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Flashcards in Chapter 10 Deck (181):
1

What is a genome?

All of the chromosomes and DNA sequences that an organism or species can possess.

2

What four important processess does chromosomal sequences facilitate?

1. Synthesis of RNA and Cellular Proteins
2. Replication of Chromosomes.
3. Segregation of chromosomes.
4. Compaction of chromosomes

3

Bacteria usually contain a single type of what? But more than one what?

Chromosome
Copy

4

What are protein-encoding genes?

Genes that produce mRNA and encode polypeptides;

5

What is another name for protein-encoding genes?

Structural genes

6

What accounts for the majority of bacterial DNA?

Protein-encoding genes

7

What are intergenic regions?

A region of DNA in a chromosome that lies between two different genes.

8

What are the key features of bacteria?

-contain circular chromosomal DNA
-contain single type of chromosome, with multiple copies
-Has a few million base pairs
-Has intergenic regions
-One origin of replication is required to initiate DNA replication
-Repetitive sequences are interspersed throught the chromosome

9

What types of sequences constitue most of a bacterial genome?

Sequences of genes

10

Other sequences in chromosomal DNA influences what?

DNA replication
Gene transcription
Chromsome structure

11

What is the origin of replication?

A nucleotide sequences that functions as an initiation site for the assembly of several proteins required for DNA replication.

12

What are repetitive sequences?

DNA sequences that are present in many copies in the genome

13

The repetitive sequences are usually what throughout the chromosome?

Interspersed within the intergenic regions throughout bacterial chromosome

14

Repetitive sequences may play a role in what?

A variety of genetic processess including DNA folding
DNA replication
Gene regulation
Genetic recombination

15

A bacterial chromosome typically contains
a. a few thousand genes
b. one origin of replication
c. some repetitive sequences
d. all of the above.

d. all of the above.

16

What is a nucleoid?

A darkly staining region that contains the genetic material of mitochondria, chloroplasts or bacteria.

17

To fit within the bacterial cell, the chromosomal DNA must be compacted ________.

1000 fold

18

What are loop domains?

A segment of chromosomal DNA that is anchored by proteins, so it forms a loop.

19

Part of the compaction process involves the formation of what?

Loop domains

20

The number of loop domains vary according to what?

The size of the bacterial chromosome and the species.

21

E. coli chromosomes contain how many loop domains?

50-100 with 40,000-80,000 bp of DNA in each loop.

22

What holds the loop domain in place?

Proteins

23

What is DNA supercoiling?

The formation of additional coils in DNA due to twisting forces. Like twisting a rubber band

24

What happens with underwinding of DNA?

The underwinding motion can cause fewer turns
Cause a negative supercoil to form.

25

Overwinding DNA can cause what?

More turns
The formation of a positive supercoil.

26

What are topoisomers?

DNA conformations that differ with regard to supercoiling

27

In living bacteria what type of supercoil is usually seen?

Negative supercoil

28

Negative supercoil occurs at how many turns of the double helix?

40 turns

29

What are the consequences of negative supercoiling?

DNA is much more compact
Affects DNA function

30

How does negative supercoiling affect DNA function?

It creates tension on the DNA strand that may be released by DNA strand separation.
So, it may promote DNA strand separation in small regions.
This enhances replication and transcription

31

Why is strand separation beneficial?

It is needed for certain processes such as DNA replication and RNA transcription

32

What is DNA gyrase?

Tpopisomerase II
An enzymes that introduces negative supercoils into DNa using energy from TAP. Gyrase can also relax positive supercoils when they occur.

33

Who discovered DNA gyrase? When?

Martin Gellert
1976

34

How does DNA gyrase alter supercoiling?

It has two sets of jaws that allow it to grab onto two regions of DNA.
The lower jaw wraps in a right-handed direction around the two A subunits. The upper jaw then clamp onto another region of DNA. The DNA in the lower jaws is cut in both strands, and the other region of DNA is released from the upper jaw and it then passes through this double-stranded break.
The double-stranded break is ligated back together at the end.

