Exam 4 DNA Metabolism

Question 1

What is chromatin?

Answer 1

Complex of DNA, proteins (histones), and RNA that makes up chromosomes.

Question 2

What are nucleosomes?

Answer 2

Repeating units where DNA is wound around an octamer of histone proteins.

Question 3

How is chromatin further condensed?

Answer 3

Into a 30-nm fiber, then loops, and finally mitotic chromosomes.

Question 4

What is the genome?

Answer 4

Complete set of genetic material (DNA) in an organism.

Question 5

How do prokaryotic and eukaryotic genomes differ?

Answer 5

Prokaryotes have a single circular chromosome; eukaryotes have multiple linear chromosomes.

Question 6

What is a point mutation?

Answer 6

Change in a single nucleotide base pair in DNA.

Question 7

What causes point mutations?

Answer 7

Errors in replication, chemical alterations (e.g., deamination), or UV radiation.

Question 8

What is mismatch repair (MMR)?

Answer 8

Corrects mispaired bases missed by DNA polymerase proofreading.

Question 9

What is base excision repair (BER)?

Answer 9

Removes and replaces damaged or altered bases (e.g., uracil from cytosine deamination).

Question 10

What is nucleotide excision repair (NER)?

Answer 10

Repairs bulky lesions/nucleotide segment like thymine dimers by excising the phosphodiester bond and resynthesizing DNA.

Question 11

Which strand serves as the template for the leading strand during replication?

Answer 11

The 3’→5’ strand.

Question 12

Which strand serves as the template for the lagging strand during replication?

Answer 12

The 5’→3’ strand.

Question 13

What is an Okazaki fragment?

Answer 13

Short segment of DNA synthesized discontinuously on the lagging strand.

Question 14

Which enzymes are required for Okazaki fragment formation in E. coli?

Answer 14

Primase (DnaG), DNA polymerase III, DNA polymerase I, and DNA ligase.

Question 15

What is the role of primase in DNA replication?

Answer 15

Synthesizes short RNA primers for DNA polymerase to begin elongation.

Question 16

What is the function of DNA polymerase III?

Answer 16

Primary enzyme for DNA replication; synthesizes DNA and proofreads errors.

Question 17

What is the role of DNA ligase?

Answer 17

Seals nicks between Okazaki fragments by forming phosphodiester bonds.

Question 18

What is the function of DNA helicase?

Answer 18

Unwinds the DNA double helix at the replication fork.

Question 19

What is the role of topoisomerases?

Answer 19

Relieves torsional stress ahead of the replication fork.

Question 20

What does the 3’→5’ exonuclease activity of DNA polymerase do?

Answer 20

Proofreads and removes mismatched nucleotides.

Question 21

What does the 5’→3’ exonuclease activity of DNA polymerase I do?

Answer 21

Removes RNA primers during DNA replication.

Question 22

Name two proteins found at the E. coli replication fork (other than DNA polymerase III).

Answer 22

DNA helicase (DnaB) and single-stranded DNA-binding proteins (SSBs).

Question 23

What is the role of SSBs in DNA replication?

Answer 23

Stabilize and protect exposed single-stranded DNA.

Question 24

What is DNA gyrase?

Answer 24

A type of topoisomerase (II) that relieves torsional stress.

Question 25

How does the cell correct errors missed by DNA polymerase proofreading?

Answer 25

Mismatch repair (MMR) and base excision repair (BER).

Question 26

What are three types of DNA damage that require repair?

Answer 26

Mismatched bases, pyrimidine dimers, and deaminated bases.

Question 27

What enzymes are involved in mismatch repair (MMR)?

Answer 27

DNA helicase II, DNA ligase, DNA polymerase III, and Exonuclease I.

Question 28

What is the difference between BER and NER?

Answer 28

BER removes only the defective base by cleavage of N-glycosidic bond; NER removes a segment of nucleotides by cleavage of phosphodiester bond.

Question 29

What does bidirectional DNA replication mean?

Answer 29

Two replication forks move in opposite directions from a single origin.

Question 30

What is the function of the β-clamp in DNA polymerase III?

Answer 30

Acts as a circular clamp to improve processivity of DNA synthesis.

Question 31

Which enzyme synthesizes RNA primers?

Answer 31

Primase.

Question 32

Why do eukaryotic chromosomes need multiple replication origins?

Answer 32

Due to their large size; multiple origins speed up replication.

Question 33

What are telomeres?

Answer 33

Protective, repetitive nucleotide sequences at chromosome ends that prevent degradation.

Question 34

What is the role of telomerase?

Answer 34

Adds repetitive DNA sequences to chromosome ends to maintain telomere length.

Question 35

In which cells is telomerase typically active?

Answer 35

Germ cells, stem cells, and certain proliferative cells.

Question 36

What is recombinant DNA?

Answer 36

Man-made DNA molecule combining genetic material from different sources.

Question 37

What enzymes are used to create recombinant DNA?

Answer 37

Restriction enzymes and DNA ligase.

Question 38

What is the role of MutS in methyl-directed mismatch repair?

Answer 38

Recognizes and binds to mismatched base pairs.

Question 39

What is the role of MutH in methyl-directed mismatch repair?

Answer 39

Nicks the newly synthesized (unmethylated) DNA strand near the mismatch.

Question 40

What is the role of DNA helicase II (UvrD) in mismatch repair?

Answer 40

Unwinds the DNA to expose the error for excision.