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Syllabus
Course: BIO 301, Fall 2009School: Bard College
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301: Biology Biochemistry Syllabus (Fall 2007) John B. Ferguson Reem-Kayden Center for Science and Computation 215 Bard College PO Box 5000 Annandale-on-Hudson, NY 12504-5000 845-752-2333 ferguson@bard.edu http://science.bard.edu/biology/ferguson/course/bio301/ SESSION DATE TOPIC AND ASSIGNMENT PROTEIN STRUCTURE 01 09-04 INTRODUCTION TO PROTEIN STRUCTURE BERG ET AL. Chapters 13 Work problems, Chapters 13, as...
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301: Biology Biochemistry Syllabus (Fall 2007)
John B. Ferguson Reem-Kayden Center for Science and Computation 215 Bard College PO Box 5000 Annandale-on-Hudson, NY 12504-5000 845-752-2333 ferguson@bard.edu http://science.bard.edu/biology/ferguson/course/bio301/
SESSION
DATE
TOPIC AND ASSIGNMENT PROTEIN STRUCTURE
01
09-04
INTRODUCTION TO PROTEIN STRUCTURE
BERG ET AL. Chapters 13 Work problems, Chapters 13, as many as you prudently can (AMAYPC)
LAB 01 02
09-04 09-06
NO LAB, BUT...
Read NINFA & BALLOU Chapter 1 for background
OXYGEN BINDING PROTEINS--MYOGLOBIN AND HEMOGLOBIN
BERG ET AL. Chapters 67 Atlas of Macromolecules: Oxymyoglobin http://molvis.sdsc.edu/fgij/fg.htm?mol=1MBO Atlas of Macromolecules: Deoxymyoglobin http://molvis.sdsc.edu/fgij/fg.htm?mol=1CQ2 Work problems, Chapter 6, AMAYPC
03
09-11
HEMOGLOBIN--AN ALLOSTERIC PROTEIN
Check out Molecular Visualization Resource's hemoglobin tutorial at http://www.umass.edu/molvis/tutorials/hemoglobin/. It takes a while to load, but no special software needs to be installed. Work problems, BERG ET AL. Chapter 7, AMAYPC
LAB 02
09-11
TITRATION OF AN AMINO ACID
NINFA & BALLOU Chapter 1, pp. 3644 FERGUSON Exercise 1
Tuesday, November 27, 2007
Page 1
7:47:24 AM
BIOLOGY 301: BIOCHEMISTRY SYLLABUS (FALL 2007) SESSION 04 DATE 09-13
Rosh Hashanah
TOPIC AND ASSIGNMENT THE LESSONS OF SICKLE-CELL ANEMIA
BERG ET AL. Chapter 7 Work problems, Chapter 7, AMAYPC
ENZYME CATALYSIS 05 09-18 ENZYME KINETICS
BERG ET AL. Chapter 8 Work problems, Chapter 8, AMAYPC Sing BAUM "The Michaelis Anthem"
LAB 03
09-18 09-19
TITRATION OF A PROTEIN
FERGUSON Exercise 2
DROP/ADD PERIOD ENDS, 5 P.M. LYSOZYME AND RIBONUCLEASE A
Atlas of Macromolecules: Lysozyme http://molvis.sdsc.edu/fgij/fg.htm?mol=1lzr
06
09-20
07
09-25
CARBOXYPEPTIDASE A AND CHYMOTRYPSIN
BERG ET AL. Chapter 9 Atlas of Macromolecules: Carboxypeptidase A http://molvis.sdsc.edu/fgij/fg.htm?mol=1CBX Work problems, Chapter 9, AMAYPC
LAB 04 08
09-25 09-27
BUFFERS
FERGUSON Exercise 3
CONTROL OF ENZYMATIC ACTIVITY--ASPARTATE TRANSCARBAMOYLASE
BERG ET AL. Chapter 10 Work problems, Chapter 10, AMAYPC
09 LAB 05 10 11 LAB 06
10-02 10-02 10-04 10-11 10-16
KINDS OF REACTIONS CATALYZED BY ENZYMES-- NUCLEOPHILIC DISPLACEMENTS REVIEW SESSION FIRST EXAMINATION FALL BREAK!! KINDS OF REACTIONS CATALYZED BY ENZYMES-- ADDITIONS, ELIMINATIONS, ETC. PROTEIN ASSAYS
NINFA & BALLOU Chapters 23
Tuesday, November 27, 2007
Page 2
7:47:24 AM
BIOLOGY 301: BIOCHEMISTRY SYLLABUS (FALL 2007) SESSION DATE TOPIC AND ASSIGNMENT
NINFA & BALLOU Experiment 3-1
12
10-16
COENZYMES I--COENZYME A, THIAMINE DIPHOSPHATE, PYRIDINE NUCLEOTIDES, FLAVINS, AND LIPOIC ACID
HORTON ET AL. Chapter 7 Work problems, Chapter 7, 17
13
10-18
COENZYMES II--BIOTIN AND PYRIDOXAL PHOSPHATE
HORTON ET AL. Chapter 7 Work problems, Chapter 7, 813
METABOLISM 14 10-23 THE THERMODYNAMICS OF METABOLISM
BERG ET AL. Chapter 15 Work problems, Chapter 15, AMAYPC
LAB 07 15
10-23 10-25
ENZYME ASSAYS
FERGUSON Exercise 6
GLYCOLYSIS
BERG ET AL. Chapter 16 Work problems, Chapter 16, AMAYPC Sing BAUM "In Praise of E.M.P." http://biotech.icmb.utexas.edu/glycolysis/glycohome.html Take a look at the two minimaps of glycolysis and gluconeogenesis and their regulation, from HANSON, RICHARD W. Metabolic minimaps of glycolysis and gluconeogenesis and their regulation, designed by Donald E. Nicholson. Biochemistry and Molecular Biology Education 30(4): 221223, July/August 2002 [RW].
