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185 Cards in this Set

  • Front
  • Back
What is the cell theory of life?
Concept developed by Schwann. All organisms are composed of cells.
What is pasteurization?
Exposing food to enough heat to destroy microorganisms without affecting quality.
What is the germ theory of disease?
Disease is caused by microorganisms. Lister.
What are Koch's postulates?
1. MO is found in diseased animals but not healthy animals.
2. MO can be grown in pure culture.
3. Healthy animals are made sick by the MO.
4. You can re-isolate the MO from these animals.
What did Tyndall do?
Helped dispel the idea of spontaneous generation. Invented tyndallization (which destroys MOs with pressure).
About how many bacteria in the oral cavity?
2 x 10^7
A bacterial ribosome is defined as__S. What two subunits does it have?
70
Subunits: 50S and 30S
Prokarya are defined by what they do not have, namely ____. This is why Pace thinks the term is outdated.
nuclei
Bacteria ribosomal RNA is defined as ___S.
What two subunits does it have?
16
subunits: 23S and 5S
What are the three domains? Which two have the closest evolutionary origin?
Eukarya, Archaea, and Bacteria

E and A are closest in origin
What RNA is used to classify bacteria? Which section is variable?
the 16S rRNA. The middle is variable.
Eubacteria lack ___ in cell membranes.
sterols
Which organelles are thought to have evolved from bacteria?
mitochondria and chloroplasts (endosymbiotic theory)
What kinds of lipids are in bacteria?
only simple phospholipids
What kinds of ribosomes do eukaryotes have?
80S (and some 70S from ribosomes)
Do eukaryotes or prokaryotes display colinearity? What is it?
Prokaryotes do. Means number of amino acids is proportional to the nucleotides. (Eukaryotes have introns)
Do viruses translate/transcribe RNA or DNA?
Do they have lipids?
No.; It is POSSIBLE for them to have a lipid coat, but this is not a biological membrane.
Why aren't bacteria giant?
Once the volume to surface area ratio gets too high, it is difficult for a cell to function.
Do bacteria have ribosomes? Do viruses?
Bacteria have ribosomes (70S) and viruses don't.
Do bacteria have DNA/RNA? Do viruses?
Bacteria have both. Viruses have one or the other, but never both.
Four basic steps of the Gram stain.
1. Crystal violet
2. Iodine (fixing in +)
3. acetone/alcohol (washing from -)
4. safranin
What's the difference between classification and taxonomy?
taxonomy is the study of classification
What did Carl Linnaeus start?
the binomial system of nomenclature
After performing the Ziehl-Neelson stain, the acid-fast bacteria are stained ____.
RED
The biggest acid-fast genus is ____. Species of this genus cause what two major diseases?
Mycobacterium
leprosy and tuberculosis
Almost all Gram + cocci n the oral cavity are ___.
Streptococcus
Almost all Gram - spirochetes in the oral cavity are ___.
Treponema (all spirochetes in general are Gram -)
Almost all Gram - cocci in the oral cavity are ____.
Veillonella
A star shaped colony indicates ____.
Aggregatibacter actinomycetemcomitans
Gram - rods with a black/brown colony from the oral cavity are usually one of what two things?
Bacteroides species or Porphyromonas gingivalis
Does Aggregatibacter actinomycetemcomitans have catalse? How can you tell?
It does have catalase! It bubbles when you add hydrogen peroxide.
Why are Bacteroides black in colonies?
melanin
What is notable about Serratia marcesens?
It is blood red in culture because of a pigment called prodigiosin.
What are some ways to identify bacteria by products?
1. their products of fermentation
2. their acid profiles
3. their fatty acid profiles
4. their protein profiles
5. their antigen profiles
What are biotypes?
classifications based on fermentation reactions
What are serotypes?
classifications based on immunospecific reactions (antigen/antibody)
How does neutral red work?
If the bacteria ferments lactose, the lactate will neutralize the red color. (this is a "biotype")
What are two typical tests for serotype?
ELISA. Adding fluorescent antibodies to a bacteria and seeing if they fluoresce.
Steps in ELISA.
1. antigens added
2. first antibody added
3. second antibody (attached to a dye) is added
What is API?
Automated phenotypic identification. Strips that you inject your bacteria into and then incubate. Pretty neat.
