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AMINO ACID FREQUENCY
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Introduction: Genetic information contained in mRNA is in the form of codons, sequences of three nucleotides, which are translated into amino acids which then combine to form proteins. At certain sites in a protein's structure, amino acid composition is not critical. Yet certain amino acids occur at such sites up to six times more often than other amino acids. In the 1960's, molecular biologists sought to determine if amino acid composition was a reflection of the genetic code or if certain amino acids were naturally selected as optimal.

Question: Are frequencies of particular amino acids simply a consequence of random permutations of the genetic code or instead a product of natural selection?

Supplement to 'The Genetic Code': https://cnx.org/contents/jVCgr5SL@15.43:aXYynRWE@10/15-1-The-Genetic-Code

Subject:
Biology
Genetics
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
ANTIBODY BINDING
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Introduction: Antibodies are proteins that react with foreign invaders during a humoral immune response. Antigens, small substituents of foreign invaders, elicit an immune response when they bind to the antibody. Variable regions of amino acid chains comprising the antibody create binding sites. A particular antibody has specificity to bind to one or more particular antigens.

Questions: How is antigen binding to an antibody related to antigen concentration? How can we determine binding properties of antibodies?

Supplement to 'Anitbodies': https://cnx.org/contents/jVCgr5SL@15.43:jN1G3E9L@10/42-3-Antibodies

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
CARDIAC OUTPUT
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Introduction: Vertebrate circulatory systems consist of blood, which transports materials to and from cells via blood vessels, and a heart to pump the blood. One important role of the circulatory system is to provide oxygen to cells. As a general rule, small animals have a higher rate of oxygen consumption per unit body mass than large animals. Therefore, the heart of a small animal must supply oxygen at a higher rate than the heart of a large animal. Since the oxygen capacity of blood is similar between small and large animals, small animals must have hearts that pump blood at a higher rate, or in other words, have a higher cardiac output.

Question: How do changes in stroke volume and heartbeat frequency affect cardiac output?

Supplement to 'Mammalian Heart and Blood Vessels': https://cnx.org/contents/jVCgr5SL@15.43:sMC0JIxR@9/40-3-Mammalian-Heart-and-Blood-Vessels

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
CELL AGGREGATION AND SPHERE PACKING
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Introduction: Many biological processes involve the aggregation of cells into a cluster. For example, in animals, small cells called platelets cluster at the site of an injury to the skin or blood vessels. Also, during the development of an embryo, space between aggregated cells decreases and cell-to-cell contact increases. The amount of space between aggregated cells can affect the permeability of solutes into the cells from the surrounding solution. The number of cell-to-cell contacts, places where the cell membranes of different cells touch, can affect flow of solutes and communication between cells.

Questions: How does the arrangement of cells within a cluster affect the space between cells and the number of cell-to-cell contacts? How do biological examples of sphere packing compare to mathematical theory?

Supplement to 'Adaptive Immune Response': https://cnx.org/contents/jVCgr5SL@15.43:3bu0TQN9@10/42-2-Adaptive-Immune-Response

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
CELL DIVISION IN THE PRESENCE OF A GROWTH FACTOR
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Introduction: Under optimal conditions, growth of cells occurs as each cell completes the cell cycle and doubles producing two daughter cells which later themselves divide. Growth factors can provoke the growth of cells. For example, interleukins are made by white blood cells to stimulate the growth of other immune system cells. Erythropoietin is made by the kidney to promote growth of red blood cells.

Question: How do growth factors affect the rate at which cell populations grow?

Supplement to 'Control of the Cell Cycle': https://cnx.org/contents/jVCgr5SL@15.43:UxhDw2_6@10/10-3-Control-of-the-Cell-Cycle

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
CELL EXPANSION
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Introduction: Plants are capable of rapidly adapting to changes in their environment. Plants can grow to replace damaged parts, bend in the direction of light cues, or elongate rapidly under good conditions. Plant hormones often play a role in plant development by affecting patterns of growth. Gibberellins, in particular, can elicit changes in growth, elongation, and flowering.
The growth of a plant cell is primarily driven by the uptake of water into the cytoplasm and vacuole of the plant cell. The vacuole expands rapidly, pressing against the cell wall. In order for the cell to enlarge, the cell wall must yield to the stress produced by cell turgor. Therefore, we would suspect that plant hormones might affect properties of the cell in order to affect plant growth.

