Lecture 4 Flashcards
what are initiator proteins?
several proteins that bind to DNA to unwind the double helix
where do initiator proteins bind?
to the origin of replication
what does helicase require?
ATP
what do initiator proteins require?
ATP
what is the job of initiator proteins?
help helicase bind
what are the two types of helicase?
one helicase the runs in the 5’ to 3’ direction and the other helicase that runs in the 3’ to 5’ direction
what is the job of ssbp?
prevent the two DNA strands from reannealing by preventing hydrogen bonds from forming
what does DNA polymerase require to begin transcription?
a bound primer
what is the job of primase?
make RNA primer
In what direction does primase synthesize the primer?
the in 3’ to 5’ direction
what are the steps in bacterial DNA replication?
1) Origin of replication
2) Binding of initiator
proteins
3) Unwinding by helicase
4) Binding of single-strand
binding protein
5) RNA primers made by
primase
what would happen if there were no sliding clamps?
DNA polymerase would constantly dissociate from the template strand
what is the job of DNA polymerase?
add nucleotides to the template stand in the 5’ to 3’ direction
what is the job of the sliding clamp?
hold DNA polymerase on the DNA template
how are the Okazaki fragments linked on the lagging strand?
DNA ligase enzyme glues the fragments together using phosphodiester bonds
how is the leading strand made in terms of continuity?
continuously
where does the leading strand start being made from?
a single RNA primer
how is the lagging strand made in terms of continuity?
discontinously
how many primers does the lagging strand have?
multiple
which strand is the predominant helicase on?
lagging strand
what is the primosome?
a group of enzymes involves in priming DNA including helicase and primase
what are Okazaki fragments made of?
RNA primer and DNA
what is the unwinding problem?
a DNA unwinds, it creates torsional strain
which type of molecule is the unwinding problem common in?
circular chromosomes and large linear eukaryotic chromosomes
how is the unwinding problem solved?
Solved by DNA topoisomerase
what happens at the end of linear chromosomes?
during DNA replication on the lagging strand, DNA polymerase can not replicate the very end of the chromosome because there is no primer
what is the direction of DNA replication?
bidirectional
why is the shortening at the ends of linear chromosomes a problem?
loss of essential genetic information
how does telomerase help the shortening of the ends of linear chromosomes?
adds repeated nucleotide sequences to the 3’ end of the parent strand
what are the steps of telomere replication?
1) RNA template
2) Resembles: Reverse Transcriptase
3) Generates: G-rich ends
4) Adds nucleotides to:
3’ ends of parental
strand template
how does loss of telomerase affect cell division?
inhibits cell division
what type of cells is telomerase abundant in?
stem and germ cells
which type of cell produces high levels
of telomerase?
cancer cells
what is the error rate of RNA polymerase?
1 in 10^4
what is the error rate of DNA polymerase?
1 in 10^9
how many times does the genome change every time a cell divides?
three times
what are the two mechanisms for proofreading DNA?
1) 3’ to 5’ exonuclease
2) stand directed mismatch repair
what is the job of the 3’-5’ exonuclease?
remove incorrect nucleotides during DNA synthesis
what is the job of stand-directed mismatch repair?
detects and repairs abnormalities after DNA synthesis has occurred
after DNA synthesis, can DNA still get damaged?
yes
what happens if there are defects in repair mechanisms?
it can lead to diseases
what can DNA damage be caused by?
oxidation, radiation, heat, chemicals
what is depurination?
loss of purine bases (adenine or guanine) from DNA, leaving a gap where the base used to be
what are the two types of spontaneous DNA damage?
depurination, deamination
what is deamination?
the removal of an amino group from a nucleotide base in DNA
what are two general mechanisms of DNA repair?
base excision repair, nucleotide excision repair
what happens to DNA that is left uncorrected?
the daughter cells inherit the mutation
what is base miexcision repair?
correcting one modified base
what is nucleotide excision repair?
correcting groups of modified bases
what are the two mechanisms to repair double-stranded bond breaks?
non-homologous end joining, homologous recombination
what is non-homologous end joining?
ligating broken parts together but there is a lack of insertion of nucleotide at the repair site
what is homologous recombination?
uses a template to repair broken DNA strand