35

What is the net result of DNA gyrase?

Two negative supercoils

36

What else can DNA gyrase do?

Untangle DNA molecules

37

Describe the steps that requires the use of ATP in recoiling of DNA?

ATP is needed so the DNA held in the upper jaws can pass through the break in the DNA and move to the region of the lower jaws

38

What is topoisomerase I?

An enzyes that alters the degree of supercoiling in DNA.

39

Topoisomerase I can do what?

Bind to a negatively supercoiled region and introduce a break in one of the DNA strands. After one DNA strand has been broken, the DNA molecule rotates to relieve the tension and relaxes supercoiling. the broken strand is then repaired.

40

What governs the overall supercoiling of the bacterial DNA?

The competing actions of DNA gyrase and topoisomerase I.

41

What is critical for bacterial survival?

The ability of gyrase to introduce negative supercoils into DNA

42

What inhibits DNA gyrase?

Quinolones
Coumarins

43

Mechanisms that make the bacterial chromosome more compact include
a. the formation of loop domains
b. DNA supercoiling
c. crossing over
d. both a and b.

d. both a and b.

44

Negative supercoiling may enhance activities like transcription and DNA replication because it
a. allows the binding of proteins to the major groove.
b. promotes DNa strand separation
c. makes the DNa more compact
d. causes all of the above.

b. promotes DNa strand separation

45

DNA gyrase
a. promotes negative supercoiling
b. relaxes positive supercoils
c. cuts DNA strands as part of its function.
d. Does all of the above.

d. Does all of the above.

46

What are the key features of Eukaryotic chromosomes?

-Usually linear
-Occur in sets usually diploid
-tens of millions to hundreds of millions of base pairs in length
-contains a few hundred and several thousand different genes
-Has many origins of replication dispersed every 100,000 base pairs.
-Has a centromere that forms a recognition site for the kinetochore proteins
-Telomeres contain specialized sequences located at both ends of chromosome
-Repetitive sequences found near centromeric and telomeric regions

47

What are some differences between the types of sequences found in eukaryotic chromosomes versus bacterial chromosomes?

Eukaryotes have centromeres and telomeres, which bacteria dont. Eukaryotes typically have much more repetitive sequences.

48

What are introns?

Intervening sequences that are found between exons. Introns are spliced out of the RNA prior to translation.

49

Protein-encoding genes tend to be much longer in eukaryotes, why?

The presence of introns

50

What are exons?

A segment of RNA that is contained within the RNA after splicing has occurred. IN mRNA, the coding sequence of a polypeptide is contained within the exon.

51

What is the range of introns?

100bp-10,000 bp

52

What are the three regions in eukaryotes chromosomes that are required fro chromosomal replication and segregation?

Origins of replication
Centromeres
Telomeres

53

What are centromeres?

A segment of eukaryotic chromosomal DNa that provides an attachment site for the kinetochore

54

What is the kinetochore?

A group of proteins that link the centromere to the spindle apparatus during mitosis and meiosis, ensuring the proper segregation of the chromosomes to each daughter cell.

55

What is a point centromere?

When centromeres have a defined DNA sequence.

56

What are regional centromeres?

Much larger centromeres that contain tandem arrays of short repetitive DNA sequences.

57

Is the repeated DNA sequences sufficient to form functional centromeres with a kinetochore?

No

58

What is a distinctive feature of all eukaryotic centromes?

Histone protein H3 is replaced with a histone variant called CENP-A

59

What are the important functions of telomeres?

Replication and stability of chromosome.

60

Telomeres prevent what?

Chromosome shortening

61

How do telomeres prevent chromosomes from shortening?

First they protect chromosomes from digestion via enzymes called exonucleases that recognize the ends of DNA.
Second, an unusual form of DNA replication occurs at the telomere to ensure that eukaryotic chromosomes do not become shortened with each round of DNa replication

62

The chromosomes of eukaryotes typically contain
a. a few hundred to several thousand different genes
b. multiple origins of replication
c. a centromere
d. telomeres at their ends
e. all of the above.

e. all of the above.

63

Is the size of the genome related to the complexity of the species?

No

64

If two different species have the same number og genes, but different genome sizes, what explains the difference in size?

It is due to the accumulation of repetitive DNa sequences present in many copies.

65

Do highly repetitive sequences encode proteins?

No

66

What are the two reasons for the wide variation in genome sizes among eukaryotic species?

The number of genes
The amount of repetitive sequences

67

What is sequence complexity?

The number of times a particular base sequence appears throughout the genome of a given species

68

What are unique or nonrepetitive sequences?

Sequences found once or a few times within the genome.

69

Protein-encoding genes are typically what?

Unique sequences of DNA

70

In humans, unique sequences make up roughly what percent of the genome?

41%
This includes 2% protein-encoding regions of genes
24% introns
15% unique regions that are not found within genes.

71

What are moderately repetitive sequences?

Sequences that are found a few hundred to several thousand times in the genome.

72

What is an example of moderately repetitive sequences?

rRNA

73

Ribosomal RNA is necessary for what?

The functioning of ribosomes

74

Why are rRNA moderatley repetitive sequences?

Ribosomes need a large amount of rRNA to make them and this is accomplished by having multiple copies of the genes that encode rRNA.

75

What is another example of moderately repetitive sequence? Why?

Genes encoding histone proteins because a large number of histone proteins are needed for the structure of chromosomes.

76

Moderately repetitive sequences may play a role in what?

Regulation of gene transcription and translation.

77

Other moderately repetitive sequences are derived from what? and thus what?

Transposable elements and thus do not play a functional role

78

What are transposable elements (TEs)?

A small genetic element that can move to multiple locations within the chromosomal DNA.

79

What are highly repetitive sequences?

Sequences that are found tens of thousands or even millions of times throughout the genome.

80

Each copy of a highly repetitive sequence is relatively what?

Short, ranging from a few nulceotides to several hundred in length.

81

What is an example of a highly repetitive sequences?

The Alu family found in humans and primates

82

The Alu sequence is how long?

300bp

83

Where does the Alu family get its name?

From the observation that it contains a site for cleavage by a restriction enzyme known as Alul

84

The Alu sequence is present in about how many copies in the human genome?

1,000,000 copies

85

The Alu sequence represents what percent of the human DNA and occurs at every ____________ bp.

10%
Occurs every 5000-6000bp

86

The Alu sequence arose from what?

Arose 65 mya from a section of a single ancestral gene known as the 7SL RNA gene.

87

What is a retroelement?

A type of transposable element that moves via an RNA intermediate

88

What is a tandem array?

A short nucleotide sequence that is repeated many times in a row.

89

What is another name for tandem array?

Tandem repeats

90

Which of the following is an example of a moderately repetitive sequence?
a. rRNA genes
b. Most protein-encoding gnes
c. both a and b
d. none of the above.

a. rRNA genes

91

If DNA from a single set of human chromosomes was stretched from end to end, the legnth would be what?

1 meter.

92

Most eukaryotic cells are only what diameter, and the cell nucleus is what diameter?

10-100 um in diameter
2-4 um in diameter

93

How is DNA in eukaryotic cells compacted?

By binding the DNA to many different cellular proteins.

94

What is chromatin?

The association between DNA and proteins that is found within chromosomes.

95

What is nucleosome?

The repeating structural unit within eukaryotic chromatin. It is composed of double-stranded DNA wrapped around an octamer of histone proteins.

96

Each octamer contains what?

Eight histone subunits:
Two copies each of four different histone proteins.

97

The DNA of eukaryotes is what over the surface of the octomer?

Negatively supercoiled. About 1.65 negative superhelical turns

98

What is the amount of DNA required to wrap around the histone octamer in eukaryotic cells?

146 or 147 bp.

99

How big is a single nucleosome?

About 11nm in diameter.

