Comparisons of amino acid sequences in specific proteins can be used to elucidate relationships between organisms. Immunological comparisons may be used to compare variations in specific proteins. Candidates should be able to interpret data relating to similarities and differences in base sequences in DNA and in amino acid sequences in proteins to suggest relationships between different organisms.

Genes code for amino acids to make proteins. So if we look at a protein in two different species and examine its amino acids, we can see how similar or different their genes are.

For example, (arbitrary data used) if we took heamaglobin from a gorilla and a human and looked at the amino acids and they looked like this:
Human: Ser; Val; Ser; Glu; Ile; Gln; Leu; Met; His; Asn
Gorilla: Ser; Val; Val; Ser; Ile; Gln Leu; Met; His; Asn
then we could see they are relatively genetically similar with  7/10 amino acids are the same.

One way to compare proteins is by comparing antigens on the body cells of a specie. This is immunological comparison:

• Extract blood serum from a species
• Put it in a second species
• This species will produce antibodies that are complimentary to the antigens of the first species
• Extract the antibodies
• Mix them with the blood serum of a third species
• A precipitate will form if the antibodies respond to the antigens of that specie

If the antibodies that were created for the antigens of the first specie can respond to antigens of the third then that means it must be complimentary to both. That means that both antigens had a similar tertiary structure, which means they had a similar primary structure, which means they had a similar sequence of amino acids which means that had a similar base sequence which means they are genetically similar. Therefore antibody can respond to both= more precipitate= more genetically similar.

If there is not very much precipitate its because the antibody can respond to the antigens in the third species because it is not sufficiently similar to the first, this shows us that they are genetically dissimilar.

The biuret test for proteins.

Place your sample in a test tube;
add an equal amount of sodium hydroxide;
add a few drops of dilute copper sulphate;
if it goes purple there are peptide bonds, if it is blue there are no peptide bonds.

http://www.youtube.com/watch?v=ufec89A47uM

The general structure of an amino acid. Condensation and the formation of peptide bonds linking together amino acids to form polypeptides. The relationship between primary, secondary, tertiary and quaternary structure, and protein function.

There are 20 different types of amino acid. In a polypeptide chain there are an average of 400 amino acids, the order of these will dictate which kind of protein it is, and therefore what its function is.

General structure of an amino acid
NH2 on the left is the amine group.

COOH on the right is carboxylic acid.

R represents the R group of the amino acid, the R group is what differs between amino acids. They can contain H, C, N and O but they can also contain Sulphur.

General structure of an amino acid

Primary structure of a protein
Amino acids join together by a condensation reaction: this produces water and a peptide bond (red line.) The oxygen and hydrogen of one amino acid, bond to the hydrogen of another forming H2O (water.) This leaves the carbon of one and nitrogen of the other free to make another bond; a peptide bond to each other.
When this is done to around 400 amino acids consecutively a polypeptide chain is formed (this is the primary structure of a protein.)
O=CNH is a peptide linkage; where as CN is the peptide bond.

Products of a condensation reaction between two amino acids

Secondary structure of a protein
Polypeptide chains bond together to form either alpha helices or beta pleated sheets.
In these structures every four amino acids has a hydrogen bond, this is a weak bond between the positive H (of the NH) and the negative O (of the CO.)

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Tertiary structure of a protein
The secondary structure is twisted and folded into an even more complex structure.
This can be held together in a variety of ways:

• Disulphide bridges can form if there are amino acids with sulphur in their R group
• Ionic bonds between carboxylic and amine groups that are not in a peptide bond
• Hydrogen bonds as in the secondary structure (but not regular)

Quaternary structure of a protein
This only happens sometimes, unlike the other stages which all have to be gone through to make a protein.
Several polypeptide chains at the tertiary level may join together to form a new protein.
An example of this is when four polypeptide chains bond around an iron making hemaglobin.

Proteins have a variety of functions within all living organisms.

Proteins can be used for many different functions, for example:

• Enzymes
• Carrier proteins
• Anti-bodies
• Hormones

They are key with in the cell; second in quantity only to water.

The two types of protein carry tend to carry out different functions:

• Fibrous proteins are formed like a rope, they are tightly twisted; this makes them very stable and good for structural functions (like collagen.)
• Globular proteins form a bundle which is more suited to carrying out metabolic functions (like enzymes.)