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BIOCHEM 200 > 2 - Nucleotides Nucleic Acids > Flashcards

2 - Nucleotides Nucleic Acids Flashcards

1
Q

What does the term amphipathic describe?

A.Something similar to frogs and other
amphibians.

B.Something shaped like a half-circle.

C.Something that has both polar and non-polar properties.

D.Something that “hates” water i.e. is poorly soluble in water

A

C.Something that has both polar and non-polar properties.

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2
Q

Amphipathic

A

Has both polar and non polar properties

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3
Q

Nucleic acids are made form monomers called

A

Nucleotides

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4
Q

What are nucleic acids

A

DNA and RNA

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5
Q 
Which of the following is NOT a component of a nucleotide?
A. A purine or pyrimidine base 
B. A carboxyl group 
C. A pentose sugar 
D. A phosphate group
A

B. A carboxyl group

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6
Q

Nucleotide structure

A
  • Phosphate group
  • sugar / ribose
  • base (either purine or pyramidine)
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7
Q

Nucleoside structure

A
  • sugar

- base

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8
Q

A nucleoside consists of a nitrogenous jbase attached to a sugar(ribose or deoxyribose) with the help of a

A

covalent bond.

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9
Q

Difference between purine and pyramidine

A
  • Pyramidine has 6 membered ring

- purine has 6 membered + 5 membered ring

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10
Q

Which N does ribose attach to on purine and pyramidine

A

N9 for purine

N1 for pyramidine

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11
Q

The ring for bases is

A

Rigid and small with very little bond rotational.

- Very planar structures.

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12
Q

The sides of the planar rings on bases are very

A

Hydrophobic because of electron delocalization

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13
Q

Bases can undergo structural rearrangements known as

A

tautomerization

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14
Q

Tautomerization is essentially a rearrangement of the

A

atoms position, not like resonance because atoms are moved. Not electrons.

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15
Q

Can bases absorb UV light?

A

Yes, at 260nm

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16
Q

How do bases absorb UV light

A

Because of electron delocalization

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17
Q

Can nucleotides and nucleic acids absorb light?

A

Yes

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18
Q

Getting a wavelength ratio of

A260/A280= 1.9 means that

A

The sample is pure DNA/RNA or pure bases.

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19
Q

A260nm can be used to measure the concentration of

A

nucleic acids in solution.

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20
Q

Absorbance of UV light and concetration of nucleic acids are

A

Directly proportional

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21
Q

If the A260:A280 ratio in your sample is 1.4, what does that mean?

A

Your sample contains proteins

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22
Q

If absorbance ratio decreases that means

A

Samples contaminated with proteins

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23
Q

The bases are ….. in water at pH 7

A

hydrophobic and relatively insoluble

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24
Q

Can bases form H-bonds?

A

Yes because of the polar side groups.

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25
Q

How many H-bonds can bases form? Dependant on what?

A

Depends on:

  • number of side groups attached
  • number of atoms on base that H bond
  • number of H bonds possible (theoretical max)
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26
Q

The base attached to the sugar through

A

C1

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27
Q

What kind of bond is used to bond base to the sugar?

A

N-B-glycerol bond

Attaches to N1 in pyramidine
Attaches to N9 in purines

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28
Q

The phosphate group is attached to the sugar at

A

C5’ via a phosphodiester bond

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29
Q

Phosphate groups only attach to sugars in

A

Nucleotides

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30
Q

Phosphoanhydride bonds

A

P-O-P bonds that hold the phosphate together within themselves.

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31
Q

Differences between phosphodiester bond and phosphoanhydride bond?

A

Phosphoanhydride bonds is within the phosphate group, whether it be mono, do, tri phosphate. [P-O-P]

Phosphodiester bond connected the phosphate group to the sugar / ribose via C5’ [P-O-C]

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32
Q

A nucleotide is a nucleoside that has

A

1,2,or 3 phosphates

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33
Q

• Deoxynucleoside =

A

2’deoxyribose + base + 1,2, or 3 phosphate groups

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34
Q

Nucleic acid primary strcure

A

Sequence of nucleotides joined by phosphodiester bonds

  • monomers joined by covalent bonds
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35
Q

What kind of bonds are phosphodiester bonds?

A

Covalent

So are phosphoanhydride bonds

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36
Q

Difference between phosphodiester bond and phosphoester bond

A

phosphodiester:
C-O-P-O-C

phosphoester:
O-P-O-C

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37
Q

Phosphodiester bonds are used to link

A

Sugars of neighbouring Nucleotides together.

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38
Q

Phosphodiester bond is in what direction

A

3’ to 5’. Cuz the one of one joins the start of the other (3’—>5’)

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39
Q

Is phosphodiester bonds charged?

A

Yes -1 charge per residue. So for 1000 residues the nucleic acid will have a net charge of -1000

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40
Q

The ends of nucleic acids are

A

Distinct and not identical

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41
Q

If your were to flip the entire phosphate sugar backbone, the geometry would be

A

Completely different, you cant flip it!

