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Biological Chemistry 1A > Nucleotides > Flashcards

Nucleotides Flashcards

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1
Q

What is a nucleotide?

A

A nucleobase bonded to a sugar which is bonded to (at least one) phosphate group

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2
Q

What is a nuceloside?

A

A nucleobase bonded to a sugar

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3
Q

Which part of ATP is attacked by a hard nucleophile?

A

The terminal phosphate group

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4
Q

What part of ATP is attacked by a soft nucleophile?

A

The bond between carbon 5 on the sugar and the O of a phosphate group

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5
Q

Apart from DNA and RNA give 3 examples of important molecules which contain nucleotides

A
  • ATP
  • NAHP
  • Coenzyme A
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6
Q

What is the general purpose of nucleotides in large molecules?

A

To bind the molecule further to proteins

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7
Q

How many rings do purines have?

A

2

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8
Q

How many rings do pyrimidines have?

A

1

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9
Q

How many hydrogen bonds do A and T make?

A

2

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10
Q

How many hydrogen bonds do G and C make?

A

3

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11
Q

Which base pairs are most strongly bonded?

A

G-C pairs

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12
Q

What is tautomerism?

A

Any reaction that involves the simple intramolecular transfer of a proton

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13
Q

What is the effect of nucelobsae tautomers on base pairing?

A

Can cause abnormal/ non-canonical base pairing

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14
Q

What is non-canonical base pairing?

A

Base pairing where bases which would not usually bond form hydrogen bonds with each other (G can bond with T and A and can bond with C)

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15
Q

How can tautomers cause abnormal base pairing?

A

Double proton transfer between H-bonded bases

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16
Q

What issues can non-canonical base pairing cause?

A

Can cause issues in replication of DNA

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17
Q

Is RNA more susceptible to hydrolysis than DNA?

A

Yes

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18
Q

Give a use of synthetic nucleotides

A

Can be used to fight HIV/AIDS by blocking the action of HIV reverse transcriptase

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19
Q

Define fluorescence

A

A type of luminescence where light is absorbed rapidly and emitted at a longer wavelength

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20
Q

Why is cytosine methylation of critical importance to organisms?

A

It is involved in gene regualtion and as a marker of self

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21
Q

Define luminescence

A

The emission of light by a substance not resulting from heat

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22
Q

Define chemiluminescence

A

The emission of light resulting from a chemical reaction

23
Q

What is used to show the electronic states of a molecule and the transitions between them?

A

Jablonski diagrams

24
Q

What is on the y axis of a morse potential curve?

A

Energy

25
Q

What is on the x axis of a morse potential energy curve?

A

Nuclear separation

26
Q

What does a Japlonski diagram show?

A

The electronic states of a molecule and the transitions between them

27
Q

What happens at the Vmax of a morse potential energy curve?

A

The bond breaks

28
Q

In general what kind of molecules for flurophores tend to be?

A

Aromatic

29
Q

Describe the position and spins of electrons in a singlet excited state

A

The electrons have opposite spins but one electron is in a higher energy level

30
Q

Describe the position and spins of electrons in a triplet excited state

A

Both electrons have the same direction of spin, one electron is in a higher energy level

31
Q

What is the loss of energy due to electrons dropping down the vibrational energy levels of the singlet excited state called?

A

Internal conversion/vibrational relaxation

32
Q

How is energy lost for absorbance?

A

As heat

33
Q

Why is the wavelength of absorbance not a single line?

A

The electrons can go into multiple vibrational energy states

34
Q

Why is a longer wavelength of light given off in fluorescence?

What is this effect called?

A

Due to energy loss

Stop shift

35
Q

How is energy emitted in fluorescence?

A

As light, by the emission of a photon

36
Q

What do you call a molecule which fluoresces?

A

Flurophore

37
Q

Which amino acid is fluroscent?

A

Tryptophan

38
Q

What affects the absorption spectrum of a molecule?

A

Temperature

39
Q

How can fluorophores help in measuring their binding affinities to proteins/DNA?

A

When bound to proteins/DNA their emission spectrum often changes

40
Q

How can some proteins become highly fluorescent?

A

An autocatalytic reaction in which cross-linking occurs between amino acid side chains

41
Q

Compare the speed of fluroscence with phosphorescence

A

Phosphorescence is much slower

42
Q

In phosphorescence what happens when an electron reaches the ground vibrational level of the excited electron state?

A
  • The electron changes spin and moves into the excited triplet state
  • The electron moves down to the ground vibrational state of the excited triplet state
  • Emission of light occurs
43
Q

What is the change in electron spin and resulting movement of an electron to the excited spin state called?

A

Intersystem crossing

44
Q

What kind of process is intersystem crossing?

A

A forbidden process

45
Q

What is a forbidden process?

A

A process (in quantum mechanics) which occurs very slowly

46
Q

How does chemiluminescence differ to fluorscence?

A

The initial energy which excites electrons is provided by a chemical reaction rather than light

47
Q

What is chemiluminescence?

A

The spontaneous emission of a photon resulting from the breakdown of a high energy molecule

48
Q

What can chemiluminescence be useful for?

A

Tracking gene expression in living organisms

49
Q

What angle is absorbance measured at relative to the light source (in an absorbance spectrometer)?

A

180°

50
Q

In a fluorescence spectrometer what angle is fluorescence measured relative to the excitation beam?

A

90°

51
Q

How does a fluroscence spectrometer work?

A
  • Light goes through the first monochromator and hits the sample
  • The fluorescent light emitted is then passed through a second monochromator
  • This light then reaches the detector
52
Q

What is FRET used for?

A

Measuring distances on a molecular scale

53
Q

What happens in FRET?

A
  • the FRET donor aborbs light, promotes an electron
  • The energy released from the electron moving energy levels is transferred to the FRET acceptor by dipole-dipole coupling mechanism

Biological Chemistry 1A (10 decks)

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