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Direct linkAurora Callahan; Todd Smith – Biochemistry and Molecular Biology Education, 2025
A common exercise given to students early in a molecular biology course is the creation of a restriction map of a plasmid "digested" by two restriction enzymes (RE). Meanwhile, students have learned from an early age about the properties and analyses of circles in their mathematics courses. But it is rare for students to learn using…
Descriptors: Problem Solving, Puzzles, Molecular Biology, Assignments
The Real Reason Why ATP Hydrolysis Is Spontaneous at pH > 7: It's (Mostly) the Proton Concentration!
Silverstein, Todd P. – Biochemistry and Molecular Biology Education, 2023
Common wisdom holds that ATP hydrolysis is spontaneous because of the weakness of its phosphoanhydride bonds, electrostatic repulsion within the polyanionic ATP[superscript 4]-molecule, and resonance stabilization of the inorganic phosphate and ADP products. By examining the pH-dependence of the hydrolysis Gibbs free energy, we show that in fact,…
Descriptors: Biochemistry, Molecular Biology, Science Education, Scientific Concepts
Murphy Angelo; Yash Bhargava; Scott Takeo Aoki – Biochemistry and Molecular Biology Education, 2024
The complexity of RNA cannot be fully expressed with the canonical A, C, G, and U alphabet. To date, over 170 distinct chemical modifications to RNA have been discovered in living systems. RNA modifications can profoundly impact the cellular outcomes of messenger RNAs (mRNAs), transfer and ribosomal RNAs, and noncoding RNAs. Additionally, aberrant…
Descriptors: Genetics, Biochemistry, Molecular Biology, College Science
Naoto Shirasu; Shin'ichiro Yasunaga – Biochemistry and Molecular Biology Education, 2024
Here, we propose a laboratory exercise to quickly determine single nucleotide polymorphisms (SNPs) in human "alcohol dehydrogenase 1B (ADH1B)" and "aldehyde dehydrogenase 2 (ALDH2)" genes involved in alcohol metabolism. In this exercise, two different genotyping methods based on polymerase chain reaction (PCR), namely…
Descriptors: Genetics, Biochemistry, Students, Science Instruction
Asmus, Stephen E.; Wells, Collin K.; Montalvo, Hanna M. – Biochemistry and Molecular Biology Education, 2023
Heart muscle cells, or cardiomyocytes, exhibit intrinsic contractility in vitro. We found that commercially-available mammalian cardiomyocytes serve as an excellent model system for studying the cytoskeleton and cellular contractility, fundamental topics in undergraduate cell and molecular biology courses. Embryonic rat cardiomyocytes were plated…
Descriptors: Anatomy, Cytology, Science Laboratories, Laboratory Equipment
Craig, Paul A.; Nash, Jessica A.; Crawford, T. Daniel – Biochemistry and Molecular Biology Education, 2022
A programming workshop has been developed for biochemists and molecular biologists to introduce them to the power and flexibility of solving problems with Python. The workshop is designed to move users beyond a "plug-and-play" approach that is based on spreadsheets and web applications in their teaching and research to writing scripts to…
Descriptors: Programming Languages, Biochemistry, Molecular Biology, Data Analysis
Representing DNA for Machine Learning Algorithms: A Primer on One-Hot, Binary, and Integer Encodings
Yash Munnalal Gupta; Satwika Nindya Kirana; Somjit Homchan – Biochemistry and Molecular Biology Education, 2025
This short paper presents an educational approach to teaching three popular methods for encoding DNA sequences: one-hot encoding, binary encoding, and integer encoding. Aimed at bioinformatics and computational biology students, our learning intervention focuses on developing practical skills in implementing these essential techniques for…
Descriptors: Science Instruction, Teaching Methods, Genetics, Molecular Biology
Ludmila Tyler; Peter J. Kennelly; Shelly Engelman; Kirsten F. Block; Jennifer C. Bobenko; Jaclyn Catalano; Jesica A. Jones; Margaret I. Kanipes-Spinks; Yang Mooi Lim; Jennifer Loertscher; Tejiri Olafimihan; Hailey Reiss; Territa L. Upchurch-Poole; Yufeng Wei; Kimberly J. Linenberger Cortes; Victoria Del Gaizo Moore; Daniel R. Dries – Biochemistry and Molecular Biology Education, 2024
