LO 4.1 : The student is able to explain the connection between the sequence and the subcomponents of a biological

1. LO 4.1: The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. SP 7.1: The student can connect phenomena and models across spatial and temporal scales. Explanation: In proteins, for example, the specific order of amino acids in a polypeptide interacts with the environment to determine the overall shape of the protein, which also involves the secondary, tertiary, and quaternary structure and, thus, its function. The R group of each amino acid in the polypeptide can be categorized by its chemical properties (hydrophilic, hydrophobic, ionic, etc.) and the interactions of these R groups determine structure and function of that region of the protein. Enzymes are examples of proteins whose functions rely on their structure. This relationship between the sequence of the subcomponents and the properties of the molecule is also evident in nucleic acids, lipids, and carbohydrates. M.C. Question: Which of the following statements concerning unsaturated fats is true? A) They are more common in animals than in plants. B) They have only single bonds in the carbon chains of their fatty acid tails. C) They’re generally a solid at room temperature b/c their molecules are closely packed together. D) They’re generally a liquid at room temperature b/c their molecules have kinks caused by double bonds. Learning Log/FRQ-style Question: Suppose you have placed a protein in an aqueous environment. Where would you expect to find a region that is rich in polar amino acids? Why? A region rich in non-polar amino acids? Why? Draw and label this hypothetical protein.

2. L.O. 4.3: The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. S.P. 6.1: The student can justify claims with evidence. Explanation: Changes in the subcomponents of a biological polymer often affect the functionality of the molecule. Nucleic acids are comprised of phosphate groups, ribose sugars, and nitrogen bases. The sequence of the nitrogen bases within DNA and RNA is essential to the function of the molecule, as slight changes in sequence can lead to different proteins being coded for from the instructions within the nucleic acid. Due to slight structural differences between subcomponents of DNA and RNA (deoxyribose sugar vs. ribose sugar, etc.), DNA and RNA have different functions. Also, the order of amino acids within proteins is essential to the secondary, tertiary, and quaternary structure of the protein, and thus, its function. Protein function (i.e. enzymes) is very closely tied to shape, and shape can be a direct result of the interactions and bonds between and among amino acids. A mutation in a single amino acid within the hemoglobin protein can lead to structural defects within the red blood cell that leads to sickle cell disease. Also, variations within the monomers and bonding patterns between monomers in carbohydrates can account for structural and functional differences between starch and cellulose, and thus impact whether these molecules can be digested by humans, for example. M.C. Question: A protein undergoes a change in which an amino acid containing a sulfhydryl R-group is replaced with an amino acid containing a cationic R-group. Which of the following will likely be a result of this change? The secondary structure of the protein will change from a pleated sheet to a helix. The tertiary structure of the protein will be altered as a result of altered disulfide bridge interactions. The protein will denature at room temperature. The protein’s properties will not change. Both B and C are true. FRQ: A) Describe the structural and functional differences between DNA and RNA. B) List and describe three specific biological examples of protein structure relating to function.

3. LO 4.4 The student is able to make a prediction about the interactions of sub cellular organelles.SP 6.4 The student can make claims and predictions about natural phenomena based on scientific theories. Explanation: The various organelles work together in order to perform many functions within the cell. The nucleus works closely with the nucleolus to provide DNA, and the nucleolus then utilizes that information and processes it to create ribosomes. The ribosomes, in turn, work to produce proteins on the rough ER, and then are shipped to the cell membrane. In order to function and regulate the transport of substances, the cell membrane uses the proteins which keep a stable environment within the cells even as the cell changes on the outside.  Simultaneously, the chloroplast receives sunlight and produces sugar, which the mitochondria then uses as energy to power the cell. Also, the smooth ER sends lipids to the Golgi apparatus which then distributes the lipids throughout the cell. These lipids are then used by the cell membrane to help the lipid bilayer function and allow materials to pass through, which aids in keeping the environment inside the cell stable. M.C. Question: Which of the following sub cellular interactions are performed with the Golgi apparatus? I. Vesicles form and the leave Golgi, carrying specific proteins to other locations or to the plasma membrane for secretion II.  Vesicles transport specific proteins backward to newer Golgi cisternae III.  Vesicles transport certain proteins back to the ER A.      I only B.      I & II only C.      I & III only D.      II &III only E.       I, II, & II Learning Log/FRQ-style Question; Explain the functions of the “cis” Golgi of verses the “trans” Golgi. Describe their interaction with another sub cellular organelle and explain how this effects where they are located. In what direction do they move in?

