This week’s lecture was about the continuation of amino acids and proteins. I learnt a lot of new things, well actually a more advanced study of proteins than I did in at A-levels. The topics covered include the different structures of proteins, types of bonds in proteins ,impacts of changes in amino acid sequences in proteins and the denaturing of proteins. This is a lot so lets get started folks.
The PRIMARY structure of the protein is quite straight forward but the SECONDARY may need a bit more elaborating on that is, features such as the alpha helix and beta pleated sheet.
In the helix, hydrogen bonds form between the carbonyl oxygen from a peptide bond and to a hydrogen of the amino group in the fourth amino acid in the chain. The hydrogen bonds run somewhat parallel to the axis of the helix. Some things to note: there are approx. 3.6 A.A per turn of the helix which covers a length of 0.54 nm,the amino acids side chains are situated on the outside of the cylindrical helix. Some amino acids are rarely found in alpha-Helices for e.g proline which 1)lacks rotation around the nitrogen-carbon bond,2)cannot form hydrogen bonds due to a lack of hydrogen atom on its nitrogen atom. Proline often acts as a molecule which ends the helix. 
Glycine is another amino acids rarely found due to its high conformational flexibility.
Factors affecting the stability of the Alpha Helix:
1)Interactions between A.A side chains- side groups with like charges causes repulsion which prevents the helix from forming
2)Steric Interference by bulky side groups can stop the formation of the helical structure-cannot fit and turn properly
3)Formation of ion pairs and hydrophobic interactions (aromatic A.A’s)- stabilize the helix
4)Peptide bonds contain miniature dipoles which ultimately form macrodipoles at the ends of the helix. Molecules close to each dipole contain opposite charge so as to stabilize the structure.
WHY DOES THE ALPHA HELIX FORM MORE READILY THAN MANY OTHER CONFORMATIONS?…this was a question posted on the lecture that need to be paid attention to and the answer is as follows:
It is formed more readily due to the more efficient use of hydrogen bonding as each peptide bond takes part except those close to the end of the chain.
Beta Pleated sheets:
In these, hydrogen bonds form between adjacent chains or sections of peptides and is positioned in such a way that the side chains protrude above and below the sheet. The bonds are planar. The sheets can be either parallel or antiparallel. The following link can give some insight into these types of sheets:
http://www.chem.wisc.edu/deptfiles/genchem/netorial/modules/biomolecules/modules/protein2/prot24.htm
TERTIARY STRUCTURE
The spatial arrangement of the polypeptide chain. It contain bonds such as disulphide,hydrogen,electrostatic and hydrophobic interactions.
QUATERNARY STRUCTURE
The way in which polypeptide chains are linked together. They contain the same forces as the tertiary structure mentioned above.
The following link explains the above information in detail:
http://themedicalbiochemistrypage.org/protein-structure.php
Denaturing of Proteins:
In denaturing of proteins, the primary structure always remain intact, it is mainly the tertiary and quaternary structure that is changed. Some proteins may or may not be able to return to its original state. Factors which denature proteins include:
1)Heat- disrupts hydrogen bonds by vibrational and translational energy
2)UV radiation-same as heat
3)Strong acids and bases-disrupts hydrogen bonds
4)Urea-competes for H- bonds
5)Organic solvents
6)Agitation
7)Chemical denaturation- chaotropes and detergents
The following link should provide ample information about denaturing of proteins:
http://www.elmhurst.edu/~chm/vchembook/568denaturation.html
WELL THIS CONCLUDES THIS LECTURE ON PROTEINS BUT BEFORE YOU GO HERE’S SOME FOOD FOR THOUGHT FOR AL YOU GYM FREAKSSS
biochemninja 