CGS 701/702 Unit Syllabi

Quicklist

• Macromolecules: Proteins (CGS 701l)
• Macromolecules: Nucleic Acids (CGS 701k)
• Metabolism and Bioenergetics (CGS 701m)
• Receptors & Signaling (CGS 701g)
• Regulation of Gene Expression (CGS 701n)
• Cellular Functions (CGS 702g)
• Cell Injury and Response (CGS 702i)
• Systems Biology (CGS 702k)

Date	Date	Flex	Instructor
Thurs Aug 21	Molecular Structure		Beeson
Fri Aug 22	Chemical Reactivity		Beeson
Mon Aug 25	Solvation and Electrostatics		Dix
Tues Aug 26	Transition State Theory		Dix/Beeson
Thurs Aug 28	Principles of X-ray Crystallography		Davies
Fri Aug 29	Protein Modification		Eblen
Tues Sept 2	Protein Folding and Stability		TBA
Thurs Sept 4	Protein-Protein Interactions		Hsu
Fri Sept 5	Enzymes and Catalysis		Krupenko
Mon Sept 8	Enzyme Kinetics		Beeson
Tues Sept 9	Protein Purification		Hennig
Thurs Sept 11	Protein Characterization/Proteomics		Ball
Fri Sept 12	Proteomics/Informatics		Schwacke
Mon Sept 15	Global Overview		Beeson/Hsu
Tues Sept 16	Unit Exam

General reading Prerequisite reading for this Unit is Stryer's Biochemistry (6^th Ed, Chapters 3, 4 and 8) or Lehninger's Principles of Biochemistry (5th Ed., Chapter 3-6).

Date	Date	Flex	Instructor
Thurs Sept 18	Introduction to Unit 1. History, DNA structure 2. A, B & Z forms, W&C, base pairing		Kurtz Schweinfest
Fri Sept 19	1. Genetic code 2. Superhelicity + topoisomerases		Schweinfest Hennig
Mon Sept 22	1. DNA replication-DNA polymerases 2. DNA replication (continued)		Brown
Tues Sept 23	1. Recombination 2. DNA repair		Brown
Thurs Sept 25	1. tRNA synthetases, translation 2. Structure of the ribosome - decoding		Davies
Fri Sept 26	1. Catalytic RNA & RNA processing 2. RNA interference		Davies
Mon Sept 29	1. Transcription in prokaryotic genes 2. Mechanisms of transcriptional regulation		Davies
Tues Sept 30	Techniques in Nucleic acids research		Kurtz
Thurs Oct 2	Pharmacogenetics		Kurtz
Fri Oct 3	Genomics/epigenetics		Wolff
Mon Oct 6	Student presentations		Kurtz
Tues Oct 7	Student presentations		Kurtz
Thurs Oct 8	Student presentations		Kurtz
Fri Oct 9	Unit Exam		Kurtz

General reading

Prerequisite: Chapters 4-7 of Molecular Biology of the Cell, 5th Ed, Alberts et al. Also useful are Chapters 4, 5, 28, 29 & 30 in Stryer, 6th ed.

Date	Date	Flex	Instructor
Mon Oct 13	1. Biological thermodynamics & kinetics 2. Overview of bioenergetics & Redox		Beeson
Tues Oct 14	1. Lipids, bilayers & membranes 2. Membrane biophysics		Beeson
Thurs Oct 16	1. Transporters & channels: classes, function 2. Transporters & channels: techniques		Covington
Fri Oct 17	1. Overview of catabolism, anabolism 2. Signaling in regulation of metabolism		Beeson
Mon Oct 20	1. Mechanisms in Glycolysis 2. Gluconeogenesis		Davies
Tue Oct 21	1. Structural Aspects of Regulation		Davies
Thu Oct 23	1. Citric Acid Cycle 2. Beta oxidation		Lemasters
Fri Oct 24	1. Electron transport chain 2. Biophysics of mitochondrial membranes		Lemasters
Mon Oct 27	1. Chemiosmotic energy transduction 2. Oxidative Phosphorylation		Lemasters
Tue Oct 28	1. Glycogen metabolism 2. Fatty acid biosynthesis		Beeson
Thu Oct 30	Integrative metabolism and metabolomics		Beeson
Fri Oct 31	Final Exam

Background Reading Material

Biochemistry	Lehninger (5th Ed)	Stryer (6th Ed.)
Intro to Metabolism	14	15
Bioenergetics	13
Lipids, membranes	10	12
Ion channels	11	13
Glycolysis	14, 15	16
TCA	16	17
Oxidative-Phosph	19	18
Fatty Acid Oxidation	17	22
Pentose Phosphate Pathway (HMP-shunt)	15	20
Gluconeogenesis	14-15	16
Glycogen Synthesis	15	21
Glycogen Catabolism	15	21
Fatty Acid Synthesis	21	22

