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).