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Amino Acids and Proteins

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1 Amino Acids and Proteins
Created By Prof. Gary F. Porter, Ph.D. Copyright © 2014 by John Wiley & Sons, Inc. All rights reserved.

2 Table of Contents (hyperlinked)
Introduction Amino Acids Synthesis of α–Amino Acids Polypeptides and Proteins Primary Structure of Polypeptides and Proteins 6. Examples of Polypeptide and Protein Primary Structure 7. Polypeptide and Protein Synthesis 8. Secondary, Tertiary, and Quaternary Structures of Proteins 9. Introduction to Enzymes 10. Lysozyme: Mode of Action of an Enzyme 11. Serine Proteases 12. Hemoglobin: A Conjugated Protein 13. Purification and Analysis of Polypeptides and Proteins 14. Proteomics © 2014 by John Wiley & Sons, Inc. All rights reserved.

3 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Introduction Amino acids are the monomeric unit for proteins. Proteins are polyamides. There are 20 different α amino acids, and 4 levels of protein structure. © 2014 by John Wiley & Sons, Inc. All rights reserved.

4 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Introduction The α carbon has the L configuration. © 2014 by John Wiley & Sons, Inc. All rights reserved.

5 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids 2A. Structures and Names The four classes of amino acids are: Neutral, Nonpolar Neutral, Polar Charged Positive, Polar Acidic (at pH 7) Charged Negative, Polar Basic (at pH 7) © 2014 by John Wiley & Sons, Inc. All rights reserved.

6 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids © 2014 by John Wiley & Sons, Inc. All rights reserved.

7 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids © 2014 by John Wiley & Sons, Inc. All rights reserved.

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Amino Acids © 2014 by John Wiley & Sons, Inc. All rights reserved.

9 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids © 2014 by John Wiley & Sons, Inc. All rights reserved.

10 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids © 2014 by John Wiley & Sons, Inc. All rights reserved.

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Amino Acids 2B. Essential Amino Acids Are not synthesized by higher animals The Essential Eight Valine Tryptophan Leucine Threonine Isoleucine Methionine Phenylalanine Lysine © 2014 by John Wiley & Sons, Inc. All rights reserved.

12 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids 2C. Amino Acids as Dipolar Ions Contain a basic group (-NH2) and an acidic group (-CO2H), and Exist as dipolar ions at physiological pH Dipolar ions are also called zwitterions. Isoelectric point (pI) is the pH at which the net charge on an amino acid is 0. © 2014 by John Wiley & Sons, Inc. All rights reserved.

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Amino Acids Alanine © 2014 by John Wiley & Sons, Inc. All rights reserved.

14 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids Note the titration curve for Alanine below. As base is added and pH is increased, the net charge on Alanine goes from positive to negative. © 2014 by John Wiley & Sons, Inc. All rights reserved.

15 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Amino Acids Practice Problem 24.1 What form of glutamic acid would you expect to predominate in (a) strongly acidic solution, (b) strongly basic solution, and (c) at its isoelectric point (pI 3.2)? (d) The isoelectric point of glutamine (pI 5.7) is considerably higher than that of glutamic acid. Explain. Practice Problem 24.2 The guanido group of arginine is the most strongly basic of all organic groups. Explain. © 2014 by John Wiley & Sons, Inc. All rights reserved.

16 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Synthesis of α–Amino Acids 3A. From Potassium Phthalimide Methionine Synthesis © 2014 by John Wiley & Sons, Inc. All rights reserved.

17 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Synthesis of α–Amino Acids 3B. The Strecker Synthesis treat aldehyde with NH3 and HCN, and produce an α amino acid. © 2014 by John Wiley & Sons, Inc. All rights reserved.

18 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Synthesis of α–Amino Acids Practice Problem 24.4 (a) Outline a Strecker synthesis of dl-phenylalanine. (b) DL-Methionine can also be synthesized by a Strecker synthesis. The required starting aldehyde can be prepared from acrolein (CH CHCHO) and methanethiol (CH3SH). Outline all steps in this synthesis of DL-methionine. © 2014 by John Wiley & Sons, Inc. All rights reserved.

19 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Synthesis of α–Amino Acids 3C. Resolution of DL-Amino Acids The two steps involve acylation with the amine, and resolving with deacylase enzyme. © 2014 by John Wiley & Sons, Inc. All rights reserved.

20 No. of Amino Acids linked together
Polypeptides and Proteins Peptides – are amino acids joined together to form a molecule. Peptide Bonds – are amide linkages between the amino acids. C terminus on right N terminus on left No. of Amino Acids linked together Name 2 Dipeptide 3 Tripeptide 3-10 Oligopeptide Multiple polypeptides Protein © 2014 by John Wiley & Sons, Inc. All rights reserved.

