DNA Flashcards
Avery, McCloud, and McCarty
Described DNA as the genetic material.
DNA isolated from virulent bacteria transformed live nonvirulent bacteria > mouse death
Chargaff’s Rules
Purines=Pyrimidines
%G=%C & %A=%T
Purine/Pyrimidine ratio is different in DNA from different organisms
What does DNA melting mean?
Temperature that separates 50% of the DNA double strand.
What factors effect melting temperature?
- Salt concentration (higher concentration increases Tm)
- Extremes of pH (effect ionization states of groups on bases)
- Chain length
- Number of GC residues
Origin binding proteins
Recognize replication origin, bind and open DNA forming a small bubble
What is the cofactor for ligase in eukaryotes/prokaryotes?
ATP/NAD+
What is PCNA?
Sliding clamp for eukaryotic DNA Pol
How does DNA polymerase discriminate between correct and incorrect nucleotides?
Hydrogen bonds
Common geometry
What polymerase has 5’-3’ exonuclease activity?
DNA Pol 1
What polymerases has a sliding clamp?
DNA Pol 3
What are the ways a nucleotide base can be damaged?
Depurination; alkylation; deamination; pyrimidine dimers; oxidative damage
What are the types of DNA repair?
Direct reversal; excision; tolerance/bypass; strand break repair
DNA ligase repair
Reversal of a specific type of single stranded DNA break
Photolyase
Reversal of UV caused base damage
MGMT
Reversal of base alkylation
BER
Repairs base damages that do not distort the DNA using base specific glycosylases
NER
Repairs base damages that distort the DNA
MMR
Removes misincorporated nucleotides during DNA replication
What are the steps common to all 3 excision repair mechanisms?
- Recognition
- Endonuclease cutting of phosphodiester backbone
- Nuclease removal of DNA fragment
- DNA polymerase mediated synthesis
- DNA ligase
Regarding BER, once a glycosylase recognizes a specific modified base, what happens?
Leaves an AP site