What's the difference between Gram negative and Gram positive bacteria?
Negative have a smaller PG layer. They also have an outer membrane.
On a Gram - bacteria, the ___ is between the inner membrane and the outer membrane.
periplasmic space
Why are bacterial membranes described as tripartate?
With the electron microscope, there are three layers.
What kind of bacteria have enclosing membranes?
acid-fast (I'm not sure why I made this question and I don't know what it means, but I'm leaving it in case I find out)
What is unique about the genus Mycoplasma?
It lacks PG. It can absorb sterols into its membrane. In these ways, they're like eukaryotes. (MYCOPLASM /= MYCOBACTERIA)
What are the three parts of PG?
1. Glycan backbone (NAG and NAM)
2. tetrapeptide side chain
3. amino acid cross-links
What is NAM? NAG?
N-acetyl muranic acid (found only in bacteria). N-acetyl glucosamine
How are NAG and NAM linked?
beta-1,4 disaccharide linkages
What are the conformations of the aas in the tetrapeptide side-chain? What does it end in?
Usually L, then D, then L/D, then D. It always ends in D-alanine.
Does the tetrapeptide chain attach to NAG or NAM?
NAM
The cross bridge of PG connects what to what?
D-alanine (position 4), to an amino acid in position 3 on a different glycan backbone.
What is the amino acid in position 3 in the tetrapeptide chain? What's unique about it.
Usually D,L-diaminopimelic acid. It's unique because it's diamino, dicarboxy, allowing it to make 3 peptide bonds, which makes crosslinking possible.
Abbreviation: meso-DAP
What doesn't the D-alanine in position 4 have to be diamino dicarboxy?
It only has to make two peptide bonds. Think about it.
What's the difference between the structure of PG in Gram - and +?
Gram - has less cross-linking. In Gram +, all the NAMs are linked.
What happens to a eukaryotic cell under hypertonic conditions? Hypotonic?
hypertonic: plasmolysis
hypotonic: cytolysis
What structural feature most explains bacteria's ability to live in weird places?
The cell wall. Keeps them from lysing/shrinking. It's also resistant to detergent and heat.
Where does lysozyme cut the cell wall?
It cleaves between NAG and NAM. (Many host cell defenses target PG)
What is the major surface polymer of (all and only) Gram positive bacteria?
Lipoteichoic acid (LTA)
The hydrophilic portion of LTA is composed of alternating phosphates and one of what two sugars?
glycerol or ribitol
What is the major surface polymer of (all and only) Gram - bacteria?
LPS (lipopolysaccharide, aka endotoxin)
What are the three parts of LPS.
1. Lipid A (in membrane)
2. Core polysaccharide (short. maybe 4-5 sugars)
3. O-polysaccharide (aka O-antigen)
What is the composition of the O-antigen?
It's got about 4 sugars that repeat many times.
Why is the O-polysaccharide helpful for serotyping?
The repeating sugars vary from bacteria to bacteria, so the antigens that respond to each one will be different.
Describe Lipid A.
Two phosphorylated NAGS with FAs attached. Lipid A is the TOXIC PORTION of LPS.
LTA attaches to the ___ and passes out through ___.
cytoplasmic membrane; PG
LPS attaches to the ____.
outer membrane
How does LPS create an asymmetrical membrane?
The outer leaflet of the outer membrane is composed mainly of the FAs and sugars of lipid A, while the inner leaflet of the outer membrane is generic phospholipid.
What's the structure of a porin? What's the biggest thing that can get through it?
It's a trimer. A pentasaccharide can get through it.
Like Gram positive bacteria, ____ have a cytoplasmic membrane and PG, but no outer membrane.
acid-fast bacteria
What is the most important surface compound of acid-fast bacteria? Describe it.
Mycolic acid. It's large and very waxy and excludes water. It makes growth difficult.
A shiny, glistening colony might indicate the presence of what?
A thick glycocalyx
Falgella are composed of ___, while pili are composed of ____.
flagellin; pilin
What are the protein surface appendages?
flagella and pili
Flagella are used for ____, while pili are used for ____.
motility; adhesion (including mating)
E. coli has a single flagellum. These are called ___.
polar flagella
When bacteria have more than one flagellum, they are called ____.
peritrichous flagella
How does a bacteria change direction?
