Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Biochemistry 2 > DNA replication > Flashcards

DNA replication Flashcards

1
Q

what kind of cells undergo DNA replication

A

somatic cells (non germ cells)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

basis for evolution

A

DNA is subject to changes that permit genetic differences

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

difference in DNA strands

A

polarity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

DNA replication overview

A

strand separation followed by copying each strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

semi-conservative replication

A

strands separate, 1 parent, 1 daughter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

what direction does DNA replication occur in

A

bidirectionally

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

where does DNA replication begin

A

at origins of replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

unwinding at double helix

A

1) helicases use ATP hydrolysis to separate strands (melt H bonds in btwn strands)
2) DNA gyrase creates negative supercoiling to overcome torsional stress that occurs during strand separation
3) single-stranded binding protein (SSB) binds to ssDNA so it doesn’t reanneal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

DNAB helicase

A

binds to lagging strand

helicase in bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

topoisomerases

A

in euks = gyrases in bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

where are gyrases located?

A

ahead of replication fork

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

semi-discontinuous replication

A

Leading strand: continuous replication

Lagging strand: discontinuous replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

in which direction do DNA polymerases move

A

3’ to 5’

so since lagging strand is opened 5’ to 3’, there is slower replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q 
summary
DNA gyrase
DnaB
DNA pol III holoenzyme
DNA pol I
A

DNA gyrase = unwinding DNA
DnaB = 5’ to 3’ helicase (DNA unwinding)
DNA polymerase III holoenzyme = elongation (DNA synthesis)
DNA polymerase I = excises RNA primer, fills in with DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

DNA pol requires

A

all 4 dNTPs = substrate to make nucleotides
a template strand = substrate to catalyze next phosphodiester bond
primer = needed bc DNApol can’t start a new strand, only elongate one that already exists

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

what enzyme adds the primer to template strands

A

primase adds a short string of RNA nucleotides complementary to DNA template

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

processivity

A

ability of DNA pol to stay associated with DNA template (how many new phosphodiester bonds it can form)
different DNA pols have diff processivities

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

how do we pick the new bases

A

DNA pol uses base-pairing
new chain grows in 5’ to 3’
DNA pol can’t initiate a DNA strand, a 3’ OH is required

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

DNA pol 3’ to 5’ exonuclease activity

A

“proofreading”
If DNApol figures out it added the wrong base before it adds the next one, it can have 3’ to 5’ exonuclease activity to remove the wrong base
uses a couple ATP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

polymerase catalytic sites

A

1) polymerase site (makes new phosphodiester bond) 2) 3’ to 5’ exonuclease hydrolysis site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

DNA pol II and II (E. coli)

A

3’ to 5’ exonuclease activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

DNA pol I (E. coli)

A

3’ to 5’ and 5’ to 3’ exonuclease activity

it can remove and replace nucleotides concurrently

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

E.coli DNApol

A

pol I, II and IV involved in DNA repair
pol I also helps with replication
DNA pol III is the replicating enzyme

24
Q

DNA pol structure

A

claw shape
Fingers (alpha helices): recognizes dNTPs
Thumb: DNA binding
Palm: contains the polymerase active site

