Understand the general mechanism of DNA replication.
Describe two mechanisms of DNA repair.
Objective 1: General Mechanism of DNA Replication What DNA Replication Requires
A template to copy: The original parental DNA strand.
Enzymes to perform the copying: Specialized proteins, primarily DNA polymerase.
Building blocks: Nucleotide triphosphates (A, T, C, G) to form the new DNA strand.
Stages of DNA Replication
Initiation:
Replication begins at specific sites called origins of replication.
Proteins bind to the origin to separate the DNA strands, forming a replication bubble.
Elongation:
DNA polymerase (chain of DNA) adds complementary nucleotides to the growing DNA strand.
Synthesis occurs in the 5' to 3' direction.
Leading strand: Synthesized continuously.
Lagging strand: Synthesized in short fragments (Okazaki fragments), which are later joined.
Termination:
Replication ends when the entire DNA molecule is copied.
Enzymes detach, and the two new DNA molecules (each with one old and one new strand) are complete.
Implications
DNA replication is highly accurate, ensuring faithful transmission of genetic information.
Errors, though rare, can occur and may lead to mutations if not repaired. This emphasizes the importance of DNA repair mechanisms.
DNA: The Genetic Material – Key Details on DNA Replication Role of DNA Polymerase
DNA polymerase is the enzyme responsible for copying DNA by:
Matching complementary bases (A with T, G with C).
Linking nucleotides to form the growing DNA strand.
Common Features of DNA Polymerases
Add new nucleotides to the 3′ end of an existing strand (synthesis runs in the 5′ to 3′ direction).
Require a short RNA primer to start replication.
Proofreading ability: Detect and correct errors using 3′ to 5′ exonuclease activity.
Types of DNA Polymerases in Prokaryotes
DNA Polymerase I (pol I):
Removes RNA primers on the lagging strand.
Replaces primers with DNA.
Also has 5′ to 3′ exonuclease activity (unique to pol I).
DNA Polymerase II (pol II):
Functions primarily in DNA repair.
DNA Polymerase III (pol III):
The main replication enzyme.
High processivity: Maintains attachment to the DNA using a sliding clamp.
Unwinding the DNA Helix
Helicases:
Use ATP to break hydrogen bonds and unwind the DNA strands.
Single-Strand Binding Proteins (SSBs):
Bind to exposed single strands to prevent them from re-pairing.
Topoisomerases:
Relieve torsional strain caused by unwinding.
Example: DNA gyrase, a topoisomerase involved in replication, prevents supercoiling.
Replication Fork
The partial opening of the DNA helix creates a replication fork where replication occurs.
DNA Primase:
An RNA polymerase that synthesizes the RNA primer.
Primer will later be removed and replaced with DNA.
Semi-Discontinuous Replication
DNA polymerase synthesizes DNA in only one direction (5′ to 3′), leading to differences in how the two strands are copied:
Leading Strand:
Synthesized continuously.
Requires a single priming event.
Extended by DNA pol III.
Lagging Strand:
Synthesized discontinuously.
Requires multiple priming events.
Forms short segments of DNA called Okazaki fragments.
Fragments are joined after RNA primers are removed by DNA pol I and replaced with DNA.
Replisome
A macromolecular assembly of enzymes involved in DNA replication.
Components:
Primosome: Includes primase, helicase, and accessory proteins.
DNA pol III complex: Two DNA polymerase III enzymes (one for each strand).
Telomeres
Specialized structures at the ends of eukaryotic chromosomes.
Functions:
Protect chromosome ends from degradation by nucleases.
Maintain the integrity of linear chromosomes.
Challenge with lagging strand: Gradual shortening of chromosomes with each cell division because the last section of the lagging strand cannot be fully replicated.
Telomere Maintenance
Composition: Telomeres consist of short, repetitive DNA sequences.
Telomerase:
Enzyme that extends telomeres by using an internal RNA template.
Ensures the leading strand is fully replicated to the end.
Developmentally regulated.
Significance:
Telomere length is linked to cellular aging (senescence).
Cancer cells often activate telomerase, promoting unlimited division.
Objective 2: DNA Repair Mechanisms Overview of DNA Repair
Sources of Errors:
Errors can arise during DNA replication.
Mutagens (e.g., radiation, chemicals) increase mutation rates above the natural background level.
Proofreading: DNA polymerases have a proofreading ability to correct replication errors.
Significance:
The importance of DNA repair is demonstrated by the variety of repair systems in cells.
Categories of DNA Repair
Specific Repair:
Targets a single type of damage or lesion in DNA.
Nonspecific Repair:
Uses a single mechanism to repair various types of DNA damage.
Specific Repair Mechanism: Photorepair
Purpose: Repairs damage caused by UV light, particularly thymine dimers (covalent bonds between adjacent thymine bases).
Mechanism:
Photolyase enzyme:
Absorbs light in the visible spectrum.
Uses this energy to break the covalent bonds in thymine dimers, restoring normal DNA structure.
Nonspecific Repair Mechanism: Excision Repair
Purpose: Repairs a wide range of DNA damage by removing and replacing damaged regions.
Steps:
Damage Recognition: Identifies the damaged DNA region.
Removal: Removes the damaged segment.
Resynthesis: Synthesizes new DNA using the undamaged strand as a template.