4. LO 4.5: The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions. SP 6.2: The student can construct explanations of phenomena based on evidence produced through scientific practices. Explanation: The endomembrane system is composed of a collection of membranes in a eukaryotic cell that are related through either direct contact or by transfer vesicles. In the endomembrane system, the nuclear envelope, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, vacuoles, and the plasma membrane interact in order to carry out a variety of tasks in the cell, including the synthesis and transport of proteins and the metabolism and movement of lipids. The nuclear envelope is connected to the rough ER, which is also continuous with the smooth ER. The smooth ER has a variety of functions in metabolic processes, such as the synthesis of lipids, the metabolism of carbohydrates, the storing of Calcium ions, and the detoxification of drugs. The rough ER, which is studded with ribosomes, synthesizes secreted proteins, membrane components, and glycoproteins, which are then transported via transport vesicles to either the Golgi apparatus for sorting or to other destinations, such as the plasma membrane for secretion. The Golgi apparatus is the center of manufacturing, sorting, and shipping for a cell. The Golgi apparatus sorts, packs, and ships numerous materials such as glycoproteins and membrane phospholipids, directs proteins to other organelles, and sorts materials for secretion outside of the cell. In addition to pinching off transport vesicles for materials leaving the Golgi, the Golgi apparatus also pinches off other vesicles that give rise to lysosomes and vacuoles. Food vacuoles both store food for the cell and carry food to lysosomes for digestion. Lysosomes contain enzymes that undergo hydrolysis in order to digest and break down macromolecules into monomers for cellular recycling. M.C. Question: All of the following are true about the Golgi apparatus except… A) The Golgi apparatus consists of stacks of flattened sacs, called cisternae, which are physically connected. B) The two poles of a Golgi stack are referred to as the cis face and the trans face, which act, respectively, as the receiving and shipping departments of the Golgi. C) In addition to sorting and shipping materials, the Golgi apparatus also manufactures certain macromolecules by itself. D) Products from the ER are usually modified during their transition from the cis region to the trans region of the Golgi apparatus. Learning Log/FRQ-style Question: Describe, using details, the process by which a cell synthesizes, modifies, transports, and then secretes the glycoproteins responsible for determining a person’s blood type. Be sure to include the roles of the endoplasmic reticulum, Golgi apparatus, vesicles, and the plasma membrane in your response. Pay particular attention to how these subcellular structures interact in order for a cell to successfully complete this process.

5. LO 4.6: The student is able to use representations and models to analyze situations qualitatively to describe how interactions of subcellular structures, which possess specialized functions, provide essential functions. SP 1.4: The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively Explanation: Subcellular structures, otherwise known as organelles, are one of several formed bodies with specialized functions that are suspended in the cytoplasm of eukaryotic cells. Prokaryotic cells do not have organelles. All of the organelles in eukaryotic cells except the ribosome are bounded by the membrane. The nucleus and mitochondria are bounded by two membranes. The mitochondria specializes in energy capture and transformation. The mitochondria’s inner folds are known as cristae, which contain enzymes important to ATP production. Chlorophyll is responsible for trapping light molecules in photosynthesis in chloroplasts, an organelle found in algae and higher plants. M.C Questions: Which is mismatched? • Smooth endoplasmic reticulum: detoxification • Centrioles: cell division • Nucleolus: ribosome synthesis • Plasma membrane: transport • Lysosome: lipid synthesis FRQ Question: Describe the structure and function of both the chloroplast and mitochondria. Then describe the probable origin of both these organelles by applying the theory of endosymbiosis.

