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Flashcards in 3B- Synthesis of DNA Deck (15)
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1
Q

Give the general steps through DNA replication

A

DNA unwound by helicase –> helicase opens DNA in 1 direction –> DNA binding proteins come and prevent re-annealing –> DNA polymerase III codes leading strand in the 5’-3’ direction

On the lagging strand RNA primer laid down by RNA primase –> DNA polymerase III lays down new DNA in 5’-3’ direction –> DNA polymerase I replaces RNA primer with DNA –> DNA ligase links the Okazaki fragments

2
Q

What is the leading strand?

A

The leading strand is the template strand of the DNA double helix so that the replication fork moves along it in the 3’ to 5’ direction.

This allows the newly synthesized strand complementary to the original strand to be synthesized 5’ to 3’ in the same direction as the movement of the replication fork.

3
Q

What is the lagging strand?

A

The lagging strand is the strand of the template DNA double helix that is oriented so that the replication fork moves along it in a 5’ to 3’ manner. Because of its orientation, opposite to the working orientation of DNA polymerase III, which moves on a template in a 3’ to 5’ manner, replication of the lagging strand is more complicated than that of the leading strand.

4
Q

What are Okazaki fragments?

A

Okazaki fragments are short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication.

DNA polymerase δ carries out a 3’ to 5’ exonuclease role

DNA ligase links the fragments together

5
Q

What is the function of topoisomerase?

A

As DNA is unwound by DNA helicase, it begins to be supercoiled.

Topoisomerase cuts the DNA to relieve the supercoiling

6
Q

Why are the ends of the chromosomes lost during replication?

A

As DNA replication approaches the end of the chromosome, the lagging strand develops a problem: you can’t put down a primase or you can’t have DNA pol bind to make DNA

Therefore the DNA strand is shorter on the 5’ end

This is fixed by telomeres

7
Q

What are telomeres?

A

They are long sequences of TTAGGG at the ends of chromosomes which fill in the end-replication problem of the 5’ strand of DNA.

THey are made by telomerase

8
Q

How does telomerase make DNA of defined sequence without an external template?

A

It contains both proteins an dRNA and acts as an RNA-dependant DNA polymerase (like reverse transcriptase).

The RNA within the telomerase complements with the 3’ overhang, uses own template and extends the 3’ end using the free -OH

A RNA primase and complements with the 3’ strand –> DNA polymerase comes and adds on 5’ strand

Bueno

9
Q

What is the process of nucleotide excision repair?

A

Happens to remove mismatched bases or bulky adducts

endonucleases cleave abnormal chain and remove distorted region –> gap filled by DNA polymerase –> DNA ligase seals the fragment

10
Q

When does base excision repair occur?

A

When there is damage to a single base

11
Q

What is the process of base excision repair?

A

DNA glycosylases recognize small distortions in the DNA –> cleaves N-glycosidic bond between base and deoxyribose –> apyrimidinic endonuclease cleaves the sugar-phosphate strand at the site –> same mechanisms to fill and seal the gap

12
Q

What is the process of mismatch repair?

A

Normal, undamaged, mismatched bases bind proteins of the mismatch repair system, the mismatch system removes the bases and re-synthesizes the portion of the new strand

13
Q

What is transcription-coupled repair?

A

the RNA polymerase transcribing the gene stalls when it encounters a damaged region of the DNA template –> repair proteins attracted to this site and repair the DNA –> RNA polymerase can resume txn

14
Q

What type of damage to the DNA is caused by UV radiation?

How is it repaired?

A

UV light can cause thymine dimers. This is when 2 thymine bases form covalent double bonds.

It is repaired by nucleotide excision repair

15
Q

What type of damage to DNA is caused by cigarette smoke?

How is it repaired?

A

cigarette smoke contains carcinogens such as the aromatic polycyclic hydrocarbon benzo[α]pyrene

this forms bulky adducts to guanine residues

it is repaired by nucleotide excision repair