SARS-CoV-2 and COVID 19 Resources

Introduction

At the time of this writing (April 2020), the world is experiencing the most significant pandemic in the last few decades, at least. (One should not forget polio and smallpox, among others, that some now living may still remember.) The causative agent is a novel Severe Acute Respiratory Syndrome Coronavirus, SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19, so called because the outbreak began in Wuhan, China in December, 2019).

This post links to a number of reliable resources about the pandemic. It provides a gateway into deeper study for those desiring or requiring a professional understanding of the situation.

This page will continue to be updated as I discover new resources.

Resources

Web sources

  1. Johns Hopkins Coronavirus Resource Center Dashboard: Provides up-t0-date data on COVID-19 epidemiology and clinical biology.
  2. Center for Disease Control and Prevention COVID-19 gateway: The CDC put together links for the general public and health-care professionals. It allows easy access to data and interpretations of the epidemic, pathology and clinical course of the disease.
  3. World Health Organization COVID-19 gateway: The WHO provides a similar page to CDC’s but with a more global focus.
  4. Morbidity and Mortality Weekly Report from CDC: The CDC publishes MMWR to keep professionals up-to-date with the major health issues facing the U.S. Over the years the MMWR has become one of the most trusted, useful sources of information for professionals, and it is doing an excellent job with this outbreak as well.
  5. Science (AAAS) Coronavirus: Research, Commentary and News: The American Association for the Advancement of Science has collected resources that they have recently published on SARS-CoV-2 into this gateway. Use with care, though, because this material is not peer-reviewed.
  6. Cell Press Coronavirus Resource Hub: Cell Press publishes very influential papers with rigorous peer review. In this hub, they provide timely resources from their suite of journals that relate to SARS-CoV-2 and COVID-19.
  7. New York Times SARS-CoV-2 Infographic: This unlikely source summarizes much of the genomic data curated by the NCBI and other sources into an outstanding outline of the virus’s genome and critical proteins.
  8. ASU COVID-19 Data Repositories: Arizona State University has collected links to a large array of data sites associated with the outbreak.

Documents

  1. Biology by the Numbers, has published an excellent information sheet about the state of the epidemic as of late March, 2020.
  2. Hoffmann et al. (2020) published a paper in Cell that shows how SARS-CoV-2 is related to 2 similar viruses, SARS-CoV and MERS-CoV, which caused similar outbreaks in China (2002, 2003) and the Middle East (2012), and elucidates how SARS-CoV-2 infects cells.
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Lecture 4.6 Competencies and Study Guide

Electron Transport Chain and OXPHOS

Vocabulary

Electron transport chain
Oxidative phosphorylation (OXPHOS)

Competencies

  1. Outline all three mechanisms of ATP production in cells that use oxygen.
  2. Explain the differences in the general purpose of the electron transport chain (ETC) and oxidative phosphorylation (OXPHOS).
  3. Name and describe the relationships of the protein complexes in the mitochondrial ETC.
  4. Identify the location in the cell of the ETC and OXPHOS.
  5. Explain the function of the ETC in general.
  6. Explain how the ETC uses free energy from redox reactions to make the mitochondrion into a battery.
  7. Explain what supplies the high energy electrons to the ETC.
  8. Explain why and how low energy electrons are oxidized off of the ETC.
  9. Explain how OXPHOS produces ATP.
  10. Explain the role of ATP synthase in this process.
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BIO 181 Lecture 4.6

Lecture 4.6: Electron Transport and Oxidative Phosphorylation

Overview

Krebs, Lipmann and others were able to work out where the carbon dioxide originated during oxidative metabolism. But the key question still lingered–it’s oxidative metabolism, so where is the oxygen used? The Krebs cycle simply doesn’t explain that. Well after the biochemical fate of pyruvate was established, the process using oxygen was discovered. That process is called the electron transport chain. But more was to be discovered, because all this process does is make mitochondria into batteries. But what happens when that battery is discharged? The answer lies in oxidative phosphorylation–using oxygen to regenerate ATP. Finally, we come full circle. We started with the observation that cells will run out of ATP is less than a minute. OXPHOS explains why they don’t.

