Out of the Rainforest - Biology 1114

For a printable copy of this page click here.

Out of the Rain Forest

Scenario: Accompany an aboriginal fishing expedition in the Amazon rainforest, in which the native people use a toxic substance from woody vines to capture fish. We will explore the action of this plant toxin, rotenone, in the context of pesticide development, coevolution, cell membrane function, and cell respiration.

Concepts Taught:

Icon Key:

activity

animation

diagram

quiz

text explanation

Cellular compartmentalization (i.e. organelles)
Cellular respiration and ATP synthesis
Coevolution (plants/herbivores)
Enzyme structure, function, regulation and inhibition
Community/ecosystem ecology (limited: trophic levels, competition, coevolution)
Mitochondrial Structure
Membrane structure and function
Natural selection

Concept Maps:

1. entire scenario
2. how parts of Cellular Respiration fit together
3. with more detail about Cellular Respiration
4. Cellular Respiration Summary
5. Cellular Respiration Diagram

Concepts Reviewed:

Metabolism
Energy
Gradient
Diffusion
Hypothesis/Prediction
Experimentation

Examples of In-Class Discussion and Thought Questions:

What is happening to the fish that are being hunted in the river?
Why do plants make toxic chemicals? Do all plants do this? Do they all make the same chemicals?
Do toxic plants win and grazers lose all the time?
Why do most living things need oxygen?
What are two ways that we could measure respiration?
What is the significance of moving hydrogen ions (H+) across the mitochondrial membrane?
How does rotenone work?
If the poisoned fish can't use the oxygen anyway, why do they gasp at the surface?

Questions:

What are some potential issues associated with pesticide use?
Can you think of coevolutionary examples of secondary metabolites relevant to humans?

Hypothesize a purpose of the cristae, infoldings of the inner mitochondrial membrane. What about bacteria that lack organelles? Where else in biology do we see this principle in action?

Major Terms Introduced:

Active Site Aerobic (cellular) respiration ATP Community (Biotic) Cell Cell membrane Chemiosmosis Coevolution Concentration gradient Ecosystem Electron transport	Enzymes (proteins) Enzyme inhibitor Eukaryote Evolution Fermentation Fluid-mosaic model Glycolysis Krebs cycle (TCA cycle or Citric acid cycle) Mitochondria Natural Selection Organelle Oxidative phosphorylation	Photosynthesis Primary consumers (herbivores) Primary producers (photoautotrophs) Prokaryote Secondary metabolites Selective Permeability Species diversity Substrate Substrate-level phosphorylation Vacuole

Related Laboratory Experiments and Tutorials:

Lab 3: How is metabolic rate influenced by ambient temperature?

Text and Recommended Readings:

Click here for Texbook Readings!

Corresponding Essential Study Partner Segments:

The Essential Study Partner is part of the McGraw-Hill Web Site.
To access it go here. Then follow these relevant paths below:

Cells > Chemistry > Proteins

Cells > Cell Structures > Prokaryotes

Cells > Cell Structure > Eukaryotes

Cells > Cell Structure > Energy Organelles

Cells > Cell Membrane > Membrane Structure

Cells > Cell Membrane > Diffusion

Cells > Cell Membrane > Osmosis

Cells > Metabolism > Thermodynamics

Cells > Metabolism > Enzymes

Cells > Metabolism > Pathways

Cells > Respiration > Glycolysis

Cells > Respiration > Krebs Cycle

Cells > Respiration > Electron Transport System

Ecology > Ecosystems > Trophic Levels

Ecology > Ecosystems > Energy Flow

Ecology > Ecosystems > Nutrient Cycles

Many of these are figures and accompanying text, but some are video clips that should help you see the process in action.

Tutorials:

Useful sites:

The site for your textbook Life by Ricki Lewis

source McGraw-Hill ATP diagram- Charts the formation of ATP from ADP (at the bottom of the page click on the square with the grey arrow; requires shockwave)

source
McGraw-Hill Electron Transport Chain Tutorial- Very informative tutorial traces the path of electrons through the electron transport chain and discusses how the electron transport chain produces ATP (takes a couple of minutes to download and requires real player)

source NPR - All Things Considered - Lake Davis
(You'll need the "RealAudio Player" plug-in or equivalent for your Web browser, probably already present on most newer computers).

source
Will rotenone save us from the Frankenfish? (NPR - Weekend Edition)
(You'll need the "RealAudio Player" plug-in or equivalent for your Web browser, probably already present on most newer computers).

