The Ph.D. Program in Biochemistry The Graduate Center, City University of New York Biochemistry U750 - Bioorganic Chemistry Syllabus, Fall 2002

General References:

• IUPAC - IUB Glossary of Terms for Bioinorganic Chemistry
• IUPAC - IUB Basic Terminology of Stereochemistry
• IUPAC Compendium of Chemical Terminology
• IUPAC Glossary of Terms used in Physical Organic Chemistry
• IUPAC Glossary of Terms used in Medicinal Chemistry
• IUPAC  Natural Products and Related Compounds
• Classic Organic Reactions..from Chempen
• Named Reactions.at UConn
• Named Organic Reactions at Merck Index
• Organic Syntheses (requires free Chemdraw Plugin, see other requirements)
• Our Library, Net, and Database Resources
• Principles of Protein Structure at Birbeck
• Glick's Glossary of Biochemistry & Molecular Biology
• Named Organic Chemistry Effects and Rules and Bordwell pKa Table at Wisconsin
• Chemexper Organic Compound Database

• IUPAC - IUB
• Nomenclature and Symbolism for Amino Acids and Peptides
• Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains
• Nomenclature of glycoproteins, glycopeptides and peptidoglycans
• Abbreviated Nomenclature of Synthetic Polypeptides
• AminoAcids.at U of Oregon
• Amino Acids at the FU of Berlin
• Amino Acids at Kenyon
• Amino Acids and Course at Brescia
• Amino Acids Repository..at IMB-Jena
• Amino Acid Derivatives at PSD
• Lecture.at the U of Michigan
• Lecture..at Haverford
• Lectures..at Vanderbilt
• Lecture Notes at MSU and at Bristol
• Structural & Functional Properties of Amino Acids at Reading
• Shorthand Symbols for the Amino Acids at Sonoma
• Amino Acid Stereo Configuration and an AA Tutorial..at Georgia
• Amino Acid Home Page,  AA Stereochemistry,.& Peptide Structure at Georgia Tech
• Amino Acids Lecture, Amines & Acid-Base Chemistry, and Proteins & Denaturation..at UIUC
• pK's of Amino Acids at MIT
• Biosynthesis of Aromatic Amino Acids at Cornell
• Amino Acids and Structure-Function Lectures at the HU of Jerusalem
• Amino Acids at Newhaven
• Amino Acid and Protein Problems at Wisconsin
• Emil Fischer at Pepnet
• History at Brescia
• Classic Papers:
• Heinrich Hlasiwetz & Josef Habermann on Peptides
• Franz Hofmeister on the Peptide Bond
• Leonor Michaelis & Maud Leonora Menten on The kinetics of invertase activity
• Gerardus Johannes Mulder on the composition of proteins (1839)
• JN Bronsted on acids and bases (1923)
• S.P.L. Sörenson on pH (1909)
• Wilhelm Ostwald on Catalysis (1894)
• Ludwig Ferdinand Wilhelmy on the action of acids on sugar (1850)
• Joseph Achille LeBel on tetrahedral carbon
• Charles Adolphe Wurtz on ammonia (1849)
• Jean-Baptiste-André Dumas on Acetic and Chloroacetic Acids (1839)
• August Wilhelm von Hofmann on the organic bases (1851)
• Jacobus Henricus van 't Hoff optical activity and the tetrahedral geometry of carbon (1874)
• Friedrich Wöhler,  The artificial synthesis of urea (1828)
• Justus Liebig, on the Nitrogen balance in Nature (1843)
• Henri Louis Le Chatelier on Chemical Equilibrium (1884)

• History, part 2
• R. Bruce Merrifield
• Linus Pauling
• Panayotis Katsoyannis
• Vincent DuVigneaud
• Wang Ying-lai (2)
• Miklos Bodanszky
• J.M. Stewart,  R.C. Sheppard, A.M. Felix,
• G. Barany, S.B.H. Kent, D. Andreu, C. DiBello, M. Goodman, J. Tam,

