BIOL 2112 Chapter Notes - Chapter 16: Okazaki Fragments, Dna Replication, Dna Ligase

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Lecture 23 – DNA replication

1) The DNA molecule of a normal mammalian chromosome is a double helix. A. What

is the term used to describe the orientation of the sugar-phosphate backbones of the

double helix? Antiparallel – their subunits run in opposite directions. B. What functional

groups distiguish the 5’ ed fro the 3’ ed of DNA? Phosphate group attahed to 5’

carbon, –OH attahed to 3’ aro. 2) A. What are Chargaff’s rules? (1) DNA base

composition varies between species (2) for each species, the percentages of A and T bases

are roughly equal, as are those of G and C bases. B. How does the Watson and Crick

model of the double helix explai Chargaff’s rules? The ratios explain that when one

strand of DNA has an A, the partner strand has a T. Similarly, G is always paired with T. In

any organism, the amount of adenine equals the amount of thymine and the amount of

guanine equals the amount of cytosine. (Confirmed by DNA sequencing to be exactly

equal). 3) Is the DNA replication model conservative, semiconservative, or dispersed?

Semiconservative – when DNA replicates, each of the daughter molecules will have one

old strand from the parent molecule and one new strand. 4) A. Where does DNA

replication begin in both prokaryotes and eukaryotes? Origins of replication – short

sequence of DNA consisting of specific nucleotides that proteins that initiate replication

a reogize ad id to, separatig the strads ad opeig up a repliatio ule.

B. How many replication bubbles can be seen in a mammalian chromosome during S

phase? Hundreds or even a few thousand 5) What is the source of energy that drives

DNA replication? DNA polymerase catalyzes the addition of each monomer via a

dehydration reaction. As each monomer is joined to the growing end of the DNA strand,

two phosphate groups are lost as a molecule of pyrophosphate (P–P). Subsequent

hydrolysis of the pyrophosphate to two molecules of inorganic phosphate (P) is a coupled

exergonic reaction that helps drive the polymerization reaction.6) Match the following

terms with the appropriate description. Untwists the DNA helix at the replication

forks, separating the DNA strands into templates available for replication. Helicase

Synthesizes a 10-nucleotide RNA primer along the DNA template strand. Primase

Elongates DNA strands in a 5’  3’ direction DNA polymerase I Replaces RNA primer

with DNA; replaceet is i a 5’3’ directio DNA polymerase III Joins the sugar-

phosphate backbone of Okazaki fragments. DNA ligase Cleaves the sugar-phosphate

backbone in order to relieve strain on the DNA strand due to torsion from the

replication forks. Topoisomerase Binds and stabilizes single-stranded DNA template

until polymerase complex moves forward. Single-stranded DNA binding protein 7) A.

How does the antiparallel structure of the double helix affect replication? Because of

struture, DNA polerases a ol add uleotides to the free 3’ ed of a prier or

groig DNA strad, eer the 5’ ed. B. How does leading strand synthesis differ from

lagging strand synthesis? Include the term Okazaki fragment in your answer. Along one

strand, DNA can synthesize a complementary strand continuously by elongating the new

DNA i the adator 5’



3’ diretio. This is the leading strand. To elongate the other

new strand of DNA i the adator 5’



3’ diretio, the DNA polymerase III must start

in the direction away from the replication fork. This is the lagging strand, and is

synthesized discontinuously as a series of fragments – Okazaki fragments (100-200

nucleotides in Eukaryotes and 1,000-2,000 in E. coli)

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Document Summary

Lecture 23 dna replication: the dna molecule of a normal mammalian chromosome is a double helix. Antiparallel their subunits run in opposite directions. Phosphate group atta(cid:272)hed to 5" carbon, oh atta(cid:272)hed to 3" (cid:272)ar(cid:271)o(cid:374). What are chargaff"s rules? (1) dna base composition varies between species (2) for each species, the percentages of a and t bases are roughly equal, as are those of g and c bases. Semiconservative when dna replicates, each of the daughter molecules will have one old strand from the parent molecule and one new strand. Hundreds or even a few thousand 5) what is the source of energy that drives. Dna polymerase catalyzes the addition of each monomer via a dehydration reaction. As each monomer is joined to the growing end of the dna strand, two phosphate groups are lost as a molecule of pyrophosphate (p p).

Related Questions

The term replication refers to DNA's abilityto

a. attack bacteriaphages

b. make copies of itself

c. respond to X-ray photography

d. twist into a helix

Meselson and Stahl performed thedensity-gradient centrifugation of DNA in a solution of calciumchloride.

a. True

b. False

Sulfur is

a. found in bacteria but not viruses.

b. found in proteins but not nucleic acids.

c. found in nucleic acid but notproteins.

d. found in viruses but not bacteria.

e. needed for bacteriophages to attach tobacteria.

