Biology Cheat Sheet

Page 1 Biology Cheat Sheet Hyperlinked Table of Contents Experimental Design—Page 3 Graphing—Page 4 Statistics—Pages 4-6 Hypothesis Testing—Pages 5-6 Chi Square Analysis—Page 5-6 Water—Important Properties—Page 6-7 Carbon—Important Properties—Page 7 Organic Macromolecules (Carbs, Lipids, Proteins, Nucleic Acids)—Pages 7-10 Endosymbiotic Hypothesis—Page 10 Surface Area to Volume Ratio for Cells—Pages 10-11 Cell Membrane—Page 11 Compartmentalization—Page 11 Endomembrane System—Page 11 Organelles/Cell Structures—Page 12 Cell Transport Mechanisms—Pages 12-13 Bioenergetics—Pages 13-14 Enzymes—Pages 14-16 Factors that Affect Enzyme Function—Pages 15-16 Metabolic Pathways—Page 16 Feedback Inhibition—Page 16 Cellular Respiration—Pages 17-19 Aerobic Respiration—Pages 17-18 Anaerobic Respiration—Pages 18-19 Coupling—Page 19 Photosynthesis—Pages 19-21 Cell Communication/Signaling—Pages 21-22 Feedback Loops—Pages 22-23 DNA Structure—Pages 23-24 Page 2 DNA Replication—Pages 24-25 Central Dogma of Genetics—Page 25-29 Exceptions to the Central Dogma—Page 26 Transcription—Page 26 RNA/Alternative Processing—Pages 26-27 Translation—Pages 27-29 Post-Translation Modification—Page 29 Mutations—Pages 29-30 Gene Regulation—Pages 30-31 Gene Regulation in Eukaryotes—Page 32 Epigenetics—Page 33 Biotechnology—Pages 33-34 Meiosis—Pages 34-37 Nondisjunction—Page 36 Meiosis and Mitosis Compared and Contrasted—Page 37 Mendelian Inheritance—Pages 37-40 Monohybrid Cross—Pages 37-38 Product Rule—Pages 38-39 Dihybrid Cross—Pages 39-40 Trihybrid Cross—Page 40 Linked Genes—Pages 40-41 Non-Mendelian Inheritance—Pages 42-43 Modes of Inheritance/Pedigree Charts—Pages 43-47 Page 3 Experimental Design • • • • • • • A hypothesis is a prediction or possible answer to the problem or question. It is a relationship between the Independent variable and Dependent variables. Independent Variable (manipulated variable) – the factor that is intentionally varied/tested by the experimenter. Dependent Variable (responding variable) – the factor that may change as a result of changes made in the independent variable (the outcome). ▪ Example: Let’s say that a sci entist wanted to know if the use of miracle-gro affected the height of tomato plants. The independent variable in the experiment would be the amount of miracle-gro applied to the plants. The dependent variable would be the height of the plants. The experiment must have a control group. The control group may be a “no treatment” or an “experimenter selected” group to use as a standard of comparison for the independent variable. A negative control group is a control group that is not exposed to the experimental treatment or to any other treatment that is expected to have an effect. For example, imagine that you wanted to know if some lettuce carried bacteria. You set up an experiment in which you wipe lettuce leaves with a swab, wipe the swab on a bacterial growth plate, incubate the plate, and see what grows on the plate. As a negative control, you might just wipe a sterile swab on the growth plate. You would not expect to see any bacterial growth on this plate, and if you do, it is an indication that your swabs, plates, or incubator are contaminated with bacteria that could interfere with the results of the experiment. A positive control group is a control group that is not exposed to the experimental treatment but that is exposed to some other treatment that is known to produce the expected effect. o As a positive control, you might swab an existing colony of bacteria and wipe it on the growth plate. In this case, you would expect to see bacterial growth on the plate, and if you do not, it is an indication that something in your experimental set-up is preventing the growth of bacteria. Perhaps the growth plates contain an antibiotic or the incubator is set to too high a temperature. o • Example: In the miracle-gro experiment described above, the negative control group would consist of plants that are not exposed to any miracle-gro. The control group is exposed to all of the same factors as the experimental group(s) except for the independent variable being tested. o Experimental group – group or groups that have the independent variable applied/manipulated. o Example: In the miracle-gro experiment, the experimental group would consist of a group of plants that are treated with miracle-gro. We might treat different subgroups with different amounts of miracle-gro to test the effect of concentration. Constants – all the factors that the experimenter attempts to keep the same/control in all of the groups in the experiment. o Example: In the miracle-gro experiment, we would want to ensure that all of the plants are of the same species, growing in the same type of soil, exposed to the same amount of light, given the same amount of water, and grown at the same temperature. o • • • • Qualitative Data - observations (using senses) written in note form. Quantitative Data- numerical measurements and calculations. Page 4 Graphing • The independent variable is plotted on the x-axis • The dependent variable is plotted on the y-axis. • The mnemonic DRY MIX, for “dependent, responding, y-axis” and “manipulated, independent, xaxis,” can help you remember this pattern. • • • Which Graph Type To Use? • • • • • • • A) Line Graph: are used for looking at the relationship between two continuous types of data. Typically, both the independent and dependent variables are numerical. B) Bar Graphs/Histogram: are used for making comparisons between discrete cases or to look for trends, such as over space or time. The independent variable is usually a category and the dependent variable is usually an average, percentage, or frequency. C) Scatter Plot: Scatter plots are used for examining relationships between two types of data. These are very similar to line graphs, just without the line. The AP Biology exam often asks students to find the rate of a process or reaction between two points on a graph. In order to find the rate, calculate the slope of the best fit line that connects the two points. Use m=y2y1/x2- x1 Be sure to include a unit with your answer. The unit for the slope/rate should be the y axis unit divided by the x axis unit. Statistics • • • • • • • • The sample standard deviation (S) is a tool for measuring the spread (variance) in the sample population, which in turn provides an estimate of the variation in the entire sample set. A large sample standard deviation indicates that the data have a lot of variability. A small sample standard deviation indicates that the data are clustered close to the sample mean. Sample standard error (SEx) is a statistic that allows students to make an inference about how well the sample mean matches up to the true population mean . The standard error of the mean utilizes the standard deviation of the sample and the sample size to estimate how closely the sample data approximates the data that would be collected if the entire population were measured. An interval within ±1 SEx of the sample mean describes the range of values about which an investigator can have approximately 67% confidence that the range includes the true population mean. Even better, a sample interval within ±2 SEx of the sample mean defines a range of values with approximately a 95% certainty that the true population mean falls within the interval. This interval is often referred at as a 95% confidence interval. You will be asked to graph 95% confidence intervals on a regular basis in this course. The Standard Error of the Mean and the 95% Confidence Interval are used to construct error bars for graphs showing the mean values of data sets. In AP Biology, the error bars usually show the range 2 standard errors above and 2 below the mean value. To create a graph with error bars, graph the means of each data set using a bar chart/histogram. Starting at the mean of the first bar, move directly up 2 times the SE x. At that point, draw a horizontal line centered over the bar. Go back to the mean, and move directly down 2 times the SEx. Again, draw a horizontal line that is in line with the line you drew above the bar. Connect the two horizonal lines with a vertical line through their centers. Repeat the process for the other bars included in the chart. The vertical space between the two horizontal lines represents a 95% confidence interval. This means that you can be 95% sure that the mean for the entire population falls within this interval. As a researcher, you may want to use your collected data to compare samples/groups and to determine if the groups are “significantly different”. Page 5 • • • A "significant difference " means that the results that are seen in the data are most likely not due to chance or sampling error. In any experiment or observation that involves sampling from a population, there is always the possibility that an observed effect could have occurred due to sampling error alone. But if a result is "significant," the investigator may conclude that the observed effect actually reflects the characteristics of the population rather than just sampling error or chance. When errors bars overlap quite a bit, it's likely that the difference between the two groups is not statistically significant and the differences are probably due to chance or sampling error. You must actually perform a statistical test to draw a valid conclusion, but in AP Biology you can simply say that if the error bars overlap that the two groups/samples are not statistically different. On the other hand, if there is no overlap between the error bars, the differences between the two groups is likely to be statistically significant. Hypothesis Testing A hypothesis is a statement explaining that a causal relationship exists between an underlying factor (variable) and an observable phenomenon. Often, after making an observation, you might propose some sort of tentative explanation for the phenomenon; this could be called your working hypothesis. Because absolute proof is not possible, statistical hypothesis testing focuses on trying to reject a null hypothesis. A null hypothesis (H 0) is a statement explaining that the underlying factor or variable is independent of the observed phenomenon —there is no causal relationship. Stated another way, a null hypothesis (H 0) is usually a statement asserting that there is no difference between treatment groups or no association between variables. The null hypothesis is a tool that makes it possible to use certain statistical tests to figure out if another hypothesis of interest is likely to be accurate or not. For example, if you were testing the idea that sugar makes kids hyperactive, your null hypothesis might be that there is no difference in the amount of time that kids previously given a sugary drink and kids previously given a sugar-substitute drink are able to sit still. After making your observations, you would then perform a statistical test to determine whether or not there is a significant difference between the two groups of kids in terms of time spent sitting still. The alternative hypothesis (HA) to the null hypothesis might be that there is a difference between the two groups of kids in terms of time spent sitting still. Usually (but not always), an investigator is trying to find an alternative to the null hypothesis —evidence that supports the alternative hypothesis by rejecting the null (based on statistical tests). If the null hypothesis (that there is no difference between the two groups of kids in terms of time spend sitting still) can be rejected, then that is support for this alternative hypothesis. If evidence to reject the null hypothesis is sufficient, what can be said is that the investigator rejects the null hypothesis —not that the investigation has proven the alternative hypothesis. Chi square Analysis The Chi-square test is a statistical method that makes a comparison between the data collected in an experiment and the data an investigator expected to find. The actual data under these categories will typically be in the form of either counts or percentages. Chi square analysis should not be used to compare averages. • There are two different ways to interpret the meaning of the chi square statistic. One way is to compare it to a critical value. Use the chi square table, included on the AP Biology formula sheet to Page 6 find this critical value. First, determine your degrees of freedom. The degrees of freedom are equal to your number of phenotypes/categories minus one. • We are always going to use the 0.05 significance level in Biology. The significance level, also denoted as alpha or α, is the probability of rejecting the null hypothesis when it is true. For example, a significance level of 0.05 indicates a 5% risk of concluding that a difference exists when there is no actual difference. This is essentially an error range. • Use the 0.05 significance level and the 1 degree of freedom to find the critical value of in the chi square table. • Compare the critical value to the chi square statistic that you calculated. If the chi square statistic is greater than the critical value, we will reject the null hypothesis. If the chi square statistic is less than the critical value, you must fail to reject the null hypothesis. This essentially means that the differences between the observed and expected values are small and likely due to chance. • The other way to interpret the chi square statistic is to use the