Primary Structure of Proteins & Acid/Base Chemistry

Lecture 3

proteins

polymers of amino acids

protein functions

• catalysis (enzymes)

• transport and storage (haemoglobin)

• movement/motion (action/myosin)

• mechanical support (collagen)

• immunity (antibodies)

• signal and nerve transmission (G-coupled receptors)

• growth, differentiation, biological control (gene expression and programming)

amino acid stereochemistry

all L (levorotatory)

all S (sinister) EXCEPT cysteine (R (rectus) because of sulfur…)

amino acid functional groups

• alkane (C_nH_2n+2)

• alcohol (-OH)

• phenol (-ArOH)

• carboxylic acid (-COOH)

• amine (-NH₂)

• amide (-CONH₂)

• thioether (-SR)

• imidazole ((CH)₃(NH)N)

• indole (C₆H₄CCNH₃)

• guanidinium (HNC(NH₂)₂)

• phenyl (-Ar)

• thiol (-SH)

Fischer Projection of amino acids

most oxidised (COOH) on top; what side is the amino acid on?

Side chain chemical properties

overlapping, but even similar residues can’t be swapped without changing structure and function of a protein

cysteine disulfide bridges

trigger massive conformational change; redox; weaker than oxygen bonds; reversible locks on structure

Tryptophan and Tyrosine chromophores

UV absorbance ~280nm can determine protein concentration; fluorescence can be used to study protein structure

Determining protein concentration

Beer’s Law (A=εcl)

acid-base properties of amino acids

Free amino acids are acids and bases in aqueous medium

amine pKa = 10

carboxylic acid pKa = 4

form amide bonds in chains

Henderson–Hasselbalch equation

describes the change in pH during titration of a weak acid or a weak base

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

Leveling Effect

An acid/base stronger than the conjugate acid/base of the solvent cannot exist in any appreciable concentration in that solvent.

Ex. in water, no acid stronger than H₃O⁺ or base stronger than OH^- can exist (pKa ~1.74 to 14)

R groups @ pH 7

pKa values of ionizable groups in proteins

1. carboxylic acid

2. amine

3. cysteine (thiol)

4. histidine (pKa ~7)

5. arginine

Isoelectric point (pI)

pH at which the overall charge of an amino acid/polypeptide is neutral; considers pKa and charge state of each ionization group; intermediate value theorem

Peptide bond formation/condensation reaction

Thermodynamically, peptide bond hydrolysis is more favorable than peptide bond formation. The rate at which this hydrolysis occurs, however, is extremely slow.

Note cancellation of amino and carboxy charges when the groups join to become amides

primary structure

the amino acid structure alone