Week 4 Textbook Reading Flashcards
what would happen if incorrect base pairs are allowed to remain?
Incorrect base pairs are formed much less frequently than correct ones, but if allowed to remain, they would result in an accumulation of mutations
what 2 special qualities does DNA polymerase have that increases the accuracy of DNA replication
- The enzyme carefully monitors the base-pairing between each incoming nucleoside triphosphate and the template strand
Only when the match is correct does DNA polymerase undergo a small structural rearrangement that allows it to re-catalyze the nucleotide-addition rxn - When DNA polymerase does make a mistake and adds the wrong nucleotide, it can correct the error through an activity called proofreading
proofreading
Proofreading takes place at the same time as DNA synthesis
-Before the enzyme adds the next nucleotide to a growing DNA strand, it checks whether the previously added nucleotide is correctly base-paired to the template strand
–If so, the polymerase adds the next nucleotide
–If not, the polymerase pauses to clip off the mispaired nucleotide and then tries again
who does the proofreading performed in dna
dna polymerases
If a DNA polymerase were to synthesize in the reverse direction, what would happen?
If a DNA polymerase were to synthesize in the reverse direction, it would be unable to proofread
-This is because if this “backward” polymerase were to remove an incorrectly paired nucleotide from the 5’ end, it would create a chemical dead end- a strand that can no longer be elongated
How can polymerase begin a completely new DNA strand?
To get the process started, a different enzyme called primase begins a new polynucleotide strand by joining two nucleotides together without the need for a base-paired end
-RNA polymerase that uses DNA as a template to produce a short RNA fragment that serves as a primer for DNA synthesis
–Primase is an example of an RNA polymerase, an enzyme that synthesizes RNA using DNA as a template
what is needed on the leading strand
For the leading strand, an RNA primer is needed only to start replication at a replication origin
At that point, the DNA polymerase simply takes over, extending this primer with DNA synthesized in the 5’ to 3’ direction
what is needed to produce okazaki fragments?
DNA polymerase then adds a deoxyribonucleotide to the 3’ end of each new primer to produce another fragment
It will continue to elongate this fragment until it runs into the previously synthesized RNA primer
To produce a continuous new DNA strand from the pieces on the lagging strand:
3 additional enzymes are needed
A nuclease degrades the RNA primer
DNA polymerase called a repair polymerase replaces the RNA primers with DNA (using the end of the Okazaki fragment as its primer)
DNA ligase joins the 5’ phosphate end of one DNA fragment to the adjacent 3’-hydroxyl end of the next
The repair polymerase involved in this process is DNA polymerase I
nuclease
degrades the RNA primer
dna polymerase
DNA polymerase called a repair polymerase replaces the RNA primers with DNA (using the end of the Okazaki fragment as its primer)
DNA ligase
DNA ligase joins the 5’ phosphate end of one DNA fragment to the adjacent 3’-hydroxyl end of the next
DNA polymerase iii
The polymerase that carries out the bulk of DNA replication at the forks is known as DNA polymerase iii
why does primase often make mistakes and how are they detected?
Unlike DNA polymerases i and iii, primase does not proofread its work and can often make mistakes
Since they’re made out of RNA, their mistakes are easily noticeable and can be easily be removed
for dna rep. to occur, the double helix must…
For DNA replication to occur, the double helix must be continuously pried apart so that the incoming nucleoside triphosphates can form base pairs with each template strand
2 types of replication proteins- DNA helicases and single-strand DNA-binding proteins- cooperate to carry out this task
dna helicase
DNA helicase is an enzyme that pries open the DNA double helix, using energy derived from ATP hydrolysis
Used to expose DNA single strands for DNA replication
single strand binding proteins
Single strand binding proteins then latch onto the single-stranded DNA exposed by the helicase, preventing the strands from re-forming base pairs and keeping them in an elongated form so that they can serve as templates
what problem does the unwinding of the dna double helix create?
As the helicase moves forward, prying open the double helix, the DNA ahead of the fork gets wound more tightly
This excess twisting in front of the replication fork creates a tension in the DNA that- if allowed to build- would make unwinding the double helix difficult and impede the forward movement of the replication machinery
Enzymes called DNA topoisomerases relieve this tension and produces a single-strand break in the DNA backbone, which releases the built-up tension
dna topoisomerases
Enzymes called DNA topoisomerases relieve this tension and produces a single-strand break in the DNA backbone, which releases the built-up tension
The enzyme then reseals the nick before falling off the DNA
function of the sliding clamp
It’s a protein that keeps DNA polymerase firmly attached to the template while it is synthesizing new strands of DNA
Left on their own, most DNA polymerase molecules will synthesize only a short string of nucleotides before falling off the DNA template strand
The sliding clamp forms a ring around the newly formed DNA double helix and, by tightly gripping the polymerase, allows the enzyme to move along the template strand without falling off as it synthesizes new DNA
function of the clamp loader
Assembly of the clamp around DNA requires the activity of another replication protein, the clamp loader, which hydrolyzes ATP each time it locks a sliding clamp around a newly formed DNA double helix
This loading needs to happen once per replication cycle on the leading strand
On the lagging strand, the clamp is removed and reattached each time a new Okazaki fragment is made
telomerase
Because DNA replication proceeds only in the 5 to 3 direction, the lagging strand of the replication fork must be synthesized in the form of discontinuous DNA fragments, each of which is initiated from an RNA primer laid down by a primase
What problem appears as the replication fork approaches the end of a chromosome?
Although the leading strand can be replicated all the way down to the chromosome tip, the lagging strand cannot
When the final RNA primer on the lagging strand is removed, there is no enzyme that can replace it with DNA
Eukaryotes get around this by adding long, repetitive nucleotide sequences to the ends of every chromosome, providing the replication machinery with “extra” DNA to complete the lagging strand
These sequences, which are incorporated into structures called telomeres, attract an enzyme called telomerase to the chromosome ends
telomeres and telomerase
These sequences, which are incorporated into structures called telomeres, attract an enzyme called telomerase to the chromosome ends
Telomerase carries its own RNA template, which it uses to add multiple copies of the same repetitive DNA sequence to the lagging-strand template
In many dividing cells, telomeres are continuously replenished and the resulting extended templates can then be copied by DNA replication, ensuring that no peripheral chromosomal sequences are lost
