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Microbio > Microbial Genetics (8 and 9) > Flashcards

Microbial Genetics (8 and 9) Flashcards

1
Q

DNA as genetic material

A
  • Griffith discovers transformation in 1928
  • cells uptake free DNA from lysed cells
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2
Q

smooth vs. rough strains of strep.pneumonieae

A

smooth: have capsule, cause pneumonia
rough: don’t have capsule, do not cause pneumonia
transformation principle: rough could take up DNA that cause pneumonia

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3
Q

flow of genetic material

A

Central Dogma
DNA to RNA to protein

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4
Q

DNA structure

A
  • nucleotide polymers
  • ATGC (adenine, guanine, cytosine, thymine)
    • A and T: 2 hydrogen bonds
    • G and C: 3 hydrogen bonds
  • phosphodiester bonds: 3’ to 5’
  • deoxyribose
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5
Q

RNA structure

A
  • nitrogenous base differs from DNA
  • AUGC (adenine, guanine, cytosine, uracil)
  • ribose
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6
Q

semi-conservative synthesis

A

separate into templates for new strand

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7
Q

patterns of DNA synthesis

A
  • most bacterial DNA is circular
  • origin of replication
    • 2 forks
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8
Q

DNA replication machinery: DNA polymerase

A
  • I through V
  • adds bases to template
    • I and III: key role in synthesis
    • 5’ to 3’ direction
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9
Q

DNA replication machinery: DnaA

A
  • initiation factor
  • assembles at origin, slowly unravels small amount of DNA
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10
Q

DNA replication machinery: DnaB

A
  • helicase
  • “unzipping” DNA to break hydrogen bonds between bases
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11
Q

DNA replication machinery: Single-stranded DNA binding proteins (SSBs)

A
  • prevent premature reconnecting (keeps zipper open)
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12
Q

DNA replication machinery: Topoisomerase IV

A

separates interlocked chromosomes

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13
Q

DNA replication machinery: gyrase

A

eases strain of DNA replication

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14
Q

DNA replication process

A
  1. DNA polymerase synthesis
  2. termination
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15
Q

DNA replication process: DNA polymerase synthesis

A

5’ to 3’ direction only
- leading strand: polymerase III
- lagging strand: okazaki fragments
- small amounts synthesized, move through SSBs

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16
Q

DNA replication process: termination

A
  • Tus @ termination site
  • topoisomerase IV separates catenones (joined chromosomes)
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17
Q

Gene structure: general info

A
  • basic unit of genetic information
  • sequence codes for a product
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18
Q

protein-coding genes: template strand

A

directs RNA synthesis

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19
Q

protein-coding genes: components

A
  • template strand
  • promot
  • pribnow box
  • shine-dalgarno sequence
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20
Q

protein-coding genes: promot

A
  • RNA polymerase recognition and binding
  • contains pribnow box
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21
Q

protein-coding genes: pribnow box

A
  • in promot
  • similar to TATA box
  • synthesizes leader, triggered to leave at terminator
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22
Q

protein-coding genes: shine-dalgarno sequence

A

on mRNA
- aligns ribosome with start codon

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23
Q

RNA synthesis: RNA polymerase

A
  • subunits: a, B, B’, W
  • sigma factor: doesn’t catalyze, helps polymerase recognize promoter
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24
Q

