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Biochemistry and Molecular Biology Education

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https://www.readbyqxmd.com/read/29131508/an-interactive-computer-lab-of-the-galvanic-cell-for-students-in-biochemistry
#1
Emma Ahlstrand, Antoine Buetti-Dinh, Ran Friedman
We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δr G, Δr H, and Δr S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29131507/the-disruptive-effect-of-lysozyme-on-the-bacterial-cell-wall-explored-by-an-in-silico-structural-outlook
#2
Emiliano D Primo, Lisandro H Otero, Francisco Ruiz, Sebastián Klinke, Walter Giordano
The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29131491/the-polygonal-model-a-simple-representation-of-biomolecules-as-a-tool-for-teaching-metabolism
#3
Carlos Francisco Sampaio Bonafe, Jose Ailton Conceição Bispo, Marcelo Bispo de Jesus
Metabolism involves numerous reactions and organic compounds that the student must master to understand adequately the processes involved. Part of biochemical learning should include some knowledge of the structure of biomolecules, although the acquisition of such knowledge can be time-consuming and may require significant effort from the student. In this report, we describe the "polygonal model" as a new means of graphically representing biomolecules. This model is based on the use of geometric figures such as open triangles, squares, and circles to represent hydroxyl, carbonyl, and carboxyl groups, respectively...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29131478/gene-isolation-using-degenerate-primers-targeting-protein-motif-a-laboratory-exercise
#4
Brandon Pei Hui Yeo, Lian Chee Foong, Sheh May Tam, Vivian Lee, Siaw San Hwang
Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the isolation and characterization of many plant resistance gene analogues (RGAs), is featured in the development of a series of laboratory experiments using important molecular biology techniques...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29105959/design-of-a-software-for-calculating-isoelectric-point-of-a-polypeptide-according-to-their-net-charge-using-the-graphical-programming-language-labview
#5
Glomen Tovar
A software to calculate the net charge and to predict the isoelectric point (pI) of a polypeptide is developed in this work using the graphical programming language LabVIEW. Through this instrument the net charges of the ionizable residues of the polypeptide chains of the proteins are calculated at different pH values, tabulated, pI is predicted and an Excel (-xls) type file is generated. In this work, the experimental values of the pIs (pI) of different proteins are compared with the values of the pIs (pI) calculated graphically, achieving a correlation coefficient (R) of 0...
November 6, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29105928/lego-bricks-and-the-octet-rule-molecular-models-for-biochemical-pathways-with-plastic-interlocking-toy-bricks
#6
Henry J Lin, Jennifer Lehoang, Isabel Kwan, Anita Baghaee, Priya Prasad, Stephanie J Ha-Chen, Tanesha Moss, Jeremy D Woods
The 8 studs on a 2 × 4 Lego brick conveniently represent the outer shell of electrons for carbon, nitrogen, and oxygen atoms. We used Lego bricks to model these atoms, which are then joined together to form molecules by following the Lewis octet rule. A variety of small biological molecules can be modeled in this way, such as most amino acids, fatty acids, glucose, and various intermediate metabolites. Model building with these familiar toys can be a helpful, hands-on exercise for learning-or re-learning-biochemical pathways...
November 6, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28902453/implementing-a-web-based-introductory-bioinformatics-course-for-non-bioinformaticians-that-incorporates-practical-exercises
#7
Antony T Vincent, Yves Bourbonnais, Jean-Simon Brouard, Hélène Deveau, Arnaud Droit, Stéphane M Gagné, Michel Guertin, Claude Lemieux, Louis Rathier, Steve J Charette, Patrick Lagüe
A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become specialized. However, biology students who are not involved in a bioinformatics program also need a solid toolbox of bioinformatics software and skills. Therefore, we have developed a completely online bioinformatics course for non-bioinformaticians, entitled "BIF-1901 Introduction à la bio-informatique et à ses outils (Introduction to bioinformatics and bioinformatics tools)," given by the Department of Biochemistry, Microbiology, and Bioinformatics of Université Laval (Quebec City, Canada)...
September 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28902439/promoting-mastery-of-complex-biological-mechanisms
#8
William S Bradshaw, Kathryn J Groneman, Jennifer Nelson, John D Bell
This article describes efforts aimed at improving comprehension and retention of complex molecular mechanisms commonly studied in undergraduate biology and biochemistry courses. The focus is on the design of appropriate assessments, an active classroom emphasizing formative practice, and more effective out-of-class study habits. Assessments that require students to articulate their understanding through writing are the most effective. Frequent formative practice improves performance on problems that require intellectual transfer, the ability to apply conceptual principles in novel settings...
