bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of the Rh factor: A practical illustrating the use of the polymerase chain reaction
Authors: Imperial Santiago , Boronat Albert 
Published: February 2007

AbstractA practical experiment on the PCR is described that has been used over several years as part of an undergraduate biochemistry and molecular biology course for chemistry students. In the first experimental session, students prepare their own DNA samples from epithelial cells of the mouth and use them as templates in the PCR. In the second session, they analyze the amplified DNA by electrophoresis and determine their Rh factor.
Software for teaching structure‐hydrophobicity relationships
Authors: White Brian , Perna Ilana , Carlson Reino 
Published: February 2007

AbstractWe have developed a lecture and laboratory curriculum for introducing beginning undergraduate Biology students to chemical structure‐function relationships. The laboratory portion of this curriculum employs cheminformatics software that provides instant feedback to help students develop an understanding of the relationship between structure and hydrophobicity. To evaluate the effectiveness of this curriculum, we measured students' understanding using an open‐ended problem‐based survey. Student responses to this survey improved significantly following the activities we describe, suggesting that they are effective teaching tools. This curriculum also provides a foundation for students' future structure‐function studies in chemistry, biochemistry, and molecular biology.
An accessible two‐dimensional solution nuclear magnetic resonance experiment on human ubiquitin*
Authors: Rovnyak David , Thompson Laura E. 
Published: February 2007

AbstractSolution‐state nuclear magnetic resonance (NMR) is an invaluable tool in structural and molecular biology research, but may be underutilized in undergraduate laboratories because instrumentation for performing structural studies of macromolecules in aqueous solutions is not yet widely available for use in undergraduate laboratories. We have implemented an experiment that is ideal for more commonly available 4.8–7.0 Tesla, double‐channel NMR instruments that would not usually be used for biomolecular NMR work. We analyzed a commercially available, 15N‐enriched human ubiquitin sample with a two‐dimensional correlation experiment using indirect 1H evolution and direct 15N detection, which produced spectra with high resolution on a spectrometer operating at 7.0 Tesla (300 MHz 1H resonance frequency). The simplicity of the experiment makes it possible to be configured by undergraduate students with minimal supervision from the instructor. Students gain experience in acquiring multidimensional biomolecular NMR experiments, confirm that ubiquitin is stably folded, and observe the correspondence between specific signals and individual amino acids in ubiquitin.
Teaching about citric acid cycle using plant mitochondrial preparations: Some assays for use in laboratory courses*
Authors: Vicente Joaquim A. F. , Gomes‐Santos Carina S. S. , Sousa Ana Paula M. , Madeira Vítor M. C. 
Published: February 2007

AbstractPotato tubers and turnip roots were used to prepare purified mitochondria for laboratory practical work in the teaching of the citric acid cycle (TCA cycle). Plant mitochondria are particularly advantageous over the animal fractions to demonstrate the TCA cycle enzymatic steps, by using simple techniques to measure O2 consumption and transmembrane potential (ΔΨ). The several TCA cycle intermediates induce specific enzyme activities, which can be identified by respiratory parameters. Such a strategy is also used to evidence properties of the TCA cycle enzymes: ADP stimulation of isocitrate dehydrogenase and α‐ketoglutarate dehydrogenase; activation by citrate of downstream oxidation steps, e.g. succinate dehydrogenase; and regulation of the activity of isocitrate dehydrogenase by citrate action on the citrate/isocitrate carrier. Furthermore, it has been demonstrated that, in the absence of exogenous Mg2+, isocitrate‐dependent respiration favors the alternative oxidase pathway, as judged by changes of the ADP/O elicited by the inhibitor n‐propyl galate. These are some examples of assays related with TCA cycle intermediates we can use in laboratory courses.
The metabolic effects of low‐carbohydrate diets and incorporation into a biochemistry course
Authors: Pogozelski Wendy , Arpaia Nicholas , Priore Salvatore 
Published: February 2007

AbstractOne of the challenges in teaching biochemistry is facilitating students' interest in and mastery of metabolism. The many pathways and modes of regulation can be overwhelming for students to learn and difficult for professors to teach in an engaging manner. We have found it useful to take advantage of prevailing interest in popular yet controversial weight‐loss methods, particularly low‐carbohydrate diets. The metabolic rationale behind these eating plans can be linked to glycolysis, the citric acid cycle, lipolysis, gluconeogenesis, ketosis, glycogen metabolism, fatty acid oxidation, and hormonal regulation. When this approach was used in undergraduate biochemistry classes at the State University of New York at Geneseo, students were highly motivated to learn the biochemical principles behind these diets. The following provides information about low‐carbohydrate diet plans that will enable professors to speak authoritatively on the subject. History and studies regarding efficacy as well as biochemical metabolic effects are included.
The early history of32P as a radioactive tracer in biochemical research: A personal memoir
Authors: Gest Howard 
Published: February 2007