RNA synthesis: phases

A

initiation, elongation, termination

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25
RNA synthesis: initiation
- starts at promoter - sigma factor - bacterial promoters - TTGACA (-35) - Pribnow-TATAAT (-10)
26
RNA synthesis: elongation
- RNA polymerase: unwinds DNA, moves along template, synthesizes
27
RNA synthesis: termination
- RNA polymerase dissociation from template DNA - terminator (intrinsic, rho factor)
28
intrinsic termination
- pauses, stem loop forms stopping RNA polymerase - uracil-rich region - factor independent
29
rho factor termination
- binds to rut site - splits DNA from RNA - breaks hydrogen bonds
30
genetic code: codon
- 3 nucleotide set - specifies amino acid
31
start codon
AUG: codes methionine
32
sense codon
- 61 total - codes amino acid
33
nonsense codon
- terminal
34
code degeneracy
mutations due to multiple options for 1 amino acid
35
polypeptide synthesis directed by?
sequence of nucleotides in mRNA
36
ribosome during polypeptide synthesis
site of translation
37
bacterial polypeptide synthesis
- 900 AA/min - coupled transcription and translation on polyribosome complex
38
tRNA during polypeptide synthesis
- anticodon to ribosome - binds to mRNA - acceptor stem - holds amino acid
39
polypeptide synthesis: initiation
- initiation complex with met-tRNA, 30s subunit, mRNA - factors 1, 2, and 3: catalyze addition of 50s subunit
40
polypeptide synthesis: elongation
- P, A, and E sites
41
polypeptide synthesis: termination
- nonsense codon - UAA, UAG, UGA - release factors: aid in recognition of stop codon
42
maturation and secretion: general rules
- function depends on 3D shape - post-translational event - requires folding - association with other proteins - proper subcellular and extracellular sites
43
translocation
- movement from cytoplasm to periplasm or plasma membrane - past membrane
44
translocation: sec
- both eukarya and bacteria - transports unfolded proteins
45
translocation: tat
- unique to bacteria - transports folded proteins
46
translocation: YidC
- unique to bacteria
47
sec proteins: 3 types
1. secA: outside pump 2. secYEG: transmembrane 3. secDF: assists
48
secretion
- movement out of cell - cytoplasm to external environment - role in toxicity
49
secretion type I
translocation through membrane, secrete out of cell
50
secretion type II
anchor, no translocation
51
secretion type III
acts like a syringe - injectisome protrudes and contacts host cell
52
secretion type IV
- can make contact - usually for conjugation
53
secretion type V
just secretion, no plasma membrane association
54
secretion type VI
- contracted and expanded versions - expanded contacts host
55
mutations: definition
changes in genetic material
56
point mutation
change in single base pair
57
spontaneous mutation
arise naturally in absence of mutagen
58
induced mutation
caused by a mutagen
59
protein coding gene mutations: silent
different code, same amino acid
60
protein coding gene mutations: missense
codes for different amino acid - severity ranges
61
protein coding gene mutations: nonsense
codes for stop - most detrimental
62
protein coding gene mutations: frameshift
insertion or deletion shifts entire sequence
63
auxotrophic mutation
unable to make an essential macromolecule ex) lysine auxotroph
64
resistance mutation
resistant to certain substance
65
DNA repair: proofreading
DNA polymerase - during replication
66
nucleotide excision repair
- UVrABCD endonuclease removes damaged nucleotides - caused by thymine dimers
67
nucleotide excision repair: UvrA
scans for damage and binds to damaged portion of DNA
68
nucleotide excision repair: UVrB
- recruited to site by UVrA - directs UVrC to cut both sides of damage
69
nucleotide excision repair: UVrC
cuts both sides of damage
70
nucleotide excision repair: UVrD
removes damaged region
71
nucleotide excision repair: DNA polymerase I and DNA ligase
fill and seal gap
72
base excision repair: DNA glycosylase
- recognizes abnormal base - cleaves bond between base and sugar
73
base excision repair: AP endonuclease
- recognizes missing base - cleaves backbone on 5' side
74
base excision repair: DNA polymerase
- uses 5'-3' exonuclease activity to remove damaged region - fills it in with normal DNA - ligase seals region
75
recombination repair
- initiates repair of DNA damage on both strands - RecA corrects damage
76
genetic recombination
new nucleotide sequence formed via rearrangement
77
horizontal gene transfer: general info
- differs from vertical gene transfer - gene transfer from one independent mature organism to another - important in evolution - antibiotic resistance - virulence
78
horizontal gene transfer: conjugation
- unidirectional - F factor (F+ and F- mating) - copy of F factor transferred to recipient
79
rolling circle mechanism: steps
1. sex pili contracts, bringing donor and recipient closer together 2. T4SS constructed and cells join 3. relaxosome cuts at oriT and begins to separate one strand 4. relaxosome accessory proteins released, coupling factor recognizes DNA/relaxase, transfers it to T4SS 5. T4SS pushes DNA/relaxase into recipient Product: 2 F+ cells
80
rolling circle mechanism: donor and acceptor
F+: donor F-: acceptor
81
transformation
uptake and incorporation of DNA by competent cells
82
s. pneumoniae transformation steps
1. fragment binds 2. nuclease activity 3. DNA enters cell 4. integrates into host chromosome
83
DNA uptake: uptake pilus
pulls DNA past peptidoglycan layer
84
DNA uptake: ComEA
directs to ComEC
85
DNA uptake: ComEC
stripped into single strand by nuclease
86
transduction
transfer of bacterial genes by viruses
87
transduction: lysogenic
1. phage integrates into chromosome 2. prophage copied during cell division 3. excision
88
transduction: lytic
1. phage injects DNA 2. phage DNA directs synthesis of new phages that can bind to cell after lysis 3. lysis

Microbio (11 decks)

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