25
WHY DNA POL ONLY WORK IN 5’ TO 3’ DIRECTION?
Release of pyrophosphate provides energy to form new bonds The pyrophosphate is released from the template strand (from incoming dNTP) when we go 5’ to 3’ → if a mistake is made, we lose a dNTP, but we have tons around If dna pol went other way, pyrophosphate would come from growing strand If a mistake → energy is spent and we couldn’t repair bc we lost energy Once phosphodiester bond is made, we don’t have energy for repair
26
WHY DO WE NEED AN RNA PRIMASE TO MAKE PRIMERS?
RNA polymerases can bind 2 nucleotides at the same time and can make phosphodiester bond between 2 NTPs DNA polymerases can’t start a strand
27
DNA pol III
multi-subunit holoenzyme core: alpha, epsilon, theta other key subunits: tau, beta, gamma, delta, delta'
28
DNA pol III beta
Beta is sliding clamp that surrounds DNA and holds core enzyme onto ssDNA Responsible for high processivity of DNA pol III
29
DNA pol III core enzyme function
exonuclease and polymerase activity alpha, epsilon, theta synthesizes lagging strand
30
gamma complex
made of one gamma, one delta, one delta prime clamp loader loads beta clamp onto DNA (uses ATP hydrolysis for energy to assemble a pair of beta subunits on to each DNA strand at replication fork)
31
tau complex
holds 2 cores together
32
how is DNA pol III removed
core polymerase synthesizing lagging strand must be released at end of each Okazaki fragment beta-clamp is released by tau and is reloaded using gamma complex onto next Okazaki fragment
33
2-beta subunits =
beta clamp
34
DNA pol III at replication fork
both strands copied at same time (coordinated by presence of 2 DNA pol II complexes at replication fork DnaB also associates with these complexes
35
in which direction do both strands elongate
5' to 3'
36
DNA ligase
seals gaps between Okazaki fragments
37
Tus proteins
required for termination of DNA replication
38
starting and stopping DNA replication in E. coli
opposite or origin (ori) is terminator (ter) sites) ori is AT rich terminator sites binds to Tus proteins Tus proteins block replication in one direction (each set (group 1 or 2) blocks in one direction) terminator = replication machinery releases template strand
39
replicons
replication factories DNA pols are in fixed locations (attached to a membrane) DNA is fed through polymerases new and parent strands emerge from factories as loops
40
DNA replication in euks
Occurs only during discrete phase of the cell cycle (S for synthesis) Progression through the cell cycle is regulated by cyclins and CDKs Cyclins are produced in a phase-specific manner Cyclins activate CDKs that stimulate phase specific events
41
which phase must DNA replication occur in?
S phase ONLY
42
origins of replication in genome
Multiple origins of replication in the genome Each replication origin fires only once per cell cycle Licensing occurs in G1, activation occurs in S
43
licensing of DNA replication
requires assembly of pre-replication complexes at each origin of replication (late M or early G1) ORC binds each origin ORC recruits Cdc6p, Cdt1, and MCMs (one is a helicase)
44
with start of S-phase,
S-cyclin binds to its CDK and activates kinase activity S-CDK phosphorylates its targets phosphorylation of MCM proteins activate helicase and recruits Cdc45 and a primase
45
how many replication forks?
2: bidirectional replication
46
cyclin licensing: when is it bad?
we need to prevent cyclins from being licensed again in S phase (this would cause another round of replication) Geminin: prevents licensing in S phase
47
Geminin
targets MCM proteins and prevents and prevents them from binding to ORC Geminin degrades in M phase
48
DNA pol alpha
has primase subunits | RNA + DNA
49
PCNA
analogous to beta clamp in bacteria It is made of 3 subunits instead of 2, but serves the same function Replication factor C (RFC) loads the PCNA clamp onto replicating DNA RFC is analogous to gamma clamp loader
50
end replication problem
DNA pol requires a 3’ OH on the previous nucleotide to extend the strand following excision of RNA primers At the extreme ends of each strand, no such 3’ OH exists Once RNA primers are removed, there’s no 3’ OH The RNA primers at the 5’ ends of each newly synthesized strand CANNOT be replaced by DNA bc DNAP can only extend a strand
51
what happens with each round of replication
Anytime somatic cells replicate, they lose a bit of DNA Telomeres help protect ends Telomerase builds telomeres
52
telomeres
GC rich repeat sequences | telomerase replicates telomeres and contains enzyme called TERT and RNA template
53
why do we need telomeres
at end of replication, RNA primers are removed and must be replaced with DNA this leaves a gap at extreme 5' end of each strand telomerase uses RNA template which hybridizes with end of completed strand this provides template to extend 3' end of top strand bottom strand is then synthesized
54
reverse transcriptase (RT)
makes DNA using ssRNA as a template Primer is dNTP from host that binds with ssRNA → forms helix with 1 ssRNA and 1 ssDNA RNase H takes RNA out and leaves us with ssDNA AIDS drugs are nucleotide analogs that block RTase activity
55
telomeres are rich in
GC | sequence depends on species
56
why do we need TERT?
DNA polymerase can’t extend both ends bc it requires DNA as a template TERT uses RNA as a template

Biochemistry 2 (32 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions