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Biochem IV > Organization of the Genome > Flashcards

Organization of the Genome Flashcards

1
Q

What are spacer sequences?

A

separate genes

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2
Q

What are Introns?

A

non-coding sequences within a gene

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3
Q

What type of RNAs do not have a protein counterpart?

A

rRNA, miRNA, snoRNA, snRNA

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4
Q

What are repetitious DNA sequences?

A

most abundant class of non-coding DNA sequences

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5
Q

What is satellite DNA also referred to?

A

simple-sequence DNA

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6
Q

What is satellite DNA?

A

comprises identical repeats of relatively short sequences

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7
Q

How long are satellite DNA?

A

14 - 500 base pairs

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8
Q

How long are satellite DNA long tandem arrays?

A

20 - 100 thousand base pairs

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9
Q

Where is most satellite DNA confined?

A

centromere or telomere

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10
Q

What is the most abundant class of repetitious DNA?

A

interspersed repeats

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11
Q

Where are interspersed repeats primarily located?

A

transposons and retrotranspsosns

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12
Q

What are exons?

A

sequences that are translated into proteins

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13
Q

What are longer, introns or exons?

A

introns

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14
Q

What are gene families?

A

redundancies in genes

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15
Q

What do gene families arise from?

A

gene duplication events

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16
Q

What are pseudogenes?

A

when the duplicate genes develop mutations and become inactivated

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17
Q

What does it mean to be clustered?

A

when a gene family is located on one chromosomal locus

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18
Q

What is the function of H5?

A

to seal the nucleosome

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19
Q

List four types of non-coding DNA

A

spacer sequences, introns, non-protein coding RNA, repetitious DNA

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20
Q

What is satellite DNA composed of? Generally, how long is satellite DNA? Where is most satellite DNA confined?

A

nearly identical repeats of short sequences

20 - 100 base pairs

centromere or telomere

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21
Q

What is the most abundant class of repetitious DNA?

A

interspersed repeats

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22
Q

How much of the total human DNA is accounted for by interspersed repeats?

A

approximately 45%

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23
Q

What two classes of DNA do interspersed repeats contribute to?

A

transposons and retrotransposons

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24
Q

Are the genes in eukaryotes continuous or discontinuous?

A

discontinuous

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25
Q

What are longer, exons or introns?

A

introns

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26
Q

Where do gene families arise from?

A

gene duplication events

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27
Q

What is a pseudogene?

A

a duplicated gene that has mutated and become inactive

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28
Q

What are the fractions of chromatin composition?

A

1/3 DNA and 2/3 protein

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29
Q

How many base pairs of DNA are wrapped around a histone protein?

A

146 bp

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30
Q

What is a nucleosome?

A

DNA wrapped around histone protein

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31
Q

What cell cycle phases are part of the division phase?

A

G2 and M

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32
Q

What is the name of the place where chromatids adhere to each other at?

A

centromeres

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33
Q

What is the role of cohesin?

A

to secure centromeres together

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34
Q

What are chromatids?

A

two identical copies of chromosomes

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35
Q

What are homologous chromosomes?

A

maternal and paternal copies of the same chromosome

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36
Q

What type of fiber is DNA condensed into for replication?

A

700 nm

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37
Q

How are prokaryotic RNA’s translated?

A

as they are synthesized

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38
Q

What is the function of the nucleolus?

A

to produce rRNA

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39
Q

Where does the assembly of ribosomal subunits take place?

A

periphery of nucleolus

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40
Q

What two nuclear constituents are attached to the nuclear envelope?

A

centromeres and telomeres

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41
Q

What is the nuclear lamina?

A

meshwork of filaments on the inner surface of the nucleus

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42
Q

Where is the perinuclear space?

A

enclosed by double nuclear membrane

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43
Q

What is the perinuclear space contiguous with?

A

endoplasmic reticulum

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44
Q

What is the function of the nuclear pore?

A

to regulate traffic between the nucleus and the cytoplasm

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45
Q

Is protein import into the nucleus energy dependent?

A

yes

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46
Q

Are mRNA, proteins and RNA-protein complex exported from the nucleus in an energy dependent process?

A

Yes

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47
Q

Where is the nuclear basket located?

A

inside of nuclear pore

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48
Q

Where is the protein ring of the nuclear pore?

A

anchored in the double membrane

49
Q

Where are the filaments of the nuclear pore located?

A

outside

50
Q

The central transporter is unspecific for size up to what size?

A

50 kDa

51
Q

What are the three molecules that must be selectively transported into/out of the nuclear pore?

A

mRNA, proteins, ribosomal subunits

52
Q

Where are ribosomal subunits synthesized?

A

cytoplasm

53
Q

Where are ribosomal subunits transported to?

A

cytoplasm –> nucleus –> nucleolus

54
Q

Import of a protein into the nucleus requires its’ association with what protein?

A

Importin

55
Q

What does importin associate with inside the nucleus? What does this cause?

A

Ran-GTP

dissociation of importin from its partner

56
Q

Export of a protein from the nucleus requires the association of Ran-GTP with what?

A

exportin

57
Q

How are the majority of RNAs exported from the cytoplasm?

