Nucleotides

Question 1

What is a nucleotide?

Answer 1

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

Question 2

What is a nuceloside?

Answer 2

A nucleobase bonded to a sugar

Question 3

Which part of ATP is attacked by a hard nucleophile?

Answer 3

The terminal phosphate group

Question 4

What part of ATP is attacked by a soft nucleophile?

Answer 4

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

Question 5

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

Answer 5

• ATP
• NAHP
• Coenzyme A

Question 6

What is the general purpose of nucleotides in large molecules?

Answer 6

To bind the molecule further to proteins

Question 7

How many rings do purines have?

Answer 7

2

Question 8

How many rings do pyrimidines have?

Answer 8

1

Question 9

How many hydrogen bonds do A and T make?

Answer 9

2

Question 10

How many hydrogen bonds do G and C make?

Answer 10

3

Question 11

Which base pairs are most strongly bonded?

Answer 11

G-C pairs

Question 12

What is tautomerism?

Answer 12

Any reaction that involves the simple intramolecular transfer of a proton

Question 13

What is the effect of nucelobsae tautomers on base pairing?

Answer 13

Can cause abnormal/ non-canonical base pairing

Question 14

What is non-canonical base pairing?

Answer 14

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)

Question 15

How can tautomers cause abnormal base pairing?

Answer 15

Double proton transfer between H-bonded bases

Question 16

What issues can non-canonical base pairing cause?

Answer 16

Can cause issues in replication of DNA

Question 17

Is RNA more susceptible to hydrolysis than DNA?

Answer 17

Yes

Question 18

Give a use of synthetic nucleotides

Answer 18

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

Question 19

Define fluorescence

Answer 19

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

Question 20

Why is cytosine methylation of critical importance to organisms?

Answer 20

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

Question 21

Define luminescence

Answer 21

The emission of light by a substance not resulting from heat

Question 22

Define chemiluminescence

Answer 22

The emission of light resulting from a chemical reaction

Question 23

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

Answer 23

Jablonski diagrams

Question 24

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

Answer 24

Energy

Question 25

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

Answer 25

Nuclear separation

Question 26

What does a Japlonski diagram show?

Answer 26

The electronic states of a molecule and the transitions between them

Question 27

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

Answer 27

The bond breaks

Question 28

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

Answer 28

Aromatic

Question 29

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

Answer 29

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

Question 30

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

Answer 30

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

Question 31

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

Answer 31

Internal conversion/vibrational relaxation

Question 32

How is energy lost for absorbance?

Answer 32

As heat

Question 33

Why is the wavelength of absorbance not a single line?

Answer 33

The electrons can go into multiple vibrational energy states

Question 34

Why is a longer wavelength of light given off in fluorescence? What is this effect called?

Answer 34

Due to energy loss Stop shift

Question 35

How is energy emitted in fluorescence?

Answer 35

As light, by the emission of a photon

Question 36

What do you call a molecule which fluoresces?

Answer 36

Flurophore

Question 37

Which amino acid is fluroscent?

Answer 37

Tryptophan

Question 38

What affects the absorption spectrum of a molecule?

Answer 38

Temperature

Question 39

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

Answer 39

When bound to proteins/DNA their emission spectrum often changes

Question 40

How can some proteins become highly fluorescent?

Answer 40

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

Question 41

Compare the speed of fluroscence with phosphorescence

Answer 41

Phosphorescence is much slower

Question 42

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

Answer 42

* 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

Question 43

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

Answer 43

Intersystem crossing

Question 44

What kind of process is intersystem crossing?

Answer 44

A forbidden process

Question 45

What is a forbidden process?

Answer 45

A process (in quantum mechanics) which occurs very slowly

Question 46

How does chemiluminescence differ to fluorscence?

Answer 46

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

Question 47

What is chemiluminescence?

Answer 47

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

Question 48

What can chemiluminescence be useful for?

Answer 48

Tracking gene expression in living organisms

Question 49

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

Answer 49

180°

Question 50

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

Answer 50

90°

Question 51

How does a fluroscence spectrometer work?

Answer 51

* 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

Question 52

What is FRET used for?

Answer 52

Measuring distances on a molecular scale

Question 53

What happens in FRET?

Answer 53

* 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