Editing 09/18/06

<h1>Amino Acids</h1>
*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

<h3>Amino Acids and Protein Structure</h3>
#Primary structure is the sequence of amino acids
#Secondary Structure is the folding caused by r-group interaction with water
#Special structural roles:
*Example of special role: proline stops alpha helices because it is an imino acid with restricted bending.

<h3>Class 2 Amino Acids: Uncharged, Polar</h3>
*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

<h4>Serine</h4>
<h5>Serine Peptidases: a family of enzymes</h5>
*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.
<h5>Phosphorylation</h5>
*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.
<h5>Phospholipid Role (Phosphatidylserine)</h5>
*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)

<h4>Tyrosine</h4>
<h5>Phosphorylation</h5>
*Again, a control mechanism
<h5>Planar</h5>
*Can lay against another planar molecule to protect the Pi electrons (e-)

<h4>Asparagine and Glutamine</h4>
*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.

<h4>Cysteine</h4>
*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.

<h4>Glycine</h4>
*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.

<h3>Class Three Amino Acids: Positively Charged (Cations)</h3>
*These have more functions than most other amino acids
*These are the really dynamic amino acids

<h4>Lysine</h4>
*Lysine likes to hang out in the active site like a fishing hook 
*Lysine is called an E-amine (or an Epsilon amine)
<h5>Lysines Many Bonds</h5>
<h6>Schiff base</h6>
*remove water between C=O and HN=R
*add H20 to make C=NH-R
*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 shift base
**color vision is dependent on formation of shift base
*exmaple: Aldolase
**an important enzyme in glycolasis
**Fructose 1,6 bisphosphate (a six-carbon chain) -- (Aldolase --> dihydroxyacetone phisphate (a two carbon chain) + glyceraldehyde-3-phosphate (a 3 carbon chain)
<h6>Amid Linkage</h6>
*same as asparagine and glutamine
*example 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.
<h6>Salt linkage</h6>
*Brings in anions
*Easiest