Proteins: from amino acids to working molecules – Chemical Basis of Life (Senior 4 Biology) | Ganzaa

Chemical Basis of Life

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Senior 4 · Biology

Chemical Basis of Life

5 lessons

Lesson 5 of 5

Proteins: from amino acids to working molecules

25 min

Why a fried egg cannot be un-fried

Break an egg into a hot pan and the clear, runny egg white turns solid and white within a minute. Cool it down and it stays white. Egg white is mostly water and protein, and heat has changed the shape of the protein molecules for good, although not one of their amino acids has been removed. That tells you the key idea of this lesson: a protein works because of its precise three-dimensional shape, and that shape is decided by the order of its amino acids.

Proteins do almost every job in a cell: enzymes, antibodies, haemoglobin, insulin, the actin and myosin of muscle, the collagen of skin and bone, the keratin of hair. They are also the nutrient most linked with growth: the Rwanda Demographic and Health Survey 2019–20 found 33 % of children under five stunted (too short for their age), a sign of long-term undernutrition.

Definition

Amino acid: the monomer of proteins: a central carbon atom bonded to an amino group ( $\mathrm{-NH_2}$ ), a carboxyl group ( $\mathrm{-COOH}$ ), a hydrogen atom and a variable R group. Proteins use 20 different amino acids. Essential amino acids (about nine for adults) cannot be made by the body and must be eaten.

Peptide bond: the C–N bond formed by condensation between the carboxyl group of one amino acid and the amino group of the next.

Polypeptide: a chain of many amino acids joined by peptide bonds. A protein is one or more polypeptides folded into a functional shape.

Denaturation: a change in the shape of a protein, caused for example by heat or extreme pH, that destroys its function without breaking its peptide bonds.

Prosthetic group: a non-protein part permanently attached to a protein, such as the haem of haemoglobin; such a protein is a conjugated protein.

Figure 1. Every amino acid has the same backbone; only the R group differs. A peptide bond forms by condensation and is broken by hydrolysis, as in digestion by protease enzymes.

Because one water molecule is lost for each peptide bond, a single chain of $n$ amino acids has $n - 1$ peptide bonds. The R groups decide the properties of each amino acid: some are non-polar and hydrophobic (valine, leucine), some polar (serine), some charged (lysine is positive, glutamic acid negative), and cysteine contains sulfur.

Four levels of structure

Figure 2. The four levels of protein structure, simplified.

Level	What it is	Bonds that hold it
Primary	The sequence of amino acids in the polypeptide, set by a gene	Peptide bonds (strong, covalent)
Secondary	Regular coiling of the backbone into an $\alpha$ -helix, or folding into a $\beta$ -pleated sheet	Hydrogen bonds between the C=O of one peptide group and the N–H of another
Tertiary	The precise three-dimensional folding of the whole polypeptide	Between R groups: hydrogen bonds; ionic bonds between charged groups; disulfide bridges (S–S, covalent) between two cysteines; hydrophobic interactions between non-polar groups, which cluster inside away from water
Quaternary	Two or more polypeptides fitted together, sometimes with prosthetic groups	The same bonds as tertiary, between the chains

Change the primary structure and the folding can change too. That is why a single wrong amino acid can wreck a protein, and why heat and pH, which break hydrogen and ionic bonds, denature it.

Worked example 1: counting peptide bonds in haemoglobin

Haemoglobin has four polypeptide chains: two $\alpha$ chains of 141 amino acids and two $\beta$ chains of 146. (a) How many amino acids are there in one molecule? (b) How many peptide bonds, and how many water molecules were released in making them?

(a) $2 \times 141 + 2 \times 146 = 282 + 292 = 574$ amino acids.
(b) Each chain of $n$ amino acids has $n - 1$ peptide bonds: $2 \times 140 + 2 \times 145 = 280 + 290 = 570$ .
One water molecule is released per peptide bond: 570. Note that it is not $574 - 1$ : the four chains are separate polypeptides, held together by weaker bonds, not peptide bonds.

A computer model of part of a human haemoglobin molecule, made from X-ray crystallography data. The coloured ribbons are the polypeptide chains, coiled into many α-helices (secondary structure); the ball-and-stick shapes held between them are haem groups, with oxygen (red) bound. Image: made with JSmol from Protein Data Bank entry 2DN1 (Park and others, 2006), CC0, via Wikimedia Commons

Globular and fibrous proteins

Feature	Globular protein, e.g. haemoglobin	Fibrous protein, e.g. collagen
Shape	Folded into a compact, roughly spherical shape	Long, thin strands; three polypeptides wound into a triple helix, cross-linked into fibres
Solubility in water	Soluble: hydrophilic R groups on the outside	Insoluble
Amino acid sequence	Irregular	Repetitive (in collagen, every third amino acid is glycine, the smallest, which lets the chains pack tightly)
Role	Metabolic: transport (haemoglobin), enzymes, hormones (insulin), antibodies	Structural: strength in tendons, skin, bone and blood-vessel walls (collagen); hair and nails (keratin)

Haemoglobin is a globular, conjugated protein. Each of its four chains holds one haem group, whose $\mathrm{Fe^{2+}}$ binds one $\mathrm{O_2}$ molecule, so one haemoglobin molecule carries up to four $\mathrm{O_2}$ .

Worked example 2: one amino acid, one disease

In sickle cell anaemia, the amino acid glutamic acid in the $\beta$ chain of haemoglobin is replaced by valine. Glutamic acid has a charged R group; valine's is non-polar. The change lies on the outside of the molecule. Explain why this one change makes red blood cells sickle-shaped when oxygen is low.

