Fund 2, Test 1

Front 1

What are the 3 domains and what are they based on?

Back 1

Eucaryotes, archaea, and eubacteria. Based on evolutionary relationships.

Front 2

What is the main difference between eukaryotes and prokaryotes?

Back 2

Eukaryotes have a true nucleus with a nuclear membrane. (animals, plants, protists)

Prokaryotes only have a primitive nucleus without a nuclear membrane. (eubacteria and archaea)

Front 3

True/False: Prokaryotes have organelles in cytoplasm.

Back 3

False.

Front 4

Which prokaryote does not have peptidoglycan?

Back 4

Mycoplasma.

Front 5

Can you find sterols in prokaryotes and eukaryotes?

Back 5

Yes in eukaryotes, but only mycoplasma for prokaryotes.

Front 6

What is the difference in ribosomes between prokaryotic and eukaryotic cells?

Back 6

Prokaryotic: 70S (50S + 30S)

Eukaryotic: 80S (60S + 40S)

Front 7

What is the order for bacterial nomenclature?

Back 7

kingdom, division, class, subclass, order, family, tribe, genus, species.

Front 8

True/False: Bacteria are mostly free-living, single-celled organisms that reproduce by simple division.

Back 8

True.

Front 9

What is an example of a bacteria that is an obligate intracellular parasite?

Back 9

Rickettsiae and chlamydiae.

Front 10

What is the average size of bacteria?

Back 10

Usually about 1 micron, (mycoplasmas as small as .2 microns, bacillus as large as 10 microns)

Front 11

What are the cell shapes?

Back 11

coccus, rod, coccobacillus, vibrio, spirillum, and spirochete.

Front 12

What is the composition of bacterial cells?

Back 12

50% protein,

20% nucleic acids (10x more RNA than DNA)

10% polysaccharides

10% lipids

Front 13

Describe bacterial chromosomes.

Back 13

Single, circular, ds DNA (except borrelia = linear)

supercoiled strand up to 1 mm in length, haploid, contained in nucleoid, 600 to >5000kb. (a gene is approximately 1 kb)

Front 14

True/False: A larger chromosome in a bacteria usually means it will be able to live in fewer environments.

Back 14

False.

Front 15

What are the 2 main types of extrachromosomal DNA?

Back 15

Plasmids - replicate in cytoplasm, independent of chromosome, dsDNA, usually circular.

Bacteriophage - virus - replicates in cytoplasm or integrates into chromosome.

Front 16

What 3 things contribute to the genome of a bacteria?

Back 16

Chromosome, plasmids, and bacteriophage.Chromosome +plasmids + bacteriophage = GENOME

Front 17

What is the purpose of detergents, polymyxins, and ionophores?

Back 17

They act as antibacterials by affecting the cytoplasmic membrane of bacteria.

Polymyxins: damage PE-containing membranes (usually gram -)

Ionophores: disrupt membrane potential.

Front 18

What are the functions of a bacterial cell wall?

Back 18

Provides shape, barrier against osmotic pressure.

Front 19

How do we take advantage of bacterial cell walls?

Back 19

We affect them with antibacterials such as beta-lactams and lysozyme. We also use it for gram stains.

Front 20

What are the components and results of gram stains?

Back 20

It involves crystal violet, potassium iodide, ethanol, and water. The crystal violet-iodide complexes get trapped in the thick cell wall, resulting in the gram + cells staining purple. Then safranin (red) counterstain is applied and the gram – cells show up red. Exceptions: mycoplasmas don’t have a cell wall, mycobaceria has lipid that interferes with the stain.

Front 21

What are the components of peptidoglycan?

Back 21

Repeating disaccharide of N-acetylglucosamine and N-acetyl muramic acid crosslinked by peptide bridges at MurNAc.

Front 22

How do beta-lactams work?

Back 22

They resemble transpeptidase substrates and block the crosslinking of the growing chain. Would not affect a fully formed peptidoglycan.

