BMMB597A
Core Concepts in Biomolecular Science - Fall 2005
9:05 to 9:55 am, 117 Thomas
e-mail to:
Ming Tien Joe Reese John Golbeck David Gilmour Wendy Hanna-Rose

Date 
Instructor 
Topic 
Tues, Aug 30
Tien
 MT 1) Acids and Bases
Wed, Aug 31
Reese
 JR 1) Nucleic acid structure: Nucleotides, Chemistry of DNA and RNA synthesis, DNA and RNA structure, DNA topology.
Thur, Sept 1
Tien
 MT 2) Amino Acids/Peptides 
-amino acid structure/properties 
-Acid base properties of amino acids
Fri, Sept 2
Reese
 JR 2) Prokaryotic and eukaryotic genomes; Chromosome structure: prokaryotic vs eukaryotic
     
Mon, Sept 5
 Labor day holiday, no class
Tues, Sept 6
 Tien
 MT 3) Peptides to Proteins 
-Primary, Secondary, tertiary structure 
-Rules that dictate conformation
Wed, Sept 7
Reese
 JR 3) Chromatin structure: nucleosome, higher order structures.
Thur, Sept 8
Tien
 MT 4) Peptides to Proteins 
-Examples of secondary structures 
-Anfinsen’s RNAase A experiments 
Fri, Sept 9
Reese
 JR 4) DNA replication: Machinery, Initiation and timing
     
Mon, Sept 12
Reese
 JR 5) Mutations, DNA damage and repair
Tues, Sept 13
Tien
 MT 5) Methods for characterizing proteins 
-Sequencing, total amino acid analysis 
-Crystallography, nmr 
Wed, Sept 14
Tien
 MT 6) Methods for characterizing proteins 
-Sequencing, total amino acid analysis 
-Crystallography, nmr 
Thur, Sept 15
Reese
 JR 6) Recombination and Mobile Genetic elements
Fri, Sept 16
Reese
 JR 7) Protein Turnover; Intro. to the Cell Cycle
     
Mon, Sept 19
Reese
 JR 8) Cell cycle: Transitions and Control
Tues, Sept 20
Tien
 MT 7) Practical Enzymology 
-Enzyme purification
Wed, Sept 21
Reese
 JR 9) Mitosis-1
Thur, Sept 22
Tien
 MT 8) Practical Enzymology 
-Enzyme purification
Fri, Sept 23
Reese
 JR 10) Mitosis and Meiosis
     
Mon, Sept 26
Reese
 JR 11) Checkpoints
Tues, Sept 27
Tien
 MT 9) Practical Enzymology 
-Activity, specific activity, etc.
Wed, Sept 28
Reese
 JR 12) Genetic Systems 1: Mutants, Screens, Suppression and Screens
Thur, Sept 29
Tien
 MT 10) Kinetics 
-Chemical 
-Steady state Assumptions 
Fri, Sept 30
Reese
 JR 13) Genetic Systems 2: Prokaryotes and Yeast
     
Mon, Oct 3
 Reese
 JR 14) Genetic Systems 3: Worms and Flies
Tues, Oct 4
Tien
 MT 11) Kinetics 
-Derivation of equations 
-Effect of pH
Wed, Oct 5
Reese
 JR 15) Genetic Systems 4: Mice; catch up
Thur, Oct 6
Tien
 MT 12) Kinetics 
-Inhibition studies 
-Kinetics with more than one substrate 
-Transient state
Fri, Oct 7
 Reese JR 16) Transcription cycle: initiation, elongation, termination (emphasis on prokaryotes).
     
Mon, Oct 10
Reese
 JR 17) Prokaryotic gene regulation: activation and repression
Tues, Oct 11
Tien
 MT 13) Examples of enzyme mechanisms
Wed, Oct 12
Reese
 JR 18) Overview of translation
Wed, Oct 12 Wednesday evening exam covering Reese's lectures JR 1 to JR 15, 7:00 pm
Thur, Oct 13
Golbeck
 JG 1) Introduction to Physical Biochemistry
Fri, Oct 14
 Study day, no class
     
Mon, Oct 17
 Reese JR 19) Regulation of translation in prokaryotes and eukaryotes
Tues, Oct 18
 Golbeck JG 2) Case Study 1: The Ribosome
Reading: pdf file (handout)
Wed, Oct 19
Reese
 JR 20) Regulation of RNA-translation and RNA stability
Thur, Oct 20
 Golbeck
JG 3) Ultracentrifugation: Theory and Practice
Reading: Dwek, Ch.6: pp 73-88 
Problems: Dwek, Ch.6: #8,10,11
Thur, Oct 20
 Thursday evening exam covering Tien's lectures MT 1 to MT13, 7:00 pm, 101 Althouse
Fri, Oct 21
 Reese
 JR 21) Regulation of prokaryotic translation
     
Mon, Oct 24
 Gilmour
 DG 1) Eucaryotic transcription units and the general transcriptional machinery.
Tues, Oct 25
 Golbeck JG 4) The First Law of Thermodynamics
Reading: Dwek, Ch.1: pp 1-6
Problems: Dwek, Ch.1: #2,3,4
Wed, Oct 26
 Gilmour DG 2) Transcriptional regulation: Cis-acting elements and Trans-acting factors.
Thur, Oct 27
 Golbeck JG 5) The Second Law of Thermodynamics
Reading: Dwek, Ch.2: pp 8-9
Problems: Dwek, Ch.2: #1
Fri, Oct 28
 Gilmour DG 3) Transcription activation domains and their mechanism of action.
     