6. 2 Posterior 1 Anterior Signal protein 4 3 Receptor EMBRYO 3 4 Signal Anterior daughter cell of 3 Posterior daughter cell of 3 Will go on to form adult intestine Will go on to form muscle and gonads Induction of the intestinal precursor cell at the four-cell stage. LO 4.7: The student is able to refine representations to illustrate how interactions between external stimuli and gene expression result in specialization of cells, tissues and organs. [See SP 1.3] SP 1.3: The student can refine representations and models of natural or man-made phenomena and systems in the domain. Explanation: Specialization of cells begins during embryonic development. Position of the cells on either the anterior or posterior sides of the embryo contributes in determining cell type. Other internal factors as well as external factors influence the determination of a cell, tissue, or organ. Cytoplasmic determinants can be found in different amounts within dividing cells, affecting the fate of a cell. External stimuli such as temperature, nutrient levels, or signals can also cause cell differentiation. Adjacent cells send signals that attach to the signal receptors of a cell, activating a regulatory gene. This gene then spurs the creation of proteins that activate other genes leading to the creation of proteins that determine the function, structure, or behavior of the cell. As these specialized cells fuse together, they form tissues which in turn fuse together to form organs that perform a specific function in the body. The creation of muscle cells from the activation of the myoD gene illustrates the specialization of cells due to signaling and gene expression. Although all DNA in cells is identical, different genes are expressed in each cell, creating specialization. M.C Question: Which of the following is the correct process of a cell becoming differentiated? A) Surrounding cells send signals; cell receives signal; creation of proteins; genes activated B) Regulatory gene activated; created proteins activate other genes; function/structural determining proteins created; cell sends signal C) Surrounding cells send signals; cell receives signal; point of no return; regulatory gene activated; function/ structural determining proteins created D) Surrounding cells send signals; cell receives signal; regulatory gene activated; proteins created; point of no return; function/structural determining proteins created     FRQ: External stimuli and gene expression work together to create specialized cells, tissues, and organs. Describe how external stimuli and gene expression contribute to the creation of muscle cells and the vulva.

7. M.C. Question: A sensory neuron of the peripheral nervous system take nerve impulses from sensory receptors to the ______ .A) motor neurons B) interneurons C) autonomic nervous system D) central nervous system Learning Log/FRQ-style Question: Communication occurs among the cells in a multicellular organism. Choose THREE of the following examples of cell-to-cell communication, and for each example, describe the communication that occurs and the types of responses that result from this communication.• Communication between two plant cells• Communication between two immune-system cells• Communication either between a neuron and another neuron, or between a neuron and a muscle cell• Communication between a specific endocrine-gland cell and its target cell LO 4.8: The student is able to evaluate scientific questions concerning organisms that exhibit complex properties due to the interaction of their constituent parts. SP 3.3: The student can evaluate scientific questions. Explanation: The Nervous system, for example, is composed of all nerve tissues in the body. The functions of the nerve tissue are to receive stimuli, transmit stimuli to nervous centers and initiate a response. Within the nervous system are many other systems that rely on each other to obtain this response. One of those systems is the central nervous system, which consist of the brain and spinal cord, and is the union of all nerve impulses. Then there is the peripheral nervous system, which connects all parts of the body to the central nervous. The peripheral system can be divided into the somatic nervous system and the autonomic nervous system. These systems go more in depth on the relay mechanisms that are involved in transmitting information to the central nervous system to acquire a response. A sensory stimuli such as a crash sound can be converted into a signal and sent to the brain or spinal cord. The generated response is a signal transmitted to organs that convert the signal into a form of action such as movement or a release of hormones by activating other parts of the body

8. LO 4.9 The student is able to predict the effects of a change in a component(s) of a biological system on the functionality of an organism(s). [See SP 6.4] SP 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Explanation: If one component of a biological system is changed or tampered with then the entire system will not function properly. Each part of a biological system is a complex building block and without each component working properly then the over all function of the system will be compromised. For example, if the root system of a plant has a deformity where it cannot take in oxygen or expel carbon dioxide then the respiration system of the plant will not function. This will lead to the plant’s death due to the lack of proper respiration from the mutated roots. M.C. Question: If a toxin was injected into a plant’s phloem which inhibited the activity of H+ pumps, what would result? A) A decreased water potential in the phloem B) An increase in photosynthesis C) A large amount of turgid cells in the plant D) Sucrose excretion from the plant’s leaves FRQ: Suppose the guard cells around the stomata of a pea plant have been killed due to a new pesticide. If the guard cells are no longer functioning, how would transpiration be altered? What would happen to the plant in a time of drought? Explain.

