1 st /2 nd /4 th Review Project Collection #2

1. 1st/2nd/4th Review Project Collection #2

2. Learning Objective 1.32: The student is able to justify the selection of geological, physical, and chemical data that reveals early Earth conditions. Science Practice 4.1: The student can justify the selection of the kind of data needed to answer a particular scientific question. Multiple Choice: Which of the following statements about the conditions of Earth’s beginning and the scientific evidence that proves that condition is TRUE? The cyanobacteria’s bacteria that metabolized dihyrogen sulfide mutated to use water rather than dihydrogen sulfide, which proves that the Earth’s atmosphere in early times had an abundance of dihydrogen sulfide. The cyanobacteria’s bacteria that metabolized dihyrogen sulfide mutated to use water rather than dihydrogen sulfide, which proves that the Earth’s atmosphere in early times had an abundance of water. The percent of common amino acids in all organisms proves that the theory of evolution is invalid. Monomers combined to make polymers which indicates that there were great amounts of volcanic activity in Earth’s early years. Explanation: At Earth’s beginning, there was very little oxygen, and a lot of water, methane, carbon monoxide, and carbon dioxide. There was no ozone layer which led to high levels of UV radiation, and lots of meteorite bombardment. There was a lot of lightening and volcanic activity. Through absolute and relative dating of fossils and rocks, and the knowledge that the environment was too hostile for life until 3.9 byo, we can conclude that the origin of life occurred between 3.5 and 3.8 billion years ago. The oldest rocks were found in Greenland 3.8 billion years ago, and the oldest fossils were dated to 3.5 byo. In 1953, the Miller-Urvey experiment was conducted to see if Earth favored reactions that formed organic compounds from inorganic compounds, which was a hypothesis made in 1920 by Oparin and Haldane. Through repeated experiments, they concluded that all monomers necessary for life (amino acids, all the components of nucleotides, sugars, lipids, etc.) could be formed from inorganic compounds. This gave evidence that living matter can come from lifeless matter, and that this is how the earth was formed since it started out with no living matter but had an abundance of free energy and barely any oxygen. These monomers connected to make polymers as Syndey Fox proved by dripping monomers onto hot sand, clay, or rocks to see if they would connect. These connected monomers created protienoids which are poly peptides created by abiotic means. These protienoids gave way to protobionts which are abiotically produced molecules surounded by a membrane. We believe that eukaryotes originated through endosymbiosis which is when molecules absorb one another and live inside of each other. This is proven by the similarities between bacteria and mitochondria & chloroplasts. They both reproduce by binary fission, have small, circular genomes, and very similar DNA sequences , along with many others. Current endosymbioticrelatationships also provide evidence… it had to start sometimes, so it could have been then. How similar all organisms DNA sequences/amino acid composure is a sign that we all are evolved from one organism and so we conclude that there is a common genetic code. There is some evidence that RNA was the first genetic material because through ribozymes, RNA can self replicate and the RNA molecules best suited for their environment replicate their DNA and reproduce so natural selection has an impact. The origin of photosynthesis tells us what the atmosphere was like during early times because the cyanobacteria used to have a bacteria that metabolized dihydrogen sulfide, and that bacteria mutated to use water. Water was abundant in the atmosphere at that time so the cyanobacteria used it in photosynthesis. The oxygen that was released from the photosynthesis reacted with dissolved iron and formed oxide precipitate and the saturated water was released into the atmosphere. FRQ: Explain the process of the origin of life on Earth and the scientific evidence that supports these theories. Begin with no life, and end with the formation of eukaryotes. Make sure that you include information about how natural selection contributed and cite the names of any scientists who contributed experimental data to help solidify this theory.

3. FRQ Answer: The Miller-Urvey experiment was conducted to see if Earth favored reactions that formed organic compounds from inorganic compounds, which was a hypothesis made earlier by Oparin and Haldane. Through repeated experiments, they concluded that all monomers necessary for life (amino acids, all the components of nucleotides, sugars, lipids, etc.) could be formed from inorganic compounds. This gave evidence that living matter can come from lifeless matter, and that this is how the earth was formed since it started out with no living matter but had an abundance of free energy and barely any oxygen. These monomers connected to make polymers as Syndey Fox proved by dripping monomers onto hot sand, clay, or rocks to see if they would connect. These connected monomers created protienoids which are poly peptides created by abiotic means. These protienoids gave way to protobionts which are abiotically produced molecules surounded by a membrane. Natural selection then comes in to play because protobionts best suited for their enviroment could reproduce and create others who were best suited for their enviroment. Coacervate is a stable protobiont droplet that self assembles when a suspension of macromolecules are shaken. Since we know that macromolecules can be created in earth’s hostile enviroment due to the findings of Miller and Urvey, we know that protobionts can also be formed. We believe that eukaryotes originated through endosymbiosis which is when molecules absorb one another and live inside of each other. This is proven by the similarities between bacteria and mitochondria & chloroplasts. They both reproduce by binary fission, have small, circular genomes, and very similar DNA sequences , along with many others. Current endosymbioticrelatationships also proof that it could have been responsible for forming eukaryotes so early because it had to have started at some point in the history of the Earth, so why not in the very beginning? Answer Key • Multiple Choice Question and Answer: Which of the following statements about the conditions of Earth’s beginning and the scientific evidence that proves that condition is TRUE? • The cyanobacteria’s bacteria that metabolized dihyrogen sulfide mutated to use water rather than dihydrogen sulfide, which proves that the Earth’s atmosphere in early times had an abundance of dihydrogen sulfide. • The cyanobacteria’s bacteria that metabolized dihyrogen sulfide mutated to use water rather than dihydrogen sulfide, which proves that the Earth’s atmosphere in early times had an abundance of water. • The percent of common amino acids in all organisms proves that the theory of evolution is invalid. • Monomers combined to make polymers which indicates that there were great amounts of volcanic activity in Earth’s early years. B is the correct answer. The other options are all wrong.

4. (LO 4.4) The student is able to make a prediction about the interactions of subcellular organelles.(SP 1.5) The student can make claims and predictions about natural phenomena based on scientific theories and models. MC Question: The endomembrane system is a complicated system involving multiple organelles. Which of the following correctly describes the movement through this system of a protein that functions best in the ER? A. The mRNA is synthesized in the ER, translated on a free ribosome to the Golgi, and then a transport vesicle carries the mRNA back to the ER for modification. The mRNA is then sent to the nucleus. B. The mRNA is synthesized in the Golgi, is translated on a free ribosome to the ER for modification, and then a transport vesicle carries the mRNA back to the Golgi. C. The mRNA is synthesized in the nucleus, is translated on a free ribosome, then is sent to the Golgi and modified. A transport vesicle carries the protein to the ER for further modification. D. The mRNA is synthesized in the nucleus, is translated on a bound ribosome, then is sent to the ER and modified. A transport vesicle carries the protein to the Golgi apparatus. After modification in the Golgi, another transport vesicle carries the protein back to the ER. FRQ Question: Organelles are found in both prokaryotic and eukaryotic cells. a. Compare and contrast prokaryotic and eukaryotic cells. b. List and describe the basic function of three organelles. c. Describe how these organelles work together to allow the animal cell to function. A eukaryotic cell has membrane-enclosed organelles, the largest of which is usually the nucleus. A prokaryotic cell is usually smaller and does not contain a nucleus or other membrane-enclosed organelles. Some organelles are animal or plant specific, but these SEVEN organelles are found in both types of cell: the nucleus, vacuole, mitochondria, the Golgi apparatus, cytoskeleton, peroxisomes, and the Endoplasmic reticulum (ER). The nucleus includes the nuclear envelope, the nucleolus, and chromatin, and is the information center of the cell. A vacuole is a membrane-bound sac that contains hydrolytic enzymes that aid in intracellular digestion and the release of cellular waste products. There is a central vacuole in plant cells. Mitochondria aid in energy capture and transformation. The Golgi apparatus, consisting of a series of flattened membrane sacs (calledcisternae), synthesizes and packages small molecules for transport in vesicles, and produces lysosomes (described later). The cytoskeleton reinforces the cell’s shape. The ER consists of a smooth and a rough ER. The rough ER gets its name from its surface containing ribosomes (small structures containing rRNA and protein) and is where protein synthesis occurs and contributes to intracellular transport. Ribosomes can be free ribosomes (suspended in the cytosol) or bound ribosomes (attached to the outside of the ER or nuclear envelope). The smooth ER synthesizes lipids. Peroxisomes are organelles that aid in metabolism and produce hydrogen peroxide. Plant cells include chloroplasts, organelles that contribute to energy capture and conversion for photosynthesis. Animal cells contain lysosomes, whichaid in intracellular digestion, apoptosis, and recycling cell material. Centrosomes are organelles where the cell’s microtubules are initiated, but in animal cells these organelles contain centrioles (function unknown). Plant cells also contain a cell wall, with plasmodesmata (channels) throughout, that help keep the cell’s shape and protect the cell from mechanical damage. (next slide has visuals)

