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How Proteins Function: Hemoglobin
File size = 360KB
This interactive exercise allows the user to explore the way in which the hemoglobin works by seeing what happens when changes are made in the molecule. The user evaluates real experiments carried out by natural selection on the functioning of a real protein, hemoglobin. By examining functional consequences of particular amino acid substitutions at different positions on the protein, the user is able to build a detailed picture of the functional importance of different proteins of the hemoglobin molecule. The substitutions examined are real alleles that actually occur in human populations (including the so-called sickle cell alleles). Both oxygen-carrying behavior, stability, and tendency of Hb molecules to stick to one another (sickling) are characterized for each version of the hemoglobin molecule.
File size = 10829KB
This interactive exercise allows the user to explore the architecture of a cell, inquiring about the influence of cell size and shape. The key parameter that is monitored is ease of access to the cell interior. The interactive exercise characterizes the ease of diffusion of metabolites entering and wastes leaving the cell, using a "molecular speedometer" that measure the relative time it takes a molecule to travel from the center of the cell to the nearest surface. To explore the implications of differences in cell size and shape, the user is able to vary four interactive parameters: cell size, cell shape (from spherical to flattened), number of dimples on the surface of the cell (which increase its surface area), and number of villi (hair-like projections that vastly increase the cell's surface area). The user soon discovers a strong relationship between cell surface area and ease of diffusion.
File size = 401KB
This interactive exercise allow student to explore how substances are transported across membranes against a concentration gradient (that is, toward a region of higher concentration). The exercise presents a diagram of a coupled channel within a membrane through which amino acids are pumped into the cell. By altering ATP concentrations, the student can speed or slow the operation of the ATP-driven sodium/potassium pump and explore the consequences for amino acid transport. Similarly, the student can alter the cellular or extracellular levels of amino acid, and investigate the effect on cellular expenditure of ATP. Because the amino acid transport channel is coupled to the ATP-driven sodium/potassium pump, students will discover that both ATP and amino acid levels have important influences.
File size = 673KB
This interactive exercise allows the user to explore the key role of cell-surface receptors and intracellular cascades in receiving and amplifying signals between cells. The user alters the design of a hypothetical receptor's intracellular amplifying system, and assesses the consequences on intercellular communication. By manipulating the efficiency of cell-surface receptor proteins, G proteins, and various components of phosphorylation cascades in amplifying a signal, the user is able to evaluate how changes in these elements alter the communication between cells.
Mitosis: Regulating the Cell Cycle
File size = 509KB
This interactive exercise permits the user to explore the ways in which our cells decide if and when they will divide, a decision that, if made inappropriately, can lead to cancer. The user investigates how different cells make the decision to divide by first selecting a particular tissue (muscle, blood, liver, etc.), and then altering the conditions to which that tissue is exposed (age, physical exercise, tissue injury/loss, adequacy of nutrition, exposure to mutagens). When a set of parameters has been chose, the particular cell type and appropriate growth factor appear on the screen, and the user monitors the intracellular chain of events that leads to dell division, noting the frequency with which the cell cycle passes through the so-called "G1 checkpoint," which in large measure determines the overall duration of the cell cycle and thus ultimately the number of cells produced. Some parameters such as frequency of cigarette smoking alter the rate of proliferation of particular tissues (the tissues exposed to the smoke) because of mutational damage to the "braking system" used by the cell to restrain cell division. Other parameters alter the level of key growth factors, or in other ways affect this complex signaling process.
Cell Chemistry: Thermodynamics
File size = 379KB
This interactive exercise allows the user to explore the way in which reaction conditions affect how an enzyme catalyzes a chemical reaction, focusing on the key roles of enzyme concentration, temperature, and pH. Every enzyme has a characteristic rate and a unique sensitivity to temperature and pH, all of this behavior depending upon its particular structure. In this interactive exercise, the user can investigate the nature of these dependencies for a variety of real enzymes. The user first specifies the enzyme to be investigated, then for each of the three parameters selects a value and observes the effect on reaction velocity. By investigating a variety of values the user is able to plot a curve representing the sensitivity of the enzyme to that variable. The three variables taken together provide quite a realistic view of the operating behavior of the enzyme. Comparing different enzymes, the user quickly gains an appreciation of how well enzymes are suited to the physiological conditions under which they operate.
