1. 5P2-1 Chapter 5: Outline Amino Acids Amino acid classesStereoisomers Bioactive AATitration of AA Modified AAAA reactions Peptides Proteins (We are here) Protein structure Fibrous proteins Globular proteins

2. 5P2-2 Protein Function 1.Catalysis 2. Structure 3. Movement 4. Defense 5. Regulation 6. Transport 7. Storage 8. Stress Response

3. 5P2-3 Proteins by Shape-1 Fibrous proteins exist as long stranded molecules: Eg. Silk, collagen, wool. A collagen segment in space-filling mode illustrates this point. Red spheres represent oxygen, grey carbon, and blue nitrogen

4. 5P2-4 Proteins by Shape-2 Globular proteins have somewhat spherical shapes. Most enzymes are globular. Eg. myoglobin, hemoglobin. Myoglobin in space-filling mode is the chosen example.

5. 5P2-5 Proteins by Composition Simple Contain only amino acids Conjugated simple protein (apoprotein) prostetic group (nonprotein) glycoproteins lipoproteins metaloproteins etc. Holo- protein

6. 5P2-6 Four Levels of Protein Structure Primary, 1 o the amino acid sequence Secondary, 2 o 3-D arrangement of backbone atoms in space Tertiary, 3 o 3-D arrangement of all the atoms in space Quaternary, 4 o 3-D arrangement of subunit chains

7. 5P2-7 Determining Primary Structure 1. Hydrolyze protein with hot 6M HCl. Identify AA and % of each. Usually done by chromatography 2. Identify the N-term and C-term AAs C-term via carboxypeptidase N-term via Sanger’s Reagent, DNFB 2,4-dinitrofluorobenzene Often step 2 can be skipped today.

8. 5P2-8 Det. Primary Structure: 2 3. Selectively fragment large proteins into smaller ones. Eg. Tripsin: cleave to leave Arg or Lys as C-term AA Eg. Chymotrypsin: cleave to leave Tyr or Trp or Phe as C-term AA Eg. Cyanogen bromide cleaves at internal Met leaving Met as C-term homoserine lactone

9. 5P2-9 Det. Primary Structure: 3 4. Determine AA sequence of peptides with AA sequencer using Edman’s reagent: phenyl isothiocyanate which reacts with the N-term AA See the next slide

10. 5P2-10 Det. Primary Structure: 3b protein Edman’s reagent Phenylthiohydantoin (PTH) derivative of N-term AA Thiazoline derivative

11. 5P2-11 Det. Primary Structure: 4 5. Reassemble peptide fragments from step 3 to give protein. An example follows on the next slide.

12. 5P2-12 Det. Primary Structure: 4b A twelve AA peptide was hydrolyzed. Trypsin hydrolysis: Leu-Ser-Tyr-Gly-Ile-Arg Thr-Ala-Met-Phe-Val-Lys Chymotrypsin hydrolysis Val-Lys-Leu-Ser-Tyr Gly-Ile-Arg Thr-Ala-Met-Phe Deduce the AA sequence One is C-term Lys is internal !

13. 5P2-13 Det. Primary Structure: 4c Tr Leu-Ser-Tyr-Gly-Ile-Arg Ct Gly-Ile-Arg Ct Val-Lys-Leu-Ser-Tyr Tr Thr-Ala-Met-Phe-Val-Lys Ct Thr-Ala-Met-Phe The complete sequence is: Thr-Ala-Met-Phe-Val-Lys-Leu-Ser-Tyr-Gly-Ile-Arg Keeping in mind the N-term AA and overlaping the sequences properly gives:

14. 5P2-14 Secondary Structure The two very important secondary structures of proteins are:  -helix  -pleated sheet Both depend on hydrogen bonding between the amide H and the carbonyl O further down the chain or on a parallel chain.

