to cause disease (can be toxic)

Front 1152

What are exotoxins?

Back 1152

Secreted protein toxins that subvert host function

Front 1153

How do exotoxins damage cellular membranes/matrices?

Back 1153

These are pore forming toxins where they insert themselves into membrane of cell and form pores

Cause ions to leak out, leading to depolarization

Most are not soluble because embedded into membrane with hydrophobic domains (are soluble in water though)

Front 1154

How do exotoxins inhibit protein synthesis?

Back 1154

One part of the toxin goes into membrane and other goes into cell to stop protein synthesis

Tends to kill the cell

Usually the intention is to make the environment more suitable for the bacteria, not to kill

Front 1155

How do exotoxins activate second messenger pathways?

Back 1155

They have proteins that affect second messenger pathways and signaling pathways

They can also interrupt these signaling pathways and stop immune system from mounting by disrupting the signal

Front 1156

What is alpha hemolysin?

Back 1156

AKA Alpha toxin

The hemolytic alpha toxin is produced by Staphylococcus aureus

Forms a transmembrane, seven-member pore in target cell membrane

Front 1157

What are AB toxins?

Back 1157

Duel component (A and B) toxins that bind to host cell and have toxic activity

Front 1158

What is the B subunit of the AB toxin?

Back 1158

Binds to host cell

Dlievers A subunit to cytoplasm

Often there are B subunits to form pore for A subunit entry

Front 1159

What is the A subunit of the AB toxin?

Back 1159

Toxic activity

Can be an ADP-ribosyltransferase: diptheria toxin or cholera toxin

Front 1160

What is diptheria toxin?

Back 1160

An ADP-ribosylating toxin

Made by gram positive bacteria, Corynebacterium diphtheriae

Encoded on a bacteriophage

Blocks ribosome function, causing cell death

Forms pseudomembrane over trachea (lethal)

Front 1161

What is cholera toxin?

Back 1161

An ADP-ribosylating toxin

Made by vibrio cholerae

Ribosylates adenylate cyclase causing hyperactivation (producing a lot of cAMP)

cAMP activates ion transport causing water to follow leading to uncontrollable diarrhea

Front 1162

What is the mechanism of cholera toxin?

Back 1162

1) AB toxin complex binds to ganglioside GM1 on host membrane lipid rafts

2) Toxin endocytosed

3) Phagosome containing cholera toxin taken to endoplasmic reticulum

4) A1 subunit removed from B sununits and exported into cytoplasm

5) A1 peptide attaches an ADP ribose to amino acid within host G protein that regulates adenylate cyclase

6) cAMP levels rise and active ion transporter causing electroylte imbalance which will cause water from ceclls to follow the ions, causing diarrhea

Front 1163

What is botulism toxin?

Back 1163

A clostridial toxin

Produced by Clostridium botulinum

On a per weight basis, most potent biological neurotoxin known

A protease that inhibits the release of acetylcholine from excitory neurons to muscle cells

Cause "flaccid paralysis" where muscles fail to work (no muscle tone)

Front 1164

What is tetanus toxin?

Back 1164

AKA Tetanospasmin

Produced by Clostridium tetani

Second most potent biological neurotoxin known

Binds inhibitory interneurons in spinal cord and prevents release of inhibitory neurotransmitters necessary for muscle relaxation

Causes "spastic paralysis" (muscles cannot relax)

Front 1165

What is flaccid paralysis?

Back 1165

Loss of muscle contraction due to botulism

Front 1166

What is spastic paralysis?

Back 1166

Excessive muscle contraction due to tetanus

Front 1167

How can botulinum toxin be used for medical purposes?

Back 1167

It is called Botox (using botulinum toxin type A)

Can be used to treat strabismus (cross eyes)

Treat muscle spasms (back pain, overactive bladder, prostate issues)

Can even treat excessive sweating

Though the effects of the toxin last 3 to 6 months

Front 1168

What is Anthrax toxin?

Back 1168

Made by Bacillus anthracis

Has two active toxins in it:

1) Edema factor (raises cAMP levels, causes fluid secretion and tissue swelling)

2) Lethal factor (cleaves protein kinases, blocks immune system from attacking)

Front 1169

How does Anthrax toxin enter the cell?

Back 1169

1) Protective antigen (PA) subunit made as single peptide

2) PA binds to host cell surface where a human protease cleaves off part of Anthrax toxin receptor

3) Seven PA fragments autoassemble in the membrane to form a pore

4) Other two components of anthrax toxin (EF and LF), bind to ring and carried into cell by endocytosis

5) EF and LF are expelled through PA pore into cytoplasm

Front 1170

What was the 2001 Anthrax Attack?

