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	Lectures	Flex	Instructor
Thurs Aug 27	Molecular Structure	Assignment 1 Distribution	Beeson (beesonc)
Fri Aug 28	Chemical Reactivity		Beeson
Mon Aug 31	Solvation and Electrostatics		Dix (dixta)
Tues Sept 1	Protein Folding and Stability		Beeson/Isaacs (isaacsj)
Thurs Sept 3	Principles of X-ray Crystallography		Davies (davies)
Fri Sept 4	Protein-Protein Interactions		Hsu (hsuy)
Tues Sept 8	Protein Modifications		Eblen
Thurs Sept 10	Protein Characterization/Proteomics		Ball (balle)
Fri Sept 11	Enzymes and Catalysis		Krupenko (krupenko)
Mon Sept 14	Enzyme Kinetics	Kinetics Questions	Beeson
Tues Sept 15	Protein Purification		Hennig (hennig)
Thurs Sept 17	Proteomics/Informatics		Schwacke (schwacke)
Fri Sept 18	Unit Exam

General reading Prerequisite reading for this Unit are Chapters 2, 3, 6, 10.3, 10.4, 23.3 and 23.3 of Stryer's Biochemistry (6^th Ed)

Date	Lectures	Flex	Instructor
Mon Sept 21	Introduction to Unit 1. History, 2. DNA structure	x-ray diffraction of DNA	Davies
Tues Sept 22	1. RNA structure		Hennig (hennig)
Thurs Sept 24	1. DNA replication 2. DNA replication (continued)	Prep for presentations	Brown (broweri)
Fri Sept 25	1. Recombination 2. DNA repair	Prep for presentations	Brown
Mon Sept 28	Student Presentations		Brown
Tues Sept 29	1. Transcription in prokaryotic genes 2. Mechanisms of transcriptional regulation in prokaryotes		Cowart (cowartl)
Thurs Oct 1	1. Genetic code 2. tRNA synthetases, translation		Davies
Fri Oct 2	1. Structure of the prokaryotic ribosome 2. Regulation of prokaryotic translation		Davies
Mon Oct 5	1. Catalytic RNA 2. RNA world hypothesis		Davies
Tues Oct 6	Techniques in nucleic acid research		Kurtz (kurtzdt)
Thurs Oct 8	Pharmacogenetics		Kurtz
Fri Oct 9	Unit Exam

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	Lectures	Flex	Instructor
Mon Oct 12	1. Biological thermodynamics & kinetics 2. Overview of bioenergetics & Redox	Redox Questions	Beeson
Tues Oct 13	1. Lipids, bilayers & membranes 2. Membrane biophysics		Beeson
Thurs Oct 15	1. Transporters & channels: classes, function 2. Transporters & channels: techniques	Transport Paper	Covington (covingt)
Fri Oct 16	1. Regulation of catabolism versus anabolism 2. Signaling in regulation of metabolism		Beeson
Mon Oct 19	1. Mechanisms in Glycolysis 2. Gluconeogenesis	Assignment 1 Due	Davies (davies)
Tue Oct 20	Structural Aspects of Regulation		Davies
Thu Oct 22	1. Citric Acid Cycle 2. Beta oxidation	Seahorse Lab	Lemasters (lemaste)
Fri Oct 23	1. Electron transport chain 2. Biophysics of mitochondrial membranes		Lemasters
Mon Oct 26	1. Chemiosmotic energy transduction 2. Oxidative Phosphorylation	Assignment 2 Due	Lemasters
Tue Oct 27	1. Mitochondrial DNA 2. Mitochondrial Diseases	Mito-DNA Paper	Chan (lamcf)
Thu Oct 29	Integrative metabolism and metabolomics	Questions Overview	Beeson
Fri Oct 30	Unit Exam

