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Biochem > Lecture 12: Chromatin Structure & DNA Replication > Flashcards

Lecture 12: Chromatin Structure & DNA Replication Flashcards

1
Q

A diploid cell has how many base pairs of DNA?

A

About 6 billion

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2
Q

DNA is organized in the nucleus as?

A

Chromatin

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3
Q

Chromatin is a complex of what two things?

A

DNA and proteins.

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4
Q

Chromatin is dynamic, it can…

A

compact or expand, depending upon the circumstances

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5
Q

What is the organization component of DNA?

A

Histones

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6
Q

Overall structure of connected nucleosomes resembles. They are called?

A

Beads on a string. Histones (histones are proteins)

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7
Q

Nucleosomes

A

Histones and their associated DNA

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8
Q

Nucleosome consists of? Shortens?

A

DNA wrapped around a core made up of different histones. This structure shortens the DNA length about 7 fold.

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9
Q

In the nucleosome, _____________ 146 bp of DNA wraps ____________ times around a histone protein

A

146 bp of DNA wraps 1.75 times around a histone protein core

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10
Q

Histone core consists of how many proteins?

A
  1. 2 molecules each of histones H2A, H2B, H3 and H4. The term nucleosome refers to the DNA and the 8 core histones.
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11
Q

Chromatosome includes the

A

DNA, the 8 core histones, and histone H1, covering 165 bp.

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12
Q

Histone H1 is involved in

A

stabilizing higher order chromatin structures (NOT part of the core)

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13
Q

Histone tails are?

A

Modification sites.

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14
Q

The tighter the histone-DNA complexes, the more?

A

Difficult access for replication or transcription becomes.

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15
Q

Acetylation of the lysine residues (positively charged) in the histone reduces?

A

Interaction with the negatively charged DNA (more relaxed)

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16
Q

Histone acetyltransferases (HATs)

A

add acetyl groups to the lysines in histone tails (more relaxed)

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17
Q

Histone deacetylases (HDACs)

A

remove the acetyl groups

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18
Q

HDAC inhibitors

A

Block HDAC function. Used in cancer treatment.

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19
Q

Naked DNA

A

fully de-condensed, transcriptionally active

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20
Q

Histones and chromatosomes are found in?

A

interphase chromatin

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21
Q

Loop domains are anchored to?

A

Scaffold proteins

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22
Q

Mitotic chromsomes

A

fully condensed, transcriptionally silent

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23
Q

The structural organization of DNA regulates

A

gene expression. Proteins needed for transcription must be able to access the DNA.

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24
Q

Euchromatin

A

When the cell is not actively dividing (during interphase), much of the DNA exists as the more de-condensed 10 and 30 nm fibers organized as loop domains (transcriptionally active).

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25
Q

Heterochromatin

A

The remaining DNA exists as highly condensed form; transcriptionally inert

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26
Q

Constitutive heterochromatin

A

DNA sequences that are not usually
transcribed (centromeres or telomeres). Compacted and gene-poor.

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27
Q

Facultative heterochromatin

A

Genes that are not transcribed in that cell type,
but may be in other cell types.

-Example is the X-chromosome in
mammalian females. One of the two X chromosomes is packaged as heterochromatin. It does this to balance the dosage of X linked genes between males and females, only one of the two chromosomes in females cells becomes inactivated. Can be altered based on stages/cell needs, dynamic.

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28
Q

Semiconservative replication

A

the process by which by which both strands of
a double-stranded piece of DNA are
copied

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29
Q

Result of semiconservative replication

A

two double stranded pieces of DNA that are identical to the original generated

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30
Q

The two strands of the parental double stranded DNA must be separated so that

A

complementary copies can be made of each strand

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31
Q

Nucleoside

A

a nitrogenous base linked to a
sugar only (without phosphates)

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32
Q

Nucleotide

A

a nitrogenous based linked to
a sugar and between to 1 – 3 phosphates

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33
Q

The sugars are

A

ribose (RNA) and deoxyribose (DNA)

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34
Q

Ribonucleoside triphosohates (NTPs, or ribonucleotides) are used to make?

A

RNA

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35
Q

Deoxyribonucleoside triphosphates (dNTPs or deoxyribonucleotides) are used to make

A

DNA

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36
Q

The N in NTP or dNTP can indicate any of the?

A

Bases (ATP or dATP, CTP or dCTP)

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37
Q

Purines

A

Double rings. Adenine (A) and Guanine (G)

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38
Q

Pyrimidines

A

Single ring. Cytosine (C), Uracil (U), Thymine (T)

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39
Q

DNA and RNA both have

A

adenine, guanine, and cytosine

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40
Q

Thymine is specific for? Uracil is specific for?

A

DNA and RNA

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41
Q

RNA is

A

single stranded (mostly)

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42
Q

What is responsible for the double stranded nature of DNA?

A

Hydrogen bonds between the bases of each DNA strand (dsDNA)

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43
Q

Each base will only “pair” with?

