BIO 181 Lecture 3.3

Lecture 3.3: Transcription

Overview

The first step in the central dogma has information flowing from DNA to RNA. That process is called translation. Conceptually, as we saw in the previous lecture, the information coded in the sequences of bases on DNA must be accurately copied into a sequence of bases on RNA. The product is called messenger RNA, or mRNA. In this lecture we begin a study of the details of the mechanisms the cell uses to accomplish this task.

Activities

  1. Read sections 17.1 and 17.2 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, Introduction to translation.
  5. Watch and take notes on video 3.3 supplement.
  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 3.4 Quiz.

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BIO 181 Lecture 3.2

Lecture 3.2: Gene Structure and Arrangement

Overview

The molecular structure of DNA provided clues to its replication, as we saw in the previous lecture. It was also fairly obvious that the information held in the DNA was somehow coded in the sequence of bases. But how is it coded? And what, precisely, is a gene? The first question was largely worked out in the decades following discovery of the molecular structure of the molecule. But the last is still open. In this lecture, we begin our study of gene function by looking first at the anatomy of a “gene” and how these information packets are arranged on chromosomes.

Activities

  1. Read sections 16.1 and 16.2 in the textbook.
  2. Download Lecture 3.2 slides.
  3. Watch and take notes on video 3.2.1, Introduction to DNA logic.
  4. Watch and take notes on video 3.2.2, Gene anatomy.
  5. Watch and take notes on video 3.2.3, Gene arrangement.
  6. Complete the questions on Study Guide 3.2 (not to be handed in).

Resources

The lectures refer to other resources that you can find here:

  1. NCBI Website.
  2. Chromosome 11 flyover.

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lec 3.2 Quiz.

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BIO 181 Lecture 3.1

Lecture 3.1: DNA Structure and Replication

Overview

One of the most fascinating aspects of DNA is that some of its function becomes obvious once its structure is known. The elucidation of its structure–a double helix with strict base pairing rules–took some time and some of the greatest minds in the history of science. In this lecture we will explore that discovery and the evidence behind it. We follow up the discovery of DNA’s structure with an observation made by one of the key architects of the theory: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possilbe copying mechanism for the genetic material.”

Activities

  1. Review sections 4.1 and 4.2 in the textbook.
  2. Read chapter 15 in the textbook.
  3. Download Lecture 3.1 slides.
  4. Watch and take notes on video 3.1.1, History and significance of DNA structure.
  5. Watch and take notes on video 3.1.2, DNA synthesis 1.
  6. Watch and take notes on video 3.1.3, DNA synthesis 2.
  7. Complete the questions on Study Guide 3.1 (not to be handed in).

Resources

The lectures refer to other resources that you can find here:

  1. NCBI Website
  2. DNA Replication Animation

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lec 3.1 Quiz.

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Sample MCAT Questions

Two sample questions from the Medical College Admission Test (MCAT)

I’ve said many, many times that BIO 181 (General Biology for Majors at Arizona public colleges and universities) just scratches the surface of what we know. I also point out that the material in the class will support upper division (300 and 400-level) study at the universities. The primary goal of the course is to educate those who wish to establish professional lives in biological sciences and (or) medicine, not to assign grades.

Here I present evidence for these statements. Below I post 2 sample MCAT questions (from the Association of American Medical Colleges website). Please read these carefully. Look for references to material taught in BIO 181 (Na+ and K+ gradients, energy metabolism, glycolysis, bar graphs, error bars, scientific reasoning). But also compare the level of understanding required to answer these questions effortlessly and accurately to the level of BIO 181. Also remember, these are just a tiny sampling of the test to get into medical school.

It’s not about grades. It’s about knowledge and skills. If you master those, the grades will take care of themselves.

Sample MCAT Questions:

Passage:

The myocellular transmembrane Na+ gradient is important for proper cellular function. During septic shock, disruption of Na+ homeostasis often occurs and leads to decreased membrane potential and increased intracellular Na+. It has been found that failure of cellular energy metabolism is a common symptom in septic patients who do not respond to therapeutics. Because normal intracellular levels of Na+ are maintained by the Na+K+ ATPase, it is important to understand how metabolic energy production is linked to cation transport.

