Chem 336 - Spring 2004
	Organic Chemistry III
	Professor Carl C. Wamser

Amino Acids & Proteins

Amino Acids

• natural amino acids are alpha (position of the amine) and L (stereochemistry)
  
• structures differ by the R groups
  there are 20 common natural amino acids
  10 amino acids are essential to human nutrition
  (we can biosynthesize the others)

Side Chains

• include a great variety of functional groups and properties
  
• glycine has no side chain

• simple alkyl groups (nonpolar)

• cyclic side chain (a secondary amine)

• aromatic side chains

• alcohol side chains

(also note that tyrosine is a phenol)

• sulfur side chains

• carboxylic acid side chains

• amide side chains (from the above acids)

• basic side chains

Acid-Base Properties of the Amino Acids

• basic amine group and acidic carboxyl group are typically both in their ionized forms in aqueous solution around biological pH values
• pKa for the alpha-amino group is about 9-10
• pKa for the carboxylic acid group is about 2-3
  
• below pH ~ 2, mainly cationic form (ammonium ion)
• between pH ~ 2 - 10, mainly zwitterionic form (both ammonium cation and carboxylate anion)
• above pH ~ 10, mainly anionic form (carboxylate anion)
• amino acids with side chains that can also ionize have more complicated behavior

The Isoelectric Point

• pH at which the major form of the molecule is neutral
  (and there are equal - but small - amounts of cationic and anionic forms)
• for most amino acids, the isoelectric point is midway between their two pKa values (the middle of their neutral range)
• for amino acids with ionizable side chains, isoelectric points are at higher pH (for basic side chains) and lower pH (for acidic side chains)

Electrophoresis

• amino acids can be separated based on their charge in solution at a given pH
  e.g., at pH 7, alanine is aprox. neutral, arginine is mainly +, glutamic acid is mainly -
• depending on their charge, the molecules migrate towards either a positive or negative electrode (moving through wet gel or paper)

Peptides - Amino Acids joined by Amide Bonds

• naming goes from N-terminus (free amine) to C-terminus (free carboxyl)
• -ine ending of the amino acids are replaced by -yl (except the last one)
  e.g., threonylvaline is a dipeptide

• note that valylthreonine would be a different dipeptide

Polypeptides

• peptides are abbreviated with 3-letter codes (sometimes 1-letter codes)
• note the huge variety of possible polypeptides, using just the 20 common amino acids as building blocks
  20 amino acids
  400 dipeptides
  8,000 tripeptides
  160,000 tetrapeptides
• typical proteins have 100 or more amino acids, so the variety is immense
• note also the variety of possible functional groups available in those 20 amino acids
• peptides have evolved with a complete array of properties useful for life processes

Amino Acid Residues

• an amino acid residue differs from an amino acid by H₂O

Disulfide Linkages

• cysteine is readily crosslinked to another cysteine by a S-S bond

• disulfide linkages can hold together parts of a peptide chain that are not necessarily close in the peptide sequence

Amino Acid Analysis

• primary structure - the order of amino acids in the peptide chain
• complete hydrolysis (extended heating in aqueous HCl) breaks all amide bonds and releases all the individual amino acids
• individual amino acids can be separated by electrophoresis and/or chromatography and detected with ninhydrin (purple spot appears on reaction with any alpha-amino acid)
• complete hydrolysis, separation, and ninhydrin analysis can give a count of all amino acids and their relative abundance in the peptide

Partial Hydrolysis of Peptides

• occasionally, partial hydrolysis is carried out and smaller peptides are isolated, which are easier to analyze completely
• from the smaller peptides, sometimes useful connection information can be determined
• chymotrypsin and trypsin (digestive enzymes) are often used because they cleave peptides selectively
  • chymotrypsin cleaves a peptide only on the carboxyl side of the aromatic amino acids (Phe, Tyr, Trp)
  • trypsin cleaves a peptide only on the carboxyl side of the strongly basic amino acids (Lys and Arg)

Peptide Sequencing

• complete sequencing of a peptide can be done for up to about 20 amino acids in a row
• Edman degradation: selective cleavage of one amino acid off the N-terminus, followed by analysis to see what amino acid was removed
  (the selective reagent is phenyl isothiocyanate, and the clipped-off product is a phenylthiohydantoin)

Peptide Synthesis

• complete synthesis of peptides was started by Emil Fischer
• the procedure now can be automated up to about 100 amino acids
• protecting groups are essential to control the coupling reactions
  • protect the N-side of AA1
    (e.g., as a BOC-amide - easily removed later)
  • activate the C-side of AA1
    (e.g., with DCC - milder than SOCl₂)
  • couple active AA1 to AA2
    to form a dipeptide (AA2-AA1)
    (note that the N-terminus is still protected)
  • activate the free carboxyl group of the dipeptide, add AA3
    (forms the tripeptide, AA1-AA2-AA3)
  • repeat for each amino acid of the polypeptide
  • eventually remove the protecting group from the N-terminus

Proteins - Natural Polypeptides

• protein classifications may be based on structure or function or origin
• proteins are always a polypeptide (sometimes more than one chain) and may also have other types of molecules associated

Conjugated Proteins are asociated with other types of molecules

• glycoproteins - sugars
• lipoproteins - lipids (nonpolar fats and oils)
• nucleoproteins - nucleic acids
• heme proteins - porphyrin molecule
• metalloproteins - metal ions (often in a heme group)

Protein Shapes

• fibrous proteins - side-by-side polypeptide chains
  usually water-insoluble, mechanically strong
  useful for structure, muscle
• globular proteins - compact, variable shapes
  usually water-soluble, transported around the body
  useful for specific functions like catalysis (enzymes)

Protein Functions

• enzymes - catalysts for controlling rates of specific reactions
• hormones - regulators of specific body processes
• transport - control of movement of other molecules or ions
• structure - muscle, skin, etc.
• storage - nutrient storage
• protection - antibodies

Protein Structure - Primary Structure

• amino acid sequence
• determination of the specific order of amino acid residues

Protein Secondary Structure

• regular conformations of the peptide chain
  • alpha-helix - a coil held together by H-bonding
  • beta-sheet (or pleated sheet) - antiparallel sections of peptide chains held together by H-bonding

Protein Tertiary Structure

• complete 3-dimensional structure of the protein
• includes disulfide bridges, ionic interactions, H-bonding, other polar interactions and nonpolar (hydrophobic) interactions

Protein Quaternary Structure

• aggregation of several peptides chains into a larger protein unit

Enzymes - Protein Catalysts

• enzymes affect the rate of a particular reaction
  usually very specific as to what reaction or family of reactions will be catalyzed
• nomenclature: -ase suffix after a description of the reaction they catalyze
  • hydrolase - hydrolysis
  • isomerase - isomerization
  • transferase - transfer of a group from one molecule to another
  • lyase - elimination or addition of a small molecule, like water
  • oxidoreductase - oxidation or reduction (usually with NADH or similar cofactor)
  • ligase - binding of two molecules (usually with ATP cofactor)
• note that enzymes can catalyze a reaction in both directions
  like any catalyst, they provide a lower-energy pathway between reactants and products
  actual direction depends on the concentrations of substrates and cofactors

Chymotrypsin - A Specific Example of a Proteolytic Enzyme

• chymotrypsin cleaves an amide bond next to an aromatic amino acid
• the imidazole ring of a nearby histidine specifically adds or removes a proton to aid in nucleophilic attack or leaving group departure