The flagellum (or flagella bundle) changes its direction of rotation.
What kinds of bacteria have axial filaments? What are they?
Spirochetes. Axial filaments are flagella that give spirochetes their corkscrew movement.
O-polysaccharide is sometimes called ____, and flagella are sometimes called ____. Capsules are sometimes called____.
O-antigen; H-antigen; K-antigen
Why do obligate anaerobes die in the presence of O2?
They cannot eliminate superoxide anions. They don't have the enzyme superoxide dismutase.
Autotrophs do not require what?
organic carbon. They use only CO2 (e.g. blue-green).
What do superoxide anions do?
they inhibit DNA (OK. Not sure, but I think they bind the two strands of DNA together...?)
Heterotrophs require ____.
an organic source of carbon
Bacteria that grow at high temperature are called? Medium temp? Cold temp?
High: thermophiles
Medium: mesophiles
Cold: psychrophiles
What is heterotrophic CO2 fixation?
The use of inorganic carbon for growth by heterotrophs (~5-10%)
How does glycerol get through the cytoplasmic membrane?
diffusion (this is rare and only for small molecules)
How do glucose, fructose, and sucrose get through the cytoplasmic membrane?
the phosphotransferase system (PTS)
[active transport]
What are the two kinds of passive transport across the cytoplasmic membrane?
simple diffusion or facilitated diffusion (as through a permease)
Describe active transport by a permease.
The permease goes through a conformation change. Once the molecule is inside, it is phosphorylated by ATP (usually), so it can't get out.
Superoxide anions are broken down by _____ into _____, which can further be broken down by ___ or _____.
superoxide dismutase; hydrogen peroxide; catalase; peroxidase
How does sugar get through the 3 layers of the Gram - bacteria?
facilitated diffusion through outer membranes, can pass through PG, and is actively transported across the cytoplasmic membrane.
What is the permease for glucose?
Enzyme IIGlu
Unlike other active transport systems, the PTS system uses ___ for phosphorylation instead of ATP.
PEP
____ takes the phosphate from PEP and puts it on ___. (re: PTS)
Enzyme I; HPr (histadine-rich protein
HPr brings phosphate to ___, which brings it to ___, which transfers it to the sugar as it enters.
Enzyme II; Enzyme III
In the PTS, sucrose binds to ____ on the cell membrane. Unlike glucose, sucrose does not have an ____.
Enzyme IIScr; Enzyme III
What are the soluble cytoplasmic components of the PTS? Which enzymes are in the membrane?
HPr and Enzyme I. Enzyme IIs are in the membrane.
What is the name for the bacterial glycolytic pathway?
The Embden-Meyerhoff-Parnas (EMP) pathway
The EMP breaks glucose down to ___.
pyruvic acid
What are the three general stages of the EMP?
1. phosphorylation
2. splitting
3. redox
What are the products of EMP?
Net 2 ATP, 2 NADH, 2 pyruvic acid
If glucose-6-P enters the PPP instead of the EMP, it will be converted first to 6-phosphogluconolactone, and ultimately will become building blocks for ___.
nucleic acids
What are the products of the pentose phosphate pathway?
1 net ATP, 1 NADH, 2 NADPH, a C4 product
Anaerobic bacteria (and facultative bacteria) will take pyruvate and make what?
alcohol, acid, and CO2
Aerobes (and facultative bacteria) take pyruvate and make what?
carboxylic acid intermediates and ATP
What process is coupled to the reduction of pyruvate to lactate (C3)?
the oxidation of NADH back to NAD+
During alcoholic fermentation, pyruvate is generally converted to ___, with ___ as an intermediate.
ethanol (C2); acetaldehyde (C2)
What kinds of bacteria are homolactic and heterolactic?
Both Streptococcus and Lactobacilli can be both
(Re: fermentation) Fusobacterium produce ____. Veillonella produce ____.
butyric acid; propionic acid
Do aerobic bacteria use the TCA cycle?
Yes, but it's modified. It's not complete. They don't have all the enzymes.
What are the main products of TCA?
NADH2 and intermediates for amino acid biosynthesis
In bacteria the ETC is in the ____. Protons are pumped ___ the cell. As protons rush back ___, they create energy.
cytoplasmic membrane; out of; in
What is the chemiosmotic hypothesis?
