B1.2 Proteins

Proteins connect amino acid structure, peptide-bond formation, dietary requirements, folding levels, R-group chemistry, denaturation, and functional protein shapes in cells.

Learning objectives

B1.2.1Generalized amino acid structure• Amino acids have an alpha carbon bonded to an amine, carboxyl, hydrogen, and R-group• The R-group varies between amino acids and determines chemical properties• Proteins contain C, H, O, N, and usually S B1.2.2Condensation reactions• Condensation joins the carboxyl group of one amino acid to the amine group of another• A peptide bond forms and water is released• Chains have an N-terminus and C-terminus and are assembled at ribosomes B1.2.3Dietary amino acids• Essential amino acids cannot be synthesized and must be obtained from dietary protein• Non-essential amino acids can be made by transamination, mainly in the liver• Deficiency of essential amino acids limits protein synthesis and can cause malnutrition B1.2.4Infinite variety of peptide chains• Twenty coded amino acids can form vast numbers of sequences• Protein diversity depends on amino acid type, number, and order• Genes encode polypeptide sequences; the proteome is the full protein set expressed B1.2.5Effect of pH and temperature• Protein shape determines function, especially enzyme active sites• High temperature or unsuitable pH disrupts weak bonds and denatures proteins• Denaturation may be reversible in small proteins but often becomes irreversible

Every protein amino acid has an α-carbon bonded to an amine group, a carboxyl group, a hydrogen atom and a variable R-group. The shared groups form peptide bonds; the R-group changes charge, polarity, size and reactivity. Proteins contain C, H, O and N, and usually S in sulfur-containing R-groups.

Clean mobile-friendly diagram of a generalized amino acid with a central alpha carbon and labelled amine group, carboxyl group, hydrogen, and R-group. Add a small note that sulfur is present in some amino acids and therefore in many proteins.

Amine and carboxyl groups: shared parts that build the repeating backbone.
R-group: variable part that changes interactions, folding and function.
Proteins contain C, H, O and N; sulfur occurs in proteins with sulfur-bearing R-groups.

The diagram shows two amino acids forming a dipeptide through a condensation reaction, producing a peptide linkage and water.

The carboxyl group of one amino acid loses OH and the amine group of another loses H. Water is released, and the remaining carbon and nitrogen form a covalent C–N peptide bond.

Two residues form one peptide bond and release one water molecule; joining $n$ residues forms $n-1$ peptide bonds and releases $n-1$ waters. Ribosomes repeat this reaction to assemble a chain with N- and C-termini.

Category	Supply to the body
Essential	cannot be synthesized in sufficient quantity; must come from food
Non-essential	can be produced from other molecules, often by transamination in the liver

Dietary protein → digestion → absorbed amino acids → amino-acid pool → ribosomes. If one required essential amino acid is scarce, it becomes limiting and synthesis of proteins containing it slows even when other amino acids are abundant.

A varied, sufficient plant-based diet can supply all essential amino acids. “Non-essential” means synthesizable, not unimportant.

Protein variety depends on amino-acid type, number and order.

$P=A^n$

$P$ counts sequences, $A$ amino-acid types and $n$ chain length. With 20 coded amino acids, $P=20^n$ and $20^5=3{,}200{,}000$ . Genes specify residue order; the proteome is the set of proteins a cell, tissue or organism expresses. Sequence positions R-groups and creates folding possibilities, although not every sequence is functional.

A folded protein loses its precise shape when heat or extreme pH disrupts stabilizing interactions.

Change	Molecular effect	Consequence
High temperature	weak interactions break	fold and binding surfaces, including active sites, change
Extreme pH	R-group charges change	ionic attractions and H-bonds break

Denaturation changes conformation and function but usually leaves the amino-acid sequence intact. Refolding requires the original interactions to reform before aggregation.

Shared amino-acid groups condense → peptide bonds build a directional backbone → genetic information specifies residue order → positioned R-groups create folding possibilities.

Limiting change	Mechanism	Consequence
Essential amino acid unavailable	a required monomer is missing	synthesis of affected proteins slows
High temperature	stabilizing interactions are disrupted	conformation and function may be lost
pH away from optimum	R-group charges change	ionic attractions and H-bond patterns can be disrupted

3 marks

The molecules of all amino acids include an amine group, a carboxyl group and an R-group. Draw a diagram to show the structure of an amino acid molecule.

4 marks

Draw molecular diagrams to show the condensation reaction between two amino acids to form a dipeptide.

2 marks

Some of the twenty amino acids that are linked together to make polypeptides in human cells are essential in the diet and others are not. Distinguish between essential and non-essential amino acids.

7 marks

Cells produce a large variety of proteins with different sequences of amino acids. Explain how this is done.

4 marks

Outline the process of protein denaturation.

Next Topic

—B2.1 Membranes and membrane transportRead

B1.2 Proteins

Learning objectives

A shared amino-acid framework, variable R-groups

Condensation forms peptide bonds

The scarcest amino acid limits protein synthesis

Sequence order creates enormous protein diversity

Heat and pH can denature a protein

Checkpoint: build a protein, then identify what can limit it

Next Topic