Chemistry 31 Course Outline + Interesting and Useful Links

Text Website: http://bcs.whfreeman.com/lehninger5e/

I Introductory Material	When I Heard the Learn’d Astronomer -- Walt Whitman What is Life? Characteristics of Living Things: http://www.cartage.org.lb/en/themes/Sciences/Zoology/AboutZoology/Characteristicslivingthings/Characteristicslivingthings.htm homeostsis: http://en.wikipedia.org/wiki/Homeostasis A. The Chemical Composition of Living Things B. The Cell Cosmic Evolution: http://www.tufts.edu/as/wright_center/cosmic_evolution/docs/splash.html Chemical Evolution: On the Origins of Life: http://www.biology-online.org/10/1_first_life.htm More Origins of Life: http://en.wikipedia.org/wiki/Origin_of_life Endosymbiosis: http://www.geocities.com/jjmohn/endosymbiosis.htm more endosymbiosis: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html More biomolecular evolution: http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/index.htm Cells Alive! http://www.cellsalive.com/ Look at cell structure: http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm "Cellupedia" http://library.thinkquest.org/C004535/ Thorough reviews of Cell Biology http://cellbio.utmb.edu/cellbio/ C. Water, Aqueous Solutions, and Buffers all about water: http://home.earthlink.net/~dayvdanls/lec2water.html more on water: http://www.sbu.ac.uk/water/explan.html Acids/ Bases fundamentals: http://www.biology.arizona.edu/biochemistry/problem_sets/ph/ph.html Clinically oriented acid/base quiz: http://www.biology.arizona.edu/biochemistry/problem_sets/medph/medph.html

II Macromolecular Structure	A. Proteins General Resources: The Home Page of the Protein Society http://www.proteinsociety.org/ Research Collaboratory for Structural Bioinformatics (RCSB): http://www.rcsb.org/pdb Protein Data Base (PDB) of the RCSB http://www.rcsb.org/pdb/ Expert Protein Analysis System http://www.expasy.ch/ European Molecular Biology Laboratory (EMBL): http://www.embl-heidelberg.de/ 1. The Amino Acids View the amino acids: http://chemistry.gsu.edu/glactone/PDB/Amino_Acids/aa.html Play the "amino acids game": http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm Quiz yourself: http://newcrop.hort.purdue.edu/rhodcv/hort640c/h640cq1/aaid.htm Amino acid titration: http://cti.itc.virginia.edu/~cmg/Demo/scriptFrame.html 2. The Primary Structure of Proteins Edman degradation animation: http://www.wiley.com/college/fob/quiz/quiz05/5-15.html Research Collaboratory for Structural Bioinformatics (RCSB): http://www.rcsb.org/pdb Protein Information Resource (PIR) - find a sequence: http://www.pir.uniprot.org/search/textSearch.shtml Entrez Protein:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein Hydropathy Plot (under "GREASE"): http://fasta.bioch.virginia.edu/fasta_www2/fasta_intro.shtml Compare sequences: http://pir.georgetown.edu/pirwww/search/pairwise.html Find a match: http://pir.georgetown.edu/pirwww/search/patmatch.html#PAT3 MIT resource: http://scansite.mit.edu Protein Music - a pitch is assigned to each amino acid of a protein sequence to generate a tune! http://www.whozoo.org/mac/Music/ 3. The 3-D Structure of Proteins - Secondary, Super Secondary, Tertiary and Quaternary Structure Protein Data Bank structure viewing: http://pir.georgetown.edu/pirwww/search/textpsd.shtml Fun with phi and psi angles: http://cti.itc.Virginia.EDU/~cmg/Demo/scriptFrame.html Plotting with Ramachandran: http://dicsoft1.physics.iisc.ernet.in/rp/index.html Another Ramachandran Plotter: http://www.fos.su.se/~pdbdna/input_Raman.html Another Ramachandran Plotter: http://swift.cmbi.ru.nl/servers/html/ramaplot.html Helical Wheel viewer: http://cti.itc.virginia.edu/~cmg/Demo/scriptFrame.html 1^o --> 2^o structure analysis: http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html 2^o and super-2^o structure: http://www.wellesley.edu/Chemistry/chem227/protstruct/prtnstrc.htm About tertiary structure: http://www.expasy.ch/swissmod/course/text/chapter4.htm