Front 23

Where do hydrolases work?

Back 23

Hydrolases such as lysozyme and mutanolysin cleave at the linkage between the sugars.

Front 24

Where do amidases cleave?

Back 24

Amidases such as autolysins cleave between NAM and its sidechain L-ala.

Front 25

What is the purpose of transglycosylases and transpeptidases?

Back 25

Transglycosylases link the sugars together while Transpeptidases link the sidechains together and make the crosslinking.

Front 26

What is an example of a beta-lactam?

Back 26

Penicillin.

Front 27

What are some of the unique aspects of gram + bacteria?

Back 27

They have unique cytoplasmic membranes, cell walls, lipoteichoic acid, teichoic acid, and proteins.

Front 28

What are Wall Teichoic Acids (WTA)?

Back 28

They are repeating unites of phosphodiester-linked (negative charge) glyderol or ribitol backbone + sidechains that are covalently linked to PG (MurNAc). Found on gram + cells.

Front 29

What are Lipoteichoic acids (LTA)?

Back 29

They are similary to WTA, but anchored to the cytoplasmic membrane lipids; phosphodiester lined (negative charge) Found on Gram + cells.

Front 30

What are the purposes of LTA and WTA?

Back 30

They help with ion binding, charge maintenance, membrane integrity, adherence, and anchor proteins.

Front 31

What is different about the gram negative bacteria from the gram + bacteria?

Back 31

It has a thin peptidoglycan (1-2 layers; 2nm), no WTA or LTA, it has a periplasmic space to hold digestive and protective enzymes, and it has an outer membrane to block entry of large molecules.

Front 32

Describe the gram negative outer membrane.

Back 32

It is not a typical lipid bilayer, is attached to PG by lipoprotein, lipopolysaccharide (LPS) forms outer leaflet, its proteins deal with transport, has porins to allow passive diffusion of low MW hydrophilic compounds (sugars and amino acids)

Front 33

What is a Lipopolysaccharide?

Back 33

It is an endotoxin that can cause toxic shock. It is made of a Lipid A (which binds it to the outer membrane and contains toxic properties), a core polysaccharide (which varies by species), and an O-antigen (polysaccharide that varies with strain). It is negatively charged and stabilized by interactions with Ca2+ and Mg2+.

Front 34

What are some additional featers that can be found in both gram + and gram – bacteria?

Back 34

Capsules, flagella, pili, surface proteins, endotoxins, enzymes, and endospores.

Front 35

What is a capsule?

Back 35

A capsule is a polysaccharide or protein layer that is covalently linked to the cell (outer membrane for Gram -, and PG or cytoplasmic membrane for Gram +),

Front 36

What is its purpose?

Back 36

It functions to block complement activation, C3b deposition or recognition (antiphagocytic), aids attachment to host surfaces, is antilytic (blockes C5-C9 MAC in gram -), and provides resistance to cationic microbial peptides (CAMPs)

Front 37

What are the functions of flagella and pili?

Back 37

Flagella is a protein that aids in motility, chemotaxis, virulence (H-antigen). Allows a cell to rotate (swims), stop (tumbles), and is mediated by attractants (supress tumbling, repellants enhance tumbling). Pili are a shorter narower protein that aid with attachment and the F-pilus is for conjugation in gram -.

Front 38

What is the purpose of an endospore?

Back 38

It forms under nutrient depletion, is resistant to heat, desiccation, and chemicals and allows the bacteria to germinate in a favorable environment when it arises. An example would be Bacillus clostridium. (gram +)

Front 39

What are the growth requirements for bacteria?

Back 39

Water, Carbon and energy source (may be same), nitrogen, oxygen (or lack of), temperature, pH, and occasionally other things.

Front 40

True/False: All pathogens are chemoheterorophs.

Back 40

True.

Front 41

How much of a cell is water?

Back 41

70 to 80%

Front 42

What are some sources of carbon/energy?

Back 42

Mono and disaccharides, organic acids (lactate, succinate), amino acids, alcohols, and fatty acids.