9. LO 4.10: The student is able to refine representations and models to illustrate bio complexity due to interactions of the constituent parts. SP 1.3: The student can refine representations and models of natural or man-made phenomena and systems in the domain. Explanation: In many important bodily functions many constituent parts work together. For example, in digestion both the small intestines and the stomach work together to break down food and absorb nutrients. In the stomach the food is churned and bathed in a strong gastric acid. At this point the food is partly digested. Then the food travels to the small intestines where bile, pancreatic enzymes, and other enzymes help to break down the food. Finally it travels to the large intestines when water and electrolytes are removed from the food. Then microbes and bacteria help digest the remaining food. Another example would include the immune system and how it uses a combination of many different chemicals and cells to fight of pathogens. All the cells have different jobs but a common goal of keeping the body healthy. The inflammatory response starts when MAST cells release histamines and prostaglandins which causes the capillaries to dilate and become more permeable. Then macrophages, RBCs, and clotting factors are delivered to the sit in order to fight off bacteria and clot the wound. Next the temperature of the area increases which slows bacterial growth and speeds up tissue repair. MC: If Henry got infected with the chicken pox virus in which order would his body respond to fight off pathogens and create future immunity? • Leukocytes kill some of the pathogens, macrophages release cytokines to raise body temperature, helper T cells recognize antigens on the surface of an APC, helper T cells release cyto- kines to make more helper T cells, numerous helper T cells release more cytokines to active cytotoxic T cells and B cells, memory T cells are produced for future immunity. • Helper T cells recognize antigens on the surface of an APC, helper T cells release cytokines to make more helper T cells, memory T cells are produced for future immunity. C. Leukocytes kill some of the pathogens, macrophages release cytokines to raise body temperature, at this point you contain the cells to have future immunity • Mast cells release histamines, capillaries dilate, macrophages come to the area, temperature rises • A B cell recognizes an antigen, that specific B cell is clones, plasma cells are released to neutralize antigen, macrophages engulf tagged antigens During blood transfusions the proper type of blood must be used for the recipient’s body to accept to blood. What causes unmatched blood to be rejected? Relate this to organ transplants and what causes the body to attack the transplanted organ if it isn’t a match.

10. LO 4.11: The student is able to justify the selection of the kind of data needed to answer scientific questions about the interaction of populations with communities.SP 1.4: The student can reexpress key elements of natural phenomena across multiplerepresentations in the domain.SP 4.1: The student can justify the selection of the kind of data needed to answer a particular scientific question.Explanation: : Individual population stability is required to maintain homeostasis within a community. In the food chain, with each level you go up, from producers to primary consumers to secondary consumers, the total amount of available energy decreases by a factor of 10. As a result of this, there are many more producers in the community than there are primary consumers, more primary consumers than secondary consumers, and so on. Also, relationships between populations have far-reaching effects on a community. Mycorrhizae and its mutual relationship with nearly all plants increases the efficiency of plants, allowing more to grow and subsequently increasing the potential for life within communities. An exotic species introduced into a community will prey on the native species while introducing new disease into the community. Data can be used to answer questions about the interaction of populations with communities. If the total biomass of secondary consumers within a community drops significantly, one can infer that the total biomass of primary consumers will drastically increase due to lack of predatory pressure. On the other hand, a decrease in the total biomass of tertiary consumers is expected because of the decrease in the amount of their prey available.M.C. Question: Which of these is true about exotic species? a. They increase biodiversity in the community by creating new divergent species. b. They are usually killed by the native species before any damage is done. c. They decrease biodiversity by introducing disease to the native community. d. Only animals can be exotic species, not plants.Learning Log/FRQ-style Question: Relationships between populations affect the whole community in different ways.Give one example each of mutualism, competition, and commensalism, and explain how they affect the populations in question and the community.