Database of tertiary structures: http://www.cbi.cnptia.embrapa.br/SMS/STINGm/ramachandran/ Proteins to study and view: http://cti.itc.virginia.edu/~cmg/Demo/scriptFrame.html A nice collection of proteins to view: http://chemistry.gsu.edu/glactone/PDB/Proteins/Classic/classic.html a protein structure quiz: http://www.bio.cmu.edu/Courses/BiochemMols/ArchQuiz/ArchQMain.htm 4. The Process of Protein Folding/Unfolding About protein folding: http://opa.faseb.org/pdf/protfold.pdf#search=%22protein%20folding%22 Molecular chaperones: http://en.wikipedia.org/wiki/Chaperone About protein denaturation: http://class.fst.ohio-state.edu/FST822/lectures/Denat.htm About Proteasomes: http://homepages.bw.edu/~mbumbuli/cell/protlec/ 5. Myoglobin and Hemoglobin Mb and Hb details (see O2 binding proteins): http://www.worthpublishers.com/lehninger3d/ Globin Gene Server (good place to study Hb variants) http://globin.cse.psu.edu/ Hb-S image: http://www.wellesley.edu/Chemistry/chem227/bindprotns/hbsickle.htm B. Carbohydrates General resources: A few carbohydrates to view via PDB http://www.nyu.edu:80/pages/mathmol/library/sugars/ The IUPAC guide to carbohydrate nomenclature http://www.chem.qmw.ac.uk/iupac/2carb/ 1. Monosaccharides A monosaccharide browser http://www.jonmaber.demon.co.uk/monosaccharide/ The making of the cyclic hemiacetal: http://www.caos.kun.nl/~borkent/wetche/bdgluc/glucanim.html 2. Disaccharides Disacchardes to view: http://www.genome.ad.jp/kegg/catalog/cpd_disacch.html 3. Polysaccharides general info glycosaminoglycans & proteoglycans: http://www.med.monash.edu.au/biochem/thcme/glycans.html a proteoglycans web site: http://bssv01.lancs.ac.uk/gig/pages/pgpage.htm a glycosaminoglycans web site: http://bssv01.lancs.ac.uk/gig/pages/gagpage.htm 4. Carbohydrate-Protein Combos - Proteoglycans and Glycoproteins a slide show on PGs and GPs: http://www.vei.co.uk/eurotron/egtm-1/Spillmann/slide1.html C. Lipids 1. Classes of Lipids Construct a phospholipid: http://www.uiowa.edu/~acadtech/ntitle_audio/flash/sjolund/3_Phospholipids.html A few lipids to view via PDB http://www.nyu.edu:80/pages/mathmol/library/lipids/ Another set of lipids to view http://www.wellesley.edu/Chemistry/chem227/lipids/lipids.htm A 3-D view of cholesterol http://www.recipnet.indiana.edu/rotate/Submit.cgi/cholesterol About Lorenzo's oil: http://carbon.cudenver.edu/~bstith/loren.htm 2. Lipid Assemblies All about liposomes http://www.unizh.ch/onkwww/lipos.htm 3. Biological Membranes Nice graphics of membranes: http://www.wellesley.edu/Chemistry/chem227/lipids/membranes.htm A membrane model-- membrane model 4. Lipid-Protein Combos - Lipid-Linked Proteins and Lipoproteins lipoproteins: cholesterol metabolism: http://www.ovc.uoguelph.ca/BioMed/Courses/Public/Pharmacology/pharmsite/98-409/Blood/Images/cholesterol_metab.gif 5. Glycolipids Blood groups: http://oregonstate.edu/instruction/bb450/stryer/ch11/Slide56.jpg

III Reactions of Biological Molecules	A. Enzymes Nice summaries: http://web.mit.edu/esgbio/www/eb/ebdir.html http://www.biochem.arizona.edu/classes/bioc462/462a/NOTES/ENZYMES/enzyme_mechanism.html http://www.biochemweb.org/fenteany/teaching/452/EnzymeMechanism.pdf 1. Overview Enzyme database: http://www.expasy.org/enzyme/ A nice summary of coenzyme structure & function: http://web.indstate.edu/thcme/mwking/vitamins.html 3-D graphical representations of common coenzymes: http://chemistry.gsu.edu/glactone/PDB/Cofactor/cofactor.html 2. Kinetics animated reviews of MM and LB kinetics http://cti.itc.virginia.edu/~cmg/Demo/scriptFrame.html An online course from Paisley University: http://orion1.paisley.ac.uk/Kinetics/contents.html see enzyme inhibition: http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm 3. Mechanism Lecture Examples: RNase: http://www.web-books.com/MoBio/Free/Ch2E3.htm http://www.nd.edu/~aseriann/rnase.html Amino Acid decarboxylase: http://cti.itc.virginia.edu/~cmg/Demo/scriptFrame.html