Useful Websites:

http://www.bmb.leeds.ac.uk/illingworth/oxphos/

http://www.esf.edu/efb/course/EFB325/default.htm

http://www.aw-bc.com/mathews/

http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/MB1index.html

Date	Date	Flex	Instructor
Mon Nov 3	1. Overview of receptors & signaling I	Methods of Studying Ligand:Receptor Interactions	Rosenzweig (rosenzsa)
Tues Nov 4	1. G protein coupled receptors	Paper discussion (1)	Blumer (blumerjb)
Thur Nov 6	G proteins and their regulatroy proteins	Paper discussion (2)	Blumer
Mon Nov 10	Photoreceptors	Paper discussion (3)	Koutaios (koutalo)
Tues Nov 12	Receptor tyrosine kinases	Paper discussion (4)	Rosenzweig
Thur Nov 13	Protein: protein interactions in signal transduction	Paper discussion (5)	Ball (balle)
Fri Nov 14	Receptor tyrosine kinase signaling to cell migration	Paper discussion (6)	Isaacs (isaacsj)
Mon Nov 17	Protein kinases: MAP kinases	Paper discussion (7)	Eblen (eblen)
Tues Nov 18	TGF- b Receptors and the Smads	Paper discussion (8)	Eblen
Thur Nov 20	Signaling to apoptosis	Methods exercise	Voelkel-Johnson (johnsov)
Fri Nov 21	Cell signaling in disease: cancer	Paper discussion (9)	Rosenzweig
Mon Nov 24	Cell signaling in disease: Animal models of Cancer	Paper discussion (10)	Neumann (neumannc)
Tues Nov 25	Unit Exam

General reading

Prerequisite: Chapters 15, 17 & 23 of Molecular Biology of the Cell, 5th Ed, Alberts et al.

Specific Reading

Papers will be posted on WebCT as required

Date	Date	Flex	Instructor
Mon Dec 1	1. Eukaryotic Transcription/Regulation of Gene Expression I 2. Eukaryotic Transcription/Regulation of Gene Expression II	Discussion of student presentations	Kyu-Ho Lee (leeh)
Tues Dec 2	3: Integrating Transcriptional Regulation Signaling Events 4: Epigenetic Regulation of Gene Expression		Kyu-Ho Lee
Thurs Dec 4	5. HDAC's and HAT's Role in Gene Expression 6. HDAC's and HAT's Role in Gene Expression II		Menick (menickd)
Fri Dec 5	7. RNA Interference I 8. RNA Interference II		Menick
Mon Dec 8	9. Regulation of mRNA Processing and Localization I 10. Regulation of mRNA Processing and Localization II		McDermott (mcdermp)
Tues Dec 9	11: Regulation of mRNA Stability and Translation Lecture 12: Regulation of Translation and Degradation	Practice talks	McDermott
Thurs Dec 11	13. Viral Models for Molecular Biology I 14. Viral Models for Molecular Biology II	Practice talks	Wright (wrightcf)
Fri Dec 12	Student presentations of research papers
Mon Dec 15	Student presentations of research papers
Tues Dec 16	Student presenations of research papers
Thurs Dec 18	Overview of Exam
Fri Dec 19	Unit Exam

Gerneral Reading

Prerequisite: Chapters 7, 8 and section 6.6 of Lodish et al, 6th Ed. Additional reading from recent reviews will be assigned by each lecturer.

Flex-Time

Primary research papers will be presented and discussed. Each student will select a current paper on gene expression (instructors will provide examples). Selected papers will be submitted for Unit leader approval by Friday, December 5, 2008. The Unit Leaders will give sample presentations, and students' initial flex-time presentations on December 9 and 11, 2008 will be in small groups (4-5 students) to maximize questions and input. Within each group, an instructor, postdoc TA or senior student will critique each presentation. Students will present to the entire class on December 12, 15, and 16, 2008. A secondary focus of Flex-times will be discussion of topics or techniques relevant to gene expression arising from lectures that day.

Grading

35% of the Unit grade will derive from in-Unit research paper presentation, and 65% will derive from the Unit exam (closed-book, in-class).