September 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28858410/intentionally-flawed-manuscripts-as-means-for-teaching-students-to-critically-evaluate-scientific-papers
#9
Jaroslav Ferenc, Filip Červenák, Erik Birčák, Katarína Juríková, Ivana Goffová, Peter Gorilák, Barbora Huraiová, Jana Plavá, Loriana Demecsová, Nikola Ďuríková, Veronika Galisová, Matej Gazdarica, Marek Puškár, Tibor Nagy, Soňa Nagyová, Lucia Mentelová, Miroslava Slaninová, Andrea Ševčovicová, Ľubomír Tomáška
As future scientists, university students need to learn how to avoid making errors in their own manuscripts, as well as how to identify flaws in papers published by their peers. Here we describe a novel approach on how to promote students' ability to critically evaluate scientific articles. The exercise is based on instructing teams of students to write intentionally flawed manuscripts describing the results of simple experiments. The teams are supervised by instructors advising the students during manuscript writing, choosing the 'appropriate' errors, monitoring the identification of errors made by the other team and evaluating the strength of their arguments in support of the identified errors...
August 31, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28858403/songs-about-cancer-gene-expression-and-the-biochemistry-of-photosynthesis
#10
Richard H Heineman
These three biology songs can be used for educational purposes to teach about biochemical concepts. They touch on three different topics: (1) cancer progression and germ cells, (2) gene expression, promoters, and repressors, and (3) electronegativity and the biochemical basis of photosynthesis. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.
August 31, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28843018/browning-in-apples-exploring-the-biochemical-basis-of-an-easily-observable-phenotype
#11
Charles E Deutch
Many fruits and vegetables undergo browning when they are cut and the tissue is exposed to the air. This is due to the activity of the enzyme polyphenol oxidase (PPO, EC 1.14.18.1) with endogenous substrates. In this laboratory experiment, students prepare slices of different varieties of apples and assess the rate of browning. They make a simple extract of the apple tissue and measure the activity of PPO using 3,4-dihydroxy-l-phenylalanine (l-DOPA) as substrate. They determine the protein concentration of the extract with the Bradford Coomassie Blue reagent and calculate the specific activity of PPO...
August 26, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28581156/the-usability-of-wechat-as-a-mobile-and-interactive-medium-in-student-centered-medical-teaching
#12
Juan Wang, Furong Gao, Jiao Li, Jieping Zhang, Siguang Li, Guo-Tong Xu, Lei Xu, Jianjun Chen, Lixia Lu
Biochemistry and cellular biology courses for medical students at Tongji University include the assessment that provides students with feedback to enhance their learning, which is a type of formative assessment. However, frequent instant feedback and guidance for students is often absent or inconsistently included in the teaching process. WeChat, the most popular Chinese social media, was introduced in biochemistry and cellular biology course. A WeChat official account (OA) was set up as an instant interactive platform...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28440901/examining-student-heuristic-usage-in-a-hydrogen-bonding-assessment
#13
Kathryn Miller, Thomas Kim
This study investigates the role of representational competence in student responses to an assessment of hydrogen bonding. The assessment couples the use of a multiple-select item ("Choose all that apply") with an open-ended item to allow for an examination of students' cognitive processes as they relate to the assignment of hydrogen bonding within a structural representation. Response patterns from the multiple-select item implicate heuristic usage as a contributing factor to students' incorrect responses...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28436090/using-augmented-reality-to-teach-and-learn-biochemistry
#14
Juan Carlos Vega Garzón, Marcio Luiz Magrini, Eduardo Galembeck
Understanding metabolism and metabolic pathways constitutes one of the central aims for students of biological sciences. Learning metabolic pathways should be focused on the understanding of general concepts and core principles. New technologies such Augmented Reality (AR) have shown potential to improve assimilation of biochemistry abstract concepts because students can manipulate 3D molecules in real time. Here we describe an application named Augmented Reality Metabolic Pathways (ARMET), which allowed students to visualize the 3D molecular structure of substrates and products, thus perceiving changes in each molecule...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28425189/the-global-ethics-corner-foundations-beliefs-and-the-teaching-of-biomedical-and-scientific-ethics-around-the-world
#15
Henry Jakubowski, Jianping Xie, Arup Kumar Mitra, Ravindra Ghooi, Saman Hosseinkhani, Mohsen Alipour, Behnam Hajipour, George Obiero
