Essential Review: Organic Chemistry
Review the basics of conformational analysis in your organic chemistry textbook.
A Powerful New Learning Tool: Molecular Modeling on Personal Computers
No single learning task will enhance your understanding of protein structure and function more than studying proteins by computer graphics, using a program like RasMol or SwissPdbViewer.
This web site provides two tutorials for helping you learn to use molecular graphics. The tutorials include links that help you get and install the programs on your own computer, and to guide you in getting structure files for any protein of known structure.
For most new biochemists, the program RasMol will take you a long way into your study of biomolecules. RasMol is used at many biochemistry web sites, so knowing how to use it will help you take advantage of new web tools. But if you think you might study biochemistry further, say in graduate school, also learn to use SwissPdbViewer, because after learning its basics, you can proceed to very sophisticated analysis of protein structure. Here are links to the tutorials:
RasMol Tutorial SwissPdbViewer Tutorial
Each tutorial, as well as teaching you the basics of a program, gives you a guided tour of an important protein. The same strategy for studying this sample protein will serve you will in studying others. Use your new-found computer skill to help you study any of the protein molecules taken up in your class. This web site provides structure files for molecules studied in many biochemistry courses. See the Chemistry 361/3 Topics List to find these files.
Learn to View Structures in Three Dimensions (Stereo)
Biomolecules are three-dimensional -- understanding them requires that you see spatial relationships within binding sites and active sites. Many scientific papers contain stereo images that can greatly enhance your understanding of the connection between structure and function. Don't be blind to these great aids:
Click here to learn stereo viewing.
Essential Memory Work: Saturation Equations
If your course includes a study of the oxygen carrier proteins myoglobin and hemoglobin, you can greatly enhance your understanding of oxygen binding by learning how to derive saturation equations from simple models of ligand binding to proteins.
For the simple dissociation model
start from the dissociation-constant expression with oxygen concentration expressed as partial pressure (KP), and derive the saturation equation Y = (pO2)/(pO2 + P50), in which pO2 is the partial pressure of O2, P50 is the partial pressure that gives half 1/2 saturation (Y = 0.5) of Mb with O2, and Y is the saturation fraction, the fraction of myoglobin molecules with O2 bound at a given pO2. The algebraic definition of Yis Y = [MbO2]/([Mb] + [MbO2]).
The derivation entails substituting for [MbO2] from the dissociation-constant expression, and simplifying. You also need to show that KP = P50.
Once you have a command of this derivation, you will find it much easier to read the discussions of oxygen transport by myoglobin and its more complex cousin hemoglobin.
Quiz for USM Biochemistry Students
(At second class on this subject -- counts as 1/10 of one exam)
In class, we will discuss the derivation described above.
For the all-or-none dissociation model for oxygen and hemoglobin,
prove that Y = (pO2)4/(pO24 + P504)
Show all algebraic manipulations, and show clearly that KP is equal to P504
THINK ABOUT THIS: Why doesn't the equation you derived here fit the hemoglogin saturation curve?
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