p-value approach. To use this approach, use the degrees of freedom and the chi square statistic that you calculated to find a p value in a provided chi square distribution table. Remember, the probability of whether the results of an investigation differ from the null results by chance alone is called the p-value. A p-value of 0.05 means that there is a 5% chance that the difference between the observed and the expected data is a random difference and a 95% chance that the difference is real and repeatable—in other words, a significant difference. Therefore, if an investigator’s p-value is greater than 0.05, he or she would fail to reject the null hypothesis —that the difference between the observed results and the expected results is due to random chance and is not significant if the p-value had been less than 0.05, we would have rejected the null hypothesis. This indicates that the differences between the observed and expected data are significant and likely due to something other than chance. Important Properties of Water Water is a Polar Molecule. Because of the high electronegativity of oxygen and the low electronegativity of hydrogen, the oxygen end of the water molecule has a slight negative charge, while the hydrogen end has a slight positive charge. The water molecule’s shape is said to be “bent”. This shape means that one side of the molecule “the hydrogen side” is positive, while the other side “the oxygen side” is negative. The polar water molecules form hydrogen bonds with each other. These bonds affect many of the biologically important properties of water. Water has a high specific heat. Specific heat refers to the amount of heat needed to change the temperature of 1 gram of a substanc e by 1 degree. Water’s specific heat is very high due to the hydrogen bonds that hold the water molecules together. Due to its high specific heat, water is excellent for helping to maintain a constant internal body temperature. Large bodies of water have fairly constant temperatures. Water also helps to moderate the air temperatures of land masses located near large bodies of water. Water is an excellent solvent. Water is often referred to as the “Universal Solvent”. This means that it is great at dissolving other materials (solutes). Due to its polarity, water is best at dissolving salts and polar molecules. This is important in Biology, because it allows vital nutrients and gases to be dissolved and transported through the body and through the ground. Water has a high heat of vaporization. Heat of vaporization refers to the amount of heat needed to convert a liquid to a gas. Due to the many hydrogen bonds which hold water molecules together, the heat of vaporization is very high for water. When the water does eventually evaporate it carries heat Page 7 away with it. This is important in Biology, because it allows processes like sweating and transpiration to cool off organisms through the process of evaporative cooling. Water is cohesive and adhesive. Due to its polarity, water molecules stick to each other (cohesion) and to other polar molecules (adhesion). This property allows transpiration, the movement of water through the xylem of plants, to move water from the ground, through the plant, and eventually out into the air. Water expands as it freezes. Like most other compounds, the volume of water contracts as it cools down, but unlike most other materials, the volume of water begins to expand after it cools to temperatures below 4 degrees Celsius. This causes ice to be less dense than liquid water. This means that ice floats on liquid water. This happens because the HYDROGEN bonds force the chains of water molecules further apart as the molecules cool down and slow down. This increased volume causes a decrease in density. This property is important to life, because as bodies of water freeze, the ice floats and insulates the liquid water underneath. This allows aquatic life to survive long, cold winters. Important Properties of Carbon Carbon has 4 valence electrons. Since carbon has 4 valence electrons, it can form four covalent bonds. This allows carbon to bond with a variety of molecules and form molecules with an almost infinite variety of shapes and functions. Carbon atoms are small. Because carbon is a small atom, its valence electrons are near the nucleus. This means that when carbon forms covalent bonds, the bonds are strong. This makes carbon an excellent building material for life. Carbon is abundant on Earth. Carbon isn’t the most abundant element on Earth, but there is a lot of carbon found on the planet. This makes it a good choice for the building block of life. Organic Macromolecules Polymers--These are large molecules that are formed by combining/bonding individual units called monomers. The monomers are linked together by covalent bonds. Remember that covalent bonds are strong. Macromolecules are formed by Dehydration Synthesis (also called Condensation) Reactions. During these reactions, monomers are covalently bonded together. The reactions release water as a byproduct. Macromolecules are broken apart into individual monomers by Hydrolysis reactions. (“lysis” means “to split.”). In these reactions, water is used as a reactant. Types of Organic Macromolecules Carbohydrates are sugars. In living things, carbohydrates serve as sources of quick energy and as structural/building materials. Most carbohydrate names end in the letters “-ose”. Monosaccharides - Are the monomers or “building blocks” of carbohydrates. (“sacch” means “sugar”.) Glucose, fructose, galactose, ribose, and deoxyribose are common monosaccharides. The general molecular formula for a monosaccharide is (C NH2NON). Polysaccharides - Are the polymers. These compounds are formed by the bonding together of several monosaccharides. Biologically important polysaccharides include: starch, glycogen, and cellulose. Page 8 Lipids--These macromolecules are fats, oils, waxes, phospholipids, and steroids. Most lipids are hydrophobic molecules. They contain little oxygen and are mostly nonpolar in nature. Two Main parts of a lipid: Fatty Acid—long chain of carbon and hydrogen atoms. 3 Carbon Glycerol molecule (alcohol) to hold the whole molecule together . Lipids use a covalent bond called an Ester Linkage to hold the fatty acids and glycerol together. Major Types of lipids: Triglycerols or Triglycerides (These are your basic fat or oil.)—These store long term energy and function to help insulate and cushion the body. Phospholipids-- These molecules replace a single fatty acid chain from a triglyceride with a single Phosphate ion. The phosphate portion of the molecule is Hydrophilic because of the charge on the phosphate ion. The remaining fatty acids chains are hydrophobic. They are mostly composed of long chains of carbon atoms that are also bonded to hydrogens. They are neutral and are not attracted to water. Phospholipids are said to be amphipathic since they have both polar and nonpolar sides. Phospholipid Bi-layers are important for the building of cell and organelle membranes. Proteins make up greater than 50% of an organism’s dry weight or biomass. The names of most proteins end in “lin” while the names of most enzymes (which are composed of proteins) usually end in “ase”. Proteins are large macromolecules which are composed of monomers “building blocks” called Amino Acids. The amino acids are connected by covalent peptide bonds. There are 20 different Amino Acids used by living things to make proteins. Proteins and enzymes usually have hundreds to thousands of Amino acids in their structure. Page 9 DNA’s only job is to code for the body ’s proteins. Amino acid structure Nucleic Acids Nucleic Acids function to store genetic information and/or to store and transfer energy. Common nucleic acids found living organisms include: DNA, RNA, ATP, cAMP, NADH, and NADPH. The monomers of nucleic acids are called nucleotides. A nucleotide consists of a 5 carbon (pentose) sugar bonded to a phosphate group and a nitrogenous base. ATP (Adenosine Triphosphate) is another important nucleic acid. An ATP molecule is composed of a single nucleotide which consists of the sugar (ribose) bonded to a nitrogenous base (always adenine), and three phosphate groups. ATP’s role in the body is to store and transfer energy. ATP is made during the process of cellular respiration. It functions to power almost every activity that occurs in the cell. Page 10 Endosymbiotic Hypothesis The Endosymbiotic Hypothesis, proposed by Lynn Margulis in the 1960s, hypothesized that some prokaryotes began to live together in symbiotic relationships with the smaller prokaryotes living inside larger ones. This gave the symbionts a survival advantage over other prokaryotes and eventually they evolved into Eukaryotic cells. Smaller organisms gained protection. Larger organisms gained energy production or faster motility. Over time DNA segments were “swapped” to create a more permanent existence. This “swapping” is referred to as genetic annealing. The smaller prokaryotes eventually became the membrane-bound organelles within the larger prokaryotes. Evidence for this hypothesis is found in mitochondria and chloroplasts. Mitochondria and chloroplasts have their own single circular chromosome like Bacteria. Mitochondria and chloroplasts have ribosomes that are similar to those found in Bacteria. Mitochondria and chloroplasts are able to independently reproduce within the eukaryotic cells. larger They use a process similar to binary fission. Mitochondria and chloroplasts have a double phospholipid bilayer cell membrane. This might be evidence of the phagocytosis of the original symbionts. Surface Area to Volume Ratios The Surface Area- to- Volume Ratio is of GREAT Importance for all cells. Page 11 As cells grow, the surface area to volume ratio for the cell decreases while the demand for internal resources increases. Think of the surface area as the cell membrane and the volume as the internal contents of the cell. As the cell gets larger, it gets harder for cells to transport in and out the required materials. This is one of the main reasons that cells must always be very small. Smaller cells have a higher surface area to volume ratio and are better able to transport materials through the cell membrane. Adaptions for increasing the surface area without increasing the volume Surface area to volume ratio can also be used to explain the shape of many cells / cellular surfaces. For example, the folds inside the mitochondria or the flat pan-cake like structures inside chloroplasts provide a greater surface area on which specific reactions can occur. The folds in the lining of our stomachs or the tiny cellular, finger-like projections that protrude from the wall of the small intestine (villi and microvilli) all act to increase the surface area without increasing the overall size or volume of the organ. In addition to being important for the transport of nutrients/wastes, the surface area to volume ratio also is very important in determining the rate of heat exchange between an organism and its environment. Cell Membrane A phospholipid bilayer makes up the majority of the cell membrane and also the organelle membranes. Phospholipids are amphipathic molecules. They have both hydrophilic and hydrophobic components/sides. These molecules form a bilayer because the hydrophilic portions of the molecule (the phosphate groups) orient themselves toward the water that is located both inside and outside the cell, while the hydrophobic portions of the molecule (the fatty acid tails) orient themselves away from the water and toward each other in the center of the membrane The current scientific model of the cell membrane is referred to as the Fluid-Mosaic model because it looks like a moving (Fluid) puzzle (mosaic). The phospholipids compose the fluid portion, while the proteins are embedded within like a mosaic. Certain membrane structures such as glycoproteins and glycolipids pieces can move laterally around the surface of the cell within the membrane, like students moving from seat to seat. The proteins moving in this sea of phospholipids are like a teacher moving around the student desks. Imagine the ceiling and floor are water molecules. The water molecules prevent vertical movement of the cell membrane. The protein embedded in the membrane acts as receptors, enzymes, transport channels, etc… Compartmentalization Membranes and membrane-bound organelles in eukaryotic cells compartmentalize/partition/divide the cell into distinct locations where specific intracellular metabolic processes and enzymatic reactions can occur. This allows for the specialization of certain cell parts and the division of labor between these specialized structures. These internal membranes and the resulting compartmentalization/partitioning, also minimize competing interactions and increase the surface area needed for some reactions to occur. Endomembrane System The endomembrane system (endo = “within”) is a group of membranes and organelles in eukaryotic cells that work together to modify, package, and transport lipids and proteins. Once the bound ribosomes make their proteins, the proteins enter the Rough ER and are eventually packaged into phospholipidbased secretory vesicles. These vesicles transport the proteins to the Golgi apparatus where they will be modified. After modification, the proteins are once again packaged into a lipid-based vesicle and shipped to the cell