AbstractThe concept of using radioactive isotopes as “tracers” of chemical conversions was conceived and developed by inorganic chemist Georg de Hevesy (Nobel Laureate in Chemistry 1943). In 1935, he began to apply the technique to various biological processes using32P, and his experiments revealed the dynamic character of physiology and metabolism. Following de Hevesy's lead, Samuel Ruben (University of California, Berkeley) exploited32P in 1937–38 for investigation of phospholipid metabolism. Between 1937 and 1940, Ruben and colleague Martin Kamen spearheaded tracer studies in various biological systems using32P, short‐lived11C, and other radioactive isotopes. During this period, Kamen was responsible for cyclotron‐produced radioactive tracers and was able to sustain de Hevesy's research by supplying him with32P. In 1940, Ruben and Kamen discovered long‐lived14C, which later proved to be a very powerful tool for analysis of complex biochemical processes, such as the path of carbon in photosynthesis. Between 1946 and 1950,32P was used in studies of bacteriophage replication and photosynthetic metabolism. This memoir surveys the history of these early investigations.
Molecular modeling of heme proteins using MOE: Bio‐inorganic and structure‐function activity for undergraduates*S
Authors: Ray Gigi B. , Cook J. Whitney 
Published: February 2007

AbstractA biochemical molecular modeling project on heme proteins suitable for an introductory Biochemistry I class has been designed with a 2‐fold objective: i) to reinforce the correlation between protein three‐dimensional structure and function through a discovery oriented project, and ii) to introduce students to the fields of bioinorganic and coordination chemistry. Students are asked to identify several unknown heme proteins based on a careful analysis of covalent and noncovalent interactions at the active site of each protein, focusing on amino acid reactivity and H‐bonding networks. Starting with the three‐dimensional crystal structures of four unknown proteins, students isolate and examine the coordination environment of the iron center in order to predict the relative reactivity toward dioxygen (O2) or hydrogen peroxide (H2O2). The central question of the project is to determine how the same iron protoporphyrin IX cofactor can be used by four different proteins to carry out diverse reactions, from electron transfer, to reversible oxygen binding to hydrogen peroxide activation. Pedagogical reasons for implementation of this biomolecular discovery‐based activity and student evaluations are discussed. In addition to developing many of the three‐dimensional visualization skills needed to successfully learn biochemistry, students also learn to use the versatile MOE molecular modeling program (Molecular Operating Environment), become familiar with metalloprotein reactivity, and are introduced to computational biochemistry research.
Isolation of Caenorhabditis elegans genomic DNA and detection of deletions in the unc‐93 gene using PCR
Authors: Lissemore James L. , Lackner Laura L. , Fedoriw George D. , De Stasio Elizabeth A. 
Published: February 2007

AbstractPCR, genomic DNA isolation, and agarose gel electrophoresis are common molecular biology techniques with a wide range of applications. Therefore, we have developed a series of exercises employing these techniques for an intermediate level undergraduate molecular biology laboratory course. In these exercises, students isolate genomic DNA from the nematode Caenorhabditis elegans and use PCR to detect deletions in the C. elegans unc‐93 gene. In advance of the exercises, wild‐type and three different unc‐93 deletion mutant strains are grown, harvested, and frozen by the instructor. In one approach, students isolate genomic DNA from each strain using a genomic DNA isolation kit and use agarose gel electrophoresis to analyze the DNA and to estimate its concentration. PCRs using primers directed to two different regions of the unc‐93 gene are carried out on the genomic DNA from wild‐type and mutant strains, and the PCR products are analyzed by agarose gel electrophoresis. Students analyze the gel to determine the approximate location and size of deletions in the three mutant strains. Alternatively, students may lyse single nematodes and carry out PCR in one laboratory session. These exercises should be easily adaptable to detection of well characterized deletions in any organism.
Developing students' awareness of public understanding of science: A matter of survival?
Authors: Castanho Miguel A. R. B. 
Published: February 2007

AbstractBiochemists and life scientists in general are now encountering a paradox regarding the public image of their work; society demands and encourages pursuit of more knowledge but at the same time is suspicious and fears the novelties it brings. At this historical moment, we are experiencing a delicate balance between the birth of a new era and a downsizing the status of biochemistry. The future can go either way, and it is up to scientists to become deeply involved to make the first scenario overturn the second. This task demands awareness and engagement in scientific communication and the promotion of science. However, the work ahead demands continuous commitment for more than one generation. If we want to leave a legacy of a well regarded and prosperous science to our students, we must let them know why public understanding is crucial, indeed vital, and show them how to cope with and actually embrace it. This may actually be a survival skill for them!
Using the discussion board in the undergraduate biochemistry classroom: Some lessons learned*
Authors: Markwell John 
Published: February 2007