E. Gross, J. Meienjofer, L. Carpino, H. Yajima, N. Fujii, S. Sakakibara,
W. DeGrado, E.T. Kaiser, V. Hruby, M. Lebl, etc.,
• Peptide Bond Synthesis & Sequencing
• Amino Acids and Peptide Synthesis at Nottingham
• Peptide Synthesis at Victoria
• Recent Papers on SPPS at 5z.com
• Peptide Structure Determination at UCSD
• Chemistry of Oligopeptide Synthesis & Protective groups at Interactiva
• Peptide Synthesis..at AnaSpec
• Structure, Sequencing and Synthesis at WSU
• Sequencing via MS at ABRF
• Sequencing via MS at Protana
• Strategies for Sequencing at MIT
• Enzymatic Peptide Synthesis at Sigma
• Intein-Based Splicing at NE Biolabs
• The Ugi Condensationat UConn
• Merrifield Peptide Synthesis at Vanderbilt
• Leuchs N-carboxyanhydrides .at Skopje
• Bailey N-Carboxyanhydride peptide synthesis at Skopje
• Polymerization via N-carboxyanhydrides at J. Mol. Evol.
• Bergmann Azlactone Peptide Synthesis &  the Bergmann-Zervas CarbobenzoxyMethodat Skopje and Chempen
• Bergman Synthesis of Azalactones, Determination of C-terminal amino acids, at Skopje
• Determination of C-Terminal Amino Acids by Thiohydantoin Formation at ABRF
• Schotten-Baumann Reaction at Chempen and at Skopje
• Simonini Reaction.for ester formation at Chempen and at Skopje
• Ester vs amide solubility from U of Texas
• Asp-Pro Lability from Medline
• Problems.and.Key at Binghamton
• Tips at ABRF
• Oligonucleotide-Peptide Adducts at Glenn
• Enzymatic Peptide Coupling at Altus
• History of Modeling at Brunel
• Proteins at Friedli
• Protein Structure at Stirling
• Protein Folding Problems. at Wisconsin
• An overview of molecular forces in relation to protein structure Oliver Smart
• Lectures on Proteins at Erlangen

• Reactions Related to Amino Acid Synthesis
• The Passerini Reaction (Medline)
• The Strecker Amino Acid Synthesis.at Bristol & Degradation..at Chempen
• The Voight Amination..at Chempen
• Amino Acid Synthesis at Vanderbilt
• Wöhler's Urea Synthesis..at Chempen and at JACS
• Akabori Amino Acid Reactions to form Aldehydes .at Chempen and at Skopje(2)
• Arndt-Eistert Synthesis of higher homologues of carboxylic acids at Skopje
• Beckmann Rearrangement at Chempen and at Skopje
• Bedoukian Synthesis of alpha-halo ketones & alpha-halo aldehydes at Skopje
• Beecham Synthesis: Ketones & aldehydes from chloroanhydrides of N-tosyl-a-aminoacids at Skopje
• Baeyer reaction of haloacetylcarbamide at Skopje
• Bischler-Möhlau Indole Synthesis at Chempen and Skopje
• Blaise Synthesis of ketones & Synthesis of aldehydes at Skopje
• Bodroux Amide Formation..at Chempen
• Bosch-Meiser Urea Process..at Chempen
• Bouveault-Blanc Synthesis of primary alcohols from esters at Skopje
• Bouveault Hydrolysis of amides at Skopje
• Bouveault-Locquin reaction of alpha-isonitroesters at Skopje
• Breckpot synthesis of substituted beta-lactams  at Skopje
• Bucherer-Bergs Reaction at Chempen and at Skopje
• Buchner-Curtius-Schlotterbeck Reaction..at Chempen
• Claisen Synthesis of esters of cinnamic acid at  Skopje
• Clibbens-Nierenstein Synthesis of halomethyl ketones at Skopje
• Curtius Rearrangement to make isocyanates and amines at Chempen and at Skopje
• Dakin-West Reaction (formation of N-acylated amino acid esters) at Chempen
• Darapasky Degradation to form amino acids at Chempen and Skopje
• Diels-Reese Reaction..for indole formation at Chempen
• Eschweiler-Clarke Methylation amines with formaldehyde at Skopje
• Fenton Reaction for formation of alpha-keto acids at Chempen
• Fischer Indole & Peptide.Syntheses..at Chempen
• Fischer-Speier Esterification Method..at Chempen
• Fossek-Page-Conant Synthesis of alpha-oxyalkylphosphonic acids at Skopje
• Frankland-Duppa Reaction..for alpha-hydroxy acid synthesis at Chempen
• Grundmann Aldehyde Synthesis..at Chempen
• Hell-Volhard-Zelinsky Halogenation. at Chempen
• Heumann Indigo Synthesis..at Chempen
• Hinsberg Reaction (Hinsberg Test). at Chempen
• Hofmann Rearrangement. to make carbamates and amines at Chempen and at UConn
• Hunsdiecker Reaction (Borodine Reaction).decarboxylation at Chempen
• Japp-Klingemann Reaction.to make alphahydrazino compounds at Chempen
• Knoop-Oesterlin Amino Acid Synthesis..at Chempen
• Lossen Rearrangement. to make isocyanates at Chempen
• Mannich Reaction.. to make beta-amino ketones at Chempen
• Mannich and other addition reactions at Iowa
• Marckwald Asymmetric Synthesis.. at Chempen
• Neber Rearrangement. to make alpha-amino ketones at Chempen
• Passerini Reaction..to make alpha-hydroxy amides at Chempen
• Reissert Indole Synthesis..at Chempen