Back 1170

After 9/11, seven letters were sent to membranes of the American congress and selected news outlet including Tom Brokaw at NBC television

The letters contained highly purified spores from Bacillus anthracis bacterium

This resulted in complete halt of governmental mail survice, close of US Capitol building

Total, 22 people contracted disease and five pepople died due to inhalation of anthrax spores

Front 1171

What are endotoxins?

Back 1171

AKA LPS

Made only by gram-negative bacteria

Present in LPS of outer membrane such as Lipid A (released as bacteria die, can cause sepsis)

Front 1172

What are intracellular pathogens?

Back 1172

Spend all or some of their time inside host cell during infection (can be within membrane-bound compartments or free within cytosol)

Can enter cells actively (bacterial driven) or passively (by host receptor-mediated uptake)

Speculated that most bacterial pathogens (except those that cause disease through toxin production) spend at least some portion of their infectious cycle within host cell niche

Front 1173

What are vacuole-adapted intracellular pathogens?

Back 1173

Can be within membrane-bound compartments

Front 1174

What are cytosol-adapted intracellular pathogens?

Back 1174

Can be free within cytosol

Front 1175

What are the advantages to being an intracellular pathogen?

Back 1175

Evasion of humoral immunity (antibodies, complement)

Evasion of specific innate immune cells (neutrophils)

Access to nutrients in host cell

Can manipulate host cell signaling, and therefore the host

Front 1176

What are the disadvantages to being an intracellular pathogen?

Back 1176

Many cellular defenses to contend with

Human cells have ways to detect many aspects of pathogen attack and initiate inflammatory response

Need a complex strategy to get into host cells, avoid being killed, acquire nutrients and then escape (failure at any step is lethal for bacterial invader)

Front 1177

TRUE or FALSE

All of the intracellular entric pathogens rely on a Type-II secretion system for the ability to reside within a host cell

Back 1177

FALSE

All of the intracellular enteric pathogens rely on a TYPE-III (3) secretion system for the ability to reside within a host cell

Front 1178

TRUE or FALSE

Some non-enteric intracellular pathogens rely on Type-IV secretion for ability to reside within a host cell

Back 1178

TRUE

Front 1179

How do phagosome going through maturation by phagocytosis on a bacterium?

Back 1179

NOTE: Each step, the pH inside endosome/phagosome decreases

1) Cell detects bacteria at surface and engulfs bacteria into early endosome/vacuole by endocytosis

Now in Early Phagosome

2) Bunch of proteins and enzymes would bind to early endosome and a multivesicular body comes and fuses to put its internal components into the early endosome

Now in Intermediate Phagosome

3) Bunch of materials interacting with bacterium as late endosome vesicle fuses and adds its components like cathepsins

Now in Late Phagosome

4) Now a lysosome will fuse with the late endosome, adding in hydrolytic enzymes that can kill the bacteria and keeping it contained in the vacuole

Now is a Phagolysosome

Front 1180

What are some phagosomal defenses against bacteria? Give examples of each

Back 1180

Acidification (V-ATPase)

ROS production (Cytochrome b558 & NADPH oxidase)

Antimicrobial peptides (Defensins)

Reactive nitrogen intermediate production (iNOS producing NO)

Nutrient limitation by pumping out or sequestering metal ions (Lactoferrin for iron)

Digestion of microbe (Proteases

Front 1181

How is acidification a phagosomal defense against bacteria?

Back 1181

Uses ATP to make protons to fill vacuole with, making it more acidic, lowing pH, inducing signaling pathways

Front 1182

How is ROS production a phagosomal defense against bacteria?

Back 1182

Produces NADPH oxidase

Gets electron from NADPH to generate oxygen radicals to react with water to make hydrogen peroxide or other radicals

Radicals are very reactive that can even split DNA

Front 1183

How are antimicrobial peptides a phagosomal defense against bacteria?

Back 1183

Punch holes in membrane

Front 1184

Why are phosphate free detergents better for lakes and streams?

Back 1184

Phosphate is a limited bioavailable nutrient for bacteria

If no phosphate in detergent, the algae will have a difficult time to grow

Front 1185

Why does iron not float freely in our body?

Back 1185

Iron is a rate-limiting nutrient/resource for microbial growth

A lot of bacteria are trying to uptake or steal iron form the host

By withholding iron, we can limit growth of bacteria in our tissues

Front 1186

What is Fenton chemistry?

Back 1186

Using iron to generate highly toxic hydroxyl radicals and peroxides

Front 1187

In the human body, where is Fe3+ stored?

