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stupid orgo > 2200 quiz 2 > Flashcards

2200 quiz 2 Flashcards

1
Q

when is the mechanism for copying DNA needed

A

DNA replication
DNA repair
DNA rocombination
RNA transcription

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2
Q

what are the problems for watson and cricks model for copying DNA

A
  1. it dosent take into account the biochem of DNA synthesis (the actual mechanism)
  2. it dosent take into account the structural organisation of DNA inside the cell (context)
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3
Q

what is watson and cricks testeable hypothesis for DNA copying

A

the two parental strands of a DNA molecule are each used to direct synthesis of a new complementary offspring strand

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4
Q

who carried out the definitive experiment to test watson and cricks hypothesis

A

matt meselson and frank stahl

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5
Q

what are the three models of copying DNA

A

semi conservative
conservative
dispersive

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6
Q

what did all three models of copying DNA share

A

the idea that the original strands of the duplex act as templates for offspring strand synthesis

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7
Q

semi conservative model

A

each progeny contains one parental and one offspring strand

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8
Q

conservative model

A

one progeny contains both parental strands and the other contain both offspring strands

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9
Q

dispersive model

A

each progeny duplex contains interspersed parental and offspring segments

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10
Q

matt meselson and frank stahls experiment

A

they prepared cells containing heavy DNA by growing e coli in a medium containing heavy nitrogen (N15) for many generations. then they grew those e coli cells in a medium containing light nitrogen (N14) and isolated the DNA after each generation or so.

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11
Q

what did matt meselson and frank stahl use to distinguish the heavy nitrogen from the light

A

cesium chloride (CsCl) density gradient centrifuge

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12
Q

what density was the isolated DNA after one round of doubling in stahl and meselsons experiment. what did this rule out

A

intermediate density. it ruled out the conservative model

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13
Q

what density was the isolated dna after two rounds of doubling. what does this rule out

A

half having equal n14 and n15 and half having only n14. this rules out the dispersive model because that would have equal of each closer to the light side

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14
Q

what is the enzyme that joins individual nuceotides into polynucleotide chains

A

dna polymerase

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15
Q

what bond does dna polymerase make

A

between the 3’ hydroxyl of first and 5’ phosphate of second

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16
Q

what does ntp stand for

A

nucleoside triphosphate

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17
Q

what does dntp stand for

A

deoxynucleotide triphosphate

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18
Q

what is the limitation of dna polymerase

A

it cant join together two free dNTPs together

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19
Q

what direction does dna polymerase work in

A

5’ to 3’

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20
Q

what is the process which activates the sugar while assmbling polynucleotides

A

the oh is activated by losing a hydrogen and now it is a nucleophile which can attack the phosphate

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21
Q

what is the full adenine molecule with the three phosphates on it called

A

deoxyadenosine triphosphate

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22
Q

is the formation of polynucleotides a favourable or unfavourable reaction

A

unfavourable

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23
Q

how can you make joining of nucleotides a reaction which proceeds

A

hydrolysis of pyrophosphate which is an energy generating reaction that is coupled with the unfavourable reaction helps the reaction proceed
-31kj/mol or -7.3kcal/mol

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24
Q

what is the byproduct of dna joining

A

pyrophosphate (PPi)

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25
Q

how many DNA polymerases do cells have

A

more than one

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26
Q

are the new daughter chains synthesised in the same or opposite directions

A

in opposite

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27
Q

how many dna polymerases work on one chromosome at a time

A

two, one for leading strand and one for lagging strand

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28
Q

what is the solution for the dna polymerases going in different directions

A

reji okazaki came up with a solution: one strand is copied continuously while the other is copied bit by bit

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29
Q

what is nucleophilic displacement

A

movement of electrons from an electron rich enviroment to an electron poor enviroment

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30
Q

how much energy does it take to join a nucleoside monophosphate NMP to a polynucleotide chain

