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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285

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Fragile States: A Case Study Exploring Genetics, Molecular Biology, and Biochemistry Through the Lens of Fragile X Syndrome

This case aims to strengthen students’ understanding of molecular biology concepts through study of Fragile X Syndrome (FXS). Students begin by learning the cause and phenotypes of FXS and related conditions. Students then apply genetics...

Courses: Biochemistry and Molecular Biology Genetics

gene regulationtranscriptiontranslationFragile X syndrometriplet repeat expansionsex linkagemetabolic pathway

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397

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Investigating Cell Signaling with Gene Expression Datasets

Modern molecular biology is a data- and computationally-intensive field with few instructional resources for introducing undergraduate students to the requisite skills and techniques for analyzing large data sets. This Lesson helps students: (i)...

Courses: Biochemistry and Molecular Biology Cell Biology

genomicstranscriptionsignaling

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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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2102

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Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

Students require a deep understanding of the central dogma before they can understand complex topics such as evolution and biochemical disorders. However, getting undergraduate biology students to apply higher-order thinking skills to the central...

Courses: Bioinformatics Genetics Science Process Skills

Protein Structurecomputational modelingcentral dogmaplant leaf structurePhenotype/Genotype

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5032

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Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

Analyzing high-throughput DNA sequence data is a fundamental skill in modern biology. However, real and perceived barriers such as massive file sizes, substantial computational requirements, and lack of instructor background knowledge can...

Courses: Biochemistry and Molecular Biology Bioinformatics

bioinformaticsDNA sequenceRNAseqgene expression

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986

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182

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From Cre/LoxP to Fate Maps: Inclusive and Equitable Approaches for Engaging Developmental Biology Students in Experimental Design

Engaging first generation underrepresented minority students in the process of inquiry in developmental biology is important to increase diversity in future graduate STEM education. One important challenge is how we design curricula to foster...

Courses: Developmental Biology

experimental designC. elegansCre/LoxPFate mapheart developmentheart regenerationmousereporter constructzebrafish

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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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83

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The Great Petunia Carnage of 2017: A Clicker Case Study Using Petunias to Describe the Effect of Genetic Modification on the Biochemistry of Flower Color and Phenotype in Plants

In this single class period case study, students examine the difference between genotype and phenotype by studying the mechanisms by which commercially available petunias have been bred to have different phenotypes (flower colors). Students review...

Courses: Genetics Introductory Biology Plant Biology

case studyGenetic ModificationsBiochemistry of Flower ColorGMO regulationsGenotype-Phenotype Connections

Teaching Tools and Strategies

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Drawing flowcharts of lab protocols helps students prepare for biology labs

With the publishing of the Vision and Change report, we know it is best practice to include authentic research experiences in our undergraduate science lab classes. One big challenge in teaching so-called "wet lab" classes is figuring...

Courses: Biochemistry and Molecular Biology Genetics Introductory Biology Science Process Skills

laboratorymolecular biologyUndergraduateprotocolflowchart

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Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson

There is a growing need for integration of “Big Data” into undergraduate biology curricula. Transcriptomics is one venue to examine biology from an informatics perspective. RNA sequencing has largely replaced the use of microarrays for whole...

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

bioinformaticscancertranscriptomicshigh-throughputData wranglingSingle cell RNA sequencingq

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1598

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344

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Investigating Gene Expression and Cell Specialization in Axolotl Embryos

The process of cell specialization is critical to the formation and function of tissues in animals and plants. Although gene expression, including the regulation of transcription, is taught in most introductory cell biology courses, the...

Courses: Biochemistry and Molecular Biology Cell Biology Developmental Biology Science Process Skills

developmenttranscriptiongene expressionmodel organismembryo

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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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A Close-Up Look at PCR

The Polymerase Chain Reaction (PCR) is a fundamental laboratory technique that allows for the amplification of many copies of a desired DNA target sequence. Despite its prevalence, undergraduate students often have poor comprehension about the...

Courses: Biochemistry and Molecular Biology Genetics Introductory Biology Science Process Skills

PCRDNA replication

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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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Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway

Students are frequently overwhelmed by the complexity of metabolic pathways and they think they have "learned" the pathway when they have memorized the individual reactions. This laboratory lesson helps students to understand the...

Courses: Biochemistry and Molecular Biology Genetics Introductory Biology Microbiology Science Process Skills

SelectionyeastMetabolismcysteinemediamethioninemutantPathwaysulfur

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Splicing it Together: Using Primary Data to Explore RNA Splicing and Gene Expression in Large-Lecture Introductory Biology

At the heart of scientific ways of knowing is the systematic collection and analysis of data, which is then used to propose an explanation of how the world works. In this two-day module, students in a large-lecture course are immersed in a...

Courses: Biochemistry and Molecular Biology Cell Biology Genetics Introductory Biology

gene regulationtranscriptiongene expressioncentral dogmarepressoralternative splicingmRNA processingActivatorTranscription factors

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Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course

The multistep nature of tumorigenesis is a foundational concept in the context of Cancer Biology. Many students do not appreciate the complex nature of cancer development nor do they understand how scientists are able to unravel the molecular...

Courses: Cell Biology Genetics Science Process Skills

pathwayscancerMolecular AlterationsRetrospective dataTumorigenesis

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Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

Teaching evolutionary theory is foundational for all biological sciences and a key aspect of overall science literacy. The conceptual framework for understanding evolution relies on thinking clearly about evolutionary trees (phylogenetics) and how...

Courses: Evolution Introductory Biology

EvolutionphylogeneticsTree thinkingbiogeography

Lesson

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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

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

Fragile States: A Case Study Exploring Genetics, Molecular Biology, and Biochemistry Through the Lens of Fragile X Syndrome

Investigating Cell Signaling with Gene Expression Datasets

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

Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

From Cre/LoxP to Fate Maps: Inclusive and Equitable Approaches for Engaging Developmental Biology Students in Experimental Design

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

The Great Petunia Carnage of 2017: A Clicker Case Study Using Petunias to Describe the Effect of Genetic Modification on the Biochemistry of Flower Color and Phenotype in Plants

Drawing flowcharts of lab protocols helps students prepare for biology labs

Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson

Investigating Gene Expression and Cell Specialization in Axolotl Embryos

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

A Close-Up Look at PCR

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

Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway

Splicing it Together: Using Primary Data to Explore RNA Splicing and Gene Expression in Large-Lecture Introductory Biology

Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course

Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

Using Raw Sequence Data to Analyze Tumor Suppressor Mutations

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