BIOMG 3320: Prelim 2
30 Cards in this Set
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Replicon
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is a DNA or RNA molecule that replicates from a single origin of replication.
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Difference B/w Eukaryotic and Prokaryotic Replication
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1) Origins of replication are much less characterized in eukaryotes.
2) Multiple Origin of replication for eukaryotes.
3)Replication fork moves much slower, the genome is much larger.
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ARS
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Also called Autonomously Replicating Sequences. They are well defined AT rich sequences of 100-150 bp that contains this sequence:
5' A/T TTT ATGTTT A/T 3'
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Yeast have welled defined origins
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In mammalian cells, replication initiation appears to occur at discrete locations.
IN yeast there are 400 origins; 10,000 in humans
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Complications of Multiple Origins
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1) Incomplete replication
2) Re-replication = Amplification of specific regions which can have crazy defects such as gene expression and all divisions.
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Cyclin-dependent kinases & how it is actively controlled throughout the cell cycle.
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proteins that are phosphorylated/dephosphorylated in response to the cell cycle – these coordinate kinase cascades that regulate DNA initiation factor loading and replication check-points
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Cyclin and Cyclin-dependent kinases
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•When to replicate •Replication is complete •Replication only once per cell cycle •Number of origins used •Timing each origin is used •Rate of DNA replication
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How do checkpoint kinases detect problems in DNA replication?
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Cyclins and CDKs interact with DNA/chromatids throughout the cell cycle.
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ribonucleotide reductase
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it is an enzyme that catalyzes the the reaction that converts ADP, and other NDPs to dNDPs.
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Why is the activity of RNR highly regulated?
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RNR activity is regulated because the enzyme need to sense the nutritional and energy state of the cell
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the advantages for cells of having early and late origins
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There are early and late origins so if the early origin doesn’t work, the late one will.
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DNA replication is under cell cycle regulation.
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•Proper cell division requires a precisely ordered sequence of biochemical events that assures every daughter cell a full complement of the molecules required for life
•Cell cycle is the series of events that takes place in a cell leading to its division and duplication
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Ensuring origin activation only once per cell cycle
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•In G1: low CDK activity: formation of pre-RC: pre-replicative complex
•In S-phase: high CDK activity: activation of pre-RCs / inhibition of pre-RC formation
•This mechanism ensures that each origin of replication is activated only once per cell cycle
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Timing of Origin Activation
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•Early origins: initiated early every cell cycle; late origins: initiated late every cell cycle •These multiple initiation events are highly coordinated
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How To control Rate of DNA replication
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The replicating fork slows down to 50nt/s
For a rapidly dividing cell replicons are small and plenty (3-5kb)
For a slowly dividing Cell they are further apart and about 100kb
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DNA clamp (PCNA)
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Serves as a processivity promoting factor for DNA replication. It binds to DNA polymerase and prevents this from dissociating from the template strand of DNA.
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Checkpoint Kinases
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They provide a cancer barrier. Prevent improper DNA replication, and thus leads to more stable genomes. Once this checkpoint is reached, leads to higher dNTPs, DNA repair, inhibition of nucleases, and arrest cell cycle progression.
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Problems with replication?
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Because DNA is linear, it is unable to replicate the extreme ends of the DNA
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How to prevent incomplete replication?
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The use of telomeres. They are highly repetitive ends of the DNA that act as a buffer at the end of DNA.
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How does the telomere work?
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Telomerase which is made up of RNA and proteins. It can conduct RNA dependent transcription. It is also known as reverse transcriptase. It works by going to the end forming the T loop, and the RNA would add Ts and Gs and then DNA polymerase would finish up the compliment.
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What does the T loop do?
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The T loop will protect the ends from attacks from nucleases and ezymes that repairs broken DNA fragments. It also differentiates DNA ends from broken DNA.
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How are DNA being damaged?
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- mismatches: replication errors
- hydrolysis: depurination and deamination
- oxidation: reactive oxygen species from metabolic processes (mitochondria)
- methylation: chemicals
- pyrimidine dimers: UV+light++
double"strand+breaks: ionizing radiation, replication fork encountering le…
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Why must DNA be repaired?
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DNA is constantly being damaged.
Unrepaired DNA when replicated leads to deletions or base pair mismatches
Mutations are permanent changes within the DNA
1/1000 would result in permanent damaged to DNA.
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Multiple Ways to repair
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Many pathways are conserved from bacteria to humans. more than >130 genes that code for repair proteins.
DNA damaged and both cause and cure cancer
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Mismatch Pair
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Repairs replication error, uses the template strand to repair.
MutL-MutS binds to all mismatches except for C-C. MutH binds to MutL and GATC. Does a loop to cleaves to leave gap at the error. Up to 1000 base pair can be fixed and thus a huge energetic cost to fix.
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Excision Repair repairs damaged Bases
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Direct Repair
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Error Prone Repair
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TLS incorporates nucleotides that are independent of base pairing. but still needs a template. It is used as a last resort.
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Recombination DNA repair
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Function of restriction endonucleases
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Cut shit up man at specific sequences. Can leave blunt ends, 5' overhang, 3' overhang.
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BIOMG 3320: Prelim 2