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SMP - Genetics > Lecture 1 - Nucleotides and DNA > Flashcards

Lecture 1 - Nucleotides and DNA Flashcards

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1
Q

What are the 3 parts of a nucleotide?

A
  1. Purine or pyrimidine base
  2. Pentose sugar
  3. Phosphate group
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2
Q

What forms the backbone of DNA?

A

Phosphoester linkages between phosphate groups and sugars

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3
Q

Order of DNA?

A

5’ => 3’

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4
Q

How to differentiate between purines and pyrimidines?

A

Longer name = smaller structure

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5
Q

2 purines?

A
  1. Adenine

2. Guanine

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6
Q

3 pyrimidines?

A
  1. Cytosine
  2. Thymine (DNA)
  3. Uracil (RNA)
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7
Q

On what part of nucleotides do mutations happen most often on?

A

Base

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8
Q

What is a nucleoside?

A

Base + sugar

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9
Q

What is a nucleotide?

A

Base + sugar + phosphate

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10
Q

What are deoxyribonucleotides?

A

Nucleotides with β-2′-deoxy-D-ribofuranose (without a 2’ (-OH) group)

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11
Q

What are deoxyribonucleotides used for?

A

DNA

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12
Q

What are ribonucleotides used for?

A

RNA

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13
Q

Order of DNA synthesis?

A

5’ => 3’

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14
Q

How many H bonds between A and T?

A

2

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15
Q

How many H bonds between C and G?

A

3

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16
Q

Why is the antiparallel structure of DNA more thermodynamically favorable/stable?

A

Because it orients the H bonds in a linear manner, in which they are the strongest

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17
Q

How was the DNA structure discovered?

A

By X-ray showing the diffraction pattern of DNA: spots forming a cross in the center denote a helical structure and heavy bands at the left and right arise from the recurring bases

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18
Q

Periodicity of the helical structure? What does it represent?

A

34 angstroms (36 in solution) = periodicity of the stacking of the bases

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19
Q

Which noncovalent bond is the strongest in the presence of water?

A

Van der Waals

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20
Q

If the H bonds contribute so significantly to the stability of DNA, then what must be true about the interior of the helix?

A

Water is excluded

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21
Q

What does the 5’ end of DNA/RNA lack?

A

A nucleotide at the 5′ position

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22
Q

What does the 3’ end of DNA/RNA lack?

A

A nucleotide at the 3′ position

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23
Q

Is the backbone of DNA/RNA polar?

A

YES, VERY

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24
Q

What is the sugar of RNA? How does it exist in solution?

A

β-D-ribofuranose: the straight-chain (aldehyde) and ring (β-furanose) forms of free ribose are in equilibrium (99% ring form)

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25
Q

What happens to DNA when put in solution?

A

B to A form

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26
Q

What is semi-conservation replication of DNA?

A

The preexisting or “parent” strands become separated, and each is the template for biosynthesis of a complementary “daughter” strand

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27
Q

What are the 3 forms of DNA? Most common one? Least common one?

A
  1. A
  2. B (most common)
  3. Z (least common)
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28
Q

Helical sense of A form DNA?

A

Right handed

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29
Q

Helical sense of B form DNA?

A

Right handed

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30
Q

Helical sense of Z form DNA?

A

Left handed

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31
Q

A form: base pairs per helical turn?

A

11

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32
Q

B form: base pairs per helical turn?

A

10.5

33
Q

Z form: base pairs per helical turn?

A

12

34
Q

What was the most significant finding of the Watson-Crick model for the structure of DNA?

A

Semi-conservation replication

35
Q

B form: angstroms per base?

A

3.4 A

36
Q

A form: angstroms per base?

A

2.6 A

37
Q

Z form: angstroms per base?

A

3.7 A

38
Q

What form does double stranded RNA take?

A

A form

39
Q

What do all DNA forms have in common?

A

Major and minor grooves

40
Q

A form: diameter?

A

26 A

41
Q

B form: diameter?

A

20 A

42
Q

Z form: diameter?

A

18 A

43
Q

More unstable form of DNA?

A

Z form

44
Q

DNA palindrome?

A

Reads the same 5’ to 3’ on each different strand

45
Q

DNA mirror repeat?

A

Reads the same 5’ to 3’ and 3’ to 5’ on same strand

46
Q

What is a hairpin?

