Proteins

*Protein Structures 
Primary Structure 
All amino acids are connected by peptide bond (O=C=N-H)
Due to the high electronegativity of Nitrogen and Oxygen, the electrons are pulled from the carbon atom toward them which form a resonance structure (C=N) and (C=O). The possibility to form C=O bond is 60% and 40% for C=N
Characteristics of peptide bond: Polar, Resonance, Non-rotatable, Planar

Primary Structure of a pentapeptide in NCC sequence

Primary structure can be written in NCC sequence or CCN sequence, which represent the same structure. Note: the orientation is very important
In NCC sequence: the first Hydrogen on alpha-carbon projects in the planar then alternating (in and out)

Secondary Structure
All primary structures are connected by hydrogen bond

Alpha-Helix characteristics  

Alpha-Helix Structure
Source: Dr. Larry Jon Freisen's Lab Manual 

1)Right handed helix
2)R-groups project outward
3)Rise angle 27 degrees
4)3.6 amino acids per turn
5)0.15nm rise
6)0.51nm interchain distance
7)0.54nm pitch
8)"Strechy"
9)Angle subtented by amino acids= 100 degrees
10)Hydrogen bonding between peptide bonds

Beta-Pleated Sheet
The folded shape of Beta-Pleated sheet allows the R groups project up and down which will able to form the tertiary and quaternary structure with the R-Group Interactions

Beta-Pleated sheet with R groups project up and downward 

Tertiary Structure 
All secondary structures are connected by the R-Group Interactions

Quaternary Structure 
All tertiary structures are connected by the R-Group Interactions


*R-Group Interactions 

Non-Covalent Type 

1) Hydrogen Bonding

Serine interacts with Glutamine under Hydrogen bonding

2) Dipole-Dipole Bonding

Serine interacts with Serine under Dipole moment 

3) Ionic Bonding
The cation of one amino acid interacts with the anion of other amino acid

Ammonium ion of Lysine interacts with acetate ions on Aspartate 

4) Cation-Pi Bonding 
The resonance of Pi bond has created electron clouds, which are able to attract the Positive cations from other amino acids.

The Electron Cloud of Phenylalanine attracts the cation of Lysine

5) Hydrophobic Bonding 

Phenylalanine is nonpolar molecule which is hydrophobic

Under the surface of tension water sphere, the electrons in electron clouds have been pushed up to the upper clouds, which created a relative strong bond.

Phenylalanines bond together under water tension

Covalent Type

1) Isopeptide Bonding 
This kind of bonding is similar with peptide bonding; however, it is not on the main chain but on the between the amine group and carboxylic group within the  R-groups. 

2) Disulfide Bonding (Only on 2 Cysteines) 
Two Cysteines joined together by releasing two protons and electrons.

Cysteine connects with Cysteine

Source: Dr. Larry Jon Friesen' s Lectures