15. 5P2-15  Helix: Peptide w Hbonds First six C=O to N hydrogen bonds shown

16. 5P2-16  Sheet: stick form Protein G Chain 1 H bonds in dotted red-blue Chain segment 1 Seg 2 Seg 3 Seg 4 H bonds shown in dotted red-blue

17. 5P2-17 B Sheet: Lewis Structure Parallel sheet Antiparallel sheet

18. 5P2-18 Supersecondary Structure Reverse turns in a protein chain allow helices and sheets to align side-by-side Common AA found at turns are: glycine: small size allows a turn proline: geometry favors a turn

19. 5P2-19 Supersecondary Structure: 2 Combinations of  helix and  sheet.    meander

20. 5P2-20 Tertiary Structure The configuration of all the atoms in the protein chain: side chains prosthetic groups helical and pleated sheet regions

21. 5P2-21 Tertiary Structure: 2 Protein folding attractions: 1. Noncovalent forces a. Inter and intrachain H bonding b. Hydrophobic interactions c. Electrostatic attractions + to - ionic attraction d. Complexation with metal ions e. Ion-dipole 2. Covalent disulfide bridges

22. 5P2-22 Tertiary interactions: diag. ionic disulfide hydrophobic H bonds or dipole Ion-dipole metal coord’n

23. 5P2-23 Domains Domains are common structural units within the protein that bind an ion or small molecule.

24. 5P2-24 Quaternary Structure-1 Quaternary structure is the result of noncovalent interactions between two or more protein chains. Oligomers are multisubunit proteins with all or some identical subunits. The subunits are called protomers. two subunits are called dimers four subunits are called tetramers

25. 5P2-25 Quaternary Structure-2 If a change in structure on one chain causes changes in structure at another site, the protein is said to be allosteric. Many enzymes exhibit allosteric control features. Hemoglobin is a classic example of an allosteric protein.

26. 5P2-26 Denaturation -loss of protein structure, 2 o  4 o, but not 1 o. 1. Strong acid or base 2. Organic solvents 3. Detergents 4. Reducing agents 5. Salt concentrations 6. Heavy metal ions 7. Temperature changes 8. Mechanical stress

27. 5P2-27 Denaturation-2 Denaturing destroys the physiological function of the protein. Function may be restored if the correct conditions for the protein function are restored. But! Cooling a hardboiled egg does not restore protein function!!

28. 5P2-28 Fibrous Proteins Fibrous proteins have a high concentration of  -helix or  -sheet. Most are structural proteins. Examples include: a-keratin collagen silk fibroin

29. 5P2-29 Globular Proteins Usually bind substrates within a hydrophobic cleft in the structure. Myoglobin and hemoglobin are typical examples of globular proteins. Both are hemoproteins and each is involved in oxygen metabolism.

30. 5P2-30 Myoglobin: 2 o and 3 o aspects Globular myoglobin has 153 AA arranged in eight  -helical regions labeled A-H. The prosthetic heme group is necessary for its function, oxygen storage in mammalian muscle tissue. His E7 and F8 are important for locating the heme group within the protein and for binding oxygen. A representation of myoglobin follows with the helical regions shown as ribbons.

31. 5P2-31 Some helical regions Myoglobin: 2 o and 3 o aspects Heme group with iron (orange) at the center

32. 5P2-32 The Heme Group Pyrrole ring N of His F8 binds to fifth site on the iron. His E7 acts as a ”gate” for oxygen.

33. 5P2-33 Binding Site for Heme Lower His bonds covalently to iron(II) Oxygen coordinates to sixth site on iron and the upper His acts as a “gate” for the oxygen.

34. 5P2-34 Hemoglobin A tetrameric protein two  -chains (141 AA) two  -chains (146 AA) four heme units, one in each chain Oxygen binds to heme in hemoglobin cooperatively: as one O 2 is bound, it becomes easier for the next to bind. Lengthy segments of the  and  chains homologous to myoglobin.

35. 5P2-35 Hemoglobin: ribbons + hemes Each chain is in ribbon form and color coded. The heme groups are in space filling form

36. 5P2-36 Oxygen Binding Curves Oxygen bonds differently to hemoglobin and myoglobin. Myoglobin shows normal behavior while hemoglobinn shows cooperative behavior. Each oxygen added to a heme makes additon of the next one easier. The myoglobin curve is hyperbolic. The hemoglobin curve is sigmoidal.

37. 5P2-37 Oxygen Binding Curves-2

38. 5P2-38 The Bohr Effect (H + and Hb) Lungs: pH higher than in actively metabolizing tissue. (Low H + ). Hb binds oxygen and releases H +. Muscle at Work: pH lower (H + product of metabolism). Hb releases oxygen and binds H +.