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Phys Pro Section 3 > Dr. Thomas lectures terms and concepts > Flashcards

Dr. Thomas lectures terms and concepts Flashcards

1
Q

What is the Messelon and Stahl experiment?

A

the N14/15 experiment that showed that DNA replication was semi conservative

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2
Q

What is DNA G

A

aka primase

RNA polymerase that makes RNA primer

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3
Q

What does DNA A do?

A

binds to the ori site and starts the open complex

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4
Q

What is DNA B?

A

helicase

unwinds DNA ahead of the replication fork

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5
Q

What is HU? what does it do?

A

Histone like protein that helps the DNA bind to the ori

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6
Q

What two repair mechanisms increase the fidelity of DNA replication?

A

missmatch repair and 3’-5’ exonuclease

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7
Q

What happens during the formation of the open complex? (3 steps, what is involved)

A
  1. DnaA binds specific sequences in oriC (with help from histone-like protein HU)
  2. DNA unwinds (stands separate) in an ATP-dependendent manner
  3. SSBs bind to keep open complex open
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8
Q

What 2 things happen to form the prepriming complex?

A
  1. DnaB (helicase) binds to both ends of open complex

2. This gives two replication forks going in opposite directions

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9
Q

What happens during the priming stage?

A
  1. DNA G (primase) lays down a 12 nt piece of RNA

2. DNA pol III initiates synthesis and adds dNTP’s to the 3’ end

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10
Q

What is different about extension on the lagging strand than the leading strand?

A

Done in 1000 bp okazaki fragments

Multiple primers laid down

Primers are removed and the space filled in by DNA pol I

Break is sealed by ligase

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11
Q

What happens during DNA synthesis termination? What proteins are involved? What is used if there are decantations?

A
  1. Tus binds Ter and the termination sequence
  2. Ter stops the replisome when it reaches the complex
  3. other replisome shows up and dislodges Tus
  4. Replication is complete

If the chromosomes are decantenated, then topoisomerase IV is used

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12
Q

What factors are involved in resolving dimers via recombination? How are they resolved?

A

Dimers resolved by site specific recombination at dif sites

The dif sites are lined up by FtsK

FtsK is localized to the septum and activates XerC/D

XerC/D are the recombinases that act on dif sites

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13
Q

what does DNA gyrase introduce?

A

Negative supercoils

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14
Q

what is supercoiling?

A

Energy stored in the DNA

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15
Q

What does topoisomerase I do?

A

Topoisomerase I removes supercoils

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16
Q

What are 5 features of histone like proteins?

A
  1. Compact DNA
  2. Small and abundant
  3. Some are site specific and some bind in a more general way
  4. Can serve as accessory factors to help initiate processes (replication, recombination)
  5. Can be general repressors
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17
Q

What are the two complexes that are formed during initiation of transcription?

A

the open and the closed complex

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18
Q

What leaves and what is formed at the start of elongation?

A
  1. sigma factor leaves

2. the transcription bubble is formed

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19
Q

What are the two forms of transcription termination

A
  1. intrinsic or factor independent

2. rho dependent termination

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20
Q

How is translation initiated? (3 things happen)

A
  1. shine dalgarno sequence is recognized by the 16s rRNA in the small subunit
  2. Scans until it finds the first AUG
  3. fMet binds at the first stop codon
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21
Q

What are the two elongation factors involved in translation?

A

EF-G is the translocase

EF-tu is elongation factor tu

Both use GTP

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22
Q

What is simple feedback inhibition?

A

A regulatory enzyme is inhibited by the end

product of a pathway

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23
Q

What is positive regulation?

A

The product of an enzyme can stimulate the activity of enzymes downstream in the pathway

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24
Q

What is cumulative feedback inhibition

A

In a branched pathway with more than one product, multiple products can inhibit the enzyme

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25
Q

What is concerted feedback inhibition?

A

Occurs in pathways with isoenzymes

multiple products of the branched pathway will inhibit each of the isozymes

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26
Q

What is forward genetics?

A

selecting for the phenotype and then identifying the mutation

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27
Q

What is reverse genetics?

A

making a mutation and then observing the phenotypes

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28
Q

What is trans complementation?

A

Providing the extrachromosomal DNA in the form of a plasmid

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29
Q

What is cis complementation ?

A

actually putting the gene back into the chromosome

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30
Q

What is a microbiome?

A

populations of cohabiting and interacting microbes.

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31
Q

a healthy microbiome is one that is?

A

stable and diverse

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32
Q

What are 3 ways to study microbiomes?

