Amino acids
An amino acid is a molecule with an amino group (–NH2) and a carboxylic acid group (–COOH). In the ones found in proteins, both groups sit on the same carbon (the α-carbon), so they are called α-amino acids. General form: R–CH(NH2)–COOH.
About 20 amino acids are common in proteins. Only R changes. Examples: glycine (R = H), alanine (R = CH3), serine (R = CH2OH), lysine (R has an extra –NH2), glutamic acid (R has an extra –COOH), phenylalanine (R has a benzene ring).
Neutral, acidic and basic amino acids
- Equal numbers of –NH2 and –COOH: neutral (glycine, alanine).
- More –COOH: acidic (aspartic acid, glutamic acid).
- More –NH2: basic (lysine, arginine).
Essential and non-essential
Non-essential amino acids can be made by our body. Essential ones cannot, so they must come from food (for example valine, leucine, lysine, phenylalanine). Pulses, milk, eggs and meat supply them.
Zwitterion
In water, the acid group gives its H+ to the amino group of the same molecule: H3N+–CHR–COO–. This form has both a plus and a minus charge and is called a zwitterion (German for "double ion"). It explains why amino acids are crystalline solids with high melting points, dissolve in water and behave like salts. It can react with both acids and bases (amphoteric).
Optical activity
Except glycine (R = H, so the α-carbon has two H), all α-amino acids are chiral. Most natural ones have the L-configuration.
The peptide bond
When the –COOH of one amino acid reacts with the –NH2 of another, a molecule of water is removed and an amide link –CO–NH– forms. In proteins this amide link is called the peptide bond.
Two amino acids joined = dipeptide; three = tripeptide; up to about ten = oligopeptide; more than ten = polypeptide. A polypeptide with more than about a hundred amino acids (molar mass above about 10 000 u) is called a protein.
Each chain has a free –NH2 at one end (N-terminal) and a free –COOH at the other (C-terminal). Because order matters, glycylalanine (Gly–Ala) and alanylglycine (Ala–Gly) are two different dipeptides.
Fibrous and globular proteins
- Fibrous proteins: chains lie side by side in long threads, held by hydrogen bonds and S–S bridges. Insoluble in water. Keratin (hair, wool, nails, silk) and myosin (muscle).
- Globular proteins: the chain folds into a round shape. Usually soluble in water. Insulin, albumin (egg white, blood), haemoglobin.
Four levels of protein structure
Primary structure
The exact order (sequence) of amino acids in each chain. Change even one and the protein changes. In sickle-cell anaemia, one amino acid in haemoglobin is swapped, and the red cells bend into sickles.
Secondary structure
The shape a stretch of chain takes, held by hydrogen bonds between the C=O of one peptide and the N–H of another.
- α-helix: the chain twists into a right-handed spring. Each C=O bonds with the N–H four units further along.
- β-pleated sheet: chains lie side by side, stretched almost flat, joined by H-bonds, with folds like a paper fan. Silk has this.
Tertiary structure
The whole chain folds further into a 3D shape. It is held by H-bonds, disulphide (S–S) bridges, ionic attractions, van der Waals forces and the pull of oily (hydrophobic) R groups towards the inside. This gives the fibrous or globular shape.
Quaternary structure
Some proteins are made of two or more chains (subunits). How these subunits sit together is the quaternary structure. Haemoglobin has four subunits.
Denaturation of proteins
A natural protein with its proper shape and job is called a native protein. When heat, a change in pH, strong acid, alcohol or heavy metal salts disturb it, the hydrogen bonds and other weak forces break. The helices unwind and the globules unfold. The protein loses its shape and its biological activity. This is denaturation.
- The primary structure stays the same: peptide bonds are not broken. Only the 2°, 3° (and 4°) structures are lost.
- Examples: boiling an egg (albumin coagulates), curdling of milk (by lactic acid from bacteria), cooking meat.
- Most denaturation is irreversible, though a few proteins can refold if conditions return slowly.
Enzymes
Enzymes are biological catalysts. Almost all are globular proteins. They make reactions in living things go millions of times faster at body temperature.
- Specific: each enzyme acts on one substance (its substrate) or one kind of bond. The substrate fits into a pocket called the active site, like a key into a lock.
- Lower the activation energy: they give the reaction an easier path. Example: an acid breaks sucrose with Ea about 104 kJ/mol; the enzyme sucrase needs only about 36 kJ/mol.
