DNA Replication and Repair

Question 1

semi-conservative replication

Answer 1

single helix separated into 2 strands, each serving as a template for replcation of a new complementary strand

each daughter molecule contains one strand from the parent helix and one new strand

Question 2

prepriming complex

Answer 2

a complex of proteins that binds to the origin of replication and begins to unwind the helix for replication

Question 3

Describe the initiation of DNA replication in both prokaryotes and eukaryotes.

Answer 3

very similar between prokaryotes and eukaryotes

Question 4

DNA helicase

Answer 4

after generation of hte replication bubble, helicase binds and starts to unwind DNA, forcing the two strands apart

ATP is required as an energy source

once the strands are opened, binding proteins attach to prevent reannealing

Question 5

MCM helicase

Answer 5

protein that binds the ORC and initiates formation of the replication bubble, only happens once per cell cycle

regulatory mechanism to ensure correct amounts of DNA are produced

separates the two strands during replication as it moves down the helix

Question 6

topoisomerases

Answer 6

two types, TOPO1 and TOPO2 to deal with supercoils generated by the unwinding of DNA

Question 7

type I DNA topoisomerases

Answer 7

reversibly cut one strand, the intact strand is passed through the break and the topoisomerase relegates the cut strand, relieving the supercoiling

relieves both positive and negative supercoiling in eukaryotes, do not use ATP

Question 8

type II DNA topoisomerases

Answer 8

make transient breaks in both strands, then passes a second stretch of the double helix through the break and religates the break

uses ATP as an energy source

called DNA gyrase in bacteria

Question 9

replication fork

Answer 9

leading strand is synthesized 5’ to 3’

lagging strand is also snythesized 5’ to 3’ but in fragments called Okazaki fragments

Question 10

primase

Answer 10

an RNA polymerase that synthesizes a short ~10 nucleotide long stretch of RNA that is complementary to the parent strand

addition of primase to the prepriming complex creates the primosome

Question 11

DNA Pol alpha

Answer 11

responsible for synthesizing RNA primeras on the lagging strand as the replication fork moves

DnaG in prokaryotes

Question 12

DNA polymerase epsilon

Answer 12

elongates the replicating DNA in the leading strand in eukaryotic cells

done by DNA polymerase II in prokaryotes

Question 13

polymerase delta

Answer 13

elongates the DNA strande in the lagging strand in eukaryotic cells

done by DNA polymerase II in prokaryotes

Question 14

PCNA

Answer 14

proliferating cell nuclear antigen - pentamer through which the DNA passes, acts as a sliding clamp around the DNA

binds polymerase and prevents it from falling off

also bound to helicase

Question 15

Flap Endonuclease I (FENI)

Answer 15

removes the RNA and DNA flap after it the RNA is displaced by pol delta

after cleavage, DNA ligase comes and seals the gap

Question 16

proofreading

Answer 16

DNA polymerase has 3’ to 5’ exonuclease activity so mispaired bases can be removed and re-polymerized

pol alpha does not have proofreading capability so errors in the Okazaki fragment are removed during its removal

Question 17

FACT

Answer 17

helps remove histones from the replication fork and then adds them back in

histone octamers stay intact when they are removed

new histones are made during the S phase when DNA is replicating

Question 18

telomerase

Answer 18

if telomeres shorten sufficiently beyond a critical length, the cell activates a pathway to permanently stop dividing

telomerase conatains a protein with reverse transcriptase activity and a small RNA that acts as a template

Question 19

retrotransposons

Answer 19

transposons that utilize RNA intermediates

Question 20

types of single-strande damage repair

Answer 20

base excision repair, nucleotide excision repair, mismatch repair

Question 21

types of double-strand break repair

Answer 21

non-homologous end joining

microhomology-mediated end joining

homologous recombination (homology directed repair)

Question 22

sources of DNA damage

Answer 22

errors in insertion, wrong base, insertion of extra molecules, environmental damage such as radiation or oxidization

Question 23

base excision repair (BER)

Answer 23

removes non-helix distorting lesions, most common form of DNA damage and involves the modification of bases by oxidation, alkylation, deamination, or misincorporation

short pathc BER, gap filled by DNA polmerase

long patch BER, a new DNA strand is laid down by the machinery and the old flap is excised by a FLAP endonuclease

Question 24

mismatch repair

Answer 24

fixes errors caused by misincorporation of bases during DNA replication, reocgnizes parental strand due to methylation in prokaryotes and maybe by nicks in eukaryotes

Question 25

nucleotide excision repair

Answer 25

removes helix distorting changes such as pyrimidine dimers and oxidized benzo[a]pyrene

endonucleases cut damaged strand on each side of the lesion, gap filled by DNA polymerase delta and epsilon, strand religated by DNA ligase

Question 26

transcription coupled repair

Answer 26

if RNA polymerase detects lesions in DNA, wills tall and signal for repair components, defects in XP proteins in this process result in xeroderma pigmentosum

Question 27

non-homologous end joining (NHEJ)

Answer 27

broken ends are recognized by the repair machinery, brought together and rejoined

process of preparing ends for ligation typically loses some of the DNA resulting in mutations

Question 28

homologous repair or homology directed repair (HR)

Answer 28

utilizes the machinery used for recombination between chromosomes during meiosis, requires that the cell has mostly completed DNA replication

Question 29

H2AX

Answer 29

histone that can detect breaks in the DNA, will spread down chromatin to indicate to the machinery that there is an error in this region

Question 30

genome surveillance complex

Answer 30

cooridnated by BRCA1

ATM and ATR are sensing kinases that phosphrylate BRCA1 an activate the complex

BLM - bloom syndrom protein, helicase involved in double stranded break repairs

Question 31

chromosome translocations

Answer 31

reciprocal translocation - exchange of two fragments

robertsonian translocation - exchange in proximal short arms, some DNA is lost

Question 32

chromothripsis

Answer 32

thousands of clustered chromosomal rearrangements occur in a single event in colcalised and confined genomic regions in one or a few chromosomes

pieces religate together differently, can generate lost segments and boule double minutes (pieces of circular DNA)

Question 33

xeroderma pigmentosum

Answer 33

AR disease that cuases extreme sensitiviety to light, abnormal skin cancers develop, cells defective at excising thymine dimers caused by UV radiation

Question 34

Bloom’s syndrome

Answer 34

patients have stunted growth, exhibit UV sensitivity and have defective DNA helicase (BLM)

Question 35

Werner syndrome

Answer 35

causes “premature aging” effects, such as graying, cataracts, osteoporosis, werner gene encodes a DNA helicase involved in repair

Question 36

hereditary nonpolyposis colorectal cancer

Answer 36

an AD condition that results from mutations in genes involved in DNA mismatch repair