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42
Q

The … is what determines the unique structure of 5’.

A

phosphoester bond that sticks out above the plane at 5’

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43
Q

RNA and DNA both have a hydroxyl group at

A

3’ on the ribose/sugar

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44
Q

Do bases form hydrophobic bonds at

their van der Waal’s radii?

A

Yes

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45
Q

Is the backbone hydrophobic or hydrophilic

A

The backbone is hydrophilic and forms

hydrogen bonds with water

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46
Q

Does the backbone form H-bonds?

A

Yes

47
Q

Are bases hydrophobic or hydrophilic ?

A

Hydrophobic, they form H-bonds because of the side groups

48
Q

The spiral staircase structure of the nucleic acid is subject to the

A

Hydrophobic effect

49
Q

The primary structure of RNA is less stable than that of DNA. Why?

A

Because RNA contains ribose and DNA contains deoxyribose.

50
Q

Hydrolysis of phosphodiester bond is done through the breaking of whihc bonds

A

The double bond between P=O and single bond between P-O

  • known as alkaline hydrolysis
51
Q

For RNA, the phosphodiester bond undergoes ______ when being broken down?

A

Autohydrolysis

52
Q

What catalyzes the hydrolysis of phosphodiester bond?

A

The 2’ hydroxyl group —> giving 2’,3’-cyclic monophosphate derivative

53
Q

Secondary structure of nucleic acids

A

Double helix structure of DNA and RNA

54
Q

What are the base compositions of DNA

A

A=T
G=C

A/T > G/C (eukaryotes)
A/T < G/C (prokaryotes)

55
Q

What is the double helix (secondary structure) of nucleic acids dependant on?

A

Base pairing

56
Q

What is base pairing held by

A

H-bonds

57
Q

Normal base paring is called

A

Watson and crick base pairing

58
Q

How many base pair H-bonds between A and T / G and C

A

A/T = 2 h bonds

G/C = 3 h bonds (stronger)

59
Q

What kind of bonds are between the polar substituents on the bases within the double helix?

A

H bonds

60
Q

What are buried in the centre of the helix?

A

H bonds (between bases)

61
Q

How many base pairs per 360 degree turn?

A

10 base pairs

62
Q

Major groove on double helix important for

A

Protein binding

63
Q

Minor groove on double helix is

A
  • deeper and fewer sides of bases exposed

- contributes to H-bond formation

64
Q

Features of double helix

A
  • double stranded NA
  • made of 2 molecules of nucleic acids
  • antiparallel
  • helical
  • complementary
65
Q

What forces stabilize the double helix?

A

Non covalent (H bonds and van derwall)

66
Q

Folding / fomration of double helix is driven by

A

Hydrophobic effect

67
Q

Single stranded helical strcure has the same

A

Secondary strcure as the double helical nucleic acids.

68
Q

Single stranded helical strcure form spontaneous base pairing is driven by the

A

Hydrophobic effect

69
Q

Secondary structure of single stranded RNA is stabilized by

A

The same non covalent forces that stabilize DNA

  • H bonds
  • base stacking (driven by hydrophobic effect)
70
Q

Both DNA / RNA, single or double stranded both have folded secondary structure. Which is stabilized by :

A
  1. H-bonds between bases, which are either inter or intra strand H-bonds, depending on whether is single or double stranded.
  2. Base stacking energies (can der walls interactions)
71
Q

Denatuation done via

A

Heat —-> melting

72
Q

Why is it easy to melt/ denature secondary structure

A

Because its stabilized by non covalent bonds like h bonds and van der waal interactions

73
Q

Double and single stranded DNA both peak at around

Which is higher?

A

260nm

Single stranded is higher

74
Q

Single stranded nucleic acid is

A

Hyperchromic: more absorptive then double stranded nucleic acid

75
Q

Double stranded nucleic acid is

A

hypochromic: less absorptive compared to single stranded nucleic acid

76
Q

Does ss or ds NA absorb more UV

A

Ss cuz its hyperchromic

77
Q

The reason why the single stranded DNA / NA is hypochromic opposed to double stranded hyperchromic NA is because the

A

secondary folded structure of DNA’s electrons are less excitable. Their excitability is “quenched”

78
Q

hyperchromic

A

When DNA is unfolded, the electrons are more excitable and therfore absorbed more UV light

79
Q

hypochromic

A

Because of the stable base stacking in the secondary folded double helix, electrons excitability is decreased

80
Q

DNA melting

A

Double stranded becomes single stranded

81
Q

Melting temp (Tm)

A

Centre of the curve

  • half are still helical
  • half are melted
82
Q

Zone of melting

A

Wider zone = broader the melting curve

Narrow zone = spiked melting curve

83
Q

Zone of melting depends on:

A
  • base sequence
  • length (#of base pairs),
    longer = broader curve
    Shorter = narrower curve
  • more varied base sequence = broader curve
84
Q

Renaturation of double stranded DNA (or ds RNA)

A

After they have been denatured,

1) cool very slowly to allow nucleation (proper alignment) to occur:
- separated complementary strands form helix
- longer the NA, the more slowly you need to cool

2) zippering (fast):
- once aligned, they zip together into helical

85
Q

Uncontrolled cooling leads to partial

A

Renaturation

86
Q

Cool to quickly

A
  • only partial realignment
  • partial nucleation
  • results having both ds and ss NA.
  • more likely to occur with longer strands to be unable to return to ds.
87
Q

Melting curve and base composition.

