bluuebunny/crossref_metadata_2025 huggingface dataset:
On the convenience of using a computer simulation to teach enzyme kinetics to undergraduate students with biological chemistry‐related curricula
Authors: González‐Cruz Javier , Rodríguez‐Sotres Rogelio , Rodríguez‐Penagos Mireya
Published: February 2007

Enzyme kinetics is a difficult subject for students to learn and for tutors to teach. During the practicals included in the biochemical courses at the Faculty of Chemistry of Universidad Nacional Autónoma de México, we found that the students acquire good training in the calculations to obtain kinetic parameters such as Km, Vmax, optimum pH, etc., but, when they are questioned about the significance of the values and their relationship to enzyme catalysis, many confusing ideas arise. To provide extended practice opportunities that could aid in the learning process we developed computer software that simulates an enzyme assay for lactate dehydrogenase, named enzsimil, that was used as well as the practical sessions. We tested three different levels of guidance to work with enzsimil, scripts where the students had to follow detailed (guided), intermediate (semiguided), or minimal (unguided) instructions, and for comparison, one group had a session of solving problems in class extracted from the program (class), and one more group had no additional sessions (control). After their respective sessions, the students either wrote a report or completed their script and undertook a laboratory practical. At the end, an exam was applied to all students. The reports and exams were graded, and the performance of the experimental groups was subjected to a statistical analysis. In addition, we carefully read the answers trying to identify the more common errors and misconceptions. The study revealed that there are statistically significant benefits in the use of the program. The semiguided scheme was more convenient to help the student in the short term for the preparation of better reports, while in the long term, both the semiguided and unguided groups performed equally well. These results are discussed in terms of the convenience of guided or unguided teaching strategies in computer‐assisted learning.
Purification of colored photosynthetic proteins for understanding protein isolation principles
Authors: Bes M. Teresa , Sancho Javier , Peleato M. Luisa , Medina Milagros , Gómez‐Moreno Carlos , Fillat María F.
Published: February 2007

The purification of a protein is the essential initial step in the study of its physical and biological properties and is one of the most common procedures in biochemistry. This article describes a method for teaching purification skills through the partial isolation of ferredoxin‐NADP+ reductase and ferredoxin from a single cell batch. The method has been used for several years in an introductory biochemistry course using spinach leaves as cellular source. The protocol gives a complete picture of the preparation of a crude extract and the subsequent isolation of both electron transport proteins on a laboratory scale. It introduces students to the use of different techniques for the purification and detection of proteins and allows them to develop a number of valuable experimental and analytical skills without necessarily resorting to complicated or expensive equipment.
Glucose transport in liposomes
Authors: Szeberényi József
Published: February 2007

Terms to be familiar with before you start to solve the test: lipoprotein membranes, liposomes, Na+,K+‐ATPase, Na+/glucose symporter, glucose transporter.
Fermentable and non‐fermentable sugars: A simple experiment of anaerobic metabolism
Authors: Paulino Tony P. , Cardoso Mauro , Bruschi‐Thedei Giuliana C. M. , Ciancaglini Pietro , Thedei Geraldo
Published: February 2007

The main objective of this class experiment is to show the time‐dependent consumption of a fermentable sugar (glucose) in the presence and absence of a non‐fermentable sugar (xylose) by bacteria in anaerobic conditions. The observation of the pH decrease due to acid production and the turbidity increase as a result of cell multiplication, both in function of time, enables an interesting discussion regarding the metabolic pathways and the products of anaerobic fermentation of carbohydrates. Also the time‐dependent disappearance of glucose due to its metabolic consumption is compared with the non‐disappearance of xylose and permits a discussion of the function of glycolysis and pentose phosphate pathways as metabolic routes.

