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Microbiology > Ch 8: Microbial genetics > Flashcards

Ch 8: Microbial genetics Flashcards

1
Q

How big is a bacterial chromosome? How many genes?

A

500 - 6000 kb

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2
Q

How big is a bacterial plasmid?

A

1.5 - 300 kb

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3
Q

What are the differences between a bacterial chromosome and a plasmid?

A
  • Chromosome carries all essential genes
  • Plasmid contains genes that are conditional
  • Plasmids replicate independently
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4
Q

Are genes for antibiotic resistance, virulence, metabolic pathways, bacteriocins, and transfer genes located on the bacterial chromosome or plasmid?

A

Plasmid

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5
Q

How long is an E. coli chromosome?

A

~1 mm

Compacted to 10% of the cell’s volume

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6
Q

What genes does a conjugative plasmid carry?

A

Genes necessary for transfer of the plasmid to another cell

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7
Q

What genes do dissimilation plasmids carry?

A

Enzymes for catabolism of unusual compounds such as:

  • Toluene
  • Camphor
  • Petroleum hydrocarbons
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8
Q

In what organism are dissimilation plasmids most prevalent?

A

Pseudomonas

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9
Q

What genes do R factors/plasmids carry?

A

Resistance to antibiotics or heavy metals

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10
Q

What genes do virulence plasmids carry?

A

Proteins that enchance pathogenicity:

  • attachment to host cell
  • Toxins, neurotoxins, shiga toxin
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11
Q

What genes do bacteriocin plasmids carry?

A

Toxic proteins that kill other bacteria

Ex: Staphylococcus epidermis produces satphylcoccin

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12
Q

What bacteriocin does Lactococcus lactis produce?

A

Nisin

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13
Q

What bacteriocin does E. coli produce?

A

Colicin

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14
Q

Genes are assigned a 3-letter designation based on either ______ (4)

A
  1. Pathway they are involved in
  2. Cell strucuture
  3. Cell function
  4. Mutant phenotype
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15
Q

Different geenes affecting the same pathway are distinguished by ______

A

Capital letters

Ex: fadA, fad B, fadD

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16
Q

Genes not listed in a genotypes are assumed _____

A

Wildtype

Ex E. coli genotypes: MC1061 araD139 Δ(araA-leu)7696 galE15 galK16 lacX74 rpsL50 hsdR2 argF2

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17
Q

Gene names should always be written in _____ and _____

A
  • lower case
  • italicized
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18
Q

Explain how they name phenotypic designations

A
  • 3-letter symbols
  • Not italicized
  • First letter is capitalized
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19
Q

“Bio-“ describes what phenotype?

A

Requires biotin added as a supplement to minimal medium

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20
Q

“Arg-” describes what phenotype?

A

Requires arginine added as a supplement to minimal medium

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21
Q

“Met-” describes what phenotype?

A

Requires methionine added as a supplement to minimal medium

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22
Q

“Lac-” describes what phenotype?

A

Cannot utilize lactoase as a carbon source

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23
Q

“Gal-” describes what phenotype?

A

Cannot utilize galactose as a carbon source

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24
Q

“Strr” describes what phenotype?

A

Resistant to streptomycin

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25
Q

“Strs” describes what phenotype?

A

Sensitive to streptomycin

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26
Q

What are ORFs?

A

Open reading frame

  • Reading frame that lacks termination codes
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27
Q

What are short tandem repeats?

A

Short DNA sequences (2-5 bps) that repeat numerous times in a head to tail manner; knowing STRs allows for DNA fingerprinting

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28
Q

What did the Messelson-Sthal experiment prove?

A

Semiconservative model: each new strand of DNA contains one whole original strand

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29
Q

What is the function of DNA gyrase?

A

Relaxes supercoiling ahead of the replication fork

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30
Q

What is the function of DNA ligase?

A

Makes covalent bonds to joint DNA strands; Okazaki fragments, and new segments in excision repair

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31
Q

What is the function of DNA polymerase?

A
  • Synthesis of new DNA
  • Proofreed and facilitate repair of DNA
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32
Q

What is the function of endonuclease?

A
  • Cut DNA backbone in a strand of DNA
  • Facilitate repair and insertion
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33
Q

What is the function of exonuclease?

A
  • Cut DNA from an exposed end of DNA
  • Facilitate repair
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34
Q

What is the function of helicase?

