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
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
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
4
Q
Unwinds DNA
A
DNA gyrase
5
Q
Binds single-stranded DNA
A
SSB
6
Q
Initiation factor, origin-binding protein
A
DnaA
7
Q
Unwinds 5’ → 3’ DNA
A
Helicase
8
Q
Synthesizes RNA Primer
A
Primase
9
Q
Elongates (DNA synthesis)
A
DNA Polymerase III holoenzyme
10
Q
Excises RNA Primer, fills in with DNA
A
DNA Polymerase I
11
Q
Covalently links Okazaki fragments
A
DNA ligase
12
Q
Terminates
A
Tus
13
Q
Binds single-stranded DNA in Eukaryotes and Prokaryotes
A
Replication Protein A (RPA)
SSB
14
Q
Synthesizes 10 nt RNA primer and then 20-30 nt DNA in Eukaryotes and Prokaryotes
A
Polymerase α
Primase/Pol I
15
Q
Synthesizes new DNA strands in Eukaryotes and Prokaryotes
A
Polymerase δ
Pol III
16
Q
Increases processivity by clamping to DNA in Eukaryotes and Prokaryotes
A
Proliferating Cell Nuclear Antigen (PCNA)
β-subunit
17
Q
Loads DNA pol onto DNA clamp in Eukaryotes and Prokaryotes
A
Replication Factor C (RFC)
γ-complex
18
Q
Removes RNA primer in Eukaryotes and Prokaryotes
A
Rnase H1
Pol I
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
20
Q
What are the steps of prokaryotic DNA replication?
A
- Recognition of the origin of replication
- Unwinding of the double-stranded helix
- Preparation of the new strand with an RNA primer
- DNA synthesis of both strands – One strand is synthesized continuously 5’→3’ – The other strand is synthesized a fragments 3’→5’
- Termination of replication
21
Q
What does DNA polymerization require to get started?
A
an RNA primer
22
Q
What is required to ensure the accurate transmission of genetic information?
A
High fidelity (specificity)
23
Q
Replication is…?
A
bi-directional and semi-conservative
24
Q
A hexamer of ___ binds several AT-rich regions on the E. coli genome, allowing the double-stranded DNA to open
A
DnaA
25
Between AT pairings and GC pairings, which are stonger?
GC
26
* Disrupts hydrogen bonds between parent strands
* Binds single-stranded DNA to start
* Requires ATP hydrolysis for energy
Helicase
27
* Type II topoisomerase that introduces negative supercoils to overcome the torsional stress of unwinding
* Requires ATP hydrolysis for energy
DNA Gyrase
28
Hold unwound strands open and prevent them from re-annealing
Single-Stranded DNA Binding Proteins (SSBs)
29
The ~10 nucleotide RNA primer is synthesized by...
a primase
30
The exonuclease activity of \_\_\_\_later replaces the RNA with DNA
Polymerase I
31
DNA is synthesized by...
DNA Polymerase
32
* 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
DNA Polymerase
33
Proofreading occurs via...
the exonuclease domain
34
adds 10 nucleotides/sec, can add ~20 dNTPs before falling off
DNA Pol I
35
adds 1,000 nucleotides/sec, can replicate the entire bacterial genome (4.6 kb) in ~40 minutes
DNA Pol III
36
the # of nucleotides that can be added before the polymerase falls off
Processivity
37
What has these catalytic activities?
* 5’→3’ exonuclease activity (RNA primer removal)
* 5’→3’ polymerase activity
* 3’→5’ exonuclease activity (proofreading)
DNA Polymerase I
38
Two core units of (βαεθ)2, one γ complex, and a dimer of τ subunits make up the holoenzyme
DNA Polymerase III
39
Processivity switch which allows release of DNA on lagging strand
τ-subunit
40
5’→3’ polymerase
α-subunit
41
Acts as sliding clamp to enhance processivity
β-subunit
42
Responsible for assembly of Pol III onto DNA
γ-complex
43
3’→5’ exonuclease
ε subunit
44
Seals nicks left from Okazaki fragments.
