***** Fundamentals of Biochemistry CH 369 - Spring 2012 *****

Instructor: David W. Hoffman, Associate Professor, Dept of Chemistry & Biochemistry
Office hours:  Mon 1-2 pm, Tues & Thurs 7:30 - 8:30 pm, or by appointment, in Welch 4.230C.
Email:  dhoffman@mail.utexas.edu    office phone: 512-471-7859  

Class meeting: Tuesday & Thursday, 6 pm - 7:30 am, in Welch 2.256 
Unique number:  69516 

Class web page:   http://hoffman.cm.utexas.edu/courses/index369_sp12.html    

You may register for this course at the UT Extension web site.  Register through UT Extension 
   
Course description:  This is a one semester course that covers the major concepts in biochemistry, including the types of biomolecules, protein and enzyme structure, membranes, and metabolism.  The course may be of interest to students who are on a path toward a health related field, or anyone interested in how living things work at the molecular level.

Textbook:  "Essential Biochemistry" by Charlotte Pratt & Kathleen Cornely. 
I'm recommending the 2nd edition, there is also a first edition.

Computer access:  There will be a class web page, and some class notes will usually be posted on the web page after each class.  It will therefore be necessary to have access to a computer and internet.

Textbook:  "Essential Biochemistry" by Charlotte Pratt & Kathleen Cornely. 
I'm recommending the 2nd edition, there is also a first edition.

Class attendance will not effect grades. However, I think it will be extremely difficult to do well in the course without attending class regularly.

Exams will be given during the regular class time. Plan to take the exams on the scheduled time. If you need to miss an exam due to extraordinary circumstances, inform me as soon as possible so that other arrangements may be made.

Schedule for Spring 2012   

Tues Jan 24     Course organization; chemical basis of life (Chapter 1)
                        class notes (PDF)      class notes (PPT)     

Thur Jan 26     Aqueous chemistry (Chapter 2)    
                        class notes (PDF)      class notes (PPT)     
                        a few practice questions to try (PDF)   
       Regarding solutions to practice problems, I will be happy to discuss any
       of the practice problems at the end of each and every class period.

Tues Jan 31     From genes to proteins (Chapter 3 and 4)
                        class notes (PDF)      class notes (PPT) 

Thur Feb 2      Proteins & protein structure (Chapter 4)   
                        class notes (PDF)      class notes (PPT) 
                         
Tues Feb 7      Proteins & protein structure (Chapter 4 & 5)
                        class notes (PDF)      class notes (PPT) 

Thur Feb 9      Protein function (Chapter 5) 
                        class notes (PDF)      class notes (PPT) 
                        some practice exam questions (PDF)
                        answers to some practice exam questions (PDF)  

Tues Feb 14    Mid-term exam #1  (covers chapters 1, 2, 3, 4, 5)

Thur Feb 16    Introduction to enzymes  (Chapter 6)
             class notes (PDF)      class notes (PPT) 

Tues Feb 21    Enzymes, kinetics and inhibition (Chapter 7)
             class notes (PDF)      class notes (PPT) 
             enzyme practice questions (PDF)                     <==

Thur Feb 23    Lipids & membranes (Chapter 8)  
             class notes (PDF)      class notes (PPT) 

Tues Feb 28    Lipids & membranes (Chapter 8 & 9)
             class notes (PDF)      class notes (PPT) 

Thur Mar 1     Membrane transport (Chapter 9)  
             class notes (PDF)      class notes (PPT) 

Tues Mar 6     Membrane transport, review (Chapter 9)
             class notes (PDF)      class notes (PPT) 
             lipid and membrane practice questions (PDF)    <==

             answers to enzymes practice questions (PDF) 
             answers to lipid and membrane practice questions (PDF) 

Thur Mar 8     Mid-term exam #2  (covers chapters 6-9 of 2nd edition, chapters 6-8 of 1st edition) 
             answers to exam 2 (PDF)   

March 10-18    Spring break

Tues Mar 20     Introduction to carbohydrate metabolism (Chapter 11-12)  
             class notes (PDF)      class notes (PPT) 