6. Organelle Interactions Now that we know the functions of the organelles, let’s look at how they interact… The nucleus houses the most of the cell’s DNA and the ribosomes use information from the DNA to make proteins. Vesicles move from the ER to the Golgi. Vesicles form and leave Golgi, carrying specific proteins to other locations or to the plasma membrane for secretion. Vesicles also transport certain proteins back to the ER. These vesicles give rise to lysosomes and vacuoles. Lysosomes are then available for fusion with another vesicle for digestion. Transport vesicles carry proteins to the plasma membrane for secretion. The Plasma membrane expands by fusion of the vesicles and the proteins are secreted from the cell. This makes up the endomembrane system. In addition to this system, mitochondria (animal cells) and chloroplasts (plant cells) contain DNA and change energy from one form to another.

7. Answer Key- LO 4.4 MC Question: The endomembrane system is a complicated system involving multiple organelles. Which of the following correctly describes a the movement through this system of a protein that functions best in the ER? A. The mRNA is synthesized in the ER, translated on a free ribosome to the Golgi, and then a transport vesicle carries the mRNA back to the ER for modification. The mRNA is then sent to the nucleus. B. The mRNA is synthesized in the Golgi, is translated on a free ribosome to the ER for modification, and then a transport vesicle carries the mRNA back to the Golgi. C. The mRNA is synthesized in the nucleus, is translated on a free ribosome, then is sent to the ER and modified. A transport vesicle carries the protein to the Golgi apparatus. After modification, another transport vesicle carries the protein back to the ER. D. The mRNA is synthesized in the nucleus, is translated on a bound ribosome, then is sent to the ER and modified. A transport vesicle carries the protein to the Golgi apparatus. After modification in the Golgi, another transport vesicle carries the protein back to the ER. The question requires background about the difference between bound and free ribosomes, the functions of each organelle in the endomembrane system, and the relationship between the different organelles in the system. First, the student must understand that the order of the endomembrane system, with the specified protein from the question, is: nucleus, ER, Golgi, back to the ER (since the protein functions best in the ER). This eliminates A and B. Between C and D, D is the only answer choice that has the correct order and mentions a bound ribosome. Understanding that this protein requires a bound ribosome is important because bound ribosomes are attached to the rough ER. FRQ: Organelles are found in both prokaryotic and eukaryotic cells. a. Compare and contrast prokaryotic and eukaryotic cells. b. List and describe the basic function of three organelles. c. Describe how these organelles work together to allow the animal cell to function. a. A eukaryotic cell has membrane-enclosed organelles, the largest of which is usually the nucleus. A prokaryotic cell is usually smaller and does not contain a nucleus or other membrane-enclosed organelles. Prokaryotes contain a single circular chromosome, while eukaryotes contain multiple linear chromosomes. b. Three animal cell organelles are the Golgi apparatus, the nucleus, and the ER. The Golgi apparatus, consisting of a series of flattened membrane sacs (called cisternae), synthesizes and packages small molecules for transport in vesicles, and produces lysosomes. Thenucleusincludes the nuclear envelope, the nucleolus, and chromatin, and is the information center of the cell. The ER consists of a smooth and a rough ER. The rough ER gets its name from its surface containing ribosomes (small structures containing rRNA and protein) and is where protein synthesis occurs and contributes to intracellular transport. Ribosomes can be free ribosomes (suspended in the cytosol) or bound ribosomes (attached to the outside of the ER or nuclear envelope). The smooth ER synthesizes lipids. c. The nucleus houses the most of the cell’s DNA and the ribosomes use information from the DNA to make proteins. Vesicles move from the ER to the Golgi. Vesicles form and leave Golgi, carrying specific proteins to other locations or to the plasma membrane for secretion. Vesicles also transport certain proteins back to the ER. These vesicles give rise to lysosomes and vacuoles. Lysosomes are then available for fusion with another vesicle for digestion. Transport vesicles carry proteins to the plasma membrane for secretion.

8. LO 1.19: The student is able to create a phylogenetic tree of simple cladogram that correctly represents evolutionary history and speciation from a provided chart. • SP 1.1: The student can use representations and models to communicate scientific problems. • Explanation: Phylogenetic trees serve to represent speciation that occurs deriving or losing traits through evolution. Relatedness of organisms is shown by how recently the two diverged into different branches, which also shows common ancestors of the two. They are constructed by comparing the similarities of fossils and DNA of species. The more two different species have in common, the more recently they diverged. Since evolution is a continuous process, phylogenetic trees and cladograms are constantly being revised in accordance to newly emerged knowledge.

9. M.C. Question: The chart below shows differences in amino acids between four insects and a wolf spider. Using the chart, determine which two organisms most likely diverged most recently.A. beetle and wolf spiderB. cricket and grasshopperC. lady bug and beetleD. Wolf Spider and the lady bugFRQ: Using the information in the chart below, create a cladogram of the evolutionary patterns of the given organisms. Explain why the cricket and grass hopper should go on the same branch. Expain two patterns of evolution and how speciation occurs as a result.

10. Multiple Choice answer • M.C. Question: The chart below (slide two) shows differences in amino acids between four insects and a wolf spider. Using the chart, determine which two organisms most likely diverged most recently. • A. beetle and wolf spider • B. cricket and grasshopper • C. lady bug and beetle • D. Wolf Spider and the lady bug • C is the correct answer because the lady bug and the beetle have only one difference in amino acids. All the other choices have more differences, so the lady bug and beetle are most similar.

11. FRQ: Using the information in the chart below, create a cladogram of the evolutionary patterns of the given organisms. Explain why the cricket and grass hopper should go on the same branch. • Explain the difference between allopatric and sympatric speciation. • Below is an example of an appropriate cladogram answer. The cricket and grass hopper belong on the same branch because they differ by only one amino acid, so it can be assumed that their speciation occurred recently in evolutionary time. • Allopatric: An extrinsic factor prevents two or more groups of a species from mating regularly, which will eventually cause a difference in the gene pool and then speciation. • Sympatric: A change in the gene pool with no geographic change or barrier in the environment. So even though the population still occupies the same area together, they will not mate and will eventually diverge because of changes in the gene pool. beetle Lady bug cricket Grass hopper Wolf spider

12. LO 2.26: The student is able to analyze data to identify phylogenetic patterns or relationships, showing that homeostatic mechanisms reflect both continuity due to common ancestry and change due to evolution in different environments.Science Practice 5.1: The student can analyze data to identify patterns or relationships.Explanation: Phylogeny is the development or evolution of a particular group of organisms. Examining fossils is a common method of seeing when groups of organisms diverged. Structures of organisms are also observed, which are divided into analogous structures and homologous structures. Analogous structures are those that have similar functions but which evolved separately within different groups of organisms and come from convergent evolution. Homologous structures have similar organs but different functions, and come from a common ancestor, or from divergent evolution. There are graphs and charts, such as phylogenetic trees and cladograms, that display evolutionary relationships.MC Question: Suppose you have encountered a dead house finch and conclude that the structure of the bird’s wing is like that of a wasp. Which of the following best describes the relationship between the structures of the organisms’ wings?A) Homologous structures because the finch and wasp derived from a shared common ancestor.B) Analogous structures because the finch and wasp derived from a shared common ancestor.C) Vestigial structures because the finch and wasp have converged over time to show a similar structure of wings, yet they did not come from a common ancestor.D) Analogous structures because the finch and wasp have converged over time to show a similar structure of wings, yet they did not come from a common ancestor.Learning Log Question: In order to discover common ancestry, what might people use to study if organisms derived from a common ancestor? (Cues: phylogenetic tree, cladogram, DNA, traits)