Question: How do osmotic potential and properties of the cell wall contribute to cell enlargement? How do plant hormones affect rates of cell enlargement?

Supplement to 'Plant Sensory Systems and Responses': https://cnx.org/contents/jVCgr5SL@15.43:eic7s50p@11/30-6-Plant-Sensory-Systems-and-Responses

Subject:
Biology
Botany
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
CHEMORECEPTION
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Introduction: Chemoreception occurs when specific receptors in the cell membrane bind with diffusing chemicals in the surrounding medium. For example, bacteria such as E. coli and Salmonella often navigate in response to chemical attractants or repellents.

Question: Should a cell invest a large amount of resources and surface area in building chemoreceptors in its cell membrane in order to detect chemicals?

Supplement to 'Signaling Molecules and Cellular Receptors': https://cnx.org/contents/jVCgr5SL@15.43:rns8-Bnk@14/9-1-Signaling-Molecules-and-Cellular-Receptors

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
CHI-SQUARE TEST
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Introduction: The chi-square test is a statistical test that can be used to determine whether observed frequencies are significantly different from expected frequencies. For example, after we calculated expected frequencies for different allozymes in the HARDY-WEINBERG module we would use a chi-square test to compare the observed and expected frequencies and determine whether there is a statistically significant difference between the two. As in other statistical tests, we begin by stating a null hypothesis (H0: there is no significant difference between observed and expected frequencies) and an alternative hypothesis (H1: there is a significant difference). Based on the outcome of the chi-square test we will either reject or fail to reject the null hypothesis.

Question: How is the chi-square test used to compare samples or populations? What does a comparison of observed and expected frequencies tell us about these samples?

Supplement to 'Laws of Inheritance': https://cnx.org/contents/jVCgr5SL@15.43:8Zft46As@11/12-3-Laws-of-Inheritance

Subject:
Biology
Ecology
Genetics
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
COHORT LIFE TABLES
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Introduction: Demographic processes such as births, deaths, immigration, and emigration, are those that affect the size and composition of a population. The timing of these processes also plays a critical role; a population with high juvenile mortality will have a very different structure from a population with high mortality in the post-reproductive years. Life tables are tables of data on survivorship and fecundity of individuals within a population. A standard method is to collect data on a cohort, or group of individuals all born in the same time period. Life tables constructed this way are called cohort life tables. They can then be used to determine age- or stage-specific fecundity and mortality rates, survivorship, and basic reproductive rates, which in turn can be compared from cohort to cohort enabling an analysis of their annual variation.

Question: How do life tables help us to understand the demography of a population?

Supplement to 'Population Demography': https://cnx.org/contents/jVCgr5SL@15.43:UNW2YGZ9@10/45-1-Population-Demography

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
DIVERSITY INDICES: SHANNON'S H AND E
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Introduction: A diversity index is a mathematical measure of species diversity in a community. Diversity indices provide more information about community composition than simply species richness (i.e., the number of species present); they also take the relative abundances of different species into account (for an illustration of this point, see below, or introduction to SIMPSON'S D AND E).

Question: How do we measure diversity?

Supplement to 'Community Ecology': https://cnx.org/contents/jVCgr5SL@15.43:2FbYMdcI@11/45-6-Community-Ecology

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
DIVERSITY INDICES: SIMPSON'S D AND E
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Introduction: A diversity index is a mathematical measure of species diversity in a community. Diversity indices provide more information about community composition than simply species richness (i.e., the number of species present); they also take the relative abundances of different species into account. Consider two communities of 100 individuals each and composed of 10 different species. One community has 10 individuals of each species; the other has one individual of each of nine species, and 91 individuals of the tenth species. Which community is more diverse? Clearly the first one is, but both communities have the same species richness. By taking relative abundances into account, a diversity index depends not only on species richness but also on the evenness, or equitability, with which individuals are distributed among the different species.

Question: How do we measure diversity?