membrane. The proteins are excreted from the cell while the phospholipids that made up the vesicle become part of the cell membrane. The general pathway is (RER →Secretory vesicle→ Golgi Page 12 →secretory vesicle → Membrane for release. In some cases, the packaged proteins/enzymes become part of lysosome instead of being transported out of the cell. Cell Structure Organelles Page 13 Cell Transport Mechanisms Passive transport mechanisms don’t require the cell to use its own ATP/energy sources to carry the transport process. These mechanisms usually move substances with the concentration gradient. Active transport mechanisms require the cell to use its own ATP/energy sources. These mechanisms usually move substances against the concentration gradient. Diffusion—a passive type of transport that moves substances from area so high concentration (of the substance) to areas of low concentration. Osmosis—the diffusion of water. Osmosis moves water from areas of high water concentration to areas of low water concentration. You can also say that osmosis moves water from areas of low solute concentration to areas of high solute concentration. This can also be stated as the movement of water from hypotonic areas to hypertonic areas. Water potential takes into account the effect of both solutes and pressure. Water moves from areas of high water potential to areas of low water potential. Facilitated diffusion—a passive type of transport that involves the movement of a large or charged object into or out of the cell through a channel or transport protein. Active transport—moves materials against the concentration. Requires the use of the cell’s energy. The sodium/potassium pump is a common example of this type of movement. Co-Transport-- Co-transport is a process in which two substances are simultaneously transported across a membrane by one protein, or protein complex which does not have ATPase activity. Co-transport is a type of active transport. Usually one of the substances moves with the concentration gradient (from high to low concentration). The movement of this substance provides the energy to transport the other substances against the concentration gradient (from low to high concentration). Bioenergetics Bioenergetics is a field of Biology that concerns energy flow through living systems. The field includes the study of the processes involved in the transferring and transforming of energy in living organisms. This includes the study of enzymatic processes, metabolic pathways, cellular respiration, and photosynthesis. The goal of bioenergetics is to describe how living organisms acquire, transfer, and transform energy in order to perform biological work. It is important to note that while matter and energy move through an ecosystem together when they are contained within organic compounds, they follow different paths at the beginning and the end of food chains and food webs. Producers (like plants and algae) get matter from carbon dioxide, water, and minerals (from the soil). They get energy from sunlight. Heterotrophs get both matter and energy from food. All of the matter is eventually converted back into carbon dioxide, water, minerals, and some metabolic wastes, while all of the energy leaves the ecosystem as heat. This heat ultimately flows out into space. Matter cycles continuously through an ecosystem, while energy flows through the ecosystem and eventually ends up in space. The energy isn’t used up or created. It is simply transformed (from one type of energy to another type) and transferred from one place or organism to another as it moves through the ecosystem. An extremely important idea from this unit is that “The highly complex organization of living systems requires a constant input of energy and the exchange of macromolecules. Page 14 Enzymes • • • • • • • • • Enzymes are proteins which catalyze chemical reactions. Enzymes increase the rate of biological reactions. They do this by lowering the activation energy required for a reaction to occur. The substance(s) acted upon by an enzyme is the substrate. The substrate binds to an area of the enzyme known as the active site. The shape of the substrate and enzyme must be complimentary. The charges of the substrate and active site must also be compatible. This ensures that each enzyme is very specific and only catalyzes one particular reaction. Once the substrate binds to the enzyme, the enzyme undergoes a slight change in shape (induced fit). This change in shape helps to catalyze the reaction. Some enzymes catalyze anabolic reactions, while others catalyze catabolic reactions. Enzymes catalyze reactions, but aren’t themselves changed by or used up during the reactions in which they take part. Each enzyme works best at a specific (optimal) temperature and pH. If the temperature and/or pH is moved away from the optimal conditions, the enzyme will begin to denature (change shape and lose function). This is largely because the changes in pH and increases in temperature disrupt the hydrogen bonds which help to provide and support the shape/structure of the enzyme. In most cases, denaturation is permanent although in some cases it can be reversible. Page 15 Factors that affect Enzyme Function Concentration of the Enzyme and Substrate —A higher concentration of either enzyme or substrate typically increases reaction rates up to the point where all of the enzymes are occupied or until the substrate is used up. pH—Any movement away from the optimum pH tends to lower reaction rates and causes denaturation of the enzymes. Salinity—Any movement away from the optimum salinity tends to lower reaction rates. Temperature—increase in temperature up to the optimum temperature tend to increase reactions rates because of an increase in molecular motion. Increases past the optimum temperature cause quick drops in reaction rate due to denaturation of the enzymes. Inhibitors—Competitive and Non-competitive—Inhibitors with slow reaction rates by either block the active site (competitive) or binding to an allosteric or cofactor/coenzyme site and causes the enzyme to change its shape to a nonfunctional conformation. Cofactors/Coenzymes—These attach to specific enzymes and activate the enzymes. Each enzyme has optimum conditions that it works best at. Page 16 Metabolic Pathways Metabolic pathways—Everything that happens in a cell happens because of chemical reactions. Most of these processes are complicated and require lots of chemical reaction steps to take place. Metabolic pathways are enzyme-regulated sets of biochemical reactions that lead to either biosynthesis (anabolic pathways) or breakdown (catabolic pathways). Examples of metabolic pathways include glycolysis, the Krebs cycle, and the Calvin Cycle. Photosynthesis, Cellular Respiration, and Digestion might also be thought of as metabolic pathways. Each step of a metabolic pathway consists of a separate chemical reaction. Metabolic pathways consist of a sequential set of chemical reactions in which the products of one reaction are typically the reactants (substrates) for the next reaction. Each step is catalyzed by a different, specific enzyme. Many of the major metabolic pathways such as glycolysis and Krebs cycle are conserved across most living things. This indicates that the organisms inherited the metabolic pathways from a common ancestor. Feedback Inhibition Feedback/Allosteric Inhibition---Temporary deactivation of an enzyme or metabolic pathway brought about by an elevation of an end product of the metabolic pathway. This is a type of noncompetitive inhibition. Typically, the product of the pathway binds to the allosteric or feedback site on one of the early enzymes in the pathway. This inhibits the action of the enzyme. Since the products of this reaction are the reactants for the next reaction, the entire metabolic pathway is inhibited. The process is dependent on the concentration of the end product. When the concentration of the end product is high, the pathway is inhibited. When the concentration is low, the pathway resumes its normal function and once again begins to produce the end product. Page 17 Feedback inhibition is an example of negative feedback. This process is an important way for cells to conserve resources. Cellular Respiration Cellular Respiration is the process of releasing the energy contained in organic molecules (mainly Glucose) to do work. (This is an example of catabolism.) The process uses the energy from the organic, biological macromolecules to make ATP. ATP then serves as the energy source for most of the body’s endergonic reactions. Cellular Respiration also releases heat (unusable energy) and free electrons. The free electrons serve as a source of energy for producing ATP. The process of cellular respiration is a metabolic pathway, a series of coordinated enzymecatalyzed reactions that capture energy from biological macromolecules. When O2 is present in the cell, aerobic respiration takes place. The first stage of this process, glycolysis, occurs in the cytoplasm/cytosol. The other two stages, Krebs Cycle and the Electron Transport Chain, take place within the mitochondria. Exceptions to these statements will be discussed below. Aerobic Cellular Respiration Chemical Equation 602 + C6H12O6 → 6CO2 + 6H2O + Free Energy +Heat Energy ∆G = -686 kcal per mole of Glucose A negative ∆ G means Free E is available to do work. During cellular respiration the free energy is used to make ATP. Without O2 present in the cell, anaerobic respiration takes place . This process also involves glycolysis as its first step. This step is again carried out in the cytoplasm/cytosol. The second step of the process is called fermentation. It too occurs in the cytoplasm. Some books/questions refer to all of anaerobic respiration as fermentation. Be sure to pay attention to the context of the question when answering questions about anaerobic respiration. Aerobic Respiration Aerobic Cellular Respiration is usually discussed as a Three Step Process: Step 1: Glycolysis—During the process, Glucose is broken into 2 three carbon molecules of pyruvate or pyruvic acid. Two net molecules of ATP and 2 molecules of NADH are generated for each glucose molecule that enters the cycle. All organisms (including bacteria and plants) can do this process since it occurs in the cytoplasm of the cell. Step 2: Krebs Cycle—In eukaryotic cells, this stage occurs in the innermost compartment of a mitochondrion, the matrix. In aerobic prokaryotes, this stage occurs in the cytoplasm. During this stage, the pyruvate molecules that were produced during Glycolysis are oxidized. The energy and electrons from the pyruvate are used to reduce electron carriers to form the energy storage molecules NADH and FADH2. Two molecules of ATP are formed during this stage for each glucose that entered into glycolysis. Most of the energy of the original glucose molecule is now contain in the electron carriers. The remains of the glucose molecules are released as carbon dioxide. Page 18 Step 3: Electron Transport Chain—In eukaryotic cells, the electron transport chain takes place on the folds of the inner mitochondrial membrane. These folds are called cristae. In aerobic prokaryotic cells, the electron transport chain takes place on the folded inner surface of the cell membrane. During the ETC, the electron carriers (NADH and FADH 2) that were formed during glycolysis and the Krebs Cycle are oxidized. The energy from these electrons is used to create large amounts of ATP. The electrons ultimately reduce oxygen gas and form water. Oxygen gas is a required reactant for this process. The process starts when NADH is oxidized by the first cytochrome in the chain (this protein is known as FMN). The 2 electrons lost from NADH pass through three proteins (proton pumps) as they move down the ETC. The electrons move from the least electronegative location (the first cytochrome/electron acceptor) toward the most electronegative location (the last cytochrome/electron acceptor). As the electrons move through the proton pumps, the energy from the electrons powers the pumping of a hydrogen ion or proton from the matrix into the intermembrane space (the space between the inner and out mitochondrial membrane). A single proton is pumped as a pair of electrons travels through each of the three proton pumps. A proton/hydrogen ion gradient is created across the inner membrane. The pumping of the protons creates an area of high proton/H+ concentration in the intermembrane space and an area of low proton/H+ concentration in the matrix. The gradient is a way to store potential energy. The bigger the gradient, the more potential energy is stored. In prokaryotes, the protons are pumped from the cytoplasm through the cell membrane and into the fluids around the cell. An enzyme, ATP synthase, embedded in the inner membrane, has a channel that will allow protons/H+ ions to move through it. Since this is the only way back into the matrix (in eukaryotes) or prokaryotic cell (because the nonpolar nature of the inner membrane won’t allow protons to cross it), the protons/H+ ions move quickly through the ATP Synthase channel. The enzyme is able to use the kinetic energy of the moving protons/hydrogen ions to add a phosphate group to ADP to make ATP. The energy from a single proton provides the energy to create a single ATP molecule. The process of using energy from a proton/H+ ion gradient to phosphorylate ADP with an inorganic phosphate group is