A

Another base that has a complimentary arrangement of atoms to allow formation of hydrogen bonds

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44
Q

What are the base pairs?

A

G-C (DNA and RNA)
A-T (DNA only)
A-U (RNA only)

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45
Q

How many hydrogen bonds per each base pair?

A

G-C = 2
A-T or A-U = 2

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46
Q

Hydrogen bonding is critical for?

A

Stabilization of dsDNA.

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47
Q

More hydrogen bonds between base pairs =

A

more energy needed to separate that pair.

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48
Q

The correct incorporation of deoxyribonucleotides into a growing DNA strand is primarily determined by?

A

Hydrogen bonding

49
Q

Hydrogen bonding is also critical for:

A

Transcription. Correct hydrogen bonding between single stranded DNA and unincorporated ribonucleotides facilitates addition of the correct bases to the growing RNA.

Note: The RNA strands do not remain bound to the DNA template
strand.

50
Q

Damage to a nucleotide that
changes its hydrogen bonding
characteristics will result in

A

the wrong nucleotide being incorporated in the new strand during DNA replication. A mutation!!

51
Q

When cytosine undergoes deamination, it becomes

(C U later)

A

Uracil. (Uracil binds adenine)

(C to G –> U to A)

(C U later)

52
Q

Deamination of adenine

A

becomes hypoxanthine. Binds Cytosine.

53
Q

Deamination is

A

spontaneous

54
Q

Deamination can create

A

mutant proteins

55
Q

The carbon positions of the ribose ring are designated with an apostrophe (’), which is referred to as

A

“prime,” to distinguish these carbon positions from those of the base

ex: 2’ = 2 prime

56
Q

Ribose contains an

A

–OH group on its 2’ carbon

57
Q

Deoxyribose lacks?

A

2’OH group

57
Q

1’ carbon

A

attaches to the nitrogenous base

57
Q

2’ carbon

A

-H (DNA) or -OH (RNA)

58
Q

3’ carbon

A

site of new nucleotide addition during replication or transcription

59
Q

4’ carbon

A

anchors the 5’ carbon

60
Q

5’ carbon

A

attaches to the phosphate groups

61
Q

The DNA strands are

A

antiparallel

62
Q

What type of bond for backbone of DNA?

A

phosphodiester bond

63
Q

The 5’ end has a free

A

phosphate

64
Q

The 3’ end has a free

A

OH group

65
Q

DNA synthesis begins at

A

replication origins (specific DNA sequences)

66
Q

Origin-binding proteins ((origin replication complexes (ORCs))

A

recognize the origins and begin to separate the DNA strands, forming a replication bubble

67
Q

Replication proceeds

A

bidirectionally form each origin until the replication forks meet each other or the end of the chromosome is reached

68
Q

What is critical fore DNA elongation?

A

A free 3’-OH group

69
Q

Because a 3’OH group is always needed, the elongation of a new DNA strand can only proceed from?

A

5’ to 3’ end

70
Q

What attaches nucleotides to the 3’ (OH) end of the DNA strand?

A

All known DNA polymerases

71
Q

DNA is built in the what direction? By creation of what bonds?

A

5’ to 3’ by the creation of phosphodiester bonds

72
Q

All DNA polymerases require a 3’-OH in order to covalently bond nucleotides
into the

A

growing daughter strand

73
Q

DNA pol a. Function.

A

RNA primer.

Has the ability to synthesize short stretches of RNA on a template without a 3’-OH.

The 3’-OH from this RNA primer serve as as the point for initiation of new DNA
synthesis

74
Q

The RNA primer is later replaced with the

A

corresponding DNA nucleotides

75
Q

DNA synthesis on both the leading and lagging strands begins with

A

DNA polymerase alpha a,
which is composed of multiple subunits that each have distinct activities (DNA primase subunit, DNA polymerase subunit)

76
Q

DNA primase subunit

A

A DNA-dependent RNA polymerase that synthesizes a short RNA primer (~10 nucleotides).

77
Q

DNA polymerase subunit

A

synthesizes a short stretch of complimentary DNA (~ 20 nucleotides)

78
Q

The bulk of DNA replication is then performed by two additional polymerases

A
  1. DNA polymerase d
  2. DNA polymerase e
79
Q

DNA polymerase d

A

synthesizes the Okazaki fragments of the lagging strand

80
Q

DNA polymerase e

A

synthesizes the new DNA on the
leading strand

81
Q

DNA primase/polymerase a first synthesizes

A

a single RNA/DNA primer (green)

82
Q

DNA polymerase ε

A

Then takes over to continue extending the new DNA strand towards the replication fork.

DNA polymerase ε can do this continuously
as long as it has a single-stranded template
with which incoming nucleotides can base
pair.

83
Q

The lagging strand synthesizes new

A

DNA in the opposite direction of the replication fork

84
Q

On the lagging strand, what synthesizes multiple RNA/DNA primers?