11. LO 4.12: The student is able to apply mathematical routines to quantities that describe communities composed of populations of organisms that interact in complex ways. • SP 2.2: The student can apply mathematical routines to quantities that describe natural phenomena. • Explanation: An example of how natural phenomena can be displayed on a graph is a predator versus prey relationship. A graph can be used to describe the population cycles of the predator and the prey, and the effect on population of the species due to interaction with one another and their surroundings.A hare and a lynx are an example of this predator and prey relationship. The population of the hare (prey) can directly affect the population of the lynx (predator), because a lynx is heavily dependent on a single prey species. This means that the lynx’s main food source is the hare, and if there is a decline in hare population due to environmental conditions (such as the winter causing food shortage) or excessive predation, then there will also be a decline in the lynx population because the lynx will experience a food shortage with the decrease in the number of hares in the area. The population of the hare and lynx are directly linked to one another. An increase in hares may allow for an increase in lynxes because they now have more prey to feed on. The opposite is also true. • M.C. Question:All of the following statements concerning characteristics of predator-prey relationships are correct except: A. A rise in the population of prey is often followed by a rise in the population of predators. B. A rise in the population of predators is followed by a decrease in the population of prey. C. The production of large numbers of offspring within very short periods of time ensures the survival of some prey populations. D. The population of predators most often eliminates the population of prey. • Learning Log/FRQ-style Question: Regulation is an important part of many biological processes. Describe the specific role of the regulator and how the process is altered if regulation is disturbed. • regulator: predators • process: prey population dynamics

12. LO 4.13The student is able to predict the effects of a change in the community’s populations on the community. SP 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Explanation: Populations depend on several factors such as density, predation and carrying capacity. Density-dependent populations will have a decreased birth rate at high density. This effectively thins the population and allows for less resource competition. Some territorial species demand space, an adaptation that allows for safe nesting and prevention of disease spread. Thus a density-dependent population will self-regulate and continue to survive in a community. Predation , when introduced to a community, is an extrinsic factor that can increase as population density increases. Predation also leads to population cycles in which predatory/prey relationships cause correlated fluctuations as animals adapt to survive. For example, lynx population will mirror hare populations and increase whenever more hares become available as prey. Thus graphs can be used to predict predator/prey relationships. M.C. Question: Scientists are studying a population of sparrows and discover that an influx of immigrant sparrows due to a hurricane has led to an increase in conflict between the birds. These sparrows are a ______ population and are exhibiting ________. Density-Independent, mating rituals Density-Dependent, territoriality Density-Independent, predation Density-Dependent, reciprocal altruism Population size (thousands) Learning Log/FRQ-style Question: An elephant population exhibits exponential population growth in its native habitat. Predict how the elephant population would change if food became a limiting factor, and what kind of population growth model should be applied.

13. LO 4.14 The student is able to apply mathematical routines to quantities that describe interactions among living systems and their environment, which result in the movement of matter and energy. SP 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Explanation: The student can use mathematics to solve problems, analyze experimental data, describe natural phenomena, make predictions, and describe processes symbolically. The student is able to estimate the answers to quantitative questions using simplifying assumptions and to use this information to help describe and understand natural phenomena. In addition, the student can estimate energy procurement and utilization in biological systems, including ecosystems. M.C. Question The following is a food web for a meadow that occupies 25.6km .The primary producers’ biomass is uniformly distributed throughout the habitat and totals 1,500 kg/km2 Developers have approved a project that will permanently reduce the primary producers’ biomass by 50 percent and remove all rabbits and deer. Which of the following is the most likely result at the completion of the project? The biomass of the coyotes will be 6kgdramatically reduced The coyotes will switch prey preference The biomass of coyotes will be and outcompete the hawks There will be a dramatic increase in voles Free Response: describe what is happening to the bacteria population between the hours of 1-4 then 5-6 then 7-8. what environmental factors made these changes happen. What environmental factors could increase or decrease the number of bacteria in this population?