The idea that the proton gradient across the membrane allows ATP synthesis
What TCA enzyme is notably inactivated in anaerobic conditions?
a-ketoglutarate oxidase (which typically converts it to succinyl-CoA)
Do facultative bacteria completely stop TCA in the absence of O2?
No. It still makes some of the intermediates. It uses different enzymes.
During heterotrophic CO2 fixation, where is the carbon used?
It is used to make oxaloacetate from pyruvate for TCA. (NB: ATP is generated from CO2 fixation.)
What is horizontal (lateral) gene transfer?
Gene transfer from one MO to another. (No sex, no children.)
What are the consequences of lateral gene transfer?
Genetic plasticity allow MOs to evade host defenses and acquire resistance to antimicrobial agents.
What are the three types of mobile genetic elements?
1. plasmids
2. transposons
3. bacteriophages
Little circles of DNA that are separate from the bacterial chromosome are called ____.
plasmids
What is the "copy number" of a plasmid?
It determines the number of copies of the plasmid that the bacteria will make.
What are bacteriocins?
Plasmids that code for proteins that kill other bacteria.
What is an F-factor?
A plasmid that codes for the sex pilus (fertility factor).
What is a colicin?
A type of bacteriocin coded by a plasmid that is toxic to E. coli.
What's the main difference between a plasmid and a transposon?
Plasmids are circular. Transposons are linear. (NB: both are dsDNA)
What is on the ends of the transposon?
inverted repeats
The RNA or DNA of a bacteriophage is always contained in a ______.
protein coat
On a bacteriophage, there may be a ____ between the tail and the tail fibers. There may be a ____ between the head and the core.
base plate; collar
What is a capsomere?
the protein coat on the genetic material of a bacteriophage
What are Bradley groups?
Different kinds of bacteriophages based on DNA/RNA, ds/ss, tail/no tail, long tail/short tail, etc.
What are the three mechanisms of lateral gene transfer?
1. transformation (naked dsDNA)
2. conjugation (plasmid or transposon)
3. transduction (bacteriophage)
What are R strains and S strains?
R = rough, no capsule
S= smooth, capsule
In Griffith's experiments, why could inactive S strain make the R strain toxic?
Because of transformation. Naked dsDNA from the lysed S strain incorporated into the R strain, inducing it to form capsule.
What is the competence factor?
A protein made by the cell that binds to other cells at high cell concentration. It turns on autolysin. (Re: transformation)
What does autolysin do?
It makes the membrane more permeable. (Re: transformation)
What does nuclease do? (Re: transformation)
It sits on the cell surface near pores and DNA-binding protein.

It degrades one strand of the dsDNA that enters the cell.
What is competence-specific protein?
It coats the ssDNA made by the nuclease in protein, allowing it to enter the cell and incorporate into the chromosome during transformation.
(NB: both DNA and the membrane are negative, so the protein allows the DNA to get through the membrane)
What are the two cell types involved in conjugation?
F+ donor cell (caries the F plasmid) and F- recipient cell (no F factor)
What happens when the F+ attaches to the F-?
The F pilus acts as a bridge and makes a copy of its plasmid for the F- cell.
What is an Hfr cell?
A high frequency recombinant cell. It's a cell that has incorporated a plasmid into its chromosome during conjugation.
What is an F' cell?
It is an cell that has received a plasmid during conjugation that has extra DNA in it from the Hfr.
What is the last piece of DNA to pass to from the Hfr to the F-?
The F gene, which is the incorporated plasmid.
What are the two types of phages?
virulent and temperate
Virulent phages ___ the cell.
lyse
Virulent phages go through the ___ cycle. Temperate phages go through the ____ cycle.
lytic; lysogenic
Why is it called the lysogenic cycle?
The prophage DNA is carried silently, but always has the potential to become lytic given the right stimulus.
What is a good example of feed forward activation in S. mutans?
When sucrose is found in excess, G6P activates pyruvate kinase. F16BP activates lactate dehydrogenase. T3P inactivates pyruvate formate lyase.

The overall effect is homolactic fermentation (the strongest acid).
1. Pyruvate kinase
2. lactate dehydrogenase
3. pyruvate formate lyase
1. PEP to pyruvate
2. pyruvate to lactate
3. pyruvate to other stuff (heterlactic fermentation)
What does beta-glactosidase do?
