From Biolk483

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 (Phosphatidylserine) 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 Amide 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 = 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

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 (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)

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

Glycine

• 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

• 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