2.1 Essential ideas
- 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.
Figure 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
- 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.
- Print Figure 2.1.4c. Study the structures of the amino acids on the chart. Circle the carboxyl and amine groups.
- 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.
Figure 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
- A polypeptide is a linear chain of amino acids. As different parts of a chain interact, the polypeptide folds and changes shape.
- The result is a three-dimensional protein. The simplest protein shape is a helix or a pleated sheet formed when a single polypeptide bends due to hydrogen bonds.
- Proteins may consist of a single polypeptide or more than one polypeptide linked together.
- 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.
- 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.
- 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?
- 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.
- Detail on the genetic code and translation is covered in 2.1.7.
- HL students can learn details about protein shape and levels of organisation in 7.1.3.
- Myoglobin and hemoglobin are both oxygen-binding proteins. See 3.2.1 and 15.2.6.
- Proteomics uses large-scale analysis techniques such as gel electrophoresis 3.1.5, ELISA 13.2.4 and mass spectrometry to identify proteins in samples taken from tissues.