Collinearity of the gene and the

protein

http://www.nottingham.ac.uk/bennett-lab/lee.html

• As we saw earlier, each gene “specifies” a protein. Therefore, you can’t understand how genes work unless you know some very simple protein biochemistry.

Proteins

• Proteins 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”.

Proteins

• Amino groups (NH2)• Carboxyl group (COOH)• Hydrogen atom• R group (different in each amino acid)

Amino Acid

Contains the following bonded to a central carbon atom:

Typical charged in the cell (-NH3

+ and COO-)

Proteins

Proteins

Proteins

20 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)

Proteins

Proteins

(Hydrophobic)

Proteins

(Hydrophilic)

Polypeptides

N-terminus C-terminus

5’ (DNA) 3’ (DNA)

Amino acids are joined to form unbranched polypeptides by a peptide bond

Proteins

Proteins

Proteins show 4 levels of structural organisation:

1. 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).

Proteins

3. 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.

Proteins

• When 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.

Proteins

• The 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.

Hemoglobin

• There 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. .

Inherited anaemias

Hemoglobin

• One 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.

Sickel cell anaemia

Normal blood Sickle cell blood

Sickel cell anaemia

• In 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.

Sickel cell anaemia

• The 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.

Sickel cell anaemia

glu gln125Hb D Punjab

val glu67Hb M Milwaukee

his+ arg+63Hb Zürich

his+ tyr+63Hb M Saskatoon

glu lys+26Hb E

glu gly7Hb G San José

glu lys+6Hb C

glu val6Hb S (sickle)

asn lys+68Hb G Philadelphia

his+ tyr58Hb M Boston

gly asp57Hb Norfolk

glu gln30Hb G Honolulu

lys+ asp16Hb I

ChangeAmino acidSubunitHaemoglobin

glu gln125Hb D Punjab

val glu67Hb M Milwaukee

his+ arg+63Hb Zürich

his+ tyr+63Hb M Saskatoon

glu lys+26Hb E

glu gly7Hb G San José

glu lys+6Hb C

glu val6Hb S (sickle)

asn lys+68Hb G Philadelphia

his+ tyr58Hb M Boston

gly asp57Hb Norfolk

glu gln30Hb G Honolulu

lys+ asp16Hb I

ChangeAmino acidSubunitHaemoglobin

Why do changes of one amino acid for another destroy the function of a protein?

1. If the protein is an enzyme, the amino acid that carries out the reaction may be changed

2. The altered amino acid may have been involved in pairing with another amino acid to maintain the shape of the protein.

Amino acid changes

• Sometimes, 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.

Amino acid changes

• The 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?

Collinearity

We 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.

Collinearity

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.

446 487 223

23 187

58 169

Positions of altered amino acids in protein chain

175 177

183

212 215

234 235

Positions of mutant loci on genetic recombination map

Collinearity

Proteins consist of chains of amino acids and genes consist of chains of nucleotides.

- so does each nucleotide specify each amino acid?

Collinearity

Collinearity

More 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 variant Amino acid at position 212

Wild type

Mutant 23

Mutant 46

Glycine

Arginine

Glutamate

It 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 variant Amino acid at position 212

Wild type

Mutant 23

Mutant 46

23 46 recombinant

Glycine

Arginine

Glutamate

Glycine

Collinearity

• In fact, each amino acid is specified by a triplet of nucleotides, known as a codon.

Collinearity

Amino acids and proteins. (2000) In: Instant Notes in Biochemistry. pp 19-42. Hames, B. D. and Hooper, N. M. (Eds). BIOS Scientific Publishers, Oxford

Molecular Genetics. (2000) In: An Introduction to Genetic Analysis. pp 271-278. Griffiths, A. J. F,. Miller, J. H., Suzuki, D. T., Lewontin, R. C. and Gelbart, W. M. (Eds). Freeman and Company, New York.