Outreach

The Center for Biological Physics is dedicated to outreach programs, especially with regard Physics Education. The CBP has been involved in summer programs to work with Arizona science teachers, exciting them with tutorials on cutting edge research, and also working alongside teachers on new pedagogical methods based on biophysical ideas. Of special note is the "Popiscle Stick Project" spearheaded by Prof Michael Thorpe, which uses ideas from ridigity theory to help children learn algebra and geometry.

 

Nanobiophysics


In 2009 the Outreach Program of the CBP was extended to experimental topics. Joanne Cox (Trevor Browne HS), Merville Nicholls (Central HS), and Trudi Wimberley (Casa Verde HS) worked in the lab of Robert Ros on imaging of individual biomolecules with Atomic Force and Confocal Laser Scanning Microscopy (see http://mstf2009.wikispaces.com/Nanobiophysics).

 

Proteins


Proteins are large organic compounds made of amino acids. In proteins, amino acids are arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acids. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic co de. Although this genetic code specifies 20 "standard" amino acids, the residues in a protein are often chemically altered in post-translational modification: either before the protein can function in the cell, or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.

Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in every process within cells. Many proteins are enzymes that catalyze biochemical reactions, and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle, and the proteins in the cytoskeleton, which forms a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Protein is also a necessary part of our diet, since animals cannot synthesise all the amino acids and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that can be used for protein synthesis.

The human body makes at least 50,000 different proteins, and possibly twice that many. They are the essential working parts of living matter. If a cell is thought of as a house, then proteins are just about everything in it. They are the furniture, the fixtures, the lumber.

Like those objects, each protein has a particular shape and function. The shapes and functions, in fact, are inextricably linked. Hemoglobin's shape lets it carry oxygen. Collagen's makes it a good connective tissue. Insulin fits in spaces like a key, enabling it to turn things on and off.

Protein Folding


Protein folding is the physical process by which a polypeptide folds into its characteristic three-dimensional structure. Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery The protein folding problem is broadly known as a grand challenge, one of the few problems in science that it is a “named problem”. It has not been solved by supercomputers, and it inspired the developments of Folding@Home a distributed computing system involving thousands of computers, in addition to IBM’s new Blue Gene computer. The new approach called ZAM (zipping and assembly method) provides the first solution to the problem that is sufficiently specific and tangible that it can guide a computer to predict protein structures at high resolution, and can predict protein folding routes in detail, which can be tested by experiments. Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes

 

http://folding.stanford.edu/education/protein.html

Conformational Changes


The powerpoint presentation can be found here.

About the Center for Biological Physics


In the Center for Biological Physics, we study biological systems from the molecular to the cell level. With improved experimental data, biology is becoming much more quantitative and at Arizona State University we are researching the underlying principles involved in the machinery of living things and searching for unifying themes both within and between organisms, in an interdisciplinary environment. Arizona State University is a leader in quantitative biology and welcomes enqueries from prospective physics graduate students who would like to join one of our exciting research areas. More information can be obtained from the center director Mike Thorpe and/or the program coordinator Jill Kolp.

http://biophysics.asu.edu

Popsicle Sticks Project


Modeling Protein Folding

pdf

PowerPoint

Notes on counting algorithms

pdf

 

Popsicle Sticks

pdf

PowerPoint

 

 

 

Rigid Body Poster 2008

 

PowerPoint2007

Rigid Body Algebra

 

PowerPoint

Rigid Body Non-Algebra

 

PowerPoint

Rigid Body, Include proofs

 

PowerPoint

Teacher's Reference

pdf

 

 


2007 school teacher presentations


 

CBP Math and Science Teaching Fellows 2007 Group 1

PDF

PowerPoint

CBP Math and Science Teaching Fellows 2007 Group 2

PDF

PowerPoint

Modeling Protein Folding Lesson

PDF

DOC

Protein Folding – Rigid/Flexible Structure Models

PDF

DOC

The Physics and Biology of Protein Folding

PDF

PowerPoint

Using Visual Python

PDF

DOC

Large Numbers

PDF

PowerPoint

Travel Times

PDF

PowerPoint

Short Times

PDF

PowerPoint

Small Things

PDF

PowerPoint

Planet Size

PDF

DOC

Zeolite movie

GIF

 

2008 lecture notes


 

June 19, 2008

Liquids

PDF

 

June 20, 2008

DNA

PDF

PowerPoint

June 23, 2008

PDB

PDF

DOC

June 24, 2008

Flexweb and First/Froda

PDF

PowerPoint

June 27, 2008

Simulation Applets

PDF

DOC

July 2, 2008

Solvation

PDF

 

July 7, 2008

Molecular Dynamics

PDF

PowerPoint

July 8, 2008

Proteins

PDF

PowerPoint

July 16, 2008

From quarks to proteins

PDF

PowerPoint

2009 lecture notes


 

Length scales

PDF

Educational Links


Annenberg Media Learner.org contains a free educational video on demand page. This page includes the "World of Chemistry" series that we watched.

 

    

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