Supplement to 'Community Ecology': https://cnx.org/contents/jVCgr5SL@15.43:2FbYMdcI@11/45-6-Community-Ecology

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
DNA AND KNOT THEORY
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Introduction: DNA is the genetic material of all cells, containing coded information about cellular molecules and processes. DNA consists of two polynucleotide strands twisted around each other in a double helix. The first step in cellular division is to replicate DNA so that copies can be distributed to daughter cells. Additionally, DNA is involved in transcribing proteins that direct cell growth and activities. However, DNA is tightly packed into genes and chromosomes. In order for replication or transcription to take place, DNA must first unpack itself so that it can interact with enzymes.
DNA packing can be visualized as two very long strands that have been intertwined millions of times, tied into knots, and subjected to successive coiling. However, replication and transcription are much easier to accomplish if the DNA is neatly arranged rather than tangled up in knots. Enzymes are essential to unpacking DNA. Enzymes act to slice through individual knots and reconnect strands in a more orderly way.

Question: How can knot theory help us understand DNA packing? How can we estimate the rates at which enzymes unknot DNA?

Supplement to 'DNA Structure and Sequencing': https://cnx.org/contents/jVCgr5SL@15.43:_N9qqIL9@10/14-2-DNA-Structure-and-Sequencing

Subject:
Biology
Genetics
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
DOUBLING TIME OF TUMORS
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Introduction: The cell cycle is divided into four stages: Gap 1, DNA synthesis or S-phase, Gap 2, and mitosis. When modelling the growth of a population of cells, it is commonly useful to assume that every individual cell doubles with every cell cycle, i.e. the daughter cells themselves divide upon completion of the next cell cycle. This is typically expressed as an exponentially growing population (see Cell Division in the Presence of a Growth Factor and Cell Division). However, in many circumstances, not all the daughter cells divide, and the rate of population growth can be affected. For example, tumor growth rate is less than that of normal cells due to the considerable loss of cells and the fact that only a fraction of the cancerous cells are dividing.

Question: Can quantitative techniques be used to more conveniently predict the doubling time of tumors?

Supplement to 'Cancer and the Cell Cycle': https://cnx.org/contents/jVCgr5SL@15.43:1dg9UsAS@11/10-4-Cancer-and-the-Cell-Cycle

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
EFFICIENCY OF ATP PRODUCTION
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Introduction: Endergonic reactions require energy input in order to proceed (see GIBB'S FREE ENERGY). Almost every time a cell performs an endergonic reaction, such as linking amino acids, synthesizing small molecules, or cellular movement, it derives the needed energy from the splitting of ATP. Aerobic organisms produce most of their ATP through respiration, a complex set of reactions that transfer electrons from glucose to oxygen. Glycolysis is the first step in glucose metabolism. The success of glycolysis lies in its ability to couple energy releasing reactions to the endergonic synethesis of ATP.

Question: How can we determine the efficiency of ATP production?

Supplement to 'Glycolysis': https://cnx.org/contents/jVCgr5SL@15.43:Hcj9xYN4@10/7-2-Glycolysis

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
ENERGY ABSORBED FROM LIGHT
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Introduction: Photosynthesis is the process by which light energy is converted to chemical energy. In plants, light is absorbed by pigments such as chlorophyll. Light hits these molecules and raises them to a higher energy. Light, however, occurs in a spectrum of wavelengths ranging from ultraviolet to visible light to infrared. The energy accompanying the absorption of light is dependent on the wavelength of the light.

Question: How is the amount of energy in a photon related to the wavelength of light?

Supplement to 'The Light-Dependent Reactions of Photosynthesis': https://cnx.org/contents/jVCgr5SL@15.43:wbPCG_pm@10/8-2-The-Light-Dependent-Reactions-of-Photosynthesis

Subject:
Biology
Botany
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
ESTIMATING TREE HEIGHTS
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Introduction: Scientists studying a forest ecosystem over a long period of time may record measurements of trees for a number of variables, including each tree's diameter at breast height, height of the lowest living branch, canopy cover, etc. One aspect of a tree's growth that can be hard to measure is tree height. Forest researchers sometimes use a piece of equipment consisting of telescoping components, which are extended until the tip reaches the same height as the tree top (this requires a second researcher standing at a distance from the tree to determine when the tip is at the correct height). This method can be cumbersome, as the equipment is bulky and the measurements require two people.

