Th1L04: Peptide, Covalent and Non-Covalent Bonds


Medicine Y1 (Theme 1 | Cells and organelles) Mind Map on Th1L04: Peptide, Covalent and Non-Covalent Bonds, created by Emma Allde on 15/08/2016.
Emma Allde
Mind Map by Emma Allde, updated more than 1 year ago
Emma Allde
Created by Emma Allde over 7 years ago

Resource summary

Th1L04: Peptide, Covalent and Non-Covalent Bonds
  1. Peptide bonds
    1. Also called amide bonds
      1. Formed via dehydration synthesis
        1. Requires energy making it kinetically stable but slow
        2. Bonds are rigid due to short length
          1. Also remain unbranched
            1. Do not rotate
              1. Trans arrangment possible
                1. Planar
                  1. Six atoms aligned
                2. Dipeptides
                  1. A few naturally occurring examples
                    1. Aspartame (asp-phe): artificial sweetener
                    2. Tripeptide
                      1. Glutathione (glu-cys-gly): natural antioxidant
                      2. Polypeptide
                        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)
                            1. Amino acid at the end of the chain carboxyl-terminal (C-terminal) residue
                            2. Rich in hydrogen bonding potential
                              1. Each residue contains a carbonyl group (hydrogen-bond acceptor)
                                1. except for proline, and an NH group, which a good hydrogen-bond donor
                                2. Short (10-40 aa)
                                  1. Hormones, NTs
                                  2. Large (<44 aa)
                                    1. Proteins
                                    2. Large protein (50 - 2,000 aa)
                                      1. Dystrophin (3684 AAs)
                                        1. Titin which is 27,000 amino acids, a muscle protein
                                      2. Uncharged, allowing polymers of amino acids to form tightly packed globular structures
                                        1. Proteins fold in such a way that to minimise contact with an aqueous environment
                                          1. These are hydrophobic regions of the protein
                                            1. Unable to form hydrogen bonds
                                        2. Covalent bonds
                                          1. 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     
                                            1. Disulphide bridges
                                              1. join cysteines together forming a subunit
                                                1. e.g. insulin
                                            2. Non-covalent bonds
                                              1. Hydrogen bonds
                                                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
                                                      1. Hydrogen-bond acceptor
                                                        1. Atom less tightly linked to hydrogen atom
                                                          1. Will have a partial negative charge
                                                            1. e.g. Trp, His
                                                        2. Longer and straighter than covalent bonds
                                                          1. Low energy
                                                        3. Weaker than covalent bonds
                                                          1. Roles
                                                            1. Responsible for maintaining the tertiary structures of proteins
                                                              1. Crucial for biochemical processes such as the formation of the double helix
                                                              2. Electrostatic interactions
                                                                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
                                                                    1. 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
                                                                    3. van der Waals
                                                                      1. The distribution of electronic charge around an atom fluctuates with time
                                                                        1. 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)
                                                                          2. 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
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