13. MC Question: Suppose you have encountered a dead house finch and conclude that the structure of the bird’s wing is like that of a wasp. Which of the following best describes the relationship between the structures of the organisms’ wings?A) Homologous structures because the finch and wasp derived from a shared common ancestor.B) Analogous structures because the finch and wasp derived from a shared common ancestor.C) Vestigial structures because the finch and wasp have converged over time to show a similar structure of wings, yet they did not come from a common ancestor.D) Analogous structures because the finch and wasp have converged over time to show a similar structure of wings, yet they did not come from a common ancestor. D is the correct answer because the bird’s wing may be similar in appearance to the wasp’s but obviously did not come from a common ancestor, considering that one is a mammal and the other is an insect. This is known as convergent evolution. This makes the structures analogous structures. A is incorrect because the two organisms do not come from a common ancestor. B is incorrect because the definition given is for homologous structures, not analogous. C is incorrect because vestigial structures are structures that are no longer in use.

14. Learning Log Question: In order to discover common ancestry, what might people use to study if organisms derived from a common ancestor? (Cues: phylogenetic tree, cladogram, DNA, traits) Cladograms are very helpful in showing common ancestry. Cladograms demonstrate ancestral relations between organisms by showing which traits organisms share and do not share. They can be used to show where an organism may have branched from one another, taking a different path. This makes cladograms very effective in finding phylogenetic relationships. Another useful method is constructing phylogenetic trees. Constructing these trees help to compare similarities of characteristics or DNA sequences of organisms. If there is common descent, phylogenetic trees should project neat lines of inheritance and ancestry.

15. LO 2.9: The student is able to represent graphically or model quantitatively the exchange of molecules between an organism and its environment, and the subsequent use of these molecules to build new molecules that facilitate dynamic homeostasis, growth, and reproduction. Explanation: Many organisms intake molecules from the environment for respiratory purposes, to generate energy for cellular work, such as synthesis and arrangement of molecules, or otherwise for doing work. For example, the Euglena protist, an organism with a chloroplast, is capable of photosynthesic light reactions where light is converted into NADPH and ATP, compounds which are then synthesized with CO2 into sugars in the dark reactions, and the sugars will be stored into cell chemical bonds as a energy supply to be oxidized in cell respiration during the nighttime. Knowing this, the exchange of molecules (light, oxygen, carbon dioxide, etc.) can be represented by respiration, a process by which thermodynamic homeostasis (regulation) may be maintained in a body, while also supplying the organism with ATP molecules that will provide energy for metabolic and reproductive processes, among other cellular processes. SP 1.1: The student can create representations and models of natural or man-made phenomena and systems in the domain. SP 1.4: The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. The graph shows an experiment in which germinating pea seeds represent organisms that respire, replacing oxygen with carbon dioxide at a 1:1 molecule exchange ratio. The oxygen thus is measured by the volume of solid potassium carbonate that is formed when cotton treated with potassium hydroxide (KOH) reacts with CO2. Diagram:

16. Multiple Choice: Which of the following cellular respiration pathways represented by a diagram will produce the most energy for cellular processes? a. b. c. d.

17. Free Response: For each of the cases, describe how ATP and/or metabolism is used to facilitate the organism’s ability to survive. A salmon exhibits osmoregulation of NaCl. Certain mammals are capable of thermoregulation. Plants construct carbohydrates out of the products of photosynthesis.

18. Multiple Choice: The correct answer is C, as it represents the Electron Transport Chain, which encompasses the two processes of chemiosmosis and oxidative phosphorylation. Using the carriers of FADH2 and the NAD+, H+ is transported across a gradient to support the ATP synthase which will phosphorylate ADP to form ATP. This metabolic pathway provides the most ATP with about 26-28 ATP molecules.a. and b. are represented by glycolysis and the Krebs cycle, which sets up and pyruvates and then uses it to form acetyl coenzyme-A and electron carriers, respectively. As such, they only generate about 2 molecules of ATP. D. represents fermentation, which is anaerobic respiration and thus won’t generate sustainable amounts of ATP. Free Response: • salmon have a special enzyme that hydrolyzes ATP and uses the released energy to actively transport Na+ and Cl-ions against their concentration gradients. These Na+-Cl- ATPase molecules 'pump' Na+and Cl- out of the salmon's blood into water, thus being resistant to NaCl overload. • In marine mammals, they can increase ATP production (increasing metabolism), and ATP can be used as heat (generation of energy). As the ATP production increases, the oxygen consumption, and circulation also increase. • In the Calvin cycle, plants use ATP as the primary energy source and reduces NADPH through three phases: Carbon fixation, Reduction of ATP and NADPH into G3P (glyceraldehyde 3-phosphate) 3-carbon carbohydrate, and Regeneration, using ATP to reform RuBP observed in carbon fixation (ribulose biphosphate) to make a round trip and continue the cycle of making sugars.

19. LO 3.18: The student is able to describe the connection between the regulation of gene expression and observed differences between different kinds of organisms. SP 7.1: The student can connect phenomena and models across spatial and temporal scales. Explanation: DNA regulatory sequences, regulatory genes, and small regulatory RNAs are involved in gene expression. Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription, (examples are promoters, terminators, or enhancers). A regulatory gene is a sequence of DNA that codes for RNA. In bacteria and viruses control mechanisms are used to regulate gene expression. These control mechanisms can either be positive or negative. Inducers have the power to turn on the expression of a gene, while repressors can inhibit it. Both inducers and repressors interact with regulatory sequences or regulatory proteins. These regulatory proteins can be a positive control and stimulate gene expression by binding to DNA and stimulating transcription, or they can be negative controls by blocking transcription and inhibiting gene expression. Genes such as the ribosomal genes are always turned on because they are continuously expressed. Gene expression is a complicated process and involves regulatory genes/elements, and transcription factors in eukaryotes. These transcription factors bind to specific DNA sequences and some of them are activators while others are inhibitors. A combination of the transcription factors is ultimately what controls how much gene product will be produced at any given time. This Gene regulation accounts for phenotypic differences in a population. Phenotypic differences are also known as observed differences. Multiple Choice Question: The Arctic Hare undergoes a complete transformation when the seasons change. In the summer, the Hare is a brown color, but when winter arrives, his fur color changes to a pure white. How does the climate of polar regions influence this change in gene expression? a) Over heating causes the fur to loose its color. b) Colder conditions cause gene regulation shifts to help the hare camouflage and preserve body heat. c) The hare doesn’t have enough pigment molecules to last all year so they are saved up during the winter d) Colder conditions cause the mitochondria to work faster and less efficiently, draining the hare of color. e) Climate has no effect on the hare’s color change Learning Log/FRQ-style Question: a. Using the model for the action of enhancers and transcription activators, label RNA Polymerase II, the DNA bending protein, activators, enhancers, promoters, and TATA box. Next, describe the role each of these parts plays in the process of the transcription initiation complex. b. Explain how a mistake in the transcription process may cause physical changes to an organism, and possibly the organisms entire species over time.