Question: Is there an efficient way to measure tree height, without heavy equipment and multiple people?

Supplement to 'The Plant Body': https://cnx.org/contents/jVCgr5SL@15.43:wNvXDeaX@10/30-1-The-Plant-Body

Subject:
Biology
Botany
Forestry and Agriculture
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
GIBB'S FREE ENERGY AND THE NATURE OF CHEMICAL REACTIONS
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Introduction: In a chemical reaction, some bonds are broken in the reactants in order to form bonds in the products. Some product molecules will participate in the reverse reaction in order to reform reactants. The initial rate of product formation depends on the initial concentrations of reactants and products. As product concentration increases, the rate of the reverse reaction increases. Eventually, the rate of forward and reverse reactions become equal. Under these circumstances, the concentrations of reactants and products are constant, and the mixture is said to be in chemical equilibrium. Since breaking bonds requires energy and forming bonds releases energy, the net energy of a chemical reaction will depend on the sum of energy absorbed and generated. Eventually, the difference in energy between the reactants and products decreases as equilibrium is achieved.

Questions: How can we measure the energy of a chemical reaction? How can we predict the direction of a chemical reaction? How do properties of the reactants and products affect the net result of a chemical reaction?

Supplement to 'Potential, Kinetic, Free, and Activation Energy': https://cnx.org/contents/jVCgr5SL@15.43:fCe9XnrW@10/6-2-Potential-Kinetic-Free-and-Activation-Energy

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
HARDY-WEINBERG EQUILIBRIUM
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Introduction: The Hardy-Weinberg model, named after the two scientists that derived it in the early part of this century, describes and predicts genotype and allele frequencies in a non-evolving population. The model has five basic assumptions: 1) the population is large (i.e., there is no genetic drift); 2) there is no gene flow between populations, from migration or transfer of gametes; 3) mutations are negligible; 4) individuals are mating randomly; and 5) natural selection is not operating on the population. Given these assumptions, a population's genotype and allele frequencies will remain unchanged over successive generations, and the population is said to be in Hardy-Weinberg equilibrium. The Hardy-Weinberg model can also be applied to the genotype frequency of a single gene.

Question: How do we use the Hardy-Weinberg model to predict genotype and allele frequencies? What does the model tell us about the genetic structure of a population?

Supplement to 'Population Evolution': https://cnx.org/contents/jVCgr5SL@15.43:OL4rARcv@10/19-1-Population-Evolution

Subject:
Biology
Ecology
Genetics
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
HEMOGLOBIN EVOLUTION
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Introduction: Different species of animals can carry different types of hemoglobins in their blood. Animals such as oligachaetes have large molecular weight hemoglobins that are carried in the plasma. In contrast, other species, such as birds and mammals, have small molecular weight hemoglobins that are packaged in red blood cells.

Questions: Do large numbers of small molecular weight hemoglobins dramatically increase the viscosity of the blood? Do smaller hemoglobins increase the supply of oxygen?

Supplement to 'Components of the Blood': https://cnx.org/contents/jVCgr5SL@15.43:toYaz2Tp@10/40-2-Components-of-the-Blood

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
INTERSPECIFIC COMPETITION
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Introduction: Interspecific competition refers to the competition between two or more species for some limiting resource. This limiting resource can be food or nutrients, space, mates, nesting sites-- anything for which demand is greater than supply. When one species is a better competitor, interspecific competition negatively influences the other species by reducing population sizes and/or growth rates, which in turn affects the population dynamics of the competitor. The Lotka-Volterra model of interspecific competition is a simple mathematical model that can be used to understand how different factors affect the outcomes of competitive interactions.

Question: Under what circumstances can two species coexist? Under what circumstances does one species outcompete another?

Supplement to 'Environmental Limits to Population Growth': https://www.oercommons.org/courses/interspecific-competition/edit

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
METABOLISM FOR ENERGY AND THE RESPIRATORY QUOTIENT
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Introduction: Animal cells obtain energy in the form of ATP by oxidizing food molecules through the process of respiration. The hydrolysis of ATP supplies energy needed for cellular processes, such as the transport of molecules or cellular movement. Carbohydrates and fatty acids are the most important fuels for generating ATP in animal cells. Respiration in animal cells depends on oxygen. Electrons from the chemical bonds of the fuel source combine with oxygen and hydrogen ions to form water and carbon dioxide. Cells couple this reaction to the production of ATP.

