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MBG* 2040 Pt. 2 > DNA Replication > Flashcards

DNA Replication Flashcards

1
Q

How many base pairs per turn DNA

A

10
And 0.34nm btw bases, so 3.4nm per helical turn

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2
Q

Semiconservative

A

Watson crock model
After one round of dna replication, each dna contains 1 parental and one newly synthesized strand

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3
Q

Modes of dna replication

A

1) theta replication
2) rolling circle replication
3) linear chromosome replication

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4
Q

Theta replication

A

Can be either bidirectional or unidirectional
Double stranded dna unwinds at the replication origin, producing single stranded templates for synthesis
- a replication bubble forms, usually with replication fork at each end
- the forks proceed around the circle
- products = two circular DNA mlc

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5
Q

Rolling circle replication

A

Specialized form of replication that occurs in the f factor of E. coli and some viruses
Only one origin of replication
Unidirectional
Replication is initiated by break in one of the nucleotide strands
- dna synth this begins at the 3 prime end of broken strand
The inner strand is used as a template
Cleavage releases a single-stranded linear DNA and a double stranded circular DNA
The linear guy can circularize and serve as a template for synthesis

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6
Q

Linear chromosome replication

A

Mode of dna replication in eukaryotes
Occurs in the linear chromosomes of eukaryotic cells
Is bidirectional
Each chromosome contains numerous origins of replication
At each origin, DNA unwinds, producing a replication bubble
- dna synthesis takes place on both strands at each end of the bubble as the replication fork proceeds outward
- eventually the forks from adjacent bubbles run into eachother and the segments of dna fuse
Produces 2 linear identical dna mlcs

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7
Q

What does dna replication require

A
  • dna dependent dna polymerase
  • four deoxyribonucleoside triphosphates (dNTPs)
  • a single stranded template of DNA to be copied
  • an RNA primer
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8
Q

What does RNA primer provide

A

A 3’ end to initiate dna synthesis by dna polymerase

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9
Q

What direction is dna always synthesized

A

5’ to 3’
It is always complementary and antiparallel to the parent strand

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10
Q

dNTP

A

Deoxyribonucleoside triphosphates
(ANTP, gNTP, cNTP and tNTP)
Have the base and sugar (deoxynucleoside) as well as three phosphates
Two phosphates are cleaved off when the chain is growing

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11
Q

What interactions take place to synthesize the new strand

A

The 3’OH group of last nucleotide on the new strand being made reacts with the 5’ phosphate group of the incoming dNTP
Two phosphates are cleaved off
A phosphodiester bod forms between the two nucleotides

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12
Q

What are Okazaki fragments

A

They are the short fragments formed when the lagging strand is synthesized

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13
Q

What are longer, Okazaki fragments in prokaryotes or eukaryotes

A

Prokaryotes
(1-2kbases)

In eaukatyotes, they are shorter (just 0.1-0.2 kbases

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14
Q

Where does dna replication start in all three modes

A

An origin of replication

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15
Q

oriC

A

Replication origin in bacteria
215 base pairs in length
Contains 4 DnaA binding sites
AT rich

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16
Q

What kind of proteins bind to the oriC

A

So obviously this is talking about prokaryotic dna replication

DnA proteins- initiator proteins that bind to oriC and cause a short stretch of DNA to unwind

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17
Q

DnaA

A

For prokaryotic dna replication
Binds to oriC
Can bind to double stranded dna
Causes stretch of dna to unwind
This allows helicase and other ssbs to attach to single stranded dna

18
Q

Helicase in prokaryotes

A

Only binds to single stranded dna
Disrupts hydrogen bonding btw complementary base pairs
Unwinds dna in 5’ to 3’ direction
Travels on the lagging strand only in prokaryotes, ahead of replication machinery

19
Q

SSBs

A

Single stranded binding proteins
Unwound single stranded dna is coated with them
They keep dna single stranded and avoid hairpins

20
Q

DNA gyrase

A

To Pom erase that makes double stranded breaks in the dna to relieve the torsinal strain that builds up from the activity of the dna helicase

