Tuesday, February 1, 2011




An amino acid is a simple organic molecule consisting of basic(H accepting), amine grp bond to an acidic(H donating) carboxyl grp via a single intermediate carbon atom.

EXAMPLE: a generic alpha amino acid. The R grp is variable and is the only difference between the 20 common amino acids. This form is called a zwitterion, because it has both positively and negatively charged atoms. The zwitteronic state results from the amino grp gaining a H atom from solution and the acidic grp losing one.

During the translation of a gene into a protein the protein is formed by the sequential joining of amino acids end to end to form a long chain like molecule or polymer.

The primary structure of a protein is easily obtainable from its corresponding gene sequence, as well as by experimental manipulation. Unfortunately, the primary structure is only indirectly related to the proteins function. Secondary structure refers to folding in a small part of the protein that forms a characteristic shape. The most common secondary structure elements are alpha helices beta shapes, one of both of which are present in almost all natural proteins.

Tertiary structure refers to the structural elements formed by bringing more distant parts of a chain together into structural domains. The spatial arrangement of these domain with respect to each other is also considered part of the tertiary structure. Finally many proteins consist of more than one polypeptide folded together and the spatial arrangement between these separate polypeptide chain is called the quaternary structure. It is imp to note that the native conformation of a protein is a direct consequence of its primary sequence and its chemical environment which for most proteins is either aqueous solution with a biological PH or the oily interior of a cell membrane.


A structure of a protein is a 3D arrangement of the atoms such that the integrity of the molecule is maintained.


The most commonly used and usually highest resolution method of structure determination is x-ray crystallography. To obtain structure by this method, laboratory biochemist obtain a very pure crystalline sample of a protein. X-rays are then passed through the sample in which they are diffracted by the electrons of each atom of the protein. The diffraction pattern is recorded and can be used to reconstruct the 3D pattern of electron density. Therefore within some error the location of each atom. A high resolution crystal structure has a resolution on the order of 1-2A.


Electron diffraction works under the same principle as x-ray crystallography but instead of x-rays electrons are used to probe the structure. Because of difficulties in obtaining and interpreting electron diffraction data,it is rarely used for protein structure determination.

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