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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
how many DNA polymerases do cells have
more than one
26
are the new daughter chains synthesised in the same or opposite directions
in opposite
27
how many dna polymerases work on one chromosome at a time
two, one for leading strand and one for lagging strand
28
what is the solution for the dna polymerases going in different directions
reji okazaki came up with a solution: one strand is copied continuously while the other is copied bit by bit
29
what is nucleophilic displacement
movement of electrons from an electron rich enviroment to an electron poor enviroment
30
how much energy does it take to join a nucleoside monophosphate NMP to a polynucleotide chain
25 kj/mol or 6kcal/mol
31
what is teh net amount of energy in joining of dna
-29kj/mol or -6.8 kcal/mol
32
what is the place where dna replication start
ori-the origin of replication
33
how many origins of replication do bacteria have
1
34
how many origins of replication do eukaryotic chromosomes have
more than one
35
what is the replication intermediate called in circular chromosomes with a single origin of replication
the replication intermediate contains a bubble like the greek letter theta
36
what is the point where the dna polymerases meet halfway around circular cells
ter- terminus of replication
37
who reported the first evidence of bacterial origins of replication
john cairns
38
what did john cairns do in his experiment
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
39
what is autoradiography
detection of radioactively labelled molecules
40
did johns cairns show us that cells replicate bidirectionally
no the info he gave didnt specify the directionality because it was consistent with both unidirectional and bidirectional replication
41
who figured out that chromosomes copy bidirectionally
ray rodriguez
42
what was ray rodriguez's experiment
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)
43
what was the result of rays experiment
he saw two radioactively labelled regions meaning there is an origin and a plaec where they meet
44
what process showed us the eukaryotic chromosomes have multiple ori
autoradiographs
45
what is the dark part in the pulse chase diagram and what is the light part
dark is pulse and light is chase
46
why does rays experiment prove bidirectionality
because thre is symmtry on both sides of origins of replication showeing that replication is proceeding bidirectionally OUTWARD from each replication origin
47
how many base pairs seperate ori in eukaryotic genomes
40 000 to 50 000
48
how many ori do eukaryotic genomes have
more than ten thousand
49
repliosomes
complex protein aggregates involved in dna synthesis
50
where are dna strands seperated
where melting is facilitated
51
why do we have unique origins of replication
from a regulatory perspective, its better to have a unique ori where dna copying can start rather than allowing random unpredictable events
52
what is e coli origin of replication called
oriC
53
how many base pairs does the sequence of e coli replication contain
245 bp
54
what bases is the origin of replication of e coli cells rich in and why
A T because they have less bonds than G C
55
what are the conserved sequences in e coli ori of replication
three conserved 13-bp sequence and at least four 9-bp sequences
56
what eukaryotic creature has the most fully characterized origin of replication
saccharomyces cerevisiae (yeast)
57
what are the multiple origins of replication called
autonomously replicating sequences (ARS)
58
what is the consensus sequence of yeast ARS
3 15 bp sequence and 1 11 bp sequence also rich in A T
59
what proteins are needed to form the initial replication bubble
DnaA DnaB DnaC
60
what is dna 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
SSB
single stranded binding protein. bind to exposed single stranded dna to protect them against degradation and prevent them from REANNEALING
62
what is Dna A and the dna wrapped aronud it with the open bubble next to it called
the open complex
63
what stabilizes the open complex and allows it to unwind further
dnaB and dnaC copmlex
64
what is dna B
a helicase
65
what does dnaB do
uses ATP to break hydrogen bonds of complementary bases thereby seperating the strands of the double helix and unwinding dna further
66
what does dnaC do
it carries dnaB to the dna helix
67
what does hexomer mean
it has 6 identical subunits
68
what is only required for the initiation of replication
DnaA and Dna C
69
when is Dna B required
throughout the rest of the process of replication
70
how many dnaB hexamers are in a circular chromosome
two, one on the leading strand of each replication fork
71
what does the unwinding of circular chromosomes lead to
tortional stress
72
what helps relieve tortional stress
topoisomerases
73
what are topoisomerases
they relieve superhelixal stress and prevent overwinding. they catalyze controlled cleavage and rejoining of dna.
74
when are topoisomerases required
throughout the whole process of dna replication process
75
when are ssb required
throughotu the whole process of dna replication
76
what end does dna polymerase add nucelotides to the previous nucleotide
the 3' end of the pre existing or primer
77
difference between dna polymerase and rna polymerase
dna polymerase needs a primer to add onto and rna polymerase can initiate rna strand synthesis on its own
78
what is the rna polymerase that is used alongside dna polymerase
primase
79
how often are primases needed
only once for the leading strand but there has to be one constantly there for the lagging strand
80
example of dna directed dna polymerase
dna polymerase
81
how many different dna polymerases does e coli have
five
82
are all the different types of dna polymerase there for ecoli at the same time
no
83
what type of dna polymerase synthesizes dna strands in e coli
dna polumerase III (pol III)
84
function of polymerase I
repair enzyme excise and replace mismatch nuceotides fill gaps
85
function of polymerase II
repair enzyme
86
function of polymerase III
major dna replicase involved in replicating the bacterial genome
87
function of pol IV and pol V
repair functions in the SOS resposne when major damage occurs
88
what is the downside of pol IV and V
they are error prone
89
what eukaryotic polymerase is similar to pol I
pol a
90
function of pol a
similar to pol I. associates with primase and adds initial primer for dna replication. carries out synthesis of rna primers
91
function of pol g
probably the major replicase for lagging strand
92
function of pol E
probably the major replication for leading strand
93
function of pol gamma
found only in mitocondria. mitochondiral dna replicase
94
what does the copying for daughter strands in bacteria
dna pol III holoenzyme
95
holoenzyme
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
how many copies of dna pol III in the replisome at each replication fork
two or maybe three
97
what direction do dna pol III work in
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
what removes the primers and fills the gaps in e coli
dna pol I
99
what is the first dna polymerase to be purified
dna pol I
100
why was dna pol I decided not to be the principal replicase
becasue it was too slow | too plentiful
101
how many enzymes are in dna pol I
three enzymes
102
what direction does dna Pol I work in
5'-3' EXONUCLEASE to remove rna primers | 5'-3' POLYMERASE activity to fill the gaps
103
which end of a molecule do exonucleases difest a nucleic acid from
the end of the molecule
104
what are exonucleases
enzymes that digest a nucleic acid from the end of the molecule
105
where can exonucleases be active
on ssDNA and or dsDNA and can also act on rna. they can be 3'-5' or 5'-3' or bidirectional
106
what does the 5'-3' exonuclease activity of dna pol I remove
rna primers
107
what does the 5'-3' polymerase activity of dna pol I do
simultaneously adds deoxynucleotides to the 3' end of the dna segment preceding the rna primer thereby filling the gaps
108
what does dna ligase do
seals the gap between the dna segments ( catalyzes phosphodiester bond bw two nucelotides)

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