This work was supported by the Universidade de Uberaba, Fundaçao de Amparo à Pesquisa do Estado de São Paulo, and Conselho Nacional de Pesquisas (Brazil).
Isolation of chicken immunoglobulins (IgY) from egg yolk*
Authors: Goldring J. P. Dean , Coetzer Theresa H. T.
Published: February 2007

Separating individual proteins from complex mixtures of molecules is the basis of many biochemical investigations. The method describes the separation of immunoglobulin Y (IgY) from chicken eggs using a series of physical and chemical separation techniques. The separation is rapid, and the success of each step is readily viewed on an SDS‐polyacrylamide gel. IgY identity can be confirmed on a Western blot probed with enzyme‐labeled anti‐IgY antibodies. The method is a good illustration of protein separation when there is no enzyme activity to follow.
It is time to update “the graduate”
Authors: Gundersen Larry E.
Published: February 2007

While leaders of the commercial biotechnology industry are impressed with the numbers and quality of science graduates, they complain that they must invest time to further train them about basic aspects of this highly regulated work environment. The addition of a small number of recommended courses would augment the students' preparation for and participation in commercial research and development (R&D). These courses include a basic understanding of the R&D process and the laws and regulations that impact this process, such as Good Laboratory Practices (GLPs) and current Good Manufacturing Practices (cGMPs). Finally it is suggested that the most likely and capable teachers of these principles are working in the biotechnology industry, and it will involve active collaboration between academia and industry to best prepare graduates for success in biotechnology R&D.
Lesson plan for protein exploration in a large biochemistry class*
Authors: Honey David W. , Cox James R.
Published: February 2007

The teaching of structural concepts plays a prominent role in many chemistry and biology courses. When it comes to macromolecular systems, a thorough understanding of noncovalent interactions lays a strong foundation for students to understand such things as protein folding, the formation of protein‐ligand complexes, and the melting of the DNA double helix. The incorporation of computer‐based molecular graphics into the biochemistry curriculum has given students unique opportunities in visualizing the structure of biological molecules and recognizing the subtle aspects of noncovalent interactions. This report describes a series of visualization‐based assignments developed to facilitate protein exploration in a large biochemistry class. A large enrollment can present special challenges for students to benefit from hands‐on use of visualization software. Three of the assignments are described in detail along with a description of an on‐line teaching tool used to manage the assignments and to coordinate the student groups participating in these exercises.
Achievement of original results in an essentially practical course in molecular biology for undergraduate students
Authors: Possik Patricia Abrão , Malagó Junior Wilson , Torres Bayardo Baptista , Henrique‐Silva Flávio
Published: February 2007

We discuss a proposal for an experimental, laboratory‐based course in molecular biology aimed at familiarizing undergraduate students with scientific research. The main advantage of this course is that it provides students with good laboratory training through the development of a scientific project and the achievement of original results. The course was implemented experimentally, with students actively involved from the elaboration to the execution of a scientific project, which included the amplification, cloning, and sequencing of DNA. The project consisted of the isolation of microsatellite arrays from ostrich using a polymerase chain reaction‐based identification of microsatellite arrays (PIMA) technique. The group successfully identified three putative microsatellites and presented its results to the National Congress of Genetics. Additionally, graduate students participated in teaching activities as tutors, monitoring class experiments and assisting the groups. An evaluation of the discipline revealed a highly positive feedback from graduate and undergraduate students.
An undergraduate biochemistry laboratory course with an emphasis on a research experience
Authors: Caspers Mary Lou , Roberts‐Kirchhoff Elizabeth S.
Published: February 2007

In their junior or senior year, biochemistry majors at the University of Detroit Mercy are required to take a two‐credit biochemistry laboratory course. Five years ago, the format of this course was changed from structured experiments to a more project‐based approach. Several structured experiments were included at the beginning of the course because not all students were familiar with computer‐based statistics and graphics programs or fundamental biochemical techniques. Finally, students were given an enzyme purification assignment and a test/control project. In the latter project, students were provided with tissue from test and control animals and were expected to propose and test a parameter that they hypothesized might be different between the two tissues. For both projects, student teams were required to search the literature, submit and orally defend their proposals, perform the experiments, and submit a report. For all experiments except the test/control project, students submitted a written report in the style of a journal paper. A poster presentation was required for the test/control project. In course evaluations, the students cited a high degree of satisfaction with the project‐based approach.
Self or help? A comparison of a personalized system of instruction biochemistry class to a standard lecture‐based biochemistry class
Authors: Ocorr Karen , Osgood Marcy P.
Published: February 2007