Back 1187

In intracellularly complexes with:

Ferritin bound by serum transferrin

OR

Lactoferrin at mucosal surfaces

Front 1188

In the human body, where is Fe2+ stored?

Back 1188

Fe2+ is complexed with haem, which is bound by haemoglobin within red blood cells

Front 1189

What are three general/common iron acquisition systems do bacteria tend to use to acquire iron?

Back 1189

Haem/hemoglobin uptake systems

Siderophores

Free iron acqusition systems

Front 1190

What is bacterial hemolysis?

Back 1190

Using hemolysins to lyse red blood cells and release the enclosed hemoglobin

Front 1191

What is the role of hemoglobin?

Back 1191

Deliver oxygen to deep tissues

Front 1192

How do gram negative bacteria do hemoglobin uptake after hemolysis?

Back 1192

Hemoglobin receptors (either Surface hemoglobin receptor or Hemophore receptors) will bind to liberated hemoglobin and takes it heme

Heme will be imported into the cell through ABC transporter

Heme will be then broken down by cytosolic oxygenase to liberate free iron for bacteria to use (sometimes bacteria will keep the whole heme)

Front 1193

When bacterial hemolysis occurs, why does it sometimes look yellow?

Back 1193

The beta-globin in it has only the heme product in it (same case for pee)

Front 1194

What is enterobactin?

Back 1194

AKA Enterochelin

Secreted by bacteria to grab iron (or more specifically ferric iron) against its concentration gradient

Extremely high affinity for ferric iron (Ka=10^52 M^-1)

This high affinity allows this molecule to scavenge iron from host proteins and from environments where it is present in very low concentrations

Outer membrane receptors (porin like) on bacteria will recognize this and import it into bacteria

Front 1195

What is FepA?

Back 1195

Outer membrane receptor that is similar to a porin but contains additional domain in center that plugs up hole

These plug domains have high affinity for their substrate (like iron bound to enterobactin)

Front 1196

How does TonB system/complex work?

Back 1196

TonB acts as a "cork" domain that blocks an outer membrane receptor until it is engaged by its substrate

When happens, TonB with ExbD and ExbB uses the proton gradient across the inner membrane as energy to drive release of the bound substrate from the outer membrane receptor

The substrate will be passed onto a Periplasmic Binding Protein (PBP) which shuttles to inner membrane to allow substrate to go through ABC-transporter to cytoplasm using ATP

Front 1197

When red blood cells are being lysed, how does the host respond?

Back 1197

Haptoglobin (HP) will bind to hemoglobin and the free haem is scavanaged by haemopexin (HPX)

Also, haem-binding protein, lipocalin 2 (neutrophil gelatinase-associated lipocalin or NGAL) binds and sequesters bacterial sideophores that chelate Fe3+

Front 1198

How does the human host counter bacterial siderophores that chelate Fe3+?

Back 1198

Haem-binding protein, lipocalin 2 (neutrophil gelatinase-associated lipocalin or NGAL) binds and sequesters bacterial sideophores that chelate Fe3+

Essentially preventing siderophore that is bound to iron from being used by bacteria

Front 1199

How does enterobactin chelate iron?

Back 1199

Using its three arms to chelate iron by coordinating it between six oxygen atoms (labeled in red)

Front 1200

What is salmochelin?

Back 1200

A specialized siderophore made by Salmonella

There are different variations of this that have high affinifty for feric iron

Front 1201

What is Salmochelin S4?

Back 1201

Produced by Salmonella as specialized specific siderophore and is closely related to enterbactin

Extremely high affinifty for ferric iron

Contains additional glucose molecules of two of the three arms that bind iron to prevent being bound by lipocalin-2

Front 1202

Why can lipocalin-2 not bind to Salmochelin S4?

Back 1202

Salmochelin S4 has two glucose molecules on two of its three arms that bind iron, preventing lipocalin-2 to bind to it

Front 1203

Why would Salmonella want to cause inflammation in the intestine upon infection?

Back 1203

A consequence of causing inflammation is the host will produce large amounts of lipocalin-2

Lipocalin-2 will prevent commensal E. coli from obtaining iron but has no effect on the ability of Salmonella

Therefore Salmonella can use inflammation to get iron it needs and simultaneously kill off its competitors

Front 1204

What protein does macrophages and neutrophils use to limit iron availability in phagosomes?

Back 1204

Natural resistance-associated macrophage protein 1 (NRAMP1)

Front 1205

What is NRAMP1?

