L2: DNA Replication (farook) Flashcards
DNA polymerase builds a new strand in which direction?
It builds a new strand in a 5’ to 3’ direction ON THE NEW STRAND
(So 3’ to 5’ in the old one)
Laish fee two names for the strands?
(Leading and lagging)
3shan DNA polymerase bas ygdar ysawee mn a 5’ to 3’ direction, il leading strand ykoon continuous etha il DNA polymerase bida mn the 3’ side of the old strand
Etha bda mn the 5’ side of the old strand it keeps breaking off w y7awil yla7g ysawee new primers fa ykoon chna fragments bdal continuous
What are the fragments on the lagging strand called?
Okazaki fragments
What are the primers originally made of?
And what do they get replaced with 3la a5r shay?
RNA, it gets replaced with DNA later
What is the role of ligase?
It fills in the gaps between Okazaki fragments of the lagging strand
What do you name the 2 new DNA molecules after replication? And why?
They’re called semi-conservative bc it contains one original strand and new strand
In prokaryotes, where does DNA replication begin? And briefly explain what happens
DNA replication starts at the site of origin which is rich with AT sequences.
Dna A binds to the origin site and stretches out the 2 complementary strands which created this bubble like structure called the replication fork.
This fork allows the replication to start bidirectionally.
What is the function of dnaA?
It binds to the site of origin which activates initiation
What does helicase do? And how does it do it?
Unwinds the 2 complementary strands from each other by breaking the hydrogen bonds by using ATP as an energy source
Function of SSB proteins?
Helps to keep the 2 strands separated so that DNA polymerase can bind and start replication
They protect the susceptible single strand DNA from nucleases that might degrade them
Who are the key players playing a role in separating the 2 strands of dna?
DnaA followed by helicase and ssb proteins
In which replication step does the DNA get prepared for the polymerase?
Initiation process
What can interfere with helicase ahead of the replication fork?
how can this problem be fixed?
When is it done?
Supercoiling of the dna strands.
It can be fixed by topoisomerase, which cuts the dna strand, unwinds it, then reseals it
It does its work at the same time as helicase but further ahead down the strand
What are the 2 types of topoisomerases?
Topoisomerase I: It breaks only one strand
Topoisomerase II: It breaks both the strands
3l saree3 summarize what happens during the replication initiation process?
IN PROKARYOTES
- DnaA identifies and binds to the site of ori and stretches out the 2 strands
- Helicase starts unwinding the 2 strands and ssb proteins keeps them separated
- Topoisomerase I and II releases tension from the supercoiling
- Primase places rna primers on the strands so DNA polymerase can do its thing now
After the separation of strands, what happens?
IN PROKARYOTES
They are ready to start replication by DNA polymerase bas lazim RNA primase synthesizes 10 nts long primers first in a 5’ to 3’ direction (so 3’ to 5’ direction in the og strand)
Why is the site of ori rich with AT sequences instead of GC?
Because the bonds are easier to break than GC
A=T : double bond
G=C: triple bond
What is the replication fork?
It’s the bubble/Y like structure that is created by the stretching of dnaA
What happens after primase synthesizes small RNA primers?
IN PROKARYOTES
Elongation:
DNA polymerase III starts synthesizing complementary strand from the last nucleotide of the RNA primer (OH’/3’ end)
It catalyzes adding deoxy nucleotide triphosphates (dATP, dTTP, dCTP, dGTP) to the elongating chain & releasing two phosphate molecules (pyro phosphate) from them thereby incorporating a deoxy nucleotide monophosphate
What is a holoenzyme? + name an example of it
DNA polymerase III:
It contains 10 different functional subunits including a polymerase core unit that contains the following enzyme activity.
a) 5 - 3’ DNA Polymerase
b) 3’- 5’ exonuclease
^2 subunits of DNA polymerase
How does DNA polymerase III holoenzyme move and work ib the elongation process?
IN PROKARYOTES
It encircles the DNA strand forming like a sliding clamp and moves along the template strand
If 2 of the subunits of DNA polymerase III are 5-3’ DNA polymerase and the other is 3-5’ exonuclease, what is the use of the other 8 subunits?
IN PROKARYOTES
They aid in holding the strand and in movement along the strand
“During replication, nucleotides mismatch can occur. DNA polymerase III can naturally make an error in every 10^7 nucleotide pairs.”
How is this mistake fixed?
IN PROKARYOTES
What differentiates DNA polymerase I from DNA polymerase III?
IN PROKARYOTES
IN PROKARYOTES
What are the 3 major activities of DNA polymerase I?
IN PROKARYOTES
After proof reading and filling of the rna primase gaps, how are the fragments gonna be linked?
They will be linked with phosphodiester bonds by LIGASE
What is 1 major difference of dna replication in eukaryotes compared to prokaryotes?
Eukaryotes have multiple sites of origin compared to prokaryotes bc of their greater length
Eukaryotes and prokaryotes have many differences in the names of the activities elly ysawoonhum, sameehum
What is a telomere
A telomere refers to the end of a chromosome
What are telomeres made of?
Repetitive sequences (tandem) of non-coding DNA that protects the dna from degradation and not fusing with other chromosomes
What is always an issue during eukaryotic cell division?
replication at the Chromosome
end (telomere) is always a problem in the lagging strand of
normal somatic cells.
Telomeres will not be shortened in eukaryotic germ cells, stem cells and cancer cells like they do in somatic cells, why?
How does telomerase extend telomeric end DNA in germ cells, stem cells & cancer cells?
Why cant telomerase enzyme synthesize telomeres in somatic cells?
Bc its activity is inhibited naturally
How is viral DNA replication inhibited in host cells?
By using nucleoside analogs:
DDI is an analog of A
AZT (azidothymidine/zidovudine) is an analog of T
They both have an H’ end instead of an OH’ end fa basically inhibits elongation
DDI and AZT are as medication for whom?
It is used as an anti-retroviral medication to treat HIV or AIDS patients
How do anti-cancer drugs inhibit DNA replication? Name some of these drugs
By inhibiting topoisomerase I & II ➡️ drug binds to any cleavage site ➡️ prevents dna uncoiling ➡️ cell undergoes apoptosis and dies
CPT (Camptothecin) inhibits topoisomerase I
Etoposide inhibits topoisomerase II
