REFLECTION 10: SECONDARY STRUCTURE

Hey guys and welcome back to my blog!! Continuing on the protein topic today, we will be looking at the secondary structure of proteins. Let’s Begin!

The secondary structure refers to the secondary level in the structure of proteins which is the folded regions along the polypeptide chain. There are two most common types of protein fold:

·         Alpha-Helix

·         Beta-Pleated Sheet

Alpha-Helix

We learnt that the amino acids are arranged in a regular helical conformation. The oxygen on the carbonyl group from each peptide bond is bonded to the hydrogen on the amino group of the 4th amino acids. The hydrogen bonds run nearly parallel to the axis of the helix. Per turn of the helix there are 3.6 amino acids which cover a distance of 0.54 nm and each amino acid residue represents an advance of 0.15 nm along the axis. Please note these figures as they may pop up in multiple choice questions. The side chains of the amino acids are all positioned along the outside of the cylindrical helix.

http://www.youtube.com/watch?v=eUS6CEn4GSA

Beta-Pleated Sheet

In the beta-pleated sheet the individual protein chains are aligned side by side with every other protein chain aligned in an opposite direction. Hydrogen bonding holds together amide groups of two separate chains. Hydrogen bonding specifically takes place between the hydrogen on the amide of one protein chain and the amide oxygen of the neighboring protein chain. We pleated sheet effect as a result of the amide structure being planar while bends occurring on the carbons containing the side chains.

http://www.youtube.com/watch?v=wM2LWCTWlrE

There are two types of Beta-pleated sheets:

·         Parallel

·         Anti-parallel

Parallel occurs when all N& C terminal ends line up.

Anti-parallel occurs when the N & C terminal ends alternate.

5 Factors affecting Alpha-Helices

·         The occurrence of Pro & Gly residues

·         The electrostatic repulsion or attraction between successive aa residues with charged R groups

·         The steric factors (bulkiness) of adjacent R groups.

·         The interactions between R groups spaced 3 or 4 residues apart

·         The interaction between aa residues at the ends of the helical segment and the electric dipole inherent to the helix

Why does the Alpha-Helix forms more readily than many other conformations?

This is due to an optimal use of internal hydrogen bonding. What this means is that within the helix every peptide bond participates in hydrogen bonding. In each successive turn of the helix there are 3-4 hydrogen bonds held, because of all the hydrogen bonds combined the helical structure is considered very stable.

Hope you guys enjoyed this post. Feel free to comment, like and share!! Take care!

References:

Youtube: BiochemJM, Leaffan27

http://www.elmhurst.edu/~chm/vchembook/566secprotein.html

Featured Image-

http://en.citizendium.org/wiki/Protein_structure

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