General Reading for the Metabolism and Bioenergetics Unit

	Lehninger (5th Ed) Chapter	Stryer (6th Ed.) Chapter
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	Lectures	Flex	Instructor
Mon Nov 2	Overview of receptors & signaling I	Methods of Studying Ligand:Receptor Interactions	Rosenzweig (rosenzsa)
Tues Nov 3	G protein coupled receptors	Paper discussion (1)	Blumer (blumerjb)
Thur Nov 5	G proteins and their regulatory proteins	Paper discussion (2)	Blumer
Mon Nov 9	Photoreceptors	Paper discussion (3)	Koutaios (koutalo)
Tues Nov 10	Receptor tyrosine kinases	Paper discussion (4)	Rosenzweig
Thur Nov 12	Protein: protein interactions in signal transduction	Methods for identifying & studying protein interactions	Ball (balle)
Fri Nov 13	Receptor tyrosine kinase signaling to cell migration	Paper discussion (6)	Isaacs (isaacsj)
Mon Nov 16	Protein kinases: MAP kinases	Paper discussion (7)	Eblen (eblen)
Tues Nov 17	TGF- b Receptors and the Smads	Paper discussion (8)	Eblen
Thur Nov 19	Signaling to apoptosis	Methods exercise	Voelkel-Johnson (johnsov)
Fri Nov 20	Cell signaling in disease: cancer	Paper discussion (9)	Rosenzweig
Mon Nov 23	Cell signaling in disease: Animal models of Cancer	Paper discussion (10)	Neumann (neumannc)
Tues Nov 24	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	Lectures	Flex	Instructor
Mon Nov 30	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 1	3: Integrating Transcriptional Regulation Signaling Events 4: Epigenetic Regulation of Gene Expression		Kyu-Ho Lee
Thurs Dec 3	5. HDAC's and HAT's Role in Gene Expression I 6. HDAC's and HAT's Role in Gene Expression II		Menick (menickd)
Fri Dec 4	7. RNA Interference I 8. RNA Interference II		Menick
Mon Dec 7	9. Regulation of mRNA Processing and Localization I 10. Regulation of mRNA Processing and Localization II		McDermott (mcdermp)
Tues Dec 8	11: Regulation of mRNA Stability and Translation 12: Regulation of Translation and Degradation	Practice talks	McDermott
Thurs Dec 10	13. Viral Models for Molecular Biology I 14. Viral Models for Molecular Biology II	Practice talks	Wright (wrightcf) Eisenman
Fri Dec 11	Student presentations of research papers
Mon Dec 14	Student presentations of research papers
Tues Dec 15	Student presenations of research papers
Thurs Dec 17	Overview of Exam
Fri Dec 18	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 4, 2009. The Unit Leaders will give sample presentations, and students' initial flex-time presentations on December 8 and 10, 2009 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 11, 14, and 15, 2009. 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	Lectures	Flex	Instructor
Tues Jan 5	Cell:Extracellular Matrix Interactions	Literature databases	Bradshaw (bradshad)
Thurs Jan 7	Cell Motility		Bradshaw
Fri Jan 8	Cytoskeletal Dynamics	Paper discussion	Krug (krugel)
Mon Jan 11	Molecular Motors		Krug
Tues Jan 12	Regulation of the Eukaryotic Cell cycle Tumor Suppressor Genes	Paper discussion	Wright (wrightcf)
Thurs Jan 14	Oncogenes Proto-oncogenes		Wright Spyropoulos (spyropdd)
Fri Jan 15	Sorting and Secretion	Paper discussion	Hunter (huntera)
Mon Jan 18	MLK Day - no classes
Tues Jan 19	Integrating Cells into Tissues		Gourdie (gourdier)
Thurs Jan 21	Cell Differentiation		Wooten-Blanks (wootenl)
Fri Jan 22	Panel Discussions of Current Literature		Faculty and Class
Mon Jan 25	Panel Discussions of Current Literature		Faculty and Class
Tues Jan 26	Unit Exam

General Reading

Chap 13, 14, 17-20, 22 and 25, Molecular Cell Biology, 6 ^th ed., Lodish

Specific Reading

Papers will be posted on WebCT before the relevant lecture.

Date	Lectures	Flex	Instructor
Thurs Jan 28	1. Introduction 2. Causes, mechanisms, morphology of cell and tissue injury	Multihead scopes with pathologists. In-Unit assign #1.	Hazen-Martin (l)* (hazenmad)
Fri Jan 29	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)*
Mon Feb 1	1. Components of immune system I 2. Components of immune system II	Chose techniques rotation. In-Unit assign #2.	London (l/f) (londonl)
Tues Feb 2	1. Immune system III	POPS**	London (l/f)
Thurs Feb 4	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)
Fri Feb 5	No lecture/all flex	Paper discussion #1	Schnellman (f) (schnell)
Mon Feb 8	No lecture/all flex	Techniques rotation; in-Unit assign #3
Tues Feb 9	1. Cellular senescence 2. Aging	Techniques follow up - discuss choice of papers with group	Zhou (l) (zhoud) Hazen-Martin (f)
Thurs Feb 11	1. Apoptosis - historical overview 2. Apoptosis - Causes, mechanisms, and detection	Promote?/Prevent? Paper discussion #2	Cunningham (l) (cunninll) Brown (f) (broweri) Wei (f) (weil)
Fri Feb 12	1. Benign and malignant neoplasms 2. Biology of tumor growth	Work on group presentations.	Metcalf (l) (metcalfj)
Mon Feb 15	Stuent Techniques Presentations
Tues Feb 16	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	Lectures	Flex	Instructor (email)
Thurs Feb 18	1. Introduction to the Unit 2. Mechanisms of Neurotransmission		Halushka (halushpv) Ramamoorthy (rama)
Fri Feb 19	The Heart and Arterial Pressure Control Mechanisms		Halushka
Mon Feb 22	Autonomic Nervous System Control of the CV System	In Unit Assignment	Webb (webbj)
Tues Feb 23	Molecular Basis of Atherosclerosis		Hammad (hammadsm)
Thurs Feb 25	Molecular Mechanism for Aspirin-mediated Cardiovascular Prophylaxis		Halushka
Fri Feb 26	Molecular Basis of Electrical Mechanical Coupling	In Unit Assignment	Menick (menickd)
Mon Mar 1	Renal Physiology		Bell (bellpd)
Tues Mar 2	Proteomic Tools for Analysis of Renal Disease	In Unit Assignment	Janech (janechmg)
Wed Mar 3	Molecular Mechanisms of Innate Immunity		Cook (cookja)
Thurs Mar 4	No Class
Fri Mar 4	Unit Exam