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Biochemistry > Replication, Repair, Transcription > Flashcards

Replication, Repair, Transcription Flashcards

1
Q

The DNA replication model where each strand of the DNA duplex is replicated and the two newly synthesized strands join to form a new duplex DNA, while the parent strands remain together.

A

Conservative

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2
Q

The DNA replication model where the two strands separate and each is copied to generate a complementary strand with each parental strand associating with a new strand.

A

Semiconservative

This is the process by which genetic information is copied

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3
Q

The DNA replication model where each of the fours strands (two daughter and two parental) contain some of both new and old DNA

A

Dispersive

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4
Q

Unwinds DNA

A

DNA gyrase

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5
Q

Binds single-stranded DNA

A

SSB

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6
Q

Initiation factor, origin-binding protein

A

DnaA

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7
Q

Unwinds 5’ → 3’ DNA

A

Helicase

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8
Q

Synthesizes RNA Primer

A

Primase

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9
Q

Elongates (DNA synthesis)

A

DNA Polymerase III holoenzyme

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10
Q

Excises RNA Primer, fills in with DNA

A

DNA Polymerase I

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11
Q

Covalently links Okazaki fragments

A

DNA ligase

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12
Q

Terminates

A

Tus

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13
Q

Binds single-stranded DNA in Eukaryotes and Prokaryotes

A

Replication Protein A (RPA)

SSB

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14
Q

Synthesizes 10 nt RNA primer and then 20-30 nt DNA in Eukaryotes and Prokaryotes

A

Polymerase α

Primase/Pol I

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15
Q

Synthesizes new DNA strands in Eukaryotes and Prokaryotes

A

Polymerase δ

Pol III

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16
Q

Increases processivity by clamping to DNA in Eukaryotes and Prokaryotes

A

Proliferating Cell Nuclear Antigen (PCNA)

β-subunit

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17
Q

Loads DNA pol onto DNA clamp in Eukaryotes and Prokaryotes

A

Replication Factor C (RFC)

γ-complex

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18
Q

Removes RNA primer in Eukaryotes and Prokaryotes

A

Rnase H1

Pol I

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19
Q

5’→3’ exonuclease

Processes the 5’ ends of Okazaki fragments

Removes 5’ overhanging flaps in DNA repair

A

Flap endonuclease I (Fen1)

Eukaryotes only

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20
Q

What are the steps of prokaryotic DNA replication?

A
  1. Recognition of the origin of replication
  2. Unwinding of the double-stranded helix
  3. Preparation of the new strand with an RNA primer
  4. DNA synthesis of both strands – One strand is synthesized continuously 5’→3’ – The other strand is synthesized a fragments 3’→5’
  5. Termination of replication
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21
Q

What does DNA polymerization require to get started?

A

an RNA primer

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22
Q

What is required to ensure the accurate transmission of genetic information?

A

High fidelity (specificity)

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23
Q

Replication is…?

A

bi-directional and semi-conservative

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24
Q

A hexamer of ___ binds several AT-rich regions on the E. coli genome, allowing the double-stranded DNA to open

A

DnaA

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25
Q

Between AT pairings and GC pairings, which are stonger?

A

GC

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26
Q
  • Disrupts hydrogen bonds between parent strands
  • Binds single-stranded DNA to start
  • Requires ATP hydrolysis for energy
A

Helicase

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27
Q
  • Type II topoisomerase that introduces negative supercoils to overcome the torsional stress of unwinding
  • Requires ATP hydrolysis for energy
A

DNA Gyrase

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28
Q

Hold unwound strands open and prevent them from re-annealing

A

Single-Stranded DNA Binding Proteins (SSBs)

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29
Q

The ~10 nucleotide RNA primer is synthesized by…

A

a primase

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30
Q

The exonuclease activity of ____later replaces the RNA with DNA

A

Polymerase I

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31
Q

DNA is synthesized by…

A

DNA Polymerase

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32
Q
  • Part of replication machinery anchored to the membrane or nuclear envelope
  • Active site selects complementary bases by Watson-Crick interactions with the template strand
  • Requires a primer oligo with a free 3’-OH to build upon
  • Has a built in proof-reading activity
A

DNA Polymerase

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33
Q

Proofreading occurs via…

A

the exonuclease domain

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34
Q

adds 10 nucleotides/sec, can add ~20 dNTPs before falling off

A

DNA Pol I

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35
Q

adds 1,000 nucleotides/sec, can replicate the entire bacterial genome (4.6 kb) in ~40 minutes

A

DNA Pol III

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36
Q

the # of nucleotides that can be added before the polymerase falls off

A

Processivity

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37
Q

What has these catalytic activities?

