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Flashcards in Chapter 9 Deck (174):
1

What is molecular genetics?

An examination of DNA structure and Function at the Molecular level.

2

What does DNA stand for?

Deoxyribonucleic Acid

3

What does RNA stand for?

Ribonucleic Acid

4

For DNA to fulfill its role as genetic material, what is the first criteria?

Information
The genetic material must contain the information necessary to construct an entire organism. It must provide the blueprint for determining the inherited traits of an organism.

5

For DNA to fulfill its role as genetic material, what is the second criteria?

Transmission
Genetic material must be passed from parent to offspring

6

For DNA to fulfill its role as genetic material, what is the third criteria?

Replication
The genetic material is passed from parents to offspring, and from mother cell to daughter cells during cell division, it must be copied.

7

For DNA to fulfill its role as genetic material, what is the fourth criteria?

Variation
Phenotypic variability must occur and that happens if the genetic material must also vary in ways that can account for the known phenotypic difference within the species.

8

What is virulence?

Ability to cause disease

9

What was Frederick Griffith's experiement?

Studied certain strains of S. penumoniae and saw that some secrete a polysaccharide capsule, wheras other strains do not. When streaked on a petri dish, capsule-secreting strains have a smooth colony morphology, while those strains unable to secrete a capsule have a rough appearance. The different strains also affect their ability to cause disease. Smooth can overcome immune system, rough is destroyed.

10

Why would a mouse infected with both rough s. pneumoniae and dead smooth S. penumoniae die?

The type R bacteria had taken up genetic material from the heat-killed type smooth bacteria, converted the rough bacteria into the Smooth bacteria. This allowed them to kill the mouse.

11

Who coined the term transformation?

Fredrick Griffith

12

What is transformation again?

When a plasmid vector or segment of chromosomal DNA is introduced into the bacterial cell.

13

What is the transforming principle?

Unidentified substance causing transformation to occur

14

How does Griffith's experiment follow the four criteria for genetic material?

The transformed bacteria acquired the information to make a capsule.
Among different strains, variation exists.
The genetic material that is necessary to create a capsule must be replicated so it can be transmitted from mother to daughter cells during cell division.

15

Generally what did Griffith's experiment show?

Some genetic material from the dead bacteria had been transferred to the living bacteria and provided them with a new trait.

16

Who used Griffith's experiment to determine what the genetic material was?

Avery
MacLeod
McCarty

17

What did Avery Macleod, and McCarty do experimentally?

Established biochemical purification procedures and prepared the S. pneumoniae strains. After many extracts, they discovered that only the extract that contained purified DNA from S bacteria, were able to convert R to S.

18

What was the purpose of adding RNase and protease to a DNA extract?

RNase and protease were added to the DNA extract to rule out the possibility that small amounts of contaminating RNA or protein was responsible for converting the type R. bacteria into type S.

19

How did Avery, MacLeod, and McCarty verify that DNA and not some contaminating substances were the source of the genetic material?

They treated the DNA extract with enzymes that digest DNA, RNA, and Protein

20

What are the three enzymes that digest DNA, RNA, and Protein?

DNase,
RNase
protease

21

What were the results when the extracts were treated with RNase and protease?

They still converted type R bacteria into type S.
Which shows that RNA and Protein were not the genetic material.

22

What was the results when the extract was treated with DNase?

It lost its ability to convert type R into type S bacteria. Thus showing DNA is the genetic material, or DNA is the transforming principle.

23

What was Alfred Hershey and Martha Chase's experiment?

They took another approach to prove DNA is the genetic material using virus T2.

24

The external structure of the T2 phage, is called what?

The capsid or phage coat

25

What does the capsid or phage coat consist of?

A head, sheath, tail fibers, and base plate.

26

Biochemically, the phage coat is composed entirely of what?

Protein, which includes several different polypeptides.

27

DNA is found where in the T2 capsid?

The head

28

Why is the T2 virus considered simple by the molecular point of view?

It is only composed of two macromolecules:
DNA and Proteins

29

The genetic material of a bacteriophage contains many genes which provide what?

The blueprint for making new viruses

30

Can a virus itself synthesize a new virus?

No

31

The virus must do what with its genetic material?

