Lecture Notes on Amino Acids and Peptides | CHEM 3550, Study notes of Biochemistry

Download Lecture Notes on Amino Acids and Peptides | CHEM 3550 and more Study notes Biochemistry in PDF only on Docsity! Chapter Three Amino Acids and Peptides Spring 2011 Dr. JDavis Chapter Outline 3.1 Amino Acids (AA) exist in a 3-D world 3.2 Structure/Properties of Amino Acids • AA sides character • Nonpolar side chains • Polar side chains • Neutral side chains • Carboxyl groups/ basic side chains 3.3 Amino acids as Acids and Bases 3.4 Peptide Bonds 3.5 Peptides with biological activity. • Also: A few Miscellaneous topics Sic — E =i Ro = or ee Ten am RLS, ies ae EA |i cot cS _ I oe Clarbwox yl romp Sool 3a 1l—za cd —Ss tick ARMIIEGreS zeecctds we awacocdeI tetrahearal sSstrwcti1res S Cengage] Leaming Names/Abbreviations of Amino Acids • Amino acids referred to by three-letter, shorthand abbreviations and by one-letter codes. • See Table 3.1 • All AA Complete structures also shown below and in the Appendix. • Students: learn the names and 3-letter symbols. Amino Acid Three-Letter Abbreviation ‘One-Letter Abbreviation Alanine Ala A Arginine Arg R Asparagine Asn N Aspartic acid Asp D Cysteine Cys Cc Glutamic acid Glu E Glutamine Gln Q Glycine Gly G Histidine His H Isoleucine Tle I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro - Serine Ser Ss Threonine Thr rr Tryptophan Trp Ww Tyrosine Tyr x Valine Val Vv Note: One-letter abbreviations start with the same letter as the name of the amino acid where this is possible. When the names of several amino acids start with the same letter, phonetic names (occasionally facetious ones) are used, such as Rginine, asparDic, Fenylalanine, tWfyptophan. Where two or more amino acids start with the same letter, itis the smallest one whose one-letter abbreviation matches its first letter. © Brooks/Cole, Cengage Learning Table 3-1, p. 69 3.2 Structures/Properties of Amino Acids General structure of amino acids in proteins  The – COOH group is acidic.  The amino group [-NH2] is basic].  Both groups are ionized at pH 7.4.  WHY?? Un-ionized AA correct ionic structure Structures/Properties of Amino Acids Classification of Amino Acids • R groups: vary in Size, Polarity, Charge and Chemical reactivity. • Classification format based on: a) polarity of the side chain R groups, plus b) presence of acidic/basic groups on side chains. Group 1: Nonpolar (hydrophobic) Group 2: Electrically neutral, polar R groups Group 3: Carboxylic acid R groups (Acidic) Group 4: Basic R groups • STUDENTS: learn these 4 classifications and the names of ~2 representative examples from each group!!! Also: Be familiar with each group’s general structural features. Q Non-polar (hydrophobic) ] cOo- l | ) HNC -H ; CHs | ) | | CH, | | | 5 | > | | CH, | ) Methionine (Met, M) , Tryptophan (Trp, W) ) per | coo- | | a | H,N'—C -H | ) CH, | HC—¢—H | | ) ye | 3 | CH, Phenylalanine (Phe, F) | ) Isoleucine (Ile, I) | © Brooks/Cole, Cengage Leaming Non-polar (Hydrophobic) - Il Fig. 3-3a (2), p. 68 Structures of Amino Acids Group 2: Neutral; Polar side chains — Ser, Thr, Tyr, Cys, Glu, and Asn. • Ser, Thr - Side chain has polar hydroxyl group • Tyr - hydroxyl group bonded to aromatic hydrocarbon group • Cysteine (Cys) - Side chain contains thiol group (-SH) • Gln, Asn - contain amide bonds in side chain**. Fig. 3-3b (1), p. 67 Polar, Uncharged AA - I Basic Amino Acids Group 4: Basic side chains – His, Lys and Arg • Side chains positively charged at pH 7 • Arg -side chain is a guanidino group • His -side chain is an imidazole group • Lys -side chain NH3 group (ε- amino group) is attached to an aliphatic hydrocarbon chain coo- H,N'‘—C —-H oO Lysine (Lys,\ Arginine (Arg, R) © Brooks/Cole, Cengage Leaming Fig. 3-3c (2), p. 68 SUMMARY: Amino acid Structures Important structural features: 1. All 20 are -amino acids; All have same basic structure. 