Amino Acids, Peptides, Proteins and Enzymes: Quick Revision

A brief note on Amino Acids, Peptides, Proteins and Enzymes. Read it before a test. Try each question at the end before you open its answer.

Amino acids

• An α-amino acid is $\text{H}_{2}\text{N}\text{-}\text{CH}(\text{R})\text{-}\text{COOH}$. Natural proteins contain L amino acids. Glycine is the only achiral one.
• In water and in the solid, it is a zwitterion: $\text{H}_{3}\text{N}^{+}\text{-}\text{CH}(\text{R})\text{-}\text{COO}^{-}$. The charge is $+1$ at low pH, $0$ at the pI and $-1$ at high pH.
• Isoelectric point: for a neutral side chain, $\text{pI} = (\text{p}K_1 + \text{p}K_2)/2$. Otherwise average the two pK values on either side of the neutral form.
• Above the pI a molecule moves to the anode. Below the pI it moves to the cathode.
• Nine amino acids are essential for an adult. NCERT lists arginine as well.
• Tests: ninhydrin gives purple (proline yellow). Nitrous acid releases $\text{N}_{2}$ from a primary amine.

Peptides and proteins

• The peptide bond is an amide formed with the loss of one water. A chain of $n$ residues has $n - 1$ bonds.
• It is flat and trans, with a C to N length of 0.133 nm, a partial double bond.
• Primary: the sequence. Secondary: α-helix (3.6 residues per turn, 0.15 nm per residue, C=O to N-H four places ahead) and β-sheet. Tertiary: the whole fold, held by disulphide bridges, hydrogen bonds, ionic attractions and hydrophobic contacts. Quaternary: several chains, as in haemoglobin.
• Fibrous proteins (keratin, collagen, silk) do not dissolve. Globular proteins (albumin, enzymes) dissolve.
• Biuret test: at least two peptide bonds give violet.

Denaturation and enzymes

• Denaturation destroys the secondary, tertiary and quaternary structures. The sequence stays. Heat, pH change, urea, solvents and heavy metal ions cause it.
• Enzymes are specific biological catalysts. They lower the activation energy and do not change the equilibrium.
• Rate ratio $= e^{\Delta E_a/RT}$. A drop of 5.7 kJ/mol gives a factor of 10 at 298 K.
• Activity has an optimum temperature (about 37 °C) and an optimum pH.

A worked example

Find the isoelectric point of glycine, with $\text{p}K_1 = 2.34$ and $\text{p}K_2 = 9.60$.

1. Which form? The neutral zwitterion lies between the two pK values.
2. Mean. $\text{pI} = (2.34 + 9.60)/2 = 5.97$.

Practice with new numbers

A program to try

Mistakes to avoid

• Averaging the wrong pK values for acidic or basic amino acids.
• Counting the peptide bonds as the number of residues. There are $n - 1$ of them.
• Saying that denaturation cuts peptide bonds. It does not.
• Thinking an enzyme shifts the equilibrium. It does not.

Check yourself

1. Which electrode does glycine move to at pH 8?

2. How many peptide bonds are in a chain of 12 residues?

3. Name two things that denature an enzyme.

4. Does an enzyme change the equilibrium constant of a reaction?

Sources

• Nelson and Cox, Lehninger Principles of Biochemistry, 8th edition, Chapters 3, 4 and 6.
• NCERT Chemistry for Class 12, Part II, the chapter Biomolecules.
• OpenStax, Organic Chemistry, Chapter 26.