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Molecular Biology > Lecture 3, 4, ~5: DNA replication, repair and recombination > Flashcards

Lecture 3, 4, ~5: DNA replication, repair and recombination Flashcards

1
Q

How does gene conversion occur

A

DNA synthesis during homologous recombination

Repair of mismatches in regions of heteroduplex DNA

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2
Q

Methylated Cytosine

A

Problematic. Deamination results in T mismatched with G
Special DNA glycosylase repairs but is relatively ineffective
Only 3% of C’s are methylated, but they account for 1/3 of all point mutations associated with inherited disease

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3
Q

Helicase loading proteins

A

Cdc6

Cdt1

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4
Q

Two outcomes of holliday junction resolution

A 
Crossing over (rare, only 2 events/chromosome)
Gene conversion (90% of the time)
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5
Q

Reader-writer complex

A

Spreads parental patterns of histone modification

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6
Q

Homologous repair differences from non homologous

A

Uses daughter DNA duplex as template
No loss or alteration of DNA at repair site
Can repair other types of DNA damage

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7
Q

Gene conversion

A

Divergence from the expected distribution of alleles during meiosis

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8
Q

Resolution of holliday junction

A

Strands of helices are cleaved by endonuclease (RuvC)

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9
Q

Telomerase

A

Replicates chromosome ends in eukaryotes
Special sequence GGGTTA repeated x1000
Elongates the parental strand, then DNA polymerase copies onto new strand

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10
Q

Type II topoisomerase

A

Creates transient DS break of DNA.
Used at points of DNA where two double strand helices cross eachother
It can separate two interlocked DNA circles and prevent severe tangling problems that could arise during replication

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11
Q

Histone octamer breaks into what as replication fork arrives

A

H3-H4 tetramer- Randomly distributed to daughter duplexes

Two H2A-H2B dimers- Released from DNA

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12
Q

MutL

A

Mismatch repair protein

Scans for nick and triggers degradation of nicked strand

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13
Q

Sliding clamp

A

Keeps DNA polymerase on DNA when moving, releases with DS-DNA is encountered

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14
Q

Transcription coupled repair

A

RNA polymerase stops at lesion and directs repair machinery

Can work with BER, NER and other mechanisms

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15
Q

Brca1

A

Regulates processing of broken ends of chromosomes

Mutations lead to use of non-homologous end joining process

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16
Q

BER

A

Repairs single base pair changes

Involves DNA glycosylase, AP endonuclease, phosphodiesterase

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17
Q

How many base pairs in each turn of the DNA helix?

A

10bp

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18
Q

Cockaynes syndrome

A

Caused by defect in transcription coupled repair

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19
Q

Non homologous end joining differences from homologous

A

No-template required
Creates mutation at site of repair
Can also create translocations

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20
Q

Causes of DS DNA breaks

A

Ionizing radiation
Replication errors
Oxidizing agents

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21
Q

Depurination

A

N-glycosyl linkage is hydrolyzed, releasing a guanine or adenine- occurs spontaneously 5000x per day

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22
Q

Holliday junction strands cut in opposite directions

A

Crossing over

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23
Q

ORI (replication origin)

A

AT rich sequences attract initiator proteins
Must have binding site for ORC origin recognition complex
Must having binding site for proteins that help attract ORC

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24
Q

SS-DNA binding proteins

A

Bind single stranded DNA
Help stabilize unwound DNA
Prevent formation of hairpins
The DNA bases remain exposed