Enzymes in Action: Kinetics
File size = 711KB
This interactive exercise allows the user to explore how an enzyme does its job. By carefully monitoring the progress of an enzyme-catalyzed reaction, it is possible to learn not only how fast a particular enzyme can carry out catalysis once a substrate has been bound to it (a function of the nature of the enzyme's active site), but also how effectively the enzyme binds its substrate in the first place (a function of the shape of its binding site). In this exploration the user carries out a chemical reaction, using one of ten enzymes [or an "unknown"] as a catalyst. Carefully monitoring the progress of the reaction, the user records the value of v (reaction velocity---amount of product produced per second) that results from different values of [S] (concentration of substrate molecules). By plotting 1/v versus 1/[S], the user obtains a straight line whose slope (called Km) is proportional to how well the enzyme binds it substrate.
File size = 484KB
This interactive exercise allow the user to explore how a mitochondrion does its job. It present a diagram of a mitochondrial membrane in cross section, in which the user can explore how electrons garnered from food molecules are use to drive proton pumps and how, by chemiosmosis, this produces ATP. The key variables manipulated by the user are oxygen levels, \the amounts of food supplied, and existing levels of ATP (high levels shut down electron extraction from food, favoring storage instead).
File size = 429KB
This interactive exercise allows the user to explore how light influences photosynthesis. On the screen can be seen a chloroplast membrane in cross section, photons of light bashing into chlorophyll molecules and ejecting energetic electrons that pass from one membrane protein to another, leading to the production of ATP and NADPH. By varying the wavelength of the incident light, the user can construct an action spectrum of the photosynthetic pigment. By varying the light's intensity, the user can explore how the rate of photosynthesis depends upon the brightness of the light.
Exploring Meiosis: Down Syndrome
File size = 1332KB
This interactive exercise allows the user to explore how the failure of chromosomes to separate during meiosis can result in Down syndrome, a congenital condition involving serious mental retardation. The user evaluates the influence of Down syndrome babies, creating in each case a graph showing the incidence as a function of age. The way in which primary nondisjunction in meiosis I produces Down children can be explored by comparing normal meiosis with on in which primary nondisjuction of chromosome 21 occurs.
Constructing a Genetic Map
File size = 449KB
This interactive exercise allows students to explore the influence of physical separation upon genetic recombination by moving the relative position of genes on a chromosome. The exercise presents a diagram of the X-chromosome of Drosophila, on which are located the genes determining yellow body color (the normal body color is gray), white eye color (the normal eye color is red), and miniature wing size (the normal wing is 50% longer). Alongside the map is a collection of flies representing the progeny of a 3-point cross. By scoring the flies and placing them in the correct phenotypic class, students build an estimate of the recombination frequency between the genes. Student may then alter the position of the genes on the map, and see what effect this has on relative recombination frequencies.
Heredity in Families
File size = 2917KB
This interactive exercise allows students to explore how the character and location of a genetic trait influence its heritability within families. The key variables are dominance/recessiveness of the inherited allele and X-linkage versus autosomal location of the gene encoding the allele. From a bank of 30 actual pedigrees, one is selected at random, and the two variables are analyzed. The program scores the answer selected and then presents another pedigree from the bank. As the 30 pedigrees are examined in random order, the program keeps score of the analyses. These pedigrees are often all a human geneticist has to work with in attempting to assess the dominance and chromosomal location of a trait.
Gene Segregation Within Families
File size = 322KB
This interactive exercise allows the user to explore how heredity affects individual families. Among the most practical questions that arise about human heredity are ones concerning the potential makeup of families. In a family with three children, what is the likelihood all three will be girls? This interactive exercise tests the ability of the user to make such predictions. The key tool in determining what a potential family is likely to consist of is a simply calculated array of possibilities, the so-called binomial distribution. Using them, it is possible to assess the probability that a family of a given size will have so many girls, or for parents heterozygous for a recessive trait, that so many of the offspring will be double-recessive.
