***** Fundamentals of Biochemistry CH 369 - Fall 2009 *****

Instructor: David W. Hoffman, Associate Professor, Dept of Chemistry & Biochemistry
Office: Room 3.422FA MBB (at the north end of 3.422)
Office hours: Monday & Thursday noon - 1 pm, or by appointment.
Email:  dhoffman@mail.utexas.edu

Class meeting: Tuesday & Thursday 8 am, in Welch 2.246.
Class unique number:  54065

Teaching Assistants:  Ken Clevenger and Cassidy Terrell (graduate students in biochemistry).
TA's emails:  kdclevenger@mail.utexas.edu ; crterrell@mail.utexas.edu 

T.A. Ken Clevenger's office hour:  Tuesday, 12-1 pm in cubicle A on the first floor of Welch. 
                                               Or, make appointment by email:  kdclevenger@mail.utexas.edu

T.A. Cassidy Terrell's office hour:  Wednesday 10-11 in MBB 3.422F, or make an appointment
                                                by email:   crterrell@mail.utexas.edu

Textbook:  "Essential Biochemistry" by Charlotte Pratt & Kathleen Cornely,
                   1st edition, 2004, ISBN # 0-471-39387-8.

Schedule for Fall 2009   

Thur Aug 27     Course organization; chemical basis of life (Chapter 1).
                                syllabus (2 pages PDF file)      slides from first class 

Tues Sept 1       Aqueous chemistry (Chapter 2).  study questions for first exam
                           slides from 2nd class as PDF file   slides from 2nd class as PPT file  

Thurs Sept 3      From genes to proteins (Chapter 3).  
                              slides from class (PDF)    slides from class (PPT)  
                               
                          schedule and locations for study groups. 

Tues Sept 8       Protein structure and function (Chapter 4). 
                           slides from class(PDF)    slides from class (PPT)  
                   Click here  for a copy of exam 1 from the last time I taught this class.
                                  
Thur Sept 10     Protein structure and function, continued (Chapter 4).  
                             slides from class (PDF)    slides from class (PPT)  

Tues Sept 15     Mid-term exam #1  (covers chapters 1, 2, 3, 4)  No calculators allowed.
                         exam #1 solutions  

Thur Sept 17      Cytoskeletal proteins and motor proteins (Chapter 5).
                              slides from class (PDF)   slides from class (PPT)  
                           To find the "inner life of a cell movie, google "inner life of cell".

                           Some study questions for the 2nd exam.   

Tues Sept 22      Introduction to enzymes  (Chapter 6).
                            slides from class (PDF)    slides from class (PPT)   
                    
Thur Sept 24      Enzymes, kinetics and inhibition (Chapter 7).
                             slides from class (PDF)    slides from class (PPT)  

                           Practice exam #2   
                                
Tues Sept 29      Enzymes, continued (Chapter 7).   
                             slides from class (PDF)    slides from class (PPT)
                                       
Thur Oct 1         Biological membranes (Chapter 8).
                            slides from class (PDF)    slides from class (PPT)

Tues Oct 6         Mid-term exam #2  (covers chapters 5, 6, 7, 8)  exam #2 solutions  

Thur Oct 8         Overview of metabolism and free energy (Chapter 9). 
                              slides from class (PDF)   slides from class (PPT)  

Tues Oct 13       Glucose metabolism part 1 (Chapter 10).
                      class slides (PDF)    class slides (PPT)    study questions for 3rd exam

Thur Oct 15       Glucose metabolism part 2 (Chapter 10).
                      class slides (PDF)    class slides (PPT) 
 
Tues Oct 20       The citric acid cycle (Chapter 11).  more study questions for 3rd exam                     
                       class slides (PDF)    class slides (PPT)  

Thur Oct 22       Oxidative phosphorylation (Chapter 12).
                       class slides (PDF)     class slides (PPT)  

Tues Oct 27       Photosynthesis, part 1 (Chapter 13). 
                       class slides (PDF)     class slides (PPT)  

Thur Oct 29       Photosynthesis, part 2 (Chapter 13).
                       class slides (PDF)    class slides (PPT) 

             schedule and locations of study groups   practice test for 3rd exam 

Tues Nov 3        Mid-term exam #3 (covers chapters 9, 10, 11, 12, 13)  
                           solution to exam #3 (PDF) 

Thur Nov 5        Lipid metabolism, part 1 (Chapter 14). 
                           class slides (PDF)    class slides (PPT)
                           study questions #1 for final exam

Tues Nov 10      Lipid metabolism, part 2 (Chapter 14).                     
                           class slides (PDF)    class slides (PPT)  

Thur Nov 12      Nitrogen metabolism (Chapter 15).
                           class slide (PDF)    class slides (PPT) 
                           study questions #2 for final  

Tues Nov 17      Regulation of metabolism (Chapter 16). 
                           class slides (PDF)   class slides (PPT)
       
Thur Nov 19      DNA replication (Chapter 17).
                           class slides (PDF)    class slides (PPT)  
                           study questions #3 for final

Tues Nov 24      DNA repair (Chapter 18).

Thur Nov 26      Thanksgiving break.   
                           my handy vitamin review (PDF)
 
Tues Dec 1         Transcription and RNA (Chapter 19).                
Thur Dec 3         Protein synthesis (Chapter 20).

                            Practice final exam  (PDF)
                           
Final exam:  Covers the entire course.  Date and time will be set by the registrar's office.
According the the registrar's web page, the final is Saturday, Dec. 12 from 9 am - noon.
The location for the final exam is Welch 1.308 (all of us in one big room).

Grading:  Midterm exams: about 100 pts each; final exam: about 200 pts.

Course grades will be based on total points earned.  Grades will be as follows:

   A    93 % of possible points ; A-  90% of possible points
   B+  87% to 90% ; B  83% to 87% ; B-  80 to 83 %
   C+  77% to 80% ; C  73% to 77% ; C-  70 to 73 %
   D+  67% to 70% ; D  63% to 67% ; D-  60 to 63 %
   F   < 60 % of possible points

There will not be make up exams, except under extraordinary circumstances, such as documented medical emergency.  There is no excuse for over-sleeping - use two alarms  to wake up if necessary!

Students with disabilities may request appropriate academic accommodations from the Division of Diversity and Community Engagement, Services for Students with Disabilities, 471-6259.

In case you are interested:  I will be teaching a course this coming spring, "Astrobiology from a biochemical perspective", on Tuesdays & Thursdays from 11-12:15.   Here is more information, including prerequisites.  Let me know if you are interested.  - David Hoffman