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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Organic Chemistry With A Biological Emphasis Volume I, Timothy Soderberg Jul 2019

Organic Chemistry With A Biological Emphasis Volume I, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for a two-semester ...


Organic Chemistry With A Biological Emphasis Volume Ii, Timothy Soderberg Jul 2019

Organic Chemistry With A Biological Emphasis Volume Ii, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for a two-semester ...


Substrate Specificity Of The Lipn Hydrolase From Mycobacterium Ulcerans, Stephanie Raynor Jan 2016

Substrate Specificity Of The Lipn Hydrolase From Mycobacterium Ulcerans, Stephanie Raynor

Undergraduate Honors Thesis Collection

Mycobacterium ulcerans is the causative agent of Buruli ulcer, a tropical skin disease that affects thousands of individuals annually. Recent studies have revealed that lipolytic enzymes are involved in the pathogenicity processes of mycobacterium and could be potential targets for novel antibiotics. LipN is one proposed serine hydrolase in Mycobacterium ulcerans that contains the conserved α/β hydrolase protein fold and utilizes the conserved catalytic traid of serine, histidine, and aspartate/glutamate. The physiological substrate and biological role of LipN from M. ulcerans have not yet been determined. In this study, LipN was cloned into a pET28a plasmid and overexpressed ...


Design, Synthesis, And Evaluation Of Molecular Inhibitors For Biologically Relevant Enzymes, Sarah Emma St. John Oct 2013

Design, Synthesis, And Evaluation Of Molecular Inhibitors For Biologically Relevant Enzymes, Sarah Emma St. John

Open Access Dissertations

The work in this thesis details the design, synthesis, and biological evaluation of molecular inhibitors for the inhibition of biologically relevant enzymes. The first three chapters of this thesis concern the polyphenol resveratrol and its inhibition of the quinone reductase 2 (QR2) enzyme. The work on this subject resulted in the complete design, synthesis, biological and structural evaluation of a second generation library of resveratrol analogues. From this work we identified a novel resveratrol analogue that inhibits QR2 in a previously unknown binding orientation. The fourth chapter of this thesis details the de novo design of molecules for the inhibition ...


Sustainable Chemistry, Synthesis And Structure-Activity Relationship Studies Of Biologically Important Small Molecules, Gerald R. Pollock, Iii Jan 2013

Sustainable Chemistry, Synthesis And Structure-Activity Relationship Studies Of Biologically Important Small Molecules, Gerald R. Pollock, Iii

Graduate Theses and Dissertations

With growing concerns for the environment, dwindling amounts of fossil fuels available for worldwide consumption and more resistant strains of diseases and infections becoming a reality, organic chemistry plays a vital role in the improvement and sustainability of modern society. Industrial chemicals from renewable sources has become an important area of research in recent years, while the synthesis and study of biologically active small molecules and their analogues leads to advancements which can help improve overall human health.

In this dissertation, we explore methods to create important industrial molecules from biorenewable sources, extend a novel cyclization to make heterocyclic compounds ...


Synthesis Of Tetrasubstituted Olefins And Aryl Ketones Via Carbopalladation Of Alkynes And Nitriles , Chengxiang Zhou Jan 2006

Synthesis Of Tetrasubstituted Olefins And Aryl Ketones Via Carbopalladation Of Alkynes And Nitriles , Chengxiang Zhou

Retrospective Theses and Dissertations

Palladium-catalyzed reactions are versatile methods for carbon-carbon bond formation due to their generality and ability to tolerate a wide range of important organic functional groups. Developing novel Palladium-catalyzed reactions has therefore been of great interest to synthetic chemists for years;The regio- and stereoselective synthesis of tetrasubstituted olefins is a long-pursuing challenge for synthetic chemists. A multi-component reaction route is ideal to generate various tetrasubstituted olefins in a very concise manner and should be highly desirable for applications in combinatorial chemistry. A highly efficient, regio- and stereoselective route to tetrasubstituted olefins has been developed by the Pd-catalyzed three-component reaction of ...


Probing Carbohydrate Biocatalysis Through The Use Of Electrospray Ionization Mass Spectrometry And Isothermal Titration Calorimetry , Corbin James Zea Jan 2005

Probing Carbohydrate Biocatalysis Through The Use Of Electrospray Ionization Mass Spectrometry And Isothermal Titration Calorimetry , Corbin James Zea

Retrospective Theses and Dissertations

Electrospray ionization mass spectrometry,(ESI-MS)-based assays have been newly developed to study three classes of enzymes (sugar nucleotidyltransferases, glycosyltransferases, and phosphorylases) from the three distinct families of life: archaea, eukaryotes, and prokaryotes. These three classes of enzymes play vital roles in carbohydrate storage, degradation and synthesis. The sugar nucleotidyltransferases from Escherichia coli and yeast that biosynthesize UDP-glucose and ADP-glucose respectively were studied using the first ESI-MS assay. Nonlinear regression of the kinetic data was comparable to those determined from the traditional UDP-glucose dehydrogenase coupled assay. This technique allowed us to determine that the yeast sugar nucleotidyltransferase has one binding ...


Cooperative Binding By A Self-Assembled Receptor: Metal In A Structural And Functional Role , Jin-Ho Lee Jan 1994

Cooperative Binding By A Self-Assembled Receptor: Metal In A Structural And Functional Role , Jin-Ho Lee

Retrospective Theses and Dissertations

Metal complexes of the amino acid, 4,4[superscript]'-phosphinylidine bis phenylalanine (PBP*, 1), self-assemble to produce a macrocyclic receptor (Co[subscript]2PBP[subscript]2, 2) with a hydrophobic cavity capable of binding aromatic compounds from water. Here we demonstrate that the metal can play a structural and a functional role: the receptor binds substrates bearing both aromatic and polar functional groups ditopically, using the hydrophobic pocket as well as the metal itself. The doubly anionic Co[superscript]2+ macrocyclic complex binds neutral aromatic guests more tightly than it does most anionic guests, as would be expected. However, carboxylates tethered ...


Sensitive Detection And Study Of Catalytic Species For Bimolecular Reactions , James William Lane Jan 1994

Sensitive Detection And Study Of Catalytic Species For Bimolecular Reactions , James William Lane

Retrospective Theses and Dissertations

In our lab, we have developed a sensitive and convenient assay for the detection of catalysts for bimolecular reactions. We have shown that catalysis of peptide synthesis by as little as 2.5 fmol (2.5 x 10[superscript]-15 mol) of a damaged enzyme can be detected using our assay. An interesting feature of our procedure is that it requires no complex apparatus, and may be carried out in parallel on many samples. We have used the assay to detect the presence of an enzyme catalyst, however the basic assay design is very versatile and may also be used ...