A

Unwinds dsDNA

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35
Q

What is the function of methylase?

A

Adds methyl groups to selected bases in newly made DNA

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36
Q

What is the function of photolyase?

A

Uses visible light energy to separate UV-induced pyrimidine dimers

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37
Q

What is the function of primase?

A

An RNA polymerase that makes RNA primers from a DNA template

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38
Q

What is an snRNP?

A

RNA-protein complex that removes introns and splices exons together

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39
Q

What is the function of topoisomerase (or gyrase)?

A
  • Relaxes supercoiling ahead of the replication fork
  • Separates DNA circles at the end of DNA replication
40
Q

What is the function of transposase?

A

Cuts DNA backbone, leaving single-stranded “sticky ends”

41
Q

Approximately 40 min is required to replicate the E. coli chromosome, yet the doubling time of the organism can be as fast as 20 minutes. How is this possible?

A

Another replication fork is initiated 20 minutes after the start of the first

42
Q

What is the start codon?

43
Q

What are the stop (nonsense) codons?

A

UAA

UAG

UGA

44
Q

In bacteria, the start codon encodes for _____

A

N-formylmethionine

45
Q

What is codon bias?

A

The probability that a given codon will be used to code for an amino acid over a different codon which codes for the same amino acid

46
Q

What is an operon?

A

A group of genes that are transcribed together and controlled by one promoter

47
Q

What are constitutive genes?

A

Unregulated genes that are expressed at a fixed rate

60-80% of bacterial genes

48
Q

What is a repressible gene?

A

Rate of transcription is decreased by a repressor; default position is on

49
Q

What are inducible genes?

A

Rate of transcription is increased by inducer; default position is off

50
Q

What is the function of the lac operon in E. coli?

A

Contains genes needed for lactose metabolism:

  1. β-galactosidase
  2. lac polymerase
  3. transacetylase
51
Q

What is the difference between the promoter and operator of an operon?

A

Promoter: where RNA polymerase starts transcription

Operator: start/stop signal for transcription; where repressor or promoter binds

52
Q

Is the lac operon inducible or repressible?

53
Q

In 1959, Francois Jacob and Jacques Monod proposed the _______.

A

Operon theory

54
Q

What is the function of the I gene on the lac operon?

A

Encodes the repressor protein that switches the operon off

55
Q

What is catabolite repression?

A

Inhibition of synthesis of alternative catabolic enzymes by a preferred carbon source

(i.e. if you have glucose, there will be repression of any enzymes that catabolize another carbon source)

56
Q

What is the function of the Trp operon?

A

Contains genes required for tryptophan synthesis; biosynthetic operon

57
Q

Transcription of the lac operon requires presence and absence of what?

A

Presence of lactose

Absence of glucose

58
Q

Is the Trp operon repressible or inducible? What is its repressor/inducer?

A

Repressible

Tryptophan is repressor

59
Q

In eukaryotes, ____ nucleotides can be methylated

60
Q

In prokaryotes, ______ nucleotides can be methylated

61
Q

What is an alarmone?

A

A chemical alarm that promotes a cellular response to environmental or nutritional stresses

Ex: cAMP when glucose is low

62
Q

What are the regulator RNA molecules of prokaryotes and eukaryotes?

A

Prokaryotes: small RNAs (sRNAs); 50-500 nucleotides

Eukaryotes: microRNAs (miRNAs); ~22 nucleotides

63
Q

What is the function of microRNAs?

A

Incorporated into a RISC and serve to target specific complementary mRNAs to alter their translation or stability

64
Q

What is the function of sRNA?

A

highly structured RNAs that bind to protein targets and modify function OR may bind to mRNA targets and regulate translation or stability

65
Q

What is the difference between a transition and transversion mutation?

A

Transitions are interchanges of two-ring purines (A G) or of one-ring pyrimidines (C T), therefore, involve bases of similar shape.

66
Q

What is an inversion mutation?

A

Deletion and reassertion with the opposite orientation

67
Q

What is a missense mutation?

A

A base substitution that results in the replacement of one amino acid for another

68
Q

What is a nonsense mutation?

A

A base substitution that creates an in-frame stop codon

69
Q

What are the spontaneous mutation rates of E. coli? (3)

A
  1. 10-9 replicated base pairs
  2. 10-6 replicated genes
  3. 10-3 replicated genomes
70
Q

Why do frameshift mutations generally lead to premature termination?

