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

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2407

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498

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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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2149

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667

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Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does "under the hood." A solid understanding of how a bioinformatics...

Courses: Biochemistry and Molecular Biology Bioinformatics Introductory Biology

BLASTmultiple sequence alignmentsequence similarityphylogramZika virusAlgorithmScoring Matrix

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4850

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Teaching the Central Dogma Using a Case Study of Genetic Variation in Cystic Fibrosis

The central dogma of biology is a foundational concept that is traditionally included in genetics curricula at all academic levels. Despite its ubiquitous presence throughout genetics education, students persistently struggle with both the...

Courses: Genetics

transcriptioncentral dogmatranslationsequence analysisDNA replicationgenetic variants

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2327

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228

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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

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246

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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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3889

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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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3792

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1247

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My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype Relationships

To facilitate understanding of the fundamental genetic concept of the genotype-phenotype relationship in our introductory biology students, we designed an engaging multi-week series of related lessons about canine genetics in which students...

Courses: Bioinformatics Genetics Introductory Biology Science Process Skills

gel electrophoresissequence analysiscanine geneticsdeoxyribonucleic acid (DNA)dog coat morphologygenotype and phenotypemutationsPolymerase chain reaction (PCR)single nucleotide polymorphism (SNP)

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348

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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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3415

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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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1734

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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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5493

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Exploring the Lytic and Lysogenic Life Cycles of Bacteriophages

The goal of this lesson is to introduce students to the lytic and lysogenic cycles of T4 and lambda bacteriophages, respectively, using student-centered pedagogies. Bacteriophages are viruses that infect bacteria and are either virulent or...

Courses: Microbiology

bacteriophagesLysogenic cycleLysogenyLytic cycle

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1299

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A CRISPR/Cas Guide RNA Design In Silico Activity

CRISPR biotechnologies inspired by the Clustered Regularly Interspaced Short Palindromic Repeat RNA-guided nuclease adaptive bacterial immune system have revolutionized biology research and become ubiquitous tools for hypothesis and...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Genetics

bioinformaticsgene expressiongenetic basis of diseaseCRISPR/Cas9genetic engineeringin silico

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685

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The Case of the Missing Strawberries: RFLP analysis

While solving the fictional mystery of the missing strawberries, students are engaged in a guided-inquiry lesson featuring small-group and class discussions, hands-on activities, and laboratory exercises related to molecular genotyping by...

Courses: Genetics Science Process Skills

process of scienceDNAforensicsgel electrophoresisMolecular genotypingRestriction endonucleaseRestriction enzymeRestriction fragment length polymorphismRFLP

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Exploration of the Human Genome by Investigation of Personalized SNPs

Students often shy away from tedious bioinformatics approaches to exploring their genomes. However, in our expanding digital world these skills are some of the most relevant and valuable. To increase students' interest in their own genomes, I...

Courses: Bioinformatics Genetics Science Process Skills

UCSC genome browsersingle nucleotide polymorphismGenome wide association studiesGenomic organization

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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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Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

One of the challenges of inquiry-based research experiences is balancing the instruction on skills and techniques with data generation and analysis. This is especially true in technique heavy disciplines such as molecular biology, where emphasis...

Courses: Biochemistry and Molecular Biology

experimental designcrisprmolecular technique

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455

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A Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research Experience

A core competency identified in Vision and Change for undergraduate biology students is the Ability to Apply the Process of Science. Here, we describe a three-week laboratory module for students in an Introductory Cell and Molecular Biology...

Courses: Science Process Skills

metacognitiongene expressionScientific ProcessExperimenal DesignHypothesis Generationmodel organisms

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3352

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275

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Application of a Bacterial Experimental Evolution System to Visualize and Teach Evolution in Action: A Course-Based Undergraduate Research Experience

Concepts of evolution are typically taught through examples of extremely long timescales, which do not always resonate broadly. Here, we describe a course-based undergraduate research experience tailored for junior and senior undergraduate biology...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Evolution Genetics Microbiology

EvolutionmutationcompetitionNatural Selectionregulationstructure and functionreproductive fitnessgenotype to phenotypehomologs

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A Laboratory Module That Explores RNA Interference and Codon Optimization Through Fluorescence Microscopy Using Caenorhabditis elegans

Scientific research experiences are beneficial to students allowing them to gain laboratory and problem-solving skills, as well as foundational research skills in a team-based setting. We designed a laboratory module to provide a guided research...

Courses: Bioinformatics Cell Biology Developmental Biology Genetics Science Process Skills

microscopyC. elegansquantitative analysisinquiry-based learninggene expressionRNA interferenceCodon UsageLaboratory Module

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

Translating Co-Translational Translocation

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Teaching the Central Dogma Using a Case Study of Genetic Variation in Cystic Fibrosis

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

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

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

My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype Relationships

A Muscular Dystrophy Case Study Illustrating the Phenotypic Effects of Mutation

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

Exploring the Lytic and Lysogenic Life Cycles of Bacteriophages

A CRISPR/Cas Guide RNA Design In Silico Activity

The Case of the Missing Strawberries: RFLP analysis

Exploration of the Human Genome by Investigation of Personalized SNPs

An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

A Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research Experience

Application of a Bacterial Experimental Evolution System to Visualize and Teach Evolution in Action: A Course-Based Undergraduate Research Experience

A Laboratory Module That Explores RNA Interference and Codon Optimization Through Fluorescence Microscopy Using Caenorhabditis elegans

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