Download S1 Genetics

Collinearity of
the gene and the
protein
http://www.nottingham.ac.uk/bennett-lab/lee.html
Proteins
• 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 Acid
Contains the following bonded to a central carbon atom:
• Amino groups (NH2)
Typical charged in the
• Carboxyl group (COOH)
cell (-NH3+ and COO-)
• Hydrogen atom
• R group (different in each amino acid)
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)
Proteins
Polypeptides
N-terminus
C-terminus
5’ (DNA)
3’ (DNA)
Amino acids are joined to form unbranched polypeptides
by a peptide bond
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
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.
Hemoglobin
• 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
Inherited anaemias
• 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. .
Sickel cell anaemia
• 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.
Haemoglobin
Hb I
Hb G Honolulu
Hb Norfolk
Hb M Boston
Hb G Philadelphia
Hb S (sickle)
Hb C
Hb G San José
Hb E
Hb M Saskatoon
Hb Zürich
Hb M Milwaukee
Hb D  Punjab
Subunit













Amino acid
16
30
57
58
68
6
6
7
26
63
63
67
125
Change
lys+  asp
glu  gln
gly  asp
his+  tyr
asn  lys+
glu  val
glu  lys+
glu  gly
glu  lys+
his+  tyr+
his+  arg+
val  glu
glu  gln
Amino acid changes
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.
Collinearity
• 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
Positions of mutant loci on genetic recombination map
446 487
223
23 187
58 169
Positions of altered amino acids in protein chain
175 177
183
212 215
234 235
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.
Collinearity
Proteins consist of chains of amino acids
and genes consist of chains of nucleotides.
- so does each nucleotide specify each
amino acid?
Collinearity
More than one mutation has been found to affect the
nature of the amino acid at position 212 in TrpA.
Genetic variant
Amino acid at position 212
Wild type
Mutant 23
Mutant 46
Glycine
Arginine
Glutamate
Perhaps one nucleotide means glycine, another means
arginine and another means glutamate. BUT…
Collinearity
It is possible to get recombination between these two
mutants.
Genetic variant
Amino acid at position 212
Wild type
Mutant 23
Mutant 46
23  46 recombinant
Glycine
Arginine
Glutamate
Glycine
Therefore, there must be more than one mutable site
(presumably more than one nucleotide) specifying each
amino acid.
Collinearity
• In fact, each amino acid is
specified by a triplet of
nucleotides, known as a codon.
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 271278. Griffiths, A. J. F,. Miller, J. H., Suzuki,
D. T., Lewontin, R. C. and Gelbart, W. M.
(Eds). Freeman and Company, New York.