2.1 Essential ideas

2.1.4 Proteins

  • Proteins are the most versatile organic molecules. They are involved in a wide range of functions.
  • Proteins are composed of polypeptides that have spontaneously folded onto themselves or associated with other polypeptides to form three-dimensional structures.

Formation of polypeptides

  • 20 different amino acids can be linked together in any sequence, giving a huge range of possible polypeptides.
  • The type and sequence of amino acids in a polypeptide is coded for by an organism’s genes.
  • Polypeptides are synthesised on ribosomes during translation.
  • Amino acids are linked together by condensation.

peptide bondFigure 2.1.4a – Peptide bond
Peptide bonds form between amino acids by condensation.

  • The carbon atom from the carboxyl group (-COOH) of one amino acid and the nitrogen atom from the amino group (-NH2) of another amino acid form a peptide bond (OC-NH) and release one molecule of water.

Skill: Drawing peptide bonds

amino acidFigure 2.1.4b – Amino acid
Molecular structure of an amino acid

  • All amino acids have the general structure shown in Figure 2.1.4b. The variable radical of an amino acid is shown as ‘R’.
  • The R-group of each of the 20 most common amino acids is different. The chemical properties of amino acids are determined by the R-groups, as shown in the chart below.

20 common amino acidsFigure 2.1.4c – 20 Common amino acids

  1. Print Figure 2.1.4c. Study the structures of the amino acids on the chart. Circle the carboxyl and amine groups.
  2. Practise drawing molecular diagrams to show the formation of peptide bonds between named amino acids of your choice. Draw polypeptide chains with three or four different amino acids.

polypeptideFigure 2.1.4d – Polypeptide with four peptide bonds

  • Drawing tips: Polypeptides have a carboxyl terminal end and an amino terminal end. R-groups should project from one side of the chain, as shown in Figure 2.1.4d.

Configuration and functions of proteins

myo-collagenFigure 2.1.4e – Myo-collagen
Collagen (left) is a fibrous protein made of three polypeptide chains. Myoglobin (right) is a globular protein made of a single polypeptide chain.

  • The amino acid sequence determines the three-dimensional conformation of a protein.
  • This is because the tendency of different amino acids to fold and interact with each other depends on the chemical composition of R-groups.
  • Fibrous proteins have an elongated shape. They are insoluble in water and have a very stable structure. They are involved in maintaining structures, support and movement.
  • Other proteins are round or globular in shape. These have many biochemical functions as plasma membrane proteins, hormones, enzymes, neurotransmitters and antibodies, as well as many others.

Every individual has a unique proteome

  • The genome of an organism contains the code for all the polypeptides produced by a species. It also contains non-coding genetic material.
  • The genome is static – it can only be altered by mutation.
  • Gene expression is influenced by internal and external factors, and proteins are modified after synthesis, so the types of proteins being produced varies throughout an individual’s life.
  • A proteome is the entire set of proteins expressed by an individual at a certain time. Every individual has a unique proteome.

Figure 2.1.4f – Proteomics
Proteomics is the large-scale study of protein structure and function.

Concept help

  • The name ‘amino acid’ comes from the combination of amine and carboxylic acid.
  • Epigenetics refers to all of the non-genetic factors that influence the expression of genes.

Exam tip

  • You do not need to name 20 amino acids or memorise the structures of R-groups, but you should be able to draw peptide bonds between generalised amino acids as shown in Figure 2.1.4b.

Food for thought

There are 203 different sequences of amino acids in a polypeptide with three residues, but most polypeptides contain hundreds of amino acids. Can you imagine how many different protein structures are possible?

inulinFigure 2.1.4g – Insulin
3D structure of insulin, a peptide hormone.

Try it!

  • ICT: You can find the 3D structures of named proteins in the protein data bank (PDB) of the Research Collaboratory for Structural Bioinformatics (RCSB): www.rcsb.org/pdb.
  • HL: To give you an idea of how R-groups interact, use cut-outs of the amino acids from Figure 2.1.4c to predict the shapes of simple proteins.
  • Link the cut-outs together with paperclips to create ‘flexible’ peptide bonds. Then try to fold them into different protein configurations by predicting where hydrogen bonds, ionic bonds and sulfide bridges will occur.
  • Create a list of all the epigenetic factors that influence gene expression.

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