Molecular genetics: proteins
1. A sequence of DNA bases gives a three letter code for the 20 amino acids. First learn the one and three letter abbreviations for the 20 amino acids. (You should memorize this)
2. Next learn how to read the genetic code for going from genes to proteins. (No need to memorize this).
3. All amino acids have a COO and a NHHH part
(or a COOH carboxyl and NHH amino part), and a distictive part called the side
chain.
4. The structure of the amino acids can be learned by
first learning their side chain topology (figure from Ponder and
Richards).
5. The topology tells only how the atoms are connected. The geometry of the amino acids, the distances between atoms and the angles between bonds, is partially determined by the tetrahedral geometry of the carbon bond. The bond directions for carbon are the same as from the centroid of a tetrahedron to the vertices. Here is a tetrahedron in Maple. You can rotate it with the mouse. The bond angles at a carbon are all approximately 110 degrees.
6. Here is a pdb (protein Data Bank) file for valine to give you an idea of the tetrahedral geometry of the carbons. Compare this with the topology of Valine above. (To view pdb files on your own computer, you need Rasmol, or related plug ins for your browser, kinemage, or the swiss pdb viewer. ) Here are some more pdb files for amino acids.
7. To form a protein, amino acids are bonded together in
sequence. The bond is called the peptide bond. The
carboxyl group of one amino acid and the amide group of the subsequent amino
acid lose an oxygen and two hydrogens, i. e., water. The bond is
more or less planar. There is a special geometry associated with this
bond.
8. Configuration of side chains are sometimes called rotamers because the tetrahedral geometry stays the same and the main degree of freedom is rotation about the carbon bonds. Here is a kinemage of rotamers for valine. This can be viewed with a java version of kinemage. For a version with more functions, dowload kinemage to your PC. Now open the kinemage file for valine.
9. Also diagrams such as these from the Birkbeck site may help you to see the 3D structures of the amino acids. Think about them in terms of tetrahedral geometry at the carbons.
10. Amino acids can be divided in 6 different groups: hydrophobic-aliphatic, hydrophobic-aromatic, neutral-polar, acidic, basic, and conformationally important. See the Birkbeck site for a good tutorial on these classifications.
11. After amino acids are bonded together they fold into a
protein. The shape of a protein is very complex because of the number of
atoms involved. Before the advent of computer graphics, only a
trained artist could render an understandable picture of a protein. One
such artist was Irving Geis. Here is his painting of sperm whale
myoglobin. You can check out a website
devoted to artistic renditions of molecular phenomena by Irving Geis and
others..
12. Although the structure of a protein is hard to describe at an atomic level, certain regular features appear at a secondary structure level. The most common secondary structural elements are the alpha-helix and the beta-sheet.
13. Now a structure such as myoglobin can be represented
as a ribbon diagram. The spiraling ribbons are alpha-helixes and the
straight ribbons are beta-sheets. You can create your own perspective
using Rasmol or Swiss prot viewer and the pdb file.
