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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

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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
Q

Brca2

A 
Maintains Rad51 (RecA) Inactive until it is at site of damage
Mutation causes RecA not to bind DNA to form invading strand
26
Q

Holliday junction definition

A

DNA intermediate containing four DNA strands from two different helices

27
Q

Checkpoints

A

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
Q

Clamp loader

A

Hydrolyzes ATP as it loads clamp. Stays near on the lagging strand to load clamp at each new fragment

29
Q

AP endonuclease and phosphodiesterase

A

Cut phosphodiester backbone to remove sugar phosphate for repair in BER

30
Q

NER

A

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
Q

Non-homologous repair

A

Most common
Nuclease processes DNA ends
Ligase seals ends

32
Q

Holliday junction strands cut the same way result in

A

Gene conversion

33
Q

Replicative senescence

A

Daughter cells have defective chromosomes after many generations and stop dividing to guard against cancer

34
Q

DNA glycosylase

A

BER enzyme
6 types, each recognize specific type of altered base and catalyzes its removal.
Cleaves glycosyl bond connecting base w/sugar

35
Q

Mismatch repair

A

Removes almost all errors missed by proofreading by detecting distortion caused by mispairing

36
Q

Human mutation rate

A

One nucleotide change per 10^8 nucleotides per generation

37
Q

ATM protein

A

Kinase that generates intracellular signals to alert cell to DNA damage and upregulate DNA repair genes

38
Q

In S phase, activated Cdks lead to:

A

Dissociation of helicase loading protein
Activation of helicase, unwinding of DNA
Loading of DNA polymerase, etc…

39
Q

Histone chaperones

A

Reassemble histones after replication

40
Q

Nucleases that generate 3’ invading strand are active in which phase(s)

A

S and G2-ensures a replicated chromosome or sister chromatid are most likely template for repair

41
Q

Heteroduplex DNA

A

Double helix from DNA strands that originate from different molecules (strand from maternal homolog is base paired with strand from paternal homolog)

42
Q

RecA

A

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
Q

Homologous recombination occurs between, begins with what, has what intermediate steps

A

Paired maternal and paternal homologous chromosomes
Begins w/double stranded break
Strand invasion and double holliday junction formation follow

44
Q

Translesion polymerase

A

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
Q

Branch migration

A

Once strand invasion occurs, the point of exchange can move through branch invasion

46
Q

Depurination repair shortcut

A

Begins directly with AP endonuclease, skips glycosylase

47
Q

Mismatch repair uses what to distinguish correct strand?

A

In E. coli: It depends on methylation to distinguish new strand
In humans: Uses single strand breaks on lagging strand

48
Q

DNA topoisomerase

A

Breaks phosphodiester bond to relieve supercoiling

49
Q

T-loops

A

structures protect ends of chromosomes and distinguishes them from broken ones that need repair

50
Q

Homologous recombination definition

A

Genetic exchange between a pair of homologous DNA sequences

51
Q

Branch migration types

A

Spontaneous (can occur in both directions)

Catalyzed by special helicase (moves in one direction)

52
Q

Exonucleolytic proofreading

A

Takes place immediately after incorrect base is added. Exonuclease clips off unpaired residue and DNA polymerase continues

53
Q

DNA helicase

A

Unwinds DNA
Protein with 6 subunits.
Binds and hydrolyzes ATP, causing conformational change that propels it like a rotary engine, unwinding DNA

54
Q

Type I topoisomerase

A

Creates single strand break of one phosphodiester bond, uses the other as a swivel point

55
Q

Homologous repair

A

Nuclease processes 5’ ends

Damage repaired accurately using sister chromatid as template

56
Q

Types of repair (4)

A

NER
BER
Transcription coupled repair
DS break repair (non homologous or homologous)

57
Q

Mre11 Nuclease complex

A

Identifies DNA damage and processes ends of DS break in meiotic recombination

58
Q

Homologous recombination uses

A

Repair of double-strand breaks
Exchange of genetic information to create new combinations of genetic sequences
Mechanical role in assuring accurate chromosome segregation

59
Q

MutS

A

Mismatch repair protein.

Binds to mismatch

60
Q

When are histone proteins synthesized

A

Mainly in S phase

61
Q

Deamination

A

Cytosine changes to Uracil, occurs spontaneously 100x per day

62
Q

ORC regulation

A

New ORC cannot be formed until next M phase resets cycle

Molecular Biology (25 decks)

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