CourseSource: Resources

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Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four...

Courses: Biochemistry and Molecular Biology Bioinformatics Science Process Skills

bioinformaticsmolecular modelingCOVID19protein structure and functionUCSF ChimeraSARS-CoV-2 spike proteinACE2 receptor

Essay

1704

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369

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Online Adaptation of the Cell Engineer/Detective Lesson

One of the most fundamental themes of biology is the relationship between structure and function, which is particularly evident when it comes to cells; however, the traditional cartoon depictions of cells that are often used to help teach the...

Courses: Cell Biology Introductory Biology Science Process Skills

cell functionCell StructureOrganelles

Lesson

1578

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350

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Understanding Protein Domains: A Modular Approach

An understanding of protein structure, function, and interaction is central to biochemistry. One angle into this topic is to engage students in considering protein domains as modules that develop form and execute function semi-independently. Here,...

Courses: Biochemistry and Molecular Biology Cell Biology Science Process Skills

Protein Structure

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3882

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209

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Isolation and Functional Analysis of a Pancreatic Enzyme in an Introductory Student Lab

Structure and function are correlated at all levels of biology. This topic is typically addressed early in an undergraduate class in general or molecular biology before students have gained much skill or knowledge in molecular biology. However, an...

Courses: Biochemistry and Molecular Biology Introductory Biology

Protein StructureproteaseEnzymechemical bondscatalysissolubility

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4196

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627

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Using Bioinformatics and Molecular Visualization to Develop Student Hypotheses in a Malate Dehydrogenase Oriented CURE

Developing student creativity and ability to develop a testable hypothesis represents a significant challenge in most laboratory courses. This lesson demonstrates how students use facets of molecular evolution and bioinformatics approaches...

Courses: Biochemistry and Molecular Biology Bioinformatics Science Process Skills

bioinformaticsNoncovalent InteractionsEnzyme CatalysisProtein Structure/function

Teaching Tools and Strategies

3637

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1718

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A 360˚ View of COVID-19

In March 2020, institutions underwent a massive transition to distance learning as a result of the COVID-19 pandemic. With so little time to devise new materials to maximize learning in the new virtual environment, instructors devised a variety of...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Evolution Genetics Immunology Introductory Biology Microbiology Science Process Skills

geneticsImmunologyBiochemistrybioinformaticsmolecular evolutionpublic healthvirusCOVID19

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2323

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227

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Sequences and Properties of Gluten Proteins From Different Grains: A Virtual-Friendly Protein Laboratory

The COVID-19 pandemic has forced much university instruction into virtual modes. As a result, many laboratory courses have either dropped content altogether or replaced hands-on activities with simulations and “dry” labs. Our goal was...

Courses: Biochemistry and Molecular Biology Bioinformatics

protein structure and functionProtein sequenceintermolecular forcesBiomacromolecules

Lesson

5361

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1394

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Teaching Cell Structures through Games

As the basic unit of life, cells are a foundational concept for all of biology. Before students can appreciate how eukaryotic cells function either in isolation or in higher order and multicellular organisms, they must first have a basic...

Courses: Introductory Biology

Cell Structurecell organellesTransmembrane Transport

Lesson

3140

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502

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Targeting Misconceptions in the Central Dogma by Examining Viral Infection

Understanding the central dogma and how changes in gene expression can impact cell function requires integration of several topics in molecular biology. Students often do not make the necessary connections between DNA structure, transcription,...

Courses: Genetics Introductory Biology

datatranscriptionvirustranslationprotein functionmembrane transportPredictions

Lesson

3406

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285

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Garden Variety Mutations: Using Primary Data to Understand the Central Dogma in Large-Lecture Introductory Biology

The ability to interpret and create an argument from data is a crucial skill for budding scientists, yet one that is seldom practiced in introductory courses. During this argumentation module, students in a large lecture class will work in groups...

Courses: Biochemistry and Molecular Biology Genetics Introductory Biology

mutationtranscriptiongene expressioncentral dogmatranslationgel electrophoresisGenotype/Phenotype

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1731

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422

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How to Find a Gene: Retrieving Information From Gene Databases

A strong understanding of distinct gene components and the ability to retrieve relevant information from gene databases are necessary to answer a diverse set of biological questions. However, often there is a considerable gap between...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Genetics Introductory Biology

NCBItranscriptiontranslationGene StructureGene databasesEnsembl

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2993

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346

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A Muscular Dystrophy Case Study Illustrating the Phenotypic Effects of Mutation

Mutations in genes can lead to a variety of phenotypes, including various human diseases. Students often understand that a particular mutation in a single gene causes a disease phenotype, but it is more challenging to illustrate complex genetic...