Chargaff's rule state that in DNA, the amount ofadenine equals

a. the amount of cytosine

b. the amount guanine

c. the amount of thymine

d. the amount of guanine and thymine

Each complete turn of the DNA helix is howlong?

b. 5.0 nm

Griffin did an experiment in which live Rbacteria was changed by dead S bacteria. Such a change is anexample of

Select one:

a. translocation

b. transformation

c. transduction

d. fertilization

One of Chargaff's rules state

a. A + T = G + C

b. A + G = T + C

c. A = G, T = C

d. A = C, T = G

The diameter of the DNA ladder is always

c. 2.0 nm

Which of the following is a purine base?

b. malomine

According to the base pairing rules, guaninebinds with

a. guanine

b. adenine

c. thymine

d. cytosine

Which of the following is a pyrimidinebase?

Select one:

a. colchicines

b. guanine

c. adenine

d. None of the answers

e. thymine

Each nucleotide in a DNA molecule is constructedof

Select one:

a. a phosphate group, a five carbon sugar, and anitrogen base

b. a phosphate group, a six carbon sugar,and a nitrogen base

c. a phosphate group, a five carbon sugar, and aoxygen base

d. a sulfur group, a five carbon sugar molecule,and a nitrogen base

champagneant40

The term replication refers to DNA's abilityto

a. attack bacteriaphages

b. make copies of itself

c. respond to X-ray photography

d. twist into a helix

Meselson and Stahl performed thedensity-gradient centrifugation of DNA in a solution of calciumchloride.

a. True

b. False

Sulfur is

a. found in bacteria but not viruses.

b. found in proteins but not nucleic acids.

c. found in nucleic acid but notproteins.

d. found in viruses but not bacteria.

e. needed for bacteriophages to attach tobacteria.

Chargaff's rule state that in DNA, the amount ofadenine equals

a. the amount of cytosine

b. the amount guanine

c. the amount of thymine

d. the amount of guanine and thymine

Each complete turn of the DNA helix is howlong?

b. 5.0 nm

Griffin did an experiment in which live Rbacteria was changed by dead S bacteria. Such a change is anexample of

Select one:

a. translocation

b. transformation

c. transduction

d. fertilization

One of Chargaff's rules state

a. A + T = G + C

b. A + G = T + C

c. A = G, T = C

d. A = C, T = G

The diameter of the DNA ladder is always

c. 2.0 nm

Which of the following is a purine base?

b. malomine

According to the base pairing rules, guaninebinds with

a. guanine

b. adenine

c. thymine

d. cytosine

Which of the following is a pyrimidinebase?

Select one:

a. colchicines

b. guanine

c. adenine

d. None of the answers

e. thymine

Each nucleotide in a DNA molecule is constructedof

Select one:

a. a phosphate group, a five carbon sugar, and anitrogen base

b. a phosphate group, a six carbon sugar,and a nitrogen base

c. a phosphate group, a five carbon sugar, and aoxygen base

d. a sulfur group, a five carbon sugar molecule,and a nitrogen base

skybeaver431

In addition to identifying the genetic material, the experiments of Avery, MacLeod, and McCarty with different strains of Streptococcus pneumoniae demonstrated that

	DNA is a double helix.
	DNA may be taken up by bacterial cells and be active.
	DNA is present in bacteriophage T2.
	eukaryotic cells may be genetically transformed.
	DNA binds to the cell wall of the bacterium.

In order to show that DNA in cell extracts is responsible for genetic transformation in Streptococcus pneumoniae, important corroborating evidence should indicate that _______ also destroy transforming activity.

	temperatures high enough to kill cells
	enzymes that hydrolyze proteins
	enzymes that hydrolyze DNA
	enzymes that hydrolyze polysaccharides
	enzymes that hydrolyze RNA

Based on what you have learned about the experiments conducted by Griffith and Avery and colleagues with bacteria, which of the following would result in transformation of living R cells?

	Pure RNA from S cells
	Cell-membrane extracts from S cells
	A mixture of pure RNA and protein from S cells
	Cell-free extracts from S cells
	Pure protein from S cells

A-T base pairs in a DNA double helix

	form three hydrogen bonds with each other.
	are more heat-stable than G-C base pairs.
	are of a substantially different length than G-C base pairs.
	are not accessible to DNA binding proteins.
	are chemically distinct from G-C base pairs.

If 23 percent of the bases in a sample of double-stranded DNA are adenine, what percentage of the bases are uracil?

	27
	50
	0
	73
	23

The uniform diameter of the DNA structure provides evidence for

	antiparallel DNA strands.
	a right-handed helix.
	a double-stranded helix.
	3â² end phosphorylation.
	purineâpyrimidine pairing.