Front 43

What are some organic and inorganic sources of nitrogen?

Back 43

Organic: amino acids. Inorganic: ammonia, nitrogen fixation, nitrate or nitrite (nitrate reduction or dentrification)

Front 44

What is the basic difference between strict aerobes and strick anaerobes?

Back 44

Strict aerobes cannot ferment, but do contain the enzymes necessary to degrade O2 metabolites while strict anaerobes lack the enzymes to degrade toxic O2 metabolites (such as catalase and superoxide dismutase), and always ferment.

Front 45

What is a faculative aerobe?

Back 45

It grows + or – O2, can respire or ferment.

Front 46

What is an aerotolerant anaerobe?

Back 46

It grows + or – O2, but always ferments.

Front 47

What is a microaerophilic bacteria?

Back 47

It grows best with low O2, but can grow without.

Front 48

What are the temperature ranges for thermophiles, psychrophiles, mesophiles?

Back 48

Thermophiles: >50 C, psychrophiles: 4 to 20 C, mesophiles: 20 to 40 C.

Front 49

What are the 4 phases of bacterial growth and when are betalacams and lysozymes effective?

Back 49

The 4 stages are the Lag phase, Log phase, stationary phase, and death phase. Lysozymes are effective for all phases, while betalatams are only effective during the xponential phase.

Front 50

What is synchronous growth?

Back 50

When all the cells divide at the same time.

Front 51

What is an open system/continuous culture/chemostat?

Back 51

It is when bacteria are given a constant source of fresh nutrients so the growth rate doesn’t change and remains linear.

Front 52

How do bacteria take in nutrients?

Back 52

Through hydrolysis of nonpenetrating nutrients by proteases, nucleases, and lipases, or through cytoplasmic membrane transport that is protein mediated (passive - facilitated diffusion; active - group translocation; active - substrate translocation)

Front 53

How are nutrients taken into the cell through facilitated diffusion kept in the cell?

Back 53

By phosphorylation of the substrate.

Front 54

How are nutrients taken into the cell through active transport (group translocation) kept in the cell?

Back 54

The substrate is altered and thereby trapped in the cell. Uses PEP or ATP.

Front 55

How are nutrients taken into the cell through active transport (substrate translocation) kept in the cell?

Back 55

The substrate remains unchanged, but the transport system has a higher affinity for the substrate outside the cell. Uses ATP or PMF (proton motor force)

Front 56

What is the major mechanism for export across cytoplasmic membrane?

Back 56

Sec.

Front 57

True/False: Bacteria have multiple mechanisms for secretion across outer membrane, and some transport directly to eukaryotic cell.

Back 57

True.

Front 58

What is the purpose of numerical classification?

Back 58

It enumerates the similarities and differences. e.g. Morphology (microscopic - size, shape, motility, spores, stains) and biochemical, physiological traits (growth under different conditions)

Front 59

What are serological classifications?

Back 59

Reactivity of specific antibodies with homologous antigens of different bacteria. Usually surface antigens (LPS, flagella, capsules. etc.) and is important in epidemiology.

Front 60

What is taken into consideration when determining genetic relatedness?

Back 60

DNA base composition, multilocus enzyme electrophoresis, ability to exchange and recombine DNA, DNA restriction profile, DNA sequence, DNA hybridization, DNA-RNA homology, DNA and rRNA, rRNA sequence

Front 61

What is multilocus enzyme electrophoresis?

Back 61

A technique used to determine genetic relatedness. It is a starch gel; enzyme assays to detect proteins that shifts in mobility due to changes in protein (amino acid) sequence.

Front 62

How do you get a DNA restriction profile?

Back 62

With a Restriction Fragment Length Polymorphism (RFLP) analysis. DNA is cut with restriction enzyme and spread on agarose gel stained with ethidium bromide.

Front 63

What is DNA hybridization?

Back 63

Taking total or specific sequences of bacterial DNA and seeing if they will hybridize with another? Also uses PCR.