Question: How can we quantify metabolism? How does the energy source affect the volume of O2 consumed and volume of CO2 produced? How do they differ among animals and how are they affected by environmental conditions?

Supplement to 'Energy in Living Systems': https://cnx.org/contents/jVCgr5SL@15.43:6gZWnxxX@10/7-1-Energy-in-Living-Systems

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
MITOTIC INDEX AND CELL DIVISION
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Introduction: Cell population growth occurs as cells pass through interphase and mitosis to complete the cell cycle. Many cells lose the capacity to divide as they mature or divide only rarely. Other cells are capable of rapid cell division. For example, as plant roots grow, cells near the tip of the root, in the apical meristem, divide rapidly to push the root through the soil. The root cap detects the pull of gravity and directs the rapid growth of cells near the tip.

Question: How do dynamics of cell division change among neighboring cells in a plant root? How does gravity affect cell division in plant roots?

Supplement to 'Cell Division': https://cnx.org/contents/jVCgr5SL@15.43:DbIdpy2Y@10/10-1-Cell-Division

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
MUSCLE CONTRACTION
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Introduction: Muscle fibers are composed of bundles of contractile muscle called myofibrils. Each myofibril is made up of smaller repeating units called sarcomeres. Thin filaments of actin and thick filaments of myosin form the muscle fibers. Myosin and actin filaments, as well as regions where the two overlap, form repeating light and dark bands in each sarcomere. These thick and thin filaments are linked at regular intervals by cross-bridges made from extensions of the myosin molecules.
Researchers from 1930 to 1960 sought to understand the mechanism of muscle contraction. The "contracting filament hypothesis" proposed that the filaments themselves contract. Electron microscope observations, however, did not support this hypothesis. Neither the thick nor thin bands changed in length when the muscle contracted. Only the degree of overlap between thick and thin filaments changed. Huxley alternatively propoded the Sliding Filament Model, suggesting muscle contraction results as the crossbridges linking the actin and myosin molecules pull the filaments over one another.

Question: Does evidence support the Sliding Filament Model? In other words, does the force generated by a muscle depend on the degree of overlap between thick and thin filaments?

Supplement to 'Muscle Contraction and Locomotion': https://cnx.org/contents/jVCgr5SL@15.43:9kpMgMgT@10/38-4-Muscle-Contraction-and-Locomotion

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
NASTIC MOVEMENTS
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Introduction: Plants are capable of rapidly adapting to changes in their environment. This can be in the form of irreversible changes in growth (See Cell Enlargement) or reversible movements in response to a stimulus. Nastic movements in plants are reversible and repeatable movements in response to a stimulus whose direction is determined by the anatomy of the plant. Examples include the diurnal movement of leaves and the response of insectivorous plants, such as the Venus fly trap, to prey. Nastic movement is generally caused by elastic changes in the size of special motor cells within the plant tissue. These changes are generally produced by changes in osmotic pressure due to an influx or efflux of ions that cause water to move in or out of the cells. In many plants, shrinkage of the motor cells causes the overall movement of the plant.

Question: How are nastic movements in plants affected by changes in osmotic pressure? Are rapid nastic movements consistent with an osmotic driven model?

Supplement to 'Leaves': https://cnx.org/contents/jVCgr5SL@15.43:N1f0e7hP@9/30-4-Leaves

Subject:
Biology
Botany
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
NUCLEOPLASMIC INDEX
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Introduction: As cells pass through the cell cycle, their nuclear volume doubles in preparation for division into two daughter cells. When cells are in resting condition, however, the ratio of nuclear volume to cytoplasmic volume remains stable. This ratio is known as the nucleoplasmic index.

Questions: How does the nucleoplasmic index change with the cell cycle? What can the nucleoplasmic index tell us about changes spinal nerves experience when lizard tails are regenerating?