A
  • Changes in frameshifts commonly make early stop codon
  • There is a 1/20 chance you will hit a stop codon in any reading from
71
Q

What is a base modifier? Example?

A
  • A mutagenic agent that alters properties of base pairs
  • Ex: nitrous acid deaminates A and C which makes them pair with C and A respectively
72
Q

What is a nucleoside analog?

A

A molecule that looks like a normal base that cannot base pair with the correct base

73
Q

What is 2-aminopurine?

A
  • Nucleoside analog
  • Takes place of A but can pair with C, so AT pair becomes CG pair
74
Q

What is 5-bromouracil?

A
  • Nucleoside analog
  • Looks like T but pairs with C, so AT pair becomes CG pair
  • Often used an anticancer drug
75
Q

What are some examples of ionizing radiation? (2)

A
  1. X-Rays
  2. Gamma Rays
76
Q

What are the direct and indirect actions of ionizing radiation as a mutagen?

A
  • Direct: physically break the sugar-phosphate backbone, bases themselves, or the connecting hydrogen bonds
  • Indirect: causes formation of ions that can oxidize bases resulting in errors in replication and repair
77
Q

What is benzopyrene?

A
  • Frameshift mutagen
  • Present in smoke and soot
77
Q

What is benzopyrene?

A
  • Frameshift mutagen
  • Present in smoke and soot
78
Q

What is aflatoxin?

A
  • Frameshift mutagen
  • Secreted by a variety of molds that grown on peanuts and grain
79
Q

What is acridine orange?

A
  • Frameshift mutagen
  • Fluorescent cationic dye
80
Q

What is azidothymidine (AZT)?

A
  • Nucleoside analog to thymidine
  • Used to treat HIV
81
Q

Describe the mechanism of action of AZT

A

Terminates the the growing DNA chain because there is no 3’ -OH

82
Q

Aside from reverse transcriptase in HIV, what else does AZT act on?

A

Mitochondrial RNA polymerase

83
Q

How does direct selection work for detection of mutants?

A
  • Grow on media supporting mutatnt, but not wild-type
  • Only rare mutants will survive
  • Ex: antibiotic resistance
84
Q

How does indirect selection work for detection of mutants?

A
  • Growth of mutant in the absence of medium or growth factor
  • Ex: replica plating
85
Q

What is phenotypic screening?

A
  • Recognizable differences in colony morphology
  • Differential breakdown of materials in media (ex. sugars, blood)
  • Not selection, just screening
86
Q

What is an Auxotroph?

A

A mutant organism that has a nutritional requirement that is absent in the parent

87
Q

What are the three mechanisms of gene transfer in bacteria?

A
  1. Transformation
  2. Conjugation
  3. Transduction
88
Q

What is homologous recombinatin?

A
  • Exchange of genes betwee two DNA molecules
  • Occurs when 2 chromosomes break and rejoin
89
Q

Homologous recombination requires what protein? What is it’s function?

A

RecA: catalyzes the joining of the two strands of DNA

90
Q

What is the main pathway used in bacteria involved in homologous recombination?

A

RecBCD pathway

91
Q

In 1944, Avery, MacLeod, and McCarty showed that DNA was responsible for converting harmless _______ into a virulent strain

A

Streptococcus pneumoniae

92
Q

Explain transformation

A
  • Direct uptake of DNA by recipient cells
  • Natural occurrence is unusual, but can be induced in the lab with almost all species
93
Q

Explain conjugation

A
  • Transfer of a plasmid from one cell to another by means of cell-to-cell contact
  • Differ between Gram-positive and Gram-negative species
94
Q

What is the F plasmid?

A
  • The first plasmid observed to transfer in conjugation
  • Most well understood
95
Q

Explain the mechanism of action of Gram-negative conjugation

A
  • Sex pilus contact
  • One donor strand grows 3’ - 5’ into recipient cell via transferasome
  • DNA polymerase regenerates complementary strands in both bacteria
96
Q

Explain the mechanism of Gram-positive conjugation

A
  • No sex pilus
  • Donor cell produces adhesion protein that allows it to attach to recipient
  • Donor and recipient each release phermones to attract each other

Microbiology (19 decks)

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