A

25 kj/mol or 6kcal/mol

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31
Q

what is teh net amount of energy in joining of dna

A

-29kj/mol or -6.8 kcal/mol

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32
Q

what is the place where dna replication start

A

ori-the origin of replication

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33
Q

how many origins of replication do bacteria have

A

1

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34
Q

how many origins of replication do eukaryotic chromosomes have

A

more than one

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35
Q

what is the replication intermediate called in circular chromosomes with a single origin of replication

A

the replication intermediate contains a bubble like the greek letter theta

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36
Q

what is the point where the dna polymerases meet halfway around circular cells

A

ter- terminus of replication

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37
Q

who reported the first evidence of bacterial origins of replication

A

john cairns

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38
Q

what did john cairns do in his experiment

A

he grew e coli cells in the presence of 3h-thymidine to radioactivly label them then he isolated the dna from the cell and put it on an electron microscope placed it next to photographic film and waited two months and he saw a replicating chormosome

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39
Q

what is autoradiography

A

detection of radioactively labelled molecules

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40
Q

did johns cairns show us that cells replicate bidirectionally

A

no the info he gave didnt specify the directionality because it was consistent with both unidirectional and bidirectional replication

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41
Q

who figured out that chromosomes copy bidirectionally

A

ray rodriguez

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42
Q

what was ray rodriguez’s experiment

A

he exposed e coli cells to low levels of 3h-thymidine to uniformly label them (pulse) and then washed and grew them in high levels of 3h-thymidine (chase)

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43
Q

what was the result of rays experiment

A

he saw two radioactively labelled regions meaning there is an origin and a plaec where they meet

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44
Q

what process showed us the eukaryotic chromosomes have multiple ori

A

autoradiographs

45
Q

what is the dark part in the pulse chase diagram and what is the light part

A

dark is pulse and light is chase

46
Q

why does rays experiment prove bidirectionality

A

because thre is symmtry on both sides of origins of replication showeing that replication is proceeding bidirectionally OUTWARD from each replication origin

47
Q

how many base pairs seperate ori in eukaryotic genomes

A

40 000 to 50 000

48
Q

how many ori do eukaryotic genomes have

A

more than ten thousand

49
Q

repliosomes

A

complex protein aggregates involved in dna synthesis

50
Q

where are dna strands seperated

A

where melting is facilitated

51
Q

why do we have unique origins of replication

A

from a regulatory perspective, its better to have a unique ori where dna copying can start rather than allowing random unpredictable events

52
Q

what is e coli origin of replication called

A

oriC

53
Q

how many base pairs does the sequence of e coli replication contain

A

245 bp

54
Q

what bases is the origin of replication of e coli cells rich in and why

A

A T because they have less bonds than G C

55
Q

what are the conserved sequences in e coli ori of replication

A

three conserved 13-bp sequence and at least four 9-bp sequences

56
Q

what eukaryotic creature has the most fully characterized origin of replication

A

saccharomyces cerevisiae (yeast)

57
Q

what are the multiple origins of replication called

A

autonomously replicating sequences (ARS)

58
Q

what is the consensus sequence of yeast ARS

A

3 15 bp sequence and 1 11 bp sequence also rich in A T

59
Q

what proteins are needed to form the initial replication bubble

A

DnaA
DnaB
DnaC

60
Q

what is dna A

A

dna binding protein. it binds to the 9-mer sequence wrapping dna at oriC into a complex that leads to destabilixation and breaking of hydrogen bonds holding two dna strands together in the A-T rich sequences of the 13-mer region

61
Q

SSB

A

single stranded binding protein. bind to exposed single stranded dna to protect them against degradation and prevent them from REANNEALING

62
Q

what is Dna A and the dna wrapped aronud it with the open bubble next to it called

A

the open complex

63
Q

what stabilizes the open complex and allows it to unwind further

A

dnaB and dnaC copmlex

64
Q

what is dna B

A

a helicase

65
Q

what does dnaB do

A

uses ATP to break hydrogen bonds of complementary bases thereby seperating the strands of the double helix and unwinding dna further

66
Q

what does dnaC do

A

it carries dnaB to the dna helix

67
Q

what does hexomer mean

A

it has 6 identical subunits

68
Q

what is only required for the initiation of replication

A

DnaA and Dna C

69
Q

when is Dna B required

A

throughout the rest of the process of replication

70
Q

how many dnaB hexamers are in a circular chromosome

A

two, one on the leading strand of each replication fork

71
Q

what does the unwinding of circular chromosomes lead to

A

tortional stress

72
Q

what helps relieve tortional stress

A

topoisomerases

73
Q

what are topoisomerases

A

they relieve superhelixal stress and prevent overwinding. they catalyze controlled cleavage and rejoining of dna.

