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BIOL 1105 > 11: DNA Structure & Replication > Flashcards

11: DNA Structure & Replication Flashcards

Module 2, Lesson 5

1
Q

The modern model of DNA was proposed by ____ in ____.

A

Watson and Crick ; 1953

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2
Q

____ used x-ray diffraction to deduce the 3D structure of DNA in ____.

A

Rosalind Franklin ; 1953

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3
Q

DNA is a…

A

Nucleic acid

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4
Q

List the three main components of a nucleotide.

A
  1. 5-carbon pentose sugar
  2. Nitrogenous base
  3. Phosphate group
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5
Q

In DNA, the chemical group attached to the 2’ carbon is…

A

Deoxyribose
(an H molecule)

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6
Q

In RNA, the chemical group attached to the 2’ carbon is…

A

Ribose
(an OH group)

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7
Q

Which carbon(s) in the pentose sugar are involved in nucleotide bonding?

A

3’ and 5’

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8
Q

What component of a nucleotide is attached the 1’ carbon?

A

Nitrogenous base

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9
Q

List the four nitrogenous bases that may be found in DNA.

A
  1. Adenine
  2. Thymine
  3. Cytosine
  4. Guanine
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10
Q

Adenine and guanine are double-ringed structures called…

A

Purines

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11
Q

Cytosine and thymine are single-ringed structures called…

A

Pyrimidines

Uracil, found in RNA, is also a pyrimidine.

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12
Q

Which component of a nucleotide is attached to the 5’ carbon?

A

The phosphate group
(PO4)

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13
Q

Nucleotides are linked together via…

A

Phosphodiester bonds

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14
Q

When nucleotides link, bonds form between the ____ end of one and the ____ end of another.

A

5’ (phosphate) and 3’ (hydroxyl)

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15
Q

Nucleotides can assemble into long strands using…

A

Dehydration synthesis reactions

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16
Q

In a strand of nucleotides, one end will always be a free ____ carbon and the other will always be a free ____ carbon.

A

5’ and 3’

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17
Q

True or false:

DNA molecules are nonpolar.

A

False

All DNA molecules have intrinsic polarity.

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18
Q

The sequence of nitrogenous bases in a strand of nucleotides is always written…

A

From the 5’ end to the 3’ end

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19
Q

Chargaff’s rules state that…

(two)

A
  1. There is always an equal proportion of purines and pyrimidines in DNA
  2. The purine:pyrimidine ratio varies between species
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20
Q

What can be inferred about nitrogenous bases from Chargaff’s rules?

A
  1. The amount of adenine equals the amount of thymine
  2. The amount of cytosine equals the amount of guanine
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21
Q

The process of shooting X-rays through a crystal of interest, then analyzing the pattern produced by the rays, is called…

A

X-ray diffraction

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22
Q

X-ray diffraction was used to determine…

(three things)

A
  1. That DNA has a helical shape
  2. The diameter of the helix
  3. The distance between helical turns
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23
Q

True or false:

In developing their model of DNA, Watson and Crick never performed a single experiment related to DNA.

A

True

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24
Q

Each molecule of DNA consists of two strands of nucleotides that twist together to form a…

A

Double helix

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25
Q

The “backbone” of each nucleotide strand is composed of…

A

Sugar and phosphate units

Hence why it is sometimes called the “sugar-phosphate backbone”.

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26
Q

Nitrogenous bases pair with a base on the opposing strand using…

A

Hydrogen bonds

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27
Q

When cytosine bonds with guanine, they form ____ H-bond(s).

A

3

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28
Q

When adenine bonds with thymine, they form ____ H-bonds.

A

2

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29
Q

The diameter of a DNA molecule is consistently…

A

2 nm

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30
Q

List the two grooves found in the sugar-phosphate backbone.

A
  1. Major groove (larger)
  2. Minor groove (smaller)
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31
Q

The two strands in a DNA molecule run ____ to each other.

A

Antiparallel

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32
Q

If one strand of DNA has a sequence of 5’-ACCTAG-3’, what is the sequence of the other strand?

A

5’-CTAGGT-3’

don’t memorize this particular sequence, I just made it up to illustrate a point

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33
Q

The Watson-Crick model suggested that the basis of copying genetic information was…

A

Complementary

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34
Q

What does it mean when we say that DNA replication is “complementary”?

A

The sequence of the parental strand determines the sequence of the daughter strand.

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35
Q

List the three proposed models of DNA replication.

A
  1. Conservative
  2. Semi-conservative
  3. Dispersive
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36
Q

Which model of DNA replication did Watson and Crick believe was most likely to be correct?

A

The semi-conservative model

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37
Q

The conservative model suggests that during DNA replication…

A

Both parent strands stay intact, and the daughter molecule contains all-new material.

