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Understanding Amino Acids and Proteins Chemistry

Learn about amino acids, protein structures, acid-base reactivity, pKa values, side-chain reactions, and post-translational modifications in proteins. Understand the importance of different amino acids in enzyme active sites.

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Understanding Amino Acids and Proteins Chemistry

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  1. iClicker question #3 3. What amino acids are in ELVIS? • (a) asp - lys - val - ile - ser • (b) asn - lys - val - ile - ser • (c) glu - leu - val - ile - ser • (d) glu - lys - val - ile - ser • (e) Thank you very much. (25 seconds) Amino Acids and Proteins

  2. … and another • 4. How many of the twenty plentiful, ribosomally encoded amino acids have exactly one chiral center? • (a) zero • (b) one • (c) seventeen • (d) eighteen • (e) twenty Amino Acids and Proteins

  3. Main-chain acid-base chemistry • Deprotonating the amine group: H3N+-CHR-COO- + OH- H2N-CHR-COO- + H2O • Protonating the carboxylate:H3N+-CHR-COO- + H+H3N+-CHR-COOH • Equilibrium far to the left at neutral pH • First equation has Ka=1 around pH 9 • Second equation has Ka=1 around pH 2 Amino Acids and Proteins

  4. Why does pKa depend on the side chain? • Opportunities for hydrogen bonding or other ionic interactions stabilize some charges more than others • More variability in the amino terminus, i.e. the pKa of the carboxylate group doesn’t depend as much on R as the pKa of the amine group Amino Acids and Proteins

  5. When do these pKa values apply? • The values given in the table are for the free amino acids • The main-chain pKa values aren’t relevant for internal amino acids in proteins • The side-chain pKa values vary a lot depending on molecular environment:a 9.4 here doesn’t mean a 9.4 in a protein! Amino Acids and Proteins

  6. How do we relate pKa to percentage ionization? • Derivable from Henderson-Hasselbalch equation • If pH = pKa, half-ionized • One unit below: • 91% at more positive charge state, • 9% at less + charge state • One unit above: 9% / 91% Amino Acids and Proteins

  7. Don’t fall into the trap! • Ionization of leucine: Amino Acids and Proteins

  8. Side-chain reactivity • Not all the chemical reactivity of amino acids involves the main-chain amino and carboxyl groups • Side chains can participate in reactions: • Acid-base reactions • Other reactions • In proteins and peptides,the side-chain reactivity is more important because the main chain is locked up! Amino Acids and Proteins

  9. Acid-base reactivity on side chains • Asp, glu: side-chain COO-: • Asp sidechain pKa = 3.9 • Glu sidechain pKa = 4.1 • That means that at pH = 5.1, a glutamate will be ~90.9% charged • Lys, arg: side-chain N: • Lys sidechain –NH3+pKa = 10.5 • Arg sidechain =NH2+pKa = 12.5 Amino Acids and Proteins

  10. Acid-base reactivity in histidine • It’s easy to protonate and deprotonate the imidazole group Amino Acids and Proteins

  11. Cysteine: a special case • The sulfur is surprisingly ionizable • Within proteins it often remains unionized even at higher pH Amino Acids and Proteins

  12. Ionizing hydroxyls • X–O–H  X–O- + H+ • Tyrosine is easy, ser and thr hard: • Tyr pKa = 10.5 • Ser, Thr pKa = ~13 • Difference due to resonance stabilization of phenolate ion: Amino Acids and Proteins

  13. Resonance-stabilized ion Amino Acids and Proteins

  14. Other side-chain reactions • Little activity in hydrophobic amino acids other than van der Waals • Sulfurs (especially in cysteines) can be oxidized to sulfates, sulfites, … • Nitrogens in his can covalently bond to various ligands • Hydroxyls can form ethers, esters • Salt bridges (e.g. lys - asp) Amino Acids and Proteins

  15. Phosphorylation • ATP donates terminal phosphate to side-chain hydroxyl of ser, thr, tyr • ATP + Ser-OH  ADP + Ser-O-(P) • Often involved in activating or inactivating enzymes • Under careful control of enzymes called kinases and phosphatases • This is an instance of post-translational modification Amino Acids and Proteins

  16. Amino acid frequencies and importance in active sites • Polaramino acids, particularly S, H, D, E, K, are at the heart of most active sites of enzymes and other globular proteins • Yet they’re relatively uncommon overall in proteins • Nonpolar amino acids (V, L, I, A) occur with higher frequencies overall Amino Acids and Proteins

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