Proteins are made of amino acids

A protein is a chain of amino acids

That fold into a particular shape

Primary Structure: Elastin

Secondary Structure: Helix

Secondary Structure: Helix

Secondary Structure: Sheet

Tertiary Structure

Carboxyl Group

Amino Group

Peptide Bond Formation

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 Cα–C bond, whose angle of rotation is called psi (ψ), and about the N–Cα 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

Proposition: One of the Motivations of Nano is to Engineer new Materials, Devices and

Machines

New Technologies

So… Why all of this biology?

Do Mechanical Engineers or

Civil Engineers or

Electrical Engineers

need to learn biology to do their jobs?

…… Engineering

Nanotechnology : Big Question#1How do we build materials or machines at the nanoscale ?

Can we just scale down macroscopic machine design?

Macroscopic Motor.Will a nanoscopic version of this motor work?

Lets say you could….

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

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….)

ATP Synthasebiology and nanotechnology

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

General Features of a Eukaryotic Cell

Mitochondria

The Power Plant (produces ATP)

Metabolism in Mitochondria

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

Bacterial Motility: Flagellaswimming rhodobacter spheroides

Armitage, J.P., and Schmitt, R. Microbiology 143, 3671-3682 (1997). http://www.rowland.org/labs/bacteria/movies_rsphe.html

TEAM 1Ahmet Serine & ProlineJessy Methionine & GlycineSam Glutamic Acid & AlanineCharlie Valine & Glutamic AcidTEAM 2Ashley Cystein &TryptophanCorey Threonine&Aspartic AcidMax Histidine & ProlineJohn Isoleucine & ThreonineTEAM 3Jeremy Glycine & ProlineZack J. Lysine & ValineCarson Asparagine & GlutamineSarah Proline & Phenylalanine

TEAM 4Sarah Proline & Histidine

Carly Phenylalanine & Glycine

Dominique Lysine & Serine

Trevor Aspartic Acid & ValineTEAM 5Aakash Leucine & Tyrosine

Zack P. Glutamine&Methionine

Shane Alanine & Cystein

Karsten Arginine & IsoleucineTeam 6Nick Phenylalanine & Glycine

Christian Tyrosine & Proline

Hunter Tryptophan & Glycine

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.