Charge and shape in biological molecules

Question 1

The nucleus consists of…

Answer 1

…protons and neutrons

Question 2

What are the mass and charges of neutrons and protons

Answer 2

Mass: 1 for both
Proton charge: +1
Neutron charge: 0

Question 3

What volume of the atom does the nucleus account for?

Answer 3

1/100,000th

Question 4

What surrounds the nucleus?

Answer 4

A cloud of electrons

Question 5

Give the nominal mass and charge of an electron

Answer 5

0 and -1

Question 6

What is atomic number?

Answer 6

The number of protons in an atom

Question 7

How are cations formed?

Answer 7

Loss of electrons

Question 8

How are anions formed?

Answer 8

Gain of electrons

Question 9

What is a covalent bond?

Answer 9

A bond that involves the sharing of electron pairs between atoms

Question 10

How strong are covalent bonds?

Answer 10

Very strong

Question 11

What is a hydrogen bond?

Answer 11

An attraction between N, O or F and a H on another molecule

Question 12

What type of bonding is present in liquid water?

Answer 12

Covalent bonds: sharing electrons between oxygen and hydrogen
Hydrogen bonds: between adjacent molecules

Question 13

What kind of environment is water?

Answer 13

Polar

Question 14

What will water easily solubilise?

Answer 14

Other polar molecules, regions of molecules or ions

Question 15

What makes something hydrophilic?

Answer 15

Charge
Hydrogen bonding potential
Low proportion of carbon atoms

Question 16

What makes something hydrophobic

Answer 16

No charge

High proportion of carbon atoms

Question 17

What is an acid?

Answer 17

A compound that can lose an H+ ion

Question 18

What is a base?

Answer 18

A compound that can form covalent bonds with a H+ ion

Question 19

What will happen to amino acids with low pKa at physiological pH?

Answer 19

They will be negatively charged and anionic

Predominantly ionised

Question 20

What will happen to amino acids with high pKa at physiological pH?

Answer 20

They will be positively charged and cationic

Predominantly ionised

Question 21

What happens to amides at physiological pH?

Answer 21

Amides are neutral at physiological pH

Question 22

What determines secondary structure?

Answer 22

Shape and conformation preference of the residues
Maintained by regular hydrogen bonding pattern
Can be predicted from primary structure

Question 23

What is tertiary structure?

Answer 23

The overall shape of a protein chain

Question 24

What determines tertiary structure?

Answer 24

Bonding interactions:
Ionic & hydrogen
Conformation of residues e.g. proline-induced turns

Question 25

How does hydrophilicity influence structure?

Answer 25

Hydrophilic residues prefer to be at the centre of the protein away from the water

Question 26

What is quaternary structure?

Answer 26

Chains forming complexes

Question 27

What determines quaternary structure?

Answer 27

Bonding between chains

Hydrophobicity

Question 28

Name three things hydrophobicity determines

Answer 28

Structure
Function
Cellular distribution

Question 29

What is pH?

Answer 29

Measure of concentration of H+

Question 30

How do we calculate pH?

Answer 30

-log10[H+]