It must introduce its genetic material into the cytoplasm of a living cell.

32

How does a T2 insert its genetic material?

Starting with its tail fibers, it attaches to the bacterial cell wall and inject the genetic material into the cytoplasm. The phage coat remains attached on the outside of the bacterium and does not enter the cell.

33

For infection to occur, what has to happen to the T2 genetic material?

It must be injected into the bacterial cytoplasm.

34

How did Hershey and Chase verify DNA is the genetic material of T2?

They devised a method to separate the phage coat from the genetic material which is injected into the cytoplasm. They exposed bacteria to T2 phage, allowig sufficient time for inject material, then sheared the phage coat from the bacteria by a blender treatment. Thus the genetic material was separated from the protein.

35

In the experiment of Avery, Mcleod, and McCarty, the addition of RNase and protease to the DNA extracts
a. prevented the conversion of type S bacteria into type R bacteria.
b. allowed the conversion of type S bacteria into type R bacteria.
c. prevented the conversion of type R bacteria into type s bacteria.
d. allowed the conversion of type R bacteria into type S bacteria.

d. allowed the conversion of type R bacteria into type S bacteria.

36

In the Hershey and Chase experiment involving T2 phage, after blender treatment and centrifugation
a. most of the 32P was in the supernatant and most of the 35S was in the pellet.
b. Most of the 35S was in the supernatant and most of the 32P was in the pellet
c. equal amounts of 32P and 35S were in the supernatant and pellet.
d. none of the above.

b. Most of the 35S was in the supernatant and most of the 32P was in the pellet

37

Who coined the term nucleic acids? When

Friedrich Miescher
1869

38

What was Friedrich Miescher's observations?

He identified a novel phosphorus-containing substance from the nuclei of white blood cells found in waste surgical bandages. He named it nuclein.

39

What was learned as the structure of DNA and RNA became better understood?

They are acidic molecules, which means they release hydrogen ions in solution and have a net negative charge at neutral pH.

40

What are the levels of nucleic acid structure?

1. nucleotides form the repeating structural unit of nucleic acids
2. Nucleotides are linked together in a linear manner to form a strand of DNA or RNA
3. Two strands of DNA (and sometimes strands of RNA) interact with each other to form a double helix
4. The three dimensional structure of DNA results from the folding and bending of the double helix. Within living cells, DNA is associated with a wide variety of proteins that influence its structure.

41

When going from simple to complex, which of the following is the proper order for DNA?
a. nucleotide, double helix, DNA strand, Chromosome
B. Nucleotide, chromosome, double helix, DNA strand
C. nucleotide, DNA strand, double helix, chromosome
D. Chromosome, nucleotide, DNA strand, double helix.

C. nucleotide, DNA strand, double helix, chromosome

42

A nucleotide has what three components?

At least one phosphate group
A pentose sugar
Nitrogenous base

43

Nucleotides vary with regard to what?

The sugar and the nitrogenous base

44

What are the two types of sugars in nucleotides?

Deoxyribose
Ribose

45

What are the two subdivisions of the five different bases in nucleotides?

Purines
Pyrimidines

46

What are the purine bases?

Adenine
Guanine

47

What are the pyrimidine bases?

Thymine
Cytosine
Uracil

48

Purine bases contain what?

A double ring structure

49

Pyrimidine bases contain what?

Single ring structure

50

Which base is not found in RNA?

Thymine

51

What is found in RNA to replace thymine?

Uracil.

52

Which bases are in both DNA and RNA?

Adenine
Guanine
Cytosine

53

The bases and sugars have a standard what?

Numbering system

54

The nitrogen and carbon atoms found in the ring structure of the bases are given what numbers for purines?

1-9

55

The nitrogen and carbon atoms found in the ring structure of the bases are given what numbers for pyrimidines?

1-6

56

The five carbons found in sugars are designated with what numbers?

Primes such as 1 to distinguish them from the number found in the bases.

57

Which components are not found in DNA?

Ribose
Uracil

58

What are important for the nucleotide's function?

The locations of the attachment sites of the base and phosphate to the sugar molecule

59

In the sugar ring, carbon atoms are numbered how?

