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PCB 3522: Molecular Biology I > Chapter 4: The Structure of DNA > Flashcards

Chapter 4: The Structure of DNA Flashcards

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1
Q

He studied proteins and isolated DNA. May have been the first.

A

Friedrich Miescher

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2
Q

He proposed the tetra-nucleotide hypothesis

A

Phoebus Levene

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3
Q

The tetra-nucleotide hypothesis suggests that …

A

Bases were in equimolar quantities in chromosomes

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4
Q

Fredrick Griffith

A

Discovered transformation while studying pneumonia

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5
Q

He showed DNA was the genetic material via transformation

A

Oswald Avery

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6
Q

He discovered A=T and G=C.

A

Erwin Chargaff

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7
Q

Worked with bacteriophage

A

Alfred Hershey and Martha Chase

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8
Q

Disproved the tetra-nucleotide hypothesis

A

Erwin Chargafff

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9
Q

He developed the idea of alpha-helix and beta sheet. Worked with keratin.

A

William Astbury

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10
Q

This is composed of a base, a sugar, and a phosphate

A

Nucleotide

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11
Q

How many hydrogen bonds are between adenine to thymine?

A

2 hydrogen bonds

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12
Q

How many hydrogen bonds are between guanine to cytosine?

A

3 hydrogen bonds

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13
Q

He discovered the alpha helix structure, inspired by Atsbury. He wrongly proposed a three chain model of DNA.

A

Linus Pauling

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14
Q

Antiparallel structures

A

Looks the same right-side up or upside down.

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15
Q

Franklin’s Photo 51 was used to show that …

A

DNA is antiparallel in nature

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16
Q

Which DNA bases identifies as a purine

A

Adenine and guanine

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17
Q

Which DNA bases identifies as a pyrimidine

A

Cytosine and thymine

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18
Q

True or False:

Purine bases has 1 ring

A

FALSE

Purine bases have 2 rings

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19
Q

Base + sugar is called a …

A

Nucleoside

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20
Q

Bases are formed with a …

A

3’5’ phosphodiester linkage

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21
Q

DNA bases are found in the …

A

amino/keto conformation

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22
Q

The purpose of the mica experiment was to …

A

determine the periodicity of DNA helix

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23
Q

What is DNA’s periodicity?

A

34 A and 10.5 bp/turn

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24
Q

The mica experiment involved …

A

binding DNA to mica and digesting with an enzyme to determine the periodicity of DNA helix

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25
Q

DNA is antiparallel. What does this mean?

A

One strand goes in the 5’–>3’ direction. The other strand goes in the 3’->5’ direction

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26
Q

In what direction does DNA polymerase synthesize?

A

5’ -> 3’ direction

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27
Q

In what direction is the DNA polymerase read?

A

3’ -> 5’ direction

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28
Q

Ribonuclease is converted into deoxyribonuclease by …

A

Reductase

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29
Q

Rare circumstances where mispairing can occurs

A

Thymine-guanine wobble

Cytosine-adenine protonated wobble

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30
Q

Most enzymes interact in the major or minor groove?

A

Major groove

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31
Q

zinc fingers interact in the major or minor groove?

A

Major groove. Can sometimes cross into the minor groove

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32
Q

True or False:

Proteins can always distinguish major groove interactions

A

True

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33
Q

Proteins cannot distinguish _______ in the minor groove

A

AT/TA

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34
Q

What strong bonds does DNA have?

A

B-S-P and 3’5’ phosphodiester linkage

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35
Q

The two DNA strands are held together via ____

A

H bonds between complementary base pairs: purine::pyrimidine

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36
Q

True or False:

Purine/pyrimidine base stacking which are van der waals that creates hydrophobic interactions

A

True

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37
Q

AT is _____ stable the GC and are _____ likely to break

A

less, more

38
Q

Heating DNA, RNA, or proteins will not break _____

A

disulfide bridges because they are covalent

39
Q

Tautomerization

A

Tautomers are in imino/enol bases should be in the amino/keto conformation.

40
Q

In typical DNA, Cytosine and Adenine are found in the amino or keto conformation?

A

Amino conformation

41
Q

In typical DNA, Guanine and Thymine are found in the amino or keto conformation?

A

Keto conformation

42
Q

Why are tautomers an issue?

A

Tautomers cannot be detected

43
Q

What is essential and limits proper base pairing to C:G and A:T?

A

Hydrogen bonding between bases

44
Q

Sugar/phosphate backbone has a negative or positive charge?

A

Negative charge

45
Q

What is the width of DNA?

A

2 nm

46
Q

Is double helix left handed or right handed?

A

Right handed

47
Q

What is the width of the minor groove?

A

12 A

48
Q

What is the width of the major groove

A

22 A

49
Q

Why does DNA have both a major and minor groove, and not two equal grooves?