source Long term effect of Rotenone Treatment on Fish in California
(Results of a study of long-term impacts of rotenone)

source Dragonfly Web Pages maintained by Miami University and NSTA
(How and why plants guard their "personal space")

source
International Center for Aquaculture and Aquatic Environments, Auburn University, Alabama
(How to eliminate unwanted fish and harmful insects from fish ponds using Rotenone and various other poisons)

source
Coevolution
(This site presents a detailed explanation with many of the examples we will use in class - and more! It presents a very "strict" definition of co-evolution, and makes the point that phylogenetic analyses of the species should be made to test hypothesese about coevolutionary relationships of any two species. In our discussions and test questions, we will assume that such analyses would uphold the relationships described. If you are having trouble with this concept, this may help - along with a discssion with your instructor and group. This web page is from the Evolutionary Biology Course that is part of the Biomedical Program at Brown University)

source
Mitochondria image from University of Pretoria
(Scanning electron Micrograph shows outside and inner folds)

source Oxidative Phorylation Home Page
(A more detailed explanation (a lot of text and additional terms) of the process of cellular respiration from the the medical curriculum and for honours degree courses in Biochemistry & Molecular Biology at the University of Leeds, UK. Nice illlustrations and animations, a history of discoveries, and additional detail that might give you a better picture of how cellular respiration works. )

source Introduction to Glycolysis
(also from the University of Leeds, this is a detailed look at glycolysis by Jon Maber, as part of an on-line learning project, BioNet. Again, more detail than you need but nicely done)

source
Cellular Metabalism and Fermentation
(A textbook quality explanation of the these processes from Michael J. Farabee's courses at Estrella Community College. Excellent illustrations and appropriate level text.)

source
This is a very useful site outlining the details of metabolism in an interactive diagram that can illustrate the fate of almost any physiologically relevant class of substance.

source
Cellular Respiration and Fermentation
(Another textbook quality explanation of the these processes by J. Stein Carter from her Biology 104 course at Clermont College, University of Cincinnati. Artistic illustrations, but some more detail than necessary. It presents some very nice connections with other processes and systems such as whole organisms respiration, genetics, and oxygen transfer )

source

Animation of Electron Transport in Mitochondria
(Straightforward illustration of ETC (respiratory Chain) with some brief textual explanation. Don't get confused by the OH- molecules, they are what is left over when some of the H+ are pumped across the inner membrane. Produced by Thomas M. Terry, The University of Connecticut. )

source Animation of ATP synthesis in Mitochondria
(The follow-up page to the one above.

3-D Animation of ATP synthase at work
This animation from the lab of Dr. Mark Girvin from the Department of Biochemsitry at the Albert Einstein School of Medicine provides an outstanding visualization of current theory on how ATPsynthase looks and works. This is well worth the long download and duration of the movie.

or here is one from our own Dr. David Demezas

Animated explanation of ETC and Chemisomosis from Thomas/Brooks Cole publshing. This explanation will whelp those who need more details. Not as much detail as the explanations below.

Animated explanation of ETC and Chemisomosis from an article in Nature Reviews Genetics 2: 342-352 (2001) THE GENETICS AND PATHOLOGY OF OXIDATIVE PHOSPHORYLATION by Jan Smeitink, Lambert van den Heuvel& Salvatore DiMauro. The animation is still schematic but describes the different protein complexes (electron carriers) in more detail. The article discusses the metabolic diseases that are are result of changes in mitochondrial DNA.

Details of Electron & Hydrogen Ion movement While it doesn't show the exact protein structures, this animation provides the details for an upper-division biochemsitry course. If you want a better idea of what molecules are moving electrons and protons and the number of steps - this is it. Reading the information on the accompanying web page from The Molecular Biochem I course at RPI will help expalin the animation. If you do what details about protein structure and biochemical reactions this is it.

source Glycolysis and more
(For the more biochemically inclined, this site presents the process along with the chemical structures and the detailed explanations of the enzymatic reactions. This is NOT something that we expect you to know, but some students like to see the chemical formulas. also available is a description of the Mitochondrion, a description of the Krebs Cycle, a description of Electron Transport and Chemiosmosis, and a description of the Formation of Acetyl-CoA. These are not quite as biochemically intense, but have considerable detail and text that goes beyond our expectations. Still, this can give you another perspective on these processes that can help. Produced by Natural Toxins Research Center at Texas A&M University - Kingsville

Textbook Flashcards:

The website for your textbook has flashcards organised by chapters. You are only responsible for topics discussed in class. For this scenario, flashcards with the Major Terms Introduced can be found in:

Chapter 3: Cells
Chapter 4: The Cell Membrane, Cytoskeleton, and Cell-Cell Interactions
Chapter 5: The Energy of Life
Chapter 7: How Cells Release Energy
Chapter 14: The Evolution of Evolutionary Thought
Chapter 43: Communities and Ecosystems

Bibliography:

French, D. 2000. Investigating Biology; A Laboratory Resource Manual. Harcourt Brace: NY.
Joyce, C. 199. Western medicine men return to the field. Bioscience 42: 399-403.
Lawson, A. 1995. Studying for Biology. Benjamin Cummings: NY.
Strauss, E. 1998. Possible new weapon for insect control. Science 280: 1543.
Lewis, R. 1998. Life. 3^rd edition. WCB/McGraw-Hill:NY.
Herbert, R.B. 1989. The Biosynthesis of Secondary Metabolites. 2^nd edition.
Chapman & Hall, pp. 1, 96-97, and 111-114.
Plotkin, M.J. 1993. Tales of a Shaman's Apprentice. Viking: NY.