In a clockwise direction, beginning with a carbon atom adjacent to the ring oxygen atom. The fifth carbon is outside the ring structure.

60

In a single nucleotide, the base is always what?

Attached to the 1' carbon atom, and one or more phosphate groups are attached at the 5' position.

61

The -OH group attached to the 3' carbon is important in what?

Allowing nucleotides to form covalent linkages with each other.

62

The terminology used to describe nucleic acid units is based on what three structural features?

The type of sugar
The type of base
The number of phosphate groups.

63

What is a nucleoside?

When a sugar is attached to only a base, the pair is called a nucleoside

64

What is a adenosine?

Ribose is attached to adenine

65

What are the names of nucleosides composed of ribose and guanine, cytosine, or uracil?

Guanosine
Cytidine
Uridine

66

What are nucleosides made of deoxyribose and adenine, guanine, thymine, or cytosine called?

Deoxyadenosine
Deoxyguanosine
Deoxythymidine
Deoxycytidine

67

What creates a nucleotide?

The covalent attachment of one or more phosphate molecules to a nucleoside.

68

One or more phosphate groups are attached to a sugar via what bond?

Ester bond.

69

If a nucleotide contains ribose, adenine, and one phosphate, what is it called?

Adenosine monophosphate
(AMP)

70

If a nucleotide composed of ribose, adenine, and three phosphate groups, what is it called?

Adenosine Triphosphate
(ATP)

71

What is a nucleotide made of deoxyribose, adenine and thre phosphate groups called?

Deoxyadenosine triphosphate (dATP)

72

Which of the following could be the components of a single nucleotide found in DNA?
a. deoxyribose, adenine, and thymine
b. ribose, phosphate, and cytosine
c. deoxyribose, phosphate, and thymine
d. ribose, phosphate, and uracil

c. deoxyribose, phosphate, and thymine

73

A key difference between the nucleotides found in DNA versus RNA is that
a. DNA has phosphate, but RNA does not
b. DNA has deoxyribose, but RNA has ribose
c. DNA has thymie, but RNA has uracil.
d. both b and c.

d. both b and c.

74

A strand of DNA or RNA has nucleotides that are linked to each other in what fashion?

Linear fashion

75

What is a phosphodiester linkage?

In a DNA or RNA strand, a linkage in which a phosphate group connects two sugar molecules together.

76

What forms the backbone of DNA or RNA strand?

The phosphates and sugar molecules.

77

What projects from the backbone?

The bases

78

The backbone is what charge? Why?

Negatively charged
Because each phosphate has a negative charge.

79

Which components of a nucleotide form the backbone of a DNA strand?

Deoxyribose and phosphate

80

What is a second important structural feature of nucleotides?

The orientation of the nucleotides.

81

A strand of DNA has a what?

Directionality

82

What is directionality?

IN DNA and RNA, refers to the 5' to 3' arrangement of nucleotides in a strand; in proteins, refers to the linear arrangement of amino acids from the N-terminal to C-terminal ends.

83

Why do DNA have directionality?

Because all sugar molecules have the same orientation.

84

The nucleotides within a strand are covalently attached to what? Via what?

Each other via phosphodiester linkages.

85

Can bases shuffle around and become rearranged?

No

86

In a DNA strand, a phosphate connects a 3' carbon atom in one deoxyribose to
a. a 5' carbon in an adjacent deoxyribose.
b. a 3' carbon in an adjacent deoxyribose.
c. a base in an adjacent nucleotide.
d. none of the above.

a. a 5' carbon in an adjacent deoxyribose.

87

What did James Watson and Francis Crick discover?

They committed themselves to determining the structure of DNA because they felt this knowledge was needed to understand the functioning of genes.

88

What did Linus Pauling discover in 1950?

Regions of proteins can fold into a secondary structure known as a helix.

89

How did Pauling prove his theory?

He built large models by linking together simple ball-and-stick units.

90

Who also used a ball-and-stick approach?

Watson and Crick

91

Why is modeling useful?

Modeling is useful because it shows how molecules can fit together in a complicated three-dimensional structure.

92

What was a second important development that let to the elucidation of the double helix?

X-ray diffraction data.

93

What happens when a purified substance, such as DNA is subject to X-ray?