 
• Amino Acid & Peptide Modification Reactions

 
• The Ninhydrin Reagent at Bryn Mawr and the U of Michigan
• Parikh-Doering Oxidation of alcohols to aldehydes at UConn
• Pinner Amidine Synthesis..at Chempen
• Sandmeyer Diphenylurea Isatin Synthesis & the Isonitrosoacetanilide Isatin Synthesis..at Chempen
• Schmidt Reaction..to make amines, nitriles, and amides at Chempen
• Sorensen Formol Titration..at Chempen
• Urech Hydantoin Synthesis..at Chempen
• Van Slyke Determination..at Chempen
• Willgerodt-Kindler reaction to make thioamides at UConn
• Voight Amination..at Chempen
• Wolff Rearrangement..via substituted ketenes to make esters and amides at Chempen
• Enantiomeric Determination via Mosher's Acid at UConn
• Chemical Modification of Amino Acid Side Chains,..Affinity Reagents, and Peptide Synthesis at Gustavus Adolphus
• Conjugation Reactions at Applied Biosystems
• Maillard Reactions at Oregon and UC Davis-2
• Tyrosine Oxidation at UC Davis
• Problem Sets at Binghamton

 
• Reactions of Amino Acids & Related Compounds that Relate to Potentially Prebiotic Chemistry

 
• The Miller-Urey Experiment from USM
• Nitrogen Fixation and Cyanamide at Britannica
• Andrussov Oxidation..of Methane and Ammonia to form cyanide at Chempen
• Calcium Carbide and Acetylene at the ACS
• Nitrogen Fixation at BYU and Kentucky
• The Chemistry of Nitrogen at Purdue
• Peptides from amino acids activated by CO and (Ni,Fe) Surfaces Wächtershäuser
• Black Smokers at USGS and at NOAA (2) and UIUC

 
• Combinatorial Chemistry
• Small Molecule Libraries at Vanderbilt
• Split Synthesis. at Vanderbilt
• Combinatorial Chemistry Review at the ACS
• Protein Expression and Display Libraries at CSU Northridge
• Genetics of Antibody Diversity at UC Davis

• Peptide Structure Determination at UCSD
• Plant Sulfur Metabolism at Kentucky
• The Sulfur Cycle at Ohio State and at Kentucky
• Possible Prebiotic Sulfur Chemistry from Indiana
• Acetylthioester formation Huber & Wächtershäuser
• The Thioester World by C. deDuve

