[sanado]

Hey guys, just started organic chem. Ive been reading over the formation of proteins and currently i understand only the primary structure. I understand how the shape changes, but i dun understand the what happens at the chemical level between the secondary and tertiary structure. What makes secondary and tertiary reactions so different? Do different parts of the chain react?

[Astrokel]

Do different parts of the chain react?

Hey, yes they do.

Secondary proteins, alpha helix and beta pleated are stabilised by the hydrogen bonds such as the C=O bond in the first amino residue forms hydrogen bond to the N=H in the 4th amino residue in an alpha helix.

Tertiary proteins, are stabilised by 4 factors at the side chains

1) Disulphide linkages.

Two cysteine molecules react at the side chain to form a disulphide 'bridge'

2) Hydrogen bonds

3) Ionic bonds between oppositely charged side chain of proteins in acidic/basic solutions

4) Dipole-dipole attractions.

K

[Yggdrasil]

Tertiary structure describes how different secondary structural elements (i.e. alpha helices, beta sheets, and loop regions) are arranged in the overall structure of the protein.  For example, two proteins that consist of mostly beta sheets can have very different arrangements of the beta sheets.  Some have a cyclical arrangement of beta sheets forming a beta barrel (e.g. http://www.rcsb.org/pdb/explore.do?structureId=1CV7) and others can have completely different arrangements of the beta sheets (e.g. http://www.rcsb.org/pdb/explore.do?structureId=1CLY)

[sanado]

OKay, trying to avoid too much detail:

During secondary stage, bonds occure between the amino acids that results in beta sheets and alpha helicas forming. During tertiary stage, these chains are arranged where certain types of bonding occur?

[Padfoot]

Mostly between the R Groups/sidechains.

This might be worth a read as well:
http://www.bio.mtu.edu/campbell/401lec9all.pdf

To go into even more detail  some proteins also have a quaternary structure:
http://en.wikipedia.org/wiki/Quaternary_structure