1. Protein : structure & function Lecture 7 Chapter 4 (part 1) Lecture 7 Chapter 4 (part 1)

2. WOW!!! Facts  Proteins are major components of all cellular systems  Proteins consist of one or more linear polymers called polypeptides  Proteins are linear and never branched  Different AA’s are linked together via PEPTIDE bonds  The individual amino acids within a protein are known as RESIDUES  The smallest known P’ is just nine residues long - oxytocin  The largest is over 25,000 residues - the structural protein titin  Proteins are major components of all cellular systems  Proteins consist of one or more linear polymers called polypeptides  Proteins are linear and never branched  Different AA’s are linked together via PEPTIDE bonds  The individual amino acids within a protein are known as RESIDUES  The smallest known P’ is just nine residues long - oxytocin  The largest is over 25,000 residues - the structural protein titin

3. WOW!!! Facts 2  Proteins are generally between 100 and 1000 residues in length.  In the absence of stabilizing forces a minimum of 40 residues is needed to adopt a stable 3D structure in water.  Protein sequence can be determined by systematically removing the AA’s one at a time from the amino end - Edman degradation  Now we just sequence the gene or cDNA for that protein and use the genetic code to determine the AA sequence  Proteins are generally between 100 and 1000 residues in length.  In the absence of stabilizing forces a minimum of 40 residues is needed to adopt a stable 3D structure in water.  Protein sequence can be determined by systematically removing the AA’s one at a time from the amino end - Edman degradation  Now we just sequence the gene or cDNA for that protein and use the genetic code to determine the AA sequence

4. Each amino acid has the same fundamental structure, differing only in the side-chain, designated the Each amino acid has the same fundamental structure, differing only in the side-chain, designated the R-group. The carbon atom to which the amino group, carboxyl group, and side chain (R-group) are attached is the alpha carbon (C).

6. 04_03_20 amino acids.jpg

7. What to learn…  You are required to learn the structure of all 20 amino acids  You are required to learn the spelling of all 20 amino acids  You are required to learn the 3 letter abbreviation of all 20 amino acids  You are required to learn the one letter abbreviation of all 20 amino acids  You are required to learn the structure of all 20 amino acids  You are required to learn the spelling of all 20 amino acids  You are required to learn the 3 letter abbreviation of all 20 amino acids  You are required to learn the one letter abbreviation of all 20 amino acids

8. 04_01_peptide bonds.jpg Peptide bond formation. Once again it is a condensation reaction

9. Each AA’ contributes three atoms to the polypeptide backbone. The side groups of adjacent AA’s protrude in an alternating manner

10. 04_04_noncovalent.jpg04_04_noncovalent.jpg Non-covalent bonds within and between P’ chains are as important in their overall conformation and function 1)Ionic bonds 2)Hydrogen bonds 3)Van der Waals forces

11. 04_05_Hydrophobic.jpg04_05_Hydrophobic.jpg The side groups of the linear unfolded polypeptide are intermingled. Only when correctly folded do we see the wonder of Nature!

12. 04_06_Hydrogen bonds.jpg The locations of the hydrogen bonds are not restricted to those between the side groups.

13. 04_07_Denatured prot.jpg The 3D folding of a P’ is governed solely by the sequence of the AA’s. Under some physiological conditions & in vitro many P’s can reversibly unfold and refold

14. Posttranslational modifications of P’s  Various AA’s are modified by enzymes after their incorporation into polypeptides  Addition of phosphate groups  Addition of methyl groups  Addition of hydroxyl groups  Formation of disulfide bonds  we learn more about these later…  Various AA’s are modified by enzymes after their incorporation into polypeptides  Addition of phosphate groups  Addition of methyl groups  Addition of hydroxyl groups  Formation of disulfide bonds  we learn more about these later…

15. cURRENT tOPICS - Prions  Prions cause diseases, but they aren't viruses or bacteria or fungi or parasites.  They are simply proteins, and proteins were never thought to be infectious on their own. Organisms are infectious, proteins are not.  ‘Mad cow’ epidemic that hit England in 1986  Scrapie in sheep and goats has the same basis.  Prions cause diseases, but they aren't viruses or bacteria or fungi or parasites.  They are simply proteins, and proteins were never thought to be infectious on their own. Organisms are infectious, proteins are not.  ‘Mad cow’ epidemic that hit England in 1986  Scrapie in sheep and goats has the same basis.