It produces a well-defined diffraction pattern if the molecule is organized into a regular structural pattern.

94

An interpretation of the diffraction pattern is done using what?

Mathematical theory

95

What did Rosalind Franklin do?

Used X-ray diffraction to study wet DNA fibers. She made advances in X-ray diffraction.

96

What modifications did Franklin make?

She adjusted her equipment to produce a extremely fine beam of x-ray

97

What did Franklin extract?

Finer DNA fibers than ever before and arranged them in parallel bundles.

98

What did Franklin study?

The DNA fibers' reactions to humid conditions.

99

What were the structural features Franklin figured out?

It was consistent with a helical structure
The diameter of the helical structure was too wide to be only a single stranded helix.
The helix contains about 10 base pairs (bp) per complete turn.

100

What did Erwin Chargaff pioneer?

He pioneered many of the biochemical techniques for the isolation, purification, and measurement of nucleic acids from living cells.

101

What was Erwin Chargaff's experiments?

He began with various types of cells as starting material. The chromosomes were extracted and treated with protease to separate the DNA. The DNA was treated with a strong acid, which cleaved the bonds between the sugars and bases, releasing the bases. The four bases were subjected to paper chromatography to separate the four types. The amounts of bases were determines spectroscopically.

102

What did Chargaff's work determine?

The amount of A equals T, and the amount of G equals C.

103

How did Watson and Crick determine the helical structure of DNA?

They tried putting (A genes with A genes, T to T, G to G, and C, to C.) It didn't work out. They then figured out that hydrogen bonding of adenine and thymine was structurally similar to guanine to cytosine.

104

Evidence or approaches that let to the discovery of the DNA double helix include
a. the determination of structures using ball-and-stick models.
b. the x-ray diffraction data of Franklin
c. the base composition data of Chargaff
d. all of the above.

d. all of the above.

105

Chargaff's analysis of the base composition of DNA is consistent with base pairing between
a. A and G, and T and C
b. A and A, G and G, T and T, and C and C.
c. A and T, and G and C
d. A and C, and T and G.

c. A and T, and G and C

106

In a DNA double helix, what is going on?

the two DNA strands are twisted together around a common axis to form a structure that resembles a spiral staircase.

107

How is the double-stranded structure stabilized?

By Base pairs (bp)

108

What are Base Pairs?

Pairs of bases in opposite strands that are hydrogen bonded to each other.

109

As you move past 10bp you have gone how many degrees around the backbone?

360 degrees

110

The linear distance of a complete turn of the double helix is what?

3.4nm

111

Each base pair traverses how far around a double helix?

.34nm

112

What holds the DNA strands together?

Hydrogen bonding between base pairs and base stacking holds the DNA strands together.

113

Describe the major and minor grooves in a double helix?

They are the indentations where the bases make contact with water. The major groove is larger then the minor groove.

114

What is the AT/GC rule?

In DNA, the phenomenon in which an Adenine base in one strand always hydrogen bonds with a thymine base in the opposite strands, and a guanine base always hydrogen bonds with a cytosine.

115

What does the AT/GC rule indicate?

That Purines always bond with pyrimidines. (T and C)

116

What keeps the width of the double helix constant?

Purines always bond with pyrimidines.

117

When do DNA sequences form more stable double-stranded structures?

DNA sequences with a high proportion of G and C because they have three hydrogen bonds compared to A and T which only have two.

118

What is complementary?

Sequences in two DNA strands that match each other according to the AT/GC rule.

119

What is the antiparallel arrangement?

An arrangement in a double helix in which one strand is running 5' to 3' direction, while the other strand runs 3' to 5'

120

What do the bases form?

Flattened planar structures.

121

In DNA, the bases are oriented how?

So the flattened regions are facing each other, an arrangement referred to as base stacking. This stabilizes the helix

122

How does base stacking stabilize the double helix?

By excluding water molecules.

123

The right handed and left handed directions are what, if laid flat in front of you?

Clockwise for right
Counter-clockwise for left.

124

The backbone of DNA is on what surface?

The outermost surface

125

The backbone of DNA has the most direct contact with what?

Water.

126

What are grooves?

The indentations where the atoms of the bases are in contact with the surrounding water.