A

in a Ran-independent fashion

58
Q

What is the function of Dbp5?

A

may be involved in RNA export from the cytoplasm

59
Q

What end of DNA do polymerases add to?

A

3’ OH

60
Q

What are the primers for DNA polymerase made of? What protein makes the primers?

A

RNA

Primase

61
Q

What protein degrades the primers?

A

exonuclease

62
Q

What is the significance of pyrophosphate?

A

its hydrolysis drives the reaction

63
Q

What type of base is incorporated into the nascent strand? (phosphate)

A

triphosphate

64
Q

What marks the origins of replication?

A

ORC (origin recognition complex)

65
Q

What cell cycle phase begins synthesis of DNA?

A

S phase

66
Q

What is the function of DNA pol alpha?

A

to synthesize RNA primers

67
Q

DNA pol alpha activity is also referred to as what?

A

primase activity

68
Q

What is the sequence of telomeres?

A

TTA-GGG

69
Q

Telomerase contains what type of complimentary molecule?

A

complimentary RNA

70
Q

What position of the ribose are bases attached?

A

1’

71
Q

What type of RNA carries the most modifications?

A

tRNA

72
Q

What is the only modification seen in DNA?

A

methylation of cytidine

73
Q

What type of base stabilizes Z-form of DNA?

A

5-methylcytidine

74
Q

How does doxorubicin work?

A

fits into the major groove of DNA

75
Q

What type of DNA mutation do intercalating agents cause?

A

insertions and deletions

76
Q

Name three intercalating agents

A

doxorubicin, ethidium, acridine dyes

77
Q

triple helical structures are formed by long runs of what base?

A

pyrimidines

78
Q

How many base pairs per turn?

A

10.4

79
Q

Negative supercoiling happens when?

A

twisted in the direction that unwinds the helix

80
Q

The majority of nuclear DNA is positively supercoiled or negatively supercoiled?

A

negative

81
Q

When does positive supercoiling of DNA occur?

A

replication and txn

82
Q

What is the MOA of type I topoisomerases?

A

cut-one strand

83
Q

What is the function of topoisomerases?

A

to supercoil DNA

84
Q

What is the MOA of type II topoisomerases?

A

cut two strands at once

85
Q

What is the MOA of doxorubicin?

A

inhibit human topo. type II

86
Q

What is the MOA of Nalidixic acid and ciprofloxacin?

A

act on bacterial topo. II

87
Q

How many bp are wrapped around a histone protein?

A

146 bp

88
Q

What is a nucleosome?

A

histone with DNA wrapped around it

89
Q

What are the stages of the division process?

A

G2 and M

90
Q

What are chromatids?

A

two identical DNA strands that make up a chromosome

91
Q

Where do chromatids adhere to each other?

A

centromere

92
Q

What is the function of cohesin?

A

to secure the chromatids together

93
Q

What are telomeres?

A

the ends of the chromatids

94
Q

Where does the assmebly of ribosomal subunits take place?

A

periphery of nucleolus

95
Q

What is the function of the nuclear envelope?

A

to stabilize the nuclear envelope

96
Q

What is the perinuclear space? What is the perinuclear space cotiguous with?

A

space between nuclear pore membranes

endoplasmic reticulum

97
Q

What are the three main types of large molecules that must be transported between the nucleus and the cytoplasm?

A

mRNA, proteins, ribosomal subunits

98
Q

What causes release of cargo from importin?

A

Importin association with Ran-GTP

99
Q

How does importin leave the nucleus?

A

via its association with Ran-GTP

100
Q

What causes dissocition of importin from Ran-GTP?

A

Ran-GTP hydrolysis to Ran-GDP

101
Q

The majority of mRNA molecules are exported from the nucleus via what mechanism?

A

Ran-independent

102
Q

What are the primers for DNA synthesis made of?

A

RNA

103
Q

What do helicases use for energy?

A

ATP

104
Q

Which DNA polymerase generates the primers?

A

DNA polymerase alpha

105
Q

Does ligase require ATP?

A

yes

106
Q

The telomere is on the end of the lagging strand or leading strand?

A

lagging strand

107
Q

How does telomerase base pair to the telomere?

A

telomerase contains complimentary RNA to the telomere

108
Q

Where are bases attached in DNA?

A

1’ position

109
Q

What is the only modification of a base in DNA?

A

methylation of cytidine to 5-methylcytidine

110
Q

What do intercalating agents most often cause regarding DNA damage?

A

insertions and deletions

111
Q

What base is involved in triple-helical structure?

A

pyrimidines

112
Q

What defines negative supercoiling?

A

when DNA is twisted in the direction it is unwound

113
Q

What causes positive supercoiling?

A

unwinding of the DNA helix

114
Q

Nucleosomes associate to form how thick of fiber?

A

30 nm

115
Q

What phase is the ORC activated?

A

S phase

116
Q

Where does topoisomerase I function?

A

at the replication fork

117
Q

The leading strand is synthesized by what polymerase?

A

DNA polymerase epsilon

118
Q

The lagging strand is synthesized by what DNA polymerase?

A

DNA polymerase delta

Biochem IV (6 decks)

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