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Transcript
Amino Acids, Peptides & Proteins amine; basic end a-amino acid: H2N R carboxylic acid; acidic end O OH H (S) absolute stereochemistry side chain O H3N R O H zwitterionic form (internal acid/base reaction): overall neutral salt H2O soluble pH = 7.3 (within cell; isoelectric point depends on R) Amino Acids O O • 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. H2N H2N OH OH H H H Valine (hydrophobic, bulky) Glycine (achiral) O O H2 N OH H2NH2CH2CH2CH2C H2N OH H H Lysine (basic, nucleophilic, often used in catalysis) O H2 N OH H CO2H Aspartic acid (acidic, used in catalysis) O NH OH SH Cysteine (nucleophilic, used in catalysis, controls shape of protein) H Proline 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. Peptides: Coupling AAs Together • Peptides & Proteins: Linear oligomers of the 20 amino acids • Peptides ≤ 20 amino acids; Proteins > 20 amino acids Functions: 1. Catalysis - enzymes 2. Membrane channels 3. Structural support (boundaries) 4. Regulate metabolites (storage & transport) 5. Antibodies; cellular signaling (recognition & binding) 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 CH3 O O Methyl ester H Phenylalanine HN H3N O H O • 4 calories per gram • 180 times sweeter than sugar Aspartic acid O Aspartame Aspartame: A Dipeptide CH3 O O Methyl ester H Phenylalanine HN H3N Two main constituents: Phenylalanine Aspartic acid O Aspartic acid H O O Goal: 1. Make the methyl ester of phenylalanine 2. Make a peptide (amide) bond between phenylalanine and aspartic acid Overall - two main steps to this synthesis Dipeptides: Coupling of 2 AAs Consider the synthesis of the dipeptide val-ala (valine-alanine): O N-terminus H2N CH3 OH C-terminus N H O 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 Merrifield’s Solid-Phase Synthesis In order to get the desired peptide (val-ala), the appropriate NH2 and CO2 units must be joined. O H2N CH3 OH OH H2N O valine's C-terminus alanine's N-terminus The selectivity is accomplished through the use of protecting groups. Merrifield’s approach: 1. Protect N-terminus of valine 2. Protect C-terminus of alanine 3. Couple valine and alanine 4. Deprotect to get dipeptide Merrifield’s Solid-Phase Synthesis 1. Protection of valine’s N-terminus: O Cl O H2N O OH (FMOC-Cl) O H N O OH Fmoc group O Merrifield’s Solid-Phase Synthesis 2. Protection of alanine’s C-terminus: Attach the C-terminus to a plastic bead (solid-phase synthesis!) CH3 CH3 OH H2N O H2N O O Benefits of solid-phase: • Ease of attachment • Ease of removal; just filter away from product solution Merrifield’s Solid-Phase Synthesis 3. Couple valine and alanine: O CH3 H N O O OH Fmoc group O H2N + N C N O Coupling agent such as DCC (dicyclohexylcarbodiimide) DCC (Used to derivatize the CO2H to make it more reactive) O CH3 H N O O N H O O Merrifield’s Solid-Phase Synthesis 3. Deprotection of Fmoc & bead: O CH3 H N O O N H O O 1. Piperidine (to remove Fmoc) 2. CF3CO2H (TFA, to remove bead) O H2N CH3 OH N H O valine alanine 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: 1. Planarity of amide bonds 2. H-bonding 3. Hydrophobic interactions 4. Electrostatic Attraction 5. Disulfide linkages Proteins 1. Planarity of amide bonds: R O H N N H O R O R O H N Barrier of rotation ~20 kcal/mol N O R H O Proteins 2. H-bonding: R O H N N O R H H-bond worth ~ 5 kcal/mol H O H-bonds orient the chain R O N N H O R O Proteins 3. Hydrophobic Interactions: Ph O O H N H N N Lots of hydrophobic interactions between Rs and H2O unstable H O Fold O Protein folds to “clump” R groups together in the interior of protein to avoid H2O - very energetically favored Hydrophobic pocket NH O NH N H O Proteins 4. Electrostatic Attraction: O NH3 O Proteins 5. Disulfide Linkages: SH HS Mild oxidant S S • Covalent S-S • Drastically alters shape • Worth ~ 50 kcal/mol 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 1. Primary structure: AA sequence 2. Secondary structure: discrete sub-structural elements (modules) a-helix & b-sheet a-helix: see board for depiction b-sheet: see board for depiction Note: 1. Internal H-bonding 2. The way the side chains line up 3. 3.6 AAs per turn Note: 1. Chain-to-chain H-bonding 2. Alternating (up-down, up-down) Pattern of R groups 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. 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: 1. Fats and oils 2. Phospholipids 3. Cholesterol & derivatives (steroids) Lipids 1. Fats & Oils Derived from glycerol and fatty acids: CH2OH H OH CH2OH + Glycerol: a triol (3 nuc sites) O OH Palmitic acid (C16 fatty acid) couple O O Weak intramolecular attractive forces between chains O O O O Triacyl glyceride Lipids 1. 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. O Unsaturated Fats: O O No contacts here due to Z-alkene Oils are polyunsaturated - lots of alkenes & have low mp due to less packing Butter has very little unsaturated & has higher mp O O O Lipids Soaps & Detergents • • Hydrolyzed fats A long chain carboxylate molecule: O O-Na+ Polar, hydrophilic end Non-polar, hydrophobic end Lipids Soaps & Detergents O-Na+ in H2O: O O H2O O-Na+ O O-Na+ +Na-O In H2O, forms a micelle. O O Hydrophobic Interior +Na-O O O O-Na+ O O-Na+ +Na-O O H2O O-Na+ O O-Na+ +Na-O O +Na-O Grease & dirt get trapped in the interior. Micelle is H2O soluble so can wash out dirt. O O-Na+ O +Na-O H2O O +Na-O O O + - Na O Hydrophilic Exterior H2O Lipids 2. Phospholipids: • Have hydrophobic and hydrophilic regions • Forms membranes • Precursors to prostaglandins O O O P O O O O N O H2O insoluble Phosphatidyl choline Highly charged H2O soluble 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. H2O outside of cell N N O O P O O O O O O O N N O O P O O O O P O O O O P O O O O O O O O O O O O O Cell membrane Hydrophobic interior O O O O O O O O O P O O O O O O O O P O O O O O O O P O O N N O N H2O inside of cell O O O P O O N Lipids 3. Cholesterol & Steroids Cholesterol: 27 carbons 4 rings 8 stereocenters Derived from terpenes H H H HO polar Cholesterol is a precursor to several steroidal hormones: Testosterone (male hormone) Estrone (female hormone) non-polar Lipids Cholesterol is a precursor to several steroidal hormones: Testosterone (male hormone) Estrone (female hormone) O OH H H H H H H HO O Testosterone Estrone These hormones operate at the genetic level (turn genes on and off) to control biochemistry. They are recognized by specific protein receptors. Antioxidants & Chocolate Antioxidants: • Protect against cardiovascular disease, cancer and cataracts • Thought to slow the effects of aging QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. 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. QuickTime™ and a TIFF (LZW) decompressor are needed to see this picture. 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.