known as chemiosmosis. This process is responsible for the creation of most of the ATP created during both aerobic cellular respiration and photosynthesis. The role of oxygen in aerobic respiration is to remove the electrons from the final cytochrome. Because of its role, oxygen is often referred to as the final/terminal electron acceptor. Oxygen is capable of this task because of its high electronegativity . Since it is more electronegative than the final cytochrome, the electrons move from the final cytochrome to oxygen. The now negatively charged oxygen, combines with hydrogen ions to form water. The electron transport chain can produce a maximum of 34 ATP molecules per glucose that initially entered glycolysis. The process also creates water and regenerates the electron acceptors NAD+ and FAD. The electron transport chain and chemiosmosis are collectively referred to as oxidative phosphorylation. This term is very descriptive of the processes since the electron carriers (NADH and FADH2) are oxidized and their energy is used to phosphorylate ADP to make ATP. Anaerobic Cellular Respiration If NO OXYGEN is present within the cell, the cell carries out anaerobic cellular respiration. Some cells solely use anaerobic cellular respiration to make ATP. This typically only works in very small and relatively inactive organisms because the process of anaerobic cellular respiration is highly inefficient and does not yield very much ATP (only 2 ATPs per glucose). Page 19 Larger and more active organisms use anaerobic cellular respiration to supplement ATP production in times of low oxygen concentration. This type of situation might arise when the organism is running at full speed or exerting the muscles with full force (lifting extremely heavy weights). The process of anaerobic respiration occurs in two phases: glycolysis and fermentation. Glycolysis occurs just as it does during aerobic cellular respiration. Each glucose is used to produce 2 net molecules of ATP, 2 molecules of pyruvate, and 2 molecules of NADH. When there is no oxygen present, the electron transport chain is not able to oxidize NADH back to NAD+. Since there is a limited amount of NAD+ in the cell, the cell must use an alternate method to regenerate NAD+ from NADH. Fermentation’s only role is to free up NAD+ so that they it is available to keep glycolysis going in the absence of oxygen gas. Pyruvate, the end product of glycolysis, serves as an electron acceptor for oxidizing NADH back to NAD+, which can then be reused in glycolysis. Anaerobic cellular respiration yields only the 2 net ATP molecules produced during glycolysis. There are many types of fermentation, but the two most commonly discussed in Biology courses are Alcoholic Fermentation and Lactic Acid Fermentation. All types of fermentation regenerate NAD+ from NADH and produce organic by-products such as alcohol or lactic acid. Coupling The energy from ATP is often used to power endergonic reactions via a process known as reaction coupling. During coupling an energetically favorable/spontaneous reaction (like ATP hydrolysis) is directly linked with an energetically unfavorable (endergonic) reaction. This essentially means that a reaction that releases energy (like the hydrolysis of ATP) is often coupled with reactions that require an input of energy. Photosynthesis During photosynthesis, energy is captured from the sun/light and converted to chemical energy stored in the bonds of glucose. Plants, algae, some protists, and some bacteria (cyanobacteria) are capable of carrying out photosynthesis. Page 20 Scientists think that photosynthesis first evolved in some prokaryotes and that the photosynthesis carried out by these organisms was responsible for the production of an oxygenated atmosphere on Earth. These original prokaryotic photosynthetic pathways served as the foundation for the evolution of eukaryotic photosynthesis. The reactants for photosynthesis include carbon dioxide (taken in from the air via the stomata), water (taken in from the ground through the roots), and light energy (absorbed by the pigment proteins in the leaves). The overall products of photosynthesis include glucose (stored energy) and oxygen gas. The balanced overall equation for photosynthesis may be written in either of the two ways illustrated below. Most textbooks teach that photosynthesis occurs in a two-phase process. Phase 1—Light Dependent Reactions —The light dependent reactions occur on the thylakoid membranes of the chloroplasts of leaf cells (in eukaryotes). In prokaryotic photosynthesizes, the light dependent reactions occur on folds of the cell membrane. The light dependent reactions involve a series of coordinated enzyme-catalyzed reaction pathways that capture energy from light. During the light dependent reactions, light energy is absorbed and used to reduce the electron acceptor NADP+ to make NADPH (a form of stored energy). NADP+ is the final/terminal electron acceptor. The light energy is also used to power the creation of a proton/H+ gradient which is used, during chemiosmosis, to create ATP (another form of stored energy). Oxygen gas is also released as a by-product of the light dependent reactions. The energy from ATP and NADPH power the production of organic molecules (like glucose) during the Calvin Cycle. The set of light wavelengths absorbed by a pigment is its absorption spectrum. In the diagram below, you can see the absorption spectra of three key pigments in photosynthesis: chlorophyll a, chlorophyll b, and β-carotene. The set of wavelengths that a pigment doesn't absorb are reflected, and the reflected light is what we see as color. For instance, plants appear green to us because they contain many chlorophyll a and b molecules, which reflect green light while absorbing and using the energy of the blue and red wavelengths. Page 21 Phase 2—Calvin Cycle/Calvin-Benson Cycle/Light Independent Reactions—The Calvin Cycle occurs in the stroma of the chloroplasts in eukaryotic cells and in the cytoplasm of photosynthetic prokaryotes. During this phase, the energy from the NADPH and ATP (formed during the light dependent reactions) is used to reduce and phosphorylate carbon dioxide gas (which enters to leaf via the stomata) to create G3P and ultimately glucose. Glucose is an energy storage molecule that can be readily stored and/or transported to other parts of the plant like the roots and stems. Cell Communication Communication between cells is essentially for the survival of both unicellular and multicellular organisms. Cells often communicate via the release of cell signaling molecules/ligand. The steps below describe the basic cell signaling process. Step 1--Reception – Reception begins when the signaling molecule binds to the ligand binding domain of a membrane receptor protein. The receptors are very specific to a particular signaling molecule. The signal molecule must fit into the receptor like a substrate fits into the active site of an enzyme. Different cells possess different receptors and are capable of interacting with different signaling molecules. Most receptors extend outside the cell membrane (extracellular receptors) because most signaling molecules are composed of proteins This means that they are too large and charged to enter the cell. After the signal molecule attaches to the receptor, the intracellular domain of the receptor protein (the part of the receptor protein that extends through the membrane and into the cytoplasm) undergoes a conformation change (change in shape). This process helps to move the signal from outside to inside the cell and initiates the transduction of the signal. Step 2--Transduction -- Since signaling systems need to be responsive to small concentrations of chemical signals and act quickly, cells often use a multi-step pathway that transmits the signal quickly, while amplifying the signal to numerous molecules at each step. Steps in the signal transduction pathway often involve the addition or removal of phosphate groups which results in the activation of proteins. Enzymes that transfer phosphate groups and energy from ATP to a protein are called protein kinases. Many of the relay molecules in a signal transduction pathway are protein kinases and often act on other protein kinases in the pathway. Often this creates a phosphorylation cascade, where one enzyme phosphorylates another, which then phosphorylates another protein, causing a chain reaction. Page 22 A benefit of transduction is that a small number of ligands (signals) can help to activate a large number of molecules at the end of the pathway. We can say that transduction often amplifies a chemical signal along the signal transduction pathway. Response – The response is the action the signal was meant to initiate and/or regulate. A signal transduction pathway regulates one or more cellular activities. Potential responses to cell signals include: The opening of an ion channel—Example: The opening of ligand gated ion channels on neurons in response to the binding of neurotransmitters. The breakdown of a substance in a cell—The breakdown of glycogen in the liver stimulated by the binding of epinephrine to receptors on the liver cells. The synthesis of enzymes or proteins (gene expression)—Rising levels of ethylene gas cause the production and activation of enzymes that cause the ripening of fruits. The turning on/off of certain genes (gene regulation)—The expression of the SRY gene triggers the development of the male sexual development pathway. Feedback Loops Homeostasis--a property of an organism or system that helps it maintain its parameters (temperature, blood glucose levels, blood calcium levels, heart rate, blood pressure, etc..) within a normal (fairly constant) range of values. One of the main functions of the endocrine system is to help maintain homeostasis. Feedback loops are mechanisms used by organisms to maintain their internal environments and respond to internal and external environmental changes. Negative Feedback Loop—A negative feedback loop occurs in biology when the product of a reaction leads to a decrease in that reaction. In this way, a negative feedback loop brings a system closer to a target set point of stability or homeostasis. Negative feedback loops are responsible for the stabilization of a system, and ensure the maintenance of a steady, stable internal state. The response of the regulating mechanism is opposite to the output of the event. Another way of thinking about negative feedback loops is that if a system is perturbed/disturbed, negative feedback mechanisms return the system to its target set point. These mechanisms operate on both the molecular and cellular levels. Examples in the human body include: Thermoregulation; Maintenance of blood glucose levels; Maintenance of blood calcium levels. Components of a Negative Feedback Loop Stimulus—a change in a variable away from the set point range. Receptor—senses a change in a variable. Control Center—compares the changes to the set point range. Sends out either nervous or endocrine signals to effectors which will reverse the change back toward the set point. In many human feedback loops, the control center is the hypothalamus. Effector—makes adjustments to the variable. Response—change in the variable caused by the effector. Page 23 Blood Glucose Feedback Loop DNA Structure Watson and Crick were eventually able to determine that the DNA molecule is composed of two strands of nucleotides that are then twisted into a double helix. The individual strands are built when the phosphate groups of the nucleotides form covalent bonds with the deoxyribose molecules of adjacent nucleotides. The actual bonds form when one deoxyribose attaches to another by connecting its 5' carbon to the 3' carbon of the next sugar in the next nucleotide using a phosphate group. The alternating sugars and phosphates form the “backbone” of the DNA molecule. The DNA molecule is composed of two strands of nucleotides held together by hydrogen bonds. Each strand has two slightly different ends. One end, known as the 5’ end, terminates with an unbound 5’ carbon on the last nucleotide in the chain. The other end, known as the 3’ end, terminates with an unbound 3’ carbon on the last deoxyribose molecule at its end. When the two strands are connected Page 24 together, they are oriented in opposite directions. Because they run parallel to each other, but have opposite directional orientations, the two strands are said to be antiparallel. DNA Replication Replication is the process in which the cell makes a complete copy of its DNA. DNA replication ensures the continuity of hereditary information by allowing copies of the DNA to be transmitted from cell to cell. The entire length of each chromosome is replicated during the process. Replication occurs during the S-Phase of Interphase as the cell prepares for mitosis or meiosis. Replication begins at locations known as origins of replication. Each eukaryotic chromosome has multiple origins, while a prokaryotic chromosome has a single origin of replication. Origins are specific nucleotide sequences encoded in the DNA strands that act as “starting points”. Replication begins when the enzyme helicase begins to unwind or unzip the two strands of the DNA at each origin of replication. This creates Replication Bubbles or Replication Forks. Both strands of DNA act as templates for the building of new DNA strands. Single-stranded binding proteins attach to the