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10. Amino acids/Proteins Chapter 17

10. Amino acids/Proteins Chapter 17. Protein - More than an Energy Source. Proteins / polypeptides - chains formed by the condensation/combination of 20 different  - amino acids. Polypeptides - may be di-, tri -, etc; up to 10 a.a.

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10. Amino acids/Proteins Chapter 17

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  1. 10. Amino acids/Proteins Chapter 17

  2. Protein - More than an Energy Source Proteins / polypeptides - chains formed by the condensation/combination of 20 different  - amino acids. • Polypeptides - may be di-, tri -, etc; up to 10 a.a. • Proteins - longer than 10 a.a. units; ie. MW>10,000

  3. Amino Acids - Protein building blocks An amino acid is a compound having both a carboxyl group(-COOH) and an amino group(-NH2). H H2N C COOH R All amino acids from protein have the -NH2 attached at the C  to the –COOH (as well as the H- & R-). All naturally occurring -amino acids, except glycine (R=H), are chiral and the ‘L’ stereoisomer.

  4. H H2N C COOH R There are 20 -amino acids in naturally occurring protein. By convention the -NH2is placed ‘to the left’. Each aa has a ‘common’ name often ending in ‘-ine’. There are ~150 other physiologically important amino acids, GABA (a neurotransmitter).

  5. Amino Acids - 1

  6. Amino Acids - 2

  7. Amino acids • Contain both an acidic functional group (COOH) and a basic one (-NH2), NH or N • Thus reactions are highly pH dependent

  8. pH dependent properties • Zwitterionic structures contain both N-H+ and COO-. • At low pH, protonate COO-. • At higher pH : lose H on N • Isoelectric pH: differs for each amino acid (due to structural differences)

  9. Leucine ionic forms • Cation below pH 2.4 • Neutral between pH 2.4 and 9.6 • Anionic above pH 9.6

  10. Leucine zwitterion • pH>2.4 • pH < 9.6

  11. Peptides – Buildup/Breakdown

  12. Dipeptides • Consider the 2 amino acids glycine (G) and alanine (A). • How many dipeptides can be made if these are randomly mixed? • GG, AA, GA and AG • N terminal on LHS; C terminal on RHS

  13. Tripeptides • Consider amino acids Glycine (G), Alanine (A) and Phenylalanine (P) • How many different tripeptides are possible if each amino acid must be present?

  14. Possible tripeptides • 3 choices for the N-terminal amino acid • 2 choices for middle • 1 choice for the C terminal amino acid • Thus 3 x2 x1 =6 choices if each aa must be present. • But total number possible is 3 x3x3 =27; includes AAA, PPP, GGG etc

  15. Protein Structure • The only unambiguous way to determine the overall structure of any molecule is………….. • Sequence of amino acids can be determined using the enzyme carboxypeptidase (cleaves one aa at a time from the C terminal end)

  16. Levels of Protein Structure Primary structure - the sequence of amino acids inthe peptide chain and the location of the disulfide bridges. Secondary structure - a description of the conformation/ shape of the backbone of the protein. Tertiary structure - a description of the 3D structure of the entire polypeptide. If the protein has more than one chain it can have a quaternary structure.

  17. Some Protein Sequences Oxytocin – contracts smooth muscle (induces ‘labour’) Phe - Gln Tyr Asn Cys Cys- S-S Pro - Arg - Gly Ile - Gln Tyr Asn Cys Cys- S-S Vasopressin - diuretic Pro - Leu - Gly

  18. Val- Glu Gln Ile-Gly Insulin (21 + 30) CysCys-Ser-Leu-Tyr-Gln-Leu-Glu-Asn-Tyr-Cys-Asn Cys-Thr-Ser-Ile Cys-Gly-Ser-His-Leu-Val-Glu-Ala-Leu-Tyr-Leu-Val-Cys-Gly Glu Arg Gly Phe Leu His Gln- Asn-Val-Phe Thr-Lys-Pro-Thr-Tyr-Phe-

  19. Secondary structure of Proteins • Is the fixed arrangement of amino acids resulting from interactions between amide linkages that are close to each other in the protein chain • Interactions can be hydrogen bonds (~ 5 kcal/mol each) • Many H bonds are sufficient to define the shape

  20. Ionic Interactions in Proteins • “salt bridges” • Involve COO- and remote NH3+ groups • Along with H bonding and dispersion forces, these are responsible for the overall shape or “conformation” of the protein

  21. Secondary (20) Structure - sheets H – bond sheets/strands, eg. fingernails, silk

  22. Secondary Structure(20) - the -Helix H-bonding - intramolecular

  23. Tertiary Structure of Proteins • Arises from weaker attractive forces (non polar dispersion forces) between hydrophobic parts of the same chain that are widely separated in the primary structure, but close in space • “intramolecular” • Results in chain twisting and folding

