1. Amino Acids and Peptides I Andy Howard Introductory Biochemistry Fall 2009, IIT

2. 01/28/08 Biochemistry: Amino Acidsp. 2 of 29 Acids, bases, amino acids We begin looking at specific categories of small molecules by examining acid-base equilibrium, both in general and in amino acids These simple molecules are inherently important, and they help illustrate some general principles

3. 01/28/08 Biochemistry: Amino Acidsp. 3 of 29 Plans iClicker stuff Acid-base equilibrium Amino acid structures Chirality Acid/base chemistry

4. 01/28/08 Biochemistry: Amino Acidsp. 4 of 29 iClicker quiz! 1. The correct form of the free energy equation is generally given as: –(a)  H =  G - T  S –(b) PV = nRT –(c)  G =  H - T  S –(d)  S =  H -  G –(e) none of the above (20 seconds for this one)

5. 01/28/08 Biochemistry: Amino Acidsp. 5 of 29 iClicker quiz, problem 2 2. Suppose a reaction is at equilibrium with  H = -6 kJ mol -1 and  S = -0.02 kJ mol -1 K -1. Calculate the temperature. –(a) 250K –(b) 280K –(c) 300K –(d) 310K –(e) 340K 45 seconds for this one

6. 01/28/08 Biochemistry: Amino Acidsp. 6 of 29 iClicker quiz, problem 3 3. Suppose the reaction A  B is endergonic with  G o = 37 kJ/mol. What would be a suitable exergonic reaction to couple this reaction to in order to drive it to the right? –(a) hydrolysis of ATP to AMP + PP i –(b) hydrolysis of glucose-1-phosphate –(c) hydrolysis of pyrophosphate –(d) none of the above 30 seconds for this one

7. 01/28/08 Biochemistry: Amino Acidsp. 7 of 29 Acid-Base Equilibrium In aqueous solution, the concentration of hydronium and hydroxide ions is nonzero Define: –pH  -log 10 [H + ] –pOH  -log 10 [OH - ] Product [H + ][OH - ] = 10 -14 M 2 (+/-) So pH + pOH = 14 Neutral pH: [H + ] = [OH - ] = 10 -7 M: pH = pOH = 7.

8. 01/28/08 Biochemistry: Amino Acidsp. 8 of 29 So what’s the equilibrium constant for this reaction? Note that the equation is H 2 O  H + + OH - Therefore k eq = [H + ][OH - ] / [H 2 O] But we just said that [H + ] = [OH - ] = 10 -7 M We also know that [H 2 O] = 55.5M (= (1000 g / L )/(18 g/mole)) So k eq = (10 -7 M) 2 /55.5M = 1.8 * 10 -16 M

9. 01/28/08 Biochemistry: Amino Acidsp. 9 of 29 Alternative approach Assume the protonated species is H 3 O + rather than H+ Then the reaction is 2 H 2 O  H 3 O + + OH - k eq = [H 3 O + ][OH - ] / ([H 2 O] 2 ) At pH=7, [H 3 O + ] = [OH - ] = 10 -7 M Dilute solution: [H 2 O] = 55.5M, so k eq = 10 -14 M 2 / [(55.5) 2 M 2 ] = 3.24*10 -18

10. 01/28/08 Biochemistry: Amino Acidsp. 10 of 29 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 K a = [A - ][H + ] / [HA] Define pK a  -log 10 K a Then pH = pK a + log 10 ([A - ]/[HA])

11. 01/28/08 Biochemistry: Amino Acidsp. 11 of 29 The Derivation is Trivial! Ho hum: pK a = -log([A-][H+]/[HA]) = -log([A-]/[HA]) - log([H+]) = -log([A-]/[HA]) + pH Therefore pH = pK a + log([A-]/[HA]) Often written pH = pK a + log([base]/[acid])

12. 01/28/08 Biochemistry: Amino Acidsp. 12 of 29 How do we use this? Often we’re interested in calculating [base]/[acid] for a dilute solute Clearly if we can calculate log([base]/[acid]) = pH - pK a then 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

13. 01/28/08 Biochemistry: Amino Acidsp. 13 of 29 Reading recommendations If the material on ionization of weak acids isn’t pure review for you, I strongly encourage you to read the relevant sections in 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!

14. 01/28/08 Biochemistry: Amino Acidsp. 14 of 29 So: let’s look at amino acids The building blocks of proteins are of the form H 3 N + -CHR-COO - ; these are  -amino acids. But there are others, e.g. beta-alanine: H 3 N + -CH 2 -CH 2 -COO -

15. 01/28/08 Biochemistry: Amino Acidsp. 15 of 29 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

16. 01/28/08 Biochemistry: Amino Acidsp. 16 of 29 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

17. 01/28/08 Biochemistry: Amino Acidsp. 17 of 29 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=-CH 2 -indole) Note that we sometimes care about  -amino acids that aren’t ribosomal— like ornithine ornithine

18. 01/28/08 Biochemistry: Amino Acidsp. 18 of 29 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

19. 01/28/08 Biochemistry: Amino Acidsp. 19 of 29 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

20. 01/28/08 Biochemistry: Amino Acidsp. 20 of 29 The simplest amino acids Glycine Alanine methyl

21. 01/28/08 Biochemistry: Amino Acidsp. 21 of 29 Branched-chain aliphatic aas Valine Isoleucine Leucine isopropyl

22. 01/28/08 Biochemistry: Amino Acidsp. 22 of 29 Hydroxylated, polar amino acids Serine Threonine hydroxyl

23. 01/28/08 Biochemistry: Amino Acidsp. 23 of 29 Amino acids with carboxylate side chains Aspartate Glutamate carboxylate methylene

24. 01/28/08 Biochemistry: Amino Acidsp. 24 of 29 Amino Acids with amide side chains asparagine glutamine Note: these are uncharged! Don’t fall into the trap! amide

25. 01/28/08 Biochemistry: Amino Acidsp. 25 of 29 Sulfur-containing amino acids Cysteine Methionine sulfhydryl

26. 01/28/08 Biochemistry: Amino Acidsp. 26 of 29 Positively charged side chains Lysine Arginine Guani- dinium

27. 01/28/08 Biochemistry: Amino Acidsp. 27 of 29 Aromatic Amino Acids Phenylalanine Tyrosine phenyl

28. 01/28/08 Biochemistry: Amino Acidsp. 28 of 29 Histidine: a special case Histidine imidazole

29. 01/28/08 Biochemistry: Amino Acidsp. 29 of 29 Tryptophan: the biggest of all Tryptophan indole