Microbiology1 > Ch 8: Microbial genetics > Flashcards

Ch 8: Microbial genetics Flashcards

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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*
  • Agrobacterium tumefaciens*
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9
Q

What genes do R factors/plasmids carry?

A

Resistance to antibiotics, bacteriophages 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
“Strs” describes what phenotype?
Sensitive to streptomycin
26
What are ORFs?
Open reading frame * Reading frame that lacks termination codes
27
What are short tandem repeats?
Short DNA sequences (2-5 bps) that repeat numerous times in a head to tail manner; knowing STRs allows for DNA fingerprinting
28
What did the Messelson-Sthal experiment prove?
Semiconservative model: each new strand of DNA contains one whole original strand
29
What is the function of DNA gyrase?
Relaxes supercoiling ahead of the replication fork Present only in Bacteria
30
What is the function of DNA ligase?
Makes covalent bonds to joint DNA strands; Okazaki fragments, and new segments in excision repair
31
What is the function of DNA polymerase?
* Synthesis of new DNA * Proofreed and facilitate repair of DNA
32
What is the function of endonuclease?
* Cut DNA backbone in a strand of DNA * Facilitate repair and insertion
33
What is the function of exonuclease?
* Cut DNA from an exposed end of DNA * Facilitate repair
34
What is the function of helicase?
Unwinds dsDNA
35
What is the function of methylase?
Adds methyl groups to selected bases in newly made DNA
36
What is the function of photolyase?
Uses visible light energy to separate UV-induced pyrimidine dimers
37
What is the function of primase?
An RNA polymerase that makes RNA primers from a DNA template
38
What is an snRNP?
RNA-protein complex that removes introns and splices exons together
39
What is the function of topoisomerase (or gyrase)?
* Relaxes supercoiling ahead of the replication fork * Separates DNA circles at the end of DNA replication
40
What is the function of transposase?
Cuts DNA backbone, leaving single-stranded “sticky ends”
41
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?
Another replication fork is initiated 20 minutes after the start of the first
42
What is the start codon?
AUG
43
What are the stop (nonsense) codons?
UAA UAG UGA
44
In bacteria, the start codon encodes for \_\_\_\_\_
N-formylmethionine
45
What is codon bias?
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
What is an operon?
A group of genes that are transcribed together and controlled by one promoter
47
What are constitutive genes?
Unregulated genes that are expressed at a fixed rate 60-80% of bacterial genes
48
What is a repressible gene?
Rate of transcription is decreased by a repressor; default position is on
49
What are inducible genes?
Rate of transcription is increased by inducer; default position is off
50
What is the function of the *lac* operon in *E. coli*?
Contains genes needed for lactose metabolism: 1. β-galactosidase 2. lac polymerase 3. transacetylase
51
What is the difference between the promoter and operator of an operon?
Promoter: where RNA polymerase starts transcription Operator: start/stop signal for transcription; where repressor or promoter binds
52
Is the *lac* operon inducible or repressible?
Inducible
53
In 1959, Francois Jacob and Jacques Monod proposed the \_\_\_\_\_\_\_.
Operon theory
54
What is the function of the *I gene* on the *lac* operon?
Encodes the repressor protein that switches the operon off
55
What is catabolite repression?
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
What is the function of the *Trp* operon?
Contains genes required for tryptophan synthesis; biosynthetic operon
57
Transcription of the *lac* operon requires presence and absence of what?
Presence of lactose Absence of glucose
58
Is the *Trp* operon repressible or inducible? What is its repressor/inducer?
Repressible Tryptophan is repressor
59
In eukaryotes, ____ nucleotides can be methylated
C\*G
60
In prokaryotes, ______ nucleotides can be methylated
GA\*TC
61
What is an alarmone?
A chemical alarm that promotes a cellular response to environmental or nutritional stresses Ex: cAMP when glucose is low
62
What are the regulator RNA molecules of prokaryotes and eukaryotes?
Prokaryotes: small RNAs (sRNAs); 50-500 nucleotides Target proteins and modify function; may bind to mRNA targets Eukaryotes: microRNAs (miRNAs); ~22 nucleotides Bind only to RNA, either degrade or inhibit the translation
63
What is the function of microRNAs?
Incorporated into a RISC and serve to target specific complementary mRNAs to alter their translation or stability
64
What is the function of sRNA?
highly structured RNAs that bind to protein targets and modify function OR may bind to mRNA targets and regulate translation or stability
65
What is the difference between a transition and transversion mutation?
