Chem 410 Biochemistry II

UPDATED SYLLABUS (click here)

Syllabus
Info on Cumulative Portion of the Final

Make Up Exam - READ INSTRUCTIONS!!!!


NEW Grades w/changes to T3 (NHCC- MSUM)

Class Notes: 

ONLINE CLASS LECTURES: When possible I will prepare online lectures. If your schedule or "other" circumstances require that you miss class the lectures are there for you. These are 10 - 20 min long and can be watched using the wimba website.

You will ALSO need to watch two guided exploration movies in chapter 21 on this book website.

FOR THE Biochemistry of Cancer, I have found a Free Online version of The Cell A Molecular Approach Geoffrey Cooper.  Chapter 15
Don't forget the handouts on Cancer as well.  Your book also has some info on cancer (chapter 13&22). Click here to get to the Chapter on Cancer for a more detailed info on the Biochemistry of Cancer.

 

Logging On to Wimba - Click on the desired lecture link in the table below. If you have not used Wimba on the computer before RUN THE WIZARD! Then click on the participant login button. The room ID is CHEM410JosephProvost .Use any name you wish. There you will see the ppt lectures, my voice and some notes written on the ppt as I give the lectures.

IF the voice or ppt does not show up, wait a moment and click on the link on the upper right hand corner of the Wimba screen marked archive start. I have had to do that two times to get the ppt to show. BUT be patient. If there are a lot of people on the server it takes time to load and run. Pushing the link button ten times does not help you.

I will be out of town to attend the American Society for Biochemistry and Molecular Bio meeting April 17 - 22. For those missed days, go to the SAC and finish the assignment as decribed on your sylabus and watch the TWO identified lectures linked below:

Wimba Online Lectures
Integration of Metabolism I Integration of Metabolism II Integration of Metabolism III
Intro to Signal Transduction I Intro to Signal Transduction II Receptors Intro to Signal Transduction III (GPCR/Tyrosine K)
Signal Transduction IV - G Proteins Signal Transduction V Small G Proteins  
     

Remember - if you are using the old version of the text book you MUST get hold of the new version for these last three sectioins, Integration of metabolism is found on chapter 22 and signal transduction and cancer are chapter 13 in the third edition of Voet Voet and Pratt. YOU MUST READ the book. ALL of this material will likely be on the test, not just the notes or the lecture recordings.

 

If you wish additional book chapters (from another textbook) have been linked at the bottom of your webpage. Older lecture recordings are also found there but are essentially the same as what are shown in the Wimba files above.

Good luck, stay dry, hope the sewer in my basement doesn't back up a third time! Dr Provost

Seminars-    You are required to attend two seminars this semester.  Each seminar/talk will be worth 5 points.  To get the points you must attend and submit a short synopsis of the talk with a review of the main point of the talk.  (10 total points).  See the class web site for the turn-in sheet.  Each assignment is due three calendar days after the talk.  Late reports will be docked 50%

-    Extra Credit Seminars -
There will be several opportunities to go to and write up a seminar/biochemical related topic for extra credit.  SEE ABOVE FOR ANNOUNCEMENTS OF THE SEMINARS.  Each event will be worth three points for a total of 21 maximum points accumulated throughout the semester. 

  • I will not review these until the end of the semester.
  • It is your responsibility to keep up on what you’ve turned in.
  • Each assignment is due three calendar days after the talk.
  • The seminar report MUST be typed for credit.
  • Late reports will be docked 50%
Seminar Participation Form - Turn in to the chemistry office only (MUST be TYPED). 
It is a word doc for your convenience.


 

Biochemistry Essay Sample Question/Answer  The essays are based on our problem based learning work on glucose transport and kinetics of glycolysis.  Your preparation for the test will need to be more than just the notes and textbook.  I will be looking for a detailed answer that is not simply a description of that happens.  Answer in terms of kinetics and metabolism.

An example of a poorly answered questions would go something like this...  blood glucose will go down as insulin levels are released by the pancreas.  Glucose will then be metabolized by the cells. 

What is wrong with answer - well at one level, nothing.  The answer is correct, but has no detail or mechanism.  I would look for values, specifics on the kinetics (actual values of glucose vs Km) what that means in terms of transport, what is specifically happening in what cells to the Glut T-porters and each of the tissues of interest...

ALSO - Remember an essay is not a table, bullets or an outline .

EC Homework -   Find a metabolic disease based on an abstract from Journal of Inherited Metabolic Disease.  You will not be able to read this article.  The paper is to be 2 pages signle spaced, 12 pt font.  The paper should focus on the biochemistry and metabolic nature of the disease (this should be the focus 80% of the paper), the cause of the disease, the implication and treatment of the disease.  8 points.  Paper due to the Chem office April 18.