The profound advances in the biomolecular sciences over the last decades have enabled similar advances in biomedicine. These advances have increasingly challenged our abilities to deploy them in an equitable and ethically acceptable manner. As such, it has become necessary and important to teach biomedical and scientific ethics to our students who will become the researchers, medical professionals, and global citizens of the future. As advances in the biosciences and medicine are made, developed, and used across the globe, our survival on an endangered planet requires global dialog and consensual action...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28419715/a-survey-on-faculty-perspectives-on-the-transition-to-a-biochemistry-course-based-undergraduate-research-experience-laboratory
#16
Paul A Craig
It will always remain a goal of an undergraduate biochemistry laboratory course to engage students hands-on in a wide range of biochemistry laboratory experiences. In 2006, our research group initiated a project for in silico prediction of enzyme function based only on the 3D coordinates of the more than 3800 proteins "of unknown function" in the Protein Data Bank, many of which resulted from the Protein Structure Initiative. Students have used the ProMOL plugin to the PyMOL molecular graphics environment along with BLAST, Pfam, and Dali to predict protein functions...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28414867/basic-education-mexican-teachers-knowledge-of-biotechnology-and-attitudes-about-the-consumption-of-genetically-modified-foods
#17
Zacarías Jiménez-Salas, Eduardo Campos-Góngora, Blanca E González-Martínez, Alexandra Tijerina-Sáenz, Angélica D Escamilla-Méndez, Erik Ramírez-López
Over the past few years, a new research field has emerged, focusing on the social-scientific criteria for the study of opinions toward genetically modified foods (GMFs), since these may be limiting factors for the success or failure of these products. Basic education is the first step in the Mexican education system, and teachers may wield an outsized influence on the attitudes and preferences of children, prospective future consumers of these products. To better understand the current state of knowledge of biotechnology issues and opinions toward the consumption of GMF of Mexican teachers, a questionnaire was distributed, and 362 Mexican teachers of basic education responded...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28407453/stressing-escherichia-coli-to-educate-students-about-research-a-cure-to-investigate-multiple-levels-of-gene-regulation
#18
Janet McDonough, Lara K Goudsouzian, Agllai Papaj, Ashley R Maceli, Vanja Klepac-Ceraj, Celeste N Peterson
Course-based undergraduate research experiences (CUREs) have been shown to increase student retention and learning in the biological sciences. Most CURES cover only one aspect of gene regulation, such as transcriptional control. Here we present a new inquiry-based lab that engages understanding of gene expression from multiple perspectives. Students carry out a forward genetic screen to identify regulators of the stationary phase master regulator RpoS in the model organism Escherichia coli and then use a series of reporter fusions to determine if the regulation is at the level of transcription or the post-transcription level...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28294503/exploring-protein-structure-and-dynamics-through-a-project-oriented-biochemistry-laboratory-module
#19
James M Lipchock, Patrick S Ginther, Bonnie B Douglas, Kelly E Bird, J Patrick Loria
Here, we present a 10-week project-oriented laboratory module designed to provide a course-based undergraduate research experience in biochemistry that emphasizes the importance of biomolecular structure and dynamics in enzyme function. This module explores the impact of mutagenesis on an important active site loop for a biomedically-relevant human enzyme, protein tyrosine phosphatase 1B (PTP1B). Over the course of the semester students guide their own mutant of PTP1B from conception to characterization in a cost-effective manner and gain exposure to fundamental techniques in biochemistry, including site-directed DNA mutagenesis, bacterial recombinant protein expression, affinity column purification, protein quantitation, SDS-PAGE, and enzyme kinetics...
September 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28251763/a-13-week-research-based-biochemistry-laboratory-curriculum
#20
Scott T Lefurgy, Emily C Mundorff
Here, we present a 13-week research-based biochemistry laboratory curriculum designed to provide the students with the experience of engaging in original research while introducing foundational biochemistry laboratory techniques. The laboratory experience has been developed around the directed evolution of an enzyme chosen by the instructor, with mutations designed by the students. Ideal enzymes for this curriculum are able to be structurally modeled, solubly expressed, and monitored for activity by UV/Vis spectroscopy, and an example curriculum for haloalkane dehalogenase is given...
September 2017: Biochemistry and Molecular Biology Education
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