16
10-30
CITRIC ACID CYCLE AND THE GLYOXYLATE BYPASS
BERG ET AL. Chapter 17 Work problems, Chapter 17, AMAYPC Sing "Waltz Round the Cycle" & "The Glyoxylate Cycle" Krebs Cycle Tutorial by Will McClure, Carnegie Mellon University (requires the Chime plug-in): http://www.bio.cmu.edu/Courses/BiochemMols/TCACycle/TCAMain.htm Take a look at the minimap of mitochondrial ATP formation, from SKULACHEV, VLADIMIR. Mitochondrial ATP formation: Revised, designed by Donald Nicholson: Commentary. Biochemistry and Molecular Biology Education 31(2): 8384, March/April 2003 [RW].
Tuesday, November 27, 2007
Page 3
7:47:24 AM
BIOLOGY 301: BIOCHEMISTRY SYLLABUS (FALL 2007) SESSION LAB 08 DATE 10-30 TOPIC AND ASSIGNMENT ENZYME KINETICS
NINFA & BALLOU Chapter 8 FERGUSON Exercise 7
17
11-01
OXIDATIVE PHOSPHORYLATION
BERG ET AL. Chapter 18 Work problems, Chapter 18, AMAYPC Sing BAUM "The Battle Hymn of the Aerobes" & "The Chemiosmotic Theory" Take a look at the minimap of approximate yield of ATP from glucose, from BRAND, MARTIN. Approximate yield of ATP from glucose, designed by Donald Nicholson. Biochemistry and Molecular Biology Education 31(1): 24, January/February 2003. [RW].
18
11-06
Election Day
GLYCOGEN AND DISACCHARAIDE METABOLISM
BERG ET AL. Chapter 21 Work problems, Chapter 21, AMAYPC Sing BAUM "Blood Sugar"
LAB 09 19
11-06
Election Day
ENZYME INHIBITION
FERGUSON Exercise 8
11-08
GLUCONEOGENESIS AND PENTOSE PHOSPHATE PATHWAY
BERG ET AL. Chapters 16 & 20 Work problems, Chapter 16 & 20, AMAYPC Sing BAUM "Blood Sugar" & "The Pentose Phosphate Shunt" Take a look at the two minimaps of glycolysis and gluconeogenesis and their regulation, from HANSON, RICHARD W. Metabolic minimaps of glycolysis and gluconeogenesis and their regulation, designed by Donald E. Nicholson. Biochemistry and Molecular Biology Education 30(4): 221223, July/August 2002 [RW].
11-09 20 11-13
LAST DAY TO WITHDRAW FROM A CLASS! AMINO ACID DEGRADATION AND THE UREA CYCLE
BERG ET AL. Chapter 23 Work problems, Chapter 23, AMAYPC Sing BAUM "We're Here Because Urea" Take a look at the minimap of the urea cycle, from HANSON, RICHARD W. The urea cycle, designed by Donald Nicholson. Biochemistry and Molecular Biology Education 30(6): 350352, November/December 2002 [RW].
