Final Exam Flashcards
enzyme primase
creates RNA nucleotides
creates 3’-OH group which allows DNA polymerase to add DNA nucleotides
leading strand
replication is continuous
Requires primer at the 5’ end
lagging strand
replication is discontinuous
Primer created at the beginning of okazaki fragments
watson and crick DNA replication mechanism
Each strand is a template for synthesis of a new strand
Semiconservative replication
based off if the template is linear (eukaryotes) or circular (bacteria)
replicon
segment that undergoes replication and has a single origin of replication
bacterial DNA has one origin
eukaryotic DNA has multiple origins
theta replication
In circular DNA
DNA unwinds at origin, exposes a single strand to act as template.
Unwinding can occur in one direction or both.
Rolling circle replication
In circular DNA
Breaks phosphodiester bond at origin
5’ end of strand is displaced
3’ end of strand grows around the circle (unidirectional)
Releases single linear strand and double circular strand
linear strand can act as template for synthesis
Linear eukaryotic replication
occurs at several origins of replication
chromosome has multiple origins
DNA unwinds at origin -> replication bubble
Replication forks proceed outwards until they reach one another and fuse creating linear DNA molecules
requirements for replication
Single stranded DNA template
Substrates (Deoxyribonucleoside triphosphates: dNTPs)
Enzymes (eg: DNA polymerases) and other proteins
dNTP:
new DNA is created from dNTP
3’-OH group of the template strand attacks the 5’-phosphate group of the dNTP
two phosphates are cleaved off
phosphodiester bond forms between the nucleotides
direction of replication
lower template strand -> DNA synthesis proceeds in the 5’ - 3’ direction
upper template strand -> DNA synthesis proceeds in the 3’ - 5’ direction until it runs out
dna synthesis starts again on the upper strand and the spaces between the replicated dna is caled the okazaki fragments (discontinuous)
direction of replication in linear eukaryotic replication
leading strand is synthesized continuously in the same direction of unwinding
lagging strand is synthesized discontinuously in the opposite direction of unwinding
three steps of bacterial replication
initiation
elongation
termination
initiation
initiator proteins (DnaA) bind to oriC and cause unwinding of a short section (breaks H-bonds) allows proteins to bind to the DNA
unwinding
DNA helicase unwinds and breaks H-bonds between two strands of DNA
binds to lagging strand and moves in 5’-3’ direction
DNA gyrase relieves strain
single strand binding proteins
bind to exposed single strands and prevents them from reannealing until replication takes place
gyrase
topoisomerase creates double-strand breaks ahead of the replication fork to relieve tension
elongation
enzyme primase synthesizes primers
primer provides 3’-OH group
DNA polymerase attaches nucleotide to 3’OH end of the primer
DNA forms loop so that both strands can replicate simultaneously
DNA polymerase III
synthesizes nucleotide strands by adding new nucleotides to the 3’ end of the growing DNA strand
has high processivity
5’->3’ polymerase activity
enables addition of nucleotides in the 5’ to 3’ direction
3’ -> 5’ exonuclease activity allows it to remove nucleotides in the 3’ -> 5’ direction
enables the removal of nucleotides in the 3’->5’ direction to correct errors in nucleotide insertion.
DNA polymerase I:
has 5’->3’ and 3’->5’ activity
has 5’->3’ exonuclease activity to remove primers created by primase and replace them with nucleotides through 5’->3’ polymerase activity
lower processivity than polymerase III
DNA poly I and DNA ligase
RNA primers in the new strands need to be removed and replaced with DNA.
After RNA nucleotides are replaced there are ‘nick’s left that are sealed by DNA ligase
termination
replication is terminated when two forks of replication bubble meet
fidelity of DNA replication
the accuracy of DNA replication
proofreading during DNA replication
if incorrect nucleotide is inserted, the 3’OH group is not properly positioned to accept the next nucleotide
this stalls polymerization
3’ -> 5’ exonuclease activity of DNA polymerase removes mispaired nucleotide
5’ -> 3’ polymerase activity inserts correct nucleotide based on complementarity to template
mismatch repair
if incorrect nucleotide remains after replication is over then there will be a deformity in structure
recognized by repair enzymes and replaces it with correct nucleotide
distinguishing between template strand and new strand
template strand has methyl and new strands dont.
mismatch repair systems look at the methylation status of strands
eukaryotic DNA replication
replication starts at multiple origins
eukaryotic chromosomes are linear
nucleosome assembly of DNA must follow after DNA replication
eukaryotic replication
must be coordinated, timely, precise, and once every cell cycle
g1 of interphase
MCM (minichromosomal maintenance) binds to origin
S of interphase:
MCM complexes with other proteins to form an active helicase -> unwinds at origin -> replication
after MCM
it is removed and prevented from rebinding
DNA polymerase alpha
complex with primase, primer synthesis, starts DNA synthesis from primer for both leading and lagging strand
DNA polymerase delta
completes replication of lagging strand
DNA polymerase epsilon
replicates the leading strand
Translesion DNA polymerase
if lesion, low fidelity Translesion DNA polymerases take over
active site of Translesion more open and accommodating to abnormal pairings.
more error prone
Bypass lesion and continue synthesis
detach from replication fork and high fidelity takes over
replication at ends of eukaryotic chromosomes
If primers at ends of chromosomes are removed during replication but not replaced, then with every round of further replication (every cell division) the new chromosomal DNA gets shorter deleterious to cell
telomeres
regions at the ends of chromosomes
have short repeated sequences
in humans: sequence is TTAGGG, G-rich strand (3’ overhang)
telomerase
protein and RNA component called ribonucleoprotein that extends the G rich 3’ overhang