For the past eight years the University of Michigan has offered two different styles of biochemistry courses each semester, one a standard lecture‐based and discussion‐section (SLB) course and one a self‐paced, non‐lecture Personalized System of Instruction (PSI) course. We tracked student responses to selected exam questions that were used in both courses for three semesters. Data on student grade point average, student satisfaction, and perceived effort in the courses were also gathered. In two of the three semesters that we monitored students there were no significant differences in performance on test questions between the two courses. In one of the three semesters there was a small but nevertheless significant difference between the two courses with junior and senior PSI students outperforming their SLB counterparts by 10 points. Student grade point average, overall satisfaction, and perceived effort were similar for both courses. Our study indicated that the PSI format works as well as the SLB model does for students in biochemistry and may be especially beneficial for more experienced students.
Evaluation of a web‐based resource to support a molecular biology practical class—does computer‐aided learning really work?
Authors: Gibbins Sue , Sosabowski Michael Hal , Cunningham Jim
Published: February 2007

In view of the increasing usage of information technology in learning and teaching there is an increasing need for meaningful evaluation of the effectiveness of information technology‐based media. The aim of this study was to investigate whether a web‐based computer‐aided learning (CAL) package enhances the learning outcomes of a laboratory‐based molecular biology class. A multiplex PCR practical exercise to detect genetically modified sequences in soybean DNA was carried out by students using either traditional (non‐electronic) teaching and learning resources or a web‐based CAL resource. The learning outcomes were evaluated by pre‐ and post‐class subject‐based comparative tests with self‐assessed confidence ratings and questionnaires. Scores relating to four modes of student learning style were assessed by questionnaire and these were correlated with the effectiveness of the support resource used. There was a significantly greater improvement in knowledge‐based test performance and self‐assessed confidence rating by students using CAL‐based learning support versus those using traditional resources. Learning style score did not correlate with the enhancement in performance by students supported by the CAL package, although one learning style did favor a response to the traditional support package. We conclude that compared with a non‐electronic alternative, the use of CAL can enhance learning and teaching outcomes in a laboratory‐based molecular biology class.
Influence of enzyme conformational changes on catalytic activity investigated by circular dichroism spectroscopy
Authors: Rigos Carolina Fortes , Santos Hérica de Lima , Thedei Geraldo , Ward Richard John , Ciancaglini Pietro
Published: February 2007

Enzyme activity is dependent on native conformational integrity. Here we present a simple laboratory exercise based on dichroism spectroscopy in which the change in enzyme structure induced by denaturation is correlated with the loss of catalytic activity. The results of circular dichroism spectra show that enzyme denaturation by either trifluoroethanol (enhancement of α‐helix structure) or guanidinium chloride (reduction of α‐helix and enhancement of random coil structure) leads to a concomitant reduction in enzyme activity, which demonstrates the relationship between structure and catalytic activity of the enzyme. This simple experimental approach demonstrates that only a single native protein (enzyme) conformation has the ability to catalyze substrate hydrolysis.
The ames test
Authors: Szeberenyi Jozsef
Published: February 2007

Terms to be familiar with before you start to solve the test: Polycyclic aromatic hydrocarbons, microsomal fraction, histidine operon, mutation, induction, repression, translation, Ca2+ channel, Ca2+ ATPase, steroid receptor, cytochrome P450, cytochrome c, direct and indirect carcinogen, procarcinogen, mutagenic compounds, tumor initiation, tumor promoter, complete and incomplete carcinogens, apoptosis.
Implementing the recommended curriculum in biochemistry & molecular biology at a Large State University: THE TEXAS A&M EXPERIENCE
Authors: Gunn J. Martyn
Published: February 2007

This article discusses how the biochemistry curriculum at Texas A&M University, a large, state‐assisted research university, fulfills the American Society for Biochemistry and Molecular Biology‐recommended guidelines. In addition, the research requirement for our degree, changes we are making to the curriculum, and the effect our large service teaching function has on implementing the guidelines are discussed.
Labeling of proteins with fluorescent probes: Photophysical characterization of dansylated bovine serum albumin
Authors: Levi Valeria , González Flecha F. Luis
Published: February 2007