unzipped DNA strands to help keep the strands separated and to stabilize them. Many replication bubbles/forks can form on each DNA strand. (This speeds up the process of replication.) A group of enzymes known as topoisomerases work to untangle/relax supercoiling of the DNA double helix ahead of the replication fork. Next, an enzyme known as Primase synthesizes short RNA sequences called primers. These primers serve as starting points for DNA synthesis. Since primase produces RNA molecules, the enzyme is a type of RNA polymerase. Primase functions by synthesizing short RNA sequences that are complementary to a single-stranded piece of DNA, which serves as its template. It is critical that primers are synthesized by primase before DNA replication can occur because the enzymes that synthesize DNA, which are called DNA polymerases, can only attach new DNA nucleotides to an existing strand of nucleotides. Therefore, primase serves to prime and lay a foundation for DNA synthesis. After replication, the RNA primers are removed and replaced with DNA. Elongation of the new DNA strands requires the enzyme DNA Polymerase. This enzyme performs the addition of new nucleotides to the new DNA strands and also acts as a proofreader to help prevent errors/mutations in construction from occurring. Page 25 DNA Polymerase can only synthesize/build new DNA strands in the 5’→ → 3’ direction. The original/parental DNA strand that runs in the 3’ to 5’ direction is used as a template for building the leading strand of DNA. This strand is built quickly and in one continuous piece. The original/parental DNA strand which runs in the 5’ to 3’ direction acts as a template for the lagging strand of DNA. This strand will run in the 3’ to 5’ direction, but must be built in the 5’ to 3’ direction. This strand must be built discontinuously. This side of the FORK has to wait for a LONG SEGMENT of DNA to become unwound and exposed before replication on the strand can start with the addition of a primer. Once the primer is in place, DNA Polymerase III will work backwards (in the 5’ to 3’ direction). Eventually a short fragment of DNA known as an Okazaki fragment is synthesized. By this time, a new segment of the double-stranded parental DNA is unzipped. RNA primase synthesizes a new primer and DNA Polymerase III synthesizes a new Okazaki fragment in the 5’ to 3’ direction. When the DNA Polymerase III, on the newly created Okazaki fragment, reaches the RNA primer of the previous Okazaki fragment, the DNA Polymerase III will remove the old RNA primer and replace it with new DNA nucleotides. The Okazaki fragments are joined/”stitched”/covalently bonded together using the enzyme Ligase. DNA replication is said to be a semiconservative process. Since each of the two original DNA strands act as a template for the building of new complementary strands, the result is the formation of two identical copies of the original double stranded molecule, each of which consists of one of the original strands and one newly synthesized strand. The Central Dogma of Genetics The central dogma of molecular biology describes the flow of genetic information in cells from a sequence of nucleotides in DNA to a sequence of bases in an messenger RNA (mRNA) molecule to a sequence of amino acids in a protein. It states that DNA (in the nucleus) is transcribed to create mRNA molecules. The mRNA molecules travel out of the nucleus and to the ribosomes where the sequence of the mRNA is translated and used to produce proteins. These proteins then determine the traits of the organism. The central dogma also includes the process of replication. Replication of DNA occurs during the S phase of Interphase and creates an identical copy of the entire genome so that when cell division occurs, both cells get an entire, complete, identical copy of the DNA. All living things carry out replication, transcription, and translation in similar ways. The central dogma is another example of a conserved trait and is further evidence of the common ancestry of all life forms on Earth. Page 26 Exceptions to the Central Dogma of Genetics There are a couple of exceptions to the Central Dogma. Retroviruses, like HIV, the influenza viruses, and the hepatitis B virus, don’t have any DNA. Their only genetic material is RNA. The viruses transcribe RNA into DNA through the use of a special enzyme called reverse transcriptase; RNA → DNA → RNA → protein. The DNA generated by reverse transcriptase integrates into the host cell’s genome and becomes transcribed and translated for the assembly of new viruses/viral progeny. Protein Synthesis The function of DNA is to code for the body’s proteins. Proteins make up a large part of the body’s structure and are responsible for many of its functions. The image below contains a brief description of just few of the roles of proteins in the body. Transcription Before proteins can be made, the DNA must first be used as a template for making messenger RNA (mRNA). This process is known as transcription. During transcription, the message contained in the DNA molecule is rewritten in the form of an RNA molecule. Messenger RNA can then leave the nucleus and go to the ribosomes where it functions as a disposable/portable copy of the protein building directions contained in the DNA. This is important because the DNA cannot leave the nucleus and the ribosomes (the protein-building factories of the cell) function outside of the nucleus. Transcription is the first step in gene expression/protein synthesis. Unlike replication in which the entire chromosome is copied at the same time, transcription occurs and is controlled on a gene by gene basis. The new RNA molecule must always be built in the 5’ to 3’ direction which means the DNA template strand must be read in the 3’ to 5’ direction. The new RNA molecule, known as the primary transcript, carries the same sequence as the non-template or coding strand of the DNA, except it has the nitrogenous base Uracil instead of Thymine. RNA Processing In prokaryotic cells, the RNA molecules produced during transcription can immediately act as messenger RNAs. Translation begins while transcription is still ongoing. In eukaryotic cells, the newly formed RNA molecule is known as pre-mRNA molecule or the primary mRNA transcript. These molecules must be processed through a series of enzyme regulated modifications before they can be used to direct translation. Splicing or Middle Modification—The RNA sequence, at this point, consists of exons (protein-coding regions) and introns (non-coding regions). For the RNA to be functional, the intron sequences must be removed or excised and the exon sequences must be retained and spliced (attached) together. This process (in multicellular eukaryotes) is carried out by spliceosomes. These structures contain snRNAs that attach to the intron sequences via complementary base pairing. The spliceosome then uses ribozymes (enzymes made of RNA) to cut and remove the intron sequences and splice together the exon sequences. Once all three steps of RNA processing are complete, the RNA is referred to as a mature mRNA. This molecule is now ready to direct the process of translation. Even though the pre-mRNA will always include all of the exons, during processing a cell may remove particular exons along with the introns. This process is known as alternative processing or alternative splicing. It allows a cell to generate multiple versions of mRNA and ultimately multiple proteins from a single gene and greatly increases the protein diversity within a cell. Page 27 Translation Translation—During translation, a cell’s ribosomes “read” the information encoded in a mRNA molecule and use the information to generate/build a polypeptide. A polypeptide is a chain of amino acids. Usually, several polypeptides are combined to form a protein. Ribosomes are present in the cytoplasm of both prokaryotic and eukaryotic cells and on the Rough Endoplasmic Reticulum of eukaryotic cells. Translation is an active process which requires the cell to use its own energy/ATP. The process consists of many coordinated, sequential steps which include initiation, elongation, and termination. Each set of three mRNA nucleotides (referred to as a codon or triplet) codes for a specific amino acid. The 4 different types of nucleotides (A, U, C, and G containing) can be combined into 64 different codons. Sixty-one of these codons code for amino acids. One of these codons (AUG) codes for the amino acid methionine, but also acts as the “start codon” to signal the beginning of protein synthesis. The other 3 codons (UAA, UAG, and UGA) act as stop codons. These codons don’t code for amino acids, but instead “tell” the cell that the polypeptide is complete and that translation should stop. In addition to mRNA molecules, tRNA molecules and ribosomes play key roles during the process of translation. Transfer RNA molecules are shaped in a cross-like arrangement. The tRNA molecule ’s job is to bind to and transport a specific amino acid to the ribosome so that it can be incorporated into the forming protein. On one side of the tRNA molecule is a set of three unpaired nucleotides called an anticodon. The anticodon of a given tRNA can bind to one or a few specific mRNA codons. The tRNA molecule also carries an amino acid: specifically, the one encoded by the codons that the tRNA binds with. The tRNA molecule is recruited to the ribosome during translation and delivers its amino acid so that the ribosome can generate/build the primary polypeptide sequence. Like replication and transcription, translation is said to occur in three major stages: initiation, elongation, and termination. The discussion below describes the process of translation as it occurs in eukaryotic cells. Initiation begins when the initiator tRNA carrying methionine attaches to the rRNA of the small ribosomal subunit. Together, they bind to the 5' end of the mRNA by recognizing the 5' cap . Then, they Page 28 "walk" along the mRNA in the 5’ to 3' direction, stopping when they reach the start codon on the mRNA (usually AUG). The initiator tRNA binds to the start codon of the mRNA. The large ribosomal subunit then attaches. The initiator tRNA sits in the P site on the ribosome. Together, the complete ribosome, the tRNA, and the mRNA are known as the initiation complex. During elongation, the sequence of nucleotides on the mRNA molecule is read in triplets/codons. Each codon encodes a specific amino acid (which can be deduced using the genetic code chart or wheel). The correct amino acids are delivered (by the tRNA molecules) to the correct place as specified by the codons on the mRNA molecule. Amino acids are added to the growing polypeptide chain and increase the chain’s length. Remember, that the original initiator tRNA molecule begins the process of elongation in the P site of the ribosome. Another codon sits (unpaired) in the A site of the ribosome. A tRNA molecule with an anticodon that is complementary to the exposed codon enters the A site. The codon and anticodon, with the addition of energy from GTP, bind together. The ribosome now catalyzes a peptide bond to form between the amino acid carried by the tRNA in the P site and the amino acid carried by the tRNA in the A site. Next, the mRNA is pulled forward through the ribosome by one codon. The original tRNA moves into the E site of the ribosome. This tRNA (which is no longer carrying an amino acid) exits the ribosome and will eventually pick up another amino acid (the same type as before) and be reused to make another protein. The second tRNA, which now has the joined amino acids attached to it, sits in the P site. A third tRNA now moves into the A site. The anticodon on this tRNA binds to the unpaired, complementary codon on the mRNA. The ribosome catalyzes the formation of a peptide bond between the second amino acid in the polypeptide chain and the amino acid transported by the tRNA. This cycle repeats itself over an over until the polypeptide chain is complete. Page 29 Termination is the process in which translation is stopped. It happens when a stop codon (UAA, UAG, or UGA) on the mRNA enters the A site of the ribosome. The stop codon is recognized by proteins known as release factors . These proteins fit into the P site and cause the ribosome to add a water molecule to the last amino acid of the polypeptide chain. This separates/releases the newly synthesized polypeptide chain/protein from the tRNA and the newly made polypeptide is released from the tRNA and the ribosome. The small and large subunits of the ribosome separate and the tRNA is freed from the complex. All of the components will likely be reused to assemble another polypeptide. Post-Translation Modification After a polypeptide chain is manufactured during translation, it must be folded into the proper threedimensional shape before it is a functional protein. Most of the folding takes place in the endoplasmic reticulum. Some polypeptides require the assistance of proteins known as chaperonins . Mutations Mutations are changes in the nucleotide sequence of DNA or mRNA that code for a protein. Mutations are the primary source of genetic variation. Mutations can occur spontaneously due to errors during DNA replication or DNA repair mechanisms. Mutations can also be caused by external factors called mutagens. Point Mutations—Point mutations (also known as substitutions) are mutations in which a single nucleotide is changed to another, incorrect