A
  1. 16s rRNA
  2. OTUs
  3. Metagenomic analysis
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33
Q

Do microbial communities have core functions?

A

yes

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34
Q

increased diversity in the gut leads to …?

A

increased colonization resistance

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35
Q

How do salmonella disrupt the microbiome to pathogenize the host?

A

Normally host secretes lipocalin-2 which sequesters enterobactin which is an iron siderophore produced by normal bacteria
- this establishes the iron homeostasis

Salmonella secretes a different iron siderophore called salmochelin which cannot be inhibited by lipocalin-2
- they take up all the iron and kill off the commensal bacteria

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36
Q

What is attenuation?

A

Way to couple transcription to nutrient supply

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37
Q

How is attenuation used in the Trp operon?

A

Low levels of trp, the ribosome stalls during translation which forms the 2’3 hairpin loop

  • signals more trp needs to be made
  • does not inhibit transcription

In high conditions, the ribosome translates quickly leading to the formation of the 3,4 hairpin loop and transcription is inhibited

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38
Q

What are repressors and where do they bind to?

A

bind to operators and black transcription by RNA polymerase

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39
Q

What factors are involed in catabolite repression?

A

Glucose regulates the activity of adenylate cyclase which makes cAMP

cAMP binds catabolite activator protein CAP

CAP is an activator that recruits RNA polymerase to promoters that would not be turned on efficiently otherwise

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40
Q

What is one of the most abundant proteins synthesized by the cell?

A

Flagellin

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41
Q

What sigma factor is involved in flagellar biosynthesis? What genes does it regulate?

A

sigma 28 regulates transcription of late genes

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42
Q

What do the early flagella genes code for?

A

make foundation and transcriptional activation complex to allow the middle genes to be transcribed

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43
Q

what is the middle gene that codes for sigma 28?

A

FliA

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44
Q

What sequesters sigma28?

A

FlgM

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45
Q

When is sigma28 uninhibited?

A

when the hook and basal body are complete and FlgM is secreted

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46
Q

What does sigma 54 need the help of?

A

NtrC bound at “enhancer” sequences far upstream from promoter

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47
Q

What is the homology of cis sRNAs like?

A

extensive homology with their target and are very specific

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48
Q

What is the homology of trans sRNAs like? what do they use?

A

have limited homology with their target and require the assistance of Hfq

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49
Q

what is Hfq?

A

A protein that stabilizes RNA RNA hybrids

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50
Q

What are riboswitches?

A

are transcripts where the RNA is regulatory and controls gene expression

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51
Q

What are 4 ways that bacteria can destroy incoming foreign DNA

A
  1. Restriction modification systems
  2. Block phage attachment
  3. Block phage infection
  4. CRISPR
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52
Q

What are restriction modification systems?

A

cleavage of foreign DNA because it is unmethylated by restriction endonucleases

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53
Q

How do cells block phage attachment?

A

can mask structural features like pili that many phages use to infect

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54
Q

How do cells block phage infection?

A

by committing cell suicide

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55
Q

What do CAS genes code for? where are they located?

A

they are found adjacent to the CRISPR locus

They code for enzymes that process the CRISPR locus

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56
Q

What is the structure of the CRISPR locus?

A

Repeated sequences of host DNA interspaced with an array of DNA fragments isolated from phage DNA

This locus has the cas genes on the 5’ end of it that are transcribed first

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57
Q

What are the three stages of CRISPR?

A
  1. immunization/adaptation
  2. crBiogenesis
  3. Interference
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58
Q

What happens during the immunization phase?

A

During an infection, a new spacer is derived from the virus/phage genome and incorporated into the CRISPR array along with a new repeated unit

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59
Q

What happens during the biogenesis stage? What is generated?

A
  1. CRISPR locus is transcribed
  2. CAS proteins process the crRNAs by endoribonuclease action
    - generates small cRNAs
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60
Q

What happens during the interference phase?

A

the crRNAs guide a complex of Cas proteins to the matching target DNA to initiate nucleolytic cleavage

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61
Q

What is the role of the PAM sequence? what does it stand for?

A

Stands for protospacer adjacent motif

Sequence of DNA that is near to the protospacer in foreign DNA but not present in the CRISPR locus

How the crRNAs recognize foreign DNA from self and cleave

Absence of a PAM sequence protects against cleavage

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62
Q

What is the protospacer?

A

the target DNA that will be acquired from the phage or plasmid and incorporated as a spacer

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63
Q

How many types of CRISPR systems are there ? How are they classified?