20. Multiple Choice Answer: The Arctic Hare undergoes a complete transformation when the seasons change. In the summer, the Hare is a brown color, but when winter arrives, his fur color changes to a pure white. How does the climate of polar regions influence this change in gene expression? a) Over heating causes the fur to loose its color. b) Colder conditions cause gene regulation shifts to help the hare camouflage and preserve body heat. c) The hare doesn’t have enough pigment molecules to last all year so they are saved up during the winter d) Colder conditions cause the mitochondria to work faster and less efficiently, draining the hare of color. e) Climate has no effect on the hare’s color change Over heating is not an issue in this cold environment, pigment molecules cannot be “saved up”, and fur color has nothing to do with the effectiveness of the mitochondria. The hare does, however, need to conserve body heat in the winter and with snow on the ground white camouflage keeps it hidden from predators. Learning Log/FRQ-style Answer: a. b. Mistakes in the transcription process lead to incorrect amino acid sequences. These incorrect amino acids lead to mutations in an organism. Although sometimes these mutations aren’t visible, often they are. When the mutation offers an advantage to an organism, they become best fit for survival and the trait is passed to younger generations and the generations that follow. Activators Activators – Bind to distal control elements Enhancer – Has three binding sites, accepts the activators Promoter – Sequence that tell other molecules where transcription begins TATA Box – Defines the direction of transcription and also indicates the DNA strand to be read. DNA Bending Protein – Brings the bound activators closer to the promoter RNA Polymerase II – Catalyzes the transcription of RNA Promoter TATA Box Enhancer DNA Bending Protein RNA Polymerase II

21. Learning Objective: 4.23 The student is able to construct explanations of the influence of environmental factors on the phenotype of an organism. Science Practice: 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Explanation: The phenotype of many organisms is dependent upon the environment. Environmental changes, both abiotic and biotic, occur every so often and they can force the organisms to either change phenotypes to adapt to the environment or die out. The changes in phenotypes of organisms is caused by changes in allelic frequencies throughout the population. Even though genotype is a critical part of development, it is the environmental factors such as temperature, diet, and availability of food that influence the phenotypes throughout an organism’s life. M.C. Question: All of the following would be an example of a phenotypic change in an organism due to environmental factors EXCEPT: A polar bear population in Antarctica’s fur coat becomes increasingly thinner as time goes by and the climate gradually becomes warmer. Two lion cubs are wrestling and one cub pulls a chunk of fur out of the other cub. This causes the second lion cub to have a permanent bald spot on the back of it’s head. A certain species of moth changes from lightly colored to black colored following the Industrial Revolution in order to be camouflage to the trees that have turned darker because of the new pollution that killed the lichens that were previously on the trees. A pair of twins are raised together until the age of 18. When they are 18 years old one twin goes to work in an office and the other twin works as a construction worker. The twin that works as a construction worker develops much larger muscles than the twin working in an office. Finches in the Galapagos are exposed to different types of seeds and nuts to eat. The finches that eat the nuts and seeds with harder shells to crack open develop thicker and more durable beaks that the finches eating nuts and seeds in soft shells. Learning Log/Free Response Question: Soon after the industrial revolution, the phenotype of many peppered moths changed from very light to almost black coloring. Peppered moths typically rest on trees. Choose an environmental factor that might have impacted this change in phenotype and explain how this phenotypic change could have been beneficial for the peppered moth species.

22. ANSWERKEY – LO4.23 All of the following would be an example of a phenotypic change in an organism due to environmental factors EXCEPT: A polar bear population in Antarctica’s fur coat becomes increasingly thinner as time goes by and the climate gradually becomes warmer. Two lion cubs are wrestling and one cub pulls a chunk of fur out of the other cub. This causes the second lion cub to have a permanent bald spot on the back of it’s head. A certain species of moth changes from lightly colored to black colored following the Industrial Revolution in order to be camouflage to the trees that turned darker because of the new pollution that killed the lichensthat were previously on the trees. A pair of twins are raised together until the age of 18. When they are 18 years old one twin goes to work in an office and the other twin works as a construction worker. The twin that works as a construction worker develops much larger muscles than the twin working in an office. Finches in the Galapagos are exposed to different types of seeds and nuts to eat. The finches that eat the nuts and seeds with harder shells to crack open develop thicker and more durable beaks that the finches eating nuts and seeds in soft shells. Learning Log/FRQ: Soon after the industrial revolution, the phenotype of many peppered moths changed from very light to almost black coloring. Peppered moths typically rest on trees. Choose an environmental factor that might have impacted this change in phenotype and explain how this phenotypic change could have been beneficial for the peppered moth species. One environmental factor that could have caused this phenotypic change in the peppered moths could be the color of the trees due to pollution from the industrial revolution. Pollution could kill the lichens that grow on trees and keep them at a lighter color. This change in phenotype to a darker coloration would benefit the moths because they would not stand out against the darker trees. Predators would not be able to spot the moths on trees as easily as they would if the moth was lightly colored and the trees was dark and vice versa. The moths that were likely colored would be the first to be eaten by predators and would not be able to reproduce moths with the same light coloring. Instead, those moths with the dark coloration would survive and be able to reproduce offspring with the same genetic coding for dark coloring.

23. LO 1.25: The student is able to describe a model that represents evolution within a population. SP 1.2: The student can describe representations and models of natural or man-made phenomena and systems in the domain. Explanation: For quite some time, there were many views on how evolution occurred within populations of organisms. Lamarck had the model of use and disuse, where parts of the body become larger and more helpful, and the ones that are not used eventually disappear. This model, however, is incorrect. Using Darwin’s correct theory, we now know more about the many factors that cause evolution within populations, including environment, predation, or other factors. Changes in allele frequencies and mutations within a population can cause evolutionary changes in the organisms within a population over a long period of time. Emergent diseases within a population can also decrease the size of that population, making it lose important alleles that can help it evolve when the environmental conditions change. The Hardy-Weinberg theorem gives a basis of comparison for determining evolutionary change within a population. It gives unrealistic, ideal situations for a population, thus serving as a basis for comparison with any real population that actually does undergo some sort of evolutionary change.

24. M.C. Question: In a population of mongooses, with genetic variation present within this particular population, environmental pressures cause one of the extreme colors of the mongooses to be favored out of all others within the population. In other circumstance, with the same population, environmental changes cause the extremes of both kinds in the mongoose population to be favored. In a third circumstance, the changes in environmental pressures cause only the mongooses with intermediate fur coat color to be favored out of the population. Which of the following statements accurately describes the phenomenon of stabilizing selection? • Evolution favors only the extremely light colored rabbits out of the populaton. • Evolution favors only the intermediate colored rabbits out of the population. • Evolution favors only the extremely dark colored rabbits out of the population. • Evolution favors both the extremely light and dark rabbits out of the population. Learning Log/FRQ-style Question: There are many types of unforeseen factors that can alter the genetic composition of a population. Describe the phenomenon of the bottleneck effect and give an example. Why is it very important that humans have a knowledge of the bottleneck effect in terms of conservation?

25. M.C. Question and Answer: Which of the following statements accurately describes the phenomenon of stabilizing selection? • Evolution favors only the extremely light colored rabbits out of the populaton. • Evolution favors only the intermediate colored rabbits out of the population. • Evolution favors only the extremely dark colored rabbits out of the population. • Evolution favors both the extremely light and dark rabbits out of the population. It stabilizes the population, removing the extremes of the organism on both sides of the population over time. Learning Log/FRQ-style Question and Answer: There are many types of unforeseen factors that can alter the genetic composition of a population. Describe the phenomenon of the bottleneck effect and give an example. Why is it very important that humans have a knowledge of the bottleneck effect in terms of conservation? The bottleneck effect is caused by some sort of sudden change in the environment, usually by a disaster. This could greatly reduce the size of the population. With only a small number of survivors from the population, the new population may not have many of the qualities the larger original population once had. This would mean that certain, important alleles from the population may be lost forever. If a population of frogs was greatly reduced due to a massive hurricane, it would lose valuable genetic qualities that may be gone for good. This may cause them to eventually go extinct, mostly because there is very little room for evolutionary improvement since they have so few alleles left. From a perspective of conservation, humans need to be informed of the dangers of the bottleneck effect. Many of the activities humans do are very harmful to wildlife populations, which can cause disasters for them, making the bottleneck effect very common in these populations.

