Amines and Amino Acids

Lessons

Senior 5 · Chemistry

Amines and Amino Acids

4 lessons

Lesson 4 of 4

Peptides, Polypeptides and Proteins

25 min

Why does egg white turn white?

Break an egg into a hot pan: the clear, runny white turns opaque and firm within seconds, and nothing you do will turn it clear again. Egg white is about one-tenth protein dissolved in water. Heat does not break the chains of amino acids in that protein; it destroys the precise way each chain is folded. To see why folding matters so much, you first need to see how amino acids join into chains.

Definition

Peptide bond (peptide link): the amide link, $\mathrm{-CO{-}NH-}$ , formed between the carboxyl group of one amino acid and the amino group of another, with loss of water.

Dipeptide, tripeptide, polypeptide: chains of two, three or many amino-acid residues. A protein is one or more polypeptide chains, usually of 50 or more residues, folded into a definite shape.

Condensation reaction: two molecules join with the loss of a small molecule such as water. Hydrolysis: the reverse, breaking a bond by reaction with water.

Denaturation: loss of a protein's folded (secondary, tertiary and quaternary) structure, with the sequence of amino acids unchanged.

Forming the peptide bond

The –OH of one amino acid's carboxyl group and an H from the next amino acid's amino group leave as water:

$\mathrm{H_2NCH_2COOH + H_2NCH(CH_3)COOH \rightarrow H_2NCH_2CONHCH(CH_3)COOH + H_2O}$

Figure 9.5: The dipeptide glycylalanine. A chain is written from the free $\mathrm{-NH_2}$ end (N-terminus) to the free –COOH end (C-terminus).

Order matters. Glycine and alanine can also join the other way round, giving alanylglycine (Ala-Gly), a different compound. With $n$ different amino acids each used once, there are $n!$ possible sequences; if each position may be any of the 20 protein amino acids, a chain of length $L$ has $20^{L}$ possible sequences. That is why proteins can be so varied.

The C–N bond in the peptide link is shorter than a normal C–N single bond, because the nitrogen lone pair is partly delocalised onto the C=O group. The six atoms around the link therefore lie in one plane, which makes the backbone stiff in some places and flexible in others.

Polyamides. The same amide link joins nylon-6,6 (from hexane-1,6-diamine and hexanedioic acid). Nylon and proteins are both polyamides; proteins differ in having a different side chain on almost every unit.

Worked example

Problem. (a) Calculate the molar mass of the tripeptide Gly-Ala-Ser. (b) How many different tripeptides contain one residue each of Gly, Ala and Ser? ( $M$ /g mol⁻¹: Gly 75.07, Ala 89.09, Ser 105.09, $\mathrm{H_2O}$ 18.02)

Solution. (a) Joining three amino acids makes two peptide bonds and releases two water molecules:

$M = 75.07 + 89.09 + 105.09 - 2 \times 18.02 = 233.21\,\mathrm{g\,mol^{-1}}$

(b) Any of the 3 can be first, either of the remaining 2 second, and the last one third: $3! = 3 \times 2 \times 1 = 6$ .

Answer: (a) 233.21 g mol⁻¹; (b) 6 (Gly-Ala-Ser, Gly-Ser-Ala, Ala-Gly-Ser, Ala-Ser-Gly, Ser-Gly-Ala, Ser-Ala-Gly).

Hydrolysis: taking proteins apart

Acid hydrolysis: heating under reflux with about 6 mol dm⁻³ hydrochloric acid for many hours. The amino acids come out as their cations, e.g. $\mathrm{H_3N^{+}CH_2COOH}$ .
Alkaline hydrolysis: heating with aqueous sodium hydroxide gives the sodium salts, e.g. $\mathrm{H_2NCH_2COO^{-}Na^{+}}$ .
Enzymes: in the stomach and small intestine, proteases such as pepsin and trypsin hydrolyse dietary protein at 37 °C, and the amino acids are absorbed into the blood.

The amino acids in a hydrolysate can be separated by paper or thin-layer chromatography and located with ninhydrin; each is identified by its $R_{f}$ value, $R_f = \frac{\text{distance moved by the spot}}{\text{distance moved by the solvent front}}$ , compared with standards run on the same plate.

