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Molecular 3rd year > Chpt 5: DNA replication > Flashcards

Chpt 5: DNA replication Flashcards

1
Q

what is a mutation rate

A

the rate at which changes occur in DNA sequences

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2
Q

are the amount of damaged genes a good indicator of the amount of mutations

A
  • no
  • many mutations are silent
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3
Q

why are the number of essential genes limited

A

if you have too many, the chances of there being a mutation in an essential gene is catastrophically high

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4
Q

what are the 2 types of cells in a sexually reproducing plant/ animal

A
  • germ transmits genetic info from parent to kid
  • somatic forms the body of the organism
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5
Q

what is DNA templating

A

the mechanism the cell uses to copy the nucleotide sequence of one DNA strand into a complementary DNA sequence

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6
Q

what is the fundamental reaction by which DNA is synthesized

A

the addition of a deoxyribonucleoside triphosphate to the 3’ end of a polynucleotide chain

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7
Q

is the DNA replication fork symmetrical

A

no

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8
Q

what direction is DNA synthesized in

A

5’ to 3’

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9
Q

what forms of proofreading are available

A
  • DNA polymerase
  • exonucleolytic proofreading
  • strand-direted mismatch repair
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10
Q

describe how DNA polymerase proofreading works

A
  • after complementary nucleotide binding, but before covalently bonding it
  • polymerase must go under a conformational change where it tightens around the active site
  • this is harder to do when the wrong bases are paired together
  • therefore more likely to diffuse away before the polymerase can mistakenly add them
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11
Q

why does DNA replication occur only in the 5’ to 3’ direction

A

the need for accuracy (if it went from 3’ to 5’, the 5’ side would need to have the energy-full bond to supply the reaction w energy, buuut then any mistakes couldn’t be hydrolyzed away, cause the bare 5’ end would immediately stop the DNA synthesis)

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12
Q

where does the energy for the polymerization reaction that occurs during DNA replication come from

A

the hydrolysis of high-energy phosphate bond in the incoming nucleoside triphosphate and the release of pyrophosphate

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13
Q

how does DNA polymerase catalyse the reaction that occurs during DNA replication

A

it positions the incoming nuceloside triphosphate to the template strand

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14
Q

does the leading or lagging strand have more primers

A

lagging

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15
Q

what makes the RNA primers

A

DNA primase

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16
Q

describe the process by which the lagging strand works

A
  • RNA primer is synthesized by primase
  • DNA polymerase adds nucleotides to 3’ end of RNA primer
  • DNA polymerase finishes okazaki fragment
  • previous RNA primer removed by nucleases and replaced w DNA by repair DNA polymerase
  • nick sealed by DNA ligase
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17
Q

which proteins are needed to open the double helix and present an appropriate single-stranded DNA template for polymerase to copy

A
  • DNA helicases
  • DNA-binding proteins
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18
Q

what do DNA helicases do and how

A
  • prys apart the DNA strands
  • by hydrolyzing ATP, which then changes the shape of a protein
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19
Q

what do single-strand DNA binding proteins do and how

A
  • straightens out the regions of single stranded DNA
  • binds tightly and cooperatively (idk thats all it says)
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20
Q

what holds moving DNA polymerase onto the DNA

A
  • a sliding ring
  • called PCNA
  • keeps polymerase on DNA, until it reaches a double-stranded portion
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21
Q

describe how DNA polymerase attaches to DNA

A
  • a clamp loader binds to a sliding clamp using ATP
  • this opens up the ring shape of the sliding clamp
  • the open clamp moves onto DNA
  • ATP hydrolysis locks sliding clamp around DNA and releases the clamp loader
  • DNA polymerase binds to the sliding clamp
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22
Q

describe the difference in the clamp loader on leading vs lagging strand

A
  • leading clamp and polymerase remain attached for a long time
  • lagging they dissociate every time the polymerase reaches the 5’ end of the preceding Okazaki fragment. it will then associate w a new clamp at the next primer
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23
Q

are all the proteins indepedent

A

nope, most of the time theyre acc in a big complex together

24
Q

is DNA replication similar in eukaryotes and bacteria

A

fundamentally yes

25
Q

how is DNA replication different in bacteria and eukaryotes

A
  • eukaryotes have 3 kinds of DNA polymerase used at the replication fork
  • diff detailed structures of their individual protein components (almost completely diff AA sequences)
26
Q