Front 64

Why is rRNA sequence useful?

Back 64

Because it can help determine the sequence of DNA encoding that rRNA.

Front 65

True/False: rRNA is very sensitive.

Back 65

True.

Front 66

What is important about rRNA.

Back 66

It binds the initiation site in mRNA, must have secondary structure (base pairs with self), changes in critical areas likely detrimental, and the DNA that encodes rRNA is highly conserved among bacteria of common ancestry.

Front 67

True/False: Phylogenetic trees are based on DNA sequences.

Back 67

False! they are based on rRNA sequences.

Front 68

What 2 very important things are found in the ribosome binding site?

Back 68

The Shine-Delgarno sequence and an initiation codon. These allow translation to initiate.

Front 69

What are operons?

Back 69

Multiple genes that are transcribed from a single promoter.

Front 70

True/False: Bacteria have introns.

Back 70

False. Although they do have non-coding sequences.

Front 71

In what direction mRNA synthesized?

Back 71

5' to 3'. and it is the complement of the DNA with U instead of T.

Front 72

True/False: Transcription can occur on either DNA strand.

Back 72

True. But the one used depends on the presence of the proper signals (promoters)

Front 73

Where would you find the Shine-Delgarno sequence and the initiation codon? What are they?

Back 73

In the Ribosome binding site between the 30S subunit and the mRNA.

The Shine-Delgarno sequence: AGGAGGU

The initiation codon: AUG

Front 74

What are the start and stop codons?

Back 74

Start: AUG (Met)

Stop: UAA, UAG, UGA. (except in mycoplasma UGA = Trp)

Front 75

True/False: Mutations are observable changes from the DNA sequence.

Back 75

False: They are any change in the DNA sequence, whether or not it is observable. Can be spontaneous or induced.

Front 76

What is the difference between missense and nonsense?

Back 76

Missense: codes for a different amino acid

Nonsense: codes for a stop codon.

Front 77

What are the mechanisms of transcriptional regulation?

Back 77

Alternative Sigma Factors, 2 component (signal transduction), and quorum sensing.

Front 78

What are sigma factors?

Back 78

Proteins that bind RNA polymerase and allow recognition of promoter sequences. Alternative sigma factors allow recognition of alternate promoters. sigma 70 is major in E. coli.

Front 79

What is involved in Signal transduction (bacterial two component regulation)

Back 79

An input signal (temp, pH, aa, etc) affecting a sensor (histidine protein kinase (HPK); autophosphorylates), and a response regulator.

Front 80

What is quorum sensing?

Back 80

Cell-cell signaling that allows them to perceive/respond to cell density via diffusible molecules. Accumulation and detection leads to transcriptional regulation. Important for competence, bioluminescence, virulence, biofilms, and sporulation.

Front 81

What are the quorum sensing signals for gram + and gram - bacteria? And how do they sense them?

Back 81

Gram +: oligopeptide: peptide transported out and is recognized by 2-component system when [out] is high.

Gram -: acyl homoserine lactone (HSL): It diffuses in/out and binds LuxR when [in] = [out]

Front 82

What is the difference between homologous and nonhomologous recombination?

Back 82

Homologous: occurs b/t regions of DNA that are highly similar, involves specific bacterial enzymes and is RecA mediated.

Non-homologous: Occurs b/t DNAs without significant similarity and can involve Transposons (mobile genetic elements: Tn)

Front 83

What is the bacterial importance of Transposons?

Back 83

They are DNA sequences that are easily transposable that encode the functions for their own transposition and often encode antibiotic resistance and virulence factors.

Front 84

What are the 3 mechanisms for bacterial gene transfer?

Back 84

Transduction: mediated by bacteriophage, does not require cell-cell contact and is DNase resistant.

Conjugation: mediated by F-factor (Gm-) and pheromones (Gm+), requires cell-cell contact, and is resistant to DNase

Transformation: mediated by free DNA, no Cell-cell contact required, is sensitive to DNase.