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38
Q

The semi-conservative model suggested that during DNA replication…

A

1 parent strand remains intact, and 1 new daughter strand is synthesized

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39
Q

The dispersive model suggests that during DNA replication…

A

Parts of both parental strands are dispersed throughout the daughter molecule and mix with newly-synthesized DNA.

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40
Q

In 1958, Meselson and Stahl’s experiments supported the ____ model.

A

Semi-conservative

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41
Q

How does a molecule of DNA replicate?

(very broadly)

A

The helix is opened and both strands are copied, so the daughter molecule has one parental strand and one new strand

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42
Q

What three things are needed for DNA replication to proceed?

A
  1. Something to copy
  2. Something to do the copying
  3. Enough relevant building blocks
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43
Q

During DNA replication, the parental molecule becomes the…

A

Template

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44
Q

The copying of DNA is facilitated by enzymes called…

A

DNA polymerase

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45
Q

The “building blocks” for new DNA are…

A

Nuceloside triphosphates

(sometimes the textbook will call these “nucleotide triphosphates”, treat both as being correct)

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46
Q

A molecule that contains only a pentose sugar and a nitrogenous base is termed a…

A

Nucleoside

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47
Q

List the three stages of DNA replication.

A
  1. Initiation - process starts
  2. Elongation - synthesis of new DNA
  3. Termination - process ends
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48
Q

What are the functions of DNA polymerase?

(two)

A
  1. Matches template strands with complementary nucleotides
  2. Links incoming nucleotides to the daughter strand
49
Q

DNA polymerase always synthesizes DNA from the ____ end to the ____ end.

A

5’ to 3’

50
Q

True or false:

DNA polymerase can start the process of DNA replication.

A

False

Starting the process requires a primer.

51
Q

The primer is made by ____ and extended by ____.

A

RNA polymerase ; DNA polymerase

52
Q

The action of DNA polymerase in the 5’ to 3’ direction is termed…

A

Writing or synthesizing

53
Q

The action of DNA polymerase in the 3’ to 5’ direction is termed…

54
Q

Many prokaryotes contain a single circular DNA molecule called a…

A

Chromosome

55
Q

DNA replication begins at the ____ and ends at the ____.

A

Origin of replication ; terminus

56
Q

What is the function of initiator proteins in DNA replication?

A

Binds to the origin and separates the two strands of DNA.

57
Q

DNA is catalyzed by ____, macromolecular complexes that contain DNA polymerase.

A

Replisomes

58
Q

True or false:

In prokaryotes, replication proceeds in one direction around the chromosome.

A

False

Replication proceeds in both directions simultaneously.

59
Q

The region of DNA controlled by the origin is called the…

60
Q

List the three major types of DNA polymerase found in prokaryotes.

A
  1. DNA polymerase 1
  2. DNA polymerase 2
  3. DNA polymerase 3

wow……so creative

61
Q

What is the function of DNA polymerase 1?

A

Replaces the RNA primers with DNA in the completed molecule.

62
Q

What is the function of DNA polymerase 2?

A

It is involved in DNA repair processes.

63
Q

What is the function of DNA polymerase 3?

A

It is the main replication enzyme and responsible for most of DNA synthesis.

64
Q

DNA polymerase has an exonuclease action in the 3’ to 5’ direction called…

A

“Proofreading”

65
Q

An exonuclease activity is one that can…

A

Break the phosphodiester bonds at the end of the molecule

66
Q

Proofreading allows DNA polymerase to…

A

Recognize and remove mis-paired bases.

67
Q

True or false:

DNA replication is a continuous process.

A

False

The process is semi-discontinuous.

68
Q

The strand that is synthesized continuously from the initial RNA primer is the…

A

Leading strand

(in the diagrams in the textbook, it’s on the bottom of the replication fork)

69
Q

The strand that is synthesized discontinuously is the…

A

Lagging strand

(in the diagrams in the textbook, it’s on the top of the replication fork)

70
Q

Because the lagging strand is synthesized discontinuously…

A

It has multiple priming and synthesis events which make short DNA fragments

71
Q

The short sequences of DNA synthesized on the lagging strand are called…

A

Okazaki fragments

72
Q

True or false:

Both the leading and lagging strands are synthesized in the same direction.

A

False

The lagging strand is synthesized in the opposite direction of the replication fork’s movement.

73
Q

List the steps involved in replication of the lagging strand.

A
  1. Primase makes a short RNA primer
  2. DNA polymerase 3 makes an Okazaki fragment from the primer
  3. DNA polymerase 1 replaces the primers with DNA
  4. DNA ligase seals the resulting gap in the backbone
74
Q

The enzyme that makes RNA primer for the lagging strand is…

75
Q

The enzyme responsible for sealing the “nicks” (gaps) in the backbone is…

A

DNA ligase

76
Q

Enzymes that use energy from ATP to unwind the DNA strands are…

77
Q

____ coat the separated DNA strands to prevent them from recombining.

A

Single-strand binding proteins
(SSBs)

78
Q

List two problems caused by unwinding DNA.