Activities

  1. Read Section 9.5 of the textbook.
  2. Download Lecture 4.6 slides.
  3. Watch and take notes on video 4.6, OXPHOS.
  4. Complete the questions on Study Guide 4.6. (Not to be handed in.)

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 4.6 Quiz.

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Lecture 4.3 Competencies and Study Guide

Enzymes

Vocabulary

Catalyst
Enzyme
Catalytic site
Activation energy
Oxidation
Reduction
Synthesis
Chemosynthesis
Photosynthesis

Competencies

  1. Explain what happens to sucrose after it is ingested into the small intestine.
  2. Explain the role of disaccharidase in that process, and express the sign of ΔG for that reaction.
  3. Define enzyme.
  4. Define catalyst.
  5. Compare and contrast Gibbs free energy with activation energy.
  6. Explain why a bag of sucrose you buy at the store does not become glucose and fructose by the time you use it in your home.
  7. Explain how enzymes act as catalysts.
  8. Define the catalytic site of an enzyme.
  9. Describe how hexokinase looks and how it changes when it binds to glucose.
  10. Describe the structural level at which this change occurs.
  11. Describe an enzyme’s catalytic cycle.
  12. Explain how hydrothermal vent ecosystems differ from other marine and terrestrial ecosystems.
  13. Define oxidation and reduction, and explain them in terms of energy transfer.
  14. Identify oxidation and reduction in chemical reaction equations by looking at transfer of O and H.
  15. Define synthesis, and compare and contrast chemosynthesis and photosynthesis.
  16. Write the equation for chemosynthesis used by archaeans (archaebacteria) living in hydrothermal vents.
  17. Identify what is being oxidized and reduced in the chemosynthesis equation.
  18. Explain how energy is transferred from the Earth’s heat to living things in hydrothermal vent ecosystems.
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BIO 181 Lecture 4.3

Lecture 4.3: Enzymes

Overview

Life is defined in part by metabolism. Although we typically define that concept by the types of chemical reactions that occur, from another viewpoint, metabolism is all about energy management. In the previous lecture we studied what energy is and is not. Managing energy in essence means we extract free energy from chemical compounds mainly to drive endergonic reactions. But, what machinery does that? The answer is, enzymes do that. Here we begin our study of enzymes before moving to our first metabolic system–the simplest one known, which powers living creatures in the deepest recesses of the ocean.

Activities

  1. Read Sections 8.3 through 8.5 of the textbook.
  2. Download Lecture 4.3 slides.
  3. Watch and take notes on video 4.3.1, Enzymes.
  4. Watch and take notes on video 4.3.2, Deep-Sea Metabolism.
  5. Complete the questions on Study Guide 4.3. (Not to be handed in.)

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 4.3 Quiz.

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BIO 181 Lecture 3.7

Lecture 3.7: SARS-CoV-2 and COVID-19

Overview

At this moment (November, 2020), the dominant thing in the lives of most people in the world is a disease called COVID-19, caused by a virus called SARS-CoV-2. We, as professional biologists, are on the front lines battling this pandemic (a global epidemic). Why us? Because we understand transcription, translation, protein expression and the function of biomolecules. This is why we study. This is why we become educated. It’s more than mere training for a job–education prepares us for leadership at times like these.

Activities

  1. Read sections 33.1 and 33.2 of the textbook.
  2. Download Lecture 3.7 slides.
  3. Watch and take notes on video 3.7.1, SARS-CoV-2 and COVID-19 Epidemiology.
  4. Watch and take notes on video 3.7.2, SARS Viruses.
  5. Watch and take notes on video 3.7.3, SARS Pathology.
  6. Complete the questions on Study Guide 3.7 (not to be handed in).

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lec 3.7 Quiz.