Melting curve vary depending on the

A

Base composition

88
Q

Poly A/T VS.
Natural A/T and G/C. VS
poly G/C

On melting curve

A

Poly A/T: curve is to the left with lower melting temp of 70C.

Natural A/T and G/C: normal curve at 90C Tm

Poly G/C: higher Tm of 110C

89
Q

G/C have greater

A

Base stacking forces and H-bonds then A/T. That’s why it has a greater Tm for denaturation.

90
Q

Regions of DNA Rich in AT Base Pairs

A

Denature Most Readily

91
Q

• For A/T rich sequences, its far more easier to convert

A

Double stranded —-> single stranded NA.

92
Q

There are regions of the DNA that denature more quickly at lower temperatures.

A

A/T regions unwind more easily. Important for transcription and replication. Therefore at the initiation sequences they are rich in A/T’s.

93
Q

If the concentration of salt is increased, Tm of a ds DNA will:

A

Increase

94
Q

Why does an increase in salt increase Tm for ds DNA?

A

Because the more salt concentration, the more energy required to unwind the helix, causing a greater Tm.

95
Q

More salt, the more

A

Stable the helix is

96
Q

Increasing salt causes increase in Tm because it

A

decreases electrostatic repulsion that is caused by the (-) charge of the backbone. Na+ ions go to phosphodiester backbone and overcome the electrostatic repulsion.

97
Q

in a test tube, salt

A

stabilized NA secondary structure, since all NA in secondary structures have (-) charged phosphodiester backbone.

98
Q

If the pH is increased or decreased notably from pH 7, Tm of a ds DNA will:

A

Decrease

99
Q

If you change pH, H-bonding groups become protonated (gain an H+), or deprotonated ( lose an H+).

What effect will that have on H-bonds and H-bonding groups?

A

When you make the H-bonds protonated and deprotonated, you change the structure of H-bonding groups, you change its ability to make the H-bonds. This then reduced H-bonding. Negatively impact the base pairing of a double stranded NA.
The melting temperature Tm decreases if you change the pH in either direction. Because the base pairing is reduced, because you lose or gain H-bonding groups that should or should be there. Prevention prompt base pairing.

100
Q

The melting temperature Tm decreases if you change the pH in

A

either direction.

101
Q

The denaturation and renaturation behaviour of nucleic acids enables.

A

hybridization

102
Q

Hybridization:

A

based on the ability of double stranded NA to nature, denature, and then renature.

103
Q

75% complentary ds VS 100% complentary ds

A

75% complentary ds

  • lower base pairing
  • lower Tm
  • less stable

100% complentary ds

  • higher base pairing
  • higher Tm
  • more stable
104
Q

Melting is done through

A

Heat and changing ph

105
Q

In hybridization, you can have two kinds of ds hybrids

A

1) DNA:DNA or RNA:RNA

2) DNA:RNA

106
Q

Hybridization involves a process called

A

annealing: when the strands fold back together.

107
Q

• Annealing depends on the degree of

A

complementarity.

• Degree of complementarity effects Tm. (Direct variables)

108
Q

If you have two strands with no complementarity, they

A

won’t form a stable double helix as there’s no H-bonding stabilizing them. 100% complementarity gives the maximum H-bonding possible.

109
Q

The hybrid annealing formation is effected by:

A
  • The concentration of salt
  • pH
  • Temperature that you do it at. (Melting temp for that sequence)
110
Q

If you want 50% complentarity, then you need to

A

Tm will be low, so you need to Lower temp

111
Q

To stabilize the helix hybrid

A
  • lower temp
  • moderate ph
  • higher salt concetration (favors stability of helix)
112
Q

You have a mixture of DNA fragments and you want only the MOST complementary fragments to hybridize. Which conditions would be best?

A. Higher temperature and lower salt
B. Lower temperature and higher salt
C. Higher temperature and higher salt
D. Lower temperature and lower salt E. High or low pH

A

A. Higher temperature and lower salt

113
Q

Why does higher temp and lower salt cause for hybridization of the most complentry strands?

A

Because it destabilizes all the low complementary strands and weeds them out, allowing only the strands with the highest complementarity to hybridize.

114
Q

Can RNA secondary structure melt?

A

Yes because secondary structure depends on base stacking (van der waal) and on base paring (H bonds).

Both are weak so can melt

BIOCHEM 200 (4 decks)

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