CW1: Protein Structure, Enzymes & Catalysis, and Protein Diversity

Question 1

How do micelles form?

Answer 1

1. DISPERSION OF LIPIDS IN H₂O
   Each lipid molecule forces surrounding H₂O molecules to become highly ordered.
2. CLUSTERS OF LIPID MOLECULES
   Only lipid portions at the edge of the cluster force the ordering of water. Fewer H₂O molecules are ordered, and entropy is increased.
3. MICELLES
   All hydrophobic groups are sequestered from water; ordered shell of H₂O molecules is minimised, and entropy is further increased.

Question 2

What is the Henderson-Hasselbalch equation?

Answer 2

pH = pK + log(^{[A<span>-</span>]}/_[HA])

Question 3

The COOH group has a pK of ~3. Which form will predominate when:

1. pH > pK
2. pH < pK
3. pH = pK?

Answer 3

1. Basic (COO^–)
2. Acidic (COOH)
3. [acidic form] = [basic form]

*N.B. Think of it in terms of [H⁺]:
When pH is low, [H⁺] is high, therefore the predominant form will have H⁺ bound to it, i.e. COOH will predominate at ph < 3.

Question 4

What are Van der Waals forces, and are they strong or weak interactions?

Answer 4

• Short-range electrostatic attractive forces between all uncharged molecules, resulting from the interaction of permanent or transient electric dipole moments.
• They occur over short distances (~3Å)
• Very weak interaction

Question 5

Which amino acid is achrial and why is this the case?

Answer 5

Glycine because it has two hydrogens bound to its α-carbon

Question 6

What are optical isomers/enantiomers?

Answer 6

Two or more forms of a compound which have the same structure but are non-superimposable mirror images of each other

Question 7

Why do amino acids exist as zwitterions at pH 7?

Answer 7

• The COOH group has a pK ≈ 3
  pH 7 is higher than the pK, so unprotonated COO^– predominates
• The NH₂ group has a pK ≈ 8
  pH 7 is lower than the pK, so protonated NH₃⁺ predominates
• Therefore, at pH 7, both the amino and the carboxyl groups will be charged, resulting in the dipolar zwitterion form

Question 8

What is the hydrophobic effect and is it a strong or weak interaction?

Answer 8

• The observed tendency of non-polar substances to aggregate in aqueous solution and exclude water molecules
• Weak interaction

Question 9

What are micelles? Define the two key terms in the definition.

Answer 9

Aggregates of surfactants dispersed in a liquid colloid

surfactants: compounds that lower the surface tension between two liquids or a liquid and a solid

liquid colloid: a mixture in which insoluble particles are suspended in another substance

Question 10

What is a covalent bond, and is it a strong or weak interaction?

Answer 10

• A shared pair of electrons between two atoms
• Strong interaction

Question 11

Define pK

Answer 11

A measure of the pH at which an ionisable group is 50% dissociated

It provides a measure of the ease of dissociation of a proton, i.e. the lower the pK, the stronger the acid

Question 12

What is a hydrogen bond, and is it a strong or weak interaction?

Answer 12

• A bond between two molecules resulting from an electrostatic attraction between a proton in one molecule and an electronegative atom in the other
• Weak interaction (one-twentieth of the strength of a covalent bond); however, many hydrogen bonds are together very strong

Question 13

Define pH and explain how the scale works

Answer 13

• pH = –log₁₀[H⁺]
• pH is a logarithmic scale:
  
  • pH 3 = [H⁺] of 10^–3 M
  • ph 7 = [H⁺] of 10^–7 M
• The higher the pH, the less acidic something is
• The lower the pH, the more acidic something is

Question 14

Which form of amino acids are found in protiens?

Answer 14

L

Question 15

What are the predominant forms of a generic amino acid at:

1. pH 1
2. pH 7
3. pH 11?

Answer 15

Question 16

What is an ionic bond, and is it a strong or weak interaction?

Answer 16

• A bond formed between two atoms of opposing charge when one atom gives up one or more electrons to the other
• Strong interaction

Question 17

What is the dissociation constant for the reaction:

HA ⇌ H⁺ + A^–

Answer 17

Question 18

What is the general structure of an amino acid? Name each functional group.

Answer 18

NH₂ = amino group

COOH = carboxylic acid group

R = side chain

C = α-carbon

Question 19

Describe the difference between the unionised form and the zwitterion form of a generic amino acid.

Answer 19

• Zwitterion form usually occurs at pH 7
• Unionised form doesn’t usually occur at pH 7
• The unionised form has no charge on the amnio and carboxyl groups

Question 20

What is the association constant for the reaction:

HA ⇌ H⁺ + A^–

Answer 20