Back 1205

Natural resistance-associated macrophage protein 1

Localizes to phagosomal membrane where it pumps Fe2+ and Mn2+ out of the phagosomal compartment, further reducing access to these metals

This starves bacteria of iron and mangenanese

Front 1206

What does Borellia burgdorferi cause and how?

Back 1206

It is a causative agent of Lyme disease

Substitutes Mn2+ in place of Fe2+ in some of its critical metabolic enzymes

For this reason, Borrelia does not require Fe2+ to infest its hosts

Front 1207

What is nutritional immunity?

Back 1207

The ability of the host to sequester critical nutrients from pathogens

These nutrients can include copper, zinc, megnesium or manganese

Front 1208

Why did the WHO gave iron supplementation to young children in third world countries and why did they have to stop?

Back 1208

Over there, there was a lack of dietary iron which was linked to poor health so WHO thought iron supplementation would improve health in children in low income regions in the world

Studies stopped prematurely when discovered that children receiving high doses of iron in form of supplements were at greatly increased risk of infectious diseases

Front 1209

What happened to Malcolm Casadaban?

Back 1209

Doing research on Yersinia pestis that was attenuated to have reduced/lack of iron uptake

Unfortunately, Malcolm Casadaban had suffered from hereditary hemochromatosis (iron overload in blood), when he was infected with the attenuated Yersinia pestis, the bacteria was able to use the excessive blood and he died

Front 1210

What happens when you infect a intestine with virulent (wild-type) and avirulent (mutant) Salmonella at the same time?

Back 1210

The avirulent will do just as well as the virulent

The virulent will create the perfect environment for the avirulent to live in

Virulent will induce inflammation which enhances colonization of avirulent

Front 1211

What is the Salmonella's metabolic paradox?

Back 1211

Under aerobic conditions, Salmonella typhimurium uses ethanolamine as sole source of carbon, nitrogen and energy (one of the few bacteria that do this)

This growth depends on exogenous cobalamin, a required cofactor that Salmonella cannot synthesize in presence of oxygen

Under anaerobic conditions, vitamin B12 is made but Salmonella cannot use thanolamine as carbon or energy source even with alternative electron acceptors nitrate or fumarate

Front 1212

How was the Salmonella's metabolic paradox solved?

Back 1212

An anaerobic electron aceptor tetrathionate allows Salmonella to use endogenously synthesized vitamin B12 to support anaerobic degradation of ethanolamine as a sole source of nitrogen, carbon and energy

The gene that encodes this tetrathionate respiration (ttr operon) is found on SPI-1

Front 1213

When does tetrathionate become available in the gut?

Back 1213

During inflammation as the white blood cells are dumping oxygen species into intestinal lumen which is usually anaerobic

Front 1214

What is an antibiotic?

Back 1214

Substance produced by a microorganism or a similar product produced wholly (synthetic) or partially (semi-synthetic) by chemical synthesis and in low concentrations inhibits the growth of or kills microorganisms

Front 1215

What antibiotic is this?

Back 1215

Salvarsan

(Notice central Arsenic group)

Front 1216

What is Salvarsan?

Back 1216

An old treatment for syphilis

Unfortunately consists of highly toxic arsenic which gave a lot of side effects

Front 1217

What is Prontosil Red (or sulphonamido-chyrsoidin)?

Back 1217

A dye for staining leather

Contains sulphanilamide in it

Front 1218

What antibiotic is this?

Back 1218

Sulfanilamide (or 4-aminobenzensulfonamide)

Front 1219

What is the antibiotic Sulfanilamide?

Back 1219

Inhibits bacterial growth by interferring with synthesis of folic acid

Front 1220

How is folic acid produced using dihydropteroate synthetase?

Back 1220

Front 1221

Why must most microorganisms must synthesize folate de novo?

Back 1221

They lack the active transport system of higher vertebrate cells that allow these organisms to use dietary folates

Front 1222

How does Sulfanilamide interfere with folic acid?

Back 1222

Sulfanilamide is a competitive inhibitor of dihydropteroate synthease

Its similar structure to PABA can block active site of enzymes such as dihydropteroate synthetase

Front 1223

Why does sulfanilamide not harm humans?

Back 1223

Humans can still obtain sufficient folic acid from their diet

Front 1224

Even though penicillium was discovered in 1928, why was it not widely used till the early 1940s?

Back 1224

Alexander Fleming could not isolate the penicillium form the fungus mold

Front 1225

Who were able to isolate penicillium from the fungus mold?

Back 1225

Florey and Chain in the 1940's

Front 1226

What core aspect makes a antibiotic good?

