Lec 30 DNA Replication

semi-conservative

- catalyzes DNA synthesis
- extremely accurate

1. A template strand
2. A primer strand w/ a 3’ free OH group
3. deoxyribonucleoside triphosphate (dNTP) --> creates base pair

5' to 3'

3' to 5'

it's bidirectional

the junction between the newly separated template strands and the un-replicated duplex DNA

Leading: synthesized in one continuous strand
Lagging strand: synthesized in discontinuous Okazaki fragments that
later combine
Both strands 5' to 3'

it is going away from the replication fork

- Gene mutations - RNA is used and degraded quite often (like your mom)

3’ OH group will attack the alpha phosphate and will release pyrophosphate (the two remaining
phosphates)
1. One of the Mg ions will activate the free OH group to make it a good nucleophile in order to attack the phosphate
2. The other ion stabilizes leaving group (pyrophosphate) as well as positions incoming nucleotide for addition

2 Mg atoms & 2 Asp residues
- helps DNA polymerase add nucleotides to the new strand

- finger
- palm
- thumb

- bends phosphodiester backbone of DNA to expose template strand
- contains O-helix
- Lys & Arg residues hold phosphates in place
- Stacked Tyr residues keep base pair together

hold metal ions in place

- catalytic site of DNA replication
- contains Arg & Gln residues that hold correct base pairs tightly in active site w/ H-bonds
- contains exonuclease which is a proofreading mechanism
- ions

- interacts w/ recently synthesized DNA
- keep the primer in its correct position

1) dNTP lines up with complementary base on template strand
2) Fingers close (O-helix) and nucleotide addition reaction occurs
3) Pyrophosphate dissociation triggers fingers to open up
4) DNA translocates one base pair over
5) Process repeats for each base pair

- steric hindrance
- 2' OH group --> prevent nucleophillic attack

the strand will drop down into the exonuclease region for repair

accurate, slower

- phosphate gorup occupying 5' end
- not enough energy for dNTP to be cleaved

DNA polymerase cannot recognize rare tautomers of bases

prevents single-stranded DNA from going back to double-stranded

unzips double-stranded DNA by using ATP

synthesize RNA primer

removes RNA primer

> combines Okazaki fragments by using energy
- Happens after RNAse H removes RNA primer
- Energy source = adenylation (ATP)
o Note: E. coli uses NAD instead of ATP

holds DNA polymerase in place

- ligase
- clamp loader
- helicase