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BIOCH 200 > Nucleotides and Nucleic Acids > Flashcards

Nucleotides and Nucleic Acids Flashcards

1
Q

What does DNA do

A

Stores information

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2
Q

What were the results of Avery-MacLoed-McCarty’s experiment

A

Rough strain (nonvirulent); mouse lives
Smooth strain (virulent); mouse dies
Heat-killed smooth strain; mouse lives
Rough strain and heat-killed smooth strain; mouse dies
There is some sort of transformative element

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3
Q

What is the basic virus structure

A

Protein coat relatively high in sulfur. DNA high is phosphorous

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4
Q

What happened to Sulfur-labeled protein after the Hershey-Chase experiments

A

After centrifugation, no sulphur was in the cells; nonradioactive viral progeny

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5
Q

What happened to Phosphorous labeled DNA after the Hershey-Chase experiments

A

After centrifugation, phosphorous was in the cells; radioactive viral progeny

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6
Q

What are the steps of the Hershey-Chase experiment

A
  1. Infection
  2. Blending
  3. Centrifugation
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7
Q

What are some roles of mono- and dinucleotides

A

Oxidation-reduction reactions. Energy transfer. Intercellular signalling and biosynthetic reaction

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8
Q

What are some roles of polynucleotides

A

Storage and decoding genetic information. As enzymes

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9
Q

What are nucleotides in a very basic sense

A

They are incorporated into nucleic acids and high-energy molecules

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10
Q

What composes a nucleotide

A

Sugar, Nitrogen-containing aromatic base and Phosphate

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11
Q

What are the common bases of nucleotides

A

Adenine, Cytosine, Guanine, Thymine and Uracil

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12
Q

What are the common sugars in nucleotides

A

Deoxyribose and ribose

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13
Q

What are the pyrimidine nucleotide bases

A

Uracil, Thymine and Cytosine

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14
Q

What are the purine nucleotide bases

A

Adenine and Guanine

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15
Q

Describe a pyrimidine

A

A 6-carbon ring with a nitrogen on the first and third carbon

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16
Q

Describe a purine

A

A 9-carbon ring (looks like hexagon attached to a pentagon). The nitrogen being attached to the first, third, seventh and ninth carbons

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17
Q

Describe the appearance of uracil

A

A pyrimidine, it has two nitrogens on the first and third positions on the carbon ring. There are two carbonyl groups attached at the 2 and 4 positions of the carbon ring

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18
Q

Describe the hydrogen bonds present in uracil

A

There is a possibility to form 6 hydrogen bonds, 2 as donors and 4 as acceptors. The 2 donors are the nitrogens. The 4 acceptors are from the lone pairs present from the carbonyl groups (2 lone pairs per oxygen)

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19
Q

Describe the appearance of thymine

A

A pyrimidine, it has two nitrogens at the first and third position on the carbon ring. There are two carbonyl groups at the 2 and 4 positions. There is also a methyl group on the fifth position of the carbon ring

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20
Q

Describe the hydrogen bonds present in thymine

A

There is a possibility to for 6 hydrogen bonds, 2 as donors and 4 as acceptors. The 2 donors the nitrogens. The 4 acceptors are from the carbonyl groups (2 lone pairs per oxygen).

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21
Q

What is the difference between uracil and thymine

A

Thymine has methyl group on the fifth carbon in the carbon ring that uracil does not have

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22
Q

Describe the appearance of cytosine

A

Cytosine is a pyrimidine. There is a nitrogen in the positions 1 and 3 on the carbon ring, a carbonyl group in position 2 and an NH2 in position 4.

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23
Q

Describe the hydrogen bonds that can be formed in cytosine

A

6 hydrogen bonds, 3 as donors and 3 as acceptors. The nitrogen in position 1 is a donor because it lacks hydrogen, the hydrogens in the NH2 in position 4 both also act as donors. The nitrogen in position 3 is an acceptor, the lone pairs from the oxygens also act as acceptors.

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24
Q

Describe the appearance of adenine

A

It is a purine, it has a nitrogen in the positions 1, 3, 7 and 9 in the carbon-ring. There is an NH2 group attached to carbon 6 in the carbon-ring

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25
Q

Describe the possible hydrogen bonds in adenine

A

There is possibility of forming 6 hydrogen bonds, 3 as donors and 3 as acceptors. The nitrogen in 1, 3, and 7 positions act as acceptors. The nitrogen in position 9, as well as the hydrogens a part of the NH2 group will act as donors

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26
Q

Describe the appearance of guanine

A

It is a purine. It has a nitrogen in positions 1, 3, 7 and 9. There is an NH2 in position 2 and a carbonyl group in position 6.