Ligase
45
Allows synchronous replication of the leading and lagging strands
DNA Pol III dimer
46
Prevents further replication by preventing unwinding
Tus protein (a contrahelicase)
47
Telomere replication is carried out by...
Telomerase
48
Faithfully replicates the DNA
DNA polymerase
49
Determines the sequence of a complementary nucleic acid
Template
50
The initial segment of a polymer that will be extended
Primer
51
Unwinds the double helix
Helicase
52
Relaxes or introduces supercoils
Topoisomerase
53
Crucial for proofreading
Exonuclease
54
Synthesizes a segment of RNA
Primase
55
Found on the lagging strand
Okazaki Fragments
56
Uses ATP to join DNA fragments
DNA ligase
57
Prevents the disappearance of the lagging strand
telomerase
58
What happens to wrongly incorporated nucleotides?
Don’t hybridize to the template strand, and are free to enter the exonuclease domain, where they are then cleaved
59
What kinds of DNA damage can occur?
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
One purine/pyrimidine replace by another, e.g. A becomes G (T→C)
Transition
61
A purine replaced by a pyrimidine or vice versa e.g T→G
Transversion
62
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
Base Oxidation
63
This can happen to A, C, and G bases, the modified bases have different base-pairings
Deamination
64
Aflatoxin is found in molds, polycyclic hydrodrocarbons found in exhaust fumes cause similar adducts, Resuts in G-C → T-A mutation
Alkylation
65
Adjacent pyrimidine residues link together, Causes bulging of the double helix
UV-induced crosslinking
66
What are the types of DNA repair?
* 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
Aberrant activity in DNA repair systems have been associated with...
Cancer
68
Photolyase cleaves UV-induced Thymidine dimers.
What kind of repair is this?
Direct Repair
69
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?
Mismatch repair
70
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?
Base Excision Repair (BER)
71
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?
Base Excision Repair (BER)
72
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?
Nucleotide Excision Repair (NER)
73
The exchange of genetic material between two daughter strands
Recombination
74
Type of exchange that occurs between sequences of high similarity
Homologous Recombination
75
Helicase & nuclease activity, drives branch migration and unwinds DNA
RecBCD
76
Binds ssDNA, invades homologous sites
RecA (RAD51 in euk)
77
Holiday Junction processing, cuts strands of like polarity and resolves junction
RuvA & RuvB/RuvC
78
Requirements for RNA synthesis
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
What catalyzes RNA synthesis?
RNA Polymerase
80
All classes of RNA are transcribed by \_\_\_\_\_in prokaryotes
a single RNA polymerase
81
Recognizes transcription start site; initiates synthesis and dissociates
σ subunit
82
Core enzyme that goes on to elongate the RNA strand after initiation
α2ββ’
83
What are the three steps RNA is synthesized in?
1. Initiation – recognition of promoter sequences
2. Elongation – extension of the RNA polymer
3. Termination – signal to stop synthesis • Rho-independent • Rho-dependent
84
Initiation of replication occurs through recognition of \_\_\_\_by the σ subunit
promoters
85
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
Initiation
86
The σ factor can go on to bind another RNA Pol and start transcribing again
Elongation
87
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
Rho-Independent Termination
88
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
Rho-Dependent Termination
89
A genetic unit containing both regulatory sequences and structural protein sequences.
Operon
90
Where RNA Pol sits down to transcribe a gene or set of genes
Promoter
91
DNA sequence that controls the expression of structural genes, normally downstream of promoter
Operator
92
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)
Repressor
93
Small molecule that binds to repressor to affect change in RNA Pol synthesis
Inducer
94
Under conditions of high glucose and low lactose, the genes of the _____ are not expressed
lac operon
95
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
CAP
96
RNA synthesis
Transcription
97
Transcriptional machinery
RNA polymerase
98
Recognizes promoter sites
Sigma (σ) factor
99
DNA sequences that determine the site of transcription initiation
Promoter
100
The average order of nucleotides
Consensus sequence
101
RNA-synthesis termination protein
Rho (ρ)
102
Consists of regulatory elements and protein coding genes
Operon
103
Repressor binding site
Operator
104
Prevents transcription of structural genes
Repressor
105
Allolactose, in the lac operon
Inducer