  • 5’→3’ exonuclease activity (RNA primer removal)
  • 5’→3’ polymerase activity
  • 3’→5’ exonuclease activity (proofreading)
A

DNA Polymerase I

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38
Q

Two core units of (βαεθ)2, one γ complex, and a dimer of τ subunits make up the holoenzyme

A

DNA Polymerase III

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39
Q

Processivity switch which allows release of DNA on lagging strand

A

τ-subunit

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40
Q

5’→3’ polymerase

A

α-subunit

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41
Q

Acts as sliding clamp to enhance processivity

A

β-subunit

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42
Q

Responsible for assembly of Pol III onto DNA

A

γ-complex

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43
Q

3’→5’ exonuclease

A

ε subunit

44
Q

Seals nicks left from Okazaki fragments.

A

Ligase

45
Q

Allows synchronous replication of the leading and lagging strands

A

DNA Pol III dimer

46
Q

Prevents further replication by preventing unwinding

A

Tus protein (a contrahelicase)

47
Q

Telomere replication is carried out by…

A

Telomerase

48
Q

Faithfully replicates the DNA

A

DNA polymerase

49
Q

Determines the sequence of a complementary nucleic acid

A

Template

50
Q

The initial segment of a polymer that will be extended

A

Primer

51
Q

Unwinds the double helix

A

Helicase

52
Q

Relaxes or introduces supercoils

A

Topoisomerase

53
Q

Crucial for proofreading

A

Exonuclease

54
Q

Synthesizes a segment of RNA

A

Primase

55
Q

Found on the lagging strand

A

Okazaki Fragments

56
Q

Uses ATP to join DNA fragments

A

DNA ligase

57
Q

Prevents the disappearance of the lagging strand

A

telomerase

58
Q

What happens to wrongly incorporated nucleotides?

A

Don’t hybridize to the template strand, and are free to enter the exonuclease domain, where they are then cleaved

59
Q

What kinds of DNA damage can occur?

A
  1. Incorrect/missing bases – replication errors
  2. Bulges – deletions or insertions
  3. Strand breaks – phosphodiester bonds OR at deoxyribose
  4. UV-induced alterations
  5. Covalent crosslinking of strands
  6. Oxidation of DNA bases
60
Q

One purine/pyrimidine replace by another, e.g. A becomes G (T→C)

A

Transition

61
Q

A purine replaced by a pyrimidine or vice versa e.g T→G

A

Transversion

62
Q

Reactive oxygen species (ROS) such as the hydroxyl radical oxidize guanine to 8-oxoguanine 8-oxoguanine base-pairs to adenine instead of cytidine, causing a G → T mutation

A

Base Oxidation

63
Q

This can happen to A, C, and G bases, the modified bases have different base-pairings

A

Deamination

64
Q

Aflatoxin is found in molds, polycyclic hydrodrocarbons found in exhaust fumes cause similar adducts, Resuts in G-C → T-A mutation

A

Alkylation

65
Q

Adjacent pyrimidine residues link together, Causes bulging of the double helix

A

UV-induced crosslinking

66
Q

What are the types of DNA repair?

A
  • Direct repair: keeps DNA strand intact
  • Mismatch Repair (MR): releases a large DNA fragment (>1000 nt)
  • Base Excision Repair (BER): releases a single damaged nt
  • Nucleotide Excision Repair (NER): releases a small oligo fragment (~ 12 nt)
67
Q

Aberrant activity in DNA repair systems have been associated with…

A

Cancer

68
Q

Photolyase cleaves UV-induced Thymidine dimers.
What kind of repair is this?

A

Direct Repair

69
Q
  1. MutS and MutL recognize the problem
  2. MutH cleaves the new strand close to the lesion
  3. An exonuclease then cleaves off ~1000 nt
  4. DNA pol III fills in the gap

What type of repair is this?

A

Mismatch repair

70
Q

Used to correct altered bases, ex. 8-oxoguanidine

First step is removing the damaged base with the action of a lesionspecific DNA glycosylase

An apurinic (AP) site is left behind

Note that the ribose-phosphate backbone remains intact

What type of repair is this?

A

Base Excision Repair (BER)

71
Q

An AP Endonuclease (APE) nicks the DNA strand adjacent to the AP site

Deoxyribose phosphodiesterase excises the residual ribose phoshate

DNA Pol I (Pol β) inserts the correct base and Ligase seals the gap

What type of repair is this?