Researchers are interested in whether the energy used for ion transport is derived from glycolysis or oxidative phosphorylation. This information would provide a better understanding of myocellular damage that occurs during critical illness. Experiments were conducted to evaluate the effects of glycolytic inhibition on cellular Na+ and K+ concentrations and lactate production in rat skeletal myocytes.

Rat skeletal muscle fibers were extracted and incubated in normal media (control), glucose-free media (G(–)), and glucose-free media with various concentrations of the glycolytic inhibitor iodoacetate (IAA). IAA directly prevents the formation of 1,3-bisphosphoglycerate. After one hour in the media, the muscle tissues were assayed for intracellular Na+ and K+ content and lactate production. Cellular viability was determined by measuring the amount of lactate dehydrogenase (LDH) released, as LDH release is an indicator of cell death. The results are displayed in Figure 1.

section 4-fig1.jpg

Figure 1 Effects of glycolytic inhibition on intracellular Na+ and K+ content and lactate production with cellular viability measured by LDH release. (Note: The * indicates p < 0.05 versus control.)

The researchers also examined the effect disruption of oxidative phosphorylation had on Na+ and K+ content. Inhibition of oxidative phosphorylation was caused by carbonyl-cyanide m-chlorophenylhydrazone (CCCP), an ionophore that allows protons to move freely through membranes. No correlation between Na+ and K+ content and oxidative phosphorylation was found.

Adapted from: Okamoto K, Wang W, Rounds J, Chambers EA, Jacobs DO. ATP from glycolysis is required for normal sodium homeostasis in resting fast-twitch rodent skeletal muscle. The American Journal of Physiology-Endocrinology and Metabolism. 2001 Sept;281(3):E479-88.

Questions:

1. The researchers chose a concentration of 0.3 mM IAA as the working concentration for any additional studies instead of 1 mM or 2 mM. What is the likely reason for this?

A) The lower concentration of IAA gave the largest Na+ response.

B) Higher concentrations induced significant cytotoxicity.

C) The solubility of IAA was not high enough.

D) The researchers were trying to mimic control conditions as closely as possible.

 

2. The information in the passage suggests that glycolysis:

A) is important for maintaining normal Na+ and K+ levels in skeletal muscle.

B) facilitates membrane permeability in skeletal muscle.

C) impedes the function of the Na+ and K+ ATPase in skeletal muscle.

D) is regulated by the Na+ and K+ ATPase in skeletal muscle.

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BIO 181 Lecture 4.7

Lecture 4.7: Photosynthesis

Overview

We saw earlier that cells only have no more than 20 of ATP reserve because it’s being oxidized at an enormous rate–100 million ATP per second. We also saw how cells regenerate that ATP using energy extracted from organic molecules. But where did the energy from these organic molecules come from, given that energy can only be transferred, not created? Ladies and gentlemen, you are walking, talking sunlight.

Activities

  1. Read Chapter 10 of the textbook.
  2. Download Lecture 4.7 slides.
  3. Watch video 4.7.1, Nature of Light.
  4. Watch video 4.7.2, Light-Dependent Reactions.
  5. Watch video 4.7.3, Light-Independent Reactions.
  6. Complete the questions on Study Guide 4.7. (Not to be handed in.)

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 4.7 Quiz.

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BIO 181 Lecture 4.5

Lecture 4.5: Krebs Cycle

Overview

Glycolysis occurs in all cells, and therefore can lay claim to being the heart of energy metabolism in all cells. However, it’s ability to transfer energy from organic compounds to ATP is very limited. Most of the available free energy that could be used to make ATP is wasted. However, when oxygen is available, and cell possess the metabolic pathways to utilize it, a great deal more energy can be extracted from compounds like glucose and used to regenerate ATP. Here, we study those metabolic pathways.

Activities

  1. Read Sections 9.3 and 9.4 of the textbook.
  2. Download Lecture 4.5 slides.
  3. Watch video 4.5.1, Introduction to Oxidative Metabolism.
  4. Watch video 4.5.2, Krebs Cycle.
  5. Complete the questions on Study Guide 4.5. (Not to be handed in.)

