Chapter 5: DNA Replication, Repair, and Recombination Flashcards
What is the error rate of P activity in DNA polymerase?
1 x 10^5
What is the error rate of E activity in DNA polymerase?
1 x 10^2
What is the combined error rate of total DNA polymerase activity?
1 x 10^7
This function occurs at the E site of DNA polymerase; identifies the polymerization of incorrect nucleic acids
exonucleolytic proofreading
This process occurs soon after DNA replication and before ligase activity seals the “nicks” of Okazaki fragments
Eukaryotic strand-directed mismatch repair
What is the error rate of eukaryotic strand-directed mismatch repair?
1 x 10^3
these are a common artifact after DNA synthesis that serve as markers to identify new strands
“nicks”
What is the total combined error rate of DNA synthesis/replication?
1 X 10^10 (1 in 10 billion)
What are the two challenges of maintaining chromosome ends
- break/error repairs
- shortening telomeres with replication
What are 3 things done to prevent the breakage-repair of chromosome ends?
- 5’ end removal (via nuclease)
- addition of protruding 3’ end (telomere)
- shelterin protein protection
What are the bases of the protruding 3’ repeat sequence added to the ends of chromosomes?
TTAGGG
about how many times are the telomere sequences repeated on a chromosome end?
~3000x
What are 3 outcomes of telomere shortening?
- loss of coding DNA
- triggering of cellular senescence
- telomerase restoration
What is cellular senescence?
the ceasing of cell division; not synonymous with cell death
How does telomerase extend the 3’ end of chromosomes?
uses RNA template to complete synthesis of the lagging strand (via DNA pol)
This is a method of DNA repair that excises ALL bases to look for errors (via 6 different enzymes)
Base excision repair
What are the 5 steps of base excision repair?
- error base recognition
- base removal
- phosphate backbone removal
- nucleotide replacement (via DNA pol)
- nick sealing (via ligase)
what are the most common DNA errors that are not caught during replication (via endonuclease activity/eukaryotic strand-directed repair)
deaminations
This is a method of post-replication DNA repair that removes whole chunks of polynucleotides
nucleotide excision repair
When does nucleotide excision repair occur most frequently? why?
during RNA transcription; RNA pol II gets stalled by bulky lesions
What is the enzyme used in nucleotide excision repair?
excision nuclease
Double-stranded break repair that occurs post-DNA replication is a subtype of what other DNA repair?
HDR (homology-directed repair)
What are the only times double-stranded break repair can occur?
during cell division (after DNA replication, before nuclear division)
what are the 3 additional methods of DNA repair that usually occur post-DNA replication?
- base excision repair
- nucleotide excision repair
- double-stranded break repair
What are the 3 main classes of transposable elements?
- transposases
- reverse transcriptase (+integrase)
- reverse transcriptase (+endonuclease)
What are the 3 methods of transposing elements?
- DNA-only transposons
- Retroviral-like transposons
- non-retroviral-like retrotransposons
transposase is coded by DNA/RNA to move the transposable elements in which method of transposition?
DNA-only transposition
DNA-only transposons are found in which organisms?
bacteria/prokaryotes ONLY
What are the 5 steps of DNA-only transposons?
- coded transposase from DNA/RNA
- transposase binds to target DNA
- target DNA is looped + broken
- target DNA is integrated into a new location
- donor region is repaired
What are the 4 steps of retroviral-like transposition?
- reverse transcriptase codes DNA from vRNA
- retrotransposon integrates DNA into new location
- copies of viral sequence are made
- protein synth from viral sequence (replication occurs)
What are the 4 steps of nonretroviral retrotransposition?
- L1 RNA sequence synthesizes reverse transcriptase
- rt protein binds to 5’ of L1 + DNA target
- rt is primed
- sequence transcribes (+ is integrated into new location)
about how many transposable elements are present in the human genome?
~3,000,000
LINE elements compose about what percentage of the human genome?
~50%
about how many nonretroviral retrotransposons are active in the human genome?
80-100
What is the TATA box?