AbstractThe discussion board feature that is included with most course management software packages is a potentially valuable tool to augment instructor‐student interactions in science lecture courses and increase student motivation. However, many teachers seem to have been frustrated that students do not readily make use of this feature when it is added to the course resources. The author has been using a discussion board in undergraduate biochemistry lecture courses for six years and has learned to use it to evolve a system that students use and that seems to increase interaction with students while requiring less time than traditional face‐to‐face meetings outside of the lecture. The aspects that the author emphasizes for efficient discussion board use are timing, creating a safe virtual environment for the students, “seeding” with simulated questions, setting boundaries, and being self‐conscious about the attitude that the instructor projects to the students.
Methionine and derivatives: Exploring chirality at sulfur
Authors: Bentley Ronald 
Published: February 2007

AbstractChiral molecules, both small and large, play important roles in biochemistry, molecular biology, and related biosciences. The central position of carbon atoms in determining chirality has received considerable attention. Less well known is the fact that chirality is also possible for sulfur atoms in certain compounds. This article introduces the role of sulfur chirality in metabolic reactions by considering methionine derivatives with chiral sulfur atoms, S‐adenosylmethionine and its decarboxylated product, methionine S‐oxide, and methionine sulfoximine.
Preparing the senior or graduating student for graduate research
Authors: Tang Bor Luen , Gan Yunn Hwen 
Published: February 2007

AbstractSenior undergraduates in the honors or graduation year with an intention to further their career in science would soon face the real world of scientific research as a junior scientist. It is important to acquaint these students with and adequately prepare them for the key aspects of a scientist's professional life. These include technical capacities indispensable for continuous and intense appraisal of data and knowledge as well as awareness that would ensure proper professional conduct within the laboratory. We have designed and conducted a module called “Scientific Critique” in the fourth year for Biochemistry majors. The module emphasizes scientific literature review and critique. It also incorporates techniques in preparing research grant proposals and an exercise in peer review of grant proposals as well as lectures and presentations on scientific integrity and research ethics. Positive response and feedback from students are indicative of an appreciation for the module contents, and we believe it of value to include such contents in any senior undergraduate life sciences curriculum.
Critical analysis on the use of poster display as an alternative evaluation method in basic biochemistry
Authors: Fernandes Patricia M. B. , Rodrigues Silas P. , Lindsey George 
Published: February 2007

AbstractThis article describes the use of poster preparation and display as an assessment tool and includes feedback from the students and academics concerned. This alternative approach has been used for four years since 2000 for biological science students studying biochemistry. The object of this approach was to get away from traditional teaching evaluation strategies, which promote passive learning and superficial memorization. Creating and presenting posters based on published manuscripts require students to understand, critically analyze, and disseminate the data, thereby promoting the understanding and retention of the material presented.
Immunoprecipitation and characterization of membrane protein complexes from yeast*S
Authors: Parra‐Belky Karlett , McCulloch Kathryn , Wick Nicole , Shircliff Rebecca , Croft Nicolas , Margalef Katrina , Brown Jamie , Crabill Todd , Jankord Ryan , Waldo Eric 
Published: February 2007

AbstractIn this undergraduate biochemistry laboratory experiment, the vacuolar ATPase protein complex is purified from yeast cell extracts by doing immunoprecipitations under nondenaturing conditions. Immunoprecipitations are performed using monoclonal antibodies to facilitate data interpretation, and subunits are separated on the basis of their molecular size by SDS‐PAGE. Both integral membrane and peripheral subunits are detected in Coomassie Blue‐stained gels, and the identity of several subunits are confirmed by Western blots. Western blots serve to illustrate reproducibility and authenticity of the results and help students understand that they could use immunoblotting to detect subunits that are not visualized by Coomassie stain. The molecular mass of the subunits is estimated by their migration relative to molecular marker proteins in the same gel and used to estimate the size of the entire complex. Just like in biochemistry research, students learn to integrate several techniques to solve the subunit composition of a protein complex. These experiments are an alternative to classical protein purification techniques and can be adapted to study most protein complexes composed of membrane‐bound and peripheral subunits from yeast. Instructors can use this approach to teaching proteomics and introduce students to systems biology. Because numerous yeast proteins are epitope tagged, instructors could use commercially available antibodies to study a protein complex of interest.
Digital learning material for student‐directed model building in molecular biologyS
Authors: Aegerter‐Wilmsen Tinri , Coppens Marjolijn , Janssen Fred , Hartog Rob , Bisseling Ton 
Published: February 2007