A

3

By the way that the cRNAs are processed

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64
Q

What is the most common type of CRISPR? what does it use?

A

Type II that uses Cas9 endonuclease

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65
Q

What is the interaction between the crRNA and the Cas9 complex?

A

After the Cas genes have processed the array products, there is a piece of crRNA bound by endonuclease Cas9

the complex can then go recognize and destroy specific DNA sequences

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66
Q

What gene editing method has CRISPR largely replaced?

A

RNAi

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67
Q

What 3 scientists were part of the phage group?

A

Max Delbrück, Salvador Luria, Alfred Hershey

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68
Q

Who figured out how lambda phage works? what else did they develop?

A

Mark Ptashne

Developed idea of “modular” nature of proteins

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69
Q

What is a plaque?

A

A zone of lysed bacteria

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70
Q

What are turbid plaques?

A

Areas where lysogenic phages have inserted themselves into the host genome and so the bacteria have replicated

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71
Q

What is the prophage?

A

The dormant phage within the host

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72
Q

What is the lysogen?

A

The host bacteria with a phage

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73
Q

What does cI encode? what does the product repress?

A

the CI repressor

represses activation of other lambda genes and can activate its own transcription

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74
Q

What is cro

A

Another repressor that represses the transcription for cI and allows for transcription of genes leading to the lytic cycle

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75
Q

How many operators are there between the cI and cro genes?

A

3

76
Q

What is the affinity of binding of CI for the operators?

A

Or1>Or2>Or3

77
Q

What is the point of cooperative binding?

A

as more CI (or cro) bind to the operators, more is recruited and it results in the shutting of of the respective genes
- how to control the amount of CI and cro

78
Q

What does binding of cI repressor at Or2 activate/recruit?

A

Repressor bound at OR2 acts as an activator. It recruits polymerase to PRM

  • the maintenance promoter
  • transcription of cI to remain in the lysogenic state
79
Q

What is the promotor for repressor maintenance?

A

Or3

80
Q

what is the promoter for repressor establishment? What is it activated by?

A

activated by the presence of one of the late lysogenic genes cII which binds to a different promoter for cI

81
Q

how does the decision occur to either go to the lysogenic or lytic states following infection?

A
  1. after infection, N protein is made
  2. N protein stimulates production of CII
  3. If the cell is healthy and there are lots of nutrients, bacterial proteases will cleave CII. The repressor is then not made and the lytic cycle is engaged

If there are not as many nutrients, CII is stable. It binds to the promotor of repressor establishment and stimulated the transcription of cI and the lysogenic cycle is initiated

82
Q

What is the enzyme involved integrating DNA into the host genome?

A

Integrase

83
Q

What two enzymes are invovled in excising the DNA from the host chromosome?

A

integrase and exisionase

84
Q

What is M13?

A

A filamentous phage with a single + strand of DNA that is surrounded by a single layer of protein

85
Q

How is M13 passed into the host cell?

A

The entire phage enters the cell

86
Q

Why are the M13 phages called “male specific”

A

because the adsorb to the sex pilus

87
Q

What are the steps of filamentous phage replication?

A
    • sense ssDNA is present in cell
  2. Copied into the dsDNA replicative form
  3. the - sense strand is used as a template to make phage proteins
  4. the RF is used to make more + strand by rolling circle replication
    - can be semi conservative
88
Q

What is the filamentous phage useful for in a laboratory setting?

A

making site directed mutations

89
Q

What two gene products are involved in the rolling circle replication process of ssDNA viruses? What do they do?

A

gene II product makes nick in the + strand and stays bound while a new + strand is synthesized

packaging of the + sense ssDNA strand is done with the help of both gene II and gene V

90
Q

What features in some bacteria originally arose from phages?

A

Pathogenicity islands

91
Q

What are colicins? what are the two types

A

toxins secreted by bacteria that either form pores in other bacteria or act as nucleases

92
Q

What are colicin systems encoded on?

A

Plasmids

93
Q

What prevents the bacteria secreting the colicins from being killed?

A

plasmid with the colicin also encodes the immunity product that neutralizes it

94
Q

What are 4 features of high copy number plasmids and what is one example of this?

A
  1. “Relaxed” control of copy number
  2. Generally small size <10 kb
  3. Replication is unlinked to cell division
  4. Random partitioning

ColE1 plasmid is best studied of this type. ColE1 make colicins that kill species related to E. coli

95
Q

What are 3 features of low copy number plasmids and what is one example?