If a sequence of one strand of DNA is 5â²-TGACTATC-3â², what is the complementary strand?

	5â²-ACTGATAG-3â²
	3â²-TGACTATC-5â²
	3â²-ACTGATAG-5â²
	3â²-ACTGATAG-3â²
	5â²-TGACTATC-3â²

What structural aspect of the DNA facilitates dissociation of the two DNA strands for replication?

	3â² end phosphorylation
	Purineâpyrimidine pairing
	Antiparallel DNA strands
	Covalent bonds between sugars and phosphate groups
	Hydrogen bonding between paired bases

If the MeselsonâStahl density gradient experiment had resulted in two bands of DNA molecules after only one round of replication, one containing only ¹⁵N and the second only ¹⁴N, this result would have indicated that replication was

	unidirectional.
	dispersive.
	conservative.
	bidirectional.
	semiconservative.

10.

The nucleoside analogue acyclovir, which is used to treat herpes simplex virus (HSV) infections, lacks a 3â² hydroxyl group (âOH). Predict what will happen if the host cell DNA polymerase incorporates a molecule of acyclovir into an elongating strand of HSV DNA.

	The replication complex will no longer bind to origins of replication.
	The DNA polymerase will only incorporate acyclovir molecules.
	Acyclovir will bind single-strand binding proteins.
	DNA polymerase will not be able to link a successive nucleotide.
	Acyclovir will block the activity of the DNA helicase.

11.

Which of the following does not demonstrate the stability of the DNA double helix?

	Single-strand binding proteins are required to keep the strands apart.
	Paired bases form hydrogen bonds.
	High temperatures are required to denature it.
	DNA synthesis requires energy.
	DNA helicases require ATP.

12.

What effect would a primase inhibitor have on DNA replication?

	DNA polymerase would not be able to add bases to the DNA.
	Primase would be blocked from joining the DNA replication complex.
	Primase would not be able to provide primers for DNA polymerases.
	DNA polymerase would not be able to use DNA as a template.
	There would be no effect on DNA replication.

13.

To replicate their DNA in a timely manner, most eukaryotic chromosomes

	normally have uncoiled DNA.
	have multiple origins of replication.
	contain linear molecules of single-stranded DNA.
	have two replication forks that move in the same direction.
	are composed entirely of DNA.

14.

Which statement about DNA replication is false?

	Okazaki fragments are synthesized as parts of the leading strand.
	Error rates for DNA replication are reduced by proofreading of the DNA polymerase.
	The sliding clamp increases the rate of DNA synthesis.
	Replication forks represent areas of active DNA synthesis on the chromosomes.
	Ligases and polymerases function in the vicinity of replication forks.

15.

In many eukaryotes, there are repetitive sequences called telomeres at the ends of chromosomes. After successive rounds of DNA replication, the _______ strand becomes shorter. In some cells, an enzyme called _______ repairs the shortened strand.

	leading; telomerase
	lagging; telomerase
	lagging; DNA polymerase I
	leading; DNA polymerase I
	leading; replicase

16.

A researcher studies normal human fibroblast cells. They can be maintained in culture but die off after about 30 cell generations. Unexpectedly, a colony of cells continues to survive and divide past 30 generations. Which scenario is most likely true for these cells?

	DNA polymerase is constantly active.
	Primase is able to extend the telomeres.
	The mismatch repair system is extra efficient.
	The telomerase gene is being expressed.
	The cells do not need the ends of their chromosomes.

17.

If DNA polymerase III introduces an incorrect nucleotide, what is the first corrective action made by the DNA repair system?

	The replication complex excises the incorrect nucleotide.
	The excision repair proteins remove the incorrect nucleotide.
	The mismatch repair system scans for base-pairing mismatches.
	There is no correction, because nucleotide errors by DNA polymerases are not repaired.
	DNA ligase connects the correct nucleotide.

18.

Choose the correct order of the following four events in the excision repair of DNA:
(1) Base-paired DNA is made complementary to the template.
(2) Damaged bases are recognized.
(3) DNA ligase seals the new strand to existing DNA.
(4) Part of a single strand is excised.

	1, 2, 3, 4
	2, 1, 3, 4
	3, 4, 2, 1
	2, 4, 1, 3
	4, 2, 3, 1

19.

Six complete cycles of PCR should result in a _______-fold increase in the amount of DNA.

	64
	32
	12
	128
	6

20.

When double-stranded DNA is heated to temperatures above 90Â°C, it denatures. Denaturation is a process that

	breaks covalent bonds.
	hydrolyzes DNA.
	separates double-stranded DNA into two single strands.
	causes new hydrogen bonds to form.
	irreversibly destroys the double helical structure.

BIOL 2112 Chapter Notes - Chapter 16: Okazaki Fragments, Dna Replication, Dna Ligase

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