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 4.5 Quiz.

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BIO 181 Lecture 4.4

Lecture 4.4: Glycolysis

Overview

The average cell contains about 2 billion ATP molecules. At rest, it “burns” (oxidizes) about 100 million per second. That gives it a reserve of about 20 seconds before the ATP is used up completely. If it runs out of ATP, as we saw in an earlier lecture, it loses control of its osmotic balance, and it will invariably swell and burst. So, something has to regenerate this ATP at the same rate it is used–viz., 100 million per second. These facts place energy metabolism–primarily metabolism revolving around ATP–at the heart of the cell’s metabolic system. ATP is regenerated by extracting energy from organic molecules. The beginning of the process that does this is glycolysis, so we start our detailed study of metabolism here.

Activities

  1. Review Section 9.1 of the textbook.
  2. Read Section 9.2 of the textbook.
  3. Download Lecture 4.4 slides.
  4. Watch and take notes on video 4.4.1, Introduction to Energy Metabolism.
  5. Watch and take notes on video 4.4.2, Glycolysis Details.
  6. Complete the questions on Study Guide 4.4. (Not to be handed in.)

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 4.4 Quiz.

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BIO 181 Lecture 4.2

Lecture 4.2: Introduction to Metabolism

Overview

Human beings are walking, talking biochemical reactors. We are part of this universe. We cannot, therefore, violate the laws that govern this universe. Among these inviolable proscriptions are the laws of thermodynamics, which ban certain things like perpetual motion machines and either de novo production or destruction of energy (at our scale). But, what is energy? Here we explore that concept and begin to see how it governs all of our metabolism. It must be conserved, and when a system, like our bodies, use it, we lose the ability to use all of it a second time.

Activities

  1. Read Section 8.1 of the textbook.
  2. Download Lecture 4.2 slides.
  3. Watch video 4.2.1, Introduction to Thermodynamics for Biology.
  4. Read Section 8.2 of the textbook.
  5. Watch video 4.2.2, Metabolic Energy Transfer.
  6. Complete the questions on Study Guide 4.2. (Not to be handed in.)

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 4.2 Quiz.

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BIO 181 Lecture 4.1

Lecture 4.1: Membranes and Membrane Transport

Overview

An essential step in the evolution of life was the compartmentalization and confinement of biochemical reactants so that metabolic reaction sequences could occur efficiently. Membranes provide the solution to the problem. Very simple in structure, membranes are made of soap. Therefore, they are actual soap bubbles. But don’t get the idea that this makes them fragile. They are extremely stable in water, and will not allow water or water-soluble materials to pass through them. However, cells need water-soluble materials; therefore, living membranes contain a variety of embedded proteins–integral membrane proteins–that control what goes into and out of the cell.

Activities

  1. Review Sections 6.1 of the textbook.
  2. Read Sections 6.2 through 6.4 of the textbook.
  3. Download Lecture 4.1 slides.
  4. Watch video 4.1.1, Membrane Structure.
  5. Watch video 4.1.2, Membrane Transport.
  6. Complete the questions on Study Guide 4.1. (Not to be handed in.)

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lec 4.1 Quiz.

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BIO 181 Lecture 2.8

Lecture 2.8: Hardy-Weinberg

Overview

Can we predict evolution? The answer is, maybe surprisingly, yes. Increasing numbers of researchers–including me–are working to predict the course of evolution in tumors under treatment. But can you tell if something is evolving? The answer also is yes, and the same reasoning can be used both to predict evolution and detect it. This lecture introduces that thought process.

Activities

  1. Read Sections 23.1, and 23.4 of the textbook.
  2. Download Lecture 2.8 Slides.
  3. Do one of the following:
    1. In-person section: Attend Lecture 2.8.
    2. Online section: Watch the following videos:
      1. Video 2.8.1, Alu Insertion.
      2. Video 2.8.2, Hardy-Weinberg Motivation.
      3. Video 2.8.3, Application of Hardy-Weinberg.
  4. Complete the questions on Study Guide 2.8.

Assessment

After completing the activities, log into Canvas, launch BIO 181 and complete Lecture 2.8 Quiz.

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