Date	Date	Flex	Instructor
Thurs Jan 8	Cell:Extracellular Matrix Interactions		Bradshaw (bradshad)
Fri Jan 9	Cell Motility	Paper discussion	Bradshaw
Mon Jan 12	Cytoskeletal Dynamics		Krug (krugel)
Tues Jan 13	Molecular Motors		Krug
Thurs Jan 15	Secretion and Vesicular Trafficking	Paper discussion	Krug
Fri Jan 16	The Eukaryotic Cell Cycle		Kurtz (kurtzdt)
Mon Jan 19	Oncogenes and cancer		Kurtz
Tues Jan 20	Tumor suppressor genes	Paper discussion	Kurtz
Thurs Jan 22	Integrating Cells Into Tissues		Gourdie (gourdier)
Fri Jan 23	Panel Discussions of Current Literature		Faculty and Class
Tues Jan 27	Panel Discussions of Current Literature		Faculty and Class
Thurs Jan 29	Unit Exam

General Reading

Chap 6, 16, 17, 19, 20, 21 and 23, Molecular Cell Biology, 5^th ed., Lodish

Specific Reading

Papers will be posted on WebCT before the relevant lecture.

Date	Date	Flex	Instructor
Fri Jan 30	1. Introduction 2. Causes, mechanisms, morphology of cell and tissue injury	Multihead scopes with pathologists. In-Unit assign #1.	Hazen-Martin (l)* (hazenmad)
Mon Feb 2	1. Cellular adaptations, cell death, and necrosis 2. Introduction to inflammation and repair	Tissue injury - a discussion of time-line of events. Assign #1 due.	Hazen-Martin (l/f)*
Tues Feb 3	1. Components of immune system I 2. Components of immune system II	Chose techniques rotation. In-Unit assign #2.	L. London (l/f) (londonl)
Thurs Feb 5	1. Immune system III	POPS**	L. London (l/f)
Fri Feb 6	1. Inflammation in acute cellular injury 2. Immunopathology - 2 examples of inflammation in disease	No flex; all lecture	Hazen-Maritn (l) S. Self (l) (selfs)
Mon Feb 9	No lecture/all flex	Paper discussion #1	Schnellman (f) (schnell)
Tues Feb 10	No lecture/all flex	Techniques rotation; in-Unit assign #3
Thurs Feb 12	1. Cellular senescence 2. Aging	Techniques follow up - discuss choice of papers with group	Zhou (l) (zhoud) Hazen-Martin (f)
Fri Feb 13	1. Apoptosis - historical overview 2. Apoptosis - Causes, mechanisms, and detection	Promote?/Prevent? Paper discussion #2	Cunningham (l) (cunninll) Brown (f) (broweri) Wei (f) (weil)
Mon Feb 16	1. Benign and malignant neoplasms 2. Biology of tumor growth	Work on group presentations.	Metcalf (l) (metcalfj)
Tues Feb 17	Stuent Techniques Presentations
Thurs Feb 19
Fri Feb 20	Unit Exam

* (l)=lecture, (f)=flex
** a group problem-solving workshop

General reading

Robbins Basic Pathology, 7^th edition (on reserve); the following chapters will supplement lecture notes:

Chapter 1:	Cellular Injury and response Aging Apoptosis
Chapter 2:	Inflammation
Chapter 5:	Diseases of Immunity
Chapter 6:	Neoplasia

If you prefer a more comprehensive version of this text try Robbins Pathologic Basis of Disease which is available on line through MD Consult. Additional articles and/or reviews may be provided in class.

Kuby's Immunology, 6^th edition (2006, by Janis Kuby, et.al.) Chapters 1-10 contain basic information that supplements lecture notes.

Specific Reading

Will be posted on WebCT before the relevant lecture and/or assignment.

Date	Date	Flex	Instructor (email)
Mon Feb 23	1. Introduction to the Unit 2. Molecular Mechanism for Aspirin Mediated Cardiovascular Prophylaxis		Halushka (halushpv)
Tues Feb 24	1. Mechanisms of Neurotransmission		Ramamoorthy (rama)
Thurs Feb 26	1. Autonomic Nervous System Control of the CV System		Webb (webbj)
Fri Feb 27	1. Molecular Basis of Electrical Mechanical Coupling		Menick (menickd)
Mon Mar 2	1. Molecular/Genetic Basis of Congenital Heart Disease		McQuinn (mcquinnt)
Tues Mar 3	1. Molecular Basis of Atherosclerosis		Hammad (hammadsm)
Thurs Mar 5	1. Molecular Basis of Neurodegenerative Diseases		Granholm (granholm)
Fri Mar 6	1. Renal Physiology		Bell (bellpd)
Mon Mar 9	1. Proteomic Tools for Analysis of Renal Disease		Arthur (arthurj)
Tues Mar 10	1. Microbial Basis of Infectious Diseases		John (johnjf)
Thurs Mar 12	1. Molecular Mechanisms of Innate Immunity		Cook (cookja)
Fri Mar 13	Unit Exam