Secondary Structure of Proteins (Alpha helices)

The only bonds in the secondary structure of a protein are regular repeated hydrogen bonds from the peptide bonds of the amide groups and carbonyl groups. You can also classify protein families by their secondary structures.

Helices 

• This is the most common secondary structure of proteins. 
• The carbonyl oxygen atom act as a hydrogen bond acceptor and the hydrogen attached to the nitrogen atom of the amide group act as the hydrogen bond donor. 
• The carbonyl oxygen atom (n) bonds to the hydrogen of the amide group four residues along (n+4) by hydrogen bonding. 
• Can be formed when the R-groups in the primary structure is not 'bulky'.
• If proline is present, the hydrogen bond formation would stop because the amine group is bonded to the R-group in proline. This is why proline is known as the 'helix breaker'.
• The first amine group and the last carbonyl group of the helix are not involved in the hydrogen bonding of the secondary structure.
• The helix forms a cylinder shape, with the hydrogen bonds forming the walls of the cylinder and the R-groups pointing outwards. 
• The properties of the R-groups that make up the primary structure dictates the interactions the helix has with other parts of the protein chain and with other molecules. It also means that the helix can be amphipathic (e.g. one side of the helix is hydrophobic and the other side is hydrophilic).
• They can be right-handed (going clockwise) or left-handed (anti-clockwise) but left-handed helices are very rare. 
• The helices can be any length because they have no limit. 
• Other variations of the alpha helix exist but are also very rare.

Primary structure of proteins

The primary structure of a protein is extremely important in governing the structure and interaction of the protein. It is made up of a chain of amino acids that are coded for by DNA.  Amino acids are always quoted/drawn from the N group to the C group. The amino acids involved also give the protein various chemical properties to allow it to arrange into the different levels of protein structure. 
These are:

• The amino acid sequence: determines everything about the protein structure.
• Peptide bonds: formed between the amino group of one amino acid to the carboxyl group of another amino acid. It can form hydrogen bonds and is involved in the secondary structure.
• R-group: extremely important in determining the tertiary structure of the protein.

The peptide bond

Polypeptides have a trans arrangement most of the time (R-groups above and below the plane of the polypeptide) because this makes the polypeptide more stable due to less obstruction from neighbouring R-groups. The peptide bonds are planar (can't rotate) but the covalent bonds either side of it can rotate depending on the R-groups of the amino acids present, which gives it the trans arrangement. This also restricts the number of arrangements the polypeptide can have. The rotation between C-C is called the psi (ψ) angle and the rotation between the N-C bond is called the phi (φ) angle.

Hydrogen bonding

They are formed when a hydrogen atom attached to a very electronegative atom is bonded to a very electronegative atom with a lone pair of electrons. The atom that is attached to the hydrogen atom is called the hydrogen bond donor and the non-bonded atom is called the hydrogen bond (H-bond) acceptor. Single H-bonds are relatively weak but many combined together can make the overall H-bond binding strength very strong.

Side chains (R-groups)

• Hydrophobic: these R-groups interact with each other by van der Waals and tend to pack together to avoid the water.
• Hydrophilic: these R-groups can interact, by hydrogen bonding, to each other, peptide bonds, organic polar molecules and water.
• Amphiphatic: these R-groups can interact with both water (by hydrogen bonding) and away from water (by van der Waals interactions).