74
Q

when are topoisomerases required

A

throughout the whole process of dna replication process

75
Q

when are ssb required

A

throughotu the whole process of dna replication

76
Q

what end does dna polymerase add nucelotides to the previous nucleotide

A

the 3’ end of the pre existing or primer

77
Q

difference between dna polymerase and rna polymerase

A

dna polymerase needs a primer to add onto and rna polymerase can initiate rna strand synthesis on its own

78
Q

what is the rna polymerase that is used alongside dna polymerase

A

primase

79
Q

how often are primases needed

A

only once for the leading strand but there has to be one constantly there for the lagging strand

80
Q

example of dna directed dna polymerase

A

dna polymerase

81
Q

how many different dna polymerases does e coli have

A

five

82
Q

are all the different types of dna polymerase there for ecoli at the same time

A

no

83
Q

what type of dna polymerase synthesizes dna strands in e coli

A

dna polumerase III (pol III)

84
Q

function of polymerase I

A

repair enzyme
excise and replace mismatch nuceotides
fill gaps

85
Q

function of polymerase II

A

repair enzyme

86
Q

function of polymerase III

A

major dna replicase involved in replicating the bacterial genome

87
Q

function of pol IV and pol V

A

repair functions in the SOS resposne when major damage occurs

88
Q

what is the downside of pol IV and V

A

they are error prone

89
Q

what eukaryotic polymerase is similar to pol I

A

pol a

90
Q

function of pol a

A

similar to pol I. associates with primase and adds initial primer for dna replication. carries out synthesis of rna primers

91
Q

function of pol g

A

probably the major replicase for lagging strand

92
Q

function of pol E

A

probably the major replication for leading strand

93
Q

function of pol gamma

A

found only in mitocondria. mitochondiral dna replicase

94
Q

what does the copying for daughter strands in bacteria

A

dna pol III holoenzyme

95
Q

holoenzyme

A

muliprotein complex in which a core enzyme subunit is associated with additional components/ subunits that are needed for the full function of the enzyme

96
Q

how many copies of dna pol III in the replisome at each replication fork

A

two or maybe three

97
Q

what direction do dna pol III work in

A

the one working on the leading strand works in the same direction as the replication fork
the one working on the lagging strand works in the opposite direction of the replication fork

98
Q

what removes the primers and fills the gaps in e coli

A

dna pol I

99
Q

what is the first dna polymerase to be purified

A

dna pol I

100
Q

why was dna pol I decided not to be the principal replicase

A

becasue it was too slow

too plentiful

101
Q

how many enzymes are in dna pol I

A

three enzymes

102
Q

what direction does dna Pol I work in

A

5’-3’ EXONUCLEASE to remove rna primers

5’-3’ POLYMERASE activity to fill the gaps

103
Q

which end of a molecule do exonucleases difest a nucleic acid from

A

the end of the molecule

104
Q

what are exonucleases

A

enzymes that digest a nucleic acid from the end of the molecule

105
Q

where can exonucleases be active

A

on ssDNA and or dsDNA and can also act on rna. they can be 3’-5’ or 5’-3’ or bidirectional

106
Q

what does the 5’-3’ exonuclease activity of dna pol I remove

A

rna primers

107
Q

what does the 5’-3’ polymerase activity of dna pol I do

A

simultaneously adds deoxynucleotides to the 3’ end of the dna segment preceding the rna primer thereby filling the gaps

108
Q

what does dna ligase do

A

seals the gap between the dna segments ( catalyzes phosphodiester bond bw two nucelotides)

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