Breaks lactose into galactose and glucose
What enzyme allows lactose to get into the cell?
galactoside permease
The lactose operon is an example of ___ and ___ control.
negative; local
What is the regulatory gene of the lactose operon?
lacI. It makes the repressor, which is always expressed in the absence of lactose.
What is the inducer of the lactose operon?
lactose. It changes the conformation of the repressor, so it can no longer block the operator.
What happens when the repressor is not bound to the operator (in negative control)
It allows lacY, lacZ, and lacA to be transcribed. (These make galactoside permease, b-galactosidase, and transacetylase, which are needed for lactose catabolism.)
What's the main difference with positive control?
The inactivated repressor binds at a different region of the operon to induce transcription.
What are the four stages of the bacterial growth cycle?
1. Lag
2. Log
3. Stationary
4. Death
Antibiotics made by...
1. fungi
2. Gram +
3. Gram -
1. beta-lactam
2. aminoglycoside
3. quinolone
What is MIC?
minimal inhibitory concentration required to inhibit bacterial growth
What are the four mechanisms of action of antibiotics we looked at?
1. inhibit cell wall synthesis
2. disrupt cell membrane
3. inhibit nucleic acid synthesis/replication
4. inhibit protein synthesis
The second part of PG is a tetrapeptide, but when it is being synthesized, it's actually a ____, with the 4th and 5th aas being ____.
pentapeptide; D-alanine
What does D-cycloserine do?
(1) Inhibits formation of the D-alanine-D-alanine bond in the pentapeptide.
What antimicrobials prevent PG precursors from getting out of the cell?
(1) vancomycin prevents transport across cell membrane.

(1) bacitracin prevents Carrier Lipid PP from dephosphoylating so it can't be recycled
What does penicillin do?
(1) prevents cleaving of the second D-alanine. Cross-links cannot be formed.
Penicillin is a close analog of ___.
D-alanyl-D-alanine
What are the two families of antimicrobials that disrupt cell membranes (2)?
a. polymyxins (for prokaryotic cells)
b. polyenes (interact with sterols -for eukaryotic cells, e.g. yeast)
What are the four families of antibiotics that inhibit DNA replication/synthesis (3)?
1. quinolones
2. metronidazole
3. rifamycins
4. sulfonamides
What do quinolones do?
(3) Inhibit DNA replication
What do metronidazoles do?
(3) Produce superoxide anion radicals to inhibit DNA replication.
What do rifamycins do?
(3) Inhibit DNA transcription by inhibiting RNA polymerase
What do sulfonamides do?
(3) block folic acid synthesis, which is needed for NA synthesis
Which antibiotics inhibit protein synthesis by inhibiting 30S (4)?
a. kanamycin
b. tetracycline
c. spectinomycin
4. streptomycin
Which antibiotics inhibit protein synthesis by binding to the 50S (4)?
a. chloramphenicol
b. erythromycin
3. clindamycin
4. lincomycin
Ethambuton, isoniazid, and pyrazinamide are all what?
Antiobiotics effective against acid-fast bacteria.
What are the four general mechanisms of antibiotic resistance?
1.Decrease cell permeability
2. Mutation to alter target site
3. Acquire gene to pump out antibiotics
4. Acquire genes to kill antibiotics
Mutations in transpeptidase might cause ____ resistance.
penicillin
Mutations in PG structure might cause ____ resistance.
vancomycin
How might bacteria become resistant to tetracyclin?
A ribosome protection gene or a tetracyline pump.
What's the last line of defense against MRSA?
vancomycin
Mutated DNA gyrase would cause resistance to ___.
quinolone
Which enzyme destroys penicillin?
beta-lactamase
Over time, pneumococci have become resistant to ____.
penicillin G
Over time, both meningococci and gonorrhea have become resistant to _____. The antibiotic of choice for gonorrhea is now ____.
sulfonamides; quinolones
Enteric bacteria are often treated with ____, but many are becoming resistant.
tetracycline
Regarding operons, ____ genes are always expressed and code for the ____.
constitutive; repressor
What is catabolite repression?
In the presence of glucose, genes that code for metabolic intermediates are repressed.

With a lack of glucose, the PTS activates cAMP, which activates these genes. This is an example of global control of several operons.