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DNA Replication
Medical School Biochem
29
Biochemistry
Graduate
08/20/2011

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Term
The fact that both strands of DNA will be copied and kept after replication means that the process of DNA replication is _________
Definition
Semi-conservative
Term
How many ORI's do prokaryotes typically have?
Definition
1
Term
Eukaryotes have _____ origins of replication
Definition
multiple
Term
What is the name of the factor that denatures DNA (prokaryotes)?
Definition
DnaA
Term
What is the name of the enzyme that unwinds DNA (prokaryotes)?
Definition
Helicase
Term
What is the name of the proteins that keep the two DNA strands separate (prokaryotes)?
Definition
ssDNA binding proteins
Term
What is the function of Topoisomerase I?
Definition
Causes a single nick in replicating DNA to relieve the tension of positive super coiling
Term
What is the function of Topisomerase II (DNA Gyrase) in prokaryotes?
Definition
Topisomerase II causes a double strand break so that prokaryotic DNA can be packed in a negative supercoil.
Term
What is the function of Topisomerase II in humans?
Definition
Changes the topography of DNA to allow gene expression and replication
Term
Drugs that inhibit Human Topoisomerase II are typically trying to combat what disease?
Definition
Cancer

these drugs stop DNA replication and cause cell apoptosis
Term
Drugs that inhibit the action of DNA gyrase are typically targeting what diseases?
Definition
Bacterial infections

Gyrase is the topoisomerase II found in prokaryotes
Term
What is the repliosome?
Definition
The protein machinery of DNA replication
Term
What is the function of Primase?
Definition
Primase creates the RNA primer that polymerase recognizes to begin synthesis
Term
[image]
Identify the structures
Definition
1: RNA Primer
2: Newly synthesized DNA strand
3: Leading Strand
4: DNA polymerase III
5: ssDNA binding proteins
6: Helicase
7: Primase
8: Okazaki Fragment
9: Lagging Strand
Term
What are Okazaki Fragments and how are they created?
Definition
Okazaki fragments are fragments of newly synthesized DNA. They are caused by synthesis on the lagging strand because DNA can only be synthesized on the 5'->3' direction which calls for periodic breaks in synthesis.
Term
What is the function of DNA ligase?
Definition
To repair nicks in DNA
Term
How are the gaps in the Okazaki Fragments filled?
Definition
DNA polymerase I excises RNA primer and synthesizes over the gaps. DNA ligase repairs the nicks.
Term
What is the function of DNA polymerase III
Definition
synthesis in the 5'->3' direction

proofreading in the 3'->5' direction
Term
What are the three steps that keep error rates low in bacterial and human genomes?
Definition
5'->3' polymerization
3'->5' exonucleolytic proofreading
Strand-directed mismatch repair
Term
What is the function of Polymerase alpha?
Definition
Primase analog, also initiates DNA synthesis
Term
What is the function of Pol Beta?
Definition
DNA repair
Term
What is the function of Pol Gamma?
Definition
Replicated Mitochondrial DNA, proof-reading
Term
What is the function of Pol Delta?
Definition
Polymerase I analog, elongates Okazaki Fragments. Also proofreads
Term
What is the function of Pol Epsilon?
Definition
Polymerase III analog, leading strand sythesis and DNA repair. Also Proofreads
Term
How does acyclovir work mechanistically to reign back Herpes Simplex 1?
Definition
Acyclovir is a nucleoside analog with no 3'OH (causes chain termination). Replaces guanisine and stops DNA polymerase from recognizing the primer
Term
What happens to nucleosomes during replication?
Definition
Nucleosomes only partially break during replication. After replication histone chaperones rebuild the partial nucleosomes mainting structural and epigenetic principles
Term
What happends to the histone code during replication?
Definition
Roughly half of the histone marks are preserved during replication but complex reader-writer proteins manage to recreate the code and preserve epigenetic gene expression
Term
What is the function of telomeres?
Definition
Telomeres protect the DNA from degradation by nucleases. Structurally this occurs by created a T-loop that leaves no ends that can be chewed
Term
What is the function of telomerase reverse transcriptase?
Definition
Prevent the shortening of telomeres after replication.

mechanistically: enzyme with associated RNA code that creates a DNA telomere repeat sequence and adds it to the parental strand
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