Fluorescence spectroscopy is a widely used technique in biophysical studies. One of the strategies frequently used consists of labeling biomolecules with fluorescent probes, which have distinctive photophysical properties. This methodology allows the study of a wide variety of structural features of the biomolecule. We describe a simple laboratory activity for undergraduate Biophysical Chemistry courses. The experimental work includes two activities: labeling BSA with dansyl chloride and analyzing the resulting absorption and fluorescence spectra. The discussion of these activities helps students to understand the basis of fluorescence spectroscopy with emphasis in the application to biological systems.
Rates of electron transport in the thylakoid membranes of isolated, illuminated chloroplasts are enhanced in the presence of ammonium chloride
Authors: Dean Rob L. , Miskiewicz Ewa
Published: February 2007

The rate of flow of electrons from water to an artificial electron acceptor, dichlorophenolindophenol (DCPIP), through photosystem II in the thylakoid membranes of isolated chloroplasts is greatly enhanced in the presence of 10 mM ammonium chloride. Rate enhancement depends on irradiance levels. Uncoupling reagents like ammonium chloride prevent the formation of a proton gradient across the thylakoid membrane and consequently remove a constraint on the rate of electron transport. The mode of action of ammonium chloride is explained. Evidence obtained using an oxygen electrode that DCPIP itself also partially uncouples the system is presented as background information for instructors. Suggestions on how this reaction may be used in laboratory classes for students from high school to the senior undergraduate level are included.
Implementing the American Society for Biochemistry and molecular biology recommended curriculum in a biochemistry and molecular biology degree program in a genetics and biochemistry department: The Clemson University experience
Authors: Zimmerman James K.
Published: February 2007

This article describes the undergraduate biochemistry degree program at a medium‐sized, “state‐supported,” land‐grant university and how this degree program implements the curriculum recommended by the Educational and Professional Development Committee of the American Society for Biochemistry and Molecular Biology.

The abbreviation used is: ASBMB, American Society for Biochemistry and Molecular Biology.
DNA isolation from a dried blood sample, PCR amplification, and population analysis: Making the most of commercially available kits
Authors: DeLong Frost Laura , Peart Sharifa T.
Published: February 2007

A 3‐week undergraduate molecular biology laboratory exercise combining commercially available kits is described. The laboratory involves DNA extraction from a human dried blood sample, amplification of an Alu‐repeat sequence found on chromosome 8, and analysis of the genetic and allelic frequency in the class population using Hardy‐Weinberg statistics. The use of the prepared kits provides a means for the instructor of an undergraduate biochemistry course to explore molecular biology techniques on a limited budget and with a minimal time investment.
Teaching structural bioinformatics at the undergraduate level
Authors: Centeno Nuria B. , Villà‐Freixa Jordi , Oliva Baldomero
Published: February 2007

Understanding the basic principles of structural biology is becoming a major subject of study in most undergraduate level programs in biology. In the genomic and proteomic age, it is becoming indispensable for biology students to master concepts related to the sequence and structure of proteins in order to develop skills that may be useful in a wide range of applications. Within this context, this article shows a scheme for teaching structural biology based on hands‐on computer approaches, including computational genomics, and structural bioinformatics tools. The students learn to use most of the leading computer programs available for the complete path that goes from sequence to structure and eventually function. During the course, they are taught to build models of proteins based on sequence and structure information. The students are also provided with a critical point of view on automatic procedures and learn to discern between likely and unlikely structures of their final models.
Assessment in a problem‐based learning course: Twelve tips for constructing multiple choice questions that test students' cognitive skills
Authors: Azer Samy A.
Published: February 2007

For over 35 years, multiple choice questions (MCQs) have been used in the assessment of students in medical, dental, nursing, and physiotherapy courses. MCQs enable educators to test a broad range of topics in the curriculum. However, the educational goals of MCQs used currently are to test factual knowledge rather than a deeper understanding or use of information. They do not focus on testing cognitive skills, and many of them test small print in textbooks. With the introduction of problem‐based learning in medical and health professional courses and a full shift from a traditional lecture‐based curriculum to a student‐centered program, many schools are currently reviewing their assessment tools and introducing new strategies that reflect the philosophy of the new curriculum. However, there is limited information in the literature to guide question writers and provide them with guidelines to construct new styles of MCQs that test higher‐order thinking skills. This article provides 12 practical tips to help question writers in creating MCQs that test cognitive skills.
Preparing undergraduates to participate in the post‐genome era: A capstone laboratory experience in proteomics*
Authors: Eberhardt Eric S. , Hansen Johanna , Riservato Luke , Cole Melissa , Smaglo Brandon , Szaniawski Paul
Published: February 2007

