Biochemistry Exam Iv - Dna Replication I

Front 1

1. Semiconservative process
2. DNA polymerase(s)
Components required for DNA synthesis
3. Origin of replication
4. Bi-directional
5. Replicating forks
6. Leading strand
7. Lagging strand (Okazaki fragments)

Back 1

General concepts of DNA replication

Front 2

These proteins need the following for DNA synthesis:

a. Substrates: dATP, dTTP, dCTP & dGTP

b. Mg2+

c. Template

d. Primer chain with free 3' hydroxyl group

Back 2

DNA polymerases

DNA polymerases can only carry out the process of elongation; they can not carry out the process of initiation.

Front 3

The addition of a deoxyribonucleotide to the __' end of a polynucleotide chain

Back 3

3' end

The fundamental reaction by which DNA is synthesized

Front 4

DNA synthesis occurs in the ____' to 3' direction.

Back 4

5'

Front 5

Site of unwinding of parental duplex and DNA synthesis

Back 5

Replication forks (two)

Front 6

Function:
DNA repair
Replication (minor)

Exonuclease activity:
- 3' to 5'
- 5' to 3' (exonuclease removes RNA primer.)

Back 6

Pol I

Replication is assisted by removal of RNA primers in conjunction with RNase H

Fills in gaps after removal of RNA primers

Front 7

Function:
DNA repair (Damage bypass)

Exonuclease activity:
- 3' to 5'

Back 7

Pol II

Front 8

Function:
DNA repair
Replication (major)

Exonuclease activity:
- 3' to 5'

Back 8

Pol III

Front 9

Pol III holoenzyme core complex:

Polymerase

Back 9

Alpha subunit

Synthesizes DNA

Front 10

Pol III holoenzyme core complex:

3' -> 5'exonuclease

Back 10

Epsilon subunit

Proofreads DNA

Front 11

Pol III holoenzyme core complex:

Stimulates 3' -> 5' exonuclease

Back 11

Theta subunit

Regulates activity of epsilon

Front 12

Pol III holoenzyme core complex:

Forms sliding clamp

Back 12

Beta subunit

Front 13

Pol III holoenzyme core complex:

Enhances dimerization of core; ATPase

Back 13

Tau subunit

Forces core to form a dimer

Protein will have two active sites.

Front 14

The number of nucleotides added before dissociation

A measure of efficiency.

Pol III holoenzyme complex processivity = >500,000 nucleotides added before dissociation

Back 14

Processivity

The high processivity of Pol III is due to the Beta subunit and Gamma complex.

Front 15

Action of helicases at the replicating fork introduces positive supercoiling ahead of the fork.

Removed through the action of DNA gyrase.

Back 15

If the positive supercoiling ahead of the fork is not removed through the action of DNA gyrase, then replication will cease.

Front 16

In the final steps of replication, the RNA primers are removed and the resulting gaps in the DNA fragments are filled in by the action of Pol ____.

Back 16

I
- Synthesizes DNA 5'-3'
- Fragments not joined together

Next the DNA fragments are joined together by DNA ligase

Front 17

- Requires NAD+ in prokaryotes

- ATP in eukaryotes

Back 17

DNA ligase

Front 18

Hydrophobic interactions

Phe, Ile interact with Ile and Leu

Ionic interaction
Glutamate and arginine

Back 18

Forces that hold the subunits together

Gamma subunit can disrupt these bond

Front 19

First step of DNA replication

Back 19

Binding of a DNA-A tetramer

Adds 20-40 DnaA monomers

Front 20

Dna-___ protein regulates activity of DNA-b protein.

Cannot bind

Back 20

C

Front 21

DNA-__

Allows DNA-b to add to each end of the open complex

Back 21

T

Front 22

Unwinds ds- DNA at the forks

Requires ATP

Displaces Dna-A proteins as it moves to the right.

Back 22

Dna-B protein = helicase

Front 23

Composed of three different proteins
DNA-b
Primase
PriA

Back 23

Primosome

- Forms at each end of open complex

Front 24

Action of Pri __ and ___ loads Primase and PriA onto DNA complex

Forms Primosome

Back 24

B and C

Front 25

1. Substrates: ATP, GTP, CTP, UTP
2. Mg2+
3. Template to direct process
4. No primer required.
5. Primer synthesized in 5'-3' direction

Back 25

Primase synthesizes RNA primers

Front 26

Need the RNA primer _____ time for the leading strand.

Back 26

one

Front 27

After synthesizing the primer for leading strand, the _______ strand primers will be formed.

Back 27

lagging

Front 28

Synthesizing DNA in 5'-3' direction

Need template to run 3'-5' direction

Have parallel orientation of both strands can synthesize two strands at one time.

Back 28

Loop converts antiparallel orientation to parallel

Front 29

Top B subunit remains attached throughout the entire process.

What about the lower B subunit?
.

Back 29

Lower B subunit has to cycle on and off as it runs out of template

Front 30

If positive supercoiling is not removed, replication wil l cease

DNA gyrase binds to this region and removes positive supercoiling.

Back 30

Major target for treating bacterial infections

Block DNA gyrase

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Front 36

This protein is used as a diagnostic marker for proliferating cells

Back 36

Proliferating cell nuclear antigen