From Biolk483


Amino Acids

  • There are 20 coded for in genetic sequences
  • A protein is a sequence of amino acids --also called a polypeptide
  • All amino acids can form peptide bonds
  • R groups interact with water
    • Negative interaction (or r-groups not wanting to be near water) is called the hydrophobic effect
    • Positive interaction = hydrophilic effect

Amino Acids and Protein Structure

  1. Primary structure is the sequence of amino acids
  2. Secondary Structure is the folding caused by r-group interaction with water
  3. Special structural roles:
  • Example of special role: proline stops alpha helices because it is an imino acid with restricted bending.

Class 2 Amino Acids: Uncharged, Polar

  • This section continues to detail the categories listed near the end of lecture on 09/13/06.
  • This group includes:
    • Alcohols: serine, threonine, tyrosine
    • Asparagine and Glutamine
    • Sulphur amino acids: cystine


Serine Peptidases: a family of enzymes
  • Cleave peptide bonds by adding water
  • Serine is at the active site
  • We need the serine at the active site so as to end with an O- after an SN2 reaction
  • Chymotrypsin is one of these enzymes --used in digestion.
  • Phosphorylation can cause a fold change in the protein when the phosphate group is added
  • This fold change could increase or decrease the protein's reactivity.
  • This is a control mechanism for turning proteins on and off.
  • Examples:
    • Glycogen phosphorilase: increases reaction rate (of something...)
    • Pyruvate dehydrogenase (an oxido-reduction reaction): decreases the reaction rate.
  • Phosphorylation is reversible.
  • Threonine and tyrosine can be phosphorylated and dephosphorylated.
  • Serines at specific locations are control points.
Phospholipid Role (Phosphatidylserine)
  • an example of nature using two chemicals it likes in non-primary roles (meaning serine and lipids are being used but not in ways that we would call primary like we would the buiding of proteins and membranes, respectively)


  • Again, a control mechanism
  • Can lay against another planar molecule to protect the Pi electrons (e-)

Asparagine and Glutamine

  • When we sequence we hydrolyse stuff and this process makes these two amino acids look the exact same
  • Asparagine has a special role as it is the only amino acid sugars can be attached to so as to make glycoproteins.


  • An oxidation reduction reaction makes disulfide bonds between two Cysteines spacially (as opposed to sequentially) near to one another in a protein
    • These disulfide bonds give a tight, precise conformation to the protein. They hold the tertiary structure together.
    • Disulfide bonding is reversible.
    • Disulfide bonds are not made by hydrolysis!
    • Two cysteine disulfide bonded are called a cystine.


  • Can be a neurotransmitter like acetylcholine (this is done as a monomer, not in a protein or polypeptide form)
  • Glycines are found in tight folding areas of proteins because they do not have an R-group to get in the way.
  • Glycines are found in porphyrins, purines and pyrimidines (the latter two from nucleic acids)
  • Nature really likes this molecule.

Class Three Amino Acids: Positively Charged (Cations)

  • These have more functions than most other amino acids
  • These are the really dynamic amino acids


  • Lysine likes to hang out in the active site like a fishing hook
  • Lysine is called an E-amine (or an Epsilon amine)
Lysines Many Bonds
Schiff base
  • Remove water between R1R2C=O and H2N-R3 to make R1R2C=N-R3
  • This shifts the wavelength longer.
  • So if we find a Schiff base on a lysine on a protein like Rhodopsin.
  • Schiff base = rhodopsin - purple when Schiff base
    • Color vision is dependent on formation of Schiff base
  • Ex.: Aldolase
    • an important enzyme in Glycolysis
    • Fructose 1,6 bisphosphate (a six-carbon chain) -- (Aldolase --> dihydroxyacetone phosphate (a 3-carbon chain) + glyceraldehyde-3-phosphate (a 3-carbon chain)
Amide Linkage
  • same as asparagine and glutamine
  • Ex.: pyruvate carboxylase
    • sticks a CO2 group on pyruvate
    • Biotin is used to get C=) group available for putting on pyruvate
      • Note, there are many drawings here.
Salt linkage
  • Brings in anions
  • Easiest
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