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Chapter 2: Protein Structure and Function

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Chapter 2: Protein Structure and Function Chapter 2: Protein Structure and Function Acid / Base chemistry is crucial for living organisms (pH control and acid/base catalysis) water as Water as the reference acid with ageneric base, B:. an acid, B donates H O H B H O a proton Hydroxide is H Kb and pKb the conjugate base of water Water as the reference base with a generic acid HA. water as a base, H O H A accepts H O H A a proton H K and pK H a a Hydronium ion is the Curved arrows emphasize electron movement. conjugate acid of water [H+][A: ] + [H O] 55.5 M [H ][A: ] 2 assumptions Keq = Ka = Keq[H2O] = [HA][H2O] [HA] T = 300 K + [A: ] pK = -(log K) (by definition) -log (Ka) = -log [H ] - log p(x) = -log (x) [HA] R=2.0cal/(mol-K) pK = pH - log [A: ] when [A: ] = [HA] R = 8.4 joule/(mol-K) a [HA] pKa = pH Also true. G = - 2.3RT logKa = 2.3RT (-log Ka) = 2.3RT (pKa) -G G=H-TS G = (constant)(pKa) Keq = 10 2.3 RT G = free energy H bond energies G = 1.4 pKa 1 pKa (kcal/mole) G = 5.8 pKa 6 pKa (kj/mole) S probabilities (randomness) 1 + -1 -2 -1 Weak acids (RCO2H, ROH, RSH, RNH3 , H3PO4, H2PO4 , HPO4 , H2CO3, HCO3 , etc.) + - B H Y B TS stronger H Y B H Y base Y B H weaker acid & base stronger acid & base weaker PE acid (more stable) endergonic G = B H Y POR = progress of reaction G = 1.4 pK 1 pK (kcal/mole) The equilibrium shifts towards the weaker conjugate a a acid and base (away from the stronger acid and G = 5.8 pKa 6 pKa (kj/mole) base). Weaker is more stable (think "less reactive"). + - B H A Strong acids (HCl, HBr, HI, H2SO4, HNO3, etc.) stronger TS PE acid potential B H A weaker energy base B H A B H A G = exergonic A B H stronger acid & base weaker acid & base (more stable) POR = progress of reaction 2 Amino Acids with Nonpolar "R" groups (have two pKa's), All aa C chiral centers are S except cysteine (because of the sulfur) O pKa=9.78 O pKa=9.87 O pKa=9.74 O pKa=9.74 pKa=2.35 pK =2.29 NH pKa=2.35 NH a NH3 3 3 pKa=2.33 NH HO HO 3 HO HO CH H H H H H3C H H3C CH2 H3C CH3 CH glycine = name alanine valine leucine Gly = 3 letter code Ala Val G = 1 letter code A body pH 7.4 CH3 Leu V L pK =9.76 pK =9.44 O a O pKa=9.18 O a O pKa=10.65 H2 pKa=2.32 pKa=2.16 pKa=2.43 pKa=1.95 2S NH3 NH3 NH3 N HO HO HO HO 3S H H H C H CH H C CH2 2 3 C CH H2 H 3 proline isoleucine phenylalanine trytophan N Trp Pro Ile Phe H P I F W Some amino acids have an additional pKa. O pKa=9.74 O K O O a1 Ka2 pK pKa=2.33 H N a1 pKa2 NH3 3 C H3N C H2N C HO CH OH CH O CH O H R S CH2 methionine R R H C C Our bodies need 20 amino acids to make our proteins 3 H Met 2 M (maybe 22 with some selenium variations). 3 Amino Acids with Polar "R" groups body pH 7.4 O pKa=9.21 O pKa=9.10 O pK =10.25 a O pKa=8.84 pKa=2.19 pK =2.09 NH a NH pKa=2.19 pKa=2.1 3 2S 3 NH3 NH HO HO 3 HO HO 3R H C H C H H 2 H2C H O CH H C 2 3 OH OH H serine threonine cysteine SH asparagine Ser pKa13 Thr pKa13 Cys pKa=8.33 NH Asn S C 2 N T pKa15 dimer pKa=9.11 O O O pKa=9.13 pKa=2.20 pK =2.17 NH3 a NH3 NH3 HO HO HO H N H H 2 H CH2 CH CH NH3 2 pKa15 2 S C H H HO O 2 pKa=10.13 S tyrosine C glutamine HO Tyr H2 Gln cystine = 2 x cysteine Q Y O with disulfide linkage Other relevant biological pKa values phosphoric acid carbonic acid H PO -2 -3 H CO -3 3 4 H2PO4 HPO4 PO4 2 3 HCO3 CO3 pKa=2.1 pKa=7.2 pKa=12.4 pKa=6.4 pKa=10.3 4 Amino Acids with Charged "R" groups (have three pKa's) body pH 7.4 O pKa=10.25 O pKa=9.90 O pKa=9.47 pKa=1.99 O pK =9.18 a pKa=2.19 NH pKa=2.10 3 NH3 NH HO 3 pKa=2.16 NH HO HO 3 HO HO H H H2C H O CH2 pK =4.07 CH H a 2 pK =10.79 H2 CH C a C 2 cysteine SH H C O 2 H Cys pK =8.33 H N CH 2 a OH asparatic acid 3 2 C glutamic acid lysine pKa=3.90 Asp Glu Lys Essential AAs Nonessential AAs D E K Histidine Alanine