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	*remove water between C=O and HN=R		*remove water between C=O and HN=R
	*add H20 to make C=NH-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
-	Arginine is used in the urea cycle.	+	**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

---

Revision as of 02:37, 14 October 2006

Contents 1 Amino Acids 1.1 Amino Acids and Protein Structure 1.2 Class 2 Amino Acids: Uncharged, Polar 1.2.1 Serine 1.2.1.1 Serine Peptidases: a family of enzymes 1.2.1.2 Phosphorylation 1.2.1.3 Phospholipid Role (Phosphotydilserine) 1.2.2 Tyrosine 1.2.2.1 Phosphorylation 1.2.2.2 Planar 1.2.3 Asparagine and Glutamine 1.2.4 Cysteine 1.2.5 Glycine 1.3 Class Three Amino Acids: Positively Charged (Cations) 1.3.1 Lysine 1.3.1.1 Lysines Many Bonds 1.3.1.1.1 Schiff base 1.3.1.1.2 Amid Linkage 1.3.1.1.3 Salt linkage

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 = ?

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

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

• 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 (Phosphotydilserine)

• an example of nature using two chemicals it likes in non-primary roles (meaing 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)

Tyrosine

Phosphorylation

• Again, a control mechanism

Planar

• 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.

Cysteine

• 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 hyrdolysis!
  • Two cysteine disulfide bonded are called a cystine.

Glycine

• Can be a neurotransmitter like acitityl coline (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 porgerins, 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

• 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 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)

Amid Linkage

• 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.

Salt linkage

• Brings in anions
• Easiest