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BIOCH 200 > Nucleotides and Nucleic Acids > Flashcards

Nucleotides and Nucleic Acids Flashcards

1
Q

What are the 4 functions of mono- and dinucleotides?

A
  1. Oxidation-reduction reactions (NAD/FAD)
  2. Energy transfer (ATP)
  3. Intracellular signalling (GTP/ cAMP)
  4. Biosynthetic Reactions (also ATP)
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2
Q

What are the two functions of polynucleotides?

A
  1. Storage and decoding genetic information (dNA/rNA)
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3
Q

What are nucleosides?

A

A base joined to a five-carbon ribose or deoxyribose.

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4
Q

How does naming change when a pyrimidine becomes a nucleoside?

A

The ending becomes “-idine”

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5
Q

How does naming change when a purine becomes a nucleoside?

A

The ending becomes “-osine”.

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6
Q

What are nucleotides?

A

A nucleoside joined to a phosphate group.

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7
Q

What is a phosphodiester bond?

A

A bond formed between phosphate and carbons that joins two nucleotides into a chain.

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8
Q

What is a phosphoanhydride bond?

A

A bond formed between phosphate groups.

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9
Q

What is the net charge of dNA?

A

Negative.

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10
Q

Is dNA backbone polar or non-polar?

A

Polar.

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11
Q

What are oligonucleotides?

A

A chain consisting of 50 or more nucleotides.

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12
Q

What are polynucleotides?

A

A chain consisting of a large number of nucleotides.

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13
Q

Why is DNA more stable than RNA in alkaline conditions?

A

The spontaneous hydrolysis of phosphodiester bonds occurs in alkaline (ph>10) conditions but is prevented in DNA due to the absence of a hydroxy group at C2.

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14
Q

What is dideoxyribose? How is it used in modern sequencing?

A

A ribose sugar without any hydroxy groups at C2 or C3. This prevents the extension of a DNA molecule by DNA polymerase during electrophoresis.

Dideoxyribose is also present at the 3’ end of a nucleic acid to prevent additional phosphodiester bonds.

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15
Q

What is the general solubility of nucleic acid bases?

A

Because they are mainly hydrophobic, the bases are primarily insoluble in water.

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16
Q

Why do nucleic acids have a ‘sense of direction?’

A

The free ends of nucleic acid are structurally different from one another, (5’ vs 3’), therefore there should be no 3’OH groups connecting to other 3’OH groups.

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17
Q

What bond interaction causes DNA chains to form a double helix?

A

Hydrogen bonds through bases.

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18
Q

What did Erwin Chargaff determine about base composition values in DNA?

A

The amount of adenosine is equal to thymidine; the amount of cytidine is equal to guanosine.

19
Q

What is a Hydrogen Bond?

A

A polar interaction in which a hydrogen atom is shared between two electronegative atoms, much weaker than covalent bonds.

20
Q

Why is adenosine specifically compatible with thymidine? Why can adenosine not pair with cytidine?

A

The amino and carbonyl functional groups between A and T allow for specific hydrogen-bonding interactions. Because A has only 2 H-bond participants when oriented toward another base, while C has 3, there would be a mismatch in hydrogen bonding and instability would ensue.

21
Q

What is B-form DNA?

A

The structure is stabilized by base stacking interactions and hydrogen bonds. The strands are antiparallel and have an overall right-handed twist.

22
Q

What is base-stacking?

A

The primary stabilizing force present in B-DNA, occurs due to VDW and hydrophobic forces between bases.

23
Q

Describe the hydrophobicity of B-form DNA, why is there a difference in hydrophobicity throughout the molecule?

A

The core of the nucleic acid is hydrophobic, while the exterior is polar. This difference is due to bases being nonpolar whereas the phosphodiester backbones are polar.

24
Q

Why are bases excluded from water in B-form DNA?

A

Water interrupts hydrogen bonding between bases, causing instability.

25
Q

What occurs during DNA denaturation?

A

Separation of paired strands due to disruption of non-covalent forces (base-stacking and hydrogen bonding).

26
Q

Why is denaturation essential?

A

Energy-dependant processes/Replication and transcription require strand separation.

27
Q

What is T(m)?

A

The temperature at which DNA melting reaches its ‘midpoint’.

28
Q

What is hyperchromicity?

A

Relatively high absorbance.

29
Q

Which nucleic acid has hyperchromicity?

A

Single-stranded DNA

30
Q

What is hypochromicity?

A

Relatively low absorbance.

31
Q

Which nucleic acid has hypochromicity?

A

Double-stranded DNA.

32
Q

What is the speed of DNA nucleation? Why does this process happen at this rate?

A

It is very slow due to the complexity of the nucleic acid, as well as it time it takes for two specific ssDNA strands to create a perfect match in a widespread environment.

33
Q

What is nucleation?

A

The initial process of DNA association characterized by the matching of ssDNA.

34
Q

What is annealation?

A

The process of reforming a heteroduplex from complementary ssDNA strands.

35
Q

What is the rate of annealation?

A

The rate is initially slow as complementary strands are matched. However, the molecule then begins to reform in a zipper-like mechanism in which hydrogen and non-covalent bonds between bases are restored quickly.

36
Q

Why does a polynucleotide with bp GC have a greater T(m) than a polynucleotide with bp AT?

A

The base-stacking between GC base pairs is more favourable. However, many believe that the hydrogen bonding between guanosine and cytidine is the cause of greater stability.

37
Q

What regions of DNA denature the easiest?

A

Regions high in A/T base-pair concentration.

38
Q

How does pH affect T(m)?

A

At extreme pH (~1) and (~14), T(m) decreases.

39
Q

How does salt concentration affect T(m)?

A

At higher salt concentrations, T(m) increases.

40
Q

Why does changing salt concentration affect DNA denaturation?

A

Ions shield negative charges on phosphate backbone (Mg2+ especially) to reduce repulsion between strands.

41
Q

How does hybridization affect T(m)?

A

If a new match is relatively poor, T(m) will decrease.

42
Q

How is RNA stabilized?

A

Intrastrand base pairing via hydrogen bonds and base stacking interactions.

43
Q

What non-Watson Crick base pairing is present in RNA?

A

G=U base pairing.

BIOCH 200 (7 decks)

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