127

The DNA double helix can form different types of what?

Structures.

128

What is B DNA?

The predominant form of DNA in living cells. It is a right-handed DNA helix with 10bp per turn. The bases tend to be centrally located and the hydrogen bonds between base pairs occur relatively perpendicular to the central axis.

129

What is Z DNA?

A left-handed DNA double helix that is found occasionally in the DNA of living cells. The backbone zigzags slightly. it has 12bp per turn. The bases are substantially tilted, relative to the central axis.

130

What determines if a B DNA can adopt a Z DNA conformation?

High ionic strength (high salt concentration) formation of a Z-DNA is favored by a sequences of bases that alternates between purines and pyrimidines.
At lower ionic strength, the methylation of cytosine bases favors Z-DNA formation.
Negative supercoiling favors Z-DNA conformation.

131

When does cytosine methylation occur?

When a cellular enzyme attaches a methyl group to the cytosine base.

132

What is the biological significance of Z DNA?

It is used in the process of transcription.

133

What did Alexander Rich and colleagues discover?

The Z DNA binding region of one protein played a role in regulating the transcription of particular genes.

134

Other researche has suggested what for Z DNA?

It plays a role in chromosome structure by affecting the level of compaction.

135

What was a discovery in 1957 by Alexander Rich, David Davies, and Gary Felsenfeld?

DNA can form a triple-helical structure called triplex DNA.

136

What is a triplex DNA?

A double stranded DNA has a third strand around it to form a triple stranded structure.

137

Does the Triplex DNA have any significant biological relevance?

NO

138

Why has interest in Triplex renewed?

Because the triplex DNA can form in vitro by mixing natural DNA stranded DNA and a third short strand that is synthetically made. The synthetic strand binds into the major groove of the naturally occuring double strand.

139

What is an interesting feature of the triplex DNA?

It is sequence specific. The synthetic third strand incorporates itself into a triple helix due to specific interactions between the synthetic DNA and the biological. The pairing rules are that a thymine in the synthetic DNA hydrogen bonds at an AT pair in the biological DNA and a cytosine in the synthetic DNA bonds with GC.

140

Why are researchers interested in the Triplex DNA medically?

It can be used as a tool for inhibiting particular genes. It can be used to silence hyperactive cancer cells.

141

Which of the following is not a feature of the DNA double helix?
a. it obeys the AT/GC rule
b. the DNA strands are antiparallel
c. the structure is stabilized by base stacking.
d. all of the above are correct features of DNA

d. all of the above are correct features of DNA

142

A groove in DNA refers to
a. the indentations where the atoms of the bases are in contact with the surrounding water.
b. the interactions between the bases in the DNA
c. the spiral structure of the DNA.
d. all of the above.

a. the indentations where the atoms of the bases are in contact with the surrounding water.

143

A key difference between B DNA and Z DNA is that
a. B DNA is right-handed, wheras Z DNA is left-handed
b. B DNA obeys the At/GC rule, Z DNA does not
c. Z DNA allows ribose in its structure, whereas B DNA uses deoxyribose.
d. Z DNA allows uracil in its strucutre, whereas B DNA uses thymine.

a. B DNA is right-handed, wheras Z DNA is left-handed

144

RNA strands are usually how long?

a few hundred to several thousand nucleotides.

145

How long is DNA?

Millions of base pairs long.

146

What happens when RNA is made during transcription?

The DNA is used as a template to make a copy of single-stranded RNA. Only one of the two DNA strands is used as a template for RNA synthesis. Therefore, only one complementary strand of RNA is usually made.

147

What types of bonds hold nucleotides together in an RNA strand?

Covalent bonds

148

What does the base pairing in RNA look like?

Short segments of RNA form a double-stranded region that is helical.

149

what is the results of different arrangements of base pairing on RNA?

Bulge loops
Internal loops
Multibranched junctions
Stem-loops

150

The Bulge loops, internal loops, multibranched junctions, and stem-loops contain regions of what?

Complementarity and noncomplementarity.

151

The complementarity regions of RNA are held together by what?

Hydrogen bonds between base pairs.

152

The noncomplementarity regions in RNA look how?

Base pairs projecting away from the double stranded regions.