• Nomenclature & Stereochemistry of Carbohydrates at Iowa State
• Monosaccharide Browser by Jon Maber
• Monosaccharides, Formation & cleavage of Glycosides, & Glycoconjugates, at Wayne State
• Carbohydrates..at Monash and Brescia
• Glycolysis by Jon Maber
• Carbohydrates at Mills
• Sugars at MIT
• Glycoside Synthesis at Clyde
• N-Glycans, Structure and Synthesis at U of Mainz
• Amadori Rearrangement at Chempen and Skopje
• Maillard Reaction at Oregon and UC Davis-2
• Caramelization at UC Davis
• Barry Oxidation of oligo- or polysacharides with periodates, followed by reaction with phenylhydrazine at Skopje
• Bergmann-Schotte Oxidation of unsaturated sugars at Skopje
• Bertrand oxidation of polyols at Skopje
• Böeseken: specific configuration at the anomeric center in aldoses. at  Skopje
• Bonner Halogenation of alkylthioglucosides at Skopje
• Buchner-Curtius-Schlotterbeck Methylation of aldehydes at  Skopje
• Corey-Winter Synthesis of olefins from sugars at Skopje
• Creighton Carbonyl Reduction at Chempen and at Skopje
• Criegee Preparation of cis-alpha-sugars and Oxidation of a-sugars at Skopje
• Delépine Reaction (Ag⁺ oxidation of aldehydes) at Skopje
• Fischer Phenylhydrazone and Osazone Reaction..at Chempen
• Mechanism of Osazone Formation at UCSD
• Imine Formation at SIU
• Haworth Methylation..at Chempen
• Helferich Method for the formation of phenylglycosides at Chempen
• Kiliani-Fischer Synthesis.of carbohydrates via cyanide at Chempen
• Koenigs-Knorr Synthesis of glycosidic linkages at Chempen and Skopje
• Lobry de Bruyn-van Ekenstein Transformation. of aldoses and ketoses.at Chempen
• Malaprade Reaction (Periodic Acid Oxidation)..at Chempen
• Purdie (Irvine-Purdie) Methylation..at Chempen
• Schiff Reaction (Schiff Bases)..at Chempen
• Tollens Reagent..at Chempen
• Walden Inversion..Sn2 Reaction at Chempen
• Weerman Degradation..at Chempen
• Wohl Degradation; Zemplen Modification..to reduce the size of a sugar at Chempen
• Woodward cis-Hydroxylation..at Chempen
• Carbohydrates..at Murdoch
• Rubisco Mechanism at Hamburg
• Triose Phosphate Isomerase at Emory
• Biotransformationat Texas A&M-Corpus Christi See sections B&D
• Drug Metabolism at UCLA
• The C4 (Hatch-Slack) Pathway at Wisconsin
• The CAM Pathway..at Wisconsin
• Dark Respiration in Plants at Wisconsin
• Photorespiration..at Marietta
• Carbohydrate Structure Exercises at MSU
• Other Compounds ... Isoprenes and alkaloids at Kentucky
• Oligosaccharide Synthesis at Glyko, at Sigma, at Glykoscience, at Alchemia, and at Hokudai
• Undergraduate Practice Problems at UCLA

• Molybdate analysis of phosphates at Clark Atlanta
• Korman and McLick's Pseudorotation Mechanism
• Psuedorotation..at Nijmegen
• Psuedorotation Movie at UNM
• The Wittig Reaction .. at Sunderland, at Old Dominion, Wayne State, & at Chempen
• Michaelis-Arbuzov Reaction..at Chempen
• The Chemistry of Phosphorous at Purdue
• The Mechanism of Ribonuclease at Virgina
• The Barnase Mechanism at Cambridge
• The Ribonuclease Mechanism at NIST
• Arginine Kinase at Florida
• AP Endonuclease at Scripps
• RNA Processing at UCSD
• Polymerases at Jena
• Hammerhead Ribozyme Mechanism at Tulane
• Structure and Function of the Hammerhead Ribozyme at Stevens
• The Transition State of Alkaline Phosphatase at Medline
• Phosphatase references at Miami
• DFP and Chymotrypsin at UBC
• Organophosphate Insecticides at U Nebraska
• Activation of Organophosphate Insecticides from UC Berkeley
• Organophosphate Cholinesterase Inhibitors at INRA Montpellier
• Phosphotriesterase..from Texas A&M
• PhosphonomethylGlycine: Herbicide and Potential Antimalarial from Medline

• DOE Primer on Molecular Genetics at JHU
• DNA/RNA Structure Tutorial at Tulane; Nucleic Acid Database at Rutgers
• Tautomerization of Nucleic Acid Bases at U. of New Hampshire
• Mutation and DNA Repair at Quinnipiac
• Biginelli Pyrimidine Synthesis at Chempen and at Skopje.
• Traube Purine Synthesis..at Chempen
• Fischer-Ach Synthesis of uric acid at Skopje
• Behrend-Roosen Synthesis of purines at Skopje
• Phosphorylimidazole-based Oligomerization of RNA at MBL and JBSD
• Ribozyme-mediated RNA Ligation at PNAS
• Ribozyme-Mediated Hydrolysis and Ligation at PNAS
• Ribozymes that ligate to form 5'-5' linkages at Harvard
• A Deoxyribozyme that Ligates DNA at PubMed
• Ribozyme Engineering at BioScience
• RNA Ligation of AMP-Activated Oligonucleotides at PubMed (see the cap structure)
• Trinucleotide Extension at PubMed
• Redox activity in RNA at PubMed
• Nucleotide Synthesis at Vanderbilt
• DNA Biosynthesis at Wisconsin
• Chemical DNA Synthesis at JHU, MSU, at NotreDame, Vanderbilt and at Interactiva
• Ribozymes at Brown  and at Bioscience
• Ribozymes and catalytic RNAs at CSU Northridge
• RNA Images at UCSD
• Deoxyribozymes..by Breaker
• The Ribosome is a Ribozyme at Colorado
• DNA Sequencing at Vanderbilt
• Intercalation at Vanderbilt
• DNA Carcinogen Adducts at Vanderbilt
• DNA Binders at Vanderbilt
• TNA at Medline
• Pentopyranosyl and Hexopyranosyl Oligonucleotides at Medline and Nucleic Acids Research
• MorpholinoNucleic Acids at Antisense & Nucleic Acid Drug Development
• Phosphoramidite-Modified DNA at LLNL
• AZT-TP at Uppsala, with Reverse Transcriptase at CMU
• EcoR1 and Modified Nucleosides at CMU and Utah
• Modified Nucleosides at Utah
• Peptide Nucleic Acids and other Nucleic Acid Structures at UMass
• Hoogsteen Base Pairs at CUNY
• PNA Clamps at Nucleic Acid Research
• Normal and Hoogsteen Base-Pairing in a PNA Clamp Triple Helix
• RNA/DNA Structures at UMD
• A Leucine Zipper at UNL
• Structures of Proteins that Bind DNA at Poznan, U Alabama-Birmingham  and UWLax

