Proteins, Enzymes, and Nucleotide Polymers

Proteins, Enzymes, and Nucleotide Polymers

1. Proteins

   • Amino acid polymer, in principle no different from a peptide beyond its size (typically contains thousands of amino acids)
     • Dipeptide
       • 2 amino acids bonded together
     • Polypetide
       • large chain of peptides (not long enough to be considered a proper protein)
   • levels of protein structure
     • primary
       • order in which amino acids are joined together
     • secondary
       • 2 dimensional coils and folds formed by hydrogen bonding between amino acids within the strand
     • tertiary
       • 3 dimensional irregular folds and contortions within the amino acid chain resulting from interactions between R-groups
     • denaturation
       • process whereby a protein's preferred tertiary structureis changed, functionally changing or more commonly inactivating that protein
       • processes that can denature proteins
         • changes in temperature
         • changes in local charge conditions (e.g. salinity)
         • changes in pH
       • protein denaturing can be temporary or permanentdepending upon the severity of the denaturing conditions and the sensitivity of the enzyme

2. Enzymes

   • enzymes are protein catalysts
   • Properties of catalysts
     • Change the rate of a chemical reaction (usually but not always speed it up)
     • Are not used up in the mediated reaction
     • Are selective as the atoms/molecules they will interact with
     • Do not have a preferred reaction direction
   • Lock and key model of enzyme function
     • Enzymes crudely possess two regions, a structural region and an active/binding site, which has a specific shape that only matches molecules with a specific shape (called a substrate)
     • When a substrate properly binds with the active/binding site of an enzyme, the enzyme changes shape
     • The shape change triggers a change in the activity of the enzyme
       • The substrate may be physically changed
       • Some catalytic process may be either turned on or off at a different region of the enzyme (e.g., the substrate acts like an on/off switch for a motor)
     • Substrate imitators
       • Are similar enough in shape to the intended substrate to interact with the active/binding site of an enzyme
       • Can have useful properties as drugs, or be poisons depending on the context
       • Agonists
         • trigger a partial to complete response in the enzyme
       • Antagonists
         • Bind to the binding/active site but do not trigger an enzyme response (deactivate the enzyme by preventing the proper substrate from reaching the binding site)