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BIOL 200 > PL1 > Flashcards

PL1 Flashcards

1
Q

how old is DNA

A

about 4 billion years old (ribosomal genes)
information storage has always been an issue in history - DNA is very stable and good for info storage

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2
Q

what happens when a cell divides

A

information stored in DNA is copied (replicated)

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3
Q

describe the main principles of what watson and crick thought

A

base pairs in center have strict pairing rules
if 2 strands come apart newly synthesized strand binds with it
contains all the info to make (replicate) the sequence

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4
Q

during replication what happens to double helix

A

denatures
each parental strand is used as template for formation of a new daughter strand (complementary to parental strand)

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5
Q

when DNA replication starts what happens (can it start from scratch)

A

DNA polymerases are enzymes that add to growing DNA strand - cannot start from
scratch, need a primer (short sequence oligonucleotide of double helix DNA being generated and elongated)
RNA can start from scratch tho - no primer needed

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6
Q

describe reaction of DNA replication

A

alpha phosphate group in incoming deoxy nucleotide triphosphate (dNTP) reacts with 3’ OH in growing DNA chain
5’ to 3’ direction - phosphate cannot attack a phosphate
pyrophosphates break down (provide energy) and phosphate bonds (reaction favoured)

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7
Q

where are the incoming dNTPs from

A

pools of dNTPs

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8
Q

how many proteins does DNA replication require

A

involves cooperation among multiple proteins

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9
Q

what is DNA helicase

A

unwinds duplex DNA
2 strands must come apart at place where replication is happening
allows DNA polymerases to work

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10
Q

what is replication fork

A

place where replication is actively happening
fork = 2 strands come apart

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11
Q

what is topoisomerase

A

relieves supercoils
the denatured DNA spreading puts torsional strain on the part (that isn’t denatured yet)
topoisomerase makes local cut and puts it back together to relieve supercoils

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12
Q

what forms primer

A

primase - specialized RNA polymerase
forms short molecule complementary to a single stranded region of the unwound duplex DNA
DNA polymerase can then extend and form
new daughter duplex DNA

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13
Q

what is direction of DNA synthesis

A

5’ to 3’
due to nature of chemical reaction

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14
Q

what is replication origin rich in

A

usually A-T rich

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15
Q

describe leading strand

A

new strand synthesized in continuous motion
only one primer

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16
Q

describe lagging strand

A

must form at various places
short stretches of DNA replication
many primers
must keep 5’ to 3’ direction
formed in opposite direction of the movement of replication fork

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17
Q

the 2 duplex DNA strands are…

A

antiparallel

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18
Q

what are okazaki fragments

A

little fragments
short discontinuous fragments consisting of RNA and DNA

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19
Q

describe informally - how okazaki fragments are joined (process)

A

starts with RNA primer and stretch of DNA
then RNA is digested then DNA is synthesized and fills in gaps
DNA ligases joins them and forms a continuous long strand

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20
Q

what happens to RNA component of okazaki fragments

A

replaced by DNA and the two adjoining DNA molecules are ligated together by DNA ligase

21
Q

what is the replisome

A

molecular machine involved in DNA replication

22
Q

how did we find out so much about DNA replication

A

studied using prokaryotes ( e. coli, viruses like SV40) and from yeast
viruses replicate like crazy and use almost the same mechanisms as our DNA replication

23
Q

describe the large complex of proteins that we will be dissecting to understand DNA replication

A

the replisome at the the SV40 replication fork

24
Q

describe large T antigen

A

hexamer (6 polypeptides)
helicase (unwinds DNA)
encoded by viral genome
unwinds double helix at replication fork (single replication origin in virus)

25
Q

describe replication protein A (RPA)

A

binds single stranded DNA
keeps single stranded DNA template in optimal conformation for DNA polymerase
important for accuracy
stabilizes single stranded DNA

26
Q

describe DNA polymerase epsilon

A

carries out leading strand DNA synthesis

27
Q

what is PCNA

A

homotrimer protein
like a collar - wraps around complex with DNA polymerase and prevents it from falling off
prevents pol epsilon or delta from dissociating from template

28
Q

describe primase/polymerase alpha

A

primase forms RNA component of the primer
and DNA pol alpha extended the primer with DNA (recognizes RNA polymerase)

29
Q

describe pol delta / Rfc / PCNA complex

A

replaces the pol alpha/primase complex and complete synthesis of okazaki fragment

30
Q

describe Rfc/PCNA complex

A

RFC is the PCNA loader
open PCNA ring and loads it at a primer on DNA

31
Q

what takes over replication after pol alpha for leading and lagging strand

A

leading = pol epsilon
lagging = pol delta takes over

32
Q

describe role of ribonuclease H and FEN 1
and subsequent steps

A

ribonuclease H (chops up primers) and FEN-1 displace the RNA component at the 5’ ends of okazaki fragments
pol delta replaces RNA with DNA
DNA fragments ligated together by DNA ligase

33
Q

describe origins of replication

A

unwinding of DNA is initiated at specific regions in duplex DNA = replication origins

34
Q

why are replication origins A-T rich

A

since A T base pairs take less energy to take a part since only 2 H bonds and not 3 like C-G base pairs

35
Q

name the steps of DNA replication

A

loading of replisome at the reapplication origin
unwinding
primer synthesis
extension
further unwinding
further extension
lagging strand primer synthesis
primer extension, primer removable and strand ligation

36
Q

is DNA replication conservative

A

it’s SEMIconservative
each progeny has 1 strand of DNA from parent

37
Q

DNA replication from replication origins is…

A

bidirectional

38
Q

describe loading of replisome at replication origin

A

helicases attracted to origin
double helix denatured and each strand is template
leading strand primer synthesis

39
Q

describe unwinding

A

catalyzed by large T antigen (helicase) driven by hydrolysis of ATP
RPA binds and stabilizes single stranded region (optimal for DNA polymerase to interact with)

40
Q

describe primer synthesis

A

primase-pol alpha complexes synthesize primer sequences that are base paired to the parental templates

41
Q

describe extension

A

pol epsilon /RFC/PCNA complexes replaces primase-pol alpha complexes and extended primer sequences
both leading strands are being synthesized

42
Q

describe further unwinding

A

further unwinding and binding of RPA to single stranded regions
bidirectionalllll

43
Q

describe further extension

A

pol epsilon Rfc PCNA complexes continues to synthesize leading strands
now lagging strand synthesis has to start

44
Q

describe lagging strand primer synthesis

A

primase pol alpha complexes form primers for
lagging strand synthesis

45
Q

describe what pol delta Rfc PCNA complexes do after the primer is synthesized

A

replace primase-pol alpha complexes and extend primer sequence

46
Q

what removes the primers

A

preformed by FEN-1 and ribonuclease H

47
Q

what replaces the primer sequences with DNA

A

pol delta / Rfc / PCNA complexes

48
Q

what puts together strands of DNA - okazaki fragments

A

strands are ligated together by DNA ligase

BIOL 200 (29 decks)

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