16. 04_08_Prion diseases.jpg Prions

17. Shapes & Sizes  There are more varieties of P’s in a cell than any other macromolecule  Filamentous & Globular  Large & Small  There are more varieties of P’s in a cell than any other macromolecule  Filamentous & Globular  Large & Small

18. 04_09_Proteins.jpg04_09_Proteins.jpg

19. 2 O Structure  The 2 O Structure of P’s is defined as the localized folding of domains of the polypeptide chain  -helices  -sheets  -barrels  coiled-coils  The 2 O Structure of P’s is defined as the localized folding of domains of the polypeptide chain  -helices  -sheets  -barrels  coiled-coils

20. 04_10_1_alpha h. beta s.jpg -sheets Right-handed -sheets

21. 04_10_2_alpha h. beta s.jpg Anti-parallel -sheets

22. 04_15_ahelix_lip_bilayer.j pg The helix is fundamental in allowing P’s to sit within the plasma membrane -it is the foundation of many many very important P’s - Visual Pigments - Immune cell receptors

23. 04_16_coiled-coil.jpg04_16_coiled-coil.jpg Coiled-coil - Coiled-coil - in which 2-6 alpha-helices are coiled together like the strands of a rope

24. 04_17_2 beta sheets.jpg Parallel and anti-parallel sheets

25. 04_19_functiondomains.jp g Individual P’ domains may and generally do consist of a combination of secondary structures

26. 04_20_protein domains.jpg

27. 04_21_Serine proteases.jpg Nature is known for reusing structures - P’ are no exception. Here two very similar P’s are built on a common theme but perform very different functions…

28. 04_22_protein subunit.jpg In other instances identical, or nearly identical, polypeptides are used in the final P’.In other instances identical, or nearly identical, polypeptides are used in the final P’.

29. 04_23_asymmetrical as.jpg Haemoglobin - is the iron-containing oxygen-transport metalloprotein in the red blood cells of the blood in vertebrates and other animals Here we see the use of two different polypeptides made by different genes

30. Experimental Procedures

31. 04_11_Mass spectrom.jpg 2D gel electrophoresis

32. 04_12_crystallography.jpg04_12_crystallography.jpg

33. 04_13_NMR.jpg04_13_NMR.jpg Nuclear magnetic resonance is used to elucidate the structural rigidity of P’s

35. Protein: structure and function 2 Lecture 8 Chapter 4 (remainder) Lecture 8 Chapter 4 (remainder)

36. 04_24_complexstructure.j pg

37. 04_25_actin filament.jpg

38. 04_26_spherical shell.jpg

39. 04_27_Viral capsids.jpg

40. 04_28_fibrous proteins.jpg

41. 04_29_Disulfide bonds.jpg

42. 04_30_selective binding.jpg

43. 04_31_specific ligands.jpg

44. 04_32_antibody.jpg04_32_antibody.jpg

45. 04_33_Lysozyme.jpg04_33_Lysozyme.jpg

46. 04_34_lysozyme bonds.jpg

47. 04_35_Enzymes.jpg04_35_Enzymes.jpg

48. 04_36_Retinal_heme.jpg04_36_Retinal_heme.jpg

49. 04_37_feed inhibition.jpg

50. 04_38_metabolic react.jpg

51. 04_39_conform.change.jp g

52. 04_40_ligand binding.jpg

53. 04_41_phosphorylation.jp g

54. 04_42_molec. switches.jpg

55. 04_43_nucleotide hydrolysis.jpg

56. 04_44_walk along.jpg

57. 04_45_motor protein.jpg

58. 04_46_Protein machine.jpg