3ProteinsAs we saw earlier, each gene “specifies” a protein. Therefore, you can’t understand how genes work unless you know some very simple protein biochemistry.
4ProteinsProteins are made by joining together amino acids to form polypeptide chains.Each amino acid in a protein has the same chemical structure except for its “R group”.
5Contains the following bonded to a central carbon atom: ProteinsAmino AcidContains the following bonded to a central carbon atom:• Amino groups (NH2)• Carboxyl group (COOH)• Hydrogen atom• R group (different in each amino acid)Typical charged in the cell (-NH3+ and COO-)
7Proteins20 different amino acids occur in living cells.4 chemical groups (composition of the R group):• Acidic (negatively charged), (n = 2)• Basic (positively charged), (n = 3)• Neutral and polar, hydrophilic, (n = 6)• Neutral and non-polar, hydrophobic, (n = 9)
11Proteins Polypeptides N-terminus C-terminus5’ (DNA) ’ (DNA)Amino acids are joined to form unbranched polypeptides by a peptide bond
12Proteins Proteins show 4 levels of structural organisation: Primary structure = amino acid sequence• Determined by the genetic code of the mRNA.2. Secondary structure = folding and twisting of a single polypeptide chain.• Result of weak H-bond and electrostatic interactions.• e.g., -helix (coiled) and -pleated sheet (zig-zag).
13Proteins3. Tertiary structure = three dimensional shape (or conformation) of a polypeptide chain.• Function of R groups contained in the polypeptide.4. Quaternary structure = association between polypeptides in multi-subunit proteins (e.g. hemoglobin).• Occurs only with two or more polypeptides.
15ProteinsWhen an enzyme carries out a chemical reaction, it is actually the R groups of several of the amino acids that are reacting with the substrate.Polypeptides have to fold up into a particular shape to be functional. It is interactions between the R groups of the amino acids that determine and maintain this shape.
16HemoglobinThe first proof of how genes specify proteins came from studies on the oxygen binding protein found in red blood cells: haemoglobin.Haemoglobin is a tetramer. It is made of four polypeptide chains – two -chains and two -chains.
17HemoglobinInherited anaemiasThere are families of people with inherited disorders causing anaemia or thallasaemia. All of the sufferers have altered haemoglobin.These disorders are caused by recessive mutations obeying Mendelian laws. .
18Sickel cell anaemiaOne of the best studied is sickle cell anaemia. When the gene defect is in the homozygous form, all of the haemoglobin is altered, the red blood cells become sickle shaped and the sufferers are very ill with severe anaemia.
20Sickel cell anaemiaIn the heterozygous form, only half of the haemoglobin is defective and the anaemia is less severe. Because the blood cells are slightly altered, the heterozygous form confers immunity to malaria. This inherited condition is, therefore, common in parts of West Africa.
21Sickel cell anaemiaThe change in the haemoglobin is very specific. The sixth amino acid is changed from glutamate to valine. This is a change from an acidic, negatively charged, hydrophilic amino acid to a hydrophobic one.Many other inherited anaemias show similarly specific changes of amino acid.
23Amino acid changesWhy do changes of one amino acid for another destroy the function of a protein?If the protein is an enzyme, the amino acid that carries out the reaction may be changedThe altered amino acid may have been involved in pairing with another amino acid to maintain the shape of the protein.
24Amino acid changesSometimes, changing one amino acid for another with very similar properties (e.g. glutamic acid to aspartic acid) might not affect the protein.Mutations in the gene might not change the amino acid – as we will see in the next lecture.Mutations that don’t affect the function of the gene product are called silent mutations.
25CollinearityThe study of haemoglobin has shown that mutations in a gene can cause specific changes in a protein. Different mutations cause different changes.Does the position of the mutation in the gene relate to the position of the changed amino acid in the protein?
26CollinearityWe can go back to the E. coli trpA cistron to find out the answer. because many mutations in trpA have been mapped and many mutant versions of the TrpA protein have been sequenced to determine the nature and order of the amino acids.
27Collinearity The tryptophan synthase (trpA) cistron The genetic map and the amino acid sequence are collinear. The mutations in the gene and the changed amino acids in the protein appear in the same relative positions.Positions of mutant loci on genetic recombination mapPositions of altered amino acids in protein chain
28CollinearityProteins consist of chains of amino acids and genes consist of chains of nucleotides.- so does each nucleotide specify each amino acid?
29CollinearityMore than one mutation has been found to affect the nature of the amino acid at position 212 in TrpA.Perhaps one nucleotide means glycine, another means arginine and another means glutamate. BUT…Genetic variantAmino acid at position 212Wild typeMutant 23Mutant 46GlycineArginineGlutamate
30CollinearityIt is possible to get recombination between these two mutants.Therefore, there must be more than one mutable site (presumably more than one nucleotide) specifying each amino acid.Genetic variantAmino acid at position 212Wild typeMutant 23Mutant 4623 46 recombinantGlycineArginineGlutamate
31CollinearityIn fact, each amino acid is specified by a triplet of nucleotides, known as a codon.
32Amino acids and proteins. (2000) In: Instant Notes in Biochemistry Amino acids and proteins. (2000) In: Instant Notes in Biochemistry. pp Hames, B. D. and Hooper, N. M. (Eds). BIOS Scientific Publishers, OxfordMolecular Genetics. (2000) In: An Introduction to Genetic Analysis. pp Griffiths, A. J. F,. Miller, J. H., Suzuki, D. T., Lewontin, R. C. and Gelbart, W. M. (Eds). Freeman and Company, New York.