The four levels of protein structure

Level	What it describes	What holds it
Primary	the sequence of amino acids in each chain	covalent peptide bonds
Secondary	local folding of the backbone into an α-helix or a β-pleated sheet	hydrogen bonds between the C=O of one peptide link and the N–H of another
Tertiary	the overall three-dimensional shape of one chain	interactions between side chains: hydrogen bonds, ionic attractions (–COO⁻ with –NH₃⁺), disulfide bridges (–S–S– between cysteines) and hydrophobic interactions
Quaternary	how several chains pack together	the same side-chain interactions, between chains

The primary structure decides all the rest: a change of a single amino acid can matter. In sickle-cell haemoglobin, the sixth amino acid of each β-chain is valine instead of glutamic acid. A charged side chain is replaced by a non-polar one, the haemoglobin molecules stick together when oxygen is low, and red cells distort into a sickle shape.

Denaturation. Heat, strong acid or alkali, heavy-metal ions and some solvents disrupt the weak interactions that hold the secondary, tertiary and quaternary structure, so the chain unfolds and the protein loses its function; an enzyme stops working. Peptide bonds are not broken, so the primary structure survives. This is what happened to the egg white.

Proteins in the diet. Your body can make some amino acids but not nine "essential" ones, which must come from food. Cereals such as maize are low in lysine, while beans are rich in lysine but low in the sulfur amino acid methionine, so a meal of beans with maize or sorghum supplies a better balance than either alone.

Warning

Hydrolysis and denaturation are different. Hydrolysis breaks covalent peptide bonds and gives amino acids. Denaturation breaks only hydrogen bonds, ionic interactions and (sometimes) disulfide bridges, leaving the chain intact. Cooking an egg denatures its proteins; digesting it hydrolyses them.

Safety: ninhydrin spray is harmful and stains skin purple; use gloves and a fume cupboard. 6 mol dm⁻³ hydrochloric acid is corrosive: on skin or in the eyes, flush with plenty of water for at least 15 minutes (CDC/ATSDR).

Tip

To draw a dipeptide quickly: write the first amino acid with its –COOH on the right, the second with its $\mathrm{H_2N-}$ on the left, cross out OH and H, and join C to N. To find the amino acids from a peptide, do the opposite: cut every C–N bond between C=O and N–H and add $\mathrm{H_2O}$ across each.

Biology Professor: Four Levels of Protein Structure (Primary, Secondary, Tertiary, Quaternary). Watch which bonds hold each level, and why only the primary structure survives denaturation.

✦

Practice

Write the structural formula of the dipeptide Ala-Gly and circle the peptide link.
Calculate the molar mass of the dipeptide Ala-Ala ( $M$ (Ala) = 89.09 g mol⁻¹).
How many tripeptides can be made if each position may be any of glycine, alanine and serine (repeats allowed)?
Give the products of complete acid hydrolysis of Gly-Ala-Gly with hot hydrochloric acid, as the ions present.
In a chromatogram the solvent front moved 8.0 cm. Spot A moved 3.6 cm and a glycine standard on the same plate moved 2.6 cm. Calculate both $R_{f}$ values. Could A be glycine?
Explain, in terms of bonds, why boiling an enzyme destroys its activity but does not change its primary structure.
Evaluate the claim: "Nylon-6,6 and proteins are the same kind of polymer."

Show answersHide answers

$\mathrm{H_2NCH(CH_3)CO{-}NH{CH_2}COOH}$ ; the peptide link is $\mathrm{-CO{-}NH-}$ .
$2 \times 89.09 - 18.02 = 160.16\,\mathrm{g\,mol^{-1}}$ .
$3^{3} = 27$ .
$\mathrm{H_3N^{+}CH_2COOH}$ (two) and $\mathrm{H_3N^{+}CH(CH_3)COOH}$ (one), with $\mathrm{Cl^{-}}$ ions.
A: $\frac{3.6}{8.0} = 0.45$ ; glycine: $\frac{2.6}{8.0} = 0.33$ . The values differ, so A is not glycine.
Heat gives molecules enough energy to break the weak hydrogen bonds, ionic and hydrophobic interactions that fix the folded shape, including the active site; the covalent peptide bonds of the primary structure need hydrolysis to break.
Partly true: both are polyamides joined by $\mathrm{-CO{-}NH-}$ links and both are hydrolysed by acid. But nylon-6,6 is made from two monomers alternating in a regular pattern, while a protein is made from up to 20 different amino acids in a precise sequence that gives it a specific folded shape and function.

1Why does egg white turn white?

2Forming the peptide bond

3Hydrolysis: taking proteins apart

4The four levels of protein structure

Why does egg white turn white?

Forming the peptide bond

Hydrolysis: taking proteins apart

The four levels of protein structure