nucleotide. This changes a single codon. There are three major types of point/substitution mutations. Silent Point Mutations—In silent point mutations, no change in the amino acid sequence occurs. This is because the new, mutated codon still codes for the same amino acid as the original codon. These mutations cause no negative effects. Missense Point Mutations—Missense point mutations cause the amino acid coded for by the original DNA sequence to be replaced by a different amino acid. The results of this type of mutation can be dramatic, especially if the chemical properties of the original and new amino acid are very different. Nonsense Point Mutations—In a nonsense point mutation, a single nucleotide substitution causes a codon which normally codes for an amino acid to instead become a stop codon. This causes premature termination of translation and none of the functional protein will be synthesized. Frameshift Mutations—In a frameshift or reading frameshift mutation (also known as either deletions or insertions), nucleotides are either deleted or inserted (in numbers that are not a multiple of 3). These mutations usually introduce premature STOP codons in addition to causing the amino acid sequence of the polypeptide to completely change in areas after the mutation. These mutations usually cause more Page 30 severe effects than point mutations because they cause extreme changes in the shape of the effected protein. Gametic vs. Somatic Cell Mutations—Mutations which occur in the germ cells (cells which undergo meiosis) or the gametes are passed on to the offspring of effected individuals. These mutations can lead to evolution. Somatic cell mutations (mutations in normal body cells) are not passed on to offspring and do not contribute to evolution of the population. Gene Regulation Every cell in a multicellular organism contains the same DNA. Even though this is true, organisms contain cells that look and function very differently from each other. This is possible because of selective gene expression. This essentially means that only certain genes are expressed (used to make proteins) in certain cells. The same genes may be inactive in different cell types within the same organism. Another way of saying this is that the phenotype of a cell or organism is determined by the combination of genes that are expressed and the levels at which they are expressed. Gene regulation results in differential gene expression and influences both the products/proteins a cell produces and the cell’s function and appearance Operons Both prokaryotes and eukaryotes have groups of genes that are coordinately regulated (regulated as a group). Prokaryotic genes tend to be physically organized into related groups. These structural genes and the other DNA sequences that help to regulate their expression are known as operons . An operon might be thought of a functional unit of transcription and gene regulation. For a gene to be expressed (on) it must be transcribed and translated. In operons, groups of related genes are transcribed into a single mRNA molecule. Operons typically consist of the following parts: Page 31 Promoter—Promotors are DNA sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription. Operator—This sequence serves as the site of repressor binding. Structural genes—The DNA sequences/genes that code for the actual proteins/enzymes of the operon. Regulatory Genes—These sequences code for repressor proteins. Repressor Proteins—In certain situations, these proteins bind to the operator and prevent the transcription and expression of the structural genes. The lac operon is an example of an inducible operon . The structural genes in this operon are usually not expressed, but their expression can be turned on when certain changes in the environment take place. The trp operon is an example of a repressible operon . The structural genes in this operon are usually expressed, but their expression can be turned off when certain changes in the environment take place. Page 32 Gene Regulation in Eukaryotes Gene Regulation in Eukaryotic Cells The expression of eukaryotic genes is controlled on several different levels. These include: 1. Chromatin Structure—In Unit 5 you learned that eukaryotic DNA is associated with proteins known as histones. The histones help to organize, compact, and regulate the expression of DNA. DNA is often organized into nucleosomes (a small portion of DNA wrapped around a group of histones). The degree to which the DNA is compacted and coiled affects the accessibility of the DNA to RNA polymerase and thus affects if the DNA can be transcribed and expressed. Active/expressed genes are typically loosely compacted and coiled and are referred to as euchromatin. Inactive genes are tightly compacted/coiled and are referred to as heterochromatin . Genes can be inactivated when methyl groups (-CH3) are attached to the cytosines of a gene. The addition of these methyl tags causes the DNA to tightly wind around the histones and become inactive and not expressed. Methylation is typically permanent. Methylation deactivates specific genes in different cells types and plays an important role in cell differentiation. Another tag that affects chromatin structure is the acetyl group (--COCH3). Acetyl groups are often attached to the histone proteins. This causes the DNA that is wrapped around the histone to uncoil and thus the genes are transcribed and expressed. Acetylation (the process of adding acetyl groups) plays an important role in allowing cells to respond to changes in their internal and/or external environments. Acetylation is a reversible process. 2. Transcriptional Control— The enzyme RNA polymerase, which makes a new RNA molecule from a DNA template, must attach to the DNA of the gene. It attaches at a spot called the promoter. In humans and other eukaryotes , there is an extra step. RNA polymerase can attach to the promoter only with the help of proteins called basal ( general) transcription factors. These transcription factors help regulate transcription (and therefore gene expression) by assisting the binding of RNA Polymerase to the promoter. There are also specialized transcription factors that control the expression of specific, individual genes. For instance, a transcription factor might activate only a set of genes needed in certain neurons. Regulatory sequences of the DNA near the genes interact with transcription activators which enhance transcription or with negative regulatory molecules which inhibit gene expression by binding to the DNA and blocking transcription. In eukaryotes, groups of genes may be influenced by the same transcription factors so that the expression of the genes can be coordinated. 3. Posttranscriptional Control—Once the pre-mRNA or primary transcript is made during transcription, it next has to be processed. One of the most important parts of RNA processing is the removal of the intron sequences and the splicing together of the exon sequences. RNA can be alternatively processed and thus one gene can actually be expressed as multiple proteins. 4. Translational Control—Small segments of RNA, known as microRNAs, can bind to and disable the translation of mRNA molecules and affect the processes of development and host/pathogen interactions. 5. Posttranslational Control—The expression of a gene can also be controlled by how the protein is folded after translation. Additionally, the lifespan of a protein in a cell, is usually regulated by enzymes known as proteases. These enzymes, usually housed in the lysosomes or proteasomes, break down proteins usually after they have been tagged by a signaling protein such as ubiquitin. Page 33 Epigenetics Acetylation and Methylation are often linked to a phenomenon known as epigenetics. Epigenetic changes can affect gene expression through reversible modifications of DNA or histones. The term epigenetics refers to inheritable changes in the expression of genes that do not depend on the nucleotide sequence itself. Epigenetics is responsible for the changes that occur through the years in identical twins. Even though the twins have identical nucleotides sequences, the patterns of methylation and acetylation in their genomes become more and more different over time due to the twins’ different lifestyles and environments. Methylation and acetylation patterns can also sometimes be inherited from parents. Although in most cases, epigenetic tags are removed from the DNA during either meiosis or events right after fertilization, there are some situations in which the methylation and acetylation patterns are transmitted from parent to child. Although scientists don’t yet know how important this epigenetic form of inheritance is, it is possible that the diet, lifestyle habits (like smoking, drug use, lack of exercise), and exposure to environmental toxins of an individual’s parents may cause epigenetic changes in the DNA of both the parent and child. These changes may then be passed on to future generations without changing the actual nucleotide sequence of the DNA. Biotechnology Genetic engineering, sometimes called genetic modification, is the process of altering the DNA in an organism’s genome. This may mean changing one base pair (A-T or C-G), deleting a whole region of DNA, or introducing an additional copy of a gene. It may also mean extracting DNA from another organism’s genome and combining it with the DNA of that individual. Genetic engineering is used by scientists to enhance or modify the characteristics of an individual organism. Genetic engineering can be applied to any organism, from a bacterium to a sheep. For example, genetic engineering can be used to produce plants that have a higher nutritional value or that can tolerate exposure to herbicides. Organisms which contain such genetic modifications are referred to as transgenic organisms. Biotechnology involves the use of living systems, organisms, or parts of organisms to manipulate natural processes in order to develop products, systems, or environments to benefit people. These may be products, such as foods, pharmaceuticals, or compost; systems, such as waste management or water purification; or environments, such as hydroponics. Biotechnology also includes genetic or biomedical engineering. Recombinant DNA technology is the process of joining together DNA molecules from two different species. The recombinant DNA is then inserted into a host organism to produce new gene products that are of value to science, medicine, agriculture, and industry. Gene Therapy-- Gene therapy is an experimental technique that uses genes to treat or prevent disease. In the future, this technique may allow doctors to treat a disorder by inserting a gene into a patient's cells instead of using drugs or surgery. DNA/gene cloning is the process of propagating specific DNA fragments or making multiple, identical copies of a particular piece of DNA. In a typical DNA cloning procedure, the gene or other DNA fragment of interest (perhaps a gene for a medically important human protein) is first inserted into a circular piece of bacterial DNA called a plasmid . The insertion is done using enzymes t hat “cut Page 34 and paste” DNA, and produces a molecule of recombinant DNA, or DNA assembled out of fragments from different organisms/sources. In some cases, we need lots of DNA copies to conduct experiments or to build new plasmids. In other cases, the piece of DNA encodes a useful protein, and the bacteria are used as “factories” to make the protein. For instance, the human insulin gene is expressed in E. coli bacteria to make insulin for use by diabetics. Restriction enzymes are enzymes that were isolated from bacteria. They are used by the bacteria to defend themselves against bacteriophages. They cut DNA after specific nucleotide sequences known as restriction sites. Restriction enzymes have strange names like EcoRI and HinDIII. Polymerase chain reaction (PCR) is a laboratory technique used to quickly produce many copies (millions or billions!) of a particular region of DNA. The process of copying is often referred to as amplification of the DNA. Gel electrophoresis is a technique used to separate DNA fragments, RNA fragments, or proteins based on their size and charge. Electrophoresis involves running a current through a gel containing the molecules of interest. Based on their size and charge, the molecules will travel through the gel in different directions or at different speeds, allowing them to be separated from one another. Meiosis Meiosis is a specialized type of nuclear division (in sexually reproducing diploid organisms) that reduces the chromosome number by half, creating four haploid cells, each genetically distinct from the parent cell that gave rise to them. The haploid cells, after undergoing a period of maturation, become gametes. The two main roles of meiosis are to create haploid gametes and to increase genetic diversity/variation within the gametes. In multicellular animals, meiosis occurs only in the sex organs/gonads . The only cells capable of doing meiosis are specialized, diploid germ cells found in the gonads. Before meiosis begins, the DNA is replicated during the S phase of interphase. Meiosis involves two rounds of a sequential series of steps. These rounds are referred to as Meiosis I and Meiosis II. Stages of Meiosis Meiosis I Prophase I Meiosis begins with Prophase I. During Prophase I, the cell’s chromatin coils and condenses to