Change and shape in biological reactions

Question 1

How are cations formed?

Answer 1

Loss of electrons

Question 2

How are anions formed?

Answer 2

Gain of electrons

Question 3

What is a hydrogen bond?

Answer 3

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

Question 4

What type of bonding is present in liquid water?

Answer 4

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

Question 5

What kind of environment is water?

Answer 5

Polar

Question 6

What will water easily solubilise?

Answer 6

Other polar molecules, regions of molecules or ions

Question 7

What makes something hydrophilic?

Answer 7

Charge
Hydrogen bonding potential
Low proportion of carbon atoms

Question 8

What makes something hydrophobic

Answer 8

No charge

High proportion of carbon atoms

Question 9

What is an acid?

Answer 9

A compound that can lose an H+ ion and become negatively charged in the process

Question 10

What is a base?

Answer 10

A compound that can (reversibly) form covalent bonds with a H+ ion to become positively charged

Question 11

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

Answer 11

They will be negatively charged and anionic

Predominantly ionised

Question 12

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

Answer 12

They will be positively charged and cationic

Predominantly ionised

Question 13

What happens to amides at physiological pH?

Answer 13

Amides are neutral at physiological pH

Question 14

What determines secondary structure?

Answer 14

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

Question 15

What is tertiary structure?

Answer 15

The overall shape of a protein chain

Question 16

What determines tertiary structure?

Answer 16

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

Question 17

How does hydrophobicity influence structure?

Answer 17

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

Question 18

What is quaternary structure?

Answer 18

Chains forming complexes

Question 19

What determines quaternary structure?

Answer 19

Bonding between chains

Hydrophobicity

Question 20

Name three things hydrophobicity determines

Answer 20

Structure
Function
Cellular distribution

Question 21

What is pH?

Answer 21

Measure of concentration of H+

Question 22

How do we calculate pH?

Answer 22

pH = -log10[H+]

Question 23

Why is water polar

Answer 23

the electrons shared in the covalent bond are attracted to it pulling the electrons away from the H, polarising the bond

• O has a partial negative charge
• each H has a partial positive charge

Question 24

What types of molecules tend to be hydrophilic?

Answer 24

molecules with charge, good H-bonding pot and a low proportion of C atoms

Question 25

What types of acid are predominately ionised (negative charge) at physiological PH?

Answer 25

Acids with a low pKA (<7.4)

Question 26

What determines the hydrophobicity/hydrophilicity in an amino acid?

Answer 26

The R group | -amides are neutral across physiological PH

Question 27

Why are weak acids usually in equilibrium?

Answer 27

Because the energy between reactants and products is very small so it is easy to go forwards and backwards

Question 28

What is Chatelier's principle?

Answer 28

If an equilibrium is disturbed by a change of environment the system will tend to shift its equilibrium position to counteract the effect of the disturbance

Question 29

What is Ka?

Answer 29

equilibrium constant

Question 30

What is the equation for KA?

Answer 30

Ka= [H+] [A-} ------------- [HA]

Question 31

What is pKA?

Answer 31

A logarithmic constant which is proportional to the free energy of the acid-base reaction which tells us how acidic/basic the compound is so can tell us the quantative behaviour of the equilibrium

Question 32

What is the equation for pKA?

Answer 32

pKa = -log10(Ka)

Question 33

When does pH =pKa?

Answer 33

When [A-] = [HA] | when the compound is 50% ionised

Question 34

What is the Henderson-Hasselbach equation?

Answer 34

pH= pKa + log ([A-]/[HA])

Question 35

How do you work out the percentage ionisation of a compound?

Answer 35

% compound ionised = 100 ------------ 1 + 10^(charge(pH-pKa) When the charge for acids = -1 charge for bases = +1

Question 36

What happens when PH =pKa -1 for an acid.

Answer 36

Acid will be around 10% disassociated

Question 37

What happenes when PH =pKa + 1 for an acid

Answer 37

Acid will be around 90% dissociated

Question 38

What happens when PH >pKa +2

Answer 38

acid will be more than 99% disassociated

Question 39

What is a deprotonated termed as and why?

Answer 39

Conjugate base because it acts as a base, receiving a proton in the reverse reaction

Question 40

What is the Ka for a base?

Answer 40

Ka = [H+] [B] ------------ [HB+]

Question 41

How can the solvent around a molecule affect pKa?

Answer 41

e.g less exposure to water (shielding) means ionisation is less likely (pKa of acids higher)

Question 42

What is the isoelectric point?

Answer 42

When there are multiple pKa values then there can be multiple different states with different charges. When the net charge is 0 it is known as the isoelectric point (the PH when theres no charge) -equal number of + and - charged groups on the protein so its at its minimum aqueous solubility

Question 43

What moves towards the cathode?

Answer 43

positively charged compounds

Question 44

What are the ionisable amino acids?

Answer 44

Aspartate Glutamate Lysine Argenine These amino acids are predmoninantly ionised at phsiological pH meaning there are very hydrophilic

Question 45

Why does pH and pKa matter?

Answer 45

Can effect the potential conformation of proteins Can effect the behaviour of certain moleules

Question 46

What influences pKa?

Answer 46

The solvent around a molecule | Accessibility to water influences the side chain ionisation properties