• General Acid-General Base Catalysis at Arizona and at the U. of the Sciences in Philadelphia
• Use of Linear Free Energy Relationships / Quantitative Structure-Activity Relationships
• At Indiana U. of PA, At U. of N. Iowa, At U of MD
• At NetScience, in JBC, at Virginia Tech, at U of MT
• at Utrecht, at Sheffield, Software at Buffalo
• The Hansch Equation at ACCVIP
• Problem Sets & Answers at Buffalo
• A Guide to LogP and pKa Measurements and Their Use Mark Earll
• Reaction Kinetics
• At U. of N. Iowa, at Portland State
• Scatchard and Kinetics Plots at UT Dallas
• The Eadie Hofstee Plot at SIU
• Kinetics Plots at OK State
• General Acid-General Base Catalysis
• Of Acid Proteases at Daresbury
• Of Model Reactions at UC Santa Cruz and at Lethbridge
• Organic Chemistry Base Catalysis at Wisconsin
• Catalysis Problems at USUHS and at Binghamton
• Introduction to Enzyme Kinetics at Paisley
• Kinetics Problems at Wisconsin and at USUHS
• Enzyme Mechanisms at Arizona, the U. of Montana and at U of Texas
• Enzymes at SDSU
• Types of Enzymes at UIUC
• Chymotrypsin at Guelph and, with Enzyme Kinetics, at UCSC
• Lysozyme at UCSC
• Enzyme Mechanisms and Transition State Analogs at University of the Sciences in Philadelphia
• Mechanisms of Catalysis, including Proximity & Orientation at Humboldt and at SIU
• Specific and General Catalysis at UT Dallas
• Strain Catalysis at Lund
• Enzymes that Cause Strain: Kinesin at MCRI,  Molecular Motors at Virginia
• Theories of Enzyme Catalysis at UCSC
• Theories of Catalysis at Reading
• Molecular Imprinting at Analytical Chemistry
• Complexes at UConn (Powerpoint)
• Cyclodextrins.at Charles U. Prague, at Bowdoin.& at Uppsala
• Cyclodextrin Glycosyltransferase at Groningen
• Cyclodextrin-based analyses at Akita
• Pericyclic Reactions in Abzymes at Imperial College
• Host-Guest Compounds at Osaka
• Calixarene at AIST and at Buffalo State
• Cryptands.at Wellesley
• Metal Ion Catalysis at MTU
• Metal Ion Activation of Water at SIU
• Proximity and Metal Ion Catalysis at Humboldt
• Lead and Lanthanide Participation in Ribozyme Reactions from J. Biochem.
• Zeolyte Structures.at CCLRC
• The ZSM-5 Zeolyte Catalyst at Oxford and at U. of Illinois at Springfield
• ZSM-5 Activity at UCSD and Structure at U. of Illinois at Springfield
• ZSM-5 Synthesis at Binghamton
• Zeolytes at Lund
• Catalysis.at Liverpool
• Reppe Chemistry at Chempen

Other Resources

• Integrated Reaction Roadmap at MSU
• CIP Nomenclature Practice at Kent State
• Nucleophilic Reactions Tutorial at Kent State