LAB 10
11-13
REVIEW SESSION Page 4 7:47:24 AM
Tuesday, November 27, 2007
BIOLOGY 301: BIOCHEMISTRY SYLLABUS (FALL 2007) SESSION 21 22 11-15 DATE 11-20 TOPIC AND ASSIGNMENT SECOND EXAMINATION LIPIDS AND BIOLOGICAL MEMBRANES
BERG ET AL. Chapter 12 Work problems, Chapter 12, AMAYPC
LAB 11
11-20
ENZYMATIC METHODS OF ANALYSIS
NINFA & BALLOU Chapter 9 NINFA & BALLOU Experiment 9-3
THANKSGIVING RECESS!! 23 11-27 DEGRADATION OF TRIGLYCERIDES AND PHOSPHOGLYCERIDES
BERG ET AL. Chapter 22 Work problems, Chapter 22, AMAYPC Sing BAUM "-Oxidation" For an animation of the interaction of LDL with its receptor by Susana Maria Halpine see: http://home.earthlink.net/~shalpine/anim/Life/endo.htm
LAB 12
11-27
LIGAND BINDING
NINFA & BALLOU Chapter 10 NINFA & BALLOU Experiment 10-1
24
11-29
BIOSYNTHESIS OF TRIGLYCERIDES AND PHOSPHOGLYCERIDES
BERG ET AL. Chapters 22 & 26 Work problems, Chapter 22 & 26, AMAYPC Sing BAUM "Fatty Acid Biosynthesis"
12-03 25 12-04
SENIOR PROJECTS DUE, 5 P.M. BIOSYNTHESIS OF CHOLESTEROL
BERG ET AL. Chapter 26 Work problems, Chapter 26, AMAYPC Sing BAUM "Cholesterol Biosynthesis"
LAB 13
12-04
CHROMATOGRAPHY
NINFA & BALLOU Chapter 4 NINFA & BALLOU Experiment 4-1
26
12-06
PHOTOSYNTHESIS--THE LIGHT REACTION
BERG ET AL. Chapter 19
Tuesday, November 27, 2007
Page 5
7:47:24 AM
BIOLOGY 301: BIOCHEMISTRY SYLLABUS (FALL 2007) SESSION DATE TOPIC AND ASSIGNMENT
Work problems, Chapter 19, AMAYPC Sing BAUM "Photosynthesis" Take a look at the minimap of chloroplastic photosynthesis, from RICH, PETER. Photosynthesis in chloroplast: Revised, designed by Donald Nicholson: Commentary. Biochemistry and Molecular Biology Education 31(5): 281282, September/October 2003 [RW].
27
12-11
PHOTOSYNTHESIS--THE CALVIN CYCLE
BERG ET AL. Chapter 20 Work problems, Chapter 20, AMAYPC Sing BAUM "Photosynthesis" Take a look at the minimap of chloroplastic photosynthesis, from RICH, PETER. Photosynthesis in chloroplast: Revised, designed by Donald Nicholson: Commentary. Biochemistry and Molecular Biology Education 31(5): 281282, September/October 2003 [RW].
LAB 14
12-11
GEL ELECTROPHORESIS OF PROTEINS
NINFA & BALLOU Chapter 5 NINFA & BALLOU Experiment 5-1 Electrophoresis Simulation by Dave Mix: http://www.rit.edu/~pac8612/electro/Electro_Sim.html
12-12 28 12-13
REGISTRATION FOR SPRING 2008 DNA--STRUCTURE AND REPLICATION
BERG ET AL. Chapter 28 Work problems, Chapter 28, AMAYPC Check out Molecular Visualization Resource's DNA tutorial at http://www.umass.edu/molvis/tutorials/dna/
12-14 29 12-18
TERM PAPER DUE! TRANSLATION
BERG ET AL. Chapter 30 Work problems, Chapter 30, AMAYPC Sing BAUM "Protein Synthesis" Ribosome Tutorial by Will McClure, Carnegie Mellon University (requires the Chime plug-in, and doesn't seem to work under Internet Explorer 6): http://www.bio.cmu.edu/Courses/BiochemMols/ribosome/70S.htm
LAB 15 30
12-18 12-20
REVIEW SESSION THIRD EXAMINATION Page 6 7:47:24 AM
Tuesday, November 27, 2007
BIOLOGY 301: BIOCHEMISTRY SYLLABUS (FALL 2007) NOTES BAUM = BAUM, HAROLD. The Biochemists' Songbook. 2nd ed. Bristol PA: Taylor & Francis, 1995. ISBN 9780748404162. BERG
ET AL.
= BERG, JEREMY M., JOHN L. TYMOCZKO, & LUBERT STRYER. Biochemistry. 6th ed. New York: W. H. Freeman, 2007. ISBN 978-0-716-78724-2.
FERGUSON = FERGUSON, JOHN B. Laboratory Manual -- Biology 301: Biochemistry. Annandale-on-Hudson NY: Bard College, 2007. HORTON ET AL. = HORTON, H. ROBERT, LAURENCE A. MORAN, RAYMOND S. OCHS, J. DAVID RAWN, & K. GRAY SCRIMGEOUR. Principles of Biochemistry, 3rd ed. Upper Saddle River NJ: Prentice Hall, 2002. ISBN 0-13-026672-8. NINFA & BALLOU = NINFA, ALEXANDER J., &a...
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Equilibrium B vectors0 1 2 1y-po sZor 3 phas e0.5angle4 50 0 6 1 0.5 os p x-XYB vectors E vectors (in x-direction)0 1 2 1y-po sZor 3 phas e0.5angle4 50 0 6 1 0.5 os p x-XYV vectors and pressure red=max, blue=
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B vectors +y propagation E vectors polarization 10 1 2 1y-po sZor 3 phas e0.5angle4 50 0 6 1 0.5 os p x-XYB vectors +y propagation E vectors polarization 20 1 2 1y-po sZor 3 phas e0.5angle4 50 0 6 1 0.5 os p x-X
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