form bivalent chromosomes. The nucleolus disappears. The centrosomes form the spindle fibers and the nuclear envelope disintegrates. Chromosomes of the same type/number (homologous chromosomes) pair up and join together during the process of synapsis to form tetrads (groups of 4 homologous chromatids). The members of each pair contain the same genes in the same order on the chromosome, but may contain different alleles or versions of the genes. After synapsis, the homologous chromosomes undergo the process of crossing over in which they physically exchange segments. This is an example of genetic recombination. The process is an important source of genetic variation/diversity in the gametes that result at the end of meiosis. Metaphase I During Metaphase I, the two members of each homologous pair of bivalent chromosomes align on each side of the metaphase plate (middle of the cell). Each chromosome also attaches to the Page 35 spindle fibers at a point on the centromere known as the kinetochore. During the process of lining up, the paternal and maternal members of each homologous pair randomly line up across from each other on either side of the metaphase plate. The pattern in which each pair arranges itself is completely independent of the other homologous pairs. This process of random alignment, known as independent assortment, can create up to 223 (8,388,608) possible alignments in human germ cells. Since the two rows of chromosomes will eventually end up in different gametes, the process of independent assortment gives each human the ability to create over 8 million genetically distinct types of gametes. Independent assortment increases genetic variation by allowing daughter cells to each randomly receive a different proportion of paternal and maternal chromosomes. Anaphase I During Anaphase I, one member of each homologous pair of chromosomes is pulled toward each pole of the cell by the microtubules of the spindle apparatus. This process is called Segregation. The individual chromatids of each bivalent chromosome are not separated as they are during the anaphase stage of mitosis. Anaphase I separates the members of the homologous pairs from each other. This process of separation ensures that each gamete receives a haploid (1N) set of chromosomes comprised of a mixture of chromosomes from both parents. Telophase I During Telophase I, the homologous chromosome pairs reach the poles of the cell, the spindle fibers disappear, nuclear envelopes form around each set of chromosomes, and cytokinesis follows to produce two cells. The two new cells are haploid and have half the number of chromosomes as the original germ cell. It is important to note that we count chromosomes by counting the number of centromeres present. Even though the chromosomes at the end of telophase I are bivalent, each bivalent chromosome has one centromere and only counts as a single chromosome. Meiosis I is often referred to as reductive division, because it halves the number of chromosomes found in the two cells which result from the process. To summarize, Meiosis I begins with 1 diploid germ cell and ends with 2 haploid cells which both possess bivalent chromosomes. Interkinesis Interkinesis is a short interphase-like period that occurs between Meiosis 1 and Meiosis 2. No DNA replication occurs during interkinesis, however it does occur during the interphase I stage that occurs before meiosis begins. During interkinesis, the single spindle of the first meiotic division disassembles and the microtubules reassemble into two new spindles for the second meiotic division. Meiosis 2 Prophase II The nuclear envelopes and the nucleoli of each of the cells produced during Meiosis 1 disintegrate during prophase II. The chromosomes condense and the centrosomes replicate and move towards opposite poles. Spindle fibers grow outward from the centrosomes. Prophase II is almost identical to the Prophase stage of mitosis. No synapsis or crossing over occur during this stage. Metaphase II The chromosomes in both cells become arranged on the metaphase plate, much as the chromosomes do in mitosis, and are attached to the now fully formed spindle. Page 36 Anaphase II During Anaphase II, the centromeres of each chromosome (in both cells) separate and the sister chromatids—now called individual chromosomes—move toward the opposite poles of the cells. Anaphase II is the process in which sister chromatids are separated from each other. Telophase II During Telophase II, a nuclear envelope forms around each set of chromosomes and cytokinesis occurs, producing four genetically different daughter cells, each with a haploid set of chromosomes. Meiosis Summary Meiosis is the first step in the process of gametogenesis or gamete creation. Meiosis happens only in the gonads and creates four haploid gametes (with single chromatid chromosomes) from each diploid germ cell that enters the process. Sexual reproduction in eukaryotes involving gamete formation/meiosis (including crossing over, the random/independent assortment of chromosomes during meiosis, and the subsequent fertilization of gametes) serves to increase the genetic variation within a population. Nondisjunction Nondisjunction is the failure of homologous chromosomes or sister chromatids to separate properly during cell division. There are three forms of nondisjunction: failure of a pair of homologous chromosomes Page 37 to separate in meiosis I, failure of sister chromatids to separate during meiosis II, and failure of sister chromatids to separate during mitosis. Nondisjunction results in daughter cells with abnormal chromosome numbers, a condition called aneuploidy. When nondisjunction occurs during meiosis, it can result in gametes with the wrong number of chromosomes. If fertilized, the most common result is miscarriage. Most human embryos cannot survive with an abnormal chromosome number. Meiosis and Mitosis Compared and Contrasted Mitosis and meiosis are both forms of nuclear division. They are similar in the way the chromosomes segregate but differ in the number of cells produced and the genetic contents of the resulting cells. The table below summarizes the key similarities and differences of the two processes. Mendelian Inheritance Mendel’s main conclusions included: 1. Each trait is controlled by a single pair of alleles. Mendel called them factors. 2. Some alleles are dominant and can mask the appearance of recessive alleles ( Law of Dominance) 3. The alleles from a pair separate (during meiosis) and only one member of each pair is transmitted to an offspring from each parent (Law of Segregation ). Realize that Mendel did not know about meiosis, but essentially predicted its existence. 4. The maternal and paternal alleles/factors from each pair assort independently from the alleles in the other pairs. All possible combinations of alleles/factors occur in the gametes. We know today that independent assortment occurs during Metaphase I of Meiosis. (Law of Independent Assortment). We know today that Mendel’s Laws of Segregation and Independent Assortment apply only to genes that are located on different chromosomes. Mendel was unaware of the existence of chromosomes and linked genes. Page 38 Punnett Square--This is a chart which shows the possible genotypic outcomes for a mating cross based on the parents’ genotypes. Monohybrid Cross Monohybrid Cross—This is a cross in which only one trait is analyzed. To complete the cross, you must first determine the possible gamete combinations of the parents. Remember that gametes are haploid. They should only contain one allele for each trait. For example: If we crossed two purple flowered plants, with the genotype Bb, the possible gametes for each plant are “B” or “b”. The gametes for one parent are written along the top of the Punnett square, one haploid gamete per column. The gametes of the other parent are written along the left hand side of the Punnett square, one haploid gamete per row. The boxes inside the square are then filled in using the column and row headers as shown below. Product Rule The cross illustrated above predicts a phenotypic ratio of 3 purple: 1 white and a genotypic ratio of 1 BB: 2Bb:1 bb The rules of probability can be applied to analyze the passage of single-gene traits from parent to offspring. The two rules commonly used in an AP Biology class are listed below: If A and B are mutually exclusive (separate, unconnected events) then: P(A or B)=P(A) + P (B) The rule listed above is used to calculate the probability (P) of either event A or event B happening. The probability that either event will occur is simply the sum of each of the individual events. Product Rule P (A and B)=P(A) X P(B) The product rule is used to calculate the probability (P) that multiple independent events will each occur. The probability that both event A and event B will occur is the product of the individual probabilities. If you were asked to determine the probability that the cross above would produce a plant with white flowers, your answer would be ¼ or 25% (from the Punnett square). If you were asked to determine the probability that the cross would produce a plant with purple flowers, your answer would be ¾ or 75%. If you were asked to determine the probability that the above cross would produce either a homozygous purple (PP) or a homozygous white (pp) plant, you would: First use the Punnett Square to determine that Page 39 the probability of getting a homozygous purple plant is ¼ and the probability of getting a homozygous white plant is also ¼. Then use: P(A or B)= ¼ + ¼= ½ Suppose you were asked to determine the probability that the cross produced two purple-flowered plants in a row? To calculate this probability, you would need to use the product rule. The product rule states that in order to determine the probability of two independent events occurring together, you must multiply the individual probabilities of each event. In this example, we should multiple ¾ X ¾ to get a probability of 9/16 or 56.25%. Dihybrid Cross Dihybrid Cross–A dihybrid cross is a cross in which the inheritance of two traits is analyzed at the same time. For example: Suppose that in pea plants “R” is the allele for round seeds, “r” is the allele for wrinkled seeds, “Y” is the allele for yellow seeds, and “y” is the allele for green seeds. The Punnett Square below illustrates the cross between two plants that are heterozygous (RrYy X RrYy) for both traits, a true dihybrid cross. To construct the cross, you must first determine the possible gametes that each parent can create. Each gamete should contain only one allele from each gene. In this case, each allele contains only one R (either upper or lowercase) and one Y (either upper or lowercase). All possible combinations of the parental alleles are possible. This means that each of the two parents can create the following gamete combinations: RY; Ry; rY; and ry. To determine the possible number of unique gamete combinations, analyze each gene pair. For the R pair, each parent has a single R and a single r, 2 different alleles. For the Y pair, each parent also has a single Y and a single y, 2 different alleles. To calculate the number of possible unique gametes, multiply the number of unique alleles in each gene pair together. In this case that would mean 2 (from the R pair) X 2 (from the Y pair) =4 unique gametes per parent. Let’s say that one of the original parents had the following genotype: rrYy To calculate the number of possible alleles from this parent, multiple 1 (from the unique alleles in the r pair) X 2 (from the unique alleles in the Y pair) to get 2 possible unique gamete combinations . In this case those would be rY and ry. Once the possible gamete combinations are determined, the gametes for one parent are written along the top of the Punnett square, one haploid gamete per column. The gametes of the other parent are written along the left- hand side of the Punnett square, one haploid gamete per row. The boxes inside the square are then filled in using the column and row headers as shown below. Page 40 In a true dihybrid cross (one in which both parents are heterozygous for both traits), the phenotypic ratio will always be 9:3:3:1 as shown in the Punnett square above. Trihybrid or Larger Cross It is possible to construct Punnett Squares for trihybrid crosses (crosses in which the inheritance of three traits are analyzed at the same time). These squares can be really large (up to 64 squares). You will typically not be asked to draw a trihybrid Punnett Square on the AP exam. You might, however, be asked to answer questions like the following: How many different possible gametes can an individual with the following genotype produce Aa Bb Dd Ee? To answer this question, use the same approach as that described above. Multiple the number of unique alleles from each pair together. In this case. 2 unique alleles from the A pair X 2 unique alleles from the B pair X 2 unique alleles from the D pair X 2 unique alleles from the E pair to yield 16 total unique allele combinations/gamete types. If the genotype of the parent had instead been AA Bb cc, the calculation would have been: 1 unique allele from the A pair X 2 unique alleles from the B pair X 1 unique allele from the c pair to yield only two possible gamete combinations. In this case, those combinations would be ABc and Abc. What is the probability that the cross between the following genotypes: Aa BB Dd Ee X Aa Bb Dd ee will