Th1L04: Peptide, Covalent and Non-Covalent Bonds

Th1L04: Peptide, Covalent and Non-Covalent Bonds

1. Peptide bonds

   • Also called amide bonds
   • Formed via dehydration synthesis
     • Requires energy making it kinetically stable but slow
   • Bonds are rigid due to short length
     • Also remain unbranched
     • Do not rotate
     • Trans arrangment possible
     • Planar
       • Six atoms aligned
   • Dipeptides
     • A few naturally occurring examples
     • Aspartame (asp-phe): artificial sweetener
   • Tripeptide
     • Glutathione (glu-cys-gly): natural antioxidant
   • Polypeptide
     • Each amino acid unit is called a residue
       • Amino acid end at the beginning of the chain is called the amino-terminal residue (N-terminal)
       • Amino acid at the end of the chain carboxyl-terminal (C-terminal) residue
     • Rich in hydrogen bonding potential
     • Each residue contains a carbonyl group (hydrogen-bond acceptor)
       • except for proline, and an NH group, which a good hydrogen-bond donor
     • Short (10-40 aa)
       • Hormones, NTs
     • Large (<44 aa)
       • Proteins
     • Large protein (50 - 2,000 aa)
       • Dystrophin (3684 AAs)
       • Titin which is 27,000 amino acids, a muscle protein
   • Uncharged, allowing polymers of amino acids to form tightly packed globular structures
   • Proteins fold in such a way that to minimise contact with an aqueous environment
     • These are hydrophobic regions of the protein
       • Unable to form hydrogen bonds

2. Covalent bonds

   • Partial dipoles
     • 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 &nbsp; &nbsp;&nbsp;
   • Disulphide bridges
     • join cysteines together forming a subunit
       • e.g. insulin

3. Non-covalent bonds

   • Hydrogen bonds
     • Peptides can from hydrogen bonds with other polar groups (including peptide bonds) in a polypeptide chain
       • e.g. alpha helix
     • Responsible for specific base-pairs
       • Hydrogen-bond donor
       • Hydrogen-bond acceptor
         • Atom less tightly linked to hydrogen atom
         • Will have a partial negative charge
           • e.g. Trp, His
     • Longer and straighter than covalent bonds
       • Low energy
   • Weaker than covalent bonds
   • Roles
     • Responsible for maintaining the tertiary structures of proteins
     • Crucial for biochemical processes such as the formation of the double helix
   • Electrostatic interactions
     • A charged group on one molecule can attract an oppositely charged group on another molecule
       • Polarity and solvent have a major effect of dielectric constant and thus on the strength of the interaction
       • Usually more attractive interactions have more negative energy
     • Energy given by Coulomb's law
       • Energy = proportions(charges of the two atoms)/distance(dielectric constant
   • van der Waals
     • The distribution of electronic charge around an atom fluctuates with time
     • Charge distribution is never perfectly symmetric resulting in a complementary asymmetry in the electron distribution within its neighbouring atoms so they attract one another
       • 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)
     • A large number of VDW forces can become substantial
       • Base stacking and associated van der Waals interactions are nearly optimal in double-helical structure

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