EXAM2_L14_DNA_Replication

Question 1

Replication reminders

Answer 1

1. duplicates entire genome
2. once per cell cycle
3. semi-conservative
4. bi-directional replication until rep forks collide or end of chromosome reached
5. semi-discontinuous (lagging strand)

Question 2

Mechanism of replication 1,2,3.

Answer 2

1. Initiation (proteins bind to DNA, open helix, prepare DNA for base pairing)
2. Elongation (proteins connect nucleotides into continuous new DNA strand)
3. Termination (proteins release replication complex)

Question 3

Origins of replication- structure, proteins used, function.

Answer 3

Multiple origins in DNA w/ TATA rich sequences.

Origin binding proteins separate DNA forming a replication bubble where other proteins recruited to replicate DNA

Question 4

DNA Helicase- function

Answer 4

unwinds and extends replication fork in 5’to3’ direction respective of leading strand.
- Req ATP

Question 5

SSBP- funciton

Answer 5

binds ssDNA to prevent strands from reattaching after helicase unwinds the DNA.

• prevents DNA degradation
• binds cooperatively
• NOT ENZYMES

Question 6

two ways of orienting 5’ to 3’

Answer 6

Growth of new daughter strand is always 5’ to 3’
or
Growth always occurs toward the 5’ end of the Parent strand

Question 7

what are 4 components req for replication?

Answer 7

1. dNTPs
2. ssDNA template
3. a free 3’ OH group
4. RNA primer (b/c dna pol cant make strands denovo)

Question 8

7 proteins of replicaiton

Answer 8

1. Helicase
2. SSB
3. Primase
4. DNA Pol
5. RNase H
6. DNA ligase
7. Topoisomerase

Question 9

What drives replication?

Answer 9

ATP and energy from phosphates on nucleotides.

-Makes it almost irreversible reaction

Question 10

Three rules for DNA Polymerase. Types of DNApol?

Answer 10

1. copy ssDNA
2. add bases ONLY to existing chains (base pairing)
3. ONLY extend from 5’ to 3’ direction
   - alpha, epsilon, gamma (major replicative DNApol)

Question 11

How does replication get started?

Answer 11

Primase makes RNA primer

• primer makes short dsRNA base-paired to DNA template with 3’-OH
• DNApol starts
• RNA portion removed/replaced with DNA later

Question 12

Inhibition of DNA synthesis (types,examples,mech)

Answer 12

-Nucleoside analogs
NRTI- nucleoside reverse transcriptase inhibitor (anti-HIV)
-ie-ddl, ZDV
Have no 3’ carbon OH so no elongation occurs

Question 13

DNA Pol alpha

Answer 13

proofreads/ manages replication

Question 14

RNase H

Answer 14

-recognizes RNA-DNA duplexes and removes the primer, leaving the DNA part intact

Question 15

Two nicks

Answer 15

1. between okazaki fragments
2. between colliding replication forks
   important for DNA to identify new daughter strand when repairing

Question 16

How are okazaki fragments numbered?

Answer 16

first fragment is #1 and counts up to the newest fragment.

Question 17

Topoisomerase

Answer 17

Supercoil unwinding ahead of helicase.
Type 1 cuts ONE strand
Type 2 cuts BOTH strands

Question 18

What are two topoisomerase inhibitors for type 1 and 2? Why used? 2 modes?

Answer 18

Camptothecin Topoisomerase I inhibitor
Doxorubicin Topoisomerase II inhibitor
-cancer Chemotherapeutic agents
1. prevent unwinding
2. prevent re-sealing
both cause cell death

Question 19

Telomeres structure funciton

Answer 19

end of linear chromosome
-ds and ss DNA
-composed of thousands of repetitive sequence of non-coding DNA
-Protects DNA from damage 
"TTAGGG"

Question 20

End-replication problem. How solved?

Answer 20

-successive rounds of DNA replication on lagging strand will produce daughter strands that are progressively shorter
When final RNA primer (lagging strand) removed, there is no way to replace it with DNA
TELOMERASE FIX!

Question 21

Telomerase

Answer 21

contains RNA template used to extend the parental DNA template.
-RNA-dep DNA polymerase (ribonucleoprotein)
Uses its own RNA template to make DNA instead of using the RNA left from RNA primer removal.
-Chromosomal end of DNA and telomerase RNA are complementary ie: telomere seq 5’-TTAGGG-3’, Telomerase 5’-CCCUAA-3’