Transitions are interchanges of two-ring purines (A G) or of one-ring pyrimidines (C T), therefore, involve bases of similar shape.
66
What is an inversion mutation?
Deletion and reassertion with the opposite orientation
67
What is a missense mutation?
A base substitution that results in the replacement of one amino acid for another
68
What is a nonsense mutation?
A base substitution that creates an in-frame stop codon
69
What are the spontaneous mutation rates of *E. coli*? (3)
1. 10-9 replicated base pairs 2. 10-6 replicated genes 3. 10-3 replicated genomes
70
Why do frameshift mutations generally lead to premature termination?
* 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
What is a base modifier? Example?
* 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
What is a nucleoside analog?
A molecule that looks like a normal base that cannot base pair with the correct base
73
What is 2-aminopurine?
* Nucleoside analog * Takes place of A but can pair with C, so AT pair becomes CG pair
74
What is 5-bromouracil?
* Nucleoside analog * Looks like T but pairs with C, so AT pair becomes CG pair * Often used an anticancer drug
75
What are some examples of ionizing radiation? (2)
1. X-Rays 2. Gamma Rays
76
What are the direct and indirect actions of ionizing radiation as a mutagen?
* 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
What is benzopyrene?
* Frameshift mutagen * Present in smoke and soot
78
What is aflatoxin?
* Frameshift mutagen * Secreted by a variety of molds that grown on peanuts and grain
79
What is acridine orange?
* Frameshift mutagen * Fluorescent cationic dye
80
What is azidothymidine (AZT)?
* Nucleoside analog to thymidine * Used to treat HIV
81
Describe the mechanism of action of AZT
Terminates the the growing DNA chain because there is no 3' -OH
82
Aside from reverse transcriptase in HIV, what else does AZT act on?
Mitochondrial RNA polymerase
83
How does direct selection work for detection of mutants?
* Grow on media supporting mutatnt, but not wild-type * Only rare mutants will survive * Ex: antibiotic resistance
84
How does indirect selection work for detection of mutants?
* Growth of mutant in the absence of medium or growth factor * Ex: replica plating
85
What is phenotypic screening?
* Recognizable differences in colony morphology * Differential breakdown of materials in media (ex. sugars, blood) * Not selection, just screening
86
What are the three mechanisms of gene transfer in bacteria?
1. Transformation 2. Conjugation 3. Transduction
87
What is homologous recombinatin?
* Exchange of genes betwee two DNA molecules * Occurs when 2 chromosomes break and rejoin
88
Homologous recombination requires what protein? What is it's function?
RecA: catalyzes the joining of the two strands of DNA
89
What is the main pathway used in bacteria involved in homologous recombination?
RecBCD pathway
90
In 1944, Avery, MacLeod, and McCarty showed that DNA was responsible for converting harmless _______ into a virulent strain
*Streptococcus pneumoniae*
91
Explain transformation
* Direct uptake of DNA by recipient cells * Natural occurrence is unusual, but can be induced in the lab with almost all species
92
Explain conjugation
* Transfer of a plasmid from one cell to another by means of cell-to-cell contact * Differ between Gram-positive and Gram-negative species
93
What is the F plasmid?
* The first plasmid observed to transfer in conjugation * Most well understood
94
Explain the mechanism of action of Gram-negative conjugation
* Sex pilus contact * One donor strand grows 3' - 5' into recipient cell via transferasome * DNA polymerase regenerates complementary strands in both bacteria
95
Explain the mechanism of Gram-positive conjugation
* 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
96
What is benzopyrene?
* Frameshift mutagen * Present in smoke and soot
97
In referring to F plasmid what is a TRA region
region of DNA responsible for conjugation, like coding for pilus
98
Transduction
Phage mediated genetic recombination in bacteria, bacterial DNA( or a phage-bacterial hybrid DNA) gets included in a phage coat
99
Generalized Transduction
a RANDOM fragment of bacterial DNA is accidentally encapsulated in a phage
100
Specialized transduction
Genes located on the bacterial genome close to the prophage insertion site can be transduced.
101
Transposons
AKA jumping genes, move from place to place. Two type replicative and non replicative
102
Replacative transposons
Once the genes move they leave a copy of itself beind
103
Nonreplacative transposons
Do no leave a copy behind after moving
104
Transposable elements
Insertion sequences Transposons use transposase and resolvase Certain phages(Mu)-not discussed
105
Transposon anatomy
Direct repeats the most outside, then its two terminal inverted repeats and the middle is the transposon
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