Summer Biochem Exam 5

Origin of Replication in prokaryotes

single point on circular chromosome, built for speed

Origin of Replication in eukaryotes

thousands of points as it would take too long if there was only a single one

Meselson and Stahl experiment

demonstrated that DNA replication was semiconservative

two DNA each made of one old strand and one new

Function of DnaA

wider, base pairs not right in middle

Function of DnaB

most common form of DNA helix

base pairs in middle

Function of Single Strand Binding Protein,

protein that binds to single strand DNA to prevent reforming of double-strands

Function of helicases

separation and unwinding of DNA helix

Function of Topoisomerases,

relieve topological stress caused by local unwinding of double helix

Function of primase

enzyme which makes a short base-paired region called RNA primer with free 3” OH group for DNA pol to add first DNA nucleotide

Function of telomerase

add nucleotides to end of telomeres to maintain length and protect genetic info in chromosomes

Function of beta-Clamp

keeps DNA pol from falling off DNA template strand

Function of PCNA

acts as sliding clamp, keeps polymerase on DNA

more processive than beta clamp

enzymatic function of DNA Pol I

replace RNA primers with DNA on okazaki fragments

exonuclease activity 5’ to 3’ (clip out bases)

proofreads activity in 3’ to 5’ direction

synthetic activity in 5’ to 3’ direction

enzymatic function of DNA pol III

main replicative polymerase, high processivity

proofreads activity in 3’ to 5’ direction

synthetic activity in 5’ to 3’ direction

DNA Pol

must work from a 3’ OH

synthesize from 5’ to 3’

needs a primer (short RNAs that must be removed after)

leading strand synthesis

continuous replication (synthesis) as DNA unwinds

lagging strand synthesis

lagging strand synthesized in fragments opposite of leading strand

synthesizes in 5’ to 3’

okazaki fragments

fragments of synthesized DNA on lagging strand

base excision repair vs nucleotide excision repair

NER- first cut phosphodiester backbone around error, refilled by DNA pol and ligase reseals backbone

BER- first clip off base, THEN phosphodiester backbone is broken then DNA pol and ligase fix

homologous recombination vs non-homologous end joining

both fix double strand breaks

homologous recombination- use one strand as guide, requires sequences to match. Leads to Holliday junction (can transfer from one chromosome to another and cause rearrangements)

non-homologous end joining- error prone, last ditch effort, no template to copy

operators

promoters

TATA box

TATA Binding protein

RNA polymerase subunits

termination via stem loop structures or Rho proteins

Eukaryotic RNA polymerases and functions

delta and epsilon are most important

e on leading strand

d on lagging strand

intron vs exons

DNA SYNTHESIS

RNA SYNTHESIS

RIBOSOME READING DIRECTION

5’ TO 3’

DNA ligase

seals phosphodiester backbone

differences in prokaryote vs eukaryote replication

prokaryotes compact DNA by using

supercoiling

eukaryotes compact DNA using

histones

terminator sequence and tus proteins

SOS system