14. L.O. 4.17: The student is able to analyze data to identify how molecular interactions affect structure and function. S.P. 6.1: The student can analyze data to identify patterns or relationships. Explanation: Molecular interactions are essential to the structure and function of biological systems. The change in the structure of a molecular system may result in a change in the function of the system. Specifically, signal transduction pathways can be altered by a change in the ligand, the receptor, or any number of relay proteins that function within the transduction pathway. Also, molecular interactions between an enzyme and a substrate can speed up necessary chemical reactions necessary for the proper functioning of an organism. The substrate must fit into an enzymes active site, and this fit is determined by the shape of the enzyme (which is determined by amino acid sequence and interactions among these amino acids.) In addition, cofactors and coenzymes may be necessary to completely activate the enzyme by inducing a structural change within the enzyme. A second binding site within the enzyme, called the allosteric site, may influence the activation or inhibition of an enzyme. For example, a toxin binding to the allosteric site of an enzyme can alter the shape of the enzyme’s active site, thus indirectly inhibiting the function of the enzyme. An enzyme’s activity, as affected by enzyme concentration, substrate concentration, and/or presence of an inhibitor, can be measured via experimentation. During our “Enzyme Lab”, a color-change indicator and a spectrophotometer were utilized to measure the rate of and enzyme-mediated reaction in the presence of varying concentrations of enzyme and substrate. M.C. Question: How does a noncompetitive inhibitor decrease the rate of an enzyme-mediated reaction? By changing the shape of a reactant By changing the free energy dynamics of the reactions By acting as a coenzyme of the reactions By decreasing the activation energy of the reactions By binding at the active site of the enzyme FRQ: An experiment was conducted to measure the reaction rate of the human salivary enzyme α-amylase. Ten mL of a concentrated starch solution and 1.0 mL of α-amylase solution were placed in a test tube. The test tube was inverted several times to mix the solution and then incubated at 25°C. The amount of product (maltose) present was measured every 10 minutes for an hour. The results are given in the table below. a) Graph the data and calculate the rate from 0 to 30 minutes. b) Explain why a change in rxn rate was observed after 30 minutes. c) Draw and label another line on the graph to predict the results if the concentration of amylase was doubled. Explain. d) Identify TWO environmental factors that can change the rate of an enzyme-mediated reaction. Discuss how each of those two factors would affect the reaction rate of an enzyme.

15. LO 4.19:The student is able to use data analysis to refine observations and measurements regarding the effect of population interactions on patterns of species distribution and abundance. SP 5.2:The student can refine observations and measurements based on data analysis. Explanation: Population dynamics are presented in graphs throughout the book. The most common may be graphs showing a change species population over a long period of time. Species interactions are demonstrated in drastic population size changes, especially when two species have a hunter-prey relationship. For example, as shown in the graph, there was a steady growth of size of the isolated moose population between 1960 and 1970. Based on the rapid population decline in 1972, we can presume the large wolf population was to blame. Populations within communities are constantly affected by distribution and abundance, as we see within the moose-wolf interactions. Other factors affecting a species population may include weather, resources, territoriality, health, and immigration. Additionally, population equilibrium plays a key role in observing data found about a specific population. Density-dependent and independent factors often affect the abundance of a population. Generally, a density-dependent death rate will increase as a population becomes denser, while a density-dependent birth rate decreases. M.C. Question: As Meerkats (Suricatasuricatta), an k-selected species, have reached their carrying capacity within their native biome of the African savannah their population size often fluctuates. What kind of data model trend would we expect to see? A) A curve of exponential growth (J-Curve) showing a seemingly limitless growth of the meerkats without any apparent affect from external environmental factors. B) A boom-and-bust cycle showing expansions and contractions within the size of the meerkat population. C) A dispersed age-structure diagram of the meerkats where majority of the population is either more than 10-years-old or younger than 8-months-old. D) A major, rapid decline in meerkat population size that comes with the change of seasons. Learning Log/FRQ-Style Question: Alaskan Grizzly Bear and Salmon populations have been measured closely over the past 75 years. These bears are known to prey on the salmon in the nearby freshwater rivers. Describe the relationship these two species share and draw a graph predicting trends you would expect to find in the data found on the populations over the past 75 years.