Biotech Seminars (14) - Click here for dates and times:  Look for Journal Club Presentation Information


 Notes
Pages
Learning Objectives
Chapter Questions
Chapter Answers
Thermodymics

Vitamins
Chpt 13



Glycolysis I

Glycolysis II

Glycolysis III

Glycolysis Regulation

Glycolysis and Diabetes & Cancer
 
Chapter 14
 Chapter 14
Study Q - 3, 4
Probs 3, 6, 9, 14
 Glucose Transport Overview    and    Diabetes   (handout info)
  Gluconeogenesis
452-459
Chpt 15 Gluconeo
Gluconeogenesis
Chapter 15
Study Q - 5, 6, 8, 9
Probs 7, 8, 9, 10
Gluconeogenesis 
Glycogen metabolism 
427-438
 Chapter 15 Glycogen
 Glycolysis
 Glycolysis
Regulation of Glycogen
438-452      
Citric Acid Cycle 
467-488
Chpt 16
Krebs Cycle
Krebs Cycle
ETS pt 1
493-526
Chpt 17
Electron Transport & OxPhos
Electron Transport & OxPhos
ETS pt 2
     
ETS pt 3




 FA Metabolism I
563-568
 Chpt 19
 Lipid transport and FA Metabolism
Lipid transport and FA Metabolism 
 FA Metabolism II
568-593   Apoprotein Class Notes Suppliment
   
Integration of Metabolism
 
 Integration of Metabolism 
 NEW - Extra Notes on Integrated Metabolism
 
Signal Transduction I
       Class Assignments
Signal Transduction II
 
 Signaling
 Signaling
Thermodynamic Homework - Due 21 Jan
PEPCK Jounal Article Review -  Write a one page review of the paper on expression oof PEPCK in muscle - super bad mouse...
Hear the podcast (MUST ALSO READ PAPER)!
Read the paper

The paper must be 11 pt font 1 page min.  Discuss the background/intro, methods, results, discussion and the overall importantce of this paper.

Due Feb 2.  Turn into the Chem Office  (20 pts)


Signal Transduction III
   
 Structural G Protein Link 
Problem based learning -TBA


Signal Transduction IV
   
Heterotrimeric G Protein-Suggested readin
PPP/HMS Assignment - Write a 1-2 page summary of the pentose phosphate pathway.  Discuss the where the pathway is found, the purpose of the pathway, the reactions and statges of the pathway, the regulation of the PPP, and any disease associated with thepathway.  Include (not in the 1-2 pages) a hand written copy of the pathway. 

Internet and Science -  TBA.
 Signal Transduction V
       
           Abl and Actin
Biochemistry of 
Cancer 1 pt 1
   
Cancer, angiogenesis and apoptosis hanout (required)
  •  G Protein Signaling
  • Lipids and Insulin
  • Protein Kinase C
  • Biochemistry of 
    Cancer 1 pt2
     
     Cancer 
     
  •  TNF Alpha
  • Ras
  • Biochemistry of 
    Cancer pt 3
       
    Nutrition, Risks and Cancer 
    (Not required just for your interest)
      Phospholipase D
            -Academic Conference - Report link   Assignment due 24 April
    Class Choice I
           Diabetes Problem Based Learning - TBA
    Class Choice II
           
    Class Choice III
           
    Class Choice IV
           
    Class Choice  V
           
    Report of the Journal of Biological Chemistry Paper

    You will write a written report of one of the Journal of Biological Chemistry papers linked above.  I will have a review paper to support each of the articles.  Your report will be typed only.  No other form will be accepted.  Your report will be two to three pages long.

    Write the report as if you were going to teach another biochemistry student.  There needs to sufficient details as to explain the mechansim / hypotyhesis and experiements described in the paper.  Your paper will have an introduction, a review of the experiements, what was done, how the experiemt was conducted and the results of the experiment and in the conclusion what the data meant as well as a larger picture of the impact of the data.  Find and discuss the hypothesis that drove the experiments and explain if the authors supported the hypothesis or not.

    Each of you are responsible for writting your own paper - I highly suggest you do not work in teams so that I do not find similar papers.

    You will need to look at other journal articles to help you understand the papers.
     

    Lectures on Tegrity
    Click below to view the lectures.  If using a Mac or a PC - use Explorer.  If you want to watch the sessions outside of the biochem lab and things aren't working, click here for help.  Each session is about 20 min long and it takes a couple of minutes to download.

    To get started click on the high speed connection if on campus


    Podcast of Signaling Intro - If you do not know how to download this, use the computers in the biochem lab.  Double click on the icon in the download window.  Do not update itunes.  Then if you click on the podcast the video should start.  If you click on the window in the lower left corner, it will enlarge in the center of the screen.  You can enlarge by dragging the bottom right corner of the window.

    Receptor Lecture Podcast -
    This is a downloaded file.  Once you click on it, look for the file to play.

    Protien Kinase Lectures I, II, III, and IV   These are Tegrity sessions and are best viewed on the biochem lab computer.
    Click here for help using Tegrity.  Use biochem lab computers if you can't get these to work on your computer.

    Cell Signaling Readings
    Chapter 15 Biochemistry 5th Ed.  Click on the link for additional chapter readings. 
    Please don't waste paper and print each chapter - read online.  We need the trees to prevent global warming!

    Intro           GPCR signaling                  PIP2 Signaling               Calcium Signaling
    Growth Factor Receptor Signaling          Signaling and Cancer      Chapter Summary