Download 4.1_Proteins_Amino_Acids_2011

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: a Helix
Secondary Structure: a Helix
Secondary Structure: b Sheet
Tertiary Structure
Amino Group
Carboxyl
Group
Peptide Bond
Formation
Steric Limitations to Bond Angles
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.)
Proposition:
One of the Motivations of
Nano is to Engineer new
Materials, Devices and
Machines
New Technologies
…… Engineering
So… Why all of this biology?
Do Mechanical Engineers or
Civil Engineers or
Electrical Engineers
need to learn biology to do their
jobs?
Nanotechnology : Big Question#1
How do we build materials or
machines at the nanoscale ?
Can we just scale down
macroscopic machine design?
Lets say you could….
Macroscopic Motor.
Will a nanoscopic version of this motor work?
Lets say the motor worked,
would the nano-car go… ?
Proteins: Natures Nanomachines
I
They work….
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 Synthase
biology 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: Flagella
swimming rhodobacter spheroides
Armitage, J.P., and Schmitt, R. Microbiology 143, 3671-3682 (1997).
http://www.rowland.org/labs/bacteria/movies_rsphe.html
TEAM 1
Ahmet Serine & Proline
TEAM 4
Sarah
Proline & Histidine
Jessy
Carly
Phenylalanine & Glycine
Methionine & Glycine
Sam
Glutamic Acid & Alanine
Charlie Valine & Glutamic Acid
TEAM 2
Ashley Cystein &Tryptophan
Dominique Lysine & Serine
Trevor
TEAM 5
Aakash
Aspartic Acid & Valine
Zack P.
Glutamine&Methionine
Shane
Alanine & Cystein
Arginine & Isoleucine
Zack J. Lysine & Valine
Karsten
Team 6
Nick
Carson Asparagine & Glutamine
Christian
Tyrosine & Proline
Hunter
Tryptophan & Glycine
Corey Threonine&Aspartic Acid
Max
Histidine & Proline
John Isoleucine & Threonine
TEAM 3
Jeremy Glycine & Proline
Sarah Proline & Phenylalanine
Leucine & Tyrosine
Phenylalanine & 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.