Proteomics is one of the important new disciplines to emerge from the genome sequencing projects of the last decade. In order to introduce our students to the techniques and promise of this emerging field, a capstone laboratory experience has been developed. The exercise involves multiple aspects of proteomics research including microbial culturing methods, two‐dimensional gel electrophoresis techniques, matrix‐assisted laser desorption‐ionization time‐of‐flight mass spectrometry, and database mining. Over a 12‐week semester, students design their own experiments and apply a proteomic approach to investigate the heat shock response in Escherichia coli. In the trial presented in this article, students successfully identified several major heat shock proteins. The laboratory outlined here can be readily adapted to explore a wide variety of responses in metabolic pathways or responses resulting from other environmental insults or stresses. Additionally, the laboratory can be modified to explore the proteomes of organelles, tissues, and other model organisms.
Contribution of each complex of the mitochondrial respiratory chain in the generation of the proton‐motive force*
Authors: Garcia‐Vallve Santiago
Published: February 2007

A new parameter is presented for considering the contribution from each complex of the mitochondrial respiratory chain to the creation of the electrochemical gradient. This parameter is the proton gradient generated in each complex per pair of electrons transported (ΔH+/2e−) and may be calculated as the sum of the electrons taken up from the N‐side and the electrons released at the P‐side. The ΔH+/2e− values take into account all the electrons taken up and released in each complex and differentiate between the contribution from protons that are translocated from the N‐side to the P‐side and the contribution of scalar protons. Using these values, the P/O ratios for the oxidation of NADH and succinate are predicted to be 2.5 and 1.5, respectively.
A spectroscopic‐based laboratory experiment for protein conformational studies*
Authors: Ramos Carlos Henrique I.
Published: February 2007

This article describes a practical experiment for teaching basic spectroscopic techniques to introduce the topic of protein conformational change to students in the field of molecular biology, biochemistry, or structural biology. The spectroscopic methods employed in the experiment are absorbance, for protein concentration measurements, and fluorescence and circular dichroism, for probing protein conformational changes.
Supplementing introductory biology with on‐line curriculum*
Authors: McGroarty Estelle , Parker Joyce , Heidemann Merle , Lim Heejun , Olson Mark , Long Tammy , Merrill John , Riffell Samuel , Smith James , Batzli Janet , Kirschtel David
Published: February 2007

We developed web‐based modules addressing fundamental concepts of introductory biology delivered through the LON‐CAPA course management system. These modules were designed and used to supplement large, lecture‐based introductory biology classes. Incorporating educational principles and the strength of web‐based instructional technology, choices were made about knowledge presentation, representation, and construction (W. A. Nelson, D. B. Palumbo (1992) J. Educ. Media Hypermedia 1, 287–299). Knowledge presentation focused on big and connecting ideas. Knowledge representation provided students the opportunity to interact with concepts in several ways using multiple representations. For knowledge construction, we facilitated students' active and meaningful interactions with content using interwoven high‐level questions. Students' extended responses to a questionnaire indicated that these modules influenced the students learning in meaningful ways. (For access to demonstration modules, go to demo.lon‐capa.org/cgi‐bin/signon.pl?hhmi.)
Innovative tools for scientific and technological education in italian secondary schools
Authors: Santucci Annalisa , Mini Roberta , Ferro Elisa , Martelli Paola , Trabalzini Lorenza
Published: February 2007

This paper describes the project “Biotech a Scuola” (“Biotech at School”), financed by the Italian Ministry of Education within the SeT program (Special Project for Scientific‐Technological Education). The project involved the University of Siena, five senior and junior secondary schools in the Siena area, and a private company. Twenty‐three teachers from diverse fields and 318 students from 15 classes were involved. The aim of the project was to improve scientific‐technological teaching by providing schools with the support and materials necessary to understand some fundamental aspects of biotechnology. With this project we propose a model of close cooperation among various educational sectors with the goal of teaching junior and senior high school students some of the theory and practice of modern biotechnology.
Adjusting a biochemistry course for physical education majors: A case study
Authors: da Costa Caetano , Torres Bayardo B.
Published: February 2007

