1. Proteins are made of amino acids

3. A protein is a chain of amino acids That fold into a particular shape

4. Primary Structure: Elastin

5. Secondary Structure:  Helix

7. Secondary Structure:  Sheet

8. Tertiary Structure

12. Carboxyl Group Amino Group Peptide Bond Formation

18. Figure 3-4. Steric limitations on the bond angles in a polypeptide chain (A) Each amino acid contributes three bonds (red) to the backbone of the chain. The peptide bond is planar (gray shading) and does not permit rotation. By contrast, rotation can occur about the C α –C bond, whose angle of rotation is called psi (ψ), and about the N–C α bond, whose angle of rotation is called phi ( ϕ ). By convention, an R group is often used to denote an amino acid side chain (green circles). (B) The conformation of the main-chain atoms in a protein is determined by one pair of ϕ and ψ angles for each amino acid; because of steric collisions between atoms within each amino acid, most pairs of ϕ and ψ angles do not occur. In this so-called Ramachandran plot, each dot represents an observed pair of angles in a protein. (B, from J. Richardson, Adv. Prot. Chem. 34:174–175, 1981. © Academic Press.) Steric Limitations to Bond Angles

25. Proposition: One of the Motivations of Nano is to Engineer new Materials, Devices and Machines New Technologies

26. So… Why all of this biology? Do Mechanical Engineers or Civil Engineers or Electrical Engineers need to learn biology to do their jobs? …… Engineering

27. Nanotechnology : Big Question#1 How do we build materials or machines at the nanoscale ? Can we just scale down macroscopic machine design?

28. Macroscopic Motor. Will a nanoscopic version of this motor work? Lets say you could….

29. Lets say the motor worked, would the nano-car go… ?

30. Proteins: Natures Nanomachines They work…. I In a very sticky, very shaky, very bumpy world. How do they do this? (if you know the answer, please come talk to me after class….)

32. ATP Synthase biology and nanotechnology

33. ATP synthase is a machine that “makes” ATP. They occur within the mitochondria at the inner mitocondrial membrane.

34. General Features of a Eukaryotic Cell

35. Mitochondria The Power Plant (produces ATP)

36. Metabolism in Mitochondria

37. ATP Synthase is a protein machine Fairly recently, it has been determined that ATP synthase is a mechanical rotary motor It is very closely related to the motor that powers flagellar motion

38. Bacterial Motility: Flagella swimming rhodobacter spheroides Armitage, J.P., and Schmitt, R. Microbiology 143, 3671-3682 (1997). http://www.rowland.org/labs/bacteria/movies_rsphe.html

44. TEAM 1 AhmetSerine & Proline JessyMethionine & Glycine SamGlutamic Acid & Alanine CharlieValine & Glutamic Acid TEAM 2 AshleyCystein &Tryptophan CoreyThreonine&Aspartic Acid MaxHistidine & Proline JohnIsoleucine & Threonine TEAM 3 JeremyGlycine & Proline Zack J.Lysine & Valine CarsonAsparagine & Glutamine SarahProline & Phenylalanine TEAM 4 SarahProline & Histidine CarlyPhenylalanine & Glycine DominiqueLysine & Serine TrevorAspartic Acid & Valine TEAM 5 AakashLeucine & Tyrosine Zack P.Glutamine&Methionine ShaneAlanine & Cystein KarstenArginine & Isoleucine Team 6 NickPhenylalanine & Glycine ChristianTyrosine & Proline HunterTryptophan & Glycine

45. Each of you will build your amino acid. Then within your group you will form peptide bonds between your amino acids to create a small “protein” or poly-peptide.