Test 4. Chapter 18

Question 1

Define DNA polymerase

Answer 1

• enzyme that synthesizes DNA, catalyzes phosphodiester linkage
• proofreading activity

Question 2

what is a template?

Answer 2

it is a sequence of nucleic acids that determines the sequence of a complementary necleic acid

Question 3

what is a primer?

Answer 3

it is the initial segment of a polymer that is to be extended on which elongation depends

Question 4

what are the key characteristics of DNA synthesis?

Answer 4

Four deoxynucleoside triphosphates (dNTPs) and Mg2+ are required.

A template strand is used to direct DNA synthesis.

A primer from which the new strand grows must be present.

Many DNA polymerases have nuclease activity that allows for the removal of mismatched bases.

Question 5

a template strand is used to ???

Answer 5

direct DNA synthesis

Question 6

A primer from which _________?

Answer 6

a primer from which the new strand grows must be present

Question 7

which polymerase is used for replication?

Answer 7

polymerase 3

Question 8

DNA polymerases catalyze the formation of a phosphodiester bridge. Elongation of the DNA strand proceeds in the __________.

Answer 8

5-to-3 direction

Question 9

DNA polymerase catalyzes _______________ linkage formation

Answer 9

phosphodiester linkage

Question 10

DNA replication starts at the ____________-

Answer 10

replication origin

Question 11

DNA must be locally unwound to expose single-stranded templates for replication. This unwinding puts a strain on the molecule by causing the overwinding of nearby regions.
Need – something to hold strands apart (___________) and something to relieve stress of overwinding (_____________)

Answer 11

helicase

topoisomerase

Question 12

the separation of DNA strands require __________ and ________-

Answer 12

specific helicases and ATP hydrolysis

Question 13

Topoisomerase prepare the double helix for _________-

Answer 13

unwinding

Question 14

What does topoisomerase I do?

what does topoisomerase II do?

Answer 14

Topoisomerase I – relaxes supercoils

Topoisomerase II (aka DNA gyrase in E. coli) - introduces supercoiling

Question 15

____________ blocks the binding of ATP to gyrase.

Nalidixic acid and ciprofloxacin are inhibitors of DNA gyrase that are used to treat bacterial infections, interfere with breakage and rejoining of DNA strands.

____________ prevents anthrax poisoning.

Answer 15

Novobiocin

Ciprofloxacin

Question 16

Replication begins in E. coli at the __________

DnaA protein binds and then recruits DnaB, a helicase.

Single-stranded-binding protein (SSB) bind to the AT-rich sites in the locus to prevent reannealing of the helix.

The resulting complex of DNA and proteins is called the prepriming complex.

Answer 16

oriC locus.

Question 17

RNA polymerase that synthesizes short RNA (≈10 nucleotides) complementary to a DNA strand that then serves as a _______for DNA synthesis.

Answer 17

primer

Question 18

Assembly of DnaA and formation of the ________

Answer 18

prepriming complex

Question 19

DNA synthesis on one of the template DNA strands is ___________: new DNA is synthesized in small pieces which then are connected together

Answer 19

discontinuous

Question 20

DNA synthesis always starts with a ___________

Answer 20

RNA primer

Question 21

DNA a

Answer 21

primase, initiates replication, generating ~ 20 dNTP

Question 22

DNA δ

Answer 22

more processive enzyme that extends the chains

Question 23

DNA δ

Answer 23

more processive enzyme that extends the chains

Question 24

The free ends of linear DNA molecules present two biochemical difficulties.
???

Answer 24

They are susceptible to damage by nucleases.

Due to the nature of DNA synthesis, one strand will shorten upon each round of DNA synthesis.

Question 25

Telomeres are replicated by __________________, a speicalized polymerase that carries its own RNA template

Answer 25

telomarase

The G-rich leading strand of the telomere can be maintained by the enzyme telomerase.

Telomerase contains an RNA template that it uses to extend the leading strand.

Question 26

huntington disease

Answer 26

triple repeat expansion of sequence CAG

Question 27

high energy electromagnetic radiation, such as __________, may cause breaks in the DNA strands

Answer 27

X-rays

Question 28

What mechanism does DNA repair systems follow?

Answer 28

Recognize the inappropriate base(s).

Remove the inappropriate base(s).

Fill in the resulting gap with DNA polymerase I and DNA ligase.

The first DNA repair mechanism occurs when DNA polymerase proofread the newly synthesized DNA and correct mismatches.

Question 29

mismatch repair

Answer 29

systems correct errors not corrected by proofreading.
In E. coli, two proteins are required for mismatch repair―one to recognize the error and one to recruit an exonuclease to cleave the DNA.

Question 30

Direct repair

Answer 30

corrects mistakes without having to remove any fragments of DNA.
DNA photolyase uses light energy to cleave pyrimidine dimers.

Question 31

Base-excision repair

Answer 31

corrects modified bases with several enzymes.
The enzyme AlkA removes the base. The site of the missing base is called an AP site.
The DNA backbone at the AP site is cleaved by AP endonuclease and a phosphodiesterase excises the deoxyribose phosphate.
The gap is repaired by DNA polymerase I and DNA ligase.
Base-excision repair corrects the most common point mutation in humans, the deamination of methyl cytosine to thymine.

Question 32

Mismatch pair

Answer 32

MutS recognizes G-T mismatch

MutH cleaves backbone at mismatch
Exonuclease I removes strand containing mismatch

DNA polymerase III synthesizes new strand

Question 33

Base excision repair

Answer 33

DNA glycosylase recognizes and excises incorrect base

AP endonuclease recognizes lesion and nicks DNA strand

DNA polymerase and DNA ligase fill the gap

Mismatch repaired

Question 34

The double strand break is recognized and the________________generating single-strand regions that are bound by RAD51.

____________ occurs when a single strand from the damaged DNA replaces a strand in the undamaged DNA. The resulting three-stranded structure is called a displacement loop.

___________ occurs, using the undamaged DNA as a template.

A __________________ occurs to complete the repair, forming a structure called a Holliday junction.

Cleavage and ligation yield two intact helices.

Answer 34

5’ ends are digested

Strand invasion

DNA synthesis

second strand invasion

Question 35

_____________ is the exchange of genetic information between two DNA molecules.

_________________ is useful for repair of extensive damage to the DNA, such as breaks in both strands of the DNA.

Answer 35

Recombination