source	McGraw-Hill ATP diagram- Charts the formation of ATP from ADP (at the bottom of the page click on the square with the grey arrow; requires shockwave)
source	McGraw-Hill Electron Transport Chain Tutorial- Very informative tutorial traces the path of electrons through the electron transport chain and discusses how the electron transport chain produces ATP (takes a couple of minutes to download and requires real player)
source	NPR - All Things Considered - Lake Davis (You'll need the "RealAudio Player" plug-in or equivalent for your Web browser, probably already present on most newer computers).
source	Will rotenone save us from the Frankenfish? (NPR - Weekend Edition) (You'll need the "RealAudio Player" plug-in or equivalent for your Web browser, probably already present on most newer computers).
source	Long term effect of Rotenone Treatment on Fish in California (Results of a study of long-term impacts of rotenone)
source	Dragonfly Web Pages maintained by Miami University and NSTA (How and why plants guard their "personal space")
source	International Center for Aquaculture and Aquatic Environments, Auburn University, Alabama (How to eliminate unwanted fish and harmful insects from fish ponds using Rotenone and various other poisons)
source	Coevolution (This site presents a detailed explanation with many of the examples we will use in class - and more! It presents a very "strict" definition of co-evolution, and makes the point that phylogenetic analyses of the species should be made to test hypothesese about coevolutionary relationships of any two species. In our discussions and test questions, we will assume that such analyses would uphold the relationships described. If you are having trouble with this concept, this may help - along with a discssion with your instructor and group. This web page is from the Evolutionary Biology Course that is part of the Biomedical Program at Brown University)
source	Mitochondria image from University of Pretoria (Scanning electron Micrograph shows outside and inner folds)
source	Oxidative Phorylation Home Page (A more detailed explanation (a lot of text and additional terms) of the process of cellular respiration from the the medical curriculum and for honours degree courses in Biochemistry & Molecular Biology at the University of Leeds, UK. Nice illlustrations and animations, a history of discoveries, and additional detail that might give you a better picture of how cellular respiration works. )
source	Introduction to Glycolysis (also from the University of Leeds, this is a detailed look at glycolysis by Jon Maber, as part of an on-line learning project, BioNet. Again, more detail than you need but nicely done)
source	Cellular Metabalism and Fermentation (A textbook quality explanation of the these processes from Michael J. Farabee's courses at Estrella Community College. Excellent illustrations and appropriate level text.)
source	This is a very useful site outlining the details of metabolism in an interactive diagram that can illustrate the fate of almost any physiologically relevant class of substance.
source	Cellular Respiration and Fermentation (Another textbook quality explanation of the these processes by J. Stein Carter from her Biology 104 course at Clermont College, University of Cincinnati. Artistic illustrations, but some more detail than necessary. It presents some very nice connections with other processes and systems such as whole organisms respiration, genetics, and oxygen transfer )
source	Animation of Electron Transport in Mitochondria (Straightforward illustration of ETC (respiratory Chain) with some brief textual explanation. Don't get confused by the OH- molecules, they are what is left over when some of the H+ are pumped across the inner membrane. Produced by Thomas M. Terry, The University of Connecticut. )
source	Animation of ATP synthesis in Mitochondria (The follow-up page to the one above.
	3-D Animation of ATP synthase at work This animation from the lab of Dr. Mark Girvin from the Department of Biochemsitry at the Albert Einstein School of Medicine provides an outstanding visualization of current theory on how ATPsynthase looks and works. This is well worth the long download and duration of the movie. or here is one from our own Dr. David Demezas
	Animated explanation of ETC and Chemisomosis from Thomas/Brooks Cole publshing. This explanation will whelp those who need more details. Not as much detail as the explanations below.
	Animated explanation of ETC and Chemisomosis from an article in Nature Reviews Genetics 2: 342-352 (2001) THE GENETICS AND PATHOLOGY OF OXIDATIVE PHOSPHORYLATION by Jan Smeitink, Lambert van den Heuvel& Salvatore DiMauro. The animation is still schematic but describes the different protein complexes (electron carriers) in more detail. The article discusses the metabolic diseases that are are result of changes in mitochondrial DNA.
	Details of Electron & Hydrogen Ion movement While it doesn't show the exact protein structures, this animation provides the details for an upper-division biochemsitry course. If you want a better idea of what molecules are moving electrons and protons and the number of steps - this is it. Reading the information on the accompanying web page from The Molecular Biochem I course at RPI will help expalin the animation. If you do what details about protein structure and biochemical reactions this is it.
source	Glycolysis and more (For the more biochemically inclined, this site presents the process along with the chemical structures and the detailed explanations of the enzymatic reactions. This is NOT something that we expect you to know, but some students like to see the chemical formulas. also available is a description of the Mitochondrion, a description of the Krebs Cycle, a description of Electron Transport and Chemiosmosis, and a description of the Formation of Acetyl-CoA. These are not quite as biochemically intense, but have considerable detail and text that goes beyond our expectations. Still, this can give you another perspective on these processes that can help. Produced by Natural Toxins Research Center at Texas A&M University - Kingsville