2. 5.1 Identity and Roles of Amino Acids Contain an amine group – Primary amine group Contain carboxyl group – Referred to as the alpha carbon R group – Variable group – 20 different groups

4. 5.1 Identity and Roles of Amino Acids Stereochemistry – All amino acids but one are chiral – Stereochemistry is L

6. 5.2 Amino Acid Individuality: The R Groups Polarity differs – Polar Amino Acids Neutral Acidic Basic – Nonpolar Alkyl Branched Aromatics Unique

7. 5.2 Amino Acid Individualities Functional Groups – Acid Groups Aspartate, Glutamate, Cysteine, Histidine, Tryosine – Basic Groups Lysine, Arginine, Histidine – Hydroxyl Groups Serine, Threonine, Tyrosine – Sulfur Groups Cysteine, Methionine

9. 5.3 Acid – Base Properties and Charge Titration and Net Charge – Henderson – Hasselbach equation illustrates the relationship between acid – base dissociation and charge – Amino acids have more than one dissociable group

12. 5.3 Acid – Base Properties and Charge Zwitterions – Two charged groups, but overall charge is zero – Most amino acids are in this form Zwitterions lead to altered pK values

14. 5.3 Acid – Base Properties and Charge Isoelectric point – pH at which zwitterion is exactly zero – Referred to as pI R groups can have dissociable groups – Acid, basic and sulfhydro groups

15. 5.4 The Peptide Bond Covalent bond between amino group and alpha carboxyl group Dehydration reaction Referred to as amide or peptide bond

17. 5.4 The Peptide Bond Resonance properties – O, C and N bonds are delocalized – Creates partial double bond

18. 5.4 The Peptide bond Amine and carboxyl groups are no longer acids or bases N- terminal end is only amino group not in peptide bond C- terminal end is only carboxyl group not in peptide bond

19. 5.5 Peptides and Proteins Peptide – short chain or less than 25 amino acids – Can have biological properties Protein – more than 25 amino acids Referred to as macromolecules – Are polymers

21. 5.6 Levels of protein structure 4 levels of hierarchy – Primary – Secondary – Tertiary – Quaternary

22. 5.6 Levels of Protein Structure Primary – Sequence of amino acids – Complete description for peptides – Determines its complete spatial arrangement

23. 5.6 Levels of Protein Structure Secondary – Regular repeating structures – Three main types Alpha helix – spiral chain – Hydrogen bonds satisified intramolecular – R groups determine water solubility – Certain amino acids favor – Certain amino acids are helix breakers

24. 5.6 Levels of Protein Structure – Three main types cont. Beta sheets – Resembles corrugate plate – Hydrogen bonds between backbone peptide bonds – Anti parallel and parallel forms Loops and Random Coils – Indeterminate in structure – Serve to link other secondary structures

26. 5.6 Levels of Protein Structure Tertiary – Three dimensional arrangement Quaternary – Three dimensional arrangement of multi subunit proteins – Individual protein chains

27. 5.6 Levels of Protein Structure Domains – Combination of secondary structural elements – Also referred to as motifs or super secondary structure

28. 5.6 Levels of Protein Structure Domain examples – TIM domain – SH2 domain – PTB domain – NAD binding domain – EF hand domain

31. 5.7 – Protein folding Two studies helped increase our understanding RNase experiment – Enzyme was inactivated with heat and then cooled – On cooling activity resumed – Suggest we can denature and refold a protein GroEL experiment – Helps protein fold correctly – Increases rate – Often referred to as a chaperone protein

33. 5.8 Oxygen binding in myoglobin and hemeglobin Myoglobin (Mb) and Hemeglobin (Hb) are oxygen binding proteins in mammals Similar protein structures – Mb – single chain Tightly bound to heme – Hb – four chains 2 Alpha and 2 Beta chains 4 heme molecules bind

34. 5.8 Oxygen binding in myoglobin and hemeglobin Heme – Prosthetic group that binds oxygen – Four linked pyrrole rings – Each Nitrogen is chelated to central Iron

35. 5.8 Oxygen binding in myoglobin and hemeglobin Binding of oxygen occurs differently – Fractional saturation of oxygen – Y = [MbO 2 ]/([Mb] + [MbO 2 ]) – Mb stores oxygen in muscle cells Releases when levels become depleted

36. 5.8 Oxygen binding in myoglobin and hemeglobin – Hb binds oxygen with positive cooperatively When one oxygen binds, it helps the other oxygen bind S shaped curve Saturated with oxygen in the lungs and releases in tissue capillaries

38. 5.8 Oxygen binding in myoglobin and hemeglobin Bohr effect – Diminished binding of oxygen when increased pH – Adaptation at high altitudes 2,3 Bisphophoglycerate – Lowers binding of O2 to hemeglobin – Provides more oxygen to tissues

39. 5.9 Protein purification and Analysis Purification – Extraction comes first Properties must be intact – Must have way to measure protein – Must minimize denaturation

40. 5.9 Protein purification and Analysis – Physical methods are often used – Fractionation depends on differences between proteins Solubility Size Charge

41. 5.9 Protein purification and Analysis Types of chromatography that may be used – Ion exchange column chromatography – Size Exclusion chromatography – High Pressure Liquid Chromatography – Gas Liquid Chromatography – Affinity Chromatography

43. 5.9 Protein purification and Analysis Analysis – UV light Tryptophan and tyrosine absorb Can estimate amount of protein – NMR Great for small molecule

44. 5.9 Protein purification and Analysis Analysis cont. – X-Ray Produce pattern of diffraction Mathematical manipulation – Mass Spectrometry – Electrophoresis Can identify various proteins present Can be a test of purity