26. Explanation: Cladograms and phylogenetic trees serve to illustrate evolutionary relationships between various organisms throughout time. They can be derived from traits including amino acid similarities/differences, similarities/differences in fossils, or relationships among protein sequences. Often times, advanced computer programs are used to analyze these patterns and determine any type of relationship. Constructing a handmade cladogram or phylogenetic tree is possible through the use of a table that may outline amino acid differences, structural characteristics, etc. These diagrams may also reflect traits that have been lost throughout evolution, and they may be used to determine if particular organisms share a common ancestor. Phylogenetic trees and cladograms are very susceptible to frequent change due to constant updates of biological information and fossil records. When updated, however, they provide extremely accurate information regarding an organism’s ancestors, evolutionary patterns and relationships with other organisms. LO 1.18 The student is able to evaluate evidence provided by a data set in conjunction with a phylogenetic tree or a simple cladogram to determine evolutionary history and speciation. SP 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question.

27. M.C Question: Consider the cladogram presented. Which organisms most likely share the greatest number of derived characteristics? A. Shark and turtle B. Tuna and frog C. Turtle and kangaroo D. Human and kangaroo E. Salamander and kangaroo FRQ-style Question: The table below expresses differences in amino acids among multiple animals. Using the data provided, draw a cladogram that accurately represents the relationships between these organisms. Explain your reasoning behind your drawing. Also, identify which organism is least related to the turtle and explain your answer. |Dog |Cow |Lemur |Ostrich |Turtle Dog 0 2 13 15 19 Cow 0 12 14 18 Lemur 0 5 16 Ostrich 0 15 Turtle 0

28. Answer Key- LO 1.18 Consider the cladogram presented. Which organisms most likely share the greatest number of derived characteristics? A. Shark and turtle B. Tuna and frog C. Turtle and kangaroo D. Human and kangaroo E. Salamander and kangaroo D is the correct answer because they are located on the same branch of the cladogram, and they are also both classified as amniotes and mammalia, implying a very close ancestral bond as well as similarities in characteristics. The answer cannot be A because the two are not in the same classification, and they share no branches on the cladogram. B is incorrect because the tuna is classified as an osteichthyes, while the frog does not have a similar classification. C is not correct because while they both belong to the amniote category, kangaroos are listed as mammals, while turtles are not. Finally, E is incorrect because salamanders are shown as amphibians, while kangaroos are mammals. Therefore, D must be the correct answer. Using the data provided, draw a cladogram that accurately represents the relationships between these organisms. Explain your reasoning behind your drawing. Also, identify which organism is least related to the ostrich and explain your answer. - The relationships among the organisms were determined by the amount of differences in amino acids- the more differences, the less closely related, and the less differences, the closer the relationship. For example, the dog and the cow are very closely related due to only having two differences in amino acids. The dog and the turtle, however, have 19 differences, reflecting very little similarities between the two. The ostrich is least related to the dog, according to the table. There are 15 amino acid differences between the two organisms, which are more than the ostrich and any other animal presented. Cow Ostrich Dog Turtle Lemur (sample cladogram)

29. LO 3.37 The student is able to justify claims based on scientific evidence that changes in signal transduction pathways can alter cellular response. SP 6.1 The student can justify claims with evidence. Explanation: A signal transduction pathway takes place during cell communication. Cells communicate by using neurotransmitters for short distances and hormones for long distances. The three stages of cell signaling include reception, transduction, and response. Reception is when a signal molecule (ligand) binds to the receptor protein on the outside of a target cell. Next, transduction (a series of events involving secondary messengers) occurs as the binding of the ligand causes a change in the receptor protein, which then brings about a specific cellular response. If there is a change in the signal transduction pathway, this can ultimately alter the cellular response, as the pathway in which the message is being carried along and amplified, controls whether or not the response occurs. Transduction occurs as a series of events, but it can also occur as a series of unfortunate events. Examples based on scientific evidence where pathways may be interrupted or altered include drugs, poisons, or diseases in the body. Poisons, such as those found in anthrax can cause a disruption in signal transduction pathways. Normally, a ligand would bind to a G-protein which then releases an alpha subunit that creates cAMP, which is a secondary messenger that amplifies the message and targets different parts within the cell. But when the poison that is found in anthrax is present, it targets the enzyme adenylatecyclase thus changing it’s shape, making it not able to convert ATP to cAMP. As a result, the signal transduction pathway is disrupted and the cellular response is altered. Another example is diabetes. Diabetes is a disease in which the body has shortage of insulin, a decreased ability to use insulin, or both. Insulin is a hormone that allows glucose to enter cells and be converted to energy. In each of our bodies there is an insulin receptor that sits on the surface of specific target cells. Once insulin binds to that receptor, a series of events occurs within the cell including an effect on the glucose transporter (GLUT) which allows the cell to take in glucose to make use of it by storing it as glycogen. With Type 1 Diabetes, a person is not producing insulin, therefore it doesn’t have the capabilities of binding with the receptor. With Type 2 Diabetes, the insulin receptor is ignoring the message that is trying to come through ultimately disrupting the signal transduction pathway by inactivating GLUT and as a result the person doesn’t take in glucose. MC Question: If the insulin receptor located on a target cell was to become inhibited, what would most likely be the result of this disruption? (Look at diagram to the right) Insulin would still bind to the receptor protein but no message would be relayed. Insulin would diffuse through the cell membrane and target an intracellular receptor that was active. The amount of glucose would increase. The cells would eventually die due to the fact that there was no cellular activity (cell communication) taking place because the receptors were inhibited. Free response: A group of scientists are designing an experiment in which they are trying to figure out how to inhibit a disruption in the signal transduction pathway via cell communication. Describe the process that occurs during normal cell communication Discuss one thing that could help the inhibition of these pathways Provide evidence of a real life disease that results in a disruption to these pathways

30. MC Question: If the insulin receptor located on a target cell was to become inhibited, what would most likely be the result of this disruption? Insulin would still bind to the receptor protein and a message would be relayed. Insulin would diffuse through the cell membrane and target an intracellular receptor that was active. The amount of glucose would increase. The cells would eventually die due to the fact that there was no cellular activity (cell communication) taking place because the receptors were inhibited. A is not correct because if insulin were to bind to a receptor that is inhibited then the message would not be relayed. B is not correct because insulin can’t diffuse through a cell because it is a protein (hormone) and it would be too big to pass through. D is not correct because cells don’t die because there isn’t any cellular activity, they die from programmed cell death or exposure to harmful environments. C is the answer because since the receptors are inhibited, insulin can’t bind which then can’t open the glucose transporter (GLUT) so the amount of glucose levels would increase since glucose can’t be taken into the cell for storage as glycogen. Free response: A group of scientists are designing an experiment in which they are trying to figure out how to inhibit a disruption in the signal transduction pathway via cell communication. Describe the process that occurs during normal cell communication Discuss one thing that could help the inhibition of these pathways Provide evidence of a real life disease that results in disruption to these pathways Cell communication can occur through short or long distances. Cell communication starts out with reception when a ligand binds to a receptor, then transduction when the message is being amplified through a series of steps with the use of secondary messengers, and it finally results in a cellular response. One way that the scientists could inhibit this disruption is to inhibit the receptor in which the ligand binds to. If that is inhibited then no message can be relayed causing no disruption in the signal transduction pathway, also creating no cellular response. A real life disease in which this occurs is diabetes. With Type 1 Diabetes, a person is not producing insulin, therefore it doesn’t have the capabilities of binding with the receptor. With Type 2 Diabetes, the insulin receptor is ignoring the message that is trying to come through ultimately disrupting the signal transduction pathway by inactivating GLUT and as a result the person doesn’t take in glucose.

31. 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 make claims and predictions about natural phenomena based on scientific theories and models Explanation: Different environmental stimuli will turn genes on or off in the processes of gene regulation and expression. These stimuli include changes in temperature, light (UV radiation), drugs, chemicals and pH. A gene for increased growth in animals could be turned on because of one of these stimuli. A specific example could be presence of the opposite mating type on pheromones production in yeast and other fungi or an environmental factor determining the sex of a reptile. M.C. Question: Hydrangeas were planted in the spring and bloomed pink, however the flowers later turned blue in the late summer/early fall. Which of the following best accounts for this change in color? A) The higher UV index denatures the color pigments in the petals and changes them from pink to blue. B) A change to the color blue serves as a defense mechanism from harmful parasites that come out during warmer seasons. C)The pH of the soil fluctuated, causing a gene in the plant that makes it blue to be turned on and expressed D)The roots of the plant become more selective during different seasons and the nutrients that are selected for during the summer change the blossom color to blue. Learning log/FRQ style Question: i. Briefly define the process of gene regulation and gene expression AND ii. Relate how a change in season could impact gene expression and the phenotype of an arctic fox. iii.Relate how removing lactose from a bacterial culture of E. coli affect the genome and phenotypic expression?

