A FATTY ACID

BIOCHEMISTRY   TRIACYLGLYCEROL OLESTRA

        phospholipid bilayer
If the  molecules above are visible, CHIME is properly configured on this computer
    ANNOUNCEMENTS
 
Grades for the semester are posted and available on-line. Final exams will not be made available for your review, however the key for the take home portion and for the extra credit quiz is in the bulletin board behind the glass.
 
Have a wonderful holiday and break! Good luck with your studies next semester.
 

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A professor was giving a big 100-point test one day to her students. She handed out all of the tests. Once the test was over, the students all handed their tests back in. The professor noticed that one of the students had attached a $100 bill to his test with a note saying "A dollar per point."

The next class the professor handed the tests back. That student got his test back and $64 change.

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Welcome to Biochemistry I- an introduction to the molecules of life, their chemical properties and how they behave according to basic  chemical principles.

Be prepared to put an extra 2 - 3 hrs/ hr of lecture time into this course STUDYING the basic chemical principles that you know so well from previous courses (equilibrium, thermodynamics, weak acids and bases, electrostatic interactions, and non-covalent bonding, etc.) and learning to apply those principles to biologically-relevant materials (proteins, nucleic acids, carbohydrates and lipids).

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Biochemistry Links
Link To PowerPoint Lectures slides are set next to each chapter below You must have PowerPoint or the PowerPoint Viewer
COURSE INFORMATION and SYLLABUS  
Study Suggestions and Helpful Hints  
   
There are many programs that you can use to view a  molecule- even large biological macromoleules!, provided its structure is known. In order to use any of these viewing programs though, you will need to get the file that contains the structural information on your protein of interest.  The Research Collaboratory for Structural Bioinformatics (RCSB) hosts a web site where data files for ALL known macmromolecular structures are stored in what is called the Protein Data Bank (or PDB for short).
THE PROTEIN DATA BANK The world's repository for protein and other macromolecular structures determined by x-ray crystallography or NMR.
PDB Tutorials Tutorials on how to search and download files from the protein data bank.
HIC-UP Where you can find PDB Files of Cofactors, Prosthetic Groups, and Other "Small" Molecules
For this class, we will be using a browser pluggin called CHIME and the molecular viewing software, "PROTEIN EXPLORER". To use the CHIME plug-in, you will need Internet Explorer or version 4.X of Netscape (or older)
CHIME Molecular Viewer Plug-in Chime is distributed by MDL software
Protein Explorer Tutorials, Instructions and other information about using the Protein Explorer
RCSB graphics help page Information from RCSB on numerous available graphics packages for visualizing macromolecules
After you have Chime and Protein Explorer installed and have completed the 1-hr tour to initiate yourself in how Protein Explorer works, the following tutorials will serve as a resource for studying concepts and lessons from the corresponding chapter in your Matthews and VanHolde textbook.
Chapter 1- The Scope of Biochemistry  
Chapter 2- Weak Interactions in an Aqueous Environment Lecture Slides Chap 1 & 2

Homework #1   Answer Key for Homework #1
Chapter 3-The Energetics of Life Lecture Slides Chap 3

Homework #2  Answer Key for Homework #2
Chapter 4- Nucleic Acids Lecture Slides Chap 4

Homework #3 Answer Key for Homework #3
Chapter 5- Amino Acids/ Peptides Lecture Slides Chap 5

Homework #4  Answer Key for Homework #4
Amino Acid Quiz Dr. William McClure has developed a super web site with links to various molecular models of biological interest for his biochemistry courses at Carnegie Mellon University.

Test your knowledge of amino acid structure- try this amino acid quiz.
 
Amino Acid Viewer Here's the link to the amino acid viewer, in case you need to refresh your memory first.
Chapter 6- Protein Structure Lecture slides Chap 6

Homework #5 Answer Key for Homework #5
Secondary Structures Tutorial Drs. Eric Martz and Timothy Drisdoll have provided an incredible resource to their students at UMass Amherst and all their biochemistry colleagues by developing this web site on Molecules in Motion: 3D tutorial on DNA and Proteins. Many of these tutorials are now spiffed up for Worth Publishing at Lehninger's "Principles of Biochemistry" Biochemistry in 3D web site.

To help you study what we learned in class, scroll down and take the Protein Secondary Structures 3.0 tutorial.
Protein Architecture/ProteinG Tutorial Here's a similar secondary structure tutorial but from a different perspective from Dr. William Mc Clure- yes he also provides a chance to test yourself. Scroll down in the top window and take the Protein Architecture quiz.
Chapter 7- Hb, Mb and Allostery Lecture Slides Chap 7

Homework #6                  
Myoglobin

Hemoglobin

 Dr. Paul Reisberg has developed a very nice web  page on Hb and Mb for his biochemistry course at Wellesley.

These pages have a link to interactive saturation curves for Mb and Hb (see how the curve changes wrt Kd for oxygen). There are also pdb images that one can manipulate to view various substituents such as the hemes and 2,3-BPG.
   
Hemoglobin Tutorial  Here's the UMass Amherst Molecules in Motion Tutorial.
Chapter 9-   Carbohydrates Lecture slides Chap 9

Homework #7               

CHO Terminology List
 

Glycoprotein Example

 

 A chime-script resource for the biochemistry course taught at Arizona
carbohydrate mobility within a glycoprotein

 

                        "      "
disaccharides                        "      "
Chapter 10- Lipids Lecture slides Chap 10

homework #8
 

Phospholipid bilayer

Diffusion within the lipid bilayer

thermodynamically unfavorable flip-flop within the lipid bilayer

 

 Chime-script and animation resources for the biochemistry course taught at Arizona
Transmembrane Protein

 

                       "      "
Valinomycin- an ion transport protein                       "      "   
Chapter 11- Enzymes Lecture slides Chap 11                           Homework #9
Enzyme Kinetics Tutorial  The University of Arizona has an on-line interactive resource called the "Biology Project" which includes links to problem sets and tutorials in various aspects of biochemistry.

For a basic understanding of the major issues in Enzyme Kinetics I recommend this particular Tutorial and problem set- to try it out yourself just follow the link to the right.
   
 
Triose Phosphate Isomerase
Chymotrypsin
Trypsin
Subtilisin
Dr. Stephen Curry at the Imperial College in London has set up a web page for his Molecular Biophysics course that includes some chime scripts for common enzymes including the evolutionarily related proteases to the right. I particularly liked the discussion in these chime scripts and recommend you visit these sites to gain further insights into how these enzymes work..

As with all chime scripts, they work best in older versions of netscape, 4.7 or older, (which is available in the chemistry department's computer lab).
Chapter 12
Metabolism Tutorial Here is the link to the University of Arizona's Biology Project Tutorial on Metabolism.