what are the different polymerases in DNA and how do they differ

A
  • Polε: synthesizes the leading strand, can bind to both sliding clamp and replicative helicate (allowing it to synthesize long stretches of DNA without dissociating)
  • Polα and Polδ: synthesize the lagging strand, Polα includes DNA primase as one of its subunits, which is needed more w the lagging strand but can’t add as much bases before dissociating…. Polδ with a sliding clamp can add more nucleotides to finish off the job
27
Q

what do mutator genes do

A

greatly increase the rate of spontaneous mutations

28
Q

describe how strand-directed mismatch repair in eukaryotes work

A
  • MutS protein recognizes and locks onto DNA mismatch
  • MutS recruits MutL and scans DNA
  • sliding clamp is rencountered, MutL nuclease is activated and initiates strand removal
  • strand is removed, and repair DNA synthesis by polymerase δ
29
Q

what happens if RNA is encorporated into DNA

A
  • it weakens the DNA chain at that point, rendering it highly susceptible to breakage
  • this can lead to high mutation rates and genome rearrangements if left unrepaired
30
Q

what prevents DNA tangling during replication

A

DNA topoisomerases

31
Q

how does DNA topoisomerase I work

A
  • produces a transient single-strand break
  • this break in the phosphodiester backbone allows the 2 sections of DNA helix on either end to rotate freely
32
Q

how does DNA topoisomerase II work

A
  • forms a covalent linkage to both strands of the DNA helix at the same time (a transient double-strand break)
  • breaks one double helix reversibly to create a DNA “gate”
  • causes the second, nearby double ehlix to pass through this opening
  • it then reseals the break and dissociates from the DNA
33
Q

what is the shape of a replication fork

A

Y

34
Q

the DNA replication process is started with which special proteins

A

special initiator ptoreins

35
Q

the positions at which the DNA helix is first opened are called what

A

replication origins

36
Q

roughly how long are replication origins

A

several hundred nucleotide pairs long

37
Q

do bacterial chromosomes have one or more replication origins

A

one

38
Q

when can e coli control DNA replication

A

only at initiation (so this is highly regulated)

39
Q

what is the other name for DNA topoisomerase II

A

DNA gyrase

40
Q

how many DNA polymerases are in a bacterial replication fork

A

2: one on leading and one on lagging

41
Q

what are 3 bacterial replication proteins

A
  • initiator protein: DnaA
  • helicase: DnaB
  • primase: DnaG
42
Q

how does exonucleolytic proofreading by DNA polymerase work

A
  • When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA and excises the mismatched base
  • then dna polymerase can keep doing its thing
43
Q

what does DnaA do

A

binds to specific sequences at oriC

44
Q

what does DnaB do

A
  • 2 helicases brought in by helicase loading proteins (DnaC proteins)
  • inhibit the helicases until they are properly loaded at oriC
45
Q

what does DnaG do

A

synthesizes initial primers

46
Q

when does DNA replication take place in eukaryotes

A
  • only at one part of the cell cycle
  • must be coordinated w mitosis and the cell cyle
47
Q

does eukaryotic DNA shorten after each replication and why

A
  • yes
  • cause when the final primer is removed, there is a section of template that remains unreplicated
  • but this is okay cause telomeres exist
48
Q

what replicates the ends of chromosomes

A

telomerase

49
Q

does bacteria DNA shorten after each replication and why

A
  • no
  • cause its a circle so there is no “end” to the dna
50
Q

what is the 5’ end

A
51
Q

what is the 3’ end

A
52
Q

what does telomerase do

A

replicates the ends of chromosomes

53
Q

describe how telomerase replicates the ends of chromosomes

A
  • telomerase binds
  • using its RNA component as the template, it adds 2 more repeats to the 3’ end of DNA
  • this is done via reverse transcription by telomerase to produce DNA from RNA template
  • DNA polymerase can then complimentary bp to it
54
Q

what is the point of a t-loop

A

to provide additional protection for the ends of chromosomes

55
Q

how do t-loops form

A

by inserting the ends of the chromosome, which is usually 3’ overhang back into the DNA of the chromosome

56
Q
A

Molecular 3rd year (9 decks)

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