100

The chromatin of eukaryotic cells contains what?

A repeating pattern in which the nucleosomes are connected by linker regions of DNA that vary in legnth from 20-100bp.

101

The overall structure of connected nucleosomes resembles what?

Beads on a string.

102

What are histone variants?

Histone proteins whose amino acid sequences are slightly different from the standard histones. They often play a specialized role in chromatin structure and function.

103

Histone proteins consists of what?

A globular domain and a flexible, charged amino terminus called an amino terminal tail.

104

Why are histone proteins very basic proteins?

They contain a large number of positively charged lysine and arginine amino acids.

105

The arginines play a major role in what?

Binding to the DNA

106

Arginines within the histone proteins form what?

Electrostatic and hydrogen-bonding interactions with the phosphate groups along the DNA backbone.

107

The octamer of histones contains what?

Two molecules each of four different histone proteins: H2A, H2B, H3, H4.

108

How determined the structure of a nucleosome by x-ray crystallography?

Timothy Richmond 1997

109

What are the core histones?

H2A, H2B, H3, H4.

110

H1 is found where and is called what?

Found in most eukaryotic cells and is called the linker histone.

111

Why is H1 called the linker histone?

It binds to the DNA in the linker region between nucleosomes and may help to compact adjacent nucleosomes.

112

The linker histones are less what?

Tightly bound to the DNA than are the core histones.

113

Non histone proteins bound to the linker region play a role in what?

The organization and compaction of chromosomes, and their presence may affect the expression of nearby genes.

114

The model of nucleosome structure was originally proposed by who? When?

Roger Kornberg 1974

115

What were the observations Kornberg based his model of the nucleosome

Biochemical experiment showed chromatin contains a ratio of one molecule of each of the four core histones per 100 bp of DNA.
Also purified core histone proteins were observed to bind to each other via specific pairwise interactions.
Subsequent x-ray diffraction studies showed that chromatin is composed of a repeating pattern of smaller units.
Finally electron microscopy of chromatin fibers revealed a diameter of approximately 11nm.

116

Who tested Kornberg's model?

Markus Noll

117

How did Noll test Kornberg's model?

By digesting chromatin with DNase I, an enzyme that cuts the DNA backbone. He then accurately measured the molecular mass of the DNA fragments by gel electrophoresis. DNase I is expected to making cuts in the linker region.

118

What was Noll's experimental protocol?

He began with nuclei from rat liver cells and incubated them with low, medium, or high concentration of DNase I. The DNA was extracted into an aqueous phase and then loaded onto an agorose gel that separated the fragments according to their molecular mass. The DNA fragments were stained with a UV-sensitive dye, ethidium bromide, which made it possible to view the DNA fragments under UV illumination.

119

Nucleosomes associate with each other to form a more compact structure that is what diameter?

30nm diameter

120

Evidence for the packaging of nucleosomes was obtained in the microscopy studies of who? When

Fritz Thoma in 1977

121

What was Thoma's study?

Chromatin samples were exposed to a solid resin that could bind to histone H1 and remove it from the DNA. The removal of H1 depends on the NaCl concentration. A moderate salt solution removed H1, while no added NaCl did not.
Both samples were observed with an electron microscope.
With salt the chromatin exhibited the classic bead-on-a-string morphology. The results suggested that the nucleosomes are packaged into a more compact unit and that H1 has a role in the packaging and compaction of nucleosomes.

122

What is 30-nm fiber?

The association of nucleosomes to form a more compact structure that is 30 nm in diameter.

123

The 30-nm fiber shortens the total length of DNa another what?

sevenfold.

124

What are the two main classes of 30-nm fiver?

The solenoid model
Zigzag model

125

The solenoid model suggests what?

A helical structure in which contact between nucleosomes produces a symmetrical compact structure.

126

The zigzag model suggests what?

Linker regions within the 30-nm structure are variably bent and twisted, and little face-to-face contact between nucleosomes.

127

Describe the distinguishing features of the solenoid model and zigzag model.