2. For 19 of the 20 AA, the -amino group is primary; for proline, it is secondary 3. Except for glycine, the -carbon for 19/20 AA is a stereocenter (Chiral; L-configuration). • Students: See Apply your Knowledge (Q. 1, p 71). **Discovery of 2 new AA (#21 & 22)**? #21 is Selenocysteine; #22 is 1-Pyrrolysine. • Selenocysteine: found in certain mammalian enzymes, i.e., glutathione peroxidase, etc. • 1-Pyrrolysine: found in microbial enzymes. • Both aa incorporated into protein via a stop codon (termination codon) from the genetic code. Vehhhhhrry, vehhhhhry STRANGE!! Biochemical Connections (Neurophysiology) See: Biochemical Connections on pg 72. • Tryptophan (Trp): AA precursor for Serotonin • Serotonin: 1 of “big 3” neurotransmitters aka Monamines) • Mental depression associated with Serotonin deficiencies; Excess serotonin associated w. manic state? • Phe & Tyr: AA precursors for other important neurotransmitters. • Phe/Tyr  L-Dopa  Dopamine  Epinephrine • Epinephrine associated with “fight-amino acids have or-amino acids have flight” 3.3 Amino acids as Acids/Bases +1 net charge 0 net charge -1 net charge Cationic form Neutral Anionic form Isoelectric zwitterion coc) r vo H pO H,N'—C—H —+_ay—e- —_— H,N—C—H | pK, = 2.34 | pK, = 9.69 | R R R © Cengage Learning Titration of Amino Acid (Alanine) w. NaOH • Amino acid titration: Titration curve represents the reaction of each functional group (containing H+ ion) with base (OH- ion) pKa Assignments for Amino Acids • Knowing about AA structures (acidic/basic forms) and properties allows prediction of the major ionic forms present at any given pH. • Will prove important when we consider protein structure and function. • See Table 3.2 The pK values for ~20 AA found in Proteins. Basicity: Amino groups • Average value of pKa for an α-NH3+ group is ~9.47. 1. Guanidine Group (pKa ~ 12.48) • Side chain of arginine is considerably stronger base than an aliphatic amine. • Basicity of guanido group attributed to large resonance stabilization of the protonated form relative to the neutral form. 2. Imidazole Group (pKa ~ 6.0) • Side chain imidazole group of histidine is a heterocyclic aromatic amine. +2 net charge +1 net charge cit) coo" nite Mele alg cy uy UY NH VA NH je! Vf ! © 0 The ionization of histidine (an amino acid wih a titrarable side chain). & Brooks/Cole, Cengage Learning pK, =6.0 0 net charge C00" | Isoelectric zwitterion pX,=9.17 Oia aH se -] net charge COO” | H,N-—C—H CH, Yn Fig. 3-5b, p. 74 Titration of Histidine with NaOH wu CH», — CH COO- = N\-NH pK, = 1.82 CHy- Cc Coon fn aN HN NH H ® Cengage Leaming T T T T 1.0 2.0 3.0 4.0 Moles of OH” per mole of amino acid • Recall: ratio for any weak acid to its conjugate base at any pH derives from the Henderson-Hasselbalch equation (Chap. 2). • Titration curves can ALSO be obtained for amino acids and used to determine charge on amino acids at any pH also (Above). • Note: Amino acids (weak acids) can also be used as buffers. BUT………………..!! [weak acid] [conjugate base]log=pH pKa + AA and Henderson-Hasselbalch Equation Biochemical Analysis of AA mixtures Biochemical Analysis of AA mixtures AA sequence & composition of proteins determined by: a) degrading proteins to their individual AA; b) separating the individual AA, and c) identifying/quantifying each one. Detection/Analysis Techniques (1) 1) Liquid Chromatography: main technique to separate, identify and measure AA from the degraded products. 2) Ion-exchange chromatography (IEC) combined with, 3) High-Pressure Liquid Chromatography [HPLC] offers improved separation capabilities. • IEC and HPLC: very effective in separating the AA via their acid-base properties [ionic charges]. • aka Sanger’s Reagent: reacts with the amino groups forming yellow derivatives [detectable in micro-molar concentrations] by spectrophotometry. (2) 1-Fluoro-2,4-Dinitro-Benzene • Forms fluorescent amino-derivatives. • Powerful technique: “highly” sensitivity method (low detection level) • Detects nanomole (10-9 M) to picomole (10-12 M) AA levels. (3) Fluorescamine • Forms fluorescent derivatives of AA. • Detects nanomole [10-9 M] to picomole [10-12 M] levels. (4) Dansyl chloride