21
Q

Primase

A

Aka rna polymerase
Synthesizes a short rna primer (10-12 nucleotides)
That provides the 3’ OH end for DNA synthesis
- binds to the helicase to initiate synthesis

22
Q

Where is primase required on leading and lagging strands

A

On leading strand, it’s required only at 5’ end of newly synthesized strand
On lagging strand, a new primer must be generated at the beginning of each okazaki fragment

23
Q

DNA polymerase projaryotes

A

Elongates new polynucleotide strand by catalyzing DNA polymerization
Requires a primer
In e. Coli there are 5 different dna polymerases

24
Q

DNA polymerase III

A

Main dna polymerase
Has 5’ to 3’ polymerase activity
Has 3’ to 5’ exonuclease activity
This means it adds a dNTP to the 3’ end but can also back up to remove a nucleotide that has been misincorporated

25
Q

Dna polymerase 1

A

Similar to dna pol III but it also has 5’ to 3’ exonuclease activity so it’s able to travel forward and remove the rna primer and replace it with dna
It does not extend the leading strand

26
Q

What happens when dna pol III reaches the 5’ end of the RNA primer?

A

It is subbed out for DNA pol I (with 5’ to 3’ exonuclease activity) which means it can remove the RNA primer and replace it with short strand DNA
Then dna ligase comes in and makes a phosphodiester bond between the 5’ phosphate group and the 3’ OH group
Okazaki fragments are thus joined together to make continuous length of dna

27
Q

Dna ligase

A

Seals the nick with a phosphodiester bond between the 5’ phosphate group of the initial nucleotide added by DNA polymerase III and the 3’OH group of the final nucleotide added by DNA pol 1

28
Q

Helicase in eukaryotes

A

Binds to double stranded dna
Involves the MCM complex of proteins

29
Q

Where does dna replication begin in eukaryotes

A

At autonomously replicating sequences (poorly understood, but generally AT rich)
Bidirectional replication

30
Q

When does dna replication occur in eukaryotes

A

During S phase of the cell cycle
(Part of interphase)

31
Q

What is the difference in length of rna primers and Okazaki fragments btw eukaryotes and prokaryotes

A

Shorter Okazaki fragments and rna primers in eukaryotes than prokaryotes

32
Q

How many dna polymerases in prokaryotes vs eukaryotes

A

Prokaryotes have 5 whereas eukaryotes have many (over 15)

33
Q

What are the three main polymerases in eukaryotes that we discussed

A

Polymerase alpha
Polymerase epsilon
And polymerase delta

34
Q

Polymerase alpha

A

Is a polymerase in eukaryotes that generates RNA primers

35
Q

Polymerase epsilon

A

Performs leading strand replication

36
Q

Polymerase delta

A

Performs lagging strand replication

37
Q

What is a key difference / additional step that needs to happen in eukaryotic dna replication

A

Nucleosomes (two each of histones H2A, H2B, H3, H4, plus H1) need to be removed from parental dna and properly reassembled on newly synthesized dna

38
Q

What is the Nucleosome problem in eukaryotes

A

Eucaryotic DNA is complex with nucleosome‘s that are modified when DNA is doubled.
The histones also need to be doubled during replication parental is stones are partially disassembled, and recycled. New histones are produced
and result in new nucleosome‘s consisting of both new and old histones.

39
Q

What are the 5 steps in histone doubling

A
  1. Chromatin disassembly
  2. Parental histone recycling
  3. New histone provision
  4. Nucleosome assembly
  5. Chromatin restoration
40
Q

What’s the end replication problem in eukaryotes

A

Telomeres/the ends of chromosomes shorten over time

41
Q

Telomerase

A

Enzyme who’s activity extends eukaryotic chromosome ends in replicating cells
The rna part of telomerase is complementary to the Grich strand and pairs with it, providing a template for the synthesis of copies of the repeats
Nucleotides are added to the 3’ end of the G rich strand
It does this without using a complementary dna template
Gap remains, but this does not matter bc the end of the chromosome is extended at each replication

42
Q

Which cells is telomerase most present

A

In highly dividing somatic and germ cells
Least present in slowly dividing cells, where lack of telomerase will result in shortening of telomeres over time

MBG* 2040 Pt. 2 (9 decks)

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