Back 1226

Selective toxicity (against target pathogen but not against host)

LD50 to be high in MIC and low in MBC

Front 1227

In clinical terms, what is MIC?

Back 1227

Minimal inhibitory concentration

Measure of concentration of antibiotic (or drug) necessary to inhibit growth of target bacterial cell

In other words, lowest concentration that prevents growth

Front 1228

In clinical terms, what does MLC stand for?

Back 1228

Minimal lethal concentration

Front 1229

In clinical terms, what is MLC?

Back 1229

Measure of the concentration of antibiotic necessary to kill target pathogen

Front 1230

How do you calculate therapeutic index?

Back 1230

Front 1231

Why is alcohol not a good antibiotic?

Back 1231

Mostlikely, the amount needed to kill bacteria, will kill a human too

Front 1232

What is Disk Diffusion Assay?

Back 1232

Also called Kirby-Bauer Assay

Measures the sensitivity of bacteria to a given antibiotic

Contains multiple disks with different antibiotics where sizes of cleared zone reflects relative sensitivity

Front 1233

How is Disk Diffusion Assay gone? Explain each step

Back 1233

Paper disc soaked in antibiotic and is placed on a petri dish coated with an overlay of bacteria (called a bacterial lawn)

As antibiotic diffuses away form the disk, it becomes increasingly dluted, providing a concnetration gradient that radiates from the center of the disk

More resistant bacteria can grow closer to the disk, where antibiotic is more concentrated

Susceptible bacteria will have a large zone around the disk where they will not grow

Front 1234

What is favourable pharmacokinetics?

Back 1234

Survive in high concentration and reach the target site (site of infection)

Front 1235

What are pharmacokinetics?

Back 1235

Actions of drugs in the body over a period of time including:

Absorption, Distribution, Localization in tissues, Biotransformation, Excretion

Front 1236

What are the general characteristics of antimicrobial drugs on effects on bacterial growth?

Back 1236

Bactericidal

Bacteriostatic

Bacteriolytic

Front 1237

What is bactericidal?

Back 1237

Kills microbes and bacteria which will not re-grow after removal of drugs

Front 1238

What is bacteriolytic?

Back 1238

Bacterial cell lysis

(Can cause immune reactions in humans)

Front 1239

What is bacteriostatic?

Back 1239

Stops growth of microorganisms without killing them

Front 1240

What is a broad-spectrum antibiotic?

Back 1240

These be indicated against polymicrobial infection

Targets multiple bacterial species, even commensal bacteria (not good)

Should not be overused as can contribute to antibiotic resistance

Front 1241

What are narrow-spectrum antibiotic?

Back 1241

Ideal for an infection caused by a single pathogen

Should only be used when pathogen has been identified to prevent selection of resistance

Front 1242

Why are natural forming antibiotic compounds usuall better than synthetic ones?

Back 1242

They are shaped by evolution and have been tailored for a specific purpose

Front 1243

Why is the Streptomyces life cycle important for antibiotic research and development?

Back 1243

During their late stages of life, they produce different kind of compounds called secondary metabolism which some have the purpose of killing other specific bacteria to increase its chances of survival

Front 1244

Why is the beta-lactam ring of penicillin important?

Back 1244

This is an active bond

R groups can be substituted near it with any number of substituents that make each pencillin different

Front 1245

How does resistance against penicillum rise?

Back 1245

Resistance arises by having a bacterial acquire a plasmid that carry a penicillinase (beta-lactamase) enzyme

Front 1246

What is natural penicillium most active against?

Back 1246

Gram-positive bacteria

Front 1247

What happens during the first steps of transpeptidation during peptidoglycan synthesis?

Back 1247

Involves a transient (temporary) acyl-enzyme itnermediate

This enzyme specifically hydrolyzes the amide bond formed between the two D-alaine amino acids

During this process, peptidoglycan subunit is attached to a serine residue on the transpeptidase enzyme

Acyl-enzyme intermediate is resolved when amino group of neighboring peptidolycan subunit attacks the intermediate and releases the free enzyme

Front 1248

How does the antibiotic penicillin work?

Back 1248

The beta-lactam ring has an amide bond that mimics the D-ala-D-ala bond in the wall peptide which is recognized by transpeptidase during cell wall synthesis

This new crossbridge between pencillin and transpeptidase inactives the enzyme

Front 1249

When you modify the position 6 of the beta-lactam ring of penicillin, what properties do you mainly change?

Back 1249

Change in stability in water

Change availability in tissues

Front 1250

When someone is allergic to penicillin, what alternatives can be used?