A
  1. “stringent” control of copy number
  2. Usually larger (like up to 300 kb)
  3. Directed partitioning systems with the replication linked to cell division

R100 plasmid is example

96
Q

What feature do low copy number plasmids often have to ensure that the progeny have it?

A

They are often conjugative which is a backup mechanisms in case there is an error in partitioning

97
Q

What is plasmid amplification? what is used/how does it work?

A

Adding drugs like chloramphenicol to to the media prevents the host cell from making new proteins

All the machinery needed to copy the plasmid is there though and so many copies can still be made

98
Q

Explain how copy number is controlled by antisense RNA. What playerzzz are involved? What type of plasmid does it control?

A

Controls high copy number plasmids like ColE1

Normally RNA II stimulates replication of the plasmid

replication of the plasmid results in the production of RNA I and rop proteins

As concentration of plasmid rise, so do rop and RNAI concentrations

rop helps RNA I (which is antisense to part of RNAII) bind to it

this stops plasmid replication

99
Q

What is the role of RepA in the replication of plasmids?

A

Binds to the OriC

100
Q

How is R100 plasmid replication controlled? What factors are involved?

A

RepA is required for initiation of replication at oriV
CopB is a repressor of repA

when the plasmid first enters the cell there are low levels of CopB and so replication proceeds

CopB initiates transcription of copA which is antisense RNA to the repA message

101
Q

What is plasmid incompatibility?

A

R100 cannot coexist with related plasmids because the copA genes are similar. Therefore they will repress the replication of the related plasmid

102
Q

Explain how replication is controlled by the presence of iterons? what are they?

A

Iterons are DNA repeats

RepA binds iterons and “handcuffs” 2 plasmids together
- prevents them from replicating again

103
Q

Can RepA cuff related plasmids?

A

Yes, form of plasmid incompatibility

104
Q

What is the stability of naturally occuring plasmids vs artificial plasmids?

A

the naturally occurring ones are more stable

105
Q

What 3 factors are associated with plasmid stability ?

A
  1. Plasmid integrity
  2. partitioning
  3. differential growth rates
106
Q

What sequences do plasmids often have that allow for deletions or inversions?

A

insertion sequences or other recombination “hotspots”

107
Q

What is the point of toxin antitoxin systems?

A

way to ensure that plasmids are inherited

108
Q

Which is usually more stable, the toxin or the antitoxin?

A

the toxin

109
Q

What are the two toxin-antitoxin systems involved in partitioning?

A
  1. CcdB-CcdA toxin-antitoxin system

2. sok and hok system

110
Q

what kind of plasmid is the CcdB/CcdA system encoded on?

A

low copy plasmid

111
Q

How does the CcdB/CcdA work? what does each factor do?

A

CcdB inhibits topoisomerase which is essential for cell functioning

CcdA (antitoxin) inhibits the action of CcdB

112
Q

What are the functions of the two factors in the sok and hok system?

A

hok encodes protein that is toxic to host (host killing)

sok encodes antisense RNA that prevents hok translation (supressor of killing)

113
Q

What happens if during partitioning the daughter cell does not receive the plasmid with the toxin antitoxin genes on it?

A

The cell will die because there will still be CcdB or hok present in the cell but no genes to transcribe CcdA or sok

114
Q

How does differential growth rate impact the stability of the plasmid?

A

if the plasmid is large and codes for lots of non-essential genes, there will be selective pressure to lose the plasmid

115
Q

What is transformation?

A

uptake of naked DNA

116
Q

What are 2 kind of extreme ways of transforming DNA?

A
  1. Biolistic transformation: shoot DNA in on gold particles
    - often done in plant cells
  2. Electroporation: shock in the DNA using a capacitor
    - used for some complex strains
117
Q

What do naturally competent bacteria become competent in response to?

A

growth phase

118
Q

what do Neisseria and Haemophilus have that allows them to selectively take up DNA?

A

proteins that bind preferred DNA sequences (usually from relates or same species)

119
Q

How does the DNA enter the bacteria during transformation?

A

As ssDNA

120
Q

Who coined the term plasmid?

A

Joshua Lederberg

121
Q

what is a self-transmissable plasmid?

A

encode machinery to initiate conjugation and transfer

122
Q

what is a mobilizable plasmid?

A

can be transferred but need Tra functions supplied in trans

123
Q

What is transconjugant?

A

progeny from a successful conjugation

124
Q

What genes encode transfer functions? which of the two cells in a conjugation event possess them?

A

tra genes

the donor has them on the plasmid

125
Q

What does the donor cell do to transfer the plasmid?