Isoleucine Arginine O pKa=8.99 Leucine Asparagine pKa=1.82 O Lysine Aspartic acid pKa=9.33 NH Methionine 3 pK =1.80 Cysteine HO a NH3 Phenylalanine Glutamicacid pK =12.48 HO a H Threonine Glutamine H2 H N CH2 H Tryptophan 2 C CH Glycine C 2 Valine Proline H2 H NH arginine N histidine Serine Arg pKa=6.04 H N NH His Tyrosine 2 R H Selenocysteine Ornithine All amino acids are "S" absolute configuration at the C position, except cysteine (because the sulfur atom changes the order of priorities). Isoleucine (3S) and theonine (3R) have a second chiral center. These are the starting points for our body's proteins. Their pKa's can change in an actual protein invironment due to nearby hydrophobic, hydrophilic and/or ionic groups. 5 extracellular blood pH 7.4 Henderson-Hasselbach Equation intracellular 6.8 [A ] stomach 1.5 - 3.5 pK = pH when [HA] = [A: ] pH = pKa+ log [HA] small intestines 8.5 a What do the amino acids look like? pH = 012 3 45678 9 10 11 12 13 14 pK 9.4 O pKa2 O a NH 3 NH2 C C R R R OH R O 100 1 1 250,000 [A] Typical aa ammonium 7.4 = 9.4 + log + 7.4 = 2 + log [A ] Typical aa carboxylic [HA ] acid ionization constant [HA] acid ionization constant [A] log + = (7.4 - 9.4) =-2.0 log [A ] = (7.4 - 2) = 5.4 [HA ] [HA] [A] -2.0 + = 10 = 1 / 100 [A ] = 105.4 = 2.5x105 = 250,000 / 1 [HA ] [HA] pKa10.8 pK 4 O a O NH 3 NH2 C C R R lysine R OH R O 2,500 1 asparatic acid pK =10.79 and 1 2,500 a [A] (third pK ) 7.4 = 10.8 + log glutamic acid a [HA+] [A ] (second pK ) 7.4 = 4 + log [A] a [HA] log = (7.4 - 10.8) = -3.4 [HA+] [A ] log = (7.4 - 4) = 3.4 [A] [HA] = 10-3.4 = 1 / 2,500 [HA+] [A ] = 103.4 = 2.5x103 = 2,500 / 1 [HA] pKa=7.2 pK =12.4 pKa2.1 a -2 -3 H PO -2 PO 3 4 H2PO4 H2PO4 HPO4 HPO4 4 1.0 1.6 6 extracellular blood pH 7.4 Henderson-Hasselbach Equation intracellular 6.8 stomach 1.5 - 3.5 [A ] pKa = pH when [HA] = [A: ] pH = pKa+ log small intestines 8.5 [HA] What do the amino acids look like? pH = 012 3 45678 9 10 11 12 13 14 pKa12.5 H2N R HN R NH NH H2N 126,000 H2N 1 histidine His pKa6 R [A] R 7.4 = 12.5 + log + H H arginine [HA ] N N [A] pKa=12.48 pK =6.04 log + = (7.4 - 12.5) = -5.1 a NH (third pK ) [HA ] (second pK ) NH a a [A] 1 25 = 10-5.1 = 1 / 126,000 [A] [HA+] 7.4 = 6 + log [HA+] pKa10.1 log [A ] = (7.4 - 6) = 1.4 OH O [HA] tyrosine pK =10.1 [A ] = 101.4 = 2.5x101 = 25 / 1 a [HA] R R (third pKa) 500 1 [A] 7.4 = 10.1 + log [HA+] Any amino acid pKa value can be shifted, left [A] log = (7.4 - 10.1) = -2.7 or right by its enzyme environment. More [HA+] hydrophobic regions will favor the neutral [A] = 10-2.7 = 1 / 500 forms (RCO2H, RNH2). A nearby opposite [HA+] charge will favor the ionic form (nearby pKa8 pK 13 positive favors negative and vice versa). An a cysteine SH OH open environment that allows access to water R S serine O pKa=8.33 R R is similar to the reference aqueous values (second pK ) threonine R a 8 1 1 (obtained in water). It is therefore hard to pKa13 340,000 [A ] (third pK ) determine the form of a functional group 7.4 = 8.3 + log a 7.4 = 13 + log [A ] [HA] [HA] (ionic or neutral) in a particular region of a [A] [A] log + = (7.4 - 8.3) = -0.9 log = (7.4 - 13) = -5.6 protein without knowing something about its [HA ] [HA+] structure. [A] [A] =10-0.9 =1/8 =10-5.6 =1/340,000 [HA+] [HA+] pK =6.4 a pKa=10.3 -2 H2CO3 HCO 3 HCO3 CO3 1 10 7 Henderson-Hasselbach Equation extracellular blood pH 7.4 intracellular 6.8 [A ] pK = pH when [HA] = [A: ] pH = pKa+ log stomach 1.5 - 3.5 a [HA] small intestines 8.5 What do the amino acids look like? pH = 012 3 45678 9 10 11 12 13 14 Typical aa ammonium O pKa4 pK 5 asparatic acid O a pKa9.4 acid ionization constant ratio = 250/1 and NH C 3 NH2 pKa8.4 glutamic acid C R R OH R O pKa5 R ratio = 10/1 (second pKa) ratio = 25/1 100 1 1 2,500 pKa7.4 ratio = 1/1 What happens to the pKa when..
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