A

DNA primase/polymerase a

85
Q

A new RNA/DNA primer is needed each time a new

A

Okazaki fragment is synthesized.

86
Q

Each Okazaki fragment is then elongated by

A

DNA polymerase d away from the replication fork until the new fragment meets a previous Okazaki fragment

87
Q

DNA primase/polymerase a then starts a new

A

RNA/DNA primer closer to the replication fork, as new single stranded DNA is revealed by the separation of the parental strands.

88
Q

RNase H

A
  1. Recognizes the RNA portion of any RNA/DNA duplexes
  2. Then removes the RNA primer, leaving the DNA part intact
89
Q

DNA polymerase d (Okazaki)

A

fills in the resulting
nucleotide gap with DNA

90
Q

Lagging strand is synthesized in what direction

A

3’ to 5’

91
Q

DNA ligase

A

repairs the nicks in the phosphodiester backbone, joining the fragments together.

92
Q

DNA ligase can also fill in other

A

phosphodiester gaps in the new DNA
strand, such as those which occur as
the result of replication forks coming
together

93
Q

Additional proteins needed at

A

replication fork

94
Q

DNA helicase

A

ravels just ahead of the leading strand DNA polymerase and uses the energy of
ATP hydrolysis to break the hydrogen bonding between individual base pairs, separating the two strands.

95
Q

Single stranded DNA binding proteins (SSB proteins)

A

bind to exposed, single-stranded DNA
of both strands once the helicase has separated them.

96
Q

SSB proteins stabilizes the

A

single-stranded molecules, preventing re-association of the two strands and intramolecular hydrogen bonding. This has the effect of straightening small
stretches of the DNA molecule, facilitating replication.

97
Q

Helicase

A

causes the DNA ahead of the replication fork to twist, forming supercoils, which would eventually DNA synthesis

98
Q

Topoisomerase

A

enzymes which relieve the strain by causing nicks in the DNA that allow one or both strands to rotate relative to the other

99
Q

Two classes of topoisomerases

A

Topoisomerase I (nicks one strand)
Topoisomerase II (cuts both strands)

100
Q

Topoisomerase I covalently attaches where? Creates what?

A

Covalently attaches to a phosphate of the DNA backbone, creating a nick in only strand of the DNA

101
Q

The strands rotate relative to?

A

each other to help relieve the strain on DNA

102
Q

The high energy bond of the topo-phosphate linkage does what?

A

Provides the energy for spontaneous reformation of the phosphodiester bond - which reseals the nick in the DNA (no ATP is required to reseal the nicked DNA)

103
Q

Topoisomerase II uses

A

ATP hydrolysis to create double stranded breaks in DNA

104
Q

Rather than cause a rotation in one strand, the creation of what allows what?

A

Creation of double-stranded break allows one segment of double-stranded DNA to pass through another.

105
Q

Topoisomerase II Steps

A
  1. Toposiomerase binds to double helix 2
  2. ATP hydrolysis is used to create a break in Helix 2
  3. The broken ends of Helix 2 are held by Topo II
  4. Double helix 1 is now able to pass between the broken strands of Helix 2
  5. Helix 1 is released
  6. The broken ends of Helix 2 are resealed
106
Q

Telomeres

A

the terminal sequences of linear DNA molecules consists of repeats of simple sequence DNA

107
Q

Telomerase

A

telomeres are maintained by telomerase, which catalyzes the synthesis of telomeres in the absence of a DNA template

108
Q

The RNA template (in telomerase) allows for

A

telomerase to extend the 3’ end by one repeat unit beyond its original length

109
Q

the complementary strand can then be synthesized by?

A

polymerase a-primase complex

110
Q

Bacterial express two different types of topoisomerase enzyme?

A

DNA Gyrase
Topoisomerase IV

111
Q

Fluroquinolones

A

a class of broad-spectrum antibacterial medications that inhibit both of these bacterial (but not human) topoisomerase enzymes, thereby affecting the ability of bacteria to synthesize new DNA

112
Q

In the US, nine different fluroquinlones are currently approved for human use, including

A

ciprofloxacin (Cipro) and levofloxacin (Levaquin) and
moxifloxacin (Avelox).

113
Q

Fluoroquinolone drugs are some of the most

A

Commonly prescribed antibiotics in the U.S. They can have some serious side effects including tendon rupture (may interfere with collagen turnover).

114
Q

Many drugs used to treat viral infections are
called

A

“chain terminators” because they
effectively terminate the construction of a
new strand of nucleic acid.

115
Q

Chain terminator drugs

A

nucleoside or nucleotide analogs. They are similar enough in structure that DNA polymerases will try to incorporate them into new nucleic acid strands during
replication.

116
Q

Acyclovir

A

antiviral drug widely used to treat HSV-1 and HSV-2 infections. This drug is an analog of the ribonucleoside guanosine (guanine + ribose sugar). It can be incorporated into the growing
strand of DNA but LACKS 3’ OH group on
which to add another nucleotide.

117
Q
A

Biochem (7 decks)

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