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

BS1030: Biochemistry > CW1: Protein Structure, Enzymes & Catalysis, and Protein Diversity > Flashcards

Flashcards in CW1: Protein Structure, Enzymes & Catalysis, and Protein Diversity Deck (20)
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1
Q

How do micelles form?

A
  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.
2
Q

What is the Henderson-Hasselbalch equation?

A

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

3
Q

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

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

4
Q

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

A
  • 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
5
Q

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

A

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

6
Q

What are optical isomers/enantiomers?

A

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

7
Q

Why do amino acids exist as zwitterions at pH 7?

A
  • 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
8
Q

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

A
  • The observed tendency of non-polar substances to aggregate in aqueous solution and exclude water molecules
  • Weak interaction
9
Q

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

A

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

10
Q

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

A
  • A shared pair of electrons between two atoms
  • Strong interaction
11
Q

Define pK

A

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

12
Q

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

A
  • 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
13
Q

Define pH and explain how the scale works

A
  • 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
14
Q

Which form of amino acids are found in protiens?

A

L

15
Q

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

  1. pH 1
  2. pH 7
  3. pH 11?
A
16
Q

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

A
  • A bond formed between two atoms of opposing charge when one atom gives up one or more electrons to the other
  • Strong interaction
17
Q

What is the dissociation constant for the reaction:

HA ⇌ H+ + A

A
18
Q

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

A

NH2 = amino group

COOH = carboxylic acid group

R = side chain

C = α-carbon

19
Q

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

A
  • 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
20
Q

What is the association constant for the reaction:

HA ⇌ H+ + A

A