A

Due to its geometry. DNA is not a ladder. It is angled, therefore when twisted it gives the major and minor groove. The base pairings are angled. The attachment of the bases and phosphate backbone is asymmetrical results in the grooves. It is not linear

50
Q

True or False:

There is a lot of information in the minor groove

A

False

The Major groove contains a lot if information

51
Q

Which groove contains more “information” and why?

A

The edges of the base pairs present a more complex environment in the major groove than the minor groove. Many proteins that bind DNA recognize specific sequences, most bind to the floor of the major groove , as it provides more chemical information for recognition than the minor groove

52
Q

In which groove do proteins interact specifically with DNA, and which type of bonds are used?

A

Proteins interact with DNA in the major groove. Base pairs are easier to distinguish in the major groove.

53
Q

True or False:

Proteins in the minor groove can distinguish TA and GC. But not AT/TA and GC/CG

A 
True
AT
TA
GC
CG
54
Q

Zinc finger recognizes …

A

Recognizes nucleotides. Need more than 3. Need four or five

55
Q

Proteins specifically recognize a sequence to activate or suppress transcription using ….

A

Zinc fingers

56
Q

Zinc fingers are …

A

Proteins held together by a zinc.

57
Q

How are zinc fingers so specific for a DNA sequence, and what is the zinc finger code?

A

Zinc finger inserts itself into the major groove and reads code. Zinc finger code dictates sequence specificity.

58
Q

True of False:

DNA’s weak interactions determines the genetic and biochemical function of the molecule

A

True

59
Q

True or False:

DNA’s weak bonds plays a critical role in determining the secondary and tertiary structures and functions

A

True

60
Q

True or False:

DNA is stabilized by H bonds and base stacking

A

True

61
Q

What is base stacking?

A

Van der waals interactions that result from the hydrophobic effect, as well as pi bonds overlapping (charge penetration)

62
Q

Which type of base pairs take the most energy to pull apart, and contribute more to Tm?

A

GC base pairs takes the most energy to pull apart and contributes more to Tm

63
Q

Why would it take longer for more complex DNA to reanneal?

A

Takes longer for matching as the strands concentrate to one another and slides

64
Q

Tm is the ….

A

melting temperature

65
Q

Tm increases with ….

A
  1. DNA length
  2. GC content
  3. Higher salt which stabilize the phosphate backbone
66
Q

The melting temperature of DNA increases as the ionic strength of the solution increases because …

A

The cations shield the negatively charged phosphoryl groups which stabilizes the helix

67
Q

DNA is typically _____ -handed (both A and B DNA)

A

Right handed

68
Q

What is the periodicity of “A form” DNA ?

A

11 bp/turn

69
Q

What is the periodicity of “B form” DNA?

A

10 bp/turn

70
Q

What is the periodicity of “Z form” DNA?

A

12 bp/turn

71
Q

True or False:

“Z form” DNA is right handed

A

FALSE

“Z form” DNA is left handed

72
Q

Which form of DNA is the longest?

A

“Z form”

73
Q

Which form of DNA is the shortest?

A

“A form”

74
Q

What is Hoogsteen base pairing, and where would it be found?

A

Purines can rotate and pair with different H bonds, which changes the shape of DNA. A and T is typically found in the anti position. In hoogsteen base pairing, A becomes/rotates syn and T is anti

75
Q

Quadruple Helix

A

Found in telomeres. Guanine-rich, parallel and antiparallel conformations

76
Q

I-Motif DNA

A

Cytosine-rich, found at promoters and telomeres

77
Q

Supercoil

A

DNA can for supercoils when two dsDNA strands cross over one another

78
Q

Linking Number

A

The number of times one strnad has to pass over the other to separate completely

79
Q

Twist:

A

Number of turns of one strand over the other

80
Q

Writhe:

A

supercoiling

81
Q

If DNA crosses up into the right, it would have a _______ supercoil

A

negatively supercoil. If wound around nucleosome, it flips

82
Q

If DNA crosses up into the left, it would have a ______ supercoil

A

positive supercoil. If wound around nucleosome, it flips

83
Q

Negative supercoil

A

Unwinding, underwinding, subtractive twisting

84
Q

Positive supercoil

A

Tighter winding, overwinding, restricted access

85
Q

Supercoils are maintained by ________

A

nucleosomes

86
Q

Topoisomerase

A

Makes ss/ds beaks, which changes supercoiling

87
Q

Topoisomerase 1

A

ssDNA cuts, steps of +/-1. Affects the twist.

88
Q

Topoisomerase 2

A

dsDNA cuts, steps of +/-2. Affects the writhe.

89
Q

True or False:

Both Topoisomerase 1 and 2 requires ATP

A

FALSE

Only topoisomerase 2 for conformational changes (rests enzyme)

90
Q

Tyrosine

A

attacks the phosphodiester bond in the DNA backbone and forms a covalent intermediate, stabilizing the other end with an OH group.

91
Q

Topoisomerase function is to …

A

relieves tension during replication

PCB 3522: Molecular Biology I (8 decks)

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