A
  1. Supercoiling
  2. Torsional strain
79
Q

Supercoiling occurs when…

A

DNA twists on itself

80
Q

Why is supercoiling a problem?

A

It can damage the DNA and block the progress of the replisome

81
Q

Torsional strain occurs when…

A

DNA strands become too twisted

82
Q

What is the function of DNA gyrase?

A

Relieves torsional strain

83
Q

DNA polymerases are kept on track by a protein complex called a…

A

Clamploader

84
Q

In order to synthesize both strands at the same time, DNA replication is thought to involve…

A

Looping the lagging strand

85
Q

DNA gyrase and helicase work together to…

A

Open the DNA helix

86
Q

DNA polymerase 3 is held to the DNA strands by the…

A

Beta clamp

87
Q

Unbound nucleotides are prevented from reforming H-bonds by the action of…

88
Q

The beta clamp protein is released from DNA polymerase 3 when…

A

It contacts an Okazaki fragment on the lagging strand

89
Q

True or false:

Eukaryotic and prokaryotic DNA replication proceeds in exactly the same fashion.

90
Q

List two factors that complicate DNA replication in eukaryotes.

A
  1. Size of the genome
  2. Structure of the genome
91
Q

True or false:

Eukaryotes only have one origin of replication.

A

False

They often have multiple origins.

92
Q

Approximately how many origins of replication are needed in the human genome?

93
Q

What additional problem is caused by eukaryotes having linear chromosomes?

A

They require a special mechanism to replicate the ends of the chromosomes

94
Q

What are the two main types of DNA polymerase in eukaryotes?

A

DNA polymerase delta (δ)
DNA polymerase epsilon (ε)

95
Q

The special structures at the ends of eukaryotic chromosomes which consist of short, repeated DNA sequences are called…

96
Q

What are the functions of telomeres?

(two)

A
  1. Protect the ends of DNA from nucleases
  2. Maintain linear chromosome integrity
97
Q

True or false:

Both the leading and lagging strands of eukaryotic DNA require extra steps to replicate their ends.

A

False

Only the lagging strands requires extra steps.

98
Q

Without extra steps, what would happen to the end of the lagging strand in eukaryotes?

A

The cell would be unable to replicate it, causing the chromosome to shorten each time the cell divides.

99
Q

Eukaryotes can replicate the last section of the lagging strand using…

A

Telomerase

100
Q

Telomerase contains an RNA template that matches…

A

The repeating telomere DNA

101
Q

How does telomerase work?

A

It binds to the telomere and extends the lagging strand with repeating stretches of DNA.

102
Q

Telomere length has been linked to…

A

Senescence
(cell aging)

103
Q

In humans, telomerase is expressed in…

A

Embryos and children

104
Q

True or false:

In human adults, telomerase is only active in stem cells.

A

True

This is why cells have a limited number of divisions they can undergo.

105
Q

Most ____ cells have active telomerase and lack telomere shortening.

106
Q

List two ways that the DNA of a cell can become damaged.

A
  1. Errors during replication
  2. Impact of mutagens (radiation and chemicals)
107
Q

True or false:

No mistakes made during DNA replication are acceptable to the cell.

A

False

Some mistakes are acceptable and remain - this causes genetic variation.

108
Q

How does the cell correct errors made during DNA replication?

A

DNA polymerase “proofreads” the new strands

109
Q

Mutagens damage DNA by…

A

Increasing the number of mistakes and mutations above normal levels

110
Q

There is a link between the failure of DNA repair systems and…

111
Q

List the two general categories of DNA repair mechanisms.

A
  1. Specific repair
  2. Nonspecific repair
112
Q

Specific repair mechanisms are a very effective means of targeting…

A

A single type of DNA damage

113
Q

Nonspecific repair mechanisms can repair multiple types of DNA damage using…

A

A single mechanism

114
Q

The specific repair mechanism used to correct damage from exposure to UV radiation is…

A

Photorepair

115
Q

How does UV radiation damage DNA?

A

It causes two adjacent thymines to covalently link (a thymine dimer) which results in replication errors.

116
Q

How does photorepair work?

A

An enzyme absorbs visible light and uses it to cleave the thymine dimers

117
Q

A nonspecific repair mechanism that removes and replaces damaged DNA is called…

A

Excision repair

118
Q

After a damaged region is removed, DNA polymerase uses ____ as the template to replace it.

A

Information on the undamaged strand

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