Amino Acids, Peptides & Proteins

1. Amino Acids, Peptides & Proteins a-amino acid:

2. Amino Acids • Are >500 naturally occurring amino acids identified in living organisms • Humans synthesize 10 of the 20 they use. The other 10 are called essential amino acids.

3. Amino Acids, Peptides & Proteins • Peptides & proteins: • Derived from amino acids through peptide or amide bonds. • The amine and acid ends of amino acids couple to form amide (peptide) bonds • in peptides/proteins/enzymes. • Proteins fold into well-defined structures. The hydrophobic residues • segregate to the water-free interior, while the polar/charged residues favor • the exterior.

4. Peptides: Coupling AAs Together • Peptides & Proteins: Linear oligomers of the 20 amino acids • Peptides ≤ 20 amino acids; Proteins > 20 amino acids • Functions: • Catalysis - enzymes • Membrane channels • Structural support (boundaries) • Regulate metabolites (storage & transport) • Antibodies; cellular signaling (recognition & binding)

5. Aspartame • Discovery story: • In 1965 by Jim Schlatter • working on discovering new • treatments for gastric • ulcers. • Made a dipeptide intermediate, • which he spilled on his hand • Tested the dipeptide in coffee Aspartame • 4 calories per gram • 180 times sweeter than sugar

6. Aspartame: A Dipeptide Two main constituents: Phenylalanine Aspartic acid Goal: Make the methyl ester of phenylalanine 2. Make a peptide (amide) bond between phenylalanine and aspartic acid Overall - two main steps to this synthesis

7. Dipeptides: Coupling of 2 AAs Consider the synthesis of the dipeptide val-ala (valine-alanine): • Coupling of amino acids is an application of nucleophilic acyl substitution • Issue of selectivity arises: • val + ala  val-ala + ala-val + • val-val + ala-ala • A mixture of 4 possible amide • products

8. Merrifield’s Solid-Phase Synthesis In order to get the desired peptide (val-ala), the appropriate NH2 and CO2 units must be joined. The selectivity is accomplished through the use of protecting groups. Merrifield’s approach: Protect N-terminus of valine Protect C-terminus of alanine Couple valine and alanine Deprotect to get dipeptide

9. Merrifield’s Solid-Phase Synthesis 1. Protection of valine’s N-terminus:

10. Merrifield’s Solid-Phase Synthesis 2. Protection of alanine’s C-terminus: Attach the C-terminus to a plastic bead (solid-phase synthesis!) • Benefits of solid-phase: • Ease of attachment • Ease of removal; just filter away from product solution

11. Merrifield’s Solid-Phase Synthesis 3. Couple valine and alanine:

12. Merrifield’s Solid-Phase Synthesis 3. Deprotection of Fmoc & bead:

13. Proteins • Amino acid polymers; when long enough, they fold back on themselves to • create intricate, well-defined 3D structures • The structure of a protein specifies its function. • The AA sequence specifies its structure. • The AA chain typically adopts regional sub-structures which sum together • to deliver the overall structure of the protein. • Forces/Factors that dictate protein folding: • Planarity of amide bonds • H-bonding • Hydrophobic interactions • Electrostatic Attraction • Disulfide linkages

14. Proteins 1. Planarity of amide bonds:

15. Proteins 2. H-bonding: H-bond worth ~ 5 kcal/mol H-bonds orient the chain

16. Proteins 3. Hydrophobic Interactions: Lots of hydrophobic interactions between Rs and H2O - unstable Protein folds to “clump” R groups together in the interior of protein to avoid H2O - very energetically favored

17. Proteins 4. Electrostatic Attraction:

18. Proteins 5. Disulfide Linkages: • Covalent S-S • Drastically alters shape • Worth ~ 50 kcal/mol

19. Proteins • Overall, these 5 structural/energetic features leads to the final 3D protein • structure. However, predicting the structure from the amino acid sequence • is still a challenge. • Hierarchy of Structural Elements of Proteins • Primary structure: AA sequence • Secondary structure: discrete sub-structural elements (modules) a-helix & b-sheet a-helix: see board for depiction Note: Internal H-bonding The way the side chains line up 3.6 AAs per turn b-sheet: see board for depiction Note: Chain-to-chain H-bonding Alternating (up-down, up-down) Pattern of R groups

20. Proteins • Hierarchy of Structural Elements of Proteins 3. Teritary Structure: the individual secondary structural elements organized in 3D. See board for depiction. 4. Quaternary Structure: non-covalent complexation of different proteins.

21. Lipids • Structurally diverse, derived from living organisms • Functional theme is hydrophobicity - water avoiding due to long alkyl chains • Often found at the interface of aqueous compartments • 3 Major Classes of Lipids: • Fats and oils • Phospholipids • Cholesterol & derivatives (steroids)

22. Lipids Fats & Oils Derived from glycerol and fatty acids: Weak intra- molecular attractive forces between chains

23. Lipids • Fats & Oils • In order for a fat to melt, these weak dispersive forces must be broken. • More contacts, the better the packing and the higher the m.p. of the fat • Less contacts, worse packing of chains, the lower the m.p. Unsaturated Fats: Oils are polyunsaturated - lots of alkenes & have low mp due to less packing Butter has very little unsaturated & has higher mp

24. Lipids Soaps & Detergents • Hydrolyzed fats • A long chain carboxylate molecule:

25. Lipids Soaps & Detergents In H2O, forms a micelle. Grease & dirt get trapped in the interior. Micelle is H2O soluble so can wash out dirt.

26. Lipids 2. Phospholipids: • Have hydrophobic and hydrophilic regions • Forms membranes • Precursors to prostaglandins

27. Lipids 2. Phospholipids: • Forms membranes: self-organize at certain concentrations to form bilayers • Membranes are largely impermeable to charged species that exist in biological environments. Cell membrane

28. Lipids 3. Cholesterol & Steroids Cholesterol: 27 carbons 4 rings 8 stereocenters Derived from terpenes Cholesterol is a precursor to several steroidal hormones: Testosterone (male hormone) Estrone (female hormone)

29. Lipids Cholesterol is a precursor to several steroidal hormones: Testosterone (male hormone) Estrone (female hormone) These hormones operate at the genetic level (turn genes on and off) to control biochemistry. They are recognized by specific protein receptors.

30. Antioxidants & Chocolate • Antioxidants: • Protect against cardiovascular disease, cancer and cataracts • Thought to slow the effects of aging • Chocolate: • High levels of antioxidants - complex mixtures of phenolic comounds • By weight, has higher concentration of antioxidants than red wine or • Green tea • 20x higher concentration of antioxidants than tomatoes Dark chocolate has more than 2x the level of antioxidants as milk chocolate. Side note: The main fatty acid in chocolate, stearic acid, does not appear to raise blood cholesterol levels the way other saturated fatty acids do.