A

forms pilus and brings cells in close contact

Pilus forms to form bridge to transfer DNA

126
Q

What 2 things are needed if you have a mobilizable plasmid?

A

Non conjugating plasmids can be transferred too if they have mob genes and bom site (often called oriT)

127
Q

What are two components of Tra genes?

A
  1. Dtr component (DNA transfer and replication): genes needed to process the DNA
  2. Mpf (mating pair formation): genes that make the sex pilus
128
Q

What 2 things do you need to have a conjugation event?

A
  1. Tra genes

2. OriT

129
Q

What factor is encoded by the Dtr component of the Tra genes? What does it do?

A

Relaxase is an endonuclease that cuts at a nick site in OriT and makes a covalent bond with the 5’ end of the DNA

130
Q

What is site specific recombination?

A

occurs at particular DNA sequences by enzymes that recognize said DNA sequences and catalyze recombination with a specific recipient DNA

131
Q

What is homologous recombination? what does it require?

A

occurs between DNA sequences that are homologous and requires RecA

132
Q

what is intramolecular recombination and what is it commonly used for?

A

Looping out of a circular piece of DNA

Commonly used to excise plasmid or phage DNA

133
Q

Increasing what 2 factors will increase the chance of recombination?

A
  1. increasing the amount of homology between the strands

2. increasing the distance between the two sites

134
Q

the frequency of co-inheritance is inversely proportional to?

A

to the distance between two DNA markers

135
Q

What are the 2 jobs of RecA overall

A
  1. cleave LexA repressor to initiate the SOS response

2. Pair homologous gene segments together so that they can exchange strands

136
Q

Describe the process of RecA mediated recombination?

A
  1. ssbp open up the DNA to be single stranded
  2. RecA binds cooperatively to the strand of DNA
  3. formation of a nucleo-protein filament
  4. RecA filament then goes looking for homology to pair with and recombine
137
Q

What are 2 features of the F plasmid?

A
  1. it can integrate into the chromosome

2. its a conjugative plasmid

138
Q

What are F’ plasmids?

A

Plasmids that incorporated some host DNA when they were excising

139
Q

What are F’ plasmids useful for?

A

constructing merodiploids

140
Q

bacteria that have integrated the F plasmid are called?

A

Hfr strains “high frequency of recombination”

141
Q

Explain how Hfr mapping works

A

lol I ain’t explaining,

get Bryn to tell you

142
Q

What is specialized transduction? when does it occur?

A

Occurs when a lysogen is induced to go into the lytic state

In excising the prophage, some host DNA is incorporated

The phage then replicates
- also replicated the host DNA

Cell lysis and phage release

The phages then go on to infect other cells

143
Q

What is generalized transduction ? when does it occur?

A

Occurs when a phage infects a cell and immediately enters the lytic cycle

Host DNA is degraded by phage enzymes

Replication of phage DNA and synthesis of new phages
- some of which accidentally take up host DNA

Transducing phages are released and will go infect other cells
- some of which contain donor DNA

144
Q

What are the 3 common transducing phages?

A

P1, P22, Mu

145
Q

what do insertion sequences encode?

A

a transposase flanked by inverted repeats

146
Q

What do transposases do?

A

duplicate a target sequence and inserts the element

147
Q

Where do insertion sequences insert themselves?

A

randomly

148
Q

What makes transposons different from insertion sequences?

A

they have a selectable marker

149
Q

What are the 2 kinds of transposons?

A
  1. composite

2. non composite

150
Q

what are composite transposons?

A

Contain 2 copies of insertion sequence flanking gene(s) for antibiotic resistance

151
Q

What two factors limit the activity of transposase?

A
  1. acts preferentially on hemimethylated DNA so works better following replication
  2. preferentially acts in cis
152
Q

Who developed the notion of gene regulation ?

A

Barbara McClintock

153
Q

How could you deliver a transposon into a cell?

A

Encode transposon on a plasmid or phage that cannot replicate in the recipient

154
Q

What is the suicide plasmid? What special site does it have and what does it need for replication?

A

Conjugative plasmid with a R6K origin of replication

Requires Pi protein supplied in trans by a temperate phage

155
Q

What is encoded on the suicide plasmid?

A

contains a transposon with antibiotic selection

156
Q

Why will the transposon be incorporated into the host DNA? how can you select for this?