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27
Q

Describe the possible hydrogen bonds in guanine

A

It is capable of 8 hydrogen bonds, 4 as acceptors and 4 as donors. The nitrogen in positions 1 and 9 and the hydrogens from the NH2 group from position 2 will act as donors. The nitrogen in positions 3 and 7 and the lone pairs from the carbonyl group from position 6 will act as acceptors.

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28
Q

What is the basic information of RNA

A

Polymer of G, A, C, or U. Sugar portion of ribose. Hydroxyl group present on 2’ carbon

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29
Q

What is the basic information of DNA

A

Polymer of G, A, C or T. Sugar portion of deoxyribose. Hydrogen present on 2’ carbon.

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30
Q

What is a nucleoside

A

A nitrogen base and a sugar

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31
Q

Where do the nitrogen bases and sugar join to form nucleosides

A

The point of attachment between the sugar and bases is carbon 1 in pyrimidine and carbon 9 in purines. They both attach to carbon 1’ of the sugar molecule

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32
Q

How are the carbons numbered in the sugar ring (pentose)

A

They are numbered from 1’ to 5’.

33
Q

What happens to the hydrogen bonds when pyrimidine is attached to a sugar

A

There are no hydrogen bond capabilities for a pyrimidine in the first position of it’s six carbon-ring. Everything else remains the same

34
Q

What happens to the hydrogen bonds when purine is attached to a sugar

A

There are no hydrogen bond capabilities for a purine in the ninth position of it’s nine carbon-ring. Everything else remains the same

35
Q

How do you name a purine nucleoside

A

-ine in purine becomes osine
Example: Adenine = adenosine
Guanine = guanosine

36
Q

How do you name a pyrimidine nucleoside

A

Pyrimidine now ends in -idine
Example: Cytosine - cytidine
Thymine = Thymidine
Uracil = Uridine

37
Q

What does a nucleotide comprise of

A

Nucleosides (nitrogen base and sugar) + phosphate

38
Q

What is a phosphoester

A

They are phosphate esters they link carbon to phosphate groups

39
Q

What is a phosphodiester

A

They link two different carbons to one phosphate group

40
Q

What is a phosphoanyhydrides

A

They link two phosphates to each other

41
Q

What is the net charge of nucleic acids

A

It is a net negative charge from the phosphate groups. Roughly consistent negative charge

42
Q

Is the backbone of nucleic acids polar or non-polar

A

The backbone is sugar-phosphate-sugar-phosphate etc. It should be polar

43
Q

Is the backbone in RNA or backbone in DNA more polar

A

Backbone in RNA is more polar than DNA because it contains the 2’ OH group, which has hydrogen bonding potential

44
Q

If you are given the nucleic acid sequence

5’-ATGCAATG-3’ what can you conclude

A

It is likely DNA, because of the presence of Thymine

45
Q

If you are given the nucleic acid sequence

5’-ACGCAAGG-3’ what can you conclude

A

Could be either RNA or DNA, there is no thymine or uracil so it’s inconclusive

46
Q

If you are given the nucleic acid sequence

5’-UCGUUCA-3’ what can you conclude

A

It is likely RNA, because of the presence of Uracil

47
Q

What are the nomenclature rules for naming nucleotides prefixes

A

1 - Mono
2 - Di
3 - Tri
4 - Tetra… etc.

48
Q

How do we name nucleotides when they pass nine nucleotides

A

They are referred to as 10-mer and that number increases as the number of nucleotides increases

49
Q

What is an oligonucleotides

A

Usually around but somewhat less than 50 nucleotides

50
Q

What are Polynucleotides

A

It is a large number of nucleotides (over 50)

51
Q

What is created in the hydrolysis of phosphodiester bonds

A

The phosphodiester bond separates and the products are 3’ hydroxyl and a 5’ phosphoester

52
Q

Where does spontaneous hydrolysis of phosphodiester bonds occur

A

It is occurs in RNA when the pH is greater than 10

53
Q

Why doesn’t spontaneous hydrolysis of phosphodiester bonds occur in DNA

A

In DNA, the absence of a 2’ OH prevents this reaction. This makes DNA more stable than RNA under alkaline conditions

54
Q

What are the two nitrogen bases that can be spontaneously converted

A

Cytosine can have a spontaneous (uncatalyzed) reaction that converts it to Uracil

55
Q

Why is the deamination of cytosine to uracil a problem

A

Uncorrected in DNA can cause a mutation. One role for thymine versus uracil isn’t present in DNA. DNA repair mechanisms will recognize uracil and remove it.

