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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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