Back 1250

Cephalosporins and its derivatives

Front 1251

What is Cephalosporin?

Back 1251

Produced by fungus Cephalosporium

Has low toxicity

Frequently given to patients that are allergic to penicillin

Active against Staphylococci, P. aeruginosa, E. cloacae and gram-negative bacteria

Front 1252

What antibiotic is this?

Back 1252

Vancomycin

(Notice large, cup-like structure)

Front 1253

What is the antibiotic vancomycin?

Back 1253

It is a large complex glycopeptide produced by Amycolatopsis orientalis

Blocks transpeptidation reaction by binding to terminal D-ala-D-ala of wall peptide and preventing it from serving as a substrate for penicillin binding proteins

It would essentially cup an enzyme that goes into the cell wall towards the D-ala-D-ala and prevent it from going in

Synthesized by non-ribosomal protein synthease

Because this can only inhibit one substrate per enzyme, it needs to be in high concentration to be efficient and is used as a last resort, usually given in IV drips

Also, poor solubility

Front 1254

Why is vanomycin a last resort antibiotic?

Back 1254

It only inhibits one substrate per enzyme, it needs to be in high concentration to be efficient

Because of this, and its poor solubility and poor ability to get through cell-wall membrane, it is used as a last resort

Front 1255

Why is vanomycin used almost exclusively on gram-positive bacteria?

Back 1255

Too big to get through a pore

Front 1256

When a drug gets bigger, is it more or less effective against gram-negative bacteria?

Back 1256

Less because it gets more difficult to get through peptidoglycan layer or fit through outer (or inner) membrane pores/channels

Front 1257

What antibiotic is this?

Back 1257

Bacitracin

(Notice exceedingly complex structure and with three layers and weird bend)

Front 1258

What is the antibiotic bacitracin?

Back 1258

Exceedingly complex peptide produced by Bacillus strains

Binds undecaprenyl phosphate (bactoprenol), a lipid caarrier, and prevents it from serving as a substrate for the attachment of NAG

Front 1259

What antibiotic is this?

Back 1259

Cycloserine

(Notice its just a simple pentagon with double O and NH2)

Front 1260

What is the antibiotic cycloserine?

Back 1260

Dy-cyclosern is a simple antimicrobial produced by Streptomyces garyphalus

Inhibits enzymes (racemases) that convert L-ala to D-ala and the enzyme that ligate the two D-ala residues to make the cell wall peptide precursor

Without the D-ala-D-ala residues cell wall synthesis cannot occur

Front 1261

Which antibiotics bind to 30S ribosomal subunit?

Back 1261

Streptomycin

Gentimicin

Tetracycline

Front 1262

What antibiotics bind to 50S ribosomal subunit?

Back 1262

Erythromycin

Chloramphenicol

Clindamycin

Front 1263

What antibiotics bind to to elongation factor G (EF-G)?

Back 1263

Fusidic acid

Front 1264

What antibiotics inhibit tRNA-synthetase?

Back 1264

Mupirocin

Front 1265

Why is targeting bacterial ribosome a great method for antibiotic targeting?

Back 1265

Bacterial and eukaryotic ribosomes are substantially different

Front 1266

What antibiotic is this?

Back 1266

Clindamycin

(Notice only one chair structure and one penta-ring)

Front 1267

What is aminoglycosides?

Back 1267

Class of antibiotics containing amino-modified sugars

They usually interfere with protein synthesis, either with tRNA translocation from A site to the P site or with proofreading during protein synthesis such that incorrect amino acids are incorporated at high frequency

They also appear to disrupt bacterial membrane

Not well absorbed by small intestine and have to be delivered to patient by injection or intravenously

Front 1268

Why do aminoglycosides have to be delievered to a patient by injection or intravenously?

Back 1268

Why are not well absorbed by the small intestines

Front 1269

What antibiotic is this?

Back 1269

Tetracycline

(Notice 4 cyclic rings)

Front 1270

What is the antibiotic tetracycline?

Back 1270

Isoalted from Streptomyces

Consists of four rings that can be derivatized to generate variant molecules

They bind to 30S subunit of ribosomes and inhibit docking of charged tRNAs, preventing protein synthesis

Readily absorbed into growing bone and tissue (therefore rarely used on children and pregnant mothers)

Cause yellow staining on growing teeth

Front 1271

Why is tetracycline rarely used with children or pregnant mothers?

Back 1271

Readily absorbed into growing bone and tissue

Also causes yellow stain on growing teeth

Front 1272

What antibiotic is this?

Back 1272

Erythromycin (class macrolides)

(Notice marcolide rings)

Front 1273

What is the class of antibiotics macrolides?

