Contents: 7 sections
Syllabus points
- Describe the structure of an amino acid and the formation of a peptide bond.
- Explain the four levels of protein structure and the bonds that hold each together.
- Compare a globular protein with a fibrous protein, using haemoglobin and collagen.
- Explain how hydrogen bonding between water molecules gives water its properties.
The amino acid
Every amino acid has the same backbone:
- a central carbon
- an amino group, NH₂
- a carboxyl group, COOH
- a hydrogen
- an R group, which is the only part that differs
There are twenty R groups in biological proteins. They may be charged, polar, or non-polar and hydrophobic, and the chemistry of the R groups is what makes one protein different from another.
The peptide bond
Two amino acids join by condensation: the carboxyl group of one reacts with the amino group of the next, water is released, and a peptide bond forms. Many joined together make a polypeptide.
Hydrolysis reverses it, adding water and breaking the bond. This is what protease enzymes do.
The four levels of structure
Primary structure
The sequence of amino acids in the chain, held by peptide bonds.
This is the level that everything else follows from. The R groups sit in a particular order, so the interactions available further up are determined here. A single change in the primary structure can change the whole molecule, which is exactly what happens in sickle cell anaemia: one glutamic acid replaced by one valine in the β-globin chain.
Secondary structure
Hydrogen bonds between the backbone, not between R groups. The slightly negative oxygen of one carboxyl group attracts the slightly positive hydrogen of an amino group further along the chain.
Two shapes result:
- the α-helix, a right-handed coil with hydrogen bonds running along it
- the β-pleated sheet, chains lying alongside one another with hydrogen bonds between them
An individual hydrogen bond is weak. There are so many of them that the structure holds, which is also why moderate heat undoes it.
Tertiary structure
The way the whole chain folds into a three-dimensional shape, held by interactions between R groups:
| Bond | Between | Strength |
|---|---|---|
| Hydrogen bond | polar R groups | weak, many |
| Ionic bond | oppositely charged R groups | stronger, pH sensitive |
| Hydrophobic interaction | non-polar R groups clustering inside | weak individually |
| Disulfide bond | two cysteine R groups | strong, covalent |
The disulfide bond is the only covalent one, so it is the one that survives conditions that break the others. Proteins that work in harsh environments, such as keratin, carry many of them.
Hydrophobic interactions deserve a note. Non-polar R groups are pushed to the inside of the molecule, away from the surrounding water, and polar ones end up on the outside. That is why most globular proteins are soluble: their outer surface is hydrophilic.
Quaternary structure
Present only in proteins made of more than one polypeptide chain, and held by the same bonds as tertiary structure.
Haemoglobin has four chains and a prosthetic group, so it has quaternary structure. Myoglobin has one chain and therefore does not.
Globular and fibrous proteins
Haemoglobin, a globular protein
Four polypeptide chains, two α and two β, each holding a haem prosthetic group containing an iron ion. Each haem group binds one oxygen molecule, so one haemoglobin molecule carries four.
The chains fold so that hydrophobic R groups face inward and hydrophilic ones face out, which makes it soluble and able to travel in blood plasma inside the red cell.
A protein with a non-protein component like haem is a conjugated protein.
Collagen, a fibrous protein
Three polypeptide chains, each a left-handed helix, wound around one another into a triple helix. Every third amino acid is glycine, which has the smallest R group, a single hydrogen. Only glycine is small enough to sit at the crowded centre where the three chains touch.
The chains are held by hydrogen bonds between them, and adjacent collagen molecules are joined by covalent cross-links that are staggered rather than aligned, so there is no line of weakness across the fibre.
Collagen is insoluble, has huge tensile strength, and is structural. It is found in tendons, skin, bone and artery walls.
The comparison
| Haemoglobin (globular) | Collagen (fibrous) | |
|---|---|---|
| Shape | roughly spherical | long and thin |
| Solubility | soluble | insoluble |
| Sequence | irregular | repeating, glycine every third |
| Role | transport, metabolic | structural |
| Prosthetic group | haem | none |
Water
Water is a polar molecule. Oxygen attracts the shared electrons more strongly than hydrogen does, so oxygen carries a slight negative charge and each hydrogen a slight positive one. Hydrogen bonds form between the slightly positive hydrogen of one molecule and the slightly negative oxygen of another.
A single hydrogen bond is weak, but each water molecule can form up to four, and that is where the properties come from.
A solvent. Polar and charged substances dissolve, because water molecules surround them and separate them. Most metabolic reactions happen in solution, and dissolved substances can be transported, which is what blood plasma and xylem sap depend on.
High specific heat capacity. A lot of energy goes into breaking hydrogen bonds before the temperature rises, so water warms and cools slowly. Cells and aquatic habitats are buffered against sudden temperature change, and enzymes are protected from denaturing.
High latent heat of vaporisation. A great deal of energy is needed to turn liquid water into vapour, so evaporation removes a lot of heat for a small loss of water. This is what makes sweating and transpiration effective as cooling.
Cohesion and surface tension. Water molecules stick to one another, so a column of water in a xylem vessel can be pulled up from above without breaking. At a surface, cohesion produces surface tension strong enough to support small organisms.
Density and ice. Ice is less dense than liquid water, because the hydrogen bonds hold the molecules in a fixed open lattice. Ice floats, insulating the water beneath, so ponds do not freeze solid and aquatic life survives the winter.
A reactant. Water is a reagent in its own right, in hydrolysis and in photosynthesis.
Common mistakes
- Saying secondary structure involves R groups. It is backbone hydrogen bonding.
- Saying every protein has quaternary structure. Only multi-chain proteins do.
- Describing the disulfide bond as strong "because there are many of them". It is strong because it is covalent.
- Saying water molecules are held together by ionic bonds. They are hydrogen bonds between polar molecules.
- Explaining ice floating as "ice is lighter". The hydrogen bonds hold the molecules further apart than in liquid water.