The purpose of this study was to investigate and analyze the events responsible for curricular characteristics that lead to positive outcomes in university teaching using a biochemistry course taught to physical education students as a model. The research was carried out as a case study, supported by questionnaires, classroom observation, document analysis, and interviews. The overall analyses of obtained data were validated by means of triangulation protocols, which proved the following reasons for the course achievements: 1) teaching staff deeply committed to the course; 2) contents adaptation to students' careers; 3) gradual adjustment of the teaching strategies and evaluation tools; 4) valorization of formative evaluation; and 5) providing a suitable affective milieu.
An introduction to mass spectrometry applications in biological research
Authors: Finehout Erin J. , Lee Kelvin H.
Published: February 2007

Mass spectrometry involves the measurement of the mass‐to‐charge ratio of ions. It has become an essential analytical tool in biological research and can be used to characterize a wide variety of biomolecules such as sugars, proteins, and oligonucleotides. In this review, a brief history of mass spectrometry is discussed, and the basic principles of the technology are introduced. A summary of some current applications is provided, as are examples of recently published research. The current methods used to identify, quantify, and characterize proteins and peptides are then reviewed. The range of applications of mass spectrometry is considerable and only promises to grow as the technology continues to improve.
Protein transport into the rough endoplasmic reticulum
Authors: Szeberenyi Joszef
Published: February 2007

Terms to be familiar with before you start to solve the test: in vitro protein synthesis, endoplasmic reticulum, [35S]methionine labeling, ribosomes, aminoacyl‐tRNA synthase, microsomes, signal recognition particle (SRP),1

The abbreviations used are: SRP, signal recognition particle; NEM, N‐ethylmaleimide; MCQ, multiple‐choice question.

SRP receptor, protease, detergent, SDS‐PAGE, autoradiography, protein glycosylation, peptidyl transferase, protein kinases, signal peptide, signal peptidase.
Virtual bioinformatics distance learning suite*
Authors: Tolvanen Martti , Vihinen Mauno
Published: February 2007

Distance learning as a computer‐aided concept allows students to take courses from anywhere at any time. In bioinformatics, computers are needed to collect, store, process, and analyze massive amounts of biological and biomedical data. We have applied the concept of distance learning in virtual bioinformatics to provide university course material over the Internet. Currently, we provide two fully computer‐based courses, “Introduction to Bioinformatics” and “Bioinformatics in Functional Genomics.” Here we will discuss the application of distance learning in bioinformatics training and our experiences gained during the 3 years that we have run the courses, with about 400 students from a number of universities. The courses are available at bioinf.uta.fi.
Gene amplification by PCR and subcloning into a GFP‐fusion plasmid expression vector as a molecular biology laboratory course*
Authors: Bornhorst Joshua A. , Deibel Michael A. , Mulnix Amy B.
Published: February 2007

A novel experimental sequence for the advanced undergraduate laboratory course has been developed at Earlham College. Utilizing recent improvements in molecular techniques for a time‐sensitive environment, undergraduates were able to create a chimera of a selected gene and green fluorescent protein (GFP) in a bacterial expression plasmid over the course of a single semester in a weekly 3‐h laboratory period. Students designed PCR primers for amplification of the selected gene using computational DNA sequence analysis tools. During the experimental portion of the course, students amplified and ligated the target DNA into a commercially available GFP expression vector. Following transformation of the ligation product, plasmids were harvested from the resulting bacterial colonies and were analyzed by restriction digestion to confirm the creation of the chimeric GFP‐DNA. This course gave students valuable experience with commonly used molecular techniques in an authentic research project. In addition, students gained experience with experimental design and execution. The techniques presented here are flexible and can be generalized for use with almost any DNA sequence and expression vector. This series also serves as an example of how faculty can adapt their ongoing research projects to the undergraduate laboratory.
cAMP Regulation of the lactose operon
Authors: Szeberenyi Jozsef
Published: February 2007

Terms to be familiar with before you start to solve the test: lactose operon, adenylate cyclase, cAMP, catabolite activator protein (CAP), expression plasmid, lac operator, lac repressor, lactose, glucose, promoter, cis‐ and trans‐acting factors.
Lucenz simulator: A tool for the teaching of enzyme kinetics
Authors: Clark Alan G.
Published: February 2007

