DNA replication

Question 1

protein-dna interactions predominantly occur in the

Answer 1

major groove through hydrogen bonds between aa and bases

Question 2

what does site specific recognition requires?

Answer 2

multiple DNA-protein interactions

Question 3

in yeast ORC does what?

Answer 3

binds to initiate replication at the origin and unwinds DNA

Question 4

true or false: exact dna sequence that mark human origins of replication have been determined

Answer 4

false, it has not

Question 5

initially used to study human DNA replication

Answer 5

SV40

Question 6

SV40 requires only one viral protein ____, the other proteins are supplies by the host cell

Answer 6

T-antigen (tag)

Question 7

multifunctional protein that not only binds to the origin of replication but act as a DNA helicase

Answer 7

T-ag

Question 8

class of enzymes that use energy released from hydrolysis of ATP to break the hydrogen bond that stabilize the double helical form of DNA, “unwinding” it

Answer 8

DNA helicase

Question 9

SSB protein

Answer 9

human single strand binding protein also called RPA

Question 10

required for dNA replication to stabilize the single stranded DNA once unwound

Answer 10

SSB

Question 11

enzyme that helps to maintain the stability of DNA by relaxing the supercoils

Answer 11

Topo I

Question 12

disorder in which cellular DNA helicase is deficient associated with a high risk of developing malignancy

Answer 12

Bloom’s synd

Question 13

associated with mutation of a gene encoding a helicase.

Answer 13

Werner’s syndrome

Question 14

characterized by premature aging

Answer 14

Werner’s syndrome

Question 15

necessary for DNA synthesis (all 5–> 3)

Answer 15

DNA pol

Question 16

needed to initiate DNA synthesis and makes an RNA primer

Answer 16

Pol alpha primase

Question 17

required for lagging strand synthesis and generate okasaki fragments

Answer 17

Pol delta

Question 18

dependent on PCNA and RF-C

Answer 18

Pol delta

Question 19

DNA clamp that facilitates binding and it is loaded on using RF-C

Answer 19

PCNA

Question 20

have 3 to 5 exonuclease activity contributing to their high fidelity through proofreading activity

Answer 20

pol delta and pol epsilon

Question 21

required for leading strand synthesis and also PCNA dependent

Answer 21

pol epsilon

Question 22

used in mitochondrial DNA synthesis

Answer 22

pol gamma

Question 23

used in DNA synthesis repair

Answer 23

pol Beta

Question 24

catalyzes the formation of a bond between two ends of DNA

Answer 24

DNA ligase

Question 25

occurs through nucleophilic attack by 3 hydroxyl on the phosphate group of incoming nucleotide

Answer 25

DNA elongation

Question 26

AZT and acyclovir

Answer 26

nucleotide analogues

Question 27

Nucleotide analogues have structures like nucleotides, but lack the __________ to permit elongation, therefore leads to _____ ___ and this inhibits ______ ______

Answer 27

Nucleotide analogues have structures like nucleotides, but lack the 3' hydroxyl required to permit elongation and therefore lead to chain termination and thus inhibits DNA replication

Question 28

therapeutic drug is limited because it blocks other pol such as DNA pol gamma causing adverse side effects

Answer 28

AZT

Question 29

Mutant forms of ______ ____ arise that have ______ affinity for AZT rendering it ineffective

Answer 29

Mutant forms of reverse transcriptase leading to lower affinity

Question 30

cell cycle composed of

Answer 30

G1, S, G2, and M

Question 31

DNA synthesis occurs during

Answer 31

S phase

Question 32

tumor suppressor that acts at the G1/S checkpoint

Answer 32

p53

Question 33

increased risk for malignant replication

Answer 33

mutated p53

Question 34

inherited disorder where a mutated p53 tumor suppressor gene leads tumors at multiple sites in the body because all cells carry the mutation

Answer 34

Li-Fraumeni

Question 35

DNA damage sense at one of the checkpoints it will undergo

Answer 35

apoptosis, cell death

Question 36

prokaryotes mismatch repair

Answer 36

MutL, MutS, MutH

Question 37

parental strand marked by

Answer 37

methylation

Question 38

recognizes the mismatched base pair in prokatyotes

Answer 38

MutS

Question 39

produces a nick at a GATC site in the daughter strand identified by lack of methylation upstream or downstream in prokaryotes

Answer 39

MutH

Question 40

facilitates an interaction between MutS and MutH

Answer 40

MutL

Question 41

___ and ___ have been isolate in humans

Answer 41

hMSH and hMLH

Question 42

mutations in genes encoding mismatch repair proteins leads to

Answer 42

hereditary non-polyposis colon cancer HNPCC

Question 43

also associated with trinucleotide repeats expansion

Answer 43

HNPCC

Question 44

x-linked dom characterized by CGG

Answer 44

fragile x

Question 45

autosomal dom characterized by CTG repeats

Answer 45

myotonic dystrophy

Question 46

autosomal dom characterized by CAG repeats

Answer 46

Huntington's

Question 47

Many proteins required for replication are also required for

Answer 47

excision repair

Question 48

___ ___causes adjacent thymine bases to form ______ bonds forming a ______ ______

Answer 48

DNA UV causes adjacent thymine bases to form covalent bonds forming a thymine dimer

Question 49

thymine dimers removed by

Answer 49

excision repair

Question 50

disease caused by defective excision repair, leading to a greatly increased risk of developing skin lesions/ cancer

Answer 50

xeroderma pigmentosum

Question 51

_____ spontaneously deaminates to _____ which can be mutagenic as it changes base-pairing

Answer 51

cytosine to uracil

Question 52

removes uracil from dNA creating an AP site

Answer 52

uracil-DNA glycosidases

Question 53

AP site

Answer 53

apurinic or apyrimidine

Question 54

acts as a chemical mutagen that can deaminate cytosine to uracil or adenine to hypoxanthine leading to mutations

Answer 54

nitrous acid

Question 55

guanine may be alkylated on

Answer 55

N7

Question 56

gives rise to insertions and deletions in DNA

Answer 56

intercalators

Question 57

examples of intercalators

Answer 57

ethidium, proflavin, acridine orange

Question 58

excision repair marked by three phases of

Answer 58

enzyme activity

Question 59

excision repair (1)

Answer 59

in e coli, exonuclease recognizes the pyrimidine dimer and cleaves on both sides creating a fragment that contains the dimer. fragment is removed leaving a gap in DNA

Question 60

excision repair (2)

Answer 60

DNA pol I fills the gap using the 3' OH end as a primer (resyntheis)

Question 61

excision repair (3)

Answer 61

DNA ligase rejoins the newly formed strand with the original DNA