WEEK 4 Flashcards
Helicase
Two types, but the predominant one moves in 5’ to 3’ direction. Both require AT. Spins along the lagging strand template.
SSBs
Single stranded DNA binding proteins, prevents strands from reannealing after helicase has separated them.
Primase
Synthesizes RNA primer that polymerase can add onto. DNA primase = RNA primase = Primase (all same thing)
Leading strand is synthesized from
a single RNA primer
Lagging strand is synthesized from
multiple primers (discontinuously)
Okazaki fragments are made of
RNA primer and DNA
Blunt ended DNA
Is damaged DNA. Body will try to fuse together.
Issues with DNA synthesis/replication
- information is lost during every replication on the lagging strand
- primase is not good at adding primer at very end
- RNA primers must be removed and then theres only a 5’ end which you can’t add to
Telomeres
Repetitive DNA sequences at ends of chromosomes that solve problem of information loss. Most eukaryotes have telomeres.
Single stranded DNA is
particularly fragile
Shortening of the 5’ end is a problem for…
the lagging strand
Telomerase
Uses RNA primer adds repeats to make 3’ end long. Adds a G rich sequence.
Topoisomerase I and II
- Breaks single strand, does not directly require ATP (DNA can rotate/unwind)
- Uses ATP, cleaves both strands
Which has a higher error rate—RNA or DNA polymerases ?
RNA polymerases have more errors
Proofreading mechanisms
- 3’ to 5’ exonuclease repair (backspace button of DNA polymerase)
- In eukaryotes, strand directed mismatch repair (occurs before ligase)
Proteins associated with strand directed mismatch repair
MutS - recognizes distortion
MutL - scans strands for nicks to see which strand is the new strand because just from distortion alone you can’t tell which one is the mismatch and which is the original strand
Prokaryote version of strand directed mismatch repair
Protein looks for unmethylated adenines, doesn’t recognize nicks in the strand
Pyrimidine Dimer
Often caused by UV light, consecutive bases on same strand are covalently bonded. Primary cause of melanoma in humans.
Types of spontaneous damage to DNA
Depurination and deamination
Depurination
Purine nucleosides are hydrolytically cleaved from DNA releasing adenine/guanine. Occurs 500 times a day.
Deamination
Cytosine turns to uracil as amine group is replaced with an oxygen (INSTANCE OF URACIL BEING IN DNA). Also occurs 500 times a day.
When does a cell have until to recognize and correct an error?
Until next replication event. If it is not resolved, the mutation becomes fixed because polymerase is dumb and just copies template strand.
BER
Base Excision Repair
Typically targets one nucleotide. Uracil-DNA glycosylase removes base, AP endonuclease cuts phosphodiester bond, and a specific DNA polymerase removes phosphate group and sugar, adds a new one.
NER
Nucleotide Excision Repair
Endonucleases cuts on either side of problem strand, specific helicase removes strand, polymerase fills in, then ligase.