Supplement to 'The Cell Cycle': https://cnx.org/contents/jVCgr5SL@15.43:SeU_rWbd@14/10-2-The-Cell-Cycle

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
OPTIMAL FORAGING
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Introduction: The absolute limits of the range of food types eaten by a consumer in a given habitat are defined by morphological constraints, but very few animals actually eat all of the different food types they are capable of consuming. Optimal foraging theory helps biologists understand the factors determining a consumer's operational range of food types, or diet width. At the one extreme, animals employing a generalist strategy tend to have broad diets; they chase and eat many of the prey/food items with which they come into contact. At the other extreme, those with a specialist strategy have narrow diets and ignore many of the prey items they come across, searching preferentially for a few specific types of food. In general, animals exhibit strategies ranging across a continuum between these two extremes.

Question: Given that a predator's diet comprises some number profitable prey items, some of which are more profitable than others, when does it make sense for that predator to broaden its diet and add the next most-profitable item?

Supplement to 'Behavioral Biology: Proximate and Ultimate Causes of Behavior': https://cnx.org/contents/jVCgr5SL@15.43:OFcY1MSo@13/45-7-Behavioral-Biology-Proximate-and-Ultimate-Causes-of-Behavior

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
OXYGEN DIFFUSION IN SIMPLE ORGANISMS
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Introduction: Many simple organisms do not have specialized respiratory structures and instead obtain oxygen by diffusion through their body surfaces.

Question: How is the oxygen need of an organism related to its metabolism and size?

Supplement to 'Prokaryotic Metabolism': https://cnx.org/contents/jVCgr5SL@15.43:ec3RcKrO@10/22-3-Prokaryotic-Metabolism

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
PERMEABILITY OF MOLECULES
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Introduction: In the late 1800's, E. Overton discovered that substances that dissolve in lipids pass more easily into the cell than those that dissolve in water. This was some of the first evidence that cells were surrounded by a lipid membrane. The phospholipid membrane of cells can greatly modify the permeation of molecules into a cell. The membrane acts as a barrier to passive diffusion of water-soluble molecules. Howeve r, substances that dissolve in lipids pass more easily into the cell. The correlation between permeability and solubility in lipidly is appropriately named Overton's Rule.

Question: How is the permeability of a molecule across the lipoprotein membrane related to the molecule's solubility in lipids and size?

Supplement to 'Passive Transport': https://cnx.org/contents/jVCgr5SL@15.43:xy5C3n_j@10/5-2-Passive-Transport

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
POPULATION BOTTLENECKS
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Introduction: Temporary but significant reductions in population size are referred to as population bottlenecks. The effects can vary depending on both the size to which the population is reduced and the duration of the bottleneck (i.e., the number of generations). Limited population size can lead to a loss of genetic variation and subsequent loss of evolutionary potential.

Question: How do we measure loss of genetic variation? Do the different measures yield similar estimates of the amount of variation lost?

Supplement to 'Population Genetics': https://cnx.org/contents/jVCgr5SL@15.43:Jf10pn9N@9/19-2-Population-Genetics

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
POPULATION GENETICS: LIMITS TO ADAPTATION
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Introduction: Organisms are generally assumed to exhibit traits that are adaptive to the specifics of the environment in which they are found, as a result of natural selection. Some studies have indicated, however, that certain traits appear to be maladaptive, yet they are maintained within a population. This maladaptation may be a result of genetic constraints (such as a trait that is genetically correlated with another trait that is changing under selection), recent or fluctuating changes in selective pressures, conflicts between natural selection and sexual selection (for example, the long tail feathers of male peacocks), or gene flow (the movement of genes between two or more populations). The latter is the focus of this module.

Question: How is gene flow measured? What conclusions can be drawn from these measurements?

Supplement to 'Adaptive Evolution': https://cnx.org/contents/jVCgr5SL@15.43:E3okHKCG@10/19-3-Adaptive-Evolution

Subject:
Biology
Ecology
Genetics
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
PREDATOR-PREY DYNAMICS: LOTKA-VOLTERRA
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Introduction: The Lotka-Volterra model is composed of a pair of differential equations that describe predator-prey (or herbivore-plant, or parasitoid-host) dynamics in their simplest case (one predator population, one prey population). It was developed independently by Alfred Lotka and Vito Volterra in the 1920's, and is characterized by oscillations in the population size of both predator and prey, with the peak of the predator's oscillation lagging slightly behind the peak of the prey's oscillation. The model makes several simplifying assumptions: 1) the prey population will grow exponentially when the predator is absent; 2) the predator population will starve in the absence of the prey population (as opposed to switching to another type of prey); 3) predators can consume infinite quantities of prey; and 4) there is no environmental complexity (in other words, both populations are moving randomly through a homogeneous environment).