56
Q

What is a dideoxynucleotide

A

It can only be incorporated at the end of the nucleic acid. There is Hydrogen on the 3’ part of the pentose.

57
Q

Why must a dideoxynucleotide be at the end of the nucleic acid chain

A

There are no phosphodiester capabilities which forces it be at the end of the chain.

58
Q

What are the properties of the nitrogen bases

A

Heterocyclic. Aromatic, electron delocalization. Basically planar, with a slight pucker in purine base. Poorly soluble in water.

59
Q

Why are nitrogen bases poorly soluble in water

A

Relatively hydrophobic, there are hydrogen bond capabilities on the outer area of the ring, but the inner ring makes it poorly soluble

60
Q

When does DNA absorb ultraviolet light

A

It absorbs at around 260 nm

61
Q

When does protein absorb ultraviolet light

A

It absorbs at around 280 nm

62
Q

Why do we use ultraviolet light to look at DNA

A

It can see if there is any protein contaminations. Lower values have typically reflected in protein contamination

63
Q

What is the ideal ratio for DNA in an absorbance of A260 nm / A280 nm

A

Approximately 1.95 for pure DNA

64
Q

What is Beer-Lambert Law

A 
A=(ϵl)c
A = Absorbance
ϵ = extinction coefficient
l = path length
c = concentration
65
Q

How do absorbance and concentration relate in the Beer-Lambert Law

A

Absorbance varies directly with concentration

66
Q

What is the primary structure of DNA

A

Primary structure is the sequence of nucleotide residues

67
Q

What do higher order structures of DNA formed by

A

Higher order structures are formed by chains of nucleotides

68
Q

What form does DNA take

A

DNA forms a double helix. Each chain is connected to the other through hydrogen bonds between the bases (non-covalent)

69
Q

In DNA structure what are the bases that go next to each other or Chargaff’s Rules

A 
Purine = Pyrimidine pairing
A = T/U
G = C
(A + G = C + T)
Chargaff's rules are only obeyed in the duplex structure
70
Q

How did Chargaff help Watson and Crick

A

Helped Watson and Crick deduce the double helical structure of DNA

71
Q

For H-bonds to form between or within biochemical macromolecules they must be shield from water?

A

In nucleic acids, hydrogen bonds are isolated from the aqueous environment to prevent it from becoming destabilized.

72
Q

What is DNA (B-form)

A

The strands are anti-parallel, with an overall right-handed twist. Stabilized by base stacking interactions and hydrogen bonds. Base stacking is the primary stabilizing force.

73
Q

What is Base stacking

A

Primarily Van der Waals. Also, hydrophobic forces

74
Q

What is the major groove in DNA good for

A

Good place for proteins to bond/interact

75
Q

What is the minor groove in DNA good for

A

It is a place for proteins to bond/interact with but it is less integral than the major groove

76
Q

What are the general features of B-form DNA

A

Hydrophobic core / polar exterior. Bases largely excluded from H2O (surrounding aqueous environment). Stabilize H-bonds. Ribose / deoxyribose and phosphates are exposed to H2O. H-bonds in pairing interactions (base pairs). ~10 base pairs per turn (one complete right-handed turn)

77
Q

What does the axial view of DNA looks like

A

The polar sugar / phosphate backbone is found on the outside with the more hydrophobic bases stack in the core of the structure.

78
Q

What is an example of complementary sequences

A

5’ - A T G C G G - 3’
3’ - T A C G C C - 5’
The strands are anti-parallel
The two polynucleotide strands are non-identical

79
Q

What must we assume if we are not told otherwise about the directions of DNA strands

A

If we are not told otherwise, we must assume that we are looking at a 5’ to 3’ strand

BIOCH 200 (8 decks)

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