A program has been developed that will produce simulated enzyme kinetic data suitable for inclusion in problem sets for undergraduates. Mechanisms simulated include one‐ and two‐substrate reactions and various types of inhibition. The effects of variation of pH and temperature may be modeled, as may the effects of random errors on the experimental procedure. The graphical output is suitable for use in lecture demonstrations.
The use of item analysis for improvement of biochemical teaching
Authors: Nagata Ryoichi
Published: February 2007

Item analysis was used to find out which biochemical explanations need to be improved in biochemical teaching, not which items are to be discarded, improved, or reusable in biochemical examinations. The analysis revealed the basic facts of which “less able” students had more misunderstanding than “able” students. Identifying these basic facts helps biochemistry teachers to improve their teaching.
An interactive introduction to protein structure
Authors: Lee W. Theodore
Published: February 2007

To improve student understanding of protein structure and the significance of noncovalent interactions in protein structure and function, students are assigned a project to write a paper complemented with computer‐generated images. The assignment provides an opportunity for students to select a protein structure that is of interest and detail three to five noncovalent interactions important for protein structure and/or function. The assignment is designed to provide a hands‐on learning experience for students in a moderately large introductory biochemistry class.
Characterization of the CCR5 chemokine receptor gene
Authors: Thomas John C.
Published: February 2007

The life cycle of retroviruses is an essential topic of modern cell biology instruction. Furthermore, the process of HIV viral entry into the cell is a question of great interest in basic and clinical biology. This paper describes how students can easily recover their own DNA, amplify a portion of the CCR5 chemokine receptor gene, characterize wild‐type and mutant genotypes, and provide a timely backdrop for learning the many molecular facets of the HIV virus. This exercise can easily lead to current and ongoing discussions of the relevance of mutant alleles in the CCR5 co‐receptor and possible HIV tolerance. Student laboratory reports often discussed the potential importance of structure to the function of CCR5 protein within the context of HIV infection and resistance. Discussions of structure linked to function are key components of student assessment.
Slow‐binding inhibition: A theoretical and practical course for students
Authors: Goliĉnik Marko , Stojan Jure
Published: February 2007

Tyrosinase (EC 1.14.18.1) catalyzes the oxidation of L‐3,4‐dihydroxyphenylalanine (L‐DOPA) to 2,3,5,6‐tetrahydro‐5,6‐dioxo‐1H‐indole‐2‐carboxylate (dopachrome), according to the classical Michaelis‐Menten kinetic mechanism. The enzyme is strongly but slowly inhibited by α‐amino‐β‐[N‐(3‐hydroxy‐4‐pyridone)] propionic acid (L‐mimosine), a toxic plant amino acid. Easily available reagents and simple spectrophotometric detection of the product make the experimental characterization and kinetic analysis of tyrosinase action convenient and interesting for teaching purposes. In the present article, we present a theoretical and practical guide to the kinetic analysis of slow‐binding inhibition. The effect of L‐mimosine on tyrosinase is established by progress curve measurements, carried out on a conventional spectrophotometer equipped with a rapid kinetic accessory. In the analysis, we recommend a classical linearization approach but we also took advantage of a more reliable nonlinear regression method to avoid subjective bias. A multistep procedure starts by careful inspection of the curves to discriminate between candidate mechanisms. Next, the evaluation of initial and steady‐state velocities provides information on the enzyme catalytic and Michaelis‐Menten constants, as well as the corresponding inhibition constants. Subsequently, an appropriate mathematical derivation enables estimation of the isomerization rate constants characteristic for a slow‐binding inhibitor. To conclude, we suggest simultaneous multivariable regression, using all the progress curve data, to cross‐check the proposed reaction mechanism and evaluated kinetic constants.
Bioinformatics in undergraduate education: Practical examples
Authors: Boyle John A.
Published: February 2007

Bioinformatics has emerged as an important research tool in recent years. The ability to mine large databases for relevant information has become increasingly central to many different aspects of biochemistry and molecular biology. It is important that undergraduates be introduced to the available information and methodologies. We present a problem‐based approach for incorporation of bioinformatics into existing courses. Examples of exercises are presented along with resources available on the World‐Wide Web.
A rapid PCR‐RFLP method for monitoring genetic variation among commercial mushroom species*
Authors: Martin Presley , Muruke Masoud , Hosea Kenneth , Kivaisi Amelia , Zerwas Nick , Bauerle Cynthia
Published: February 2007