A

Secondary structure of palindromic SINGLE stranded DNA (or RNA) sequences formed by intrastrand base pairing

47
Q

How to superimpose palindromic sequences?

A

Must be rotated 180˚ about the horizontal axis then 180˚ about the vertical axis

48
Q

How to superimpose mirror repeat sequences?

A

Requires only a single 180˚ rotation about the vertical axis

49
Q

What is a cruciform?

A

Secondary structure of palindromic DOUBLE stranded DNA (or RNA) sequences formed by intrastrand base pairing

50
Q

Role of hairpins and cruciforms?

A

Regulatory sequences or DNA binding domains

51
Q

What is a Hoogsteen base pair? What does it imply?

A

Alternative base pairing

Means we can have a triplex or tetraplex DNA

52
Q

Are Hoogsteen base pairs pathological?

A

Probably not

53
Q

Are triplex and tetraplex forms of DNA parallel or antiparallel?

A

Both

54
Q

What is particular about triplex DNA segments in vivo?

A

They are very short

55
Q

What is the 3rd strand of triplex DNA called?

A

Triplex-forming oligonucleotide (TFO)

56
Q

Is the TFO DNA or RNA?

A

Can be both!

57
Q

To what do DNA binding proteins bind?

A

Double stranded DNA

58
Q

What do Hoogsteen nucleotides and DNA binding proteins have in common?

A

They bind to DNA in the minor and major grooves

59
Q

What could be a possible role for triplex DNA segments?

A

May regulate transcription (or even replication) by:

  1. Blocking binding of transcriptional factors
  2. Blocking elongation by being downstream of transcriptional start site
60
Q

How can triplex sequences be identified experimentally?

A

Immunofluorescent monoclonal antibodies

61
Q

What is the role of human replication proteins A? 2 examples?

A

They melt and disrupt DNA triplex structures

Jel 466 and DAPI

62
Q

What could be a reason why DNA is the genetic language instead of RNA?

A

Maybe because RNA duplexes are unable to accommodate Hoogsteen base pairing, which may make DNA more stable than RNA because when mutations happen, DNA can flip the base so that a Hoogsteen pairing happens inside the helix until full repair happens ==> DNA can better accommodate mutations

63
Q

What pattern does single stranded RNA form?

A

Typical right-handed stacking pattern

64
Q

Which is more stable: double-stranded DNA or RNA? How come?

A

RNA, most likely because of ribose

65
Q

What are 3 tertiary structures of RNA?

A
  1. tRNA
  2. Ribozyme
  3. Ribozyme intron
66
Q

Which reforms faster: denatured DNA or proteins? Why?

A

DNA because only 4 bases compared to 20 AAs

67
Q

What does the melting temperature of DNA represent?

A

Temp at which you’ve lost 50% of the standard shape

68
Q

What increases the melting temp of DNA? Why?

A

Higher G-C content because 50% more H bonds

69
Q

Describe the relationship between G-C content and melting temp of DNA.

A

Linear relationship

70
Q

DNA melting temp with 0% G-C?

A

Below 70 degrees Celcius

71
Q

What do DNA regions high in A-T content represent? What is this called?

A

Likely to be separated therefore points at which transcription bubbles and replications forks can be most easily inserted = DNA breathing

72
Q

Describe the geometry of the bases.

A

Planar

73
Q

Name of A nucleoside?

A

Adenosine

74
Q

Name of A nucleotide?

A

Adenylate

75
Q

Which DNA form corresponds the most to the model made by Watson and Crick?

A

A form

76
Q

Is DNA denaturing via salt or high temps relevant in vivo?

A

Nope, only happens in the lab

77
Q

Watson-Crick model: how many base pairs and angstroms per turn of the helix?

A

10 base pairs, or 34 Å (3.4 nm), per turn of the helix

78
Q

What does the melting temp of DNA depend on? 2

A
  1. pH and ionic strength

2. Size and base composition of the DNA

79
Q

What happens during DNA hybridization?

A

Two DNA samples to be compared are completely denatured by heating. When the two solutions are mixed and slowly cooled, DNA strands of each sample associate with their normal complementary partner and anneal to form duplexes. If the two DNAs have significant sequence similarity, they also tend to form partial duplexes or hybrids with each other: the greater the sequence similarity between the two DNAs, the greater the number of hybrids formed. Hybrid formation can be measured in several ways. One of the DNAs is usually labeled with a radioactive isotope to simplify the measurements.

SMP - Genetics (16 decks)

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