1、Chapter 1 Amino acidsOutlineStructure and classification of AAProperties and function of AASeparation and purification of AAAmino acid structureDifferent side-chain (R group)Different chemical and physical propertiesAmino groupCarboxylic acid groupProteinogenic AA & non-protenogenic AAProteinogenic

2、AA or canonical AA. Encoded by genetic codes and directly introduced into protein during translationDiffer in side chain (R group) 20 commonly foundAll organisms have same set of 202 rarely found (selenocysteine and pyrrolysine)Non-proteinogenic AA or non-canonical AANever directly introduced into p

3、roteins during translationCan be naturally-occurring or chemical modifications of proteinogenic AAAmino Acid ClassificationAliphaticAromaticSulfur containingPolar/unchargedbasic/acidicHydrophobic: water fearing. non-polar side chainsHydrophillic:water loving. polar, neutral chains, negatively charge

4、d, positively charged6 Non-polar Amino Acids6 Polar, Uncharged Amino Acids3 Aromatic Amino Acids6 Polar, Charged Amino Acids21st & 22nd AAsEssential Amino AcidsAll 20 common amino acids are required for protein synthesis, but the human body is able to synthesize only 12 of them. The other 8 (the ess

5、ential amino acids) must be obtained from food, which include threonine, isoleucine, phenylalanine, methionine, tryptophan, valine, leucine, and lysine. Histidine and arginine are called semi-essential amino acids because they are also required to be obtained from food under some conditions.Abbrevia

6、tions for 22 amino acidsAlanine - Ala - A Arginine - Arg - R Asparagine - Asn - N Aspartic Acid - Asp - D Cysteine - Cys - C Glutamine - Gln - Q Glutamic Acid - Glu - E Glycine - Gly - G Histidine - His - H Isoleucine - Ile - I Leucine - Leu - L Lysine - Lys - K Methionine - Met - M Phenylalanine -

7、Phe - F Proline - Pro - P Serine - Ser - S Threonine - Thr - T Tryptophan - Trp - W Tyrosine - Tyr - Y Valine - Val - V Asparagine/Aspartic Acid - Asx - B Glutamine/Glutamic Acid - Glx - Z Selenocysteine-sec-uPyrrolysine-pyl-oDiagrammatic representation of AA classificationProperties of 20 Common Am

8、ino AcidsAmino Acids not found in ProteinsProperties of Amino AcidsCapacity to polymerizeChiralityNovel acid-base propertiesVaried structure and chemical functionalityAA Condensation and Peptide Bond FormationA Peptide Bond is an amide bond linking together amino acids forming peptides and proteins.

9、Peptide bondL-Amino AcidsSince all amino Acids but glycine are chiral molecules, its possible to have enantiomers. However, nature uses only one enantiomer, the L-amino acid.L-glyceraldehydeL-amino acidZwitterions and pIA Zwitterion is a dipolar ion. Since amino acids contain both an acid and a base

10、, an internal acid-base reaction forms a zwitterion.Amino acidZwitterionAmino acids exist primarily as zwitterions.ZwitterionsAmino acid zwitterions are amphoteric. They can react as either acids or bases.In acid solutionIn base solutionzwitterionprotonatedzwitteriondeprotonatedIsoelectric PointsThe

11、 isoelectric point of an amino acid occurs at the pH where the amino acid exists as the zwitterion.deprotonatedbase solutionhigh pHprotonated acid solutionlow pHzwitterionisoelectric pointTitration Curve for AlaninepI (isoelectric point) = the pH at which the number of positive and negative charges

12、on a population of molecules is equal (i.e. no net charge). pK1 carboxylic acid = 2pK2 amino group = 10pI = (pK1+ pK2)/2Titration Curve for Glutamic AcidpK1 carboxylic acid = 2.2pK2 R group = 4.3pK3 amino group = 9.7pI = (pK1+ pK2)/2pI = (2.2+4.3)/2pI = 3.25pK1 carboxylic acid = 2.2pK2 amino group =

13、 9.0pK3 R group = 10.5pI = (pK2+ pK3)/2pI = (9+10.5)/2pI = 9.75Titration Curve for LysineNo net chargeMinimum solubility in waterprotein will precipitate out at its isoelectric pointcan separate amino acids and peptides based in electrophoresis:+ charged amino acids move to electrode- charged amino

14、acids move to + electrode0 amino acids at their isoelectric points do not moveIsoelectric Points Reaction with NinhydrinUsed to visualize spots or bands of amino acids separated by chromatography or electrophoresis.Deep purple color formed with traces of any amino acid except Pro (yellow). Reaction

15、with HNO2 and Van Slyke DeterminationPro can not react with HNO2Reaction with DNFB and PITCUV-absorbing Properties of Amino AcidsOnly three amino acids, Phe, Tyr, and Trp, absorb light in the near UV range (230 nm-300 nm). These amino acids dominate the UV absorption spectra of proteins. The wavelen

16、gth maxima for tyrosine and tryptophan are around 280 nm. In contrast, nucleic acids have absorption maximum of 260 nm. Thus a simple UV scan can allow one to distinguish between protein and nucleic acids. Functional Significance of AA R-Groups In solution it is the nature of the amino acid R-groups

17、 that dictate structure-function relationships of peptides and proteins. The hydrophobic amino acids will generally be encountered in the interior of proteins shielded from direct contact with water. Conversely, the hydrophilic amino acids are generally found on the exterior of proteins as well as i

18、n the active centers of enzymes. The imidazole ring of histidine allows it to act as either a proton donor or acceptor at physiological pH. Hence, it is frequently found in the reactive center of enzymes. The primary alcohol of serine and threonine as well as the thiol (-SH) of cysteine allow these

19、amino acids to act as nucleophiles during enzymatic catalysis. Additionally, the thiol of cysteine is able to form a disulfide bond with other cysteines: Cysteine-SH + HS-Cysteine Cysteine-S-S-CysteineDisulfide bonding between cysteines in different polypeptide chains of oligomeric proteins plays a

20、crucial role in ordering the structure of complex proteins, e.g. the insulin receptor. Separation and Analysis of AA MixturesSeparating amino acids in mixtures is usually based on relative differences in their physical and chemical traits. These are all mediated by their “R” or functional groups.The general strategy is to exploit the ability of a given amino acid to partition between two different phases. It could be two liquid phases, a solid-liquid phase, or a gas-liquid phase. In particular, solid-liquid phase methods