We report the development of a simplified procedure for restriction fragment length polymorphism (RFLP) analysis of mushrooms. We have adapted standard molecular techniques to be amenable to an undergraduate laboratory setting in order to allow students to explore basic questions about fungal diversity and relatedness among mushroom species. The streamlined protocols allowed students to practice important molecular techniques within the context of self‐designed investigative projects. This laboratory experience provided opportunities for students to practice strategies for examining molecular diversity among species.
Solving an ethical issue involved in experimentation with animals in a brazilian teaching laboratory*
Authors: Loureiro Natália I. V. , Viana Henrique V. , Rodrigues Carlos R. , Cabral Lúcio Mendes , Silva Thaís D. N. , Cardoso Fernanda Serpa , Santos Dilvani Oliveira , Castro Helena C.
Published: February 2007

Changes are occurring within Brazilian institutes of higher education; currently several universities are reviewing their course offerings and teaching approaches to determine if they meet the needs of today's undergraduate students. When changes are made to the curriculum of experimental courses, there should be an understood guarantee that all efforts to avoid ethical and biosafety issues have been diligently considered. Ethical considerations lead us to create an alternative experimental session to be conducted that eliminated the use of rats, the conventional in vivo model employed for learning metabolism of glycogen in our university. To avoid possible biosafety issues, we prepared an alternative sample to simulate human urine, which we called guarurine. Using our new method, it is possible to verify positive results imitating a diabetic and starving people samples for detection of glucose and ketone. The alternative tool described herein is not only particularly suited to bypass the ethics of using animals for teaching, but also permits the discussion of significant aspects of pathological and physiological situations such as diabetics and starvation in a simple, safe, and interesting way.
Introductory course based on a single problem: Learning nucleic acid biochemistry from AIDS research
Authors: Grover Neena
Published: February 2007

In departure from the standard approach of using several problems to cover specific topics in a class, I use a single problem to cover the contents of the entire semester‐equivalent biochemistry classes. I have developed a problem‐based service‐learning (PBSL) problem on HIV/AIDS to cover nucleic acid concepts that are typically taught in the second semester of a biochemistry class. Use of research articles on a specific topic allows developing problems such as one discussed here. The implementation of this problem is similar to teaching literature‐based courses but is tailored to undergraduate work. Details of designing and setting up this problem, along with the pros and cons of this approach, are discussed here.
A new literary metaphor for the genome or proteome
Authors: Pappas Gus
Published: February 2007

Previously, the idea of a blueprint has been used to explain the genome. The concept of a play's cast of characters, the Dramatis Personae, is a more fluid metaphor that allows for mutations and time‐dependent phenomena to be taken into account. It also provides an educational and mnemonic exercise for students.
Use of visible light‐based photodynamic therapy to bacterial photoinactivation
Authors: Paulino Tony P. , Magalhães Prislaine P. , Thedei Geraldo , Tedesco Antônio C. , Ciancaglini Pietro
Published: February 2007

The main focus of this laboratory exercise was to investigate the photodynamic therapy (PDT) acting over Streptococcus mutans. A handheld photopolymerizer and a classical photosensitizer (Rose Bengal) were used to induce photodynamic response. In this way, a suspension of S. mutans was treated with different concentrations of Rose Bengal (0–10 μmol/liter), irradiated with a light (400–600 nm) for 20 s, and then cell viability was evaluated. It was observed that the light (per se) is not toxic, and in the dark, Rose Bengal is toxic only to the cells tested at concentrations above 5.0 μmol/liter. Under light exposure, concentrations of Rose Bengal above 0.5 μmol/liter killed all S. mutans. Therefore, for the purpose of our work, the photoactivation of Rose Bengal using the handheld photopolymerizer was efficient in bacteria inactivation.
Determination of the Rh factor: A practical illustrating the use of the polymerase chain reaction
Authors: Imperial Santiago , Boronat Albert
Published: February 2007

A 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

We 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

Solution‐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

Potato 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

One 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

The 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.