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Biochemistry > DNA Replication and Repair > Flashcards

DNA Replication and Repair Flashcards

1
Q

What is semiconservative replication?

A

the use of each strand as a template for synthesis

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1
Q

What is base pairing?

A

the recognition of the parental nucleotide and the incorporation of a complementary base in the newly synthesized strand

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2
Q

What is DNA polymerase I and what are the requirements for its function? What is the alternative name?

A

Catalyzed the polymerization of nucleotides. It requires: all four deoxyribonucleotides (dATP, dGTP, dCTP, dTTP), Mg, a 3’ OH primer and a template

  • The function of the primer is to start the polymerization, then it will be replaced by polymerase I
  • Polymerase I is also called Kornberg enzyme. It synthesizes in 5’ to 3’ direction and has exonuclease activity (providing both repair and proofreading)
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3
Q

In which direction does proof reading progress?

A

3’ to 5’
* The wrong nucleotide can not hydrogen bond to the opposing template and causes polymerization to stop until the error is repaired

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4
Q

In which direction does the repair progress?

A

5’ to 3’

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5
Q

What is the function of polymerase II , III?

A

polymerase II function is unknown

polymerase III function is similar to polymerase I

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6
Q

What is DNA ligase?

A

Forms phosphodiester bonds between 3’ OH and 5’ mono phosphate groups. This is an endergonic reaction requiring energy by NAD (bacteria) or ATP (viruses and animals)

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7
Q

What is primase?

A

An enzyme that synthesizes a short RNA strand (4-10 bases) complementary to the template (a primer), required by polymerase for DNA synthesis. Its growing end is 3’ OH

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8
Q

What is the helicase enzyme?

A

unwind the double DNA helix before replication can occur. It requires ATP

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9
Q

What is the Single strand binding protein SSB?

A

It prevents the re-annealing of the DNA strand and also protects it from the cleavage of nucleases

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10
Q

What is the functions of topoisomerase enzymes?

A

create swivel points in the DNA to relieve the strain created by the replication fork by cutting and resealing the DNA

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11
Q

What is the function of the two topoisomerase enzyme?

A
  1. Topoisomerase I: relaxes the DNA in front of the replication fork by creating a transient nick in one strand. Doesn’t require ATP
  2. Topoisomerase II: introduces negative supercoils in the molecule by cutting and resealing the two strands. Requires ATP.
    * Gyrase is similar to topoisomerase II in E.Coli (introduces negative supercoils)
    see p. 378
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12
Q

What is the difference between the leading strand and Okazaki fragment in DNA synthesis?

A
  1. The leading strand: the one continuously synthesized in 5’-3’ direction (complementary to parental 3’ - 5’)
  2. The lagging strand: this one is synthesized in short fragments which are joined later by ligase
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13
Q

The replication fork is …..

A

the site where the two strands are unwound. It can move in either direction from the origin of replication (called ori)

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14
Q

The separation of the strands is maintained by …..

A

binding of several Single strand binding proteins

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15
Q

The synthesis of each of the Okazaki strands require …….

A

a short RNA primer

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16
Q

Two replication forks forms at each …. site and move in an opposite direction

A

ori

17
Q

E Coli has ….. site, while the eukaryotic DNA has many

A

one ori

18
Q

The RNA primer (for DNA synthesis) is synthesized by a complex containing …… & …..

A

primase & single strand binding protein

19
Q

The primer on the lagging strand is located near ……

A

the replicating fork

20
Q

The free 3’-OH on the primer serve as the binding site for …..

A

the first deoxyribonucleotide added by the polymerase

21
Q

In the lagging strand, replication continues until ……

A

it reaches another RNA primer

22
Q

What happens when polymerase III reach another primer in Okazaki fragment?

A

It dissociates, allowing polymerase I to enter and erase the ribonucleotides one at a time from the 5’ end, then add deoxyribonucleotides to fill the gap
Ligase then forms the phosphodiester bonds between the fragments

23
Q

DNA replication is inhibited by analogs of ….., …. & ….

A

pyrimidines, purines & folate

* used to slow division of cancer cells

24
Q

Thymidylate synthase is an enzyme critical for ……., inhibited by …..

A

DNA synthesis

Pyrimidine analogs

25
Q

Cytosine arabinoside is an analog of the pyrimidine ……, used to ……

A

cytosine nucleoside
stop elongation of the DNA chain
* It lacks 3’-OH

26
Q

Aminopterin and methotrexate are …..

A

inhibitors of DHF acid reductase

see p. 380

27
Q

Define Mutation and Mutagen

A
  • Mutation: is heritable change in DNA

* Mutagen is a chemical that alter the nucleotides in DNA

28
Q

Point mutation is a ….., and it is of two types, ….. & …..

A

change in a single nucleotide

transition, transversion

29
Q

What is transition mutation?

A

Transition: is the change of one purine or pyrimidine with another purine or pyrimidine respectively, due to mispairing of bases during replication or chemical insult.

30
Q

What is transversion mutation?

A

The exchange of a purine to pyrimidine or vice verse

31
Q

The nucleotide excision-repair mechanism repairs …..

A

UV damage

32
Q

Dimers are formed between …….. due to UV light exposure. It prevents ……

A 
adjacent pyrimidines (usually thymidines)
normal gene expression and replication
33
Q

Explain the nucleotide excision-repair theory

A
  1. incision: by endonuclease in the phosphodiester bonds several nucleotides away from the dimer
  2. Removal: by helicase which removes the hydrogen bonds
  3. Polymerization: by polymerase I, which fills the gap in 5’ - 3’ direction
  4. Ligation: by ligase
34
Q

Explain the base excision repair theory

A

Repairs most common error of deamination of cytosine to uracil (transition) causing U-G instead of C-G

  1. Removal of Uracil base: by glycosidase
  2. Cleavage of the phosphodiester bond next to missing base by endonuclease (belong to AP nucleases family)
  3. Insertion of cytosine and ligation
35
Q

The enzymes topoisomerase II, ligase & helicase require …..

A

ATP to function

36
Q

What is Missense mutation??

A

A codon with an altered amino acids sequence

* example is valine replaces glutamate causing sickle cell anemia

37
Q

What is a nonsense mutation??

A

A stop codon that causes polypeptide chain termination

38
Q

What is the wobble effect??

A

in translation, only the first two base pairs of the codon is translated into anticodon by tRNA, ignoring the last (3rd) base pair

39
Q

What is the frameshift mutation??

A

the deletion of insertion of one or more base pairs in the template

40
Q

What is the function of the enzyme reverse transcriptase?

A

formation of a complementary DNA strand from RNA template..

  • HIV has this enzyme
  • AZT is a reverse transcriptase inhibitor
41
Q

Polymerase chain reaction is used in …..

A

forensic medicine

* The lab sequence is : splitting the DNA strands, annealing primers to each one, copying each strand with polymerase

Biochemistry (13 decks)

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