IB Biology HL B1.2 Proteins Notes

Every amino acid has the same backbone: an alpha carbon bonded to an amine group, a carboxyl group, a hydrogen atom, and an R-group. The R-group is the variable part, so it determines properties such as charge, polarity, hydrophobicity, and later folding behaviour. Proteins contain C, H, O, N, and usually S because some amino acids contain sulfur.

Use the shared backbone to recognize any amino acid, then look to the R-group for its chemistry.

Peptide bonds form by condensation. The carboxyl group of one amino acid reacts with the amine group of another, water is released, and a peptide bond links the residues. The chain has direction: an N-terminus at one end and a C-terminus at the other. Ribosomes assemble polypeptides in this directional order.

Track which atoms leave as water, then identify the new peptide bond and chain direction.

Essential amino acids are “essential” because the body cannot synthesize enough of them, so they must come from dietary protein. Non-essential amino acids can be made by transamination, mainly in the liver. If an essential amino acid is missing, protein synthesis is limited because the ribosome cannot complete all needed polypeptides, which can contribute to malnutrition.

Protein diversity comes from sequence possibilities. Twenty coded amino acids can be combined in different types, numbers, and orders, creating vast numbers of polypeptide sequences. Genes encode those sequences, and the proteome is the full set of proteins expressed by a cell, tissue, or organism at a given time.

Protein shape determines function, especially for enzyme active sites. High temperature or unsuitable pH can disrupt weak bonds that maintain the folded shape. When the active site changes shape, the substrate no longer fits properly and function falls. Small proteins may sometimes refold, but denaturation is often irreversible.

R-groups are the chemical personalities of amino acids. They may be acidic, basic, polar hydrophilic, or non-polar hydrophobic. This chemistry determines solubility, interactions, folding, and function. In soluble proteins, hydrophobic R-groups are often buried away from water, while polar or charged groups are more likely to face water.

Primary structure is the ordered amino acid sequence joined by peptide bonds. DNA controls that sequence through mRNA during translation. Because the sequence determines which R-groups appear and where, even one amino acid substitution can change interactions, conformation, and protein properties.

Secondary structure is local folding of the polypeptide backbone. Some regions coil into alpha helices; others pleat into beta-sheets. Both are stabilized by regular hydrogen bonding between backbone groups, not mainly by R-group interactions. These motifs can combine into domains such as coiled coils or beta sandwiches.

Both patterns come from regular hydrogen bonding, but one coils and the other pleats.

Tertiary structure is the unique 3D folding of one polypeptide chain. It is stabilized by interactions between R-groups: hydrogen bonds, ionic bonds, disulfide covalent bonds between cysteine residues, and hydrophobic interactions that cluster non-polar groups away from water. This folding creates the final shape needed for function.

Different side-chain interactions all help stabilize one functional 3D shape.

Residue placement depends on environment. In soluble globular proteins, hydrophobic residues are often buried in the core, while polar and charged residues are commonly exposed to water. Integral membrane proteins reverse part of that logic: hydrophobic regions face lipid tails in the bilayer, while hydrophilic regions face watery environments.

Quaternary structure means two or more polypeptide chains join into one functional protein. Haemoglobin is conjugated because it has four globin chains plus non-polypeptide haem groups with iron. Insulin and collagen are non-conjugated examples: insulin is stabilized by disulfide bonds, while collagen forms a triple helix.

All three are quaternary examples, but they are built and stabilized in different ways.

Globular and fibrous proteins differ in shape, solubility, and job. Globular proteins are compact, often soluble, and suited to transport, signalling, or catalysis; insulin is a small globular hormone stabilized by disulfide bridges. Fibrous proteins are long, insoluble, and structural; collagen provides tensile strength.

The core protein story is build -> vary -> function. Amino acids share a backbone but differ in R-groups. Peptide bonds form by condensation between carboxyl and amine groups. Some amino acids must come from diet, or protein synthesis is limited. Twenty coded amino acids create many sequences by type, number, and order. Finally, shape determines function, so denaturation changes performance.

Use this for core protein questions on amino acid structure, peptide-bond formation, essential amino acids, sequence diversity, or denaturation.

HL protein questions are level-control questions. R-group chemistry predicts solubility and interactions. Primary structure is the DNA-coded amino acid sequence. Secondary structure is local alpha helix or beta-sheet stabilized by backbone hydrogen bonds. Tertiary structure is one polypeptide’s 3D fold stabilized by R-group interactions. Quaternary structure joins multiple chains. Examples such as haemoglobin, insulin, and collagen anchor these levels in real proteins.

Use this for HL questions on R-group chemistry, protein-structure levels, residue placement, and named examples.