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Biochemistry > BB451 exam 2 - DNA Replication, Recombination, Repair > Flashcards

BB451 exam 2 - DNA Replication, Recombination, Repair Flashcards

1
Q

DNA structure

A

double helix, phosphodiester linkages of nucleotides, alternating sugar/phosphate links

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2
Q

complementary base pairs held by

A

H bonds

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3
Q

anti parallel

A

one strand 5’ to 3’ paired with other 3’ to 5’

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4
Q

phosphodiester bonds

A

linkage between 5’ phosphate group of incoming nucleotide and 3’ hydroxyl of previous nucleotide in chain

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5
Q

base pairings

A

AT with 2 H bonds

CG with 3 H bonds (harder to break)

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6
Q

start with ___ only 1 phosphate added

A

start with triphosphate, only 1 phosphate added to the strand

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7
Q

major and minor groove from…

A

asymmetric glycosidic linkage between deoxyribose sugar and each base in double helix

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8
Q

3 major forms of DNA

A

A, B, Z

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9
Q

A form DNA

A

right handed helix, franklin published, found only when dehydrated, more compressed/tilted, double stranded RNA (or RNA-DNA duplex)

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10
Q

B form DNA

A

most common, right handed helix, Watson and Crick published, stole from Franklin, 10.5 base pairs per turn

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11
Q

Z form DNA

A

left handed helix, marking location of genes in eukaryotic chromosomes

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12
Q

semiconservative replication

A

each daughter has 1 new strand + 1 old strand

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13
Q

DNA polymerase I function

A

5’ to 3’ DNA polymerase activity to make DNA
3’ to 5’ exonuclease activity (proofreading)
5’ to 3’ exonuclease activity (remove RNA primer)

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14
Q

most abundant DNA polymerase

A

DNA polymerase I

falls off

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15
Q

structure of DNA polymerase I

A

hand structure

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16
Q

bacteria have ____ chromosomes

A

circular

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17
Q

all DNA polymerases require a ___ to start DNA synthesis

A

primer formed by primase

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18
Q

DNA polymerase II

A

repair mechanisms

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19
Q

DNA polymerase III

A 
responsible for most replication 
very processive - stays on (don't need as many as Pol I) 
fast - 1000 nucleotides/sec 
does have proofreading 
dimer
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20
Q

subunits of DNA polymerase III

A

2 identical sets of subunits (dimer)
2 cores: where catalysis occurs
beta clamp/sliding clamp - hold to DNA
clamp loader - closes clamp around DNA

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21
Q

helicase

A

pull strands apart using energy from ATP hydrolysis

fast enough to not slow down Pol III (1000 nucleotides/sec=100 turns/sec=6000 rpm)

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22
Q

single strand binding protein

A

covers up bases and protects strand after pulled apart

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23
Q

topoisomerase II (gyrase)

A

relieves tension, changes superhelical density

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24
Q

topoisomerases can…

A

increase or decrease superhelical density

don’t usually bring it to 10.5 base pairs/ turn (relaxed)

25
Q

okazaki fragments

A

segments synthesized on lagging strand

must be combined together

26
Q

ligase

A

connects okazaki fragments (after Pol I removes primer)

biotechnologists use to join DNA fragments to create recombinant molecules

27
Q

___ is faster so..

A

leading strand is faster so lagging strand loops around –> trombone

28
Q

removal of RNA primers requires

A

Pol I’s 5’ to 3’ exonuclease activity

-remove RNA at front end of enzyme as polymerase activity (at back of Pol I) fills in space behind it as it moves along

29
Q

topoisomerases…

A

change topological structure of DNA molecule

30
Q

supercoiling can occur when..

A

it has something other than 10.5 base pairs per turn

31
Q

tension relived by

A

supercoiling

-double strands twist over each other –> helix goes back to approximately 10.5 base pairs per turn

32
Q

2 types of topoisomerase

A

type 1 - cut one strand

type 2 - cut both strands (ex: gyrase)

33
Q

drugs that inhibit topoisomerases..

A

can be effective antibiotics

ex: naladixic acid, ciprofloxacin

34
Q

topoisomerase 7

A

only in E. coli/bacteria
good for antibiotics
unwinds strands, kill them, no effects on us

35
Q

linking number

A

L=T+W

twits + writhes

36
Q

twists (T)

A

number of times 2 helices cross each other

37
Q

writhes (W)

A

number of superhelical turns
can be + or -
when not 0, it is a superhelical, has superhelicity

38
Q

writhing occurs in an attempt of…

A

DNA to relax

relaxed = number of base pairs per twist = 10.5

39
Q

initiation of replication in E. coli occurs at

A

OriC (origin of replication)

contains 3 repeats of an AT rich sequence

40
Q

DNA A

A

several copies bind at origin of replication

DNA wraps around it –> superhelical tension –.strands come apart (AT only 2 H bonds, weak)

41
Q

DNA BC complex

A

bind when strands come apart from DNA A

dnaB = helicase, dnaC released

42
Q

DNA A released when

A

SSB and primase bind the exposed single strands

43
Q

eukaryotic chromosomes..

A

linear, multiple origins or replication

44
Q

telomeres

A

at linear ends, junk DNA

thousands of copies of repeats of short sequences

45
Q

telomerase

A

builds telomeres
found predominantly in fetal and cancer cells and fertilized eggs, differentiated cells do not appear to have active telomerase
reverse transcriptase -

46
Q

reverse transcriptase

A

telomerase
use an RNA template (that it carries) to synthesize DNA
other in retroviruses (HIV)

47
Q

deamination of adenine –>

A

hypoxanthine (chemical damage to DNA)

48
Q

oxidation damage to DNA –>

A

creation of 8-oxo-guanine

49
Q

aflatoxin

A

made by mold, from peanut butter

causes damage to DNA

50
Q

UV light causes..

A

dimerization of thymines

51
Q

lack of repair of DNA sliding (amid repeating sequences) –>

A

Huntington’s disease

52
Q

proofreading

A

3’ to 5’ exonuclease activity, as DNA is being replicated

53
Q

mismatch repair

A

fix mismatches, after replication

54
Q

nucleotide excision repair

A

excision of group of nucleotides followed by replacement w/ correct ones
by exonucleases
ex: removal of thymine dimers (segment removed by nuclease) or remove aflatoxin

55
Q

base excision repair

A

uracil repair
excision of damaged base, nicking by endonuclease, repair
ex: remove U from DNA by uracil glycosylase

56
Q

deamination of cytosine

A

–> uracil –> GU base pairs

57
Q

mismatch repair in E. Coli

A

MutS recognizes mismatch
MutL recruits MutH
MutH nick newly synthesized strand to allow exonuclease removal of nucleotides around mismatch

58
Q

p53

A

critical protein for monitoring DNA for damage prior to division
stop cell cycle is senses damage
if repair cant be performed –> induce apoptosis

59
Q

which strand made error?

A

strand that is being copies is methylated

new strand with error is not

Biochemistry (11 decks)

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