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Amino Acids

Amino Acids. Andy Howard Introductory Biochemistry Fall 2014, IIT. Amino acids and what they do. We ’ ll show you all 20 ribosomally encoded amino acids and discuss their reactivities … but first we ’ ll review acid-base equilibrium!. Plans. Amino acid properties Amino Acid Structures

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Amino Acids

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  1. Amino Acids Andy Howard Introductory BiochemistryFall 2014, IIT

  2. Amino acids and what they do • We’ll show you all 20 ribosomally encoded amino acids and discuss their reactivities • … but first we’ll review acid-base equilibrium! Amino Acids and Proteins

  3. Plans • Amino acid properties • Amino Acid Structures • Proline • Simple aa’s • More complex aa’s • Chirality • Acid-base behavior • Abbreviations • Side-chain reactivity Amino Acids and Proteins

  4. Let’s begin, chemically! • Amino acids are important on their own and as building blocks • We need to start somewhere: • Proteins are made up of amino acids • Free amino acids and peptides play significant roles in cells, even though their resting concentrations are low • We’ll build from small to large Amino Acids and Proteins

  5. Acid-Base Equilibrium • In aqueous solution, the concentration of hydronium and hydroxide ions is nonzero • Define: • pH  -log10[H+] • pOH  -log10[OH-] • Product [H+][OH-] = 10-14 M2 (+/-) fact • So pH + pOH = 14 derived formula • Neutral pH: [H+] = [OH-] = 10-7M:pH = pOH = 7. Amino Acids and Proteins

  6. So what’s the equilibrium constant for this reaction? • Note that the equation isH2O  H+ + OH- • Therefore keq = [H+][OH-] / [H2O] • But we just said that [H+] = [OH-] = 10-7M • We also know that [H2O] = 55.5M(= (1000 g / L )/(18 g/mole)) • So keq = (10-7M)2/55.5M = 1.8 * 10-16M Amino Acids and Proteins

  7. Henderson-Hasselbalch Equation • If ionizable solutes are present, their ionization will depend on pH • Assume a weak acid HA  H+ + A-such that the ionization equilibrium constant is Ka = [A-][H+] / [HA] • Define pKa -log10Ka • Then pH = pKa + log10([A-]/[HA]) Amino Acids and Proteins

  8. The Derivation is Trivial! • Ho hum: Ka= [A-][H+]/[HA] • pKa= -log10([A-][H+]/[HA])= -log10([A-]/[HA]) - log10([H+])= -log10([A-]/[HA]) + pH • Therefore pH = pKa + log10([A-]/[HA]) • Often writtenpH = pKa + log([base]/[acid]) Amino Acids and Proteins

  9. How do we use this? • Often we’re interested in calculating [base]/[acid] for a dilute solute • Clearly if we can calculatelog([base]/[acid]) = pH - pKathen you can determine [base]/[acid] = 10(pH - pKa) • A lot of amino acid properties are expressed in these terms • It’s relevant to other biological acids and bases too, like lactate and oleate Amino Acids and Proteins

  10. Reading recommendations • If the material on ionization of weak acids isn’t pure review for you, I strongly encourage you to the relevant section of Garrett & Grisham • We won’t go over this material in detail in class because it should be review, but you do need to know it! Amino Acids and Proteins

  11. pKa values for weak acids Acid Base pKa Acid Base pKaForm Form Form Form Formic acid Formate 3.8 Acetic acid Acetate 4.8 Lactic acid Lactate 3.9 H3PO4 H2PO4- 2.2 H2PO4- HPO4-2 7.2 HPO4-2 PO4-3 12.7 H2CO3 HCO3- 10.2 NH4+ NH3 9.2 CH3NH3+ CH3NH2 10.7 Alanine+ Alanine0 2.4 Alanine0 Alanine- 9.9 Amino Acids and Proteins

  12. So: let’s look at amino acids • The building blocks of proteins are of the form H3N+-CHR-COO-;these are -amino acids. • But there are others,e.g. beta-alanine:H3N+-CH2-CH2-COO- Amino Acids and Proteins

  13. These are zwitterions • Over a broad range of pH: • the amino end is protonated and is therefore positively charged • the carboxyl end is not protonated and is therefore negatively charged • Therefore both ends are charged • Free -amino acids are therefore highly soluble, even if the side chain is apolar Amino Acids and Proteins

  14. At low and high pH: • At low pH, the carboxyl end is protonated • At high pH, the amino end is deprotonated • These are molecules with net charges Amino Acids and Proteins

  15. Identities of the R groups • Nineteen of the twenty ribosomally encoded amino acids fit this form • The only variation is in the identity of the R group (the side chain extending off the alpha carbon) • Complexity ranging from glycine (R=H) to tryptophan (R=-CH2-indole) • Note that we sometimes care about-amino acids that aren’t ribosomal—like ornithine ornithine Amino Acids and Proteins