Enolase: Lysozyme: http://employees.csbsju.edu/hjakubowski/classes/ch331/catalysis/olcatenzmech.html animated!: http://www.angelo.edu/faculty/nflynn/Biochemistry/Lysozyme%20Catalytic%20Mechanism.htm Serine Protease: http://cgat.ukm.my/protease/serinemech.html http://wps.prenhall.com/wps/media/objects/726/744224/0120f.html http://www.bio.cmu.edu/courses/03231/Protease/SerPro.htm Aspartate Protease: http://cti.itc.virginia.edu/~cmg/Demo/scriptFrame.html http://cgat.ukm.my/protease/asparticmech.html Other Examples: Carboxypeptidase: http://www.angelo.edu/faculty/nflynn/Biochemistry/CA%20Catalytic%20Mechanism.htm Carbonic Anhydrase: http://oregonstate.edu/instruction/bb450/lecturenoteskevin/catalyticstrategiesoutline.html A nice lecture from biochemweb: http://www.biochemweb.org/fenteany/teaching/452/EnzymeMechanism.pdf B. Metabolism 1. General Concepts Pathways galore: http://www.genome.ad.jp/kegg/metabolism.html 2. Glycolysis a) Reactions Glycolysis reactions: http://ull.chemistry.uakron.edu/Pathways/glycolysis/index.html Glycolysis animated: http://www.gwu.edu/~mpb/glycolysis3d.htm Others ---- glycolysis in action Glycolysis, the Movie Glycolytic enzymes highlighted: http://chemistry.gsu.edu/glactone/PDB/Proteins/glycolys/glyco.html b) Regulation Regulation of the Phosphofructokinases and the Bisphosphatases: http://web.indstate.edu/thcme/mwking/glycolysis.html#regulation c) Fates of pyruvate fates illustrated: http://ull.chemistry.uakron.edu/Pathways/pyruvate/index.html an animation of pyruvate dehydrogenase http://www.chembio.uoguelph.ca/educmat/chm258/pdhanim.shtml another: http://www.med.unibs.it/~marchesi/Animation_PDH.gif step-by-step: http://www.brookscole.com/chemistry_d/templates/student_resources/shared_resources/animations/pdc/pdc.html see pyruvate dehydrogenase complex: http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm 3. The Citric Acid Cycle reactions of citric acid cycle: http://ull.chemistry.uakron.edu/Pathways/Citric_acid_cycle/index.html The Citric Acid cycle : http://www.gwu.edu/~mpb/citric3d.htm interactive citric acid cycle: http://www.wiley.com/legacy/college/boyer/0470003790/animations/tca/tca.swf Another - citric acid cycle in action Following the carbons The Cycle highlighting the enzymes: http://chemistry.gsu.edu/glactone/PDB/Proteins/Krebs/BACKUP/Krebs.html#1pyd (4. The Glyoxalate Pathway) 5. Electron Transport and the Synthesis of ATP A good discussion of ET/OxPhos: http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/oxphos.htm#animat2 electron transport animated (Note Complex 2 is equivalent in this diagram to our Complex III with a link to OxPhos http://www.sp.uconn.edu/~terry/images/anim/ETS.html Another view of ET and OxPhos http://www.gwu.edu/~mpb/oxidativephos.htm A more detailed animation of OxPhos http://www.harcourtcollege.com/chem/biochem/Campbell/Animations/OxidativePhosphorylation.html The structure of ATP F1: http://info.bio.cmu.edu/courses/03740/ATPase/BMFMain.htm http://plantcell.lu.se/ltm/05/chime.html About ATP synthase: http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/f1fo.htm#animat1 Watch ATP synthase in action animated ATP synthase Another pair of animations: •http://www.stolaf.edu/people/giannini/flashanimat/metabolism/atpsyn1.swf • •http://www.stolaf.edu/people/giannini/flashanimat/metabolism/atpsyn2.swf ATP synthase movies: http://nature.berkeley.edu/~hongwang/Project/ATP_synthase/ 6. Transport Mechanisms 7. Gluconeogenesis reactions of gluconeogenesis: http://ull.chemistry.uakron.edu/Pathways/gluconeogenesis/index.html Gluconeogenesis/Glycolysis animated http://www.gwu.edu/~mpb/gluco3d.htm 8. Glycogenesis / Glycogenolysis glycogen synthesis/usage: http://ull.chemistry.uakron.edu/Pathways/glycogen/index.html glycogen phosphorylase cascade glycogen synthase cascade (9. Pentose Phosphate Shuttle) Pentose Phosphate Pathway animated http://www.gwu.edu/~mpb/pentphos3d.htm (10 b-oxidation of Fatty Acids)