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Abnormal Amnio > Biochem - DNA Replication > Flashcards

Biochem - DNA Replication Flashcards

(48 cards)

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1
Q

Central Dogma

A

DNA —> RNA –> Protein

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2
Q

Central dogma for all organisms except…

A

some viruses

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3
Q

Significance of DNA replication

A

transmit genetic info to offspring, be performed with high fidelity, defects –> genetic instability –> mutations and disorders

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4
Q

Semiconservative DNA replication

A

parental strands are permanently separated

each forms a duplex molecule with the new complementary daughter strand

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5
Q

AT, GC H bonds

A

2 H bonds for A-T

3 H bonds for G-C

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6
Q

Substrates for DNA polymerases?

A

Deoxyribonucleoside triphosphates (dNTPs)

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7
Q

What actually gets added to the growing DNA chain?

A

dNMPs - processive process

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8
Q

How a dNTP –> dNMP and adds to the DNA chain

A

Incoming dNTP forms bp with complementary NT on parental strand
phosphodiester bond is formed
Pyrophosphate is released (PPi)
generates large energy change –> drives DNA synthesis

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9
Q

Type of bond made between incoming NT to the DNA chain

A

phosphodiester bond made between 5’ phosphate of incoming dNTP and free 3’ OH of the end of the chain
Bond is a 3’-5’ phosphodiester bond

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10
Q

Hydrolysis of PPi

A

PPi –> 2Pi generates a large energy change

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11
Q

DNA replication occurs in …

A

S phase of cell cycle in eukaryotic cells

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12
Q

oriC

A

origin of replication in E. coli

contains short AT rich sequences

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13
Q

Primosome

A

Protein complex that initiates DNA synthesis
Initiate unwinding of the duplex DNA
stabilize the DNA template single strands
initiate the synthesis of the RNA primers required for DNA synthesis

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14
Q

Primosome proteins?

A 
DnaA
DnaC
DnaB (Helicase)
SSB
DnaG (DNA primase)
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15
Q

DnaA

A

tetrameric DNA binding protein with specificity for oriC
Involved in directing other primosome proteins to the origin
ATP required for initial melting of AT region

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16
Q

DnaC

A

Helicase inhibitor that is required for loading DnaB onto the strand

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17
Q

DnaB

A

DNA helicase
further separates the duplex DNA
ATP is hydrolyzed

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18
Q

SSB

A

Single stranded DNA binding protein

Stabilized ssDNA

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19
Q

DnaG

A

DNA Primase

generates short RNA primers for DNA synthesis

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20
Q

Primosome binding process

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A 
DnaA binds to the replication origin
DnaB binds to the DNA
DnaB opens the helix and binds DnaG to form primosome
RNA primer synthesis
DNA polymerase can start first DNA chain
21
Q

Semidiscontinuous manner

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A

DNA has anti-parallel structure
DNA synthesis can only occur in 5–>3’ direction
Replication fork moves in 5–>3 for one strand but 3–>5 for the lagging strand

22
Q

Leading strand

Study These Flashcards
A

Synthesized continuously in 5–>3’ direction

Moves in same direction as fork

23
Q

Lagging strand

Study These Flashcards
A

Synthesized in opposite direction

Discontinuous DNA fragments must be joined together by DNA ligase

24
Q

Okazaki fragments

Study These Flashcards
A

discontinuous DNA fragments on the lagging strand

25
Replisome
elongation of DNA requires additional proteins
26
Replisome proteins
DNA polymerase DNA ligase - ATP hydrolysis Topoisomerases Sliding clamp
27
Sliding clamp
Made up of 2 halves Clamp loader places clamp on DNA in ATP dependent process Clamp keeps DNA pol to be processive
28
DNA ligase
seals nicks between DNA fragments Seals in 3'-->5' fashion ATP hydryolysis E. coli is NAD-dependent
29
E. coli DNA pol I
``` Monomeric 5-->3' elongation 3-->5' exonuclease proofreading 5-->3' exonuclease Remove RNA primers Replace RNA primers with DNA Slow, low processivity ```
30
E. coli DNA pol III
``` 5-->3' elongation 3-->5' exonuclease proofreading No 5-->3' exonuclease Recognizes RNA primers Fast, high processivity Major replicative polymerase ```
31
Termination of replication
replication forks meet in region with multiple copies of ter sequence Proteins bind and trap/arrest the fork by inhibiting DnaB
32
Why PPi --> 2Pi
If you keep taking out the product, then you can keep pushing the reaction to go forward
33
Why is eukaryotic DNA replication more complicated?
Size and organization of euk DNA Multiple origins of replication, many forks Primer removal (5-->3' exonuclease) is done by RNaseH
34
ORC in eukaryotes
Origin recognition complex - 6 proteins Analogous to DnaA Phosphorylation of ORC allows binding of proteins like primosome Onset of S phase - DNA pol alpha-primase binds to make it an active complex
35
DNA pol alpha
Nuclear Initiation, primase activity, synthesize 20nt 5-->3' polymerase No 3-->5' exonuclease
36
DNA pol beta
Nuclear DNA repair 5-->3' polymerase 3-->5' exonuclease
37
DNA pol delta
Nuclear Elongation - chromosomal DNA replication 5-->3' polymerase (highly processsive) 3-->5' exonuclease
38
DNA pol epsilon
Nuclear Elongation - chromosomal DNA replication 5-->3' polymerase (highly processive) 3-->5' exonuclease
39
DNA pol gamma
Mitochondrial Replication of mitochondrial genome 5-->3' polymerase 3-->5' exonuclease
40
Nucleosomes
``` H1, H2A, H2B, H3, H4 Positively charged (ionic bond with DNA) Core histones = 2A, 2B, 3, 4 + Linker H1 Duplicated during DNA synthesis Synthesized mostly in S phase ```
41
Telomere
non-coding NT sequences at ends of linear chromosomes Maintain the structural integrity of eukaryotic chromosomes Protozoa - GGGGTT Euk - AGGGTT
42
Telomere sequences
Protozoa - GGGGTT | Euk - AGGGTT
43
Shelterin
Protein in telomeres that functions to protect ends from being recognized as DNA breaks
44
Problem with telomeres?
RNA primer on the end of lagging strand at 5' is shorter with each DNA replication Removal of the primer leads to a shorter strand
45
Telomerase
Ribonucleoprotein Contains RNA molecule that serves as template for elongation of G rich strand of telomeric DNA Has a protein with polymerase activity Only found in - germ cells, early embryonic cells, cells that divide continuously
46
Telomerase process
Telomerase extends the 3' end of DNA RNA primer is synthesized by primase at end of 3' end RNA primer serves as primer for DNA polymerase Polymerase extends in 5'-->3' RNA primer is removed
47
Hutchinson-Guilford Progeria
Disease of very premature aging Due to mutations in nuclear proteins - lamins Dramatically shortened telomeres at early age
48
Why do SSB proteins exist?
Don't let ssDNA base pair, get degraded, form a duplex | Cell thinks ssDNA is a virus

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