Lecture 1 - Nucleotides and DNA Flashcards Preview

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Flashcards in Lecture 1 - Nucleotides and DNA Deck (79):
1

What are the 3 parts of a nucleotide?

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

2

What forms the backbone of DNA?

Phosphoester linkages between phosphate groups and sugars

3

Order of DNA?

5' => 3'

4

How to differentiate between purines and pyrimidines?

Longer name = smaller structure

5

2 purines?

1. Adenine
2. Guanine

6

3 pyrimidines?

1. Cytosine
2. Thymine (DNA)
3. Uracil (RNA)

7

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

Base

8

What is a nucleoside?

Base + sugar

9

What is a nucleotide?

Base + sugar + phosphate

10

What are deoxyribonucleotides?

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

11

What are deoxyribonucleotides used for?

DNA

12

What are ribonucleotides used for?

RNA

13

Order of DNA synthesis?

5' => 3'

14

How many H bonds between A and T?

2

15

How many H bonds between C and G?

3

16

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

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

17

How was the DNA structure discovered?

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

18

Periodicity of the helical structure? What does it represent?

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

19

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

Van der Waals

20

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

Water is excluded

21

What does the 5' end of DNA/RNA lack?

A nucleotide at the 5′ position

22

What does the 3' end of DNA/RNA lack?

A nucleotide at the 3′ position

23

Is the backbone of DNA/RNA polar?

YES, VERY

24

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

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

25

What happens to DNA when put in solution?

B to A form

26

What is semi-conservation replication of DNA?

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

27

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

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

28

Helical sense of A form DNA?

Right handed

29

Helical sense of B form DNA?

Right handed

30

Helical sense of Z form DNA?

Left handed

31

A form: base pairs per helical turn?

11

32

B form: base pairs per helical turn?

10.5

33

Z form: base pairs per helical turn?

12

34

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

Semi-conservation replication

35

B form: angstroms per base?

3.4 A

36

A form: angstroms per base?

2.6 A

37

Z form: angstroms per base?

3.7 A

38

What form does double stranded RNA take?

A form

39

What do all DNA forms have in common?

Major and minor grooves

40

A form: diameter?

26 A

41

B form: diameter?

20 A

42

Z form: diameter?

18 A

43

More unstable form of DNA?

Z form

44

DNA palindrome?

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

45

DNA mirror repeat?

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

46

What is a hairpin?

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

47

How to superimpose palindromic sequences?

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

48

How to superimpose mirror repeat sequences?

Requires only a single 180˚ rotation about the vertical axis

49

What is a cruciform?

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

50

Role of hairpins and cruciforms?

Regulatory sequences or DNA binding domains

51

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

Alternative base pairing

Means we can have a triplex or tetraplex DNA

52

Are Hoogsteen base pairs pathological?

Probably not

53

Are triplex and tetraplex forms of DNA parallel or antiparallel?

Both

54

What is particular about triplex DNA segments in vivo?

They are very short

55

What is the 3rd strand of triplex DNA called?

Triplex-forming oligonucleotide (TFO)

56

Is the TFO DNA or RNA?

Can be both!

57

To what do DNA binding proteins bind?

Double stranded DNA

58

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

They bind to DNA in the minor and major grooves

59

What could be a possible role for triplex DNA segments?

May regulate transcription (or even replication) by:
1. Blocking binding of transcriptional factors
2. Blocking elongation by being downstream of transcriptional start site

60

How can triplex sequences be identified experimentally?

Immunofluorescent monoclonal antibodies

61

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

They melt and disrupt DNA triplex structures

Jel 466 and DAPI

62

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

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

What pattern does single stranded RNA form?

Typical right-handed stacking pattern

64

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

RNA, most likely because of ribose

65

What are 3 tertiary structures of RNA?

1. tRNA
2. Ribozyme
3. Ribozyme intron

66

Which reforms faster: denatured DNA or proteins? Why?

DNA because only 4 bases compared to 20 AAs

67

What does the melting temperature of DNA represent?

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

68

What increases the melting temp of DNA? Why?

Higher G-C content because 50% more H bonds

69

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

Linear relationship

70

DNA melting temp with 0% G-C?

Below 70 degrees Celcius

71

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

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

72

Describe the geometry of the bases.

Planar

73

Name of A nucleoside?

Adenosine

74

Name of A nucleotide?

Adenylate

75

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

A form

76

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

Nope, only happens in the lab

77

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

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

78

What does the melting temp of DNA depend on? 2

1. pH and ionic strength
2. Size and base composition of the DNA

79

What happens during DNA hybridization?

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.