Courses: Developmental Biology Genetics

mutationProtein Structureethicscentral dogmahuman disease

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81

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Using Raw Sequence Data to Analyze Tumor Suppressor Mutations

Learning to identify DNA sequence variants from raw sequencing data (electropherograms) is a basic molecular biology skill with applications to basic research and clinical practice. Yet learning to map DNA sequence variants to functional regions...

Courses: Bioinformatics Genetics

bioinformaticsmutationDNAgenomic visualizationparts of a geneclinical consequencesraw data

Science Behind the Lesson

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202

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The Science Behind the ACTN3 Polymorphism

A common polymorphism in the alpha-actinin-3 (ACTN3) gene results in the lack of ACTN3 protein expression in fast twitch muscle fibers in ~16% of the human population (1). This genetic change has been linked with muscle performance in humans (2)...

Courses: Anatomy-Physiology Genetics

protein structure and functionhuman genetic variationskeletal muscle physiology

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460

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The Avocado Lab: An Inquiry-Driven Exploration of an Enzymatic Browning Reaction

Typical biochemistry labs exploring basic enzyme activity rely on costly, time-consuming protein purification and rarely explore enzyme function in situ. Further, complex purification procedures leave little room for novelty in experimental...

Courses: Biochemistry and Molecular Biology Introductory Biology

enzymescontrolsenzyme inhibition

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240

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21

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Protein Import Into the ER: Understanding Experimental Methods for Old and New Cellular Discoveries

Process Oriented Guided Inquiry Learning (POGIL) is an effective approach for group work in STEM courses. POGIL-style lessons foster active learning because they require students to communicate and co-construct knowledge to solve problems. Here,...

Courses: Cell Biology Science Process Skills

Necessary and sufficientsignal sequenceProtein SynthesistrafficER importTranslocation

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497

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Translating Co-Translational Translocation

Understanding the process of proteins targeting to specific locations within a cell is a fundamental part of cell biology. Synthesis of proteins by co-translational translocation, which also determines the resulting protein topology, is a complex...

Courses: Cell Biology

Topologyco-translational translocationendoplasmic reticulumprotease protection assaysecretory proteinssignal sequencetransmembrane proteins

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An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and...

Courses: Biochemistry and Molecular Biology Bioinformatics Genetics

bioinformaticsGenome BrowsergenomicsRNAseqsplicingComputer ModelGene Structure

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907

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A Structured Inquiry-Based Module for the Undergraduate Cell Biology Laboratory That Teaches Fundamental Concepts of Cell Differentiation

Pedagogical research in science education has shown that students effectively learn science by doing science. As a result, there is increased interest in bringing research-like experiences into the classroom, particularly for laboratory courses....

Courses: Cell Biology

fluorescence microscopygene expressionpolymerase chain reactionCell Structurecell culturewestern blottingdifferentiationreverse transcription

Lesson

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612

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Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function: Introductory Biology (identifying new promoters)

Students often memorize the definition of a transcriptional promoter but fail to fully understand the critical role promoters play in gene expression. This laboratory lesson allows students to conduct original research by identifying and...

Courses: Genetics Introductory Biology Science Process Skills

bacteriasynthetic biologygene regulationtranscriptionstudent researchcentral dogmacloningpromoterreporter gene/protein

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Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

Online Adaptation of the Cell Engineer/Detective Lesson

Understanding Protein Domains: A Modular Approach

Isolation and Functional Analysis of a Pancreatic Enzyme in an Introductory Student Lab

Using Bioinformatics and Molecular Visualization to Develop Student Hypotheses in a Malate Dehydrogenase Oriented CURE

A 360˚ View of COVID-19

Sequences and Properties of Gluten Proteins From Different Grains: A Virtual-Friendly Protein Laboratory

Teaching Cell Structures through Games

Targeting Misconceptions in the Central Dogma by Examining Viral Infection

Garden Variety Mutations: Using Primary Data to Understand the Central Dogma in Large-Lecture Introductory Biology

How to Find a Gene: Retrieving Information From Gene Databases

A Muscular Dystrophy Case Study Illustrating the Phenotypic Effects of Mutation

Using Raw Sequence Data to Analyze Tumor Suppressor Mutations

The Science Behind the ACTN3 Polymorphism

The Avocado Lab: An Inquiry-Driven Exploration of an Enzymatic Browning Reaction

Protein Import Into the ER: Understanding Experimental Methods for Old and New Cellular Discoveries

Translating Co-Translational Translocation

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

A Structured Inquiry-Based Module for the Undergraduate Cell Biology Laboratory That Teaches Fundamental Concepts of Cell Differentiation

Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function: Introductory Biology (identifying new promoters)

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