"Bioenergetics and Metabolism"







Spring 2009     CRN: 65050

Lectures:        Tuesdays and Thursdays, 1:40 – 3:00 p.m., 198 Young Hall

Instructor:              Steffen Abel (210 Asmundson Hall, Phone: 752-5549, The ABEL LAB
               Office Hours: Fridays 9:30 – 11:30 am, Asmundson Hall, Room 210 (Office) or 242 (Hanna Conference Room for larger groups of students) 
Teaching               Rebecca Shipman 
Assistants:            Office Hours: Wednesdays 11 am – 1 pm, Asmundson Hall, Hanna Room Annex (2. Floor) 
                               Katrina Edgar
                               Office Hours: Mondays 1 – 3  pm,  Asmundson Hall, Hanna Room Annex (2. Floor)

Text:                      I typically recommend the following texts: 
                                              Biochemistry by Garrett & Grisham (3rd edition)
                                              Fundamentals of Biochemistry by Voet, Voet & Pratt (upgrade edition)
                                              Principles of Biochemistry by Lehninger, Nelson & Cox (4th edition)
                               However, because BIS103 covers basic metabolism only, any other biochemistry text should be sufficient.
Booklet:                A collection of visual aids specifically prepared for this class is available for purchase at the
                               UCD Bookstore, which you need to bring to every lecture.   However, the booklet is not a substitute for a textbook!
                               To do well in class, you need to study the relevant chapters in a biochemistry text!!!

Prerequisites:      General/Organic Chemistry, BIS102
Exams:                Midterm 1                           (33.3%)                Tuesday, April 21, in class
                               Midterm 2                           (33.3%)                Tuesday, May 19, in class
                               Final Exam                         (33.3%)                Saturday, June 6, 10:30 a.m. -12:30 p.m.
                               Exams will be given at the assigned times only. No early final will be given. Exceptions may 
                               be granted to students with documented verification of personal loss or sickness and if the 
                               instructor was contacted before the exam. Regrade requests for midterms must be submitted 
                               in writing within one week after returning of the tests and will only be considered if permanent ink 
                               has been used during the exam.

Schedule of Lectures and Exams
Lecture Audio Files (Podcast)

Power Point


 Lecture Topics

Lecture 1

March 31

Introduction to Metabolism (Thermodynamics; ATP; Enzymes; Amino acids; Co-factors; Regulation of enzyme activity)

Lecture 2

April 2

Lecture 3

April 7

Carbohydrate Catabolism (Carbohydrates; Glycolysis; Substrate level phosphorylation; Breakdown of other sugars and carbohydrates;

Pyruvate dehydrogenase (PDH) complex; Tricarboxylic acid (TCA) cycle; Anaplerotic reactions)   


Lecture 4

April 9

Lecture 5

April 14

Lecture 6

April 16

Essentials 1

April 21

 MIDTERM 1 (Answer Key)

Lecture 8

April 23

ATP Synthesis   (Electron transport chain; oxidative phosphorylation; ATP synthase; photophosphorylation

ATP Synthase Animations: One, Two, Three, Four

Lecture 9

April 28

Lecture 10

April 30

Carbohydrate Anabolism (Gluconeogenesis; Synthesis of other sugars and carbohydrates; Pentose phosphate pathway; Calvin cycle)

Lecture 11

May 5

Lecture 12

May 7

Lecture 13

May 12

Lipid Metabolism (Lipid degradation; Ketogenesis; Lipid and isoprenoid synthesis; Glyoxylate cycle)

Lecture 14

May 14

Essentials 2

May 19

MIDTERM 2 (Answer Key)

Lecture 16

May 21

Amino Acid Metabolism  (Amino acid degradation; Urea cycle; Nitrogen and sulfur assimilation; Amino acid reactions)

Lecture 17

May 26

Lecture 18

May 28

Nucleotides (Metabolism of purines and pyrimidines; Carcinogenesis)

Lecture 19

June 2

Regulation (Principles of global regulation; Hormonal regulation; Integration of metabolism)

2009 Review in the Science Magazine on Metabolic Regulation (Warburg Effect)

Lecture 20

June 4

Final Essentials

June 6

FINAL EXAM (Answer Key)    Rate My Professor

Folks, that’s it for us. Get through finals week and enjoy the summer break. 
All the best to all of you! – Dr. Abel, Rebecca & Katrina
Beyond the textbooks... (you may totally ignore this section)
Why nature chose phosphates.
Understanding nature's catalytic toolkit.
Tracing Oxygen's Imprint on Earth's Metabolic Evolution.
Life, the Universe, and Body Temperature (Uncoupling Protein)
NAD Metabolism in Health and Disease
Out of thin air (The roots of photosynthesis)
Frontiers in Cancer Research 


