Week 4 (amino acids)

Question 1

What is a salt bridge?

Answer 1

An ionic interaction within a protein

Question 2

Which amino acids have acidic side groups?

Answer 2

Tyrosine

Aspartic acid

Glutamic acid

Question 3

Which amino acids are basic?

Answer 3

• Histidine
• Lysine
• Arginine

Often found in active site of enzymes AND On surface because their side chains interact well with water

Question 4

Which amino acids are amides?

Answer 4

Asparagine

Glutamine

(Tryptophan- amine)

Question 5

which amino acids are Hydrophobic?

Answer 5

Alanine

Valine

Leucine

Isoleucine

Methionine

Proline

Phenylalanine

Question 6

What amino acids are Nucleophilic?

Answer 6

Serine

Threonine

Cysteine

Question 7

Which amino acids are hydrophilic?

Answer 7

Aspartic acid

Glutamic acid

Asparagine

Glutamine

Serine

Threone

Tyrosine

cysteine

Lysine

Arginine

Histidine

Question 8

What is the isotonic point? What is this equal to for amino acids?

Answer 8

• The pH at which predominates in aqueous solution
• This means it is the pH at which the amino acid is neutral, i.e. the zwitterion form is dominant.
• For AAs this is equal, to the isoelectric point

Question 9

What happens To an AA at low pH?

Answer 9

Everything that can be protonated will be:

NH3+ and COOH

Question 10

What happens at high pH?

Answer 10

Everything that can be deprotonated will be:

NH₂ and COO-

Question 11

Why is proline special?

Answer 11

• Only amino acid where the side chain is connected to the protein backbone twice, forming a five-membered nitrogen-containing ring.
• The only imino acid
• Can change the direction of a polypeptide chain

Question 12

What is special about tryptophan?

Answer 12

• Aromatic indole (heterocyclic) ring-: The lone pair of electrons is part of the delocalised Pi system not available for bonding
• It has a nitrogen containing side chain (amine)

Question 13

Why is pH measured using a glass electrode?

Answer 13

• A glass electrode is selectively permeable to hydrogen ions and is used for measuring the pH of solution
• A combination electrode (double electrode system) consisting of a glass electrode and a calomel electrode combined in one probe

Question 14

How does a glass electrode work?

Answer 14

1. The glass electrode consists of a Ag-Cl electrode in a reference solution of hydrochloric acid contained in a glass membrane
2. The membrane is made of a special glass, selectively permeable to hydrogen ions
3. The potential that develops across the membrane depends upon the hydrogen ion concentration of the test solution compared with the reference acid solution inside the electrode
4. This potential is measured against a reference calomel electrode
5. For ease of operation the glass electrode is often combined with a reference calomel electrode in a single probe.

6 There is an almost linear relationship between potential and pH range of 2-10

Question 15

What pH promotes the formation of the zwitterion?

Answer 15

pH 7

Question 16

How do you calculate the pH of the isoelectric point?

Answer 16

pKa₁+pKa₂

pI= –————––

2

• The average pKa for the ionisable groups
• Where pKa₁ and pKa₂ is the ionisable groups (NH₂ and COOH)

Question 17

Ionisation of the terminal carboxyl

Answer 17

COOH—> COO- + H+

Question 18

Ionisation of the amino terminal

Answer 18

NH3+—> NH2 + H+

Question 19

which ammonium group is deprotonated first in an AA with multiple NH groups

Answer 19

The NH₂ attached to the alpha carbon

Question 20

Which COOH group inonises first in an AA with multiple COOH?

Answer 20

The COOH attached to the alpha carbon

Question 21

What is the Henderson Hasselbach equation for a weak acid?

Answer 21

pH= pKa + log (([conjugate base] (ionised form)/acid)

where the square brackets indicate the molar concentration of the named substance

Question 22

What is the Henderson Hassalbach equation for a weak base?

Answer 22

pH= pKa + log (( [base] (unionised form)/ [conjugate acid] (ionised form))

where the square brackets indicate the molar concentration of the named substance

Question 23

Explain the titration curve for alanine

Answer 23

• At a pH equivalent to pKa₁ there are equal amounts of forms 1 and 2
• at a pH equivalent to pKa₂, forms 2 and 3 are in equal concentrations
• the pI value for alanine is 6 and is the mean of pKa 1(2.4) and pKa 2 (9.6)
• at a pH below it’s pI value an amino acid will carry a net positive charge it it will carry a net negative charge at pH greater than pI

(Typical curve of an amino acid with only two ionizable groups (one carboxyl and one amino)

Question 24

What are the labels on this diagram?

Answer 24

Question 25

What do the the two shaded areas of a titration curve show?

Answer 25

The two shaded areas show the pH range over which the addition of alkali results in only a very small change in pH and where the amino acid exhibits its most significant buffering action

Question 26

What is K, Ka and pKa?

Answer 26

The dissociated and undissociated forms of each group exist in equilibrium having the equilibrium constant K often termed Ka because it refers to the dissociation of groups that liberate protons.

The actual values for Ka are often very small and are conventionally expressed as the negative logarithm of the value, a term known as the pKa value: pKa = -log Ka

Question 27

What does the Henderson-Hasselbalch equation show?

Answer 27

How the concentration of hydrogen ions liberated by the dissociation of an acid is related to the dissociation constant for that acid.

Question 28

What are the 4 key points of amino acids and titration?

Answer 28

1. The nature of the amino acid species present in solution will depend upon the pH.
2. For amino acids, at the isoelectric point (pI), the molecule carries no net charge and is electrophoretically immobile.
3. 7 of the 20 common amino acids have readily ionisable side chains
4. Amino acids with ionizable side chains give complex titration curves.