32. Answer Key-LO 4.24 Hydrangeas were planted in the spring and bloomed pink, however the flowers later turned blue in the late summer/early fall. Which of the following best accounts for this change in color? A) The higher UV index denatures the color pigments in the petals and changes them from pink to blue. B) A change to the color blue serves as a defense mechanism from harmful parasites that come out during warmer seasons. C)The pH of the soil fluctuated, causing a gene in the plant that makes it blue to be turned on and expressed D)The roots of the plant become more selective during different seasons and the nutrients that are selected for during the summer change the blossom color to blue. Answer C is the only choice that makes sense because a color change in a flower is from a gene being activated or deactivated and this affects the phenotype of the flower. The rest of the answer choices do not involve an environmental factor changes gene expression and regulation. i. Define the process of gene regulation and gene expression AND ii. relate how a change in season could impact gene expression and the phenotype of an arctic fox. iii. Relate how removing lactose from a bacterial culture of E. coli affect the genome and phenotypic expression. i. Gene regulation is the process of turning genes on and off to ensure they are expressed at the proper time. Also gene regulation can help an organism respond to its environment. Gene expression refers to whether a gene is activated and being used or not and if it is, the genotype and phenotype reflects it. In order to do this in eukaryotes, a gene must undergo transcription into RNA, which is then processed into mRNA and transported to the cytoplasm. Here, some mRNA is degraded but some is translated to a polypeptide. The polypeptide then may be cleaved or chemically modified to form an active protein which might denature and transform into a degraded protein. • During the winter, the fur coat of the arctic fox usually lightens due to a decrease in the amount of daylight. This lack of daylight causes a genetic change in the animal and the fur to lighten. • When genes in the lacoperon are transcribed, a single mRNA is produced. In the absence of lactose, the operon is turned off. The regulatory gene lacI produces an mRNA that produces a lac repressor protein, which can bind to the operator of the lacoperon. The lac regulatory protein is called a repressor because it keeps RNA polymerase from transcribing the structural genes. It would be inefficient for e. coli to express lac genes with no lactose present which is why the lac repressor prevents transcription of the gene.

33. How genes can be turned on (above) Various levels of gene expression and regulation (left)

34. LO 2.30 The student can create representations or models to describe nonspecific immune defenses in plants and animals.[See SP 1.1, 1.2] SP 1.1: The student can create representations and models of natural or man-made phenomena and systems in the domain. SP 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Explanation: A nonspecific immune responses can be defined as the generalized line of defense which an organism innately has. These nonspecific responses attempt to fend off all prospective threats to the organism, hence the “nonspecific.” Invertebrates are limited to these nonspecific mechanisms, lacking the secondary line of defense which are pathogen specific in vertebrates. Nonspecific defenses include but are not limited to: barriers (skin), phagocytosis, elimination, unfavorable pH/environments, systematic cell destruction, lysozyme action, the inflammatory response and traps (mucus membranes). Plant defenses are also limited to nonspecific responses which overlap with animals. Plant defenses against pathogens include molecular recognition systems with systemic responses; infection triggers chemical responses that destroy infected and adjacent cells, thus localizing the effects and removing anything that could be afflicted. Students should fully grasp these concepts, and in turn, be able to produce visual representations or models of the nonspecific immune processes. M.C Question: Which of the following isn’t an innate immunity that protects an individual as they are riding the subway from contracting a bacterial infection? a.) Natural killer cells b.) skin c.) memory B cells d.) mucous membranes Learning Log Question: Plants and animals have myriad nonspecific immune responses that are the first line of defense for organisms. a.) Discuss three nonspecific immune system responses that hinder the establishment of a pathogen within the body. Provide a diagram to support your response with at least one of the nonspecific responses you explain. b.) Plants only have a nonspecific immune responses. Discuss an immune defense mechanisms of a plant and provide a diagram to illustrate this process. Skin: our body’s barrier and primary defense mechanism

35. Answer Key M.C Question: • Which of the following isn’t an innate immunity that protects an individual as they are riding the subway from contracting a bacterial infection? a.) Natural killer cells b.) skin c.) memory B cells d.) mucous membranes • All of the choices above are nonspecific immune defensives , with the exception of C. Memory B cells are specific to antigens that infect our bodies; they “remember” how to fend off the infection so that our bodies won’t have to fight the same infection twice. (The reason we only get the chicken poxs once) Learning log Question: Plants and animals have myriad nonspecific immune responses that are the first line of defense for organisms. a.) Discuss three nonspecific immune system responses that hinder the establishment of a pathogen within the body. Provide a diagram to support your response with at least one of the nonspecific responses you explain. Sample response A: Our skin acts as a defensive barrier to bacteria and viruses in the environment; it prevents bacteria from reaching inner cells that which would suffer if otherwise breeched. The opening of our bodies are protected by traps such as ear wax, hair or mucus membranes which essentially “catch” pathogens as they attempt to enter the body. Mucus membranes contain pathogen destroying enzymes which kill pathogens, further shielding the body from infection. The inflammatory response is induced in situations when the body becomes vulnerable- for instance, paper cuts. Cells of the afflicted area send out histamines, attracting macrophages. Vasodilation occurs, increasing blood flow to the area in order for more macrophages to inhibit and engulf pathogens. • Other responses could reference: Phagocytosis (white blood cells), Elimination (coughing, sneezing, urination) Unfavorable pH /environment (stomach acid, sweat, saliva, urine), Cellular destruction (i.e natural killer cells, complement), Interference with viral replication (interferon), Lysozyme action (excretion of sweat/ tears) Diagram of Inflammatory Response

36. Answer Key Continued LL Question Part B: b.) Plants only have a nonspecific immune responses. Discuss an immune defense mechanism of a plant . Sample Response B: Plants nonspecific response to pathogens include the Hypersensitive Response (HR). Essentially, HR is a form of apoptosis or programmed cell death. If the plant cells are presented with some sort of foreign cell, then the afflicted cells breakdown along with those adjacent to them to minimize the prospective diseased area and preventing the spread of microbial pathogens.

37. LO 1.17: The student is able to pose scientific questions about a group of organisms whose relatedness is described by a phylogenetic tree or cladogram in order to (1) identify shared characteristics, (2) make inferences about the evolutionary history of the group, and (3) identify character data that could extend or improve the phylogenetic tree. SP 3.1: The student can pose scientific questions. Explanation: Due to evolution, organisms share many common biological processes that are necessary for survival. The presence of these common processes serves as evidence that all organisms are linked to some kind of common ancestry. Phylogenetic trees show evolutionary history, representing both acquired traits and traits lost during evolution by means of natural selection. Phylogenetic trees and cladograms model speciation that has occurred. For example, the relatedness of any two groups on the tree is shown by how recently two groups had a common ancestor. Phylogenetic trees and cladograms serve as means by which inferences can be drawn about why species have a particular trait and can answer questions about a specie’s history. M.C. : The following cladogram shows the distribution of five different derived characteristics in six different species. The cladogram can provide insight into vertebrate phylogeny for all of the posed questions EXCEPT: A. Why do all the vertebrates in the ingroup have backbones? B. Why are hinged jaws a character absent in lampreys but present in other members of the ingroup? C. What is the evolutionary history of each of the species? D. Why is lancelet considered as part of the outgroup? FRQ: You are attempting to convert this cladogram into a phylogenetic tree. Answer the following questions to serve as the premise for your research: (a) How do you identify shared characteristics on a cladogram? (b) What inference can be drawn about the evolutionary history of the group? (c) What character data could extend or improve the phylogenetic tree? Identify at least two mechanisms.

