University:
Amherst College
Course:
BIOL 330 | Biochemical Principles of Life at the Molecular Level
Academic year:

2011
Views:

372

Pages:

27
Author:

ice0ver13toy

BioChem 330 - Course Outline • Bio-molecular Structure/Function (I) – PROTEINS • Structure – – – – Chemistry of amino acid building blocks Primary, secondary and tertiary structure Protein folding, thermodynamics and kinetics Predictions of protein folding, dynamics • Function – Binding ….a tale of two globins (hemoglobin and immunoglobulin) BioChem 330 - Course Outline • Bio-molecular Structure/Function (I) – PROTEINS • Structure – Chemistry of amino acid building blocks » Structure » Chirality » Functionality » Acid/base behavior Amino Acid building blocks Amino Acid building blocks Amino Acid building blocks Amino Acid building blocks – 20 fundamental amino acid monomers • • • • Gly Ala Val Leu Ile Ser Thr Asp Asn Glu Gln Lys G A V L I S T D N E Q K Arg His Trp Phe Tyr Pro Cys Met R H W F Y P C M – polymer is ___________? • < ~60 monomers is polypeptide • 60 < monomers < 600 makes up a typical protein • Nearly infinite variety for even small protein The α carbon is a chiral center • Nearly all amino acids have at least one chiral center, the α carbon. Which amino acid has none? _________ Why is that carbon called alpha? _______ • All proteins incorporate the L stereoisomer into their backbones. • D isomers have other uses – D-glu (DE) is a neurotransmitter – dipeptide (DA-DA) crosslinks bacterial cell walls and is target of antibiotics such as penicillin and vancomycin Remember L for Life Functionality of R groups Aliphatic Amino Acids: Gly is difficult to characterize; here, it’s grouped with the aliphatic a.a.’s, yet there’s no carbon in the R group! Val, Leu, and Ile are strongly hydrophobic amino acids Functionality of R groups Aromatic Amino Acids These amino acids are quite different from each other, with Phe being very nonpolar and Tyr sometimes becoming deprotonated to form tyrosinate, Trp sometimes participating in H bonding through N-H. Functionality of R groups Alcohol functionality •We’ll see Ser in many different catalytic roles, where O acts as a nucleophile to initiate peptide bond cleavage (trypsin) •Thr are also complicated, partial hydrophobic character but with H bonding possibilities…… Functionality of R group Thiol Functionality w/o terminal methyl, homocysteine • Cysteines can dimerize to make disulfide bonds that hold a protein together. In air, cysteine will oxidize and form a sulfoxide. • Methiones are really subtle Functionality of R groups Basic Amino Acids Why are these amino acids called bases? What is being depicted? Functionality of R group Acidic Amino Acid Family Why are these amino acids called acids? What is being depicted? Functionality of R group Proline, the Helix Breaker In a polypeptide, the trans/cis change is often regulatory switch to turn off, on catalysis Charge is Critical to Behavior •All amino acids exhibit acid/base behavior in the ionization of their carboxyl and amino groups. •At neutral pH, amino acids are zwitterions (have positive and negative charges for net neutral). Acidity is characterized by pKa Acids:" Chemical Equilibrium: K = [H3O+][A-]/[HA][H2O] 3.5 x 10-7 [1] Ka = [H3O+][A-]/[HA] 1.9 x 10-5 [2] pKa = -logKa 4.7 [3] stronger acid = larger Ka = ________ pKa weaker acid = smaller Ka = ________pKa How do we characterize basicity? bases: B + H2O = HB+ + OH– Kb = [HB+][OH-]/[B] [4] conjugate acids of bases, BH, act as acids HB+ + H2O = B + H3O+ – Ka’ = [H3O+][B]/[HB+]= 1/Kb [5] – pKa’ = -log Ka’ [6] Note: pK'a is of the conjugate acid. stronger base = weaker conj. acid = _______pKa’ weaker base = stronger conj. acid = _______ pK'a Important pKas to remember for amino acids • Each of the pKa numbers listed Amino Acid Group -Carboxy Terminal [R1-COOH] 1.7-2.4 at right can vary depending -Asp and Glu [R2-COOH] ~4.4 on the -His [His+] ~6.5 environment + • Do positive neighbors cause pKa to go up, or down? _____ Why?? _____ -Amino Terminal [R- H3N ] -Cys -Tyr [R-S-H] [R-O-H] 8.8-10.9 ~ 8.5 ~ 10.0 -Lys [R-NH3+] ~ 10.0 -Arg [R-N=C-NH3+] ~ 12.0 NH2 App 1: How do you predict the outcome of a reaction between a weak acid and a weak base? + • • • • = H+ + AB + H+ = HB+ B + HA = HB+ + AHA Ka 1/K'a Keq= Ka * 1/Ka’ pKeq = pKa - pK'a App 2: How do you predict the pH of a buffered solution knowing pKa’s and concentrations? (Henderson-Hasselbach) ++ pH = pKa - log [HA]/[A-] So what does this have to do with Amino Acids? • Asp has three titratable groups – HA1 is -COOH carboxy group 2.09 – HA2 is -COOH R group 3.86 – HA3 is -NH3+ amino terminal 9.82 •What species coexist at pH = 7? log [A-]/[HA] = pH - pKa carboxy Log (A1-/HA1) =7.00-2.09 = 5.91 R group Log (A2-/HA2) =7.00-3.86 = 3.14 Amino Log (A3/HA3+)=7.00-9.82 = -2.82 •At what pH would asp be a good buffer? (a good buffer resists changes in pH with addition of acid/base) • Asp – pKa 1 -CO2H – pKa 2 -CO2H – pKa 3 -NH3+ pKa 2.09 3.86 9.82 A: when pH = pKa, so the 3 pHs at left see graph At what pH are amino acids neutral? • Isoelectric point (pI) is pH at which molecule has no net charge. • pI is calculated by averaging pKa’s on either side of neutral form of molecule. For simple ser, where there are no titratable side groups. pI = 5.68 At what pH would Asp be neutral? Will pI of asp be higher or lower than ser (5.68)? • Expect pI to be lower than ser since there’s an extra group (the R group) that goes from neutral to negative when it titrates. • You have to go to lower pH to have the molecule have no charge. • Which titrations in asp bring it from + to - in net charge? • pH 1 3 5 11 • carboxy2.09 neu. neg neg neg. • R group3.86 neu neu neg neg • amino9.82 pos pos pos neu • net +1 0 -1 -2 •So, pI for asp is (2.09 + 3.86)/2 = 2.97 •So yes, this is indeed lower than pI for serine. Acid Base Behavior Charge is Critical to Function • Isoelectric Precipitation: Amino acids with net charges repel each other and do not easily crystallize from solution - solubility is lowest at the isoelectric point • CaM, protein that binds to Ca+2 ions, pI= 3, this protein has many many negative side groups such as glu and asp. At neutral pH, CaM is very negatively charged (-27). • Histones, proteins that bind to DNA (polyanion) have very high pI, 10 - 11 because they must be positively charged at neutral pH to bind to DNA Clip this and put it in the front of your notebook, or in your wallet, or under your pillow so that you’ll learn the one and three letter codes for the amino acids and their chemical structures. Short hand code for the structure of the individual amino acids

BioChem 330 - Course Outline Bio-molecular Structure Function (I) Aminoacids

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