Biochemistry Chapter 25

Question 1

List fundamental rules of DNA replication

Answer 1

DNA replication is semi-conservative, both parents contributing half of the DNA

DNA replication begins at the origin, meaning it starts at the same spot on the DNA each time

DNA replication usually proceeds bidirectionally, mostly as a fork

DNA synthesis proceeds in a 5’ to 3’ direction

DNA replication is semi-discontinuous, meaning leading strand is continuous and lagging strand is discontinuous

DNA synthesis is catalyzed by very specific enzymes, each one catalyzing only specific DNA sequences

Question 2

Name critical enzymes and factors associate with initiation of E. coli DNA replication and describe their specific functions

Answer 2

Critical enzymes and factors:
Deoxyribonucleotides
Template DNA
Cell extract
Mg2+

Functions:
Mg2+: Essential for initiation reaction
DNA unwinding, primer synthesis

Question 2

DNA replication steps

Answer 2

1. Initiation: DNA unwinding and primer synthesis
2. Elongation: dNTPs incorporation and fork movement
3. Termination: Primer removal and fragment ligation

Question 3

Two critical aspects of DNA replication in all organisms

Answer 3

Fidelity: How accurate an enzyme system is in making two complete sets of DNA

Catalytic efficiency: How high the processivity of the enzyme is and how strongly the enzyme sticks to the template

Question 4

Initiation part for DNA replication

Answer 4

Need: DNA polymerase 1, Mg2+,

Question 5

Two critical factors for accurate DNA synthesis

Answer 5

1. Base-pair geometry: A-T and G-C pairing, any errors get removed
2. Proof-reading activity of DNA polymerase 1: Allows any mismatched pairs to be removed

Question 6

Multiple proteins required for initiation of E. coli DNA replication

Answer 6

Primase: synthesizes RNA primers

DNA gyrase: Relieves torsional strain generated by DNA unwinding

Question 7

Prokaryotic DNA Replication: Elongation

Answer 7

Leading strand synthesis is continuous and lagging is discontinuous

Both synthesized at the same time

Lagging strand proceeds opposite of the fork movement direction

Primase makes the primer (RNA)

DNA Pol 3 extends each primer

New primer synthesized at end of fork begins new process

Question 8

Prokaryotic DNA Replication: Termination

Answer 8

Specific sequences define termination sites

Proteins bind to them and terminate DNA replication

DNA Pol 1 removes primer and put correct NTP in the gap

DNA ligase joins the Okazaki fragments

Question 9

Eukaryotic DNA Replication

Answer 9

Mechanistically similar to prokaryotic DNA replication

More complex enzymology

Single chromosome may have multiple origins of replication

Question 10

Drugs that affect DNA replication in Prokaryotes

Answer 10

Acyclovir for HSV

Lamivudin for HBV

Question 10

What can cause DNA damage

Answer 10

Environmental: Physical, Chemical, and Biological

Physiological: Metabolites, DNA replication, and recombination

Pharmacological: Drugs and Drug metabolites

Question 11

Drugs that affect DNA replication in Eukaryotes

Answer 11

Aphidicolin

Cytarabine

Phoscarnet

Gemcitabine

Question 12

Human DNA repair pathways and what they repair

Answer 12

Mismatch repair (MMR): Mismatch

Base excision repair (BER): Deamination and depurination

Nucleotide excision repair (NER): Bulky base modification

Homologous and non-homologous recombination: DS breaks