Primary structure: a change in the gene changes one amino acid in the sequence.
A charged, hydrophilic group on the surface is replaced by a non-polar, hydrophobic one.
When the haemoglobin is not carrying oxygen, these hydrophobic patches stick to neighbouring haemoglobin molecules, which join into long fibres inside the cell.
The fibres distort the red blood cell into a stiff sickle shape. Sickled cells carry less oxygen, are destroyed early (anaemia) and can block small blood vessels.

The biuret test for proteins

Add an equal volume of biuret reagent (sodium hydroxide solution with a little copper(II) sulfate) to the sample. Alternatively, add sodium hydroxide solution, then a few drops of dilute copper(II) sulfate solution.
Shake gently and leave for a few minutes. No heating is needed.
A change from blue to lilac or purple shows protein. In alkaline solution, copper(II) ions form a coloured complex with the nitrogen atoms of peptide bonds, so the test detects peptides and proteins, not free amino acids.

The depth of the purple colour increases with protein concentration, so, like Benedict's test, it can be made semi-quantitative with colour standards or a colorimeter. Sodium hydroxide is corrosive: wear eye protection.

Protein in the diet

Animal foods (milk, eggs, meat, fish) contain all the essential amino acids. Plant proteins are often short of one: beans are relatively low in methionine and cereals such as maize in lysine. Eating beans together with maize, sorghum or cassava-leaf dishes in the same day supplies a complete set, which is one reason why the traditional mixed Rwandan plate of beans and a starchy food works well.

The lilac-purple colour of a positive biuret reaction in a test tube: copper(II) ions in alkaline solution bound to peptide-like bonds. (This tube contains biuret, the small compound that gives the test its name; a protein solution gives the same colour.) Photo: Ozone aurora (Philip Evans), CC BY-SA 3.0, via Wikimedia Commons

Amoeba Sisters: "Protein Structure and Folding". Watch for the four levels of structure (from about 2:06) and what denaturing does to a protein (from about 6:40).

Warning

Common mistakes

Saying denaturation breaks peptide bonds. It breaks the hydrogen bonds, ionic bonds and (sometimes) disulfide bridges that hold the shape; the primary structure stays.
Calling the bonds of the secondary structure "bonds between R groups". $\alpha$ -helices and $\beta$ -sheets are held by hydrogen bonds between backbone C=O and N–H groups; R-group bonds hold the tertiary structure.
Writing that every protein has a quaternary structure. Only proteins made of two or more polypeptides do.
Heating in the biuret test. It is not needed; heating belongs to Benedict's test.

Tip

Memory hook for tertiary bonds: "HIDS": Hydrogen bonds, Ionic bonds, Disulfide bridges, hydrophobic interactions that Shield the core. In any question about a protein's function, connect: primary sequence → folding → specific shape → function (active site, binding site or strong fibre).

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Practice: proteins

Draw the general structure of an amino acid and label the amino group, the carboxyl group and the R group.
A polypeptide is made of 250 amino acids. How many peptide bonds does it contain, and how many water molecules were released when it was made?
Insulin has two chains, of 21 and 30 amino acids, joined by disulfide bridges. Taking the mean $M_{r}$ of an amino acid as 130 (illustrative), estimate the $M_{r}$ of insulin.
Explain why a protein denatured by heat no longer works although its primary structure is unchanged.
Describe how you would show that milk contains protein. State the positive result.
Compare the structure of haemoglobin with that of collagen and relate each to its function.
A pupil says: "Beans and maize are both incomplete proteins, so a meal of both is still incomplete." Evaluate this statement.

Show answersHide answers

A central carbon atom bonded to H, to $\mathrm{-NH_2}$ (amino group), to $\mathrm{-COOH}$ (carboxyl group) and to R (the variable side chain), as in Figure 1.
$250 - 1 = 249$ peptide bonds and 249 water molecules.
51 amino acids; peptide bonds $= 20 + 29 = 49$ . $M_r \approx 51 \times 130 - 49 \times 18 = 6630 - 882 = 5748$ , about 5700 (the true value is about 5800).
Heat makes the molecule vibrate until hydrogen and ionic bonds break; the polypeptide unfolds and loses the precise three-dimensional shape (for example of an active site or binding site) on which its function depends. The shape does not return on cooling.
Add an equal volume of biuret reagent (or sodium hydroxide followed by a few drops of dilute copper(II) sulfate) and shake; a lilac-purple colour shows protein.
Haemoglobin is globular: four folded chains with haem groups, soluble, with an irregular sequence; its shape lets it carry oxygen in the blood. Collagen is fibrous: three chains in a tight triple helix with a repeating sequence, cross-linked into insoluble fibres; this gives great tensile strength in tendons, skin and bone.
Wrong. Each lacks a different essential amino acid: beans are low in methionine, maize in lysine. Together they supply all the essential amino acids, so the mixed meal provides complete protein.

Quick check

Key points

Amino acids (20 kinds, differing only in R) join by condensation to form peptide bonds; a chain of $n$ has $n - 1$ bonds.
Primary structure (sequence) → secondary ( $\alpha$ -helix, $\beta$ -sheet; hydrogen bonds) → tertiary (3D fold; H bonds, ionic bonds, disulfide bridges, hydrophobic interactions) → quaternary (several chains).
Globular proteins (haemoglobin, enzymes) are soluble and metabolic; fibrous proteins (collagen, keratin) are insoluble and structural.
Heat and extreme pH denature proteins; the biuret test (purple) detects them.

1Why a fried egg cannot be un-fried

2Four levels of structure

3Globular and fibrous proteins

4The biuret test for proteins

5Protein in the diet

Why a fried egg cannot be un-fried

Four levels of structure

Globular and fibrous proteins

The biuret test for proteins

Protein in the diet