Front 85

True/False: Homologous DNA taken into cell cannot recombine into chromosome.

Back 85

False. It can recombine into the chromosome.

Front 86

Where can you find extrachromosomal DNA?

Back 86

Bacteriophages - virus; replicates in cytoplasm or integrates into chromosome.

Plasmids - replicate in cytoplasm, independent of chromosome.

Front 87

What are the types and characteristics of bacteriophages?

Back 87

They are viruses that can be seen with an electron microscope, contain DNA or RNA in phage head, do not contain metabolic apparatus, and are specific phages infect specific bacteria. They can be virulent (kills bacterial host) or temperate (symbiotic with host, may give virulence factors, and these are >90% of known phages)

Front 88

What is the significance of bacteriophages?

Back 88

Phage (lysogenic) conversion is an observable effect of phage carried by bacterium and is medically important. Every bacterium may carry a phage. e.g. Corynebacterium diptheriae - Gm + rod; diptheria toxin = phage-encoded.

They also aid in gene transfer (transduction)

Front 89

Describe Transduction.

Back 89

It is the accidental packaging of bacterial DNA during the lytic cycle. It is rare ( about 1/10^6) and can transfer bacterial DNA to new host. Can be virulent or temperate phage.

Front 90

What is the purpose of F-factors?

Back 90

They mediate conjugation and can encode antibiotic resistance (R factor). They can replicate in cytoplasm and be transferred. Both donor and recipient = F+ at the end (Recipient begins as F-)

Front 91

Describe Transformation.

Back 91

It is the uptake and integration into chromosome (usually) of free DNA (or plasmids).

Front 92

True/False: For transformation, you need both the capsule and the live strain in order for it to be effective.

Back 92

True. But the capsule can be heat-killed and still effective.

Front 93

How does natural transformation occur?

Back 93

Homologous DNA is integrated from lysed bacteria or secretion. This only occurs when, through quorum sensing, the bacteria know they are near other like bacteria. Then the uptake machinery is expressed (it is highly regulated)

Front 94

What is antigenic variation?

Back 94

It is a permanent change that occurs via antigenic drift (slow accumulation of point or other 'small' mutations like in flu virus) or antigenic shift (major change from recombination)

Front 95

What is Phase variation?

Back 95

A.K.A. microbial variation. It is a non-permanent change (can revert back to original type). The bacteria can switch back and forth between expressing/not expressing. Helps pathogens avoid antibody and allows it to only express antigen when important (e.g. attachment)

Front 96

What are the main mechanisms of action for antibiotics?

Back 96

Inhibition of protein synthesis: rifampin, erythromycin, kanamycin, tetracyclines.

Inhibition of DNA synthesis: fluoroquinolones (ciprofloxacin)

Inhibition of metabolic activity: sulfonamides-bactrim (inhibit tetrahydrofolate production)

Cell wall synthesis: penicillins, vancomycin.

Front 97

What allows antibiotics to be specific for bacteria?

Back 97

Differences between bacteria (70S) and mammalian ribosomes (80S), analogous mammalian enzymes insensitive, antibiotic doesn't enter mammalian cells, or absence of PG in mammalian cells

Front 98

How can bacteria overcome the antibiotics?

Back 98

DNA replication (gyrase): Uses altered gyrase that doesn't bind antibiotic. (point mutation)

Transcription (RNA polymerase): Uses altered RNA polymerase. (point mutation)

Translation (ribosome): uses altered ribosome, develops enzyme to inactivate antibiotic, or prevention of antibiotic entering cell.

Cell wall synthesis: Altered cell wall synthesis proteins, or enzymes to inactivate antibiotic.

Front 99

What aids in the development and spread of antibiotic resistance?

Back 99

Mutations (point, in chromosome)

Plasmids, transposons

Gene transfer

Mutations arise at a low but constant frequency

Antibiotics SELECT FOR naturally-occurring resistant isolates.