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Lecture 3.6 Competencies and Study Guide

Cancer

Vocabulary

Metastasis
Carcinoma
Ipsilateral
Contralateral
Primary tumor
Secondary tumor

Competencies

  1. Explain the properties that make a tumor malignant (cancer).
  2. Explain what it means for a tumor to be invasive.
  3. Describe the process of metastasis in cancer.
  4. Describe at least 2 of the hallmarks of cancer presented by Hanahan and Weinberg (2000).
  5. Explain the 2 major signaling concepts–proliferative signals and proliferation suppressors–that control how and when healthy cells exit G0 and reenter G1.
  6. Describe in detail the type of mutation and its consequences in the child described with retinoblastoma. (Note: this is a classic case that helped determine the role of inherited mutations in cancer.)
  7. Describe the cytogenetic location of the RB1 gene.
  8. Describe the function of the pRB protein in molecular detail–how is it related to E2F?
  9. Explain how a single mutation in the RB1 gene that inactivates the pRB protein is related to the cause of cancer.
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BIO 181 Lecture 3.6

Lecture 3.6: Cancer

Overview

Why is the Central Dogma important? Why are we spending so much time learning about transcription and translation? This lecture will help answer that question. Cancer is one of the most significant diseases in human history. It was recognized by Aristotle around 350 B.C.E., and even today it is the second leading cause of death worldwide. Nevertheless, our ability to treat this disease successfully has improved a great deal over the last 20 years. That improvement came only after our understanding of the molecular mechanisms of gene function, the very same mechanisms that we have studied in this unit. This lecture will open the door to the deeper world of application of our basic biological knowledge.

Activities

  1. Read sections 17.3 through 17.5 in the textbook.
  2. Download Lecture 3.6 slides.
  3. Watch and take notes on video 3.6.1, Introduction to Cancer.
  4. Watch and take notes on video 3.6.2, Malignancy.
  5. Watch and take notes on video 3.6.3, pRB.
  6. Complete the questions on Study Guide 3.6 (not to be handed in).

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lec 3.6 Quiz.

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BIO 181 Lecture 2.6

Lecture 2.6: Evidence for Evolution

Overview

In the past, the Earth supported a variety of interesting creatures that are quite different than anything alive today: carnivores–dog- or cat-like creatures–that had hooves like a deer; a little racoon-like critter that also had hooves; a large mammal shaped like a crocodile, which had hooves, too. All of these had ear bones and other features unique to whales and dolphins. Modern creatures have a variety of odd characteristics: whales have hind limb bones but no hind limbs; they develop hair and whiskers as fetuses but then lose them before birth; you have broken versions of genes from other species in your DNA. In this lecture, we observe these and other strange patterns and discuss why they exist. This discussion leads us to one of the most useful and successful theories–as professional scientists, not the general public uses that term–in all of science.

Activities

  1. Download Lec 2.6 slides.
  2. Watch video 2.6.1, Synapomorphies.
  3. Watch video 2.6.2, Vestiges.
  4. Watch video 2.6.3, Molecular evidence for evolution.
  5. Read Sections 22.1 and 22.2 of the textbook.

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 2.6 Quiz.

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BIO 181 Lecture 3.5

Lecture 3.5: Translation

Overview

The second step in the central dogma has information flowing from RNA to protein. That process is called transcription. Conceptually the information coded in the sequences of bases on RNA informs the cell of the proper sequence of amino acids on a particular poplypeptide or protein. In this lecture we begin a study of the details of the mechanisms the cell uses to accomplish this task.

Activities

  1. Read sections 17.3 through 17.5 in the textbook.
  2. Download Lecture 3.5 slides.
  3. Watch and take notes on video 3.5.1, Translation initiation.
  4. Watch and take notes on video 3.5.2, Mutation.
  5. Complete the questions on Study Guide 3.5 (not to be handed in).

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lec 3.5 Quiz.

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BIO 181 Lecture 3.3

Lecture 3.3: Basic Gene Function

Overview

What does DNA and its genes, whatever those are, actually code for? This question is also still evolving. At one point in time, around the 1980s, we were fairly certain that we knew the answer: genes code for proteins. That made sense, given that proteins perform most cellular functions. Now, however, we have learned that our theory, while correct, was woefully incomplete. Here we begin to look at the older theory, which details the functions of what we now call protein-coding genes. The processes involved are not simple, so this and the next 2 lectures will be devoted to them.

Activities

  1. Read sections 16.3 and 16.4 in the textbook.
  2. Download Lecture 3.3 slides.
  3. Watch and take notes on video 3.3.1, Introduction to gene expression.
  4. Watch and take notes on video 3.3.2, Mutation.
  5. Watch and take notes on video 3.3.
  6. Complete the questions on Study Guide 3.3 (not to be handed in).

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lec 3.3 Quiz.

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