Question: What are the predictions of the Lotka-Volterra model? Are they supported by empirical evidence?

Supplement to 'Environmental Limits to Population Growth': https://cnx.org/contents/jVCgr5SL@15.43:m1xWhyxP@9/45-3-Environmental-Limits-to-Population-Growth

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
QUANTIFYING CELL DIVISION
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Introduction: It is often necessary in experimental research to quantify the dividing capabilities of cells when investigating manipulations of the cells or their environment. The growth of cell populations can be modelled by assuming each cell divides into two, and the rate of growth depends on the length of the cell cycle. However, the simplicity of this idea may lead to misinterpretations in some circumstances. The growth rate of a population may be reduced if the length of the cell cycle increases. However, the growth rate may also be reduced if only a fraction of the cells are dividing.

Questions: How does the growth of a cell population change if only a fraction of the cells are dividing?

Supplement to 'The Cell Cycle': https://cnx.org/contents/jVCgr5SL@15.43:SeU_rWbd@14/10-2-The-Cell-Cycle

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
QUANTIFYING CURVATURE IN PLANTS
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Introduction: Plants adjust to the conditions of their environment through growth responses. For example, plant stems generally bend toward light sources while roots grow away from light sources. This process is called phototropism. Substances called auxins play a strong role in controlling various plant responses. Auxin increases the plasticity of plant cell walls causing them to stretch more during active plant growth. During phototropism, the auxin concentration in stem cells is usually higher on the side of the stem away from light. These cells will stretch more during active growth, causing the plant to move toward the light source. In gravitropism, plants respond to gravity, generally causing shoots to grow up and roots to grow down.

Question: How is plant curvature measured? How does curvature change over time in response to gravity or a light source?

Supplement to 'Stems': https://cnx.org/contents/jVCgr5SL@15.43:BPr6NhL7@9/30-2-Stems

Subject:
Biology
Botany
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
QUANTITATIVE CYTOLOGICAL CHARACTERISTICS
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Introduction: Cytological characteristics of a cell can vary from cell to cell and frequently depend on properties of the cell's environment. We might expect cytological characteristics to change when a cell needs to increase or decrease rates of diffusion. For example, plant cells may be stressed under photorespiratory conditions (high temperature, low CO2, high O2). Photorespiration interferes with photosynthesis and inhibits ATP formation. We can use quantitative cytological techniques to gain information about cells under stressful environmental conditions.

Question: How do quantitative characteristics of the cell change when a cell is under stress?

Supplement to 'Overview of Photosynthesis': https://cnx.org/contents/jVCgr5SL@15.43:dEDuZRSu@10/8-1-Overview-of-Photosynthesis

Subject:
Biology
Botany
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
RHYTHMS IN BREATHING AND LUNG CAPACITY
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Introduction: The respiratory system functions to filter, warm, and humidify the air we breathe, and to supply cells with oxygen while removing carbon dioxide. In animals that breathe with lungs, air moves into the lungs through the trachea and then back out again. When each breath is completed, the lung still contains a volume of air, called the residual volume. Each inhalation adds additional air. Each exhalation removes approximately the same volume as was inhaled.

Questions: How does lung capacity change over time? How does activity affect lung capacity?

Supplement to 'Breathing': https://cnx.org/contents/jVCgr5SL@15.43:TaqOW3G8@10/39-3-Breathing

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
SPECIES-AREA RELATIONSHIPS
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Introduction: The relationship between island area and number of species is well known: larger islands contain more species than smaller islands. "Islands" can be used to refer not only to pieces of land surrounded by water, but to habitat islands as well (lakes, forest fragments, etc.). Although the relationship is clearly demonstrated by many taxa, the causes of the relationship are less clear. This is possibly the most general pattern found in ecology, and many explanations have been proposed.

Question: What factor(s) may account for the species-area relationship? What other factors may come into play in determining the number of species on an island?