16. LO 4.20: The student is able to explain how the distribution of ecosystem changes over time by identifying large-scale events that have resulted in these changes in the past. SP 6.3: The student can articulate the reasons that scientific explanations and theories are refined or replaced. Explanation: After some type of disturbance (such as a volcanic eruption or a glacier), all existing vegetation is stripped away causing changes in the community. Gradually, the disturbed area which was once inhabited by many species will be replaced with other species; this is called ecological succession. If the process takes place in a “lifeless” area where soil has not yet formed, it is called primary succession. Lichens and mosses are usually the first to colonize in the area. Soil starts to develop as rocks weather and organic matter accumulates. When the soil is present, mosses and lichens are replaced by shrubs, trees, and grasses. Eventually, the area is colonized by plants and become proper vegetation. This process is gradual and could take hundreds of years. Secondary succession follows the destruction of existing vegetation, either naturally or by human activity (soil is already present). For example, section of a forest destroyed by fire.  Often, the area starts to return to something similar to its original state. If an area has not been burned or heavily grazed, woody shrubs may replace some of the species. M.C. Question: Which is not an example of primary succession? Vegetation colonizing on a volcanic island years after an eruption Salt marsh vegetation on a mud flat Moss growing on a mountain top Grassland growing on a site of a previous rainforest Learning Log/FRQ-style Question: The diagram shows the succession of a community over the course of 150 years. Describe the changes in biodiversity as succession progresses over the period of time. How do primary and secondary succession differ?

17. A) LO 4.21 The student is able to predict consequences of human actions on both local and global ecosystems.[See SP 6.4] B) 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. C) The impact of humans on the environment is noticeable in almost all organisms and ecosystems. The phenotypic expression of organisms can even be affected by the environment, and human interaction plays a major role in this. By releasing chemicals into the air, pH can be changed. Certain species of plants’ flower colors are determined by the pH of air, and because pollination is often dependent on attracting a specific species of pollinator, this could cause decreased effectiveness in survival and reproduction of plant species. At the same time, humans are notorious for habitat destruction and water pollution. Runoff from fertilizing fields can lead to increased nitrate and phosphate concentrations in water which leads to algal blooms, mass death, and thus cultural eutrophication and decreased dissolved oxygen content in water. D) Multiple choice: As human interaction with the environment continues, which of the following is NOT a likely consequence of human interference in natural ecosystems? A. Uncontrolled erosion and water pollution from runoff B. Increased dissolved oxygen concentration in available water sources C. Phenotypic expression in plant flowers D. Rising sea levels and temperatures Marine biologists studying coral populations in the Gulf of Mexico have found that coral bleaching, a phenomenon that occurs when coral polyps expel a symbiotic zooplankton from their surfaces has rapidly increased due to environmental stress on the colony of coral. Discuss human impact on coral bleaching based on the following: -Decreased dissolved oxygen content in oceans - Increased salinity of oceans -Temperature increases

18. LO 4.23 The student is able to construct explanations of the influence of environmental factors on the phenotype of an organism. • SP 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. • Explanation: Phenotypes are defined as the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment. In Mendelian genetics, each of the two parents have a set of genes that are passed down to the offspring in some way. If the offspring is homozygous dominant or heterozygous, then they are dominant for the trait that that gene is associated to, and therefore their phenotype(or physical appearance) is dominant for that trait. If the organism is homozygous recessive for that trait then in turn they are also recessive for the phenotype linked with the genotype of that particular trait(the genotype is the specific allelic combination for a certain gene). Certain environmental factors such as diet, temperature, humidity, light cycles, and others can have a significant effect on the phenotypes of an organism by the way that the physical appearance could change. The arctic hare is an example of an animal that has the ability to provide camouflage for itself by having a white fur in the winter to blend in with the snow but changing to a grayish fur color in the spring to help blend in with the rocks and vegetation. In this case, the hare is able to change its phenotype without the entire genetic makeup changing. • M.C. Question: Which pair of organism and physical change is due to genetic/phenotypic reasons? A) Moose; losing antlers B) Elderly man; graying of hair C) Arctic Hare; White Fur turning into gray fur D) Snake; Shedding skin • Learning Log/ FRQ-style question: Explain how diet can have an impact on the phenotypic traits of a person. How is this significant to the overall health of a person?