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25
Brca2
``` Maintains Rad51 (RecA) Inactive until it is at site of damage Mutation causes RecA not to bind DNA to form invading strand ```
26
Holliday junction definition
DNA intermediate containing four DNA strands from two different helices
27
Checkpoints
DNA damage triggers pause of cell cycle Blocks entry from G1-->S phase Slows progression through S phase Blocks transition from G2-->M phase
28
Clamp loader
Hydrolyzes ATP as it loads clamp. Stays near on the lagging strand to load clamp at each new fragment
29
AP endonuclease and phosphodiesterase
Cut phosphodiester backbone to remove sugar phosphate for repair in BER
30
NER
Can repair any bulky lesion Multienzyme complex scans DNA for distortion in double helix instead of specific base change Cleaves phosphodiester bond, DNA helicase peels lesion containing stand away
31
Non-homologous repair
Most common Nuclease processes DNA ends Ligase seals ends
32
Holliday junction strands cut the same way result in
Gene conversion
33
Replicative senescence
Daughter cells have defective chromosomes after many generations and stop dividing to guard against cancer
34
DNA glycosylase
BER enzyme 6 types, each recognize specific type of altered base and catalyzes its removal. Cleaves glycosyl bond connecting base w/sugar
35
Mismatch repair
Removes almost all errors missed by proofreading by detecting distortion caused by mispairing
36
Human mutation rate
One nucleotide change per 10^8 nucleotides per generation
37
ATM protein
Kinase that generates intracellular signals to alert cell to DNA damage and upregulate DNA repair genes
38
In S phase, activated Cdks lead to:
Dissociation of helicase loading protein Activation of helicase, unwinding of DNA Loading of DNA polymerase, etc...
39
Histone chaperones
Reassemble histones after replication
40
Nucleases that generate 3' invading strand are active in which phase(s)
S and G2-ensures a replicated chromosome or sister chromatid are most likely template for repair
41
Heteroduplex DNA
Double helix from DNA strands that originate from different molecules (strand from maternal homolog is base paired with strand from paternal homolog)
42
RecA
Binds the 3' end of single stranded invading strand and directs it to a homologous sequence to form heteroduplex. Requires at least 15 base pairs of homology
43
Homologous recombination occurs between, begins with what, has what intermediate steps
Paired maternal and paternal homologous chromosomes Begins w/double stranded break Strand invasion and double holliday junction formation follow
44
Translesion polymerase
Used to repair extensive damage, less accurate though 7 types, all lacking exonuclease proofreading ability Adds only a couple nucleotides before real polymerase reassociates
45
Branch migration
Once strand invasion occurs, the point of exchange can move through branch invasion
46
Depurination repair shortcut
Begins directly with AP endonuclease, skips glycosylase
47
Mismatch repair uses what to distinguish correct strand?
In E. coli: It depends on methylation to distinguish new strand In humans: Uses single strand breaks on lagging strand
48
DNA topoisomerase
Breaks phosphodiester bond to relieve supercoiling
49
T-loops
structures protect ends of chromosomes and distinguishes them from broken ones that need repair
50
Homologous recombination definition
Genetic exchange between a pair of homologous DNA sequences
51
Branch migration types
Spontaneous (can occur in both directions) | Catalyzed by special helicase (moves in one direction)
52
Exonucleolytic proofreading
Takes place immediately after incorrect base is added. Exonuclease clips off unpaired residue and DNA polymerase continues
53
DNA helicase
Unwinds DNA Protein with 6 subunits. Binds and hydrolyzes ATP, causing conformational change that propels it like a rotary engine, unwinding DNA
54
Type I topoisomerase
Creates single strand break of one phosphodiester bond, uses the other as a swivel point
55
Homologous repair
Nuclease processes 5' ends | Damage repaired accurately using sister chromatid as template
56
Types of repair (4)
NER BER Transcription coupled repair DS break repair (non homologous or homologous)
57
Mre11 Nuclease complex
Identifies DNA damage and processes ends of DS break in meiotic recombination
58
Homologous recombination uses
Repair of double-strand breaks Exchange of genetic information to create new combinations of genetic sequences Mechanical role in assuring accurate chromosome segregation
59
MutS
Mismatch repair protein. | Binds to mismatch
60
When are histone proteins synthesized
Mainly in S phase
61
Deamination
Cytosine changes to Uracil, occurs spontaneously 100x per day
62
ORC regulation
New ORC cannot be formed until next M phase resets cycle

Molecular Biology (25 decks)

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