153

What does a bulge loop look like?

A zit
One strand bulges out

154

What does a internal loop look like?

A bulge in someones throat.
Both strands have unattracted bases going away from each other.

155

What does a multibranched junction look like?

A four way stop with a square in the middle.
No bases make up the middle.

156

What does a stem-loop look like?

A coup-de-sac part of a three way stop.

157

What are the base-pairing rules in RNA?

A bonds with U and G bonds with C

158

What factors contribute to the structure of RNA?

Hydrogen bonding between base pairs.
Stacking between bases
Hydrogen bonding between bases and backbone regions.
Interactions between ions, small molecules, and large proteins

159

What is the structure of tRNA?

It has several double-stranded and single-stranded regions,
the Helices are antiparallel and right-handed, with 11-12 pb per turn. In living cells, the various regions of an RNA molecule fold and interact with each other to produce the three-dimensional structure.

160

The folding of RNA into a three-dimensional structure is important for what?

Its function.

161

What are the two key functional sites of a tRNA?

an anticodon
3' acceptor site.

162

What do the key functional sites of tRNA play a important role in?

Translation.

163

Why is the fold important in tRNA?

It allows the two key sites to be exposed on the surface of the molcule to perform their roles.

164

A double-stranded region of RNA
a. forms a helical structure.
b. obeys the AU/GC rule.
c. may promote the formation of different structures, such as bulge loops and stem loops.
d. does all of the above.

d. does all of the above.

165

After the DNa from type S bacteria is exposed to type R bacteria, list all of the steps that you think must occur for the bacteria to start making a capsule.

1. fragment of DNA binds to the cell surface
2. it penetrates the cell wall
3. it enters the cytoplasm
4. it recombines with the chromosome.
5. the genes within the DNA are expressed
6. the gene products create a capsule. They are enzymes that synthesize a capsule using cellular molecules as building blocks.

166

What are the building blocks of a nucleotide? With regard to the 5' and 3' positions on a sugar molecule, how are nucleotides linked together to form a strand of DNA?

Sugar, a nitrogenous base, and a phosphate group.
The phosphate is already linked to the 5' position on the sugar. When two nucleotides are hooked together, a phosphate on one nucleotide forms a covalent bond with the 3' hydroxyl group on another nucleotide.

167

If one DNA strand is 5'-GGCATTACACTAGGCCT-3' what is the complementary strand?

3'-CCGTAATGTGATCCGGA-5'

168

Compare the structural features of a double-stranded RNA structure with those of a DNA double helix.

RNA and DNA both form a helical structure due to base pairing. They are different in that the number of base pairs per turn is slightly different and RNA follows an AU/GC base pairing rule where DNA follows AT/GC

169

What structural features allows DNA to store information?

The nucleotide base sequence

170

An organism has a G + C content of 64% in its DNA. What are the percentages of A, T, G, and C?

G=32%
C=32%
A=18%
T=18%

171

A double stranded DNA molecule contains 560 nucleotides. How many complete turns would be found in this double helix?

The DNA molecule contains 280bp. There are 10bp per turn, so 28 turns.

172

What chemical groups (phosphate group, hydroxyl group, or nitrogenous base) is found at the 3' end of a DNA strand? What group is found at the 5' end?

Hydroxyl at 3
Phosphate at 5

173

The genetic material found within some viruses is single-stranded DNA. Would this genetic material contain equal amounts of A and T and equal amounts of G and C?

No necessarily.
The At/GC rule is required only of a double stranded DNA molecule.

174

A double stranded DNA moelcule is 1 cm long, and the percentage of adenine is 15%. How many cytosines would be found in this DNA molecule?

First determine how many base pairs are in the DNA. The linear length of 1 bp is 0.34nm, which equals .34X 10^29m. ONe centimeter equals 10^-2 meters.
((10^2/ 0.34X10^-9)= 2.9 X 10^7bp)
2.9 X 10^7 bp= 5.8 X 10^ nucleotides. If 15 % are adenine, then 15% are thymine. That leaves 70% for cytosine and guanine. So 35% cytosine.
(5.8X 10^7) (0.35)= 2.0 X10^7 or about 20 million cytosines.