21 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Polypeptides and Proteins 4A. Hydrolysis Peptide bond cleavage occurs in 6 M HCl for 24 h. AAs separate on cation-exchange resin. AAs will bind at low pH Amino Acids (AA) AAs release as pH increases. Resin © 2014 by John Wiley & Sons, Inc. All rights reserved.

22 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Polypeptides and Proteins Detect AAs Ninhydrin Reagent λmax = 570nm Formation of blue complex occurs with this reagent. © 2014 by John Wiley & Sons, Inc. All rights reserved.

23 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Primary Structure of Polypeptides and Proteins Primary Structure is defined by the molecular weight, amino acid composition, and amino acid sequence. Edman Degradation Involves identification of N-Terminus, sequential degradation of AAs from N- terminus, And is good up to 60 AAs. © 2014 by John Wiley & Sons, Inc. All rights reserved.

24 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Primary Structure of Polypeptides and Proteins 5A. Edman Degradation © 2014 by John Wiley & Sons, Inc. All rights reserved.

25 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Primary Structure of Polypeptides and Proteins 5B. Sanger N-Terminus Analysis involves sequential Analysis, and use of a 2,4-dinitro-flourobenzene dye. © 2014 by John Wiley & Sons, Inc. All rights reserved.

26 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Primary Structure of Polypeptides and Proteins 5C. C-Terminus Analysis uses carboxypeptidases, continually cleaves carboxyl AAs, and can only be used with smaller peptide chains. © 2014 by John Wiley & Sons, Inc. All rights reserved.

27 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Primary Structure of Polypeptides and Proteins 5D. Complete Sequence Analysis starts with C & N Terminus Identification followed by fragment analysis Practice Problem 24.9 © 2014 by John Wiley & Sons, Inc. All rights reserved.

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Primary Structure of Polypeptides and Proteins 5E. Peptide Sequencing Use Mass Spectrometry and Sequence Databases Ladder Sequence uses carboxypeptidases, analyzes the molecule weight of the polypeptides (PPs) which have been degraded, and each PP is one AA larger than the last. Tandem Mass Spectrometry analyzes fragments generated by MS. Partial Hydrolysis and Sequence Comparison is used for analyzing small chains within known PP databases, and identification of a known PP is possible. © 2014 by John Wiley & Sons, Inc. All rights reserved.

29 © 2014 by John Wiley & Sons, Inc. All rights reserved.
6. Examples of Polypeptide and Protein Primary Structure 6A. Oxytocin and Vasopressin Oxytocin stimulates uterine contractions during childbirth. Vasopressin stimulates peripheral blood vessel contraction. © 2014 by John Wiley & Sons, Inc. All rights reserved.

30 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Examples of Polypeptide and Protein Primary Structure 6B. Insulin is secreted by pancreas, and regulates (lowers) blood glucose. Thousands of other polypeptides and protein structures are known. © 2014 by John Wiley & Sons, Inc. All rights reserved.

31 © 2014 by John Wiley & Sons, Inc. All rights reserved.
7. Polypeptide and Protein Synthesis Protecting Groups Used to prevent C-terminus from reacting with N-Terminus. Examples of N-Terminus protecting groups are below. © 2014 by John Wiley & Sons, Inc. All rights reserved.

32 © 2014 by John Wiley & Sons, Inc. All rights reserved.
7. Polypeptide and Protein Synthesis © 2014 by John Wiley & Sons, Inc. All rights reserved.

33 © 2014 by John Wiley & Sons, Inc. All rights reserved.
7. Polypeptide and Protein Synthesis 7B. Activation of the Carboxyl Group is needed to get the C-Terminus to react, form an anhydride, and uses ethyl chloroformate. © 2014 by John Wiley & Sons, Inc. All rights reserved.

34 © 2014 by John Wiley & Sons, Inc. All rights reserved.
7. Polypeptide and Protein Synthesis 7C. Peptide Synthesis Involves several steps: N-Terminus Protection C-Terminus Activation Amino Acid Addition © 2014 by John Wiley & Sons, Inc. All rights reserved.

35 © 2014 by John Wiley & Sons, Inc. All rights reserved.
7. Polypeptide and Protein Synthesis 7D. Automated Peptide Synthesis Involves solid phase addition, addition of AA, and followed by wash. High yield at each step is realized © 2014 by John Wiley & Sons, Inc. All rights reserved.

36 © 2014 by John Wiley & Sons, Inc. All rights reserved.
8. Secondary, Tertiary, and Quaternary Structures of Proteins Secondary Structure is defined by local conformation of polypeptides. Specific types are α helix, β sheets, and coil or loop. Rotation AA have limited or no rotation. The side groups have free rotation. There is free rotation about the Peptide bond. © 2014 by John Wiley & Sons, Inc. All rights reserved.