produce an offspring with the genotype Aa BB dd Ee? To answer this question, you could draw a huge Punnett Square, but the easiest and fastest approach is to use the product rule. First, analyze each gene pair separately. Think of doing four separate Punnett squares. What is the probability that AA (from parent 1) and Aa (from parent 2) will yield (Aa) in the offspring? The answer is ½. Page 41 What is the probability that BB (from parent 1) and Bb (from parent 2) will yield BB in the offspring? Again, the answer is ½. What is the probability that Dd (from parent 1) and Dd (from parent 2) will yield dd in the offspring? This time, the answer is ¼. What is the probability that Ee (from parent 1) and ee (from parent 2) will yield Ee in the offspring? This time the answer is ½. To determine the overall probability that the cross between parents Aa BB Dd Ee X Aa Bb Dd ee will produce an offspring with the genotype Aa BB dd Ee, multiply the probabilities from each gene pair (in bold above). In this case, the calculation is ½ (from the A pair) X ½ (from the B pair) X ¼ (from the C pair) X ½ (from the D pair) to yield an overall probability of 1/32. Linked Genes and Dihybrid Crosses Linked genes occur on the same chromosome, and therefore, tend to be inherited together (i.e., do not segregate independently). When two heterozygotes are mated in a normal dihybrid cross with independent assortment of alleles, the expected ratio in the offspring is 9:3:3:1. However, as shown in the figure below, in cases of dihybrid crosses involving linkage, the ratio of the offspring produced is 3:1 and only the parental types, with no recombinants, are expected. Page 42 The table below includes the actual observed results of the dihybrid cross involving the two heterozygotes described above. Even though offspring with long wings/white eyes and offspring with short wings/red eyes weren’t expected, some were produced. This often occurs in crosses involving linked genes because of the genetic recombination that occurs during crossing over. Non-Mendelian Inheritance Although Mendel discovered some of the most basic laws of inheritance, scientists have discovered many exceptions to the so-called laws of Mendelian inheritance. The processes/conditions described below are all examples on non-mendelian inheritance patterns. In these situations, the patterns of inheritance do not follow the ratios predicted by Mendel’s laws. Quantitative analysis of the results of such crosses reveals that the observed phenotypic ratios statistically differ from the ratios predicted by Mendel’s laws. 1. Incomplete Dominance is a form of intermediate inheritance in which one allele for a specific trait is not completely expressed over its paired allele. This results in a third phenotype in which the expressed physical trait is a combination or blending of the phenotypes of both alleles. In some plants, there are alleles for red flowers (R) and for white flowers (r). Heterozygous plants (Rr) end up with pink flowers (a blend between red and white). 2. Codominance—This is a condition in which both alleles in a pair are expressed at the same time. They are both equally present in the phenotype (not blended). An example of codominance is human blood type. There are alleles for Type A blood (IA), Type B (IB), and type O (i) blood. The alleles for type A and B code for different cell surface proteins that occur on the surface of the red blood cells (RBCs). Individuals with two O alleles (ii) lack these proteins. Individuals with either I AIA or IAi possess the type A proteins on their RBCs. Individuals with either IBIB or IBi possess the type B proteins on their RBCs. Individuals with the I AIB genotype possess both the A and B proteins on the surface of their RBCs. 3. Multiple Alleles—This is when three or more alternative forms of a gene (alleles) can occupy the same locus (location) . However, only two of the alleles can be present in a single organism. For example, the ABO system of blood types is controlled by three alleles (IA, IB, i), only two of which are present in an individual. Page 43 4. Pleiotropy is a condition in which one gene affects multiple (seemingly unrelated) characteristics. Sickle Cell Disease is a great example. The gene AFFECTS the shape of one of the polypeptide chains that make up hemoglobin (the molecule that allows red blood cells to transport oxygen). The change in the polypeptide’s shape also causes the red blood cells to change shape (from round to sickle shaped). This impedes the flow of blood and leads to multiple symptoms all over the body such as anemia, physical weakness, impaired mental function, lowered disease resistance, and paralysis. Individuals who are heterozygous for the sickle cell mutation also possess resistance to the protozoan that causes malaria. This heterozygote advantage explains why the normally harmful mutation is so common in human populations where malaria has consistently been a problem. Epistasis is a condition in which a gene at one locus affects a gene at a second locus. Albinism in humans is a good example of epistasis. Albinism arises when individuals inherit two defective copies of the allele that normally codes for the enzyme necessary for melanin (pigment) synthesis. Even though alleles at other loci may code for brown eyes, skin, or hair, these individuals are albinos because they lack the ability to produce the pigment (melanin). 6. Polygenic Inheritance occurs when a trait is governed by two or more sets of alleles. Examples of human traits that are polygenic include height, skin color, and the prevalence of diabetes. Each individual possesses a copy of all the allelic pairs. These may be located on different chromosomes. Each dominant allele has a quantitative effect on the phenotype and the effects are additive. The population typically exhibits continuous phenotypic variations. If the frequency of the different phenotypes were graphed, the graph would look like a bell curve. Human skin color is thought to be controlled by 3 pairs of alleles (A, B, C). A person with the alleles AABBCC is very dark skinned, a person with aabbcc alleles is very light skinned, and a person with AaBbCc (or any combo) has an intermediate skin color. 7. Multifactorial traits are those controlled by multiple genes that are also affected by physiological and environmental influences. Hypertension, diabetes, schizophrenia, and allergic conditions are probably all multifactorial traits. Such traits do not segregate in the predicted Mendelian patterns. 5. Modes of Inheritance/Pedigree Charts Mode of Inheritance--The manner in which a genetic trait or disorder is passed from one generation to the next. Autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive, Y-linked, and mitochondrial inheritance are examples. The diagram included below illustrates the symbols commonly used in pedigree charts. Page 44 Modes of Inheritance—Autosomal Dominant The genes for autosomal dominant traits are located on one of the 44 autosomes in a human cell. The genes are dominant, which indicates that individuals with only one copy of the gene are affected. Characteristics of autosomal dominant traits include: • Males and females are equally likely to have the trait. • Traits do not skip generations because there are no carriers for the traits. • The trait is present whenever a single copy of the corresponding allele is present. • There is male-to-male transmission. This means that fathers can pass to trait to their sons. Some examples of human genetic conditions that are transmitted via the autosomal dominant mode of inheritance include: Huntington’s Disease, Achondroplasia, Polycystic Kidney Disease, and Familial Hypercholesterolemia. The pedigree chart included below depicts the transmission of an autosomal dominant trait. Modes of Inheritance—Autosomal Recessive The genes for autosomal recessive traits are located on one of the 44 autosomes in a human cell. The genes are recessive, which indicates that individuals must possess two copies of the recessive allele in order to exhibit the trait. Characteristics of autosomal recessive traits include: • • • Males and females are equally likely to have the trait. Traits often skip generations (due to the possibility of carriers). Only homozygous recessive individuals have the trait. Page 45 • • • Traits may appear in siblings without appearing in their parents. If a parent has the trait, those offspring who do not have it are heterozygous carriers of the trait. Some examples of human genetic conditions that are transmitted via the autosomal recessive mode of inheritance include: Tay Sachs Disease, PKU, and Cystic Fibrosis. The pedigree chart included below depicts the transmission of an autosomal recessive trait. Modes of Inheritance—X-linked Dominant Some traits are determined by genes located on sex chromosomes (either X or Y). Such traits are known as sex-linked traits. The genes for X-linked dominant traits(a type of sex-linked trait) are located on the X chromosome in a human cell. The alleles are dominant, so individuals with only one copy of the allele exhibit the trait. X-linked traits (whether dominant or recessive) are always expressed in males (if the male’s X carries the allele) because males possess only one X chromosome. Characteristics of X-linked dominant traits include: • The trait is present whenever the corresponding gene is present. • There is no male-to-male transmission. Fathers cannot pass the trait to their sons. • A female who has the trait may or may not pass the allele for the trait to her son or daughter. • All of the daughters of a male with the trait will inherit the trait. Some examples of human genetic conditions that are transmitted via the X-linked dominant mode of inheritance include: hypertrichosis, porphyria, and Rett syndrome. The pedigree chart included below depicts the transmission of an X-linked dominant trait. Page 46 Modes of Inheritance—X-linked Recessive The alleles for X-linked recessive traits are located on the X chromosome in a human cell. The alleles are recessive, so for a female to exhibit the trait she must possess the allele on both of her X chromosomes. Since a male has only one X chromosome, he is affected if his X chromosome carries the allele. Characteristics of X-linked recessive traits include: • • • • • These traits are far more common in males than in females. Traits may skip generations. All daughters of a male who has the trait are either affected or are heterozygous carriers. The son of a female carrier has a 50 percent chance of having the trait. Mothers of males who have the trait are either heterozygous carriers or homozygous and express the trait. There is no male-to-male transmission. Fathers cannot pass the trait to their children. • • Some examples of human genetic conditions that are transmitted via the X-linked recessive mode of inheritance include: hemophilia, red/green colorblindness, Duchenne Muscular Dystrophy, and Lesch-Nyhan syndrome. The pedigree chart included below depicts the transmission of an X-linked recessive trait. Page 47 Modes of Inheritance—Y-linked The alleles for Y-linked traits are located on the Y chromosome in a human cell. Since males possess only one Y chromosome, the traits aren’t usually referred to as dominant or recessive. A man who possesses a Y-linked allele will exhibit the trait it controls. Since females don’t possess a Y chromosome, they are not affected by Y-linked traits. Characteristics of Y-linked traits include: • • Only males are affected. • All sons of an affected male will also be affected. Females can’t possess or pass on the trait. Some forms of Retinitis pigmentosum (a form of progressive blindness) are transmitted via the Ylinked mode of inheritance The pedigree chart included below depicts the transmission of an Y-linked trait. Modes of Inheritance—Mitochondrial Some traits result from non-nuclear inheritance. The alleles for mitochondrial traits are located on the small circular chromosome found in the mitochondria. Since children (in animals) of both sexes inherit their organelles (including the mitochondria) from the egg of the mother, mitochondrial traits are always transmitted from mother to child. Since the mitochondria only have one chromosome each, there are no dominant or recessive mitochondrial traits. Individuals who possess a single copy of a mitochondrial allele express the trait. Characteristics of mitochondrial traits include: • • All of the children of an affected female will express the trait. These traits are always maternally inherited. Males can express the trait but are unable to pass it on to their offspring. The human mitochondrial chromosome is a very small piece of DNA and codes for only 13 proteins which are part of the electron transport chain. Disorders related to mutations in the mitochondrial chrom osome usually affect one’s ability to make ATP. In plants, both mitochondria and chloroplasts are transmitted in the ovule and not in the pollen. Since both organelles contain their own single, circular chromosome, traits determined by the Page 48 genes on the mitochondrial and chloroplast chromosomes are always maternally inherited. Because chloroplasts and mitochondria are randomly assorted to gametes and daughter cells, traits determined by chloroplast and mitochondrial DNA do not follow simple Mendelian rules. The pedigree chart included below depicts the transmission of a mitochondrial trait.