Back 1273

They have 14 to 16 marcolide rings that can be substitued at certain positions with various modifications

Inhibit protein synthesis by binding to 23S rRNA in the 50S ribosomal subunit

Front 1274

What is the antibiotic erythromycin?

Back 1274

Belongs to class of antibiotics, marcolides

Binds to ribosomes so they cannot shift (translocate) tRNAs from A-site to P-site and fail to transfer amino acids from tRNAs into growing peptide chains

Front 1275

What antibiotic is this and what does it do? And what class on antibiotics does it belong to?

Back 1275

Ciprofloxacin (class fluoroquinolones)

Inhibits DNA gyrase

(Notice triangle)

Front 1276

What antibiotic is this?

Back 1276

Rifampin

(Notice how bulky it looks in 2D)

Front 1277

What antibiotic is this?

Back 1277

A basic fluoroquinolone

(Notice the fluorine)

Front 1278

What are the class of antibiotics fluoroquinolones?

Back 1278

They inhibit gyrases which are lethal for bacterial cells

Front 1279

What is rifampin?

Back 1279

Bacteriocidal antibiotic that binds to beta-subunit of RNA polymerase

Blocks channel that newly synthesized mRNA goes through and stops RNA elongation when transcript is a few nucleotides long

Only active on RNA polymerase if it binds before transcription starts

Front 1280

What antibiotic is this?

Back 1280

Polymyxin

(Notice giant circular ring)

Front 1281

What is the basis of antimicrobial peptide selectivity?

Back 1281

Antimicrobial peptides have positively charged residues and ydrpohobic residues that are arranged in a fashion that can interact first with negative charges on bacterial surface then hydrophobic lipids in bilayers

Animal cell lipid bilayers are generally low in negative charges in their outer leaflet but rather usually loaded with cholesterol and zwitterionic lipids

Front 1282

How come Vanomycin took a long time to develop antibiotic resistance?

Back 1282

We used it as a last resort

Its evolutionary and mechanically changing to the change the D-ala-D-Ala it was targeting

Front 1283

What is the superbug NDM-1?

Back 1283

New Delhi Metallo-beta-lactamase 1

Cleaves almost anything with beta-lactam bond in it with broad specificity

Often found in strains that were already resistant to fluoroquinolones and amino-glycosides (making them superbugs)

Front 1284

How is the Netherlands fighting against antibiotic resistance?

Back 1284

They have strict laws on how they use antibiotics and where they can be sold

Front 1285

What is inherent resistance or natural resistance against antimicrobial drugs?

Back 1285

Lack of target (lacking targets like peptidoglycan)

Membrane permeability barrier (outermembrane of gram-negative bacteria)

Efflux (pumps like the ArcAB/TolC)

Metabolic shutdown (dormant persister state)

Front 1286

What is acquired resistance against antimicrobial drugs?

Back 1286

Alteration of target (genetic mutations leads to loss of affinity for drugs)

Efflux (production of proteins that pump out specific drugs)

Alteration or inacivation of drugs (production of enzymes to destroy the drug itself)

Front 1287

How has Streptomycin resistance develop?

Back 1287

Streptomycin binds to the 30S subunit of bacterial ribosome via contact with 16S RNA and ribosome subunit S12

Mutations arose spontaneously in S12 protein that decreased affinity for streptomycin, making the bacteria antibiotic resistant

Front 1288

What is MRSA?

Back 1288

Methicillin resistant Staphylococcus aureus

Group of Staphylococci that have high levels of resistance against the majority of beta-lactam antibiotics

MRSA strains harbor an alternative transpeptidase called MecA that has low affinity for beta-lactams but can still function to cross-link cell wall subunits

MecA gene is encoded on a genomic island (acquired by horizontal gene transfer) and appears to have been derived from a transpeptidase from closely related but non-pathogenic bacterial strain Staphylococcus scuiri

Front 1289

What is MecA?

Back 1289

MRSA strains harbor an alternative transpeptidase called MecA that has low affinity for beta-lactams but can still function to cross-link cell wall subunits

MecA gene is encoded on a genomic island (acquired by horizontal gene transfer) and appears to have been derived from a transpeptidase from closely related but non-pathogenic bacterial strain Staphylococcus scuiri

Front 1290

What is resistance to tetracycline due?

Back 1290

Due to efflux from specific transporter called TetA

This transporter is under negative regulation of repressor called TetR

When TetR binds tetraclycline, it falls off DNA and allows transcription of TetA antiporter

The TetRA genes are usually acquired by horizontal gene transfer

Front 1291

What is the beta-lactamase enzyme?