Thur Mar 22     Glucose metabolism (Chapter 12,13)
             class notes (PDF)      class notes (PPT) 
  
Tues Mar 27     The citric acid cycle (Chapter 14)
             class notes (PDF)      class notes (PPT) 

Thur Mar 29     Oxidative phosphorylation (Chapter 15)   
             class notes (PDF)      class notes (PPT) 

Tues Apr 3       Oxidative phosphorylation (Chapter 15)
            class notes (PDF)      class notes (PPT) 

Thur Apr 5       Metabolism topics & review day  
            class notes (PDF)      class notes (PPT) 

 glycolysis, Krebs cycle & oxidative phosphorylation practice questions (PDF)     <==
 answers to some of the practice questions (PDF)  

 practice exam 3 questions (PDF)         <==
 answers to practice exam 3 questions (PDF)    <== (with answer to #13 fixed) 

Tues Apr 10     Mid-term exam #3 (covers chapters 11-15 of 2nd edition, chapters 9-12 of 1st edition)
  
      ==>  Exam 3 will be in Painter 4.42 (PAI 4.42)  <==
      
  exam 3 answers (PDF)     
 
Thur Apr 12     Photosynthesis (Chapter 16)  
          class notes (PDF)      class notes (PPT) 
       
Tues Apr 17    Photosynthesis (Chapter 16)
          class notes (PDF)      class notes (PPT) 

Thur Apr 19    Lipid metabolism (Chapter 17)  
          class notes (PDF)      class notes (PPT)    
          study questions for photosynthesis & lipid metabolism (PDF)   

Tues Apr 24     Nitrogen metabolism (Ch. 18). 
          class notes (PDF)      class notes (PPT)      
          some nitrogen study questions (PDF)   

Thur Apr 26     Finish metabolism, then DNA topics. (chapters 19-20)  
          class notes (PDF)      class notes (PPT)      

Tues May 1      Topics from chapters 20, 21, 22.   DNA replication, transcription, translation.
         class notes (PDF)      class notes (PPT)   
         the last study questions (PDF)  

Thur May 3      Review day.   class notes (PDF)      class notes (PPT)   
                     
The final exam is on Tuesday, May 8, from 6 to 9 pm, in the
usual place:  Painter 4.42.


Final exam:  Covers the entire course, and is required.  The date and time are set by UT Extension, and appear on the UT Extension web page (see "calendar"). 

Grading:  Midterm exams are 100 pts each; the final exam will be 160 pts.
Your grade will be based on the total points you earn on the midterm exams, plus the final exam. 
The final exam is required.  Grades will be as follows:

   A    92 % 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

Incomplete grades will only be given in the case of truly extraordinary circumstances.

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

Regarding exam regrades:  I you believe there has been an error in grading your exam, I am willing to consider re-grade requests. Submit regrade requests in writing along with your graded exam; include a brief written description of the grading error.  Re-grade requests should be submitted within one week of when the exam is returned.

UEX Policy on Scholastic Dishonesty:  In promoting a high standard of academic integrity, the University broadly defines scholastic dishonesty—basically, all conduct that violates this standard, including any act designed to give an unfair or undeserved academic advantage, such as falsifying academic records, cheating, plagiarism, unauthorized collaboration, collusion, misrepresenting facts (e.g., providing false information to postpone an exam, obtain an extended deadline for an assignment, or even gain an unearned financial benefit). Any other acts (or attempted acts) that violate the basic standard of academic integrity (e.g., multiple submissions—submitting essentially the same written assignment for two courses without authorization to do so).  Several types of scholastic dishonesty—unauthorized collaboration, plagiarism, and multiple submissions—are discussed in more detail on this Web site to correct common misperceptions about these particular offenses and suggest ways to avoid committing them.  For the University’s official definition of scholastic dishonesty, see  Section 11-802, Institutional Rules on Student Services and Activities.

Miscellaneous stuff that may be useful:  
   my handy vitamin review (PDF)
   diagram of the EM spectrum (PDF)  
   I like to read daily science news at  Science Daily 
   Every day I look at Astronomy Picture of the Day 
   Positive thought:  Try to make the world a slightly better place, one day at a time,
      one person at a time.