Mon, Oct 31
Gilmour
 DG 4) Transcription and chromatin.
Tues, Nov 1
 Golbeck JG 6) Gibbs Free Energy: Theory and Application
Reading: Dwek, Ch.2: pp 10-14
Problems: Dwek, Ch.2: #4,5,8
Wed, Nov 2
 Gilmour
 DG 5) Transcription and chromatin.
Thur, Nov 3
 Golbeck
 JG 7) Chemical Equilibrium
Reading: Dwek, Ch.3: pp 16-28
Problems: Dwek, Ch.3: #2,11,12
Fri, Nov 4
 Gilmour
 DG 6) Transcriptional repression
     
Mon, Nov 7
Gilmour
 DG 7) Transcription elongation and RNA processing
Tues, Nov 8
 Golbeck
 JG 8) Case Study 2: The Photosynthetic Reaction Center
Reading: pdf file handout
Wed, Nov 9
 Gilmour DG 8) Biological membranes
Thur, Nov 10
 Golbeck
 JG 9) Marcus Theory
Fri, Nov 11
 Gilmour DG 9) Membrane transport of small molecules and electrical properties of membranes.
     
Mon, Nov 14
 Gilmour DG 10) Visualizing cells, internal organization of eukaryotic cells
Tues, Nov 15 Changed to Wednesday evening
Tues, Nov 15
 Golbeck JG 10) Optical Spectroscopy, Beer’s Law
Reading: Dwek, Ch.11: pp 205-211
Problems: Dwek, Ch.11: #1,3,4
Wed, Nov 16
 Gilmour DG 11) Secretory pathway
Wed. Nov 16
 Wednesday evening exam covering Reese's lectures JR 16 to JR 21 and Gilmour's lectures DG 1 to DG 7, 7:00 pm, 101 Althouse
Thur, Nov 17
 Golbeck JG 11) Electrochemistry
Reading: Dwek, Ch.8: pp 107-124
Problems: Dwek, Ch.8:#7,8,9
Fri, Nov 18
 Gilmour DG 12) Secretory pathway, lysosomal biosynthesis
     
Mon, Nov 21
Gilmour
 DG 13) Endocytosis
Tues, Nov 22
 Gilmour
 DG 14) Nuclear and mitochondrial transport
Wed, Nov 23
Thanksgiving Break - No Class
Thur, Nov 24
Thanksgiving Break - No Class
Fri, Nov 25
Thanksgiving Break - No Class
     
Mon, Nov 28
Golbeck
 JG 12) Biological Oxidation/Reduction: Anaerobes
Problems: Handout
Tues, Nov 29
 Golbeck  		 JG 13) Biological Oxidation/Reduction: Aerobes
Problems: Handout
Wed, Nov 30
 Golbeck
 JG 14) Energy, Entropy, Information Theory, and Evolution
Thur, Dec 1
 Hanna-Rose WHR 1) Signal Transduction in Prokaryotes I. 
Two Component Systems
Fri, Dec 2
 Hanna-Rose WHR 2) Signal Transduction in Prokaryotes II. 
Two Component Systems (cont) 
Chemotaxis
     
Mon, Dec 5
Hanna-Rose
 WHR 3) Signal Transduction in Eukaryotes I. 
An Overview of the Players
G protein coupled receptors
Tues, Dec 6
 Hanna-Rose WHR 4) Signal Transduction in Eukaryotes II. 
Players (cont)
Wed, Dec 7
Hanna-Rose
 WHR 5) Signal Transduction in Eukaryotes III. 
tyrosine kinases, ras and MAPK
Thur, Dec 8
 Hanna-Rose WHR 6) Signal Transduction in Eukaryotes IV. 
tyrosone kinases (cont)
Fri, Dec 9
Hanna-Rose
  WHR 7) Signal Transduction in Eukaryotes V.
wnt and Notch
     
Mon, Dec 12
 7:00 PM, 101 Althouse, Exam 1: Golbeck's lectures JG 1 to JG 14
Tues, Dec 13
 7:00 PM, 101 Althouse, Exam 2: Gilmour's lectures DG 8 to D 14 and Hanna-Rose's lectures WHR 1 to WHR 7

Exams: Students are required to take all five exams, and each exam will contribute equally to the final grade.  Missed exams must be made-up, and the format of the make-up exam is at the discretion of the examiner.

Final Grades: The division between B+ and A- will be the overall mean in the course.  Students with a final average within one standard deviation below the mean will be assured of receiving a letter grade of at least a B.  The letter grade for students falling below one standard deviation could be B- or lower as decided by a majority vote of the course instructors. 

Academic integrity: The students and instructors are bound by the rules and procedures on academic integrity set by the Eberly College of Science Academic Integrity Committee. A complete listing of these policies can be found at the following web site: http://www.science.psu.edu/academic/Integrity/index.html.

It is the student's responsibility to know and abide by these policies. Failure to do so may result in sanctions or expulsion.