Solenoid model depicts the nucleosomes in a repeating, spiral arrangement, whereas the zigzag model depicts a more irregular and dynamic arrangement of nucleosomes.

128

What is the nuclear matrix?

A group of proteins that anchor the loops found in eukaryotic chromosomes.

129

What are the two parts consists of the nuclear matrix?

Nuclear lamina
Internal nuclear matrix.

130

What are nuclear lamina?

A collection of fibers that line the inner nuclear membrane.

131

Nuclear lamina are composed of what?

intermediate filament proteins.

132

What are internal nuclear matrix?

A network of irregular protein fibers and other proteins that is connected to the nuclear lamina and fills the interior of the nucleus.

133

What is the hypothesis of the role of the internal nuclear matrix?

An intricate fine network of irregular protein filaments plus many other proteins that bind to these filaments.

134

Is the internal nuclear matrix a static structure?

no.

135

What is the function of the nuclear matrix?

It helps to organize and compact the chromosomes within the cell nucleus and also aids in the condesnation during cell division.

136

The proteins of the nuclear matrix are involved in what?

Compacting the DNA into radial loop domains

137

The chromosomal DNA of eukaryotic species contains sequences called what?

Matrix-attachment regions (MARs) or another name
Scaffold-attachment region (SARs)

138

What is the matrix-attachment region?

A site in the chromosomal DNa that is anchored to the nuclear matrix or scaffold.

139

Why is the attachment of radial loops to the nuclear matrix important?

The nuclear matrix serves to organize the chromosomes within the nucleus.

140

What is a chromosome territory?

IN the cell nucleus, each chromosome occupies a nonoverlapping region
A discrete region in the cell nucleus that is occupied by a single chromosome.

141

When can chromosome territories be viewed?

When interphase cells are exposed to multiple fluorescent molecules that recognize specific sequences on particular chromosomes.

142

What did Emil Heitz observe?

The variability of compaction level of interphase chromosomes

143

What is heterochromatin?

Highly compacted DNA. It is usually transcriptionally inactive.

144

What is euchromatin?

DNA that is not highly compacted and may be transcriptionally active.

145

In euchromatin, the 30-nm fiber forms what?

Radial loop domains.

146

In heterochromatin, what happens to the radial loops domains?

They become more compact.

147

Heterochromatin is most abundant in what regions?

Centromeric regions of the chromosome and, to a less extent, the telomeric regions.

148

What is constitutive heterochromatin?

Regions of chromsomes that are always heterochromatic and are permanently transcriptionally inactive.

149

Constitutive heterochromatin usually contains what?

highly repetitive DNA sequences, such as tandem repeats, rather than gene sequences.

150

What is facultative heterochromatin?

Heterochromatin that is derived from the conversion of euchromatin to heterochromatin

151

What is an example of a faculatative heterochromatin?

In female mammals when one of the two x chromosomes is converted to a heterochromatic Barr body.

152

Would you expect to find active genes in heterochromatic or euchromatic regions?

Active genes are found in more loosely packed euchromatic regions.

153

What are components of a single nucleosome?
a. About 146bp of DNA and four histone proteins
b. About 146 bp of DNA and eight histone proteins
c. About 200bp of DNA and four histone proteins
d. About 200 bp of DNA and eight histone proteins.

b. About 146 bp of DNA and eight histone proteins

154

IN Noll's experiment to test the bead-on-a-string model, exposure of nuclei to a low concentration of DNase I resulted in
a. a single band of DNA with a size of approximately 200bp
b. several bands of DNA in multiples of 200bp
c. a single band of DNA with a size of 100bp
d. several bands of DNA in multiples of 100 bp.

b. several bands of DNA in multiples of 200bp

155

With regard to the 30-nm fiber, a key difference between the solenoid and zigzag models is
a. the solenoid model suggests a helical structure.
b. the zigzag model suggests a more irregular pattern of nucleosomes
c. the zigzag model does not contain nucleosomes.
d. both a and b are correct.

d. both a and b are correct.