  16. Let’s learn the ribosomal amino acids • We’ll walk through the list of 20, one or two at a time • We’ll begin with proline because it’s weird • Then we’ll go through them sequentially • You do need to memorize these, both actively and passively Amino Acids and Proteins

  17. But first: a reminder • We often characterize a carbon atom by specifying how many hydrogens are attached to it • –CH3 is methyl • –CH2– is methylene • –CH– is methine | Amino Acids and Proteins

  18. Quick non-iClicker non-quiz… 1. The standard form of the free-energy equation is • (a) H = G - TS • (b) G = H - TS • (c) PV = nRT • (d) none of the above. Amino Acids and Proteins

  19. iClicker quiz question 2 2. A reaction in which reactants are spontaneously being converted to products is • (a) unlikely • (b) endergonic • (c) exergonic • (d) endothermal • (e) exothermal Amino Acids and Proteins

  20. Special case: proline • Proline isn’t an amino acid: it’s an imino acid • Hindered rotation around bond between amine N and alpha carbon is important to its properties • Tends to abolish -helicity because of that hindered rotation Amino Acids and Proteins

  21. The simplest amino acids • Glycine • Alanine These are moderately nonpolar methyl Amino Acids and Proteins

  22. Valine Isoleucine Leucine Branched-chain aliphatic aas Seriously nonpolar isopropyl Amino Acids and Proteins

  23. Serine Threonine Hydroxylated, polar amino acids hydroxyl Amino Acids and Proteins

  24. Aspartate Glutamate Amino acids with carboxylate side chains carboxylate methylene Amino Acids and Proteins

  25. asparagine glutamine Amino Acids with amide side chains amide Note: these are uncharged! Don’t fall into the trap! Amino Acids and Proteins

  26. Cysteine Methionine Sulfur-containing amino acids sulfhydryl Two differences:(1) extra methylene(2) methylated S Amino Acids and Proteins

  27. Lysine Arginine Positively charged side chains Guani-dinium Amino Acids and Proteins

  28. Phenylalanine Tyrosine Aromatic Amino Acids phenyl Amino Acids and Proteins

  29. Histidine: a special case • Histidine imidazole Amino Acids and Proteins

  30. Tryptophan: the biggest of all • Tryptophan indole Amino Acids and Proteins

  31. Chirality • Remember:any carbon with four non-identical substituents will be chiral • Every amino acid except glycine is chiral at its alpha carbon • Two amino acids (ile and thr) have a second chiral carbon: C Amino Acids and Proteins

  32. Ribosomally encoded amino acids are L-amino acids • All have the same handedness at the alpha carbon • The opposite handedness gives you a D-amino acid • There are D-amino acids in many organisms • Bacteria incorporate them into structures of their cell walls • Makes those structures resistant to standard proteolytic enzymes, which only attack amino acids with L specificity Amino Acids and Proteins

  33. The CORN mnemonicfor L-amino acids • Imagine you’re looking from the alpha hydrogen to the alpha carbon • The substituents are, clockwise:C=O, R, N: Amino Acids and Proteins

  34. Abbreviations for the amino acids • 3-letter and one-letter codes exist • All the 3-letter codes are logical • Most of the 1-letter codes are too • 6 unused letters, obviously • U used for selenocysteine • O used for pyrrolysine • B,J,Z are used for ambiguous cases:B is asp/asn, J is ile/leu, Z is glu/gln • X for “totally unknown” • http://www.chem.qmul.ac.uk/iupac/AminoAcid/A2021.html Amino Acids and Proteins

  35. Acid-base properties • -amino acids take part in a variety of chemical reactivities, but the one we’ll start with is acid-base reactivity • The main-chain carboxylate and amine groups can undergo changes in protonation • Some side chains can as well Amino Acids and Proteins

  36. Letters A-F: acid-base properties Amino Acids and Proteins

  37. Letters G-L Amino Acids and Proteins

  38. Letters M-S pyrrolysine Amino Acids and Proteins

  39. Letters T-Z Amino Acids and Proteins

  40. Remembering the abbreviations • A, C, G, H, I, L, M, P, S, T, V easy • F: phenylalanine sounds like an F • R: talk like a pirate • D,E similar and they’re adjacent • N: contains a nitrogen • W: say tryptophan with a lisp • Y: second letter is a Y • Q: almost follows N, and gln is like asn • You’re on your own for K,O,J,B,Z,U,X Amino Acids and Proteins

  41. Do you need to memorize these structures? • Yes, for the 20 major ones(not B, J, O, U, X, Z) • The only other complex structures I’ll ask you to memorize are: • DNA, RNA bases • Ribose, glucose, glyceraldehyde • Cholesterol, stearate, palmitate • A few others I won’t enumerate right now. Amino Acids and Proteins

  42. How hard is it to memorize the structures? • Very easy: G, A, S, C, V • Relatively easy: F, Y, D, E, N, Q • Harder: I, K, L, M, P, T • Hardest: H, R, W • Again, I’m not asking you to memorize the one-letter codes, but they do make life a lot easier. Amino Acids and Proteins

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