A

there won’t be any Pi protein in the cell it is introduced into

Since it can’t replicate, the transposon will “hop” to the host DNA

you can select because the transposon will encode antibiotic resistance genes

157
Q

What is the Luria and Delbruck Fluctuation Test? What were the outcomes

A

T1 is a phage that can kill E-coli

mutants that are resistant are easily isolated

Showed that mutations are spontaneous because each time they did the experiment, there were a different number of mutants

158
Q

What would have been the result of the fluctuation test if mutation was directed?

A

you would have had the same number of mutants each time

159
Q

What do deletions and rearrangements arise from?

A

recombination

160
Q

What are conditional mutants?

A

Have a mutation where they can live in one condition but die in another

161
Q

What 2 kinds of mutations are often polar?

A

nonsense and insertion mutations

162
Q

Why would mutations affect translational coupling?

A

the recognition of an initiation codon may be dependent on translation of the gene upstream

163
Q

What are 3 types of “pseudoreversion” or intragenic supression?

A
  1. same codon or same nucleotide
  2. different codon but in the same gene
  3. frame shift
164
Q

What are the stop codon “alternate names” and what do they correspond to

A 
amber = UAG 
opal = UAA
ochre = UGA
165
Q

What are tRNA suppressors?

A

tRNA that have mutations in the anticodon that allow them to bind to the mutated codon and still incorporate the correct amino acid

166
Q

What is a bypass suppressor?

A

If you have a mutation in one pathway you can have other products from other pathways “bypassing” the mutation to still give you your product

167
Q

What are 3 common types of mutation types in bacteria?

A
  1. require additional supplements
  2. loss of ability to use a nutrient source
  3. resistance
168
Q

What do E-coli mutator strains have?

A

A defect in proofreading

169
Q

What does ethidium bromide do ?

A

Inserts between paired bases, acts as an intercalating agent

170
Q

What is nitrosoguanadine (NTG)?

A

An alkylating agent

171
Q

What is EMS and what does it do?

A

Ethyl methanesulfonate

Reacts with guanine to make O-6-methylguanine

Causes polymerase to pair it with a thymine instead of a cytosine

172
Q

What does nitrous acid do?

A

Deaminates bases

173
Q

What does UV radiation cause?

A

crosslinks between adjacent pyrimidines

174
Q

What is the result of a thymine dimer occurring?

A

causes polymerase to see them as one base instead of two

Results in a frameshift mutation

175
Q

How does the Ames test work? what is it testing for?

A

tests to see if something is a mutagen

If you plate mutant bacteria on a deficient medium with the carcinogen, you can count the number of “revertants” that are able to now grow

176
Q

How does the blockage of DNA replication stimulate the SOS response?

A

If the polymerase is blocked, the helicase is going to keep unwinding the DNA, leaving more ssDNA to be bound by RecA

This binding of RecA activates its protease activity and it cleaves LexA to relieve repression

177
Q

What is the first stage of the SOS response (after cleavage of the repressor)

A

Nucleotide excision repair

178
Q

What are the 3 proteins involved in the nucleotide excision repair?

A

UvrA, B, C, and D

179
Q

What occurs during nucleotide excision repair?

A
  1. two UvrA and one UvrB protein binds to DNA nonspecifically
  2. translocate via an ATP dependent process until they find the mutation
  3. when they find the mutation, UvrA leaves and a stable UvrB-DNA complex is formed
  4. UvrC comes and binds to the UvrB-DNA complex and makes a nick on either side of the damage, resulting in a 12nt fragment
  5. UvrD helicase action then removes the fragment
  6. the space is filled in by Pol I and ligase
180
Q

What are the 2 alternate polymerases?

A

Pol IV and PolV

181
Q

What are the 2 subunits of Pol IV?

A

UmuD and UmuC

182
Q

What gene codes for PolV? What kind of gene is it?

A

DinB, an SOS induced gene

183
Q

Which of the 2 alternate polymerases causes a frameshift mutation?

A

Pol IV

184
Q

What factors are involved in mismatch repair

A

Mut H, Mut S, Mut L, DNA helicase II and exonucleases

185
Q

What are the steps in mismatch repair?

A
  1. MutH binds to hemimethylated DNA at GATC sequences following replication
  2. complex of MutS and MutL bind to mismatched DNA between the two
  3. DNA is threaded through the MutS MutL complex until it reaches the MutHs
  4. MutH cleaves unmethylated DNA
  5. DNA helicase II and exonucleases complex
    degrades the unmethylated DNA towards the mismatch
  6. gap is filled in by DNA polymerase III
    and the nick is sealed by DNA ligase

Phys Pro Section 3 (5 decks)

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