DNA Structure and Replication Flashcards
Base pairing. Which is stronger?
G-C and A-T. G-C stronger due to extra H-bond.
DNA replicates ____. Each round of replication results in ___.
Semiconservatively. Each replication results in a daughter strand with a parent strand. Meselson-Stahn experiment with Nitrogen-15.
Replication forks
Active zones of DNA replication
Leading strand replication occurs in ___ direction _____. While lagging strand is made in _____.
Leading strand replication occurs in 5’–> 3’ direction continuously while lagging strand is made in Okazaki fragments.
RNase H does what?
DNA Pol I?
DNA ligase?
RNase H removes the RNA primer fragments in the lagging strand during replication.
DNA Pol I replaces gaps with DNA. Also has 5’–>3’ exonuclease activity that removes RNA primer.
DNA ligase seals backbone
DNA helicase does what?
Unwinds DNA at replication fork
Single strand DNA binding proteins
Prevents DNA from folding back on itself during replication
Sliding clamp
Supports DNA and DNA pol, making replication a processive process
Contents of replisome and what they do
Replisome = set of proteins and enzymes required for DNA replication. Include:
(1) Helicase: unwinds DNA
(2) Topoisomerase: removes DNA supercoild
(3) single-stranded binding proteins: stabilize ssDNA
(4) Primase: lay down RNA primers on lagging strand
(5) DNA ligase: ligates Okazaki fragments on logging strand
Exonuclease domain
Domain in all DNA pols 3’–>5’ that allows DNA pol to backspace removing most incorrectly inserted bases
Main DNA pol is ___. It is a ___.
DNA pol III. It is a dimer. One domain binds leading strand, the other the lagging strand.
Replication initiates at ___ and ends at ___.
Origins of replication (ori) and ends at termination points.
Main sources of DNA damage (3)
(1) Reactive oxygen species
(2) Ionizing radiation
(3) Chemical exposure
Oncogenes
Tumor-suppressor genes
Oncogenes are genes that can lead to cell cycle disregulation if they experience a gain-of-function mutation.
Tumor-suppressor genes can lead to cell cycle disregulation if they experience a loss-of-function mutation.
Types of DNA damage repair
(1) Direct repair
(2) Excision repair (a) base excision (b) mismatch repair (c) nucleotide excision repair
(3) Recombination repair
Base excision repair
- Timing of repair?
- Does what? Steps?
- Failure could lead to?
- Repairs DNA damage throughout cell cycle
- Removes small, non-helix distorting base lesions (e.g. oxidized/alkylated bases, uracil incorporation
(1) Glycosylase removes base
(2) Endonuclease and phosphodiesterase removes sugar phosphate
(3) DNA polymerase adds new nucleotide and ligase seals - Failure could lead to breaks in DNA
Mismatch repair
- Does what? Mistake corrected where?
- Can be detected in prokaryotes via?
- Steps
- Corrects errors of DNA replication that result in mispaired nucleotides.
- Strand specific –> corrects mistake on new daughter strand
- Look for unmethylated DNA in prokaryotes
(1) MutS binds mismatched DNA and MutL scans DNA for nick
(2) MutL removes DNA in mismatched strand
(3) DNA polymerase synthesizes new DNA
Nucleotide excision repair
- Does what?
- Steps?
- Removes bulky DNA lesions due to UV, tobacco smoke, etc.
(1) Exonuclease binds to DNA at side of lesion and cleaves damaged DNA around lesion
(2) DNA strand removed by helicase
(3) Gap filled by DNA polymerase and nick filled by ligase
Nonhomologous end-joining
- Does what?
- Occurs when?
- Can lead to?
- What is used to recognize and process broken ends?
- Repairs double stranded DNA break by altering DNA sequence at break to join ends together
- Occurs before cells duplicate DNA
- Can lead to deletions and translocations
- Ku protein used to recognize and process broken chromosome ends
Homologous recombination
- Does what?
- Can be used when?
- Repairs double stranded DNA breaks by using duplicated sister chromatids as template to repair sequence lost in break
- Restores original DNA sequence but can only be used after DNA duplication (S/G2 phases)