                       Recommended Reading (Old Text Book Editions)
                       Jessie's Crossword Puzzle
Problem Sets:            Set 1                             Set 2                                Set 3
                                              Set 4                                    Set 5                                     Set 6
Exams of 2007:          Midterm 1                           Midterm 2                            Final Exam
                                              Answer Key 1                    Answer Key 2                    Final Key

Google                                Periodic Table                   Biochemical Nomenclature
Google Scholar                Molecules R US                Glossary (Org. Chem.)


Wikipedia                           3-D Library








Nobel Prizes to Biochemists
(Click and read their stories)


 Emil Fischer

 1902, Carbohydrates and purines

 Eduard Buchner

 1907, Cell-free fermentation

 Richard Willstaetter

 1915, Chlorophyll

 Theodor Svedberg

 1926, Biophysical studies

 Heinrich Wieland

 1927, Bile acid

 Adolf Windaus

 1928, Sterols and vitamins

 Arthur Harden and Hans von Euler-Chelpin

 1929, Sugar fermentation

 Hans Fischer and Walter Haworth

 1930, Heme and chlorophyll

 Paul Karrer

 1937, Vitamins

 Richard Kuhn

 1938, Vitamins

 Adolf Butenandt and Leopold Ruzicka

 1939, Hormones

 James Sumner

 1946, Crystallization of urease

 Arne Tiselius

 1948, Electrophoresis

 Alexander Todd

 1957, Nucleotides and co-enzymes

 Frederick Sanger

 1958, Protein structure, insulin

 Melvin Calvin

 1961, Photosynthetic carbon fixation

 Max Perutz and John Kendrew

 1962, Protein structure, myoglobin

 Robert Woodward

 1965, Vitamin B12

 Luis Leloir

 1970, Sugar nucleotides

 Christian Anfinsen

 1972, Protein structure, ribonuclease

 Peter Mitchell

 1978, Chemiosmotic hypothesis

 Paul Berg, Walter Gilbert,and Frederick Sanger

 1980, DNA biochemistry

 Robert Merrifield

 1984, Peptide synthesis

 Johann Deisenhofer, R. Huber, and H. Michel

 1988, Photosynthetic reaction center

 Sidney Altman and Thomas Cech

 1989, Catalytic RNA

 Kary Mullis and Michael Smith

 1993, Polymerase Chain Reaction

 Paul Boyer, John Walker, and Jens Skou

 1997, Mechanism of ATP synthesis

 John Fenn, Koichi Tanaka, Kurt Wuthrich

 2002, Structure analyses of biological macromolecules

 Peter Agre, Roderick MacKinnon

 2003, Membrane channels

 Aaron Ciechanover, Avram Hershko, Irwin Rose

 2004, Regulated proteolysis

 Roger Kornberg (son of Arthur Kornberg)

 2006, Molecular basis of eukaryotic transcription


 Archibald Hill and Otto Meyerhof

 1922, Glycolysis

 Frederick Banting and John Macleod

 1923, Discovery of insulin

 Otto Warburg

 1931, Respiration

 Albert von Szent-Gyorgyi

 1937, Carbohydrate metabolism

 Carl and Gerty Cori

 1947, Glycogen metabolism

 Edward Kendall

 1950, Hormones

 Hans Krebs and Fritz Lipmann

 1953, TCA cycle

 Axel Theorell

 1955, Oxidation enzymes

 Severo Ochoa and Arthur Kornberg

 1959, DNA and RNA biosynthesis

 Francis Crick, James Watson and Maurice Wilkins

 1962, Structure of DNA

 Konrad Bloch and Feodor Lynen

 1964, Fatty acid metabolism

 Earl Sutherland

 1971, Hormone action

 Michael Brown and Joseph Goldstein

 1985, Cholesterol metabolism

 Edmond Fischer and  Edwin Krebs

 1992, Reversible protein phosphorylation

 Alfred Gilman and Martin Rodbell

 1994, G-proteins

 Robert Furchgott, Louis Ignarro, and Ferid Murad

 1998, Function of NO

 Gunter Blobel

 1999, Protein topogenesis

 Arvid Carlsson, Paul Greengard, Eric Kandel

 2000, Signal transduction in the nervous system

 Richard Axel, Linda Buck

 2004, Olfactory sensation

 Andrew Fire, Craig Mello

 2006, RNA interference