19. LO 4.24: The student is able to predict the effects of a change in an environmental factor on the genotypic expression of the phenotype. SP 6.4: The student can construct explanations of phenomena based on evidence produced through scientific practices. Explanation: In plants and animals, an organism’s genotype is the set of genes that it carries. The organism’s phenotype is all of its observable characteristics. A genotype-environment interaction has an effect on the phenotypic interactions between genes and the environment. In both plants and animals, phenotypic plasticity allows an organism to change its phenotype in response to changes in the environment. The environment can also influence the expression of traits by natural selection. The phenotype of an individual can depend directly on the environment in which it develops and/or lives in. Plants and animals, usually plants however (since they are stationary), must deal with whatever the weather throws at them. Plants can produce anti-freezing proteins in order to stay alive during winter. Bacteria can use galactose as a carbon source instead of sucrose due to changes in gene expression. Animals, when exposed to disease, can cope with it by alternating the expression of genes. M.C. Question: Which of the following does not affect gene expression? • Epigenetics via target gene • Lac operons, which digest lactose • Bacterial conjugation (bacterial sex) • Intensive radiation situations • Transcription (Proteins and RNA) Learning Log/FRQ-style Question: Based on the life cycle of non-evergreen trees, what environmental effect causes the trees to change their leaf colors from green to orange and yellow? What causes the trees’ leaves to fall down? How do these trees accomplish this task of color changing and leaf falling in autumn and winter?

20. LO 4.26: The student is able to use theories and models to make scientific claims and/or predictions about the effects of variation within a population on survival and fitness. SP 6.4: Student make claims and predictions about phenomena based on scientific theories. Explanation: Genomic diversity measures the level of fitness of organisms, survival and reproduction of the fittest is what causes natural selection. A population with little genetic diversity is at a higher risk for extinction. Such as, the Tasmanian devil population in which an infectious cancer spreads rapidly due to lack of genetic variation. Without a mutation that protects against the infectious cancer the population is on the verge of extinction. Genetic diversity allows individuals in a population to respond differently to the same changes in environmental conditions. For example, as the Flu spreads throughout a population not all individuals are equally affected by the disease outbreak. M.C. Question: Of all mutations that occur, why do only a small fraction become widespread in a gene pool? A)Mutation rates tend to be low in animals and plants. B)Most mutations occur in somatic cells that do not produce gametes and die out with the organism. C)Gene duplication is a more important source of variation. D)Most mutations occur in gametes and without sexual recombination the mutation only spreads through a small population. Learning Log/FRQ-style Question: Genetic variation is the raw material for evolution. A)Explain three cellular and/or molecular mechanisms the introduce genetic variation into the gene pool of a plant or animal population.

21. LO 4.27 The student is able to make scientific claims and predictions about how species diversity within an ecosystem influences ecosystem stability. SP 6.40 The student can make claims and predictions about natural phenomena based on scientific theories and models. Explanation Because of the network of community interactions among populations of different species, the local extinction of one species (e.g. a keystone predator) can have a negative impact on the overall species richness of the community. In addition, each ecosystem has characteristic patterns of energy flow and chemical cycling that can affect the whole biosphere. For example, the productive “pastures” of phytoplankton in the oceans may help moderate the greenhouse effect by consuming massive quantities of CO2 for photosynthesis and for building shells made of bicarbonate. MC Question: Which of the following would be most immediately disrupted by the extinction of a keystone predator species in a local ecosystem? A) Natural resource availability B) Food web relationships C) Population of producer species D) Population of primary and secondary level species FRQ: What are some potential consequences caused by a loss in biodiversity? How could the introduction of a new species into an ecosystem disrupt it? What could the extinction of a keystone species cause within its ecosystem? Larger food webs are more stable than simple, smaller food webs, which are disrupted more by one species’ extinction. A complex food web, heavily dependent on krill for stability. Community 1 has a high level of biodiversity; Community 2 has a very low level of biodiversity.