37 © 2014 by John Wiley & Sons, Inc. All rights reserved.
8. Secondary, Tertiary, and Quaternary Structures of Proteins Secondary Structure β pleated sheet (below) has high nonpolar AA content, and predominates in silk. α helix (right) has 3.6 AA’s per right handed turn, and is in fibrous proteins. © 2014 by John Wiley & Sons, Inc. All rights reserved.

38 © 2014 by John Wiley & Sons, Inc. All rights reserved.
8. Secondary, Tertiary, and Quaternary Structures of Proteins 8B. Tertiary Structure has a three dimensional shape that arises from secondary structures orientation to each other, and results in two classes of proteins. Fibrous Proteins have mainly α helices. Globular Proteins have all types of secondary structure. AA classes have specific locations: nonpolar in the interior and polar in the exterior. © 2014 by John Wiley & Sons, Inc. All rights reserved.

39 © 2014 by John Wiley & Sons, Inc. All rights reserved.
8. Secondary, Tertiary, and Quaternary Structures of Proteins Carbonic Anhydrase Myoglobin © 2014 by John Wiley & Sons, Inc. All rights reserved.

40 © 2014 by John Wiley & Sons, Inc. All rights reserved.
8. Secondary, Tertiary, and Quaternary Structures of Proteins 8C. Quaternary Structures Three dimensional shape that arises from polypeptide chain orientation to each other. See the four polypeptide chains of hemoglobin to the right. © 2014 by John Wiley & Sons, Inc. All rights reserved.

41 © 2014 by John Wiley & Sons, Inc. All rights reserved.
9. Introduction to Enzymes Enzymes catalyze all chemical reactions found in cellular metabolism, have highly specific reactants called substrates, form an enzyme-substrate complex, and are stereospecific. Enzyme-substrate complex induces conformational changes in the enzyme, is the place where the reaction is catalyzed, and resides within the active site. © 2014 by John Wiley & Sons, Inc. All rights reserved.

42 © 2014 by John Wiley & Sons, Inc. All rights reserved.
9. Introduction to Enzymes Competitive Inhibitors have a similar structure to substrate and binds to the active site instead of the substrate. Cofactors is an extra molecule required for enzyme activity. i.e. metal ions Coenzyme – Organic cofactor © 2014 by John Wiley & Sons, Inc. All rights reserved.

43 © 2014 by John Wiley & Sons, Inc. All rights reserved.
10. Lysozyme: Mode of Action of an Enzyme Lysozymes cleave the cell wall of gram positive bacteria. Lysozymes hydrolyze the glycosidic linkages in peptoglycans. Blue AAs are found at the active site. © 2014 by John Wiley & Sons, Inc. All rights reserved.

44 © 2014 by John Wiley & Sons, Inc. All rights reserved.
10. Lysozyme: Mode of Action of an Enzyme Below is the substrate that Lysozyme reacts with. © 2014 by John Wiley & Sons, Inc. All rights reserved.

45 © 2014 by John Wiley & Sons, Inc. All rights reserved.
10. Lysozyme: Mode of Action of an Enzyme Below is the AA in Lysozyme that reacts with the substrate. © 2014 by John Wiley & Sons, Inc. All rights reserved.

46 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Serine Proteases Pancreatic digestive enzymes Chymotrypsin is activated from Chymotrypsinogen is a peptidase Catalytic triad - Asp 102, His 57, Ser 195 The triad only forms in Chymotrypsin The inactive form exists in the pancreas to avoid damage © 2014 by John Wiley & Sons, Inc. All rights reserved.

47 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Serine Proteases The active site © 2014 by John Wiley & Sons, Inc. All rights reserved.

48 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Hemoglobin: A Conjugated Protein Hemoglobin is a conjugated protein with a nonprotein prosthetic group. Heme is the prosthetic group. Fe2+ © 2014 by John Wiley & Sons, Inc. All rights reserved.

49 © 2014 by John Wiley & Sons, Inc. All rights reserved.
13. Purification and Analysis of Polypeptides and Proteins 13A. Purification Involves chemical and chromatographic means. Depends upon molecular weight pI, and stability. © 2014 by John Wiley & Sons, Inc. All rights reserved.

50 © 2014 by John Wiley & Sons, Inc. All rights reserved.
13. Purification and Analysis of Polypeptides and Proteins 13B. Analysis Methods Gel Electrophoresis (based upon pI) Mass Spectroscopy Obtains molecular weight Electrospray Ionization (ESI) uses peak corresponds to m/z ratio and mixtures separated by HPLC Matrix-assisted Laser Desorption Ionization (MALDI) Used for ionization of nonvolatile molecules © 2014 by John Wiley & Sons, Inc. All rights reserved.

51 © 2014 by John Wiley & Sons, Inc. All rights reserved.
Proteomics Involves the identification, structure, and function of proteins © 2014 by John Wiley & Sons, Inc. All rights reserved.

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