Evolution and proteins• You can see the effects of evolution, not

only in the whole organism, but also in its molecules - DNA and protein

• For a mutation to have an effect on the phenotype (and be subject to selection) it must (usually) affect the structure or function of a protein

• You can learn a lot about evolution by studying the structure of proteins

Chapter 26 Purves 7th edition

• Figures 26.2, 26.3, 26.5, 26.9

Reminder - protein structure• The primary structure of a protein is its sequence

of amino acids, e.g. Glu-Asp-Gly-Leu-Asp----• The secondary structure is how the chain of AAs

coils up into helices, loops and sheets• The tertiary structure is the 3-dimensional folding

of the secondary structures• The quaternary structure is the way in which some

proteins are made of 2 or more separate subunits (e.g. haemoglobin, a tetramer)

Some protein structures

Protein sequence alignments• How can you show 2 proteins (e.g. from 2

different species) are homologous (i.e. have the same evolutionary origin?

• Make an alignment: write the 2 sequences side-by-side so they match up as far as possible (you may need to introduce gaps): ASDFGFGHRTED * *** *** * TS-FGFSHRTDD

How often do changes occur?

• Mutations in the DNA can either be in the parts that code for a protein (coding sequences) or in the parts that don’t (non-coding sequences)

• Mutations in coding DNA can be either synonymous (“neutral”, do not change an amino-acid) or non-synonymous (changes an amino-acid)

Amino-acids are not equally “swappable”

• If we compare many examples of homologous proteins, we can count how many times each amino-acid can be substituted by any of the others

• The degree to which this happens, depends on how similar the amino-acids are

• Glutamate and aspartate both have acidic side-chains and often “swap”

• The position in the protein structure also makes a difference - some positions are always the same

A molecular clock

• Plot the number of changes in amino-acids between the same protein in different species (such as cytochrome C) against the time since the species diverged

• Gives a straight line - so evolution of a protein sequence proceeds at a constant rate and therefore can be used as a clock

The origin of new proteins

• Genomes are full of “paralogues” - two or more homologous versions of a gene and protein, forming a gene (or protein) “family”

• These arose by a duplication of that part of the genome

• Once duplicated, the 2 genes can evolve independently

• This may lead to the evolution of a new protein function, e.g. haemoglobin and myoglobin

The homeobox gene family

• Homeobox (Hox) proteins are “master switch” proteins that control development in all metazoan organisms

• The number of Hox genes is from one (in sponges) up to 13 (in vertebrates)

• All Hox genes are homologous. The Hox system was created once only in early evolution

• You’ll get more lectures on this later

Homeobox protein