Exam 2: DNA & Replication Flashcards Preview

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Flashcards in Exam 2: DNA & Replication Deck (38)
1

3 parts of a nucleotide

sugar

phosphate

nitrogenous base

2

complementary base pairs

A---T with 2 bonds

G---C with 3 bonds

3

what is needed to make dsDNA

antiparallel strands with complementary base pairs

4

what stabilizes dsDNA

Mg2+ ions

5

Watson-Crick Model

2 antiparallel strands
right-handed double helix
phosphate backbones on the outside
h-bonding from the bases on the inside
complementary pairs
Mg2+ ions to stabilize helix backbone

6

in vitro

in glass (test tube)

7

in vivo

in life

8

DNA replication in vitro is a ____

cell free system

you only use chemicals

9

5 things needed for in vitro DNA replication

DNA nucleotides in triphosphate form

a ssDNA template strand

a DNA primer

DNA polymerase enzyme

Mg2+ ions

10

what happens in in vitro DNA replication

DNA polymerase binds at the 3' end of the primer

DNA polymerase extends the primer from 3' to 5'

5'---3'(primer)-DNA polymerase--->>
3'-----------template--------------------5'

11

what yields E for synthesis?

2 phosphates from the triphosphate nucleotides are lost in synthesis

12

Mg 2+

2 ions involved in each nucleotide addition (stabilization)

a cofactor of DNA polymerase

neutralizes charge repulsion of oxygens in DNA backbone

13

complications of in vivo DNA replication in E. coli

2 strands are wrapped around eachother and have to separate and replicate in opposite directions

unwinding can cause supercoiling

there is no primer when the two strands open up and separate

14

how many forks does in vivo DNA replication have?

two forks going in opposite directions at the same time

15

is there a primer in natural DNA replication?

no, there is a temporary short primer made of RNA

16

primase

an enzyme that makes short temporary primers from RNA

17

semidiscontinuous replication

differences in the way synthesis occours on the leading and lagging strand

18

the leading strand

is replicated continuously towards the fork

19

the lagging strand

is replicated discontinuously away from the fork

20

supercoil

when DNA unravels the strand uncoils and supercoils into loops

21

supercoils on short pieces of dsDNA

don't last long, they spin out

22

supercoils on long linear DNA or circular DNA

accumulate

23

should supercoils be removed?

yes they must in both replication and transcription

24

how are supercoils removed?

with the enzyme topoisomerase

25

topoisomerase

2 types (1 & 2)

enzymes that cut dsDNA either in one strand or 2 strands

26

topoisomerase 1

cuts dsDNA on 1 strand

1) nick
2) rotate
3) ligate

27

topoisomerase 2

cuts dsDNA on 2 strands

1) double-strand break
2) pass through
3) rejoin

28

okazaki fragments

created during discontinuous synthesis on the lagging strand

contains an RNA primer on 5' end and attached strand of ssDNA to 3' end

5'-RRRRDDDD,RRRRDDDD-3'

29

DNA polymerase 1

connects Okazaki fragments by removing RNA nucleotides one by one from right of nick

attaches DNA nucleotides to left of the nick

RRRRDDDD
D,RRRDDDD
DD,RRDDDD

30

3 major differences in DNA replication in eukaryokes

chromosomes

packaging of DNA

rate of replication

31

chromosomes in eukaryote DNA replication

long, linear, end in telomeres

telomerase enzyme needed to restore chromosome ends

32

in eukaryotes, replication starts at...

replicon origins/bubbles that extend and meet each other

early and late replicating areas are organized locally into replicon families

33

DNA packaging in eukaryotes

chromatin has nucleosome (spooled) structure

histone proteins for nucleosomes are synthesized

nucleosome cores are replicated dispersively-old and new are divided randomly into new strands

34

eukaryoke DNA replication rate

movement of forks is slower

rate is 2000-10000 bp/min

~ 10,000 origins in mammalian genome

300,000 bp/replicon

35

what end does the primer go on?

3'

36

semiconservative replication

in every dsDNA one strand is the parent of the other

37

ori

single origin of replication in circular chromosome of a bacterium like E. coli

38

where on E. coli does replication begin and end

begins at ori and ends on other side of circular chromosome where the forks meet