156

A chromosome territory is a region
a. along a chromosome where many genes are clustered.
b. along a chromosome where the nucleosomes are close together.
c. in a cell nucleus where a single chromosome is located.
d. in a cell nulceus where multiple chromosomes are located.

c. in a cell nucleus where a single chromosome is located.

157

What is the first level of compaction of metaphase chromosomes?

The wrapping of DNA around histone octamers to form nucleosomes.

158

What is the second level of compaction of metaphase chromosomes?

The formation of a 30-nm fiber in which nucleosomes from a zigzag or spiral structure via histone H1 and nonhistone proteins that bind to the DNA.

159

What is the third level of compaction of metaphase chromosomes?

The 30-nm fivers form radial loops by anchoring to protein filaments of the nuclear matrix. The average distance that the loops radiate is 300nm.

160

What structural changes covnert a region that is 300nm in diameter to one that is 700nm in diameter?

The radial loop domains become more tightly packed.

161

By the end of prophase, sister chromatids are entirely what?

Heterochromatin.

162

The overall size of a metaphase chromosome is _____________ than a chromosome territory found in the cell nucleus during interphase.

much smaller

163

The structure of metaphase chromosomes is determined by what?

Nuclear matrix proteins (which form a scaffold) and by histones (which are needed to compact the radial loops)

164

What are the two multiprotein complexes?

Condensin
Cohesin

165

What is condensin?

A protein complex that plays a role in the condensation of interphase chromosomes to become metaphase chromosomes.

166

What is cohesin?

A protein complex that facilitates the alignment of sister chromatids.

167

Condensin and cohesin contain a category of proteins called what?

SMC proteins.

168

What are SMC proteins?

Proteins that use energy from ATP to catalyze changes in chromosome structure.

169

What does SMC stand for?

Structural maintenance of chromosomes

170

Together with topoisomerases, SMC proteins have been shwon to promote what?

Major changes in DNA structure.

171

SMC proteins actively do what?

Fold, tether and manipulate DNA strands.

172

The monomers, which are connected at a hinge region, have two what?

Long coiled arms with a head region that binds ATP.
Length of each monomer is about 50nm, which about 150bp of DNA

173

Prior to M phase, condensin is found where?

Outside the nucleus.

174

As m phase begins, what happens with condensin?

The nuclear envelope breaks apart and condensin is observed to coat the individual chromatids as euchromatin is condensed into heterochromatin. Condensin proteins fform a ring around the DNA. Multiple condensin proteins bring chromatin loops closer together and hold them in place.

175

The function of cohesin is to promote what?

Binding between sister chromatids.

176

After S phase and until the middle of prophase, sister chromatids remain what?

Attached to each other along their length. due to cohesion

177

What happens to cohesin during prophase?

It is released along the arms, but stays attached at the centromeric regions.

178

What happens to cohesin during anaphase?

The cohesins bound to the centromere are rapidly degraded by a protease named separase, thereby allowing sister chromatid separation.

179

The compaction leading to a metaphase chromosome involves which of the following?
a. the formation of nucleosomes
b. the formation of the 30-nm fiber
c. anchoring and further compaction of the radial loops
d. all of the above.

d. all of the above.

180

The role of cohesin is to
a. make chromosomes more compact
b. allow for the replication of chromosomes
c. hold sister chromatids together
d. promote the separation of sister chromatids.

c. hold sister chromatids together

181

On rare occasions, a chromosome can suffer a small deletion that removes the centromere. When this occurs, the chromosome usually is not found within subsequent daugther cells. Explain why a chromosome without a centromere is not transmitted very efficiently from mother to daughter cells.

The centromere is the attachment site for the kinetochore, which attaches to the spindle. If a chromosome is not attached to the spindle, it is free to "float around" within the cell, and it may not be near a pole when the nuclear membrane re-forms during telophase. If a chromosome is left outside of the nucleus, it is degraded during interphase. That is why the chromosome without a centromere may not be found in daughter cells.