Back 1291

It cleaves beta-lactam rings in penicillins and cephalosporins

Use serine to attack beta-lactam ring and allows water to enter that can hydrolyzed penicillin from the active site, deactivating it

Front 1292

What antibiotic is this?

Back 1292

Carbapenems

Front 1293

What are carbapenems?

Back 1293

Class of beta-lactam derived antibiotics from naturally occuring beta-lactam produced by Streptomyces cattleya

These antibiotics are structurally distinct from penicillin and cephalosporin deriviates and highly resistant to inactivation by most beta-lactamases

Typically last resort in clinics

Front 1294

What is Aspergillomarasime A (AMA)?

Back 1294

A inhibitor of metallo-beta-lactamase

Front 1295

What modification can be done to small molecules to make them resistant to aminoglycosides?

Back 1295

1) Acetylation by acetylase enzymes using acetyl-CoA as donor

2) Phosphorylation by phosphotransferase enzymes (ATP as donor)

3) Adenlyation by adenyl-transferase (AMP attached to aminoglycoside)

Front 1296

Can Aspergillomarasime A (AMA) kill bacteria on its own?

Back 1296

No, it needs to work with meropenem

Front 1297

What is combinatorial chemistry?

Back 1297

Make libraries of compounds that are related or have different functional groups or atoms around the molecule which you would test its activity on certain bacteria or enzymes

Find different versions of drugs that are better or less effective

Front 1298

What is rational drug design?

Back 1298

Decide on particular target that you want drug against

Try and find some particular enzyme/protein that is only found in that bacteria and not human so if you inhibit that E/pep, you will kill that bacteria but not the humans

In silico drug screening (bioinformatics)

Front 1299

What are anti-infective drugs?

Back 1299

They inhibit virulence proteins

Drugs that inactivate the toxin and once done, can remove harmful effects of bacteria without needing to kill bacteria itself

If you do this, you are less likely to resistance to drug as you are not killing the bacteria, allowing the surviving ones to reproduce, here you kill none, just the toxin

Front 1300

What is Phage Therapy?

Back 1300

Make concoctions of phages and give it to patients so the phages can kill/disable the bacteria

Front 1301

What is the fear/problem with phage therapy?

Back 1301

There is no inherent danger to having phages in our body as they cannot infect us

The fear is that there is immune reactions to them or they can pick up virulence genes and spread them

So you could end up treating one infection while spreading genes to other bacteria, creating different infection

Front 1302

What are the advantages to phage therapy?

Back 1302

Bacterial host range and killing ability of a phage is generally restricted to one species of bacteria which helps maintain balance of natural flora (killing only target)

Limited host range decreases risk of developing resistant in strains not specifically targeting

Resistance to phage cocktails are unlikely

Pathogens that forms biofilms are innately resistant to antibiotics and host immune defenses but phages are able to degrade biofilms using exopolysaccharide-degrading enzymes that exist as spike attached to tails (digging through biofilms)

Front 1303

What are phage tail-like bacteriocins (also known as tailocins)?

Back 1303

Bacteriocins are bactericidal compounds made by bacteria which are generally effective only against same or closely related species

Pseudomonas aeruginosa makes bacteriocins called Pycins where R-pyocins resemble myophage tails (contractile) and F-pyocins that resemble siphophage tails (non-contractile)

Front 1304

What do R-pyocins resemble?

Back 1304

Myophage tails (contractile)

Front 1305

What do F-pyocins resemble?

Back 1305

Siphophage tails (non-contractile)

Front 1306

TRUE or FALSE

R- and F-Pyocins are related to phage tails

Back 1306

TRUE

Front 1307

How are expression of Pyocins controlled?

Back 1307

In a manner similar to prophages

When they are induced and released, they kill the cell they were released from

A repressor, PrtR, would be cleaved by RecA, allowing transcription of PrtN which creates pyocin proteins

Altraistic mechanism

Front 1308

How does R-Pyocin kill bacteria?

Back 1308

By making holes in their cell membrane and letting intracellular molecules leak out and ATP levels drop

Usually, when viruses poke into bacteria, the hole will remain plugged so cell does depolraize and die but not with R-pyocin

Front 1309

How can R-pyocins be engineered to kill specific bacterial species?

Back 1309

You can modify the fibers at the end of the tail through gene manipulation that bind to specific proteins on specific bacteria

Front 1310

What is Lysin CF-301?

Back 1310

Can be used in combination therapy with antibiotics, it can treat MRSA

Together they will kill the bacteria more effectively than antibiotic alone