Supplement to 'The Biodiversity Crisis': https://cnx.org/contents/jVCgr5SL@15.43:2gggXk15@10/47-1-The-Biodiversity-Crisis

Subject:
Biology
Ecology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
SPERM MOTILITY
Conditions of Use:
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Introduction: Mammalian sperm cells consist of a head, midpiece, and flagellum. The midpiece is densely packed with mitochondria. These mitochondria provide energy in the form of ATP to the flagellum to propel the cell.

Question: How can we quantify sperm movement? How efficient are mammalian sperm at converting ATP to flagellar movement?

Supplement to 'Fertilization and Early Embryonic Development': https://cnx.org/contents/jVCgr5SL@15.43:shbyUxdz@10/43-6-Fertilization-and-Early-Embryonic-Development

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
STRESS-STRAIN CURVES AND YOUNG'S MODULUS
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Introduction: Solid materials are often categorized by their mechanical behavior. One such category is tensile materials, which operate by resisting being pulled upon. Four common types of tensile materials are found in living organisms: silk, collagen, cellulose, and chitin. Silk and collagen are both composed of proteins, while cellulose and chitin are composed of polysaccharides (sugars). The properties of tensile materials are often investigated using stress-strain tests, which involve pulling on a sample from each end. Spider webs, which function in prey capture for many species, are made of silk, a well-studied example of a tensile material.

Question: How does the web of a spider balance the conflicting requirements of being strong enough to trap prey, fine enough to resist wind disturbance, and flexible enough to resist deformation from struggling insects and movement of anchoring substrate?

Supplement to 'Features of the Animal Kingdom': https://cnx.org/contents/jVCgr5SL@15.43:KOCX7qJQ@10/27-1-Features-of-the-Animal-Kingdom

Subject:
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019
SYNAPSE TRANSMISSION
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Introduction: The nervous system depends on neurons working together to transmit signals. Neurons are special cells that have plasma membranes capable of generating and conducting electric impulses. Each neuron is composed of dendrites that collect information from other neurons, a cell body where nerve impulses are initiated, an axon along which impulses are conducted, and axon terminals that synapse with a target cell such as another neuron or muscle tissue.
The electric potential of neurons is responsible for signal transmission. The inside of a neuron generally has an excess of negative charges. When a neuron is unstimulated, the difference in electric charge across the plasma membrane is the resting potential. A neuron is sensitive to physical or chemical changes that cause changes in the resting potential. A sudden and rapid reversal in charge across the membrane is called an action potential. When a neuron is stimulated, the action potential moves along the axon to the axon terminals to the target cell. The post-synaptic membrane of the target cell integrates the information it receives. In order for the target cell to be stimulated, the stimulus must be greater than the target cell's action potential. Neurotransmitters that affect the membrane bring about an excitatory postsynaptic potential (EPSP). When several EPSP's arrive at the cell body simultaneously, the potential is summed over the number of synaptic knobs, and an action potential may be reached.

Question: How do membrane potential, action potential thresholds, and properties of neurons affect how nerve impulses stimulate muscles?

Supplement to 'How Neurons Communicate': https://cnx.org/contents/jVCgr5SL@15.43:KXC_-MaB@10/35-2-How-Neurons-Communicate

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/17/2019
TENSION IN BLOOD VESSELS: LAPLACE'S EQUATION
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Introduction: The closed circulatory system of vertebrates is composed of arteries, veins, and capillaries. Arteries are thick walled and carry blood away from the heart. Veins carry blood to the heart. Capillaries are small tubes that connect arterioles (small arteries) and venules (small veins).

Questions: How does is the tension in the walls of blood vessels affected by their thickness and size? Does the size and thickness of blood vessels make sense considering their particular roles?

Supplement to 'Blood Flow and Blood Pressure Regulation': https://cnx.org/contents/jVCgr5SL@15.43:OiYUUgCL@9/40-4-Blood-Flow-and-Blood-Pressure-Regulation

Subject:
Anatomy/Physiology
Biology
Material Type:
Activity/Lab
Provider:
University of Tennessee Knoxville
Provider Set:
The Institute for Environmental Modeling
Author:
L. Gross
M. Beals
S. Harrell
Date Added:
05/20/2019