A

Base Excision Repair (BER)

72
Q
  1. UVrABC exinuclease cleaves DNA strand upstream and down stream of the damage
  2. An ~12 nucleotide fragment is released
  3. DNA Pol I (Pol δ or ε) synthesizes the corrected strand
  4. Ligase seals the gap

What type of repair is this?

A

Nucleotide Excision Repair (NER)

73
Q

The exchange of genetic material between two daughter strands

A

Recombination

74
Q

Type of exchange that occurs between sequences of high similarity

A

Homologous Recombination

75
Q

Helicase & nuclease activity, drives branch migration and unwinds DNA

A

RecBCD

76
Q

Binds ssDNA, invades homologous sites

A

RecA (RAD51 in euk)

77
Q

Holiday Junction processing, cuts strands of like polarity and resolves junction

A

RuvA & RuvB/RuvC

78
Q

Requirements for RNA synthesis

A
  1. Duplex DNA Template – template strand (antisense) is complement – coding strand (sense) has same sequence (T for U)
  2. Ribonucleoside triphosphate monomers (rATP, rGTP, rUTP, rCTP)
  3. Divalent cations (Mg2+, Mn2+) as cofactor
79
Q

What catalyzes RNA synthesis?

A

RNA Polymerase

80
Q

All classes of RNA are transcribed by _____in prokaryotes

A

a single RNA polymerase

81
Q

Recognizes transcription start site; initiates synthesis and dissociates

A

σ subunit

82
Q

Core enzyme that goes on to elongate the RNA strand after initiation

A

α2ββ’

83
Q

What are the three steps RNA is synthesized in?

A
  1. Initiation – recognition of promoter sequences
  2. Elongation – extension of the RNA polymer
  3. Termination – signal to stop synthesis • Rho-independent • Rho-dependent
84
Q

Initiation of replication occurs through recognition of ____by the σ subunit

A

promoters

85
Q

The σ factor lowers affinity of RNA Pol for DNA, allowing it to bind and slide along DNA, as well as recognize the specific promoter site

Topoisomerases are necessary at each end to unwind/rewind the DNA RNA Pol has lower overall fidelity than DNA Pol III, along with lower proofreading ability

A

Initiation

86
Q

The σ factor can go on to bind another RNA Pol and start transcribing again

A

Elongation

87
Q

Occurs at palindromic GC rich regions followed by a sequence of T in the DNA template strand

The palindromic sequence forms a stem loop in the RNA sequence that pauses the RNA polymerase

The uridines paired with the DNA template are weaker than the A:T duplex DNA strand, making the RNA fall off and allowing DNA to reanneal

A

Rho-Independent Termination

88
Q

Pausing of the RNA Pol occurs, which allows the Rho protein to catch up to the nascent RNA strand and knock it off the DNA

A

Rho-Dependent Termination

89
Q

A genetic unit containing both regulatory sequences and structural protein sequences.

A

Operon

90
Q

Where RNA Pol sits down to transcribe a gene or set of genes

A

Promoter

91
Q

DNA sequence that controls the expression of structural genes, normally downstream of promoter

A

Operator

92
Q

Protein that binds to operator region to normally decrease RNA synthesis by obstructing RNA Pol access to structural genes (has allosteric sites for binding of small molecules)

A

Repressor

93
Q

Small molecule that binds to repressor to affect change in RNA Pol synthesis

A

Inducer

94
Q

Under conditions of high glucose and low lactose, the genes of the _____ are not expressed

A

lac operon

95
Q

Stimulates transcription

Senses the energy state of the cell

Binds upstream of promoter regions for alternative sugar metabolism operons

Bends the DNA, making it easier to unwind

When cAMP is high (glucose low), activated

A

CAP

96
Q

RNA synthesis

A

Transcription

97
Q

Transcriptional machinery

A

RNA polymerase

98
Q

Recognizes promoter sites

A

Sigma (σ) factor

99
Q

DNA sequences that determine the site of transcription initiation

A

Promoter

100
Q

The average order of nucleotides

A

Consensus sequence

101
Q

RNA-synthesis termination protein

A

Rho (ρ)

102
Q

Consists of regulatory elements and protein coding genes

A

Operon

103
Q

Repressor binding site

A

Operator

104
Q

Prevents transcription of structural genes

A

Repressor

105
Q

Allolactose, in the lac operon

A

Inducer

Biochemistry (12 decks)

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