Chapter 11 Flashcards
Define DNA replication
Copying of DNA during S-phase
When does DNA replication occur?
S-phase (prior to mitosis or meiosis)
What are the DNA replication steps?
- DNA strand opens up
- DNA polymerase comes in and adds nucleotides
Define leading strand
Continuous synthesis of 5’ -> 3’ in the same direction as the replication fork
Define lagging strand
Discontinuous synthesis in the opposite direction of the replication fork, but still synthesizing in the 5’ -> 3’
Why did scientists first identify DNA Polymerase I?
It is the most abundant polymerase found in bacteria.
Define Okazaki fragments
Discontinuous bursts of DNA on the lagging strand
What does DNA polymerase I need to synthesize DNA?
dNTPs, a template strand, and a small starting complementary strand (primer)
What is the difference between eukaryotic and bacterial chromosomes?
Eukaryotes have linear chromosomes, bacteria has circular chromosomes.
Results in slight differences in replication
How does DNA polymerase I add nucleotides?
From 5’ to 3’, it adds a dNTP to the 3’ hydroxyl group of the previous nucleotide.
2 phosphates must be released to gain enough energy to power this reaction.
What is the function of DNA polymerase I?
Removes and replaces the primer using the 5’ to 3’ exonuclease function. lays down new DNA in the primer’s place.
What are DNA pol II, IV, and V’s function?
Main function is with DNA repair
What functions do the majority of the DNA polymerases have? (4)
-Require DNA/RNA to extend of of (like a primer)
-Have a 5’ -> 3’ polymerase activity
-Have a 3’ -> 5’ exonuclease activity
- SOME 5’ -> 3’ exonuclease activity
Define exonuclease
Remove nucleotides in a specific direction starting from the end of the strand. Allows for proofreading
Define proofreading
Removal of its mistakes
Define endonuclease
Cuts middle of strand to remove nucleotides.
How many subunits does DNA polymerase have?
~10 distinct proteins/subunits. Each subunit performs a different role
Define holoenzyme
The collective subunits of DNA polymerase III
What is the core enzyme?
Subunit of DNA Pol III, responsile for the 5’->3’ polymerization and the 3’->5’ exonuclease function.
2 core enzymes per holoenzyme
What is the γ complex?
Assists the core enzymes to get loaded/placed onto the DNA. Loads the enzyme ono the template
(AKA CLAMP LOADER)
What is the β Clamp?
Holds the core enzyme to the DNA. (AKA sliding clamp). Enhances the processivity of DNA pol III
Define processivity
How many nucleotides a polymerase adds before it falls off.
What is the processivity of DNA poly III with and without the β clamp?
Without: ~10nucleotides
With: >100,000 nucleotides
What does the τ subunit do?
Dimerizes the core complex. Keeps 2 core complexes attached to the clamp loader (γ complex)
Define helicase
Unwinds the DNA
Define Single-stranded binding proteins (SSBP)
Holds the parent strands apart
Define topoisomerase
AKA DNA Gryase. Cuts DNA upstream to relieve torsional stress caused by Helicase
Define Primase
Adds an RNA primer
Define DNA ligase
Seals the gaps between adjacent Okazaki Fragments
What is the difference between eukaryotic and prokaryotic DNA polymerases?
Eukaryotes have different polymerases for strands and DNA repair
Eukaryotes have 2 different polymerases for each strand (1 for lagging, 1 for leading)
What are the first 4 steps in recombination?
- Endonuclease creates nick in the strand
- Nicked strand from each duplex invades the other duplex
- Innervating strands are ligated to a new duplex. Forms a heteroduplex
- Branch migration occurs
What are the last 4 steps in recombination?
- Duplex separates/is bent
- Duplex rotates 180 degrees
- New nicks are generated that separate the OG duplexes from each other.
- Nicks are ligated so that the opposite duplexes are now joined together
Define endonuclease
Enzyme that cuts nucleic acids in the middle
Define nick
Severing of a covalent bond within a strand
Define heteroduplex
2 connected DNA duplexes
Define branch migration
Point of connection of the heteroduplexes is moved down the heteroduplex slightly.
Define holliday junction
When the duplex rotates 180 degrees