38. ANSWER KEY– LO 1.17 M.C. The following cladogram shows the distribution of five different derived characteristics in six different species. The cladogram can provide insight into vertebrate phylogeny for all of the posed questions EXCEPT: A. Why do all the vertebrates in the ingroup have backbones? Incorrect– The cladogram shows that all of the vertebrates in the ingroup have backbones. This is because it is a shared primitive character that was present in the ancestral vertebrate, though not in the outgroup. B. Why are hinged jaws a character absent in lampreys but present in other members of the ingroup? Incorrect– The cladogram shows that lampreys do not have this character; this character is the early branch point in the vertebrate clade. C. What is the evolutionary history of each of the species? Correct– A cladogram is not a phylogenetic tree and cannot show this information. Phylogenetic trees depict hypotheses about evolutionary relation while cladograms only show patterns of shared characteristics. To covert this cladogram into a phylogenetic tree would require more information from fossils, for example. D. Why is lancelet considered as part of the outgroup? Incorrect– The cladogram shows that the lancelet less closely related than any of the ingroup members are to each otherirtually no shared characteristics. FRQ: You are attempting to convert this cladogram into a phylogenetic tree. Answer the following questions to serve as the premise for your research: (a) How do you identify organisms with shared characteristics on a cladogram? (b) What inference can be drawn about the evolutionary history of the group? (c) What character data could be used to help convert the cladogram into phylogenetic tree? Identify at least two mechanisms. A cladogram will begin by grouping organisms based on a characteristics displayed by ALL the members of the group. Subsequently, the larger group will contain increasingly smaller groups that share the traits of the groups before them. The hinged jaw character absent in lampreys is present in other members of the ingroup; this character helps us identify an early branch point in the vertebrate clade. This provides evidence of the possible evolution of a new species. To convert this cladogram into a phylogenetic tree we would need more information-for example, from fossils, which can indicate when, and in which groups, the characters first appeared. Identifying more branching points by extending the pool of organisms would broaden the scope of the phylogenetic tree and allow for more accurate history of the evolution of the species.

39. LO 3.16: The student is able to explain how the inheritance patterns of many traits cannot be accounted for by Mendelian genetics. • SP 6.3: The student can articulate the reasons that scientific explanations and theories are refined or replaced. • Mendelian genetics occur when the offspring follows the predictable pattern of a 3:1 phenotypic ratio and 1:2:1 genotypic ratio. But, epigenetic inheritance, polygenetic inheritance, and many other variables can interrupt the Mendelian inheritance patterns. • Which is an example of non-Mendelian inheritance? a. hitchhiker’s thumb c. widow’s peak b. skin color d. earlobe detachment • Mendelian inheritance with non-Mendelian inheritancehave several differences. a) List and explain three facets of Mendelian genetics. b) List and explain three facets of non-Mendelian genetics.

40. D. The answer is “B” because skin color is an example of polygenetic inheritance, but the other traits are distributed through Mendelian genetics. E. a) Mendel has three laws, which involve segregation, dominance, and independent assortment. Segregation is when chromosome pairs are separated into individualgametes to carry genetic information to their offspring. Dominant and recessive alleles are also important parts of Mendel genetics because dominant alleles cancel out the affect of recessive alleles. Independent assortment is when alleles on different chromosomes are distributed randomly to individual gametes. b) Polygenetic traits are determined by the combined effect of more than one pairs of genes. Co-dominance is when the two alleles are both expressed in a heterozygote, instead of a recessive allele’s expression being blocked. Pleiotropy occurs when a single gene is responsible for more than one trait, like in sickle cell anemia and albinism.

41. LO 1.4 The student is able to evaluate data-based evidence that describes evolutionary changes in the genetic makeup of a population over time. SP 5.3 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Explanation: According to Darwin’s theory of natural selection, competition for limited resources results in differential survival. Individuals with more favorable phenotypes are more likely to survive and produce more offspring, thus passing traits to subsequent generations. Although natural selection is usually the major mechanism for evolution, genetic variation in populations can occur through other processes, including mutation, genetic drift, sexual selection and artificial selection. Inbreeding, small population size, nonrandom mating, the absence of migration and a net lack of mutation can lead to a loss of genetic diversity. Using evidence given from a diagram or chart, students should be able to describe what changes caused the differences in the genetic make up of a population. Cross 2 Learning Log/FRQ-style Question: A new species of fly was discovered in the South Pacific. Several different crosses were performed, each using 100 females and 100 males. The phenotypes of the parents and the resulting offspring were recorded. Cross I. All F1 offspring had bronze eyes. F1 flies were crossed, and the data for F2 flies are given below. Cross II: All F1 offspring had stunted wings. F1 flies were crossed, and the data for F2 flies are shown to the right. Cross III: All F1 offspring had bronze eyes and stunted wings. F1 flies were crossed with true-breeding red-eyed, normal-winged flies, and results are shown to the right. Based on the information given in the charts above, what conclusions can be draw from cross I and II? What data can then be drawn from Cross III? Explain how the data supports your conclusion Cross 3 M.C. Question: Using the charts above and to the left, which of the following factors would affect whether the island’s fly population is in Hardy-Weinberg equilibrium for the gene above? A) There is a large population size so it maximizes genetic drift B) Random mating causes gene pool changes due to mate preferences. C) There are no mutations meaning that there are no new alleles in the population. D) There is no immigration but there are gene pool changes caused by the addition and subtraction of alleles. E) There is no natural selection even though there are alleles favored or disfavored by the environment. Cross 1

42. Answer Key – LO 1.4 M.C. Question: Using the charts above and to the left, which of the following factors would affect whether the island’s fly population is in Hardy-Weinberg equilibrium for the gene above? A) There is a large population size so it maximizes genetic drift B) Random mating causes gene pool changes due to mate preferences. C) There are no mutations meaning that there are no new alleles in the population. D) There is no immigration but there are gene pool changes caused by the addition and subtraction of alleles. E) There is no natural selection even though there are alleles favored or disfavored by the environment. FRQ Answer: For cross I, bronze is dominant and red is recessive, and non-sex-linked are also autosomal. All F1 or heterozygotes express dominant traits such as the bronze flies. The F2 generation shows a 3 to 1 ratio. There is an equal distribution of F2 phenotypes for both genders. For cross 2, the stunted is dominant and the normal is recessive, and the non-sex-linked are also autosomal. All F1 heterozygotes express dominant traits because they are stunted, and F2 shows a 3 to 1 ratio. There is also an equal distribution of F2 phenotypes for both genders. For cross 3, the genes are linked, there is crossing over, and genes are 10 map units apart. That is due to how there is not a 1:1:1:1 ratio as predicted by independent assortment. There is also not a 1:1 ratio or two recombinant phenotypes that are unexpected. The frequency of recombinant phenotypes was also 10%.

43. LO 2.25 The student can construct explanations based on scientific evidence that homeostatic mechanisms reflect continuity due to common ancestry and/or divergence due to adaptation in different environments SP 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Explanation: A Homeostatic mechanism is the property of a system in which variables are regulated so that internal conditions remain stable and relatively constant. In other words homeostasis is an internal stable environment. Many organisms have similar mechanisms to restore homeostasis against certain factors such as dehydration. A disrupted environment due to natural disasters such as a drought or water limitation, can cause the organism to be faced with a lack of water resources in the environment. The excretory system tries conserve the water already retained by minimizing the water loss through urine and sweat glands and releasing anti-diuretic hormones. Also most animals respond in a similar way towards fighting infection through the action of the immune system such as signaling the white blood cells (B and T cells) to fight pathogens and kill infected cells. When we look at a variety of organisms and how they maintain homeostasis we discover a continuity or a simple strategy once developed,which run through an entire lineage or ancestry. Change can result from different environmental factors being pressured onto the organism living in the new environment. In 2004 the Tiktaalik experiment conducted by Neil Shubin proved that the Tiktaalik (an extinct four legged organism that had gills to swim in water, lungs to breathe on land, 4 fins/leg to live on land and swim in the water) stood as a representative of the evolutionary transition from fish to amphibians. This was due to a change to adapt to different environments. Tiktaalik was an important transitional fossil that enabled us to understand how different environmental pressures result in certain characteristics to become favored over time. Although certain systems, such as the excretory system (used for getting rid of waste and blood filtration) in earthworms, vertebrates, and flatworms serve the same purpose and remain unchanged over the last millions of years resulting in continuity. M.C. Question: Which of the following statements below is FALSE concerning the scientific evidence of homeostatic mechanisms with regards to EVOLUTION in the excretory system? A) Invertebrates and vertebrates both evolved to having an excretory system extremely similar to each other in the function of getting rid of excess solutes or water due to sharing a common ancestor B) Excretion can vary greatly between invertebrates and vertebrates, depending on the complexity of the organism. C) An organisms morphology is developed through specialized structures that makeup the excretory system D) Osmoregulation (control of levels of water and mineral salts in blood) in the excretory system required no evolution Amphibian Learning Log/FRQ-style Question: Consider the situation of a marine organism obtaining oxygen from the water and into animal cells, to transitioning to a terrestrial organism obtaining oxygen through the air and into animal cells. Through this evolutionary process, what adaptations would be favored by natural selection? Tiktaalik Fish