We present as a case study the evolution of a series of participant-centered workshops designed to meet a need in the life sciences education community--the incorporation of best practices in the assessment of student learning. Initially, the ICABL (Inclusive Community for the Assessment of Biochemistry and Molecular Biology/BMB Learning) project…
Descriptors: Science Education, Science Teachers, Teacher Workshops, Biological Sciences
Chang, Ming-Mei – Biochemistry and Molecular Biology Education, 2022
Southern blot analysis is an important molecular biology technique for identifying a specific sequence in DNA samples. Although it is no longer used extensively in recent years, the steps and underlying principles of Southern blot are applicable to modern biology. High sensitivity and limited background are keys to successful Southern blots,…
Descriptors: Molecular Biology, Science Instruction, Genetics, Hands on Science
Singh, Anoushka; Miller, Ryan C.; Archuleta, Stephen R.; Kugel, Jennifer F. – Biochemistry and Molecular Biology Education, 2023
Transcription is the critical first step in expressing a gene, during which an RNA polymerase (RNAP) synthesizes an RNA copy of one strand of the DNA that encodes a gene. Here we describe a laboratory experiment that uses a single assay to probe two important steps in transcription: (1) RNAP binding to DNA, and (2) the transcriptional activity of…
Descriptors: Molecular Biology, Science Instruction, Genetics, Teaching Methods
Sievers, Matt; Reemts, Connor; Dickinson, Katherine J.; Mukerji, Joya; Beltran, Ismael Barreras; Theobald, Elli J.; Velasco, Vicente; Freeman, Scott – Biochemistry and Molecular Biology Education, 2023
Researchers have called for undergraduate courses to update teaching frameworks based on the Modern Synthesis with insights from molecular biology, by stressing the molecular underpinnings of variation and adaptation. To support this goal, we developed a modified version of the widely used Assessing Conceptual Reasoning of Natural Selection…
Descriptors: Student Evaluation, Knowledge Level, Molecular Biology, Evolution
Maurye, Praveen; Basu, Arpita; Jana, Chayna; Devi, Manoharmayum Shaya; Kumari, Kavita; Naskar, Malay – Biochemistry and Molecular Biology Education, 2022
Gel electrophoresis (GE) is the most preferred and adapted technique for the separation and identification of biological molecules like proteins/peptides and nucleic acids from diverse types of organisms. All over the world, researchers, educators, and students aspiring to work in biochemistry and molecular biology disciplines use the…
Descriptors: High School Students, Biochemistry, Molecular Biology, Laboratory Procedures
Meftahi, Gholam Hossein; Bahari, Zahra; Zarei Mahmoudabadi, Ali; Iman, Maryam; Jangravi, Zohreh – Biochemistry and Molecular Biology Education, 2021
Western blot (WB) or immunoblot is a workhorse method. It is commonly used by biologists for study of different aspects of protein biomolecules. In addition, it has been widely used in disease diagnosis. Despite some limitations such as long time, different applications of WB have not been limited. In the present review, we have summarized…
Descriptors: Biochemistry, Molecular Biology, Clinical Diagnosis, Literature Reviews
Bubis, José – Biochemistry and Molecular Biology Education, 2021
Protein molecular weight standards are routinely employed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to estimate the apparent sizes of unknown proteins within a sample. For training students, a laboratory course based on the production of marker proteins is proposed. Following fractionation by column chromatography, a…
Descriptors: Molecular Biology, Science Laboratories, Molecular Structure, Scientific Concepts
Castro, Claudia; Johnson, R. Jeremy; Kieffer, Bruno; Means, John A.; Taylor, Ann; Telford, Jason; Thompson, Lynmarie K.; Sussman, Joel L.; Prilusky, Jaime; Theis, Karsten – Biochemistry and Molecular Biology Education, 2021
Proteopedia (proteopedia.org) is an open resource to explore the structure--function relationship of proteins and other biomolecules. This guide provides practical advice on how to incorporate Proteopedia into teaching the structure and function of proteins and other biomolecules. For 11 activities, we discuss desired outcomes, setting…
Descriptors: Science Instruction, Open Educational Resources, Molecular Biology, Science Activities
