BIOCHEMISTRY: DNA Structure, Replication and Repair

DNA Replication

• the process by which DNA makes an exact copy of itself

• synthesis of 2 daughter DNA from a single parental DNA molecule

Origin of Replication

• Replication begins at the point called _____

DnaA

• a proten that binds to a specific nucleotide sequence

DNA helicase

• enzyme that unwinds double helix

SBB Protein

• helps to keep the strand separated

DNA Topoisomerase

• responsible for removing supercoils in the helix

Nuclease

Activity:

• strand cutting

Ligase

Activity:

• strand resealing

DNA Polymerase

• responsible for the replication

• are only able to “read” the parental nucelotide sequences in the 3 —> 5 direction

• syntesize new DNA strands only in the 5 —> 3 direction

Primase

• syntesizes the short streches of RNA that are complementary and anti-parallel to DNA template

DNA Polymerase III

• catalyzes DNA elongation

Pyrophosphate (PP)

• is released when each new deoxynucleoside monophosphate is added to the growing chain

DNA Polymerase I

• removes the RNA primer and fills the gap between Okazaki Fragments

DNA ligase

• catalyzed the final phosphodiester linkage between the 5’-phosphate group and the 3’-hydroxyl group chain

TUS (Terminus Utilization Substance)

DNA repair

• failure to this causes mutation

• incredibl accurate

Cellular Metabolism, UV light exposure, Ionizing radiation, Chemical Exposure, Replication errors

Agents that Damage DNA

Prokaryotic DNA Replication

• Single origin of Replication

Prokaryotic DNA Replication

• Three types of DNA Polymerase

DNA Polymerase III

• In prokaryotic DNA replication, which enzyme carries out both initiation and elongation

DNA Polymerase I

• In prokaryotic DNA replication, DNA repair and gap filling are done by which polymerase?

DNA Polymerase I

• In prokaryotic DNA replication, RNA primer is removed by which polymerase?

Eukaryotic DNA Replication

• Multiple origin of Replication

Eukaryotic DNA Replication

• It has 5 types of DNA POL

DNA Polymerase Alpha

• In eukaryotic DNA Replication, initiation is carried by which polymerase?

DNA Polymerase delta and epsilon

• In eukaryotic DNA Replication, elongation is carried out by which polymerase?

DNA Polymerase beta and epsilon

• In eukaryotic DNA Replication, DNA repair and gap filling are done by which polymerases?

DNA Polymerase beta

• In eukaryotic DNA Replication, RNA primer is removed by which polymerase?

DNA Polymerase Gamma

• In eukaryotic DNA Replication, this replicated mitochondrial DNA

Direct Damage Reversal and Excision of DNA Damage

• Types of DNA Repair

Direct Damage Reversal

• involves enzymatic properties which binds to the damage and restores the DNA to its normal state

Base Excision Repair, Nucleotide Excision Repair, Mismatch Repair

Types of Repairs under Excision of DNA Damage:

uracil DNA glycosylase

• removes the uracil created by spontaneous deamination of cytosine in the DNA

Endonuclease

• cuts the backbone near the defect

DNA Polymerase

• Defect is filled by the action of a DNA polymerase

Ligase

• rejoining of strands

Damage recognition

NER:

• The cell detects the distorted DNA

Excision

NER:

• A small segment of DNA containing the damage (about 12-30 nucleotides) is cut out.

DNA Synthesis

NER:

• DNA polymerases fills in the gap using the undamaged strand as a template

Ligation

NER:

• DNA ligase seals the backbone, restoring DNA integrity

Exonuclease

• when a new strand containing mismatch is identified, ________ removes mismatched bases

DNA Polymerase I

MMR:

• the gap left by removal of mismatchd nucleotides is filled using ________