- Named by adding "-ase" to the substrate or reaction: maltase (maltose → glucose), sucrase/invertase (sucrose → glucose + fructose), lipase (fats), protease (proteins), oxidoreductase (redox).
- Best conditions: work best near 37 °C and at a particular pH. High heat or wrong pH denatures them.
The detailed mechanism of enzyme action is covered in the unit on Chemical Kinetics and surface chemistry; here, remember the lock-and-key picture.
Try it at home
- Take two spoons of raw egg white in two small cups.
- Predict first: what happens if you add a spoon of lemon juice to one cup and leave the other?
- Wait 10 minutes. The lemon cup turns cloudy white: acid has denatured the albumin, just like heat does. The other cup stays clear.
- Bonus: put a slice of fresh pineapple (it has a protein-cutting enzyme) on a bit of set jelly or cheese overnight. It softens. A slice of cooked pineapple does not, because cooking denatured the enzyme. Compare with the 3D temperature slider in step 6.
Key formulas and definitions
- α-amino acid: R–CH(NH₂)–COOH · zwitterion: R–CH(NH₃⁺)–COO⁻
- Amino acid + amino acid → dipeptide + H₂O (peptide bond –CO–NH–)
- n amino acids in one chain → (n − 1) peptide bonds and (n − 1) H₂O removed
- Mass of peptide = sum of amino acid masses − 18 × (n − 1)
- Number of different chains of length n from k kinds of amino acid = kⁿ
- Glycine 75, alanine 89 g/mol · 1 residue in a chain ≈ amino acid mass − 18
Worked examples
1. Show the formation of the dipeptide Gly–Ala.
Step 1: Glycine H₂N–CH₂–COOH and alanine H₂N–CH(CH₃)–COOH. Step 2: –COOH of glycine + –NH₂ of alanine lose H₂O. Step 3: H₂N–CH₂–CO–NH–CH(CH₃)–COOH. Answer: glycylalanine, with one peptide bond.
2. How many peptide bonds are there in a chain of 51 amino acids (like insulin, if it were one chain)?
Step 1: n amino acids in one chain are joined by n − 1 bonds. Step 2: 51 − 1 = 50. Answer: 50 peptide bonds.
3. Find the molar mass of the tripeptide Gly–Gly–Ala (Gly = 75, Ala = 89 g/mol).
Step 1: Sum = 75 + 75 + 89 = 239. Step 2: 3 amino acids → 2 bonds → 2 H₂O lost = 36. Step 3: 239 − 36 = 203 g/mol. Answer: 203 g/mol.
4. How many different dipeptides can be made from glycine and alanine (each may be used twice)?
Step 1: Position 1 has 2 choices, position 2 has 2 choices. Step 2: 2 × 2 = 4: Gly–Gly, Gly–Ala, Ala–Gly, Ala–Ala. Answer: 4. Gly–Ala and Ala–Gly are different because order matters.
5. A protein has molar mass 11 000 g/mol. If the average residue mass is 110 g/mol, estimate the number of amino acids.
Step 1: n ≈ 11 000 ÷ 110 = 100. Step 2: It has more than ~100 residues, so it counts as a protein. Answer: about 100 amino acids.
6. Glycine melts at about 500 K while acetic acid melts at about 290 K, though they are similar in size. Why?
Step 1: Glycine exists as a zwitterion, H₃N⁺–CH₂–COO⁻. Step 2: The + and − ends of neighbouring molecules attract strongly, like in a salt crystal. Step 3: Acetic acid has only H-bonds between neutral molecules. Answer: strong ionic attractions between zwitterions make glycine melt much higher.
7. An egg is boiled. Which levels of structure of albumin change, and which stays? Explain.
Step 1: Heat shakes the chain and breaks H-bonds and other weak forces. Step 2: Helices unwind (2° lost) and the ball unfolds (3° lost). Step 3: Peptide bonds are strong covalent bonds and do not break. Answer: 2° and 3° change; 1° (sequence) stays.
Common mistakes
- Thinking denaturation breaks peptide bonds. It only breaks weak forces; the sequence stays.
- Treating Gly–Ala and Ala–Gly as the same. The N-terminal end is written first; order makes them different.
- Saying all amino acids are optically active. Glycine is not (its R is H).
- Mixing up secondary and tertiary structure. Secondary = local coils/sheets by H-bonds; tertiary = the whole chain's 3D fold.