Biochemistry COVID/SARS Teaching Materials

Description and use of materials: This website is for faculty interested in creating, adopting, stealing, materials to teach biochemistry and molecular biology using COVID as a theme. Online or in-person the material uses several different pedagogies and approaches to engage students.  Videos, discussion boards, flipped classrooms, personal videos from scientists on the leading edge of COVID research are all included.

The work here was used and created to teach important biochemistry concepts and techniques. These materials are primarily meant to used to teach a biochemistry/biology/chemistry major-level junior/senior course. The teaching materials shared here can be used after teaching the key concepts of molecular biology and protein biochemistry or interspersed as a theme throughout a semester. With minimal alteration, each assignment could be performed independently, grouped or done as an extended learning module.

Use the material as you see fit. However, use at your own risk. Caveat emptor or the buyer alone is responsible for checking the quality and suitability of the goods. These were used with good success in a remote format and many, most, but not all errors or mistakes have been corrected. There are many additional outstanding resources, these are presented because they worked for me. Adopt and change as you see fit.  If you wish to make kind suggestions (I am fragile ;>) feel free to email me with your ideas.

This is part of a larger project called “COVID 360” lead by Jennifer Roecklein-Canfield with Lisa Scheifele, Mike Wolyniak, and Victoria Moore.  Together we are gathering COVID-centered teaching resources in several subject/discipline areas: Biochemistry and Molecular Biology Structure Function, Immunology, Genomic Analysis, Vaccinology, Pharmacology/Medicinal Chemistry, Systems and Synthetic Biology.  The project will be shared on CourseSource… 

Teaching Materials (downloaded as word files for adoption)

  • Biochem COVID teaching learning objectives
  • Activity Description
  • COVID Virus Introduction PPT
  • Mind/Concept Map Assignment
  • COVID Presentations and Critique Instructions
  • COVID Theraputic Activity Instructions
  • Research Publication Activity I- ACE-Spike Protein
  • Research Publications Activity II- Mutational Analysis
  • Required Video - Dr. Erik Procko on his COVID Research on ACE2-S Protein
  • Required Video - Molecular Memories Video on COVID-19 Structure (Dr. Kristin Procko)

ASBMB Presentation Handout

  • Resources
    • Nice illustrated summary of COVID-19  YouTube
    • Simple Life Cycle of Virus Tutorial  YouTube
    • Lecture on COVID-19 and ACE2  stop at ~4:50  Youtube
    • Detailed Video of Molecular Virology of CoronaVirus Youtube
    • Review- Coronaviruses: An Overview of their replication and pathogenesis  NCBI Site
    • J Advanced Research COVID-19 Review  HTML Version
    • Review of COVID-19   Springer HTML
    • ASBMB Today – Article on Spike Protein  WebVersion
    • The Proximal Origin of SARS-CoV-2  Nature Article with S protein alignment
    • Genomic Anaylsis of COVID-19 Strains Science Mag Discussion
    • Phylogenic Evolution of COVID-19 Nextstrain
    • Structural analysis of COVID  MolecularMemories
    • Deep Look into the Biology and Evolution of COVID-19  UCSD
    • SARS Coronavirus E Protein PDB Website
    • SARS Coronavirus S Protein PDB Website
    • SARS Coronavirus M Protein PDB Website
    • Protein E and M alignment
    • COVID M-Membrane Protein Structure PubMed
    • Vaccine Simple Approach Nature
    • ASBMB Today – Article on Chloroquine Website
    • Repurposing Drugs for COVID Website
    • Open-Data Repository on Hydroxychloroquine Website Collection
    • Collection of COVID-19 Drug Therapy-Potential Option  Elsevier PDF
    • Antimicrobial Agents and Chemotherapy Journal  Article on Potential COVID Therapies
    • ASBMB Today – What makes remdesivir unique? Web Article
    • AAAS Science Translational Medicine Blog on Drugs in the Pipeline
    • Video on ACE and Coronavirus-19  YouTube
    • Erik Procko’s Paper on ACE2 Binding to Spike Protein Preprint HTML Version
    • RT-PCR ThermoFisher – Authorized for in vitro diagnostic use.
    • PCR Information for Laboratories – From the CDC Website

INSTRUCTIONS FOR STUDENTS-HOW TO ALIGN PROTEIN SEQUENCES:  To align the primary amino acid sequence of proteins, use either the pre-supplied sequences in the resource link.  You may be interested in expanding your comparisons.  To do so, the simplest way is to click on the UniProt link to bring you to a program that includes protein sequence alignment called Clustal.  The alignment requires you find the PROTEIN sequence (you can search in UniProt or NCBI) but make sure you have the protein and not nucleotide record ID number/sequence.  Following the instructions in this video, you can use a FASTA sequence or other options to paste protein data for comparison.  Not sure how to find the FASTA or other ways to do an alignment?  Click here for a tutorial.

For those interested in learning PyMOL (Molecular Memory) and (bottom left page of link - a collection of video tutorials on PyMOL)

(Back)

For Faculty Interested in Adopting: A few thoughts to further develop and add modules – Have students analyze (and notate?) the entire genome of SARS, MERS and COVID-19.  Identify where they are unique and find the function of these.   Additionally search the additional set of aa that were inserted when COVID-19 jumped into the human population.  These might be a sight of interesting biochemistry. 

  • There are a set of molecular biology – bioinformatics case studies
  • There is interesting physiology on how the virus “hides” or suppresses the host immune system until the titer (MOI) is high – this creates the “cytokine storm”  lots of interesting stuff
  • The genetics of how the “slip” of polymerases that increase both the diversity and number of possible genes/genetic expression control is fascinating. 

Additional COVID Related Teaching Materials/Activities -

Genomic alignment of different strains of viruses in the Coronaviridae family and PCR Coronavirus diagnostic design (Nik Tsotakos and Lisa Scheifele)

Questions - email: josephprovost@sandiego.edu