  24. Dispersion forces • Attractive when nuclei are separated by the sum of their van der Waals radii

  25. Tertiary structure of protein: braids and globs • Collagen-a fibrous protein (precursor of gelatin) has a triple helix structure-some elasticity due to interchain interactions • Hemoglobin (a globular protein)

  26. Tertiary Structure (30) - braids & globs collagen hemoglobin

  27. Hemoglobin(H) and Myoglobin (M) • H has 4 polypeptide chains : carries O2, CO2 and H+ in the blood, and possesses quaternary structure • M has a single chain of 153 amino acids: carries O2 from the blood vessels to the muscles and stores it until needed. • Both have Fe II containing heme unit in each chain that binds O2.

  28. Myoglobin Structure

  29. To summarize • Myoglobin cannot have quaternary structure since it has only one polypeptide chain • Hemoglobin has 4 polypeptide chains and possesses quaternary structure

  30. Enzyme structure • Many enzymes are proteins and their specific binding properties to a substrate depend on their overall molecular shape or “conformation” Lock and key mechanism for activity

  31. Active Site of Enzymes

  32. Denaturation - any physical or chemical process that changes the protein structure and makes it incapable of performing its normal function. Whether denaturation is reversible depends on the protein and the extent of denaturation. Examples:·heating egg whites (irreversible) ·‘permanent’ waving of hair (reversible)

  33. Protein Chemistry and your hair • Forces combining to keep hair (a) straight (b) in loose waves or (c) in tight curls are: • Disulfide linkages (part of 10 structure) • Salt bridges • Hydrogen bonds

  34. Protein in Human hair • Keratin (fibrous protein) has the S containing amino acid cystine (14~18%) . • S-S bonds (disulphide linkages) between cystine units give hair its strength by connecting the strands and keeping them aligned

  35. Removing the grey (Grecian Formula) • Active constituent is lead acetate • Reacts with the disulfide links in keratin to produce what black compound? • Also does some structural damage

  36. Animal hair protein composition • Sheep’s wool: also the fibrous protein keratin, but with high glycine & tyrosine content

  37. Do you want change a bad hair day?

  38. To a Good Hair day?

  39. Perm(?) – have your keratin 1o structure modified HSCH2COOH H2O2

  40. Use some Protein Chemistry on your hair! • Slightly basic solution of thioglycolic acid is used: cleaves the disulfide links and makes new SH bonds (reset hair) • Then Dilute! Peroxide used in final Oxidation step of “perm” (otherwise bleaching effect!) • Covalent S-S bonds in new positions give permanent structure (recall : position of the disulfide linkages is part of 1o structure)

  41. Hydrogen bonding and your hairdo • Hydrogen bonds N-H....O=C Between adjacent strands of fibrous protein are much weaker than the S-S covalent bonds, but there are many more hydrogen bonds, which form a large part of hair structure • Hence excess water will break these up and permit restructuring of hair upon drying • Water not strong enough to break S-S bonds

  42. Hair gels • First ingredient is water • Contain “protein mimics” • Water miscible copolymers with low melting points • Dimethylaminomethacrylate

  43. Coloured gels

  44. Protein mimics in hair gels • Y=N , thus an amide ; EO & PO are polymer chains

  45. Protein Denaturation • Heat • Mechanical agitation • pH change • Inorganic salts • polar organic solvents • Soaps and detergents

  46. Heating of protein causes denaturation • Frying eggs • Cooking meat-insoluble collagen protein is converted into soluble gelatin to be used in Jello, gravy, or glue (from horses)

  47. Mechanical Agitation • Beating egg whites-proteins denature at the surface of the air bubbles • Cream of tartar (the dipotassium salt of tartaric acid) is added to beaten egg whites to keep them stiff for mousse and meringue preparation, by raising the pH

  48. Disinfection by denaturation • Ethanol acts via denaturation of bacterial protein • Detergents and soaps disrupt association of protein sidechains of bacterial protein

  49. Protein Denaturation: Origin of Cheese? • Arab merchant carrying milk across the desert in a pouch made from sheep’s stomach • Action of heat caused milk to form a watery liquid and a soft curd with a “pleasing taste” • Rennet containing the enzyme Rennin in the sheep’s stomach caused curd formation

  50. Sour milk , Cheese • Increased amount of lactic acid (from fermentation of lactose by lactobacillus bacteria) causes lower pH • Induces protein denaturation and then coagulation • Casein proteins make up 80% of protein in skim milk • Precipitation of casein by low pH results in curds, essential to cheese making

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