Chemistry 103                                                                            Spring 2008

Biochemical Structures, Reactions, and Energetics

General Information 

Last Updated:   3/31/08 12:26 PM
Instructor:    Prof. Thomas Schleich   Lecture:     M, W, F, 9:30 AM –  10:40 AM
Office:     252 PSB   Location:    PSB 114
Phone:    831 - 459 - 2067  

Office Hours:    W, 2:00 - 4:00 PM   (or by   appointment)

Email: mailto:schleich@chemistry.ucsc.edu

Introduction

      Chemistry 103, Biochemical Structure, Reactions, and Energetics, is a one-quarter survey introduction to modern biochemistry.  Emphasis will be placed on those fundamental topics pertinent to the biochemistry of living systems.  Aspects of molecular biology involving the flow of biological information will not be covered (DNA replication, repair, recombination, transcription, translation, recombinant DNA, and cloning technology) nor will photosynthesis.  We will strive for an aggressive reading and lecture schedule, roughly two-thirds of a chapter per lecture from the recommended text (Fundamentals of Biochemistry – Life at the Molecular Level, Third Edition, by Voet, Voet, and Pratt) (ISBN-13  978-0470-12930-2) per lecture.  If necessary, the pace will be varied.  Some topics may be expanded whereas others may be truncated, condensed, or even eliminated.

Two take home exams will be given.  The first will be approximately at mid quarter (Parts 1, 2, and 3 and Chap. 23 of the text) and the second at the conclusion of the quarter (Part 4 of text).  In addition, a special project will be required and is due at the end of the quarter.  Projects may take the following form: (1) Research paper on some aspect of biochemistry; (2) Analysis of a procedure to analyze some aspect of biochemistry; (3) Critique of a paper in the peer reviewed scientific literature; (4) Development of a computer program to enable investigation (modeling) of a biochemical process; (5) Other (by prior approval).

Disability Statement

If you have a disability that interferes with your learning I encourage you to talk with me about it on a confidential basis so that we might collectively devise a strategy to overcome whatever barriers might exist. You should also consult with the Disability Resource Center .

Lecture Schedule

(subject to minor revision as the need arises)

Lecture Notes (requires Adobe Acrobat and Password)

DATE

TOPIC

READING

3/31

  Course Outline
  Setting the Stage

 

 Chapter 1    

4/2

  Physical Biochemistry of Water


 Chapter 2         

4/4

  Amino Acids

 

 Chapter 4     

4/7

  Proteins: Primary Structure


 Chapter 5  (Parts 1, 3 & 4)     

4/9

  Proteins: Three Dimensional Structure

 

  Chapter 6  (Parts 1, 2 & 3)  

4/11

  Proteins: Three Dimensional Structure

 

  Chapter 6  (Parts 3, 4 & 5)

4/14

  Protein Function (Myoglobin and Hemoglobin)


  Chapter 7  (Part 1)        

4/16

  Enzymatic Catalysis

  Chapter 11  (Parts 1, 2 & 3)   

 

4/18

  Enzymatic Catalysis


  Chapter 11 (Parts 4 & 5)

4/21

  Enzymatic Kinetics, Inhibition, and Control

  Chapter 12  (Parts 1 & 2)

     

4/23

  Enzymatic Kinetics, Inhibition, and Control

  Chapter 12  (Parts 3 & 4)  

4/25

  Carbohydrates


  Chapter 8      

4/28

  Lipids and Biological Membranes


  Chapter 9  (Parts 1 & 2)   

4/30

  Lipids and Biological Membranes

 

  Chapter 9  (Parts 3 & 4)       

5/2

  Membrane Transport

  Chapter 10

   

5/5

  Nucleic Acid Structure

 

  Chapters 3 (Parts 1, 2 & 4) & 24 (Parts 1, 2 & 4)    

5/7

  Introduction to Metabolism


  Chapter 14     

5/9

  Glucose Metabolism

 

  Chapter 15  (Parts 1, 2 & 3) 

5/12

  Glucose Metabolism

 

  Chapter 15  (Parts 4, 5 & 6)    

5/14

  Glycogen Metabolism and Gluconeogenesis

 

  Chapter 16  (Parts 1, 2 & 3)

5/16

  Glycogen Metabolism and Gluconeogenesis

 

  Chapter 16  (Parts 4 & 5)  
5/19

  Citric Acid (TCA) Cycle

 

  Chapter 17  (Parts 1, 2 & 3)  

5/21

  Citric Acid (TCA) Cycle


  Chapter 17  (Parts 4 & 5)  

5/23

  Electron Transport and Oxidative Phosphorylation

 

  Chapter 18  (Parts 1 & 2)

5/26

  Holiday

 

     

5/28

  Electron Transport and Oxidative Phosphorylation

 

  Chapter 18  (Parts 3 & 4)    

5/30

  Lipid Metabolism

 

  Chapter 20 (Parts 1 & 2)
     
6/2

  Lipid Metabolism

 

  Chapter 20  (Parts 4, 5 & 7)  

6/4

  Amino Acid Metabolism

 

  Chapter 21     
6/6

  Mammaliam Fuel Metabolism

 

  Chapter 22    

 

  Nucleotide Metabolism

 

  Chapter 23     

6/9
  Project Due       
     

 

Suggested Study Strategy for Chemistry 103


Useful Links

Molecular Graphics Programs for Viewing Structures

WPDB -  http://www.sdsc.edu/pb/wpdb/wpdb.htm

Protein Explorerhttp://molvis.sdsc.edu/protexpl/frntdoor.htm

Molecules in Motion - http://www.moleculesinmotion.com/

Molecular Visualization - http://www.umass.edu/microbio/rasmol/

Chime (molecular graphics plug-in for web browsers) - http://www.mdl.com/  (required for the software packages)

Lecture Notes and Other Course Material