Biol/Chem 410 Biochemistry II
Syllabus
Info on Cumulative Portion of the Final

Make Up Test (Click  here)

GRADES


TEGRITY and ON-LINE TEXTBOOK - The links have been fixed - "sort of".  Click here to go to my Tegrity Page.  The Protein kinase lectures with protein kinase written on the RIGHT column under "description" are those that work.  They take a min or two to start as they are larger files.

I have also made links for an online textbook for the signaling and cancer at the bottom of this webpage.  These pages PLUS your textbook and notes will cover what you need for the test.  We will NOT cover apoptosis on this test, but will get through cancer.

Have fun, Dr P

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 Regulation

NEW - Glycolysis and Diabetes & Cancer
  

 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  NEW 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 18 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 March 19th.  Turn into the Chem Office  (10 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
       Paper assignment. The report format is described below.  Pick from one of the following Journal Articles.  If you wish to find one of your own, please submit the paper to me ASAP:  Due TBA in April
           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 16 April
    Nutrition I
    		        Diabetes Problem Based Learning - TBA
    Nutrition II
    		        
    Neurochemistry I
    		        
    Neurochemistry II
    		        
    Neurochemistry III
    		        
    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
    Cancer Readings - 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.
    Intro        Development and Causes of Cancer      Tumor Viruses      Oncogenes      Tumor Suppressor Genes   

    Finding and Capturing Videos of Lectures:  Each day's lecture will be videotaped and placed on the web for downloading.  Only one day's video will be up at a time.  Between 11:00 and 1:00 on lecture days, I will remove the old movie and upload the next.  There are no archives.  Each movie is about 1gig of memory so most of you will have to burn them for storage.

    Students access material by browsing to:
    http://sws.mnstate.edu/chem410
    username    chem410
    password    biochem

    To download the file you need to RIGHT-click on it and choose the menu item that pops up saying Save link as…or Save target as… or whatever language your browser uses that sounds like that.  It will then download directly to you hard drive.  The files are going to be around 1 GB is size and that is quite large.  Expect a long download time and be sure you are downloading on a broadband link.  If you have a cable modem at home, I would expect it to take around 15 minutes to download.
     
    To view on a PC, download the file and name as an .mp4 file, you can use quicktime.  I also think Windows Media will play it.  The coming files will be in the .mod format.  You will need to use Windows Media player to play those back.  You can also use a free program called VLC. 
     
    To view on a MAC, download the file, change the .MOD tag to .MPG (ie.  filename.mpg instead of filename.mod) and view using VLC.
     
    You can get VLC for free at http://www.videolan.org/vlc/