Revise Proteins for IB Biology (B1.2)

Proteins are polymers assembled from monomers called amino acids, and living organisms use 20 different ones. Every amino acid shares the same core: a central carbon atom (the alpha-carbon) bonded to four groups — an amine group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain called the R-group. The first three are identical in all 20; only the R-group changes. That single variable is what gives each amino acid its own chemistry — acidic or basic, positively or negatively charged, polar (hydrophilic) or non-polar (hydrophobic) — and it is these R-group properties that will later decide how a chain folds.

Amino acids are joined by condensation reactions. In a condensation, the carboxyl group ($-COOH$) of one amino acid reacts with the amine group ($-NH_2$) of the next; a molecule of water is removed and a covalent peptide bond forms between them. Two amino acids joined this way make a dipeptide, and many joined in a chain make a polypeptide. Because the bond is covalent, it is strong and stable — this is why the sequence of a protein survives conditions that destroy its shape. The reverse reaction, hydrolysis, adds water back to break the peptide bond, which is how proteins are digested. The order in which amino acids are joined is dictated by the sequence of bases in the gene that codes for the polypeptide.

A polypeptide does not stay as a straight chain. It folds, in stages, into a specific three-dimensional shape. Biologists describe this in four hierarchical levels, and a key exam skill is knowing which bonds stabilise each one.

The distinction to hold onto is what stabilises each level. Secondary structure comes from hydrogen bonds along the backbone, so it forms regular repeating patterns regardless of the R-groups. Tertiary and quaternary structure come from interactions between R-groups, so they depend directly on which amino acids are present and where. This is precisely why the primary sequence, by fixing the R-groups, ultimately controls the higher levels.

This is the central idea of the whole topic. The primary sequence is not just the first level of structure; it is the instruction set for all the others. Each R-group can only bond with a partner if the sequence places a suitable partner within reach as the chain folds. So the order of amino acids fixes where hydrogen bonds, ionic bonds, hydrophobic clusters and disulfide bridges can form, and those interactions pull the chain into one specific, reproducible three-dimensional conformation. A given sequence therefore folds the same way every time. That final shape creates the functional features of the protein — the precisely shaped active site of an enzyme, the antigen-binding site of an antibody, the oxygen-binding pockets of haemoglobin. Because function depends on shape, and shape depends on sequence, the amino-acid sequence ultimately determines the protein's function. Change the sequence and you may move an R-group, change a bond, alter the fold, and so change (or abolish) the function.

Because a chain can be built from the 20 amino acids in almost limitless orders, proteins can fold into an enormous variety of shapes — and so perform an enormous variety of jobs. Enzymes (such as amylase and catalase) act as biological catalysts, each with an active site shaped for its substrate. Structural proteins such as collagen in skin and tendon and keratin in hair and nails provide strength and support. Transport proteins carry cargo: haemoglobin transports oxygen in the blood, and membrane carrier proteins move solutes across cell membranes. Hormones such as insulin act as chemical messengers. Antibodies (immunoglobulins) defend against pathogens by binding specifically to antigens. Contractile proteins such as actin and myosin drive muscle movement, and receptor proteins receive signals at the cell surface. In every case the specific function traces back to a specific shape, and the shape back to a specific sequence.

Denaturation is a change in the three-dimensional conformation of a protein that leads to loss of function. It is not a change to the primary structure: the peptide bonds are covalent and are not broken, so the sequence of amino acids stays the same. What is disrupted are the weaker interactions that hold the higher levels together. High temperature increases the kinetic energy of the molecule, so atoms vibrate more and the hydrogen bonds (and other weak interactions) stabilising the secondary and tertiary structure break. Extreme pH adds or removes hydrogen ions, changing the charges on acidic and basic R-groups, so the ionic bonds (and hydrogen bonds) between R-groups are disrupted. In both cases the chain unfolds and loses its specific shape. Because function depends on shape — for example an enzyme's active site can no longer bind its substrate — the denatured protein no longer works. This is usually irreversible, as when the clear albumin of an egg white turns solid and white on heating.

Explanation questions in B1.2 are marked analytically: each distinct valid point is worth one mark. Answer marks (A) credit a correct link or conclusion, and error-carried-forward (ECF) means the points are independent, so a weak line early on does not cost you the marks that follow. Study how each mark below is tied to a specific, named idea rather than to loose phrasing.

The sequence-shape-function logic underpins much of the rest of biology. It is the basis of enzyme action and its sensitivity to temperature and pH, of how a single DNA base change can alter a protein (as in sickle-cell anaemia), and of how antibodies achieve their exquisite specificity. Master the habit of running the full chain — sequence fixes R-group interactions, interactions fold the chain, shape makes the functional site, site does the job — and you have a template that explains protein behaviour anywhere it appears.