DNA Fingerprinting: You Be the Judge
File size = 1708KB
In this interactive exercise the user analyzes the DNA evidence presented in real courtroom trials, attempting to ascertain the guilt or innocence of the suspect in each instance. The exercise selects a case at random from its library of real cases, and presents the user with physical evidence (DNA samples from victim, perpetrator, and suspect) and a variety of DNA probes (RFLPs) to use as tools in the analysis. Selecting a probe, the user treats the DNA samples and examines the gel banding patterns that result. The user notes any differences between suspect and perpetrator (a difference would indicate innocence of the suspect), and, if no differences occur, uses the frequency of matches to estimate the probability that two randomly selected people would match that well. Then, by selecting a second and a third enzyme, the user can repeat the analysis to gain a clearer statistical picture.
File size = 394KB
This interactive exercise allows the user to explore what might at first seem a puzzling contradiction: how can regulatory proteins "read" the DNA double helix without unzipping it when the base pairs of the two strands point inward toward the center of the helix? As the user can see from the animation, the proteins slide along the major groove of the helix, feeling the edges of the hydrogen bonds for clues. The user investigates the nature of this protein-DNA interaction by designing proteins with structural motifs, including leucine zippers and homeodomains, and testing these hypothetical proteins against particular DNA sequences, including promoters and homeoboxes.
File size = 897KB
In this interactive exercise the user explore the various strategies employed by organisms to regulate the transcription of genes. Two strategies are explored: bacterial gene regulation, with the focus on rapid adaptation to environmental changes, and eukaryotic gene regulation, with the focus on complex, hard-wired programs dictating fixed patterns of gene activity. In the bacterial simulation, the user will design a regulatory mechanism for a sugar-utilizing enzyme, selecting elements from among activator and repressor proteins, and locating their binding sites on the DNA. The user then varies the level of sugar in the environment and assesses the success of the proposed regulatory mechanisms in optimizing use of the sugar. In the eukaryotic simulation, the user will have a broader choice of regulatory tools, including transcription factors, and the ability to locate regulatory genes at far distant sites. The challenge is to design a regulatory mechanism that will permit the various mammalian globin genes to be expressed at different times during development.
Making a Restriction Map
File size = 531KB
In this interactive exercise the student constructs a restriction map by entering measured band position data from a set of electrophoresis gels. The data may be supplied by the user from real lab experiments, or the user may choose to analyze one of several data sets provided by the interactive exercise. Maps such as these, based on determining the relative positions of overlapping DNA restriction fragments, are the principle way in which today's geneticists construct physical maps of genes.
File size = 366KB
The animated diagram shows a portion of a cell membrane that consists of a lipid bilayer with 3 embedded transport channels -- two chloride ion channels and one water channel. You watch what happens to the water movement across the membrane of a person with no cystic fibrosis alleles, a person heterozygous for the allele, and a person homozygous for the allele. Blue molecules represent water and green molecules represent chloride ion. The top portion of the screen is the outside of the cell. Two scales in the upper left of the screen record quantitatively the chloride ion concentration and mucus buildup on both sides of the membrane as the simulation runs.
Evolution of the Heart
File size = 502KB
This animation allows you to compare the hearts of fish, primitive amphibians, advanced amphibians, reptiles, and mammals. Each simulation shows an outline of a heart and animates the passage of blood through it. The color red indicates the presence of oxygenated blood; the color blue indicates the presence of deoxygenated blood; the color purple indicates a mixture of both oxygenated and deoxygenated blood. The meters at the bottom of the screen contain quantitative data about the heart's pumping efficiency, the delivery rate of oxygen to tissues, and the degree of separation of oxygenated and deoxygenated blood. As you move between vertebrate categories, you can observe changes in the data and relate those changes to what is happening in the animation.
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