AbstractThe building of models to explain data and make predictions constitutes an important goal in molecular biology research. To give students the opportunity to practice such model building, two digital cases had previously been developed in which students are guided to build a model step by step. In this article, the development and initial evaluation of a third digital case is described. It concerns the selection of bristles during Drosophila development. To mimic a real research situation in a more realistic way, students are given much more freedom while building their models and can thus follow their own model‐building approach. At the same time, however, students are provided with a sufficient amount of support to ensure that they can build their models without the requirement of intensive supervision.
A docking interaction study of the effect of critical mutations in ribonuclease a on protein‐ligand binding
Authors: Mukherjee Sayan , De Soumya , Ghosh Zhumur , Dasgupta Swagata 
Published: February 2007

AbstractEnzymes with ribonucleolytic activity play a pivotal role in gene expression and cellular homeostasis by altering the levels of cellular RNA. Ribonuclease A has been the most well studied of such enzymes whose histidine residues (His12 and His119) play a crucial role in the catalytic mechanism of the protein. The ligands chosen for this study, 2′CMP and 3′CMP, act as competitive substrate analog inhibitors of this enzyme. Using molecular graphics software freely available for academic use, AutoDock and PyMol, we demonstrate that substitution of either histidine residue by alanine causes marked changes in the distances between these critical residues of the enzyme. The ligands in the docked conformation (particularly on mutation of His119 to Ala) compensate for the altered free energy and hydrogen bonding abilities in these new protein‐ligand complexes.
Simplifying structure analysis projects with customizable chime‐based templates*
Authors: Thompson Scott E. , Sears Duane W. 
Published: February 2007

AbstractStructure/function relationships are fundamental to understanding the properties of biological molecules, and thus it is imperative that biochemistry students learn how to analyze such relationships. Here we describe Chime‐based web page templates and tutorials designed to help students develop their own strategies for exploring macromolecular three‐dimensional structures like those on our course website. The templates can easily be customized for any structure of interest, and some templates include a Command Entry Line and a Message Recall Box for more refined macromolecular exploration using RasMol/Chime image modification commands. The tutorials present students with an integrated overview of the image modification capabilities of the Chime plug‐in and its underlying RasMol‐based command structure as accessed through the Command Entry Line. The tutorial also illustrates how RasMol/Chime command syntax addresses specific formatted structural information in a standard Protein Data Bank file. Judging by the high quality of structure‐based presentations given by students who have used these templates and tutorials, it appears that these resources can help students learn to analyze complex macromolecular structures while also providing them with convenient tools for creating scientifically meaningful and visually effective molecular images to share with others. (The templates, tutorials, and our course website can be viewed at the following URLs, respectively: tutor.lscf.ucsb.edu/instdev/sears/biochemistry/presentations/demos‐downloads.htm, tutor.lscf.ucsb.edu/instdev/sears/biochemistry/tutorials/pdbtutorial/frontwindow.html, and tutor.lscf.ucsb.edu/instdev/sears/biochemistry/.)
Modular laboratory courses: An alternative to a traditional laboratory program
Authors: Caprette David R. , Armstrong Sarah , Beason K. Beth 
Published: February 2007

AbstractOur modular laboratory teaching program is characterized by two major features. First, each course is taught independently and not linked with a particular lecture course. Second, each course is designed to be completed within one‐half semester or less. The modular organization has allowed incorporation of the latest technology, reduction of class sizes, and a greater number of choices to permit students to pursue their own interests. Full‐time laboratory teaching personnel work together on the organization of the program as well as design and teach individual courses. The program has distinct and separate instructional goals, namely introduction, reinforcement, and advancement of fundamental scientific capacities. Such focus has facilitated efforts to coordinate laboratory courses within the biological sciences and among other departments in natural sciences and engineering, raising expectations as students progress through a program.
Use of solid phase extraction in the biochemistry laboratory to separate different lipids
Authors: Flurkey William H. 
Published: February 2007

AbstractSolid‐phase extraction (SPE) was used to demonstrate how various lipids and lipid classes could be separated in a biochemistry laboratory setting. Three different SPE methods were chosen on their ability to separate a lipid mixture, consisting of a combination of a either a fatty acid, a triacylglycerol, a mono‐ or diacylglycerol, phospholipid, cholesterol, or cholesteryl ester into distinct lipid fractions. These mini‐scale SPE methods used aminopropyl‐bonded silica columns or silica Sep‐Pak cartridges suitable for completion in a 2‐ to 3‐h time block. Thin‐layer chromatography of the isolated lipid fractions was used to show separation characteristics and to evaluate the utility and reproducibility of each SPE method.
Poem: A is for alanine
Authors: Crowther Gregory J. 
Published: February 2007

AbstractThe poem below presents a brief review of amino acid abbreviations and structures. Among the featured facts are the following: histidine has a pKa close to the normal pH of the cytosol and therefore is an effective intracellular buffer, the R group of isoleucine is hydrophobic, and many protein kinases add a phosphate at the ‐OH site of tyrosine.This work is just one of many science songs and poems that may be used for educational purposes. A comprehensive database of over 2,000 songs is available online at www.science‐groove.org/MASSIVE/.