Th1L04: Peptide, Covalent and Non-Covalent Bonds

1. Requires energy making it kinetically stable but slow

1. Also remain unbranched
2. Do not rotate
3. Trans arrangment possible
4. Planar
   1. Six atoms aligned

1. A few naturally occurring examples
2. Aspartame (asp-phe): artificial sweetener

1. Glutathione (glu-cys-gly): natural antioxidant

1. Each amino acid unit is called a residue
   1. Amino acid end at the beginning of the chain is called the amino-terminal residue (N-terminal)
   2. Amino acid at the end of the chain carboxyl-terminal (C-terminal) residue
2. Rich in hydrogen bonding potential
3. Each residue contains a carbonyl group (hydrogen-bond acceptor)
   1. except for proline, and an NH group, which a good hydrogen-bond donor
4. Short (10-40 aa)
   1. Hormones, NTs
5. Large (<44 aa)
   1. Proteins
6. Large protein (50 - 2,000 aa)
   1. Dystrophin (3684 AAs)
   2. Titin which is 27,000 amino acids, a muscle protein

1. These are hydrophobic regions of the protein
   1. Unable to form hydrogen bonds

Annotations:

• Nuclei of the hydrogen atoms naturally repel when close together because they are both positively charged at certain distance away from each other there is a slight dipole attraction that strengthens the bond that requires very low energy     

1. join cysteines together forming a subunit
   1. e.g. insulin

1. Peptides can from hydrogen bonds with other polar groups (including peptide bonds) in a polypeptide chain
   1. e.g. alpha helix
2. Responsible for specific base-pairs
   1. Hydrogen-bond donor
   2. Hydrogen-bond acceptor
      1. Atom less tightly linked to hydrogen atom
      2. Will have a partial negative charge
         1. e.g. Trp, His
3. Longer and straighter than covalent bonds
   1. Low energy

1. Responsible for maintaining the tertiary structures of proteins
2. Crucial for biochemical processes such as the formation of the double helix

1. A charged group on one molecule can attract an oppositely charged group on another molecule
   1. Polarity and solvent have a major effect of dielectric constant and thus on the strength of the interaction
   2. Usually more attractive interactions have more negative energy
2. Energy given by Coulomb's law
   1. Energy = proportions(charges of the two atoms)/distance(dielectric constant

1. The distribution of electronic charge around an atom fluctuates with time
2. Charge distribution is never perfectly symmetric resulting in a complementary asymmetry in the electron distribution within its neighbouring atoms so they attract one another
   1. Result is that atoms come closer to one another until they are separated by van der Waals constant distance where stronger repulsive forces become dominant (outer electron clouds overlap)
3. A large number of VDW forces can become substantial
   1. Base stacking and associated van der Waals interactions are nearly optimal in double-helical structure