Amino Acids & Proteins

Question 0

What bonds are involved in macromolecular structures?

Answer 0

COVALENT = shared pair of electron bonds e.g. disulfide bonds
NON-COVALENT:
- Hydrogen bonds = Weak electrostatic interaction between hydrogen atoms, covalently bound to an electronegative atom, and another electronegative atom.
- Ionic interactions = Electrostatic bond between two ions formed through the transfer of one or more electrons
- Hydrophobic interactions = Interaction of polar (hydrophilic) and non-polar (hydrophobic) molecules with each other and water
- Van der Waals’ Force = Force between instantaneous dipoles (formed by movement of electrons in one atom, inducing a dipole in another atom)

Question 1

What are some of the differences between eukaryotic and prokaryotic cells?

Answer 1

EUKARYOTIC = nuclear membrane, DNA wrapped around histone complexes (chromosomes); membrane-bound organelles (chloroplasts, mitochondria, ER, Golgi complex, vacuoles); transcription in nucleus and translation in cytoplasm; transcription factors bind directly to promoter sequences independently of RNA polymerase.

PROKARYOTIC = no nucleus, DNA tightly coiled with associated RNA and proteins (nucleoid); no membrane-bound organelles but have specialised internal membranes where ATP is generated; transcription & translation occur concurrently; cell wall (peptidoglycan or periplasm + lipopolysaccharide layer).

Question 2

How do hydrophobic and hydrophilic molecules differ in behaviour in water?

Answer 2

Hydrophobic regions cluster together and are shielded from water by a bilayer/shell of hydrophilic regions.

Amphipathic molecules (molecule with hydrophobic and hydrophilic regions) form the lowest energy conformation in water.

Question 3

What is the isoelectric point of an amino acid?

Answer 3

ISOELECTRIC POINT = pH at which a protein has no overall net charge

Basic proteins: pI>7 (mostly positively charged)
Acidic proteins: pI<7 (mostly negatively charged)

Question 4

Define an acid/base.

Answer 4

ACID = substance which ionises in water to produce protons (proton donor/electron-pair acceptor)
NEGATIVE CHARGE

BASE = substance which ionises in water to produce hydroxide ions
(proton acceptor/electron-pair donor)
POSITIVE CHARGE

Question 5

Define pKa and explain how the relationship between pH and pKa affects the charge of an acid/base.

Answer 5

pH > pKa = protonation (accepted proton/donated electron)

pH < pKa = deprotonation (donated proton/accepted electron)

Question 6

What is a buffer?

Answer 6

Solution that resists changes in pH following the addition of an acid/base (mix weak acid with its conjugate base).

Maximum buffering capacity when pH = pKa
(+-1pH of pKa)

Question 7

How does the peptide bond contribute to the conformation of the amino acid.

Answer 7

Peptide bond = partial double bond characteristics (electron delocalisation)

• rigid (no free rotation of groups around bond)
• planar
• shorter than normal C-N bonds

Trans conformation is the lowest energy

Question 8

How can amino acids be classified? Give an example of each group.

Answer 8

Non-polar (hydrophobic) e.g. glycine, proline, methionine (“hidden” sulfur)

Polar, uncharged (hydrophilic) e.g. cysteine (exposed sulfur), serine (side chain: -CH2OH)

Polar, charged (hydrophilic) e.g. +ve lysine (basic), -ve glutamate (acidic)

Question 9

What is the acid dissociation constant?

Answer 9

pH > pKa = deprotonated
pH < pKa = protonated

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

Question 10

What is the Henderson-Hasselbalch equation?

Answer 10

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