44. Answer Key- LO 2.25 M.C. Question: Which of the following statements below is FALSE concerning the scientific evidence of homeostatic mechanisms with regards to EVOLUTION in the excretory system? A) Invertebrates and vertebrates both evolved to having an excretory system extremely similar to each other in the function of getting rid of excess solutes or water due to sharing a common ancestor B) Excretion can vary greatly between invertebrates and vertebrates, depending on the complexity of the organism. C) An organisms morphology is developed through specialized structures that makeup the excretory system D) Osmoregulation (control of levels of water and mineral salts in blood) in the excretory system required no evolution M.C. Question Answer: The correct answer for this question was D due to the fact that osmoregulation did require evolution. There is scientific evidence that Cetaceans had to adapt to new environmental changes by maintaining their salt and water balance to survive. This also suggests that cetaceans may have evolved an effective and complex mechanism for osmoregulation used today in organisms. Learning Log/FRQ-style Question: Consider the situation of a marine organism obtaining oxygen from the water and into animal cells, to transitioning to a terrestrial organism obtaining oxygen through the air and into animal cells. Through this evolutionary process, what adaptations would be favored by natural selection? Learning Log/FRQ-style Answer: (Each explanation for a favored adaptation is a point, 3 points max.) Adaptations favored would include tissues of the respiration system to adapt from a wet/moist environment to a dry environment. Also tissues must be adapted to going from an environment of low oxygen levels in the water to an environment of high oxygen levels on land. Another adaptation would include a change in homeostatic mechanisms going from gills in species such as fish processing oxygen through counter current exchange to developing lungs in species such as mice to maintain water levels.

45. LO 2.23: The student is able to design a plan for collecting data to show that all biological systems (cells, organism, populations, communities and ecosystems) are affected by complex biotic and abiotic interactions. SP 4.2: The student can design a plan for collecting data to answer a particular scientific question. SP 7.2: The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Explanation: All biological systems, from cells to ecosystems, are influenced by complex biotic and abiotic interactions. The availability of resources influences activities in cells and organisms; examples include responses to cell density, biofilm(s) formation, temperature responses, and responses to nutrient and water availability. Cell activities are affected by interactions with biotic and abiotic factors; high temperatures denature important proteins in cells disrupting its activity. The activity of organisms can also be influenced by biotic and abiotic factors, these influences can be observed with symbiosis, predator-prey relationships and how these organisms react to environmental changes such as temperature, water and nutrient availability and pH. Water and nutrient availability affect the primary producers and this in turn disrupts food chains and food webs that affect the stability of populations, communities and ecosystems. To collect data to show how biological systems are affected by complex biotic and abiotic interactions one could design an experiment or conduct an observational study. The scientific method should be used for an effective experiment, the steps of the scientific method are: the formulation of a question, make a hypothesis, experiment, and analyse the data. The information is collected in the experiment (testing) part of the scientific method. After the collected data is analyzed, the problem in question is answered. Learning Log/ FRQ-style Question: Figure 1 illustrates the symbiotic mutualistic relationship between the clownfish and sea anemone. The clownfish’s fecal matter provides nutrients to the sea anemone while the clownfish feeds on small invertebrates that could harm the sea anemone it also protects it from predators with its stinging cells to which the clownfish is immune to. a. Design an experiment whose outcome would support the idea that the mutualistic relationship is beneficial for both animals. M.C. Question: Which of the following is NOT a cell's response to high temperatures? A. Proteins denature. B. Kinetic energy of the cell decreases. C. The phospholipid bilayer behaves like a liquid. D. Respiration rates increase. Figure 1 Figure 1 source: http://en.wikipedia.org/wiki/File:Common_clownfish_curves_dnsmpl.jpg

46. Answer Key- LO 2.23 M.C. Answer: Which of the following is NOT a cell's response to high temperatures? A. Proteins denature. B. Kinetic energy of the cell decreases. C. The phospholipid bilayer behaves like a liquid. D. Respiration rates increase. Learning Log/ FRQ-style Answer: a. Experiment; -Question: Is symbiotic mutualistic relationships actually beneficial for both organisms? -Hypothesis: If symbiotic mutualistic relationships benefit both organisms, then when separated, the organisms would have lower survival rates. -Test: Have three separate tanks modeling coral reefs where clownfish and sea anemones usually live. One (the control group) would have a normal coral reef model with the clownfish and the sea anemone living together. The second model would have a regular coral reef with clownfish but no sea anemone and the third model will be a regular coral reef with sea anemones but not clownfish. Leave the three models alone, untouched for a month so they model a real coral reef and after the month has passed calculate the survival rate of each organism. *Independent variable: Whether or not the two organisms are together *Dependent variable: Survival rate -Collect and record data -Reach a conclusion Learning Log/ FRQ-style Question: Figure 1 illustrates the symbiotic mutualistic relationship between the clownfish and sea anemone. The clownfish’s fecal matter provides nutrients to the sea anemone while the clownfish feeds on small invertebrates that could harm the sea anemone it also protects it from predators with its stinging cells to which the clownfish is immune to. Design an experiment whose outcome would support the idea that the mutualistic relationship is beneficial for both animals.

47. LO 3.30 - The student is able to use representations and appropriate models to describe how viral replication introduces genetic variation in the viral population. SP 1.4 – The student can use representations and models to analyze situations or to solve problems quantitatively and qualitatively. Explanation – Viruses have great genetic variation when a single species of virus is compared with the rest of its population. First off viruses can replicate efficiently and at an incredibly high rate which makes the RNA coding errors that already have a high rate of occurrence because of a lack of replication error-checking mechanisms happen more frequently. Viruses also increase their replication rate by simply replication using a component assembly model (lytic cycle) which allows for one virus to make plenty of offspring with just itself and a host organism. M.C. Question Which stage is the selection point for the virus to choose between the lytic cycle or the lysogenic cycle? A: E B: B C: C D: D Free Response Question The graph to the right is the population of a bacteria in a given area and time. In section C a virus is introduced into the bacteria’s environment. Predict what will happen to the population of the bacteria after the virus is introduced.

48. Answers to LO 3.30 M.C. Question Which stage is the selection point for the virus to choose between the lytic cycle or the lysogenic cycle? A: E B: B C: C D: D Free Response Question The graph to the right is the population of a bacteria in a given area and time. In section C a virus is introduced into the bacteria’s environment. Predict what will happen to the population of the bacteria after the virus is introduced. Answer The Bacteria will likely follow suit with the new graph to the right. This is because the rapid amount of reproduction of the virus causes the bacteria population to plummet. The reproductive method kills the host bacteria so the large amount of viruses made after the plummet will not be able to find bacteria to infect. After a certain amount of time both the viruses and the bacteria hit their carrying capacity.

49. Learning Concept 3.27 : The student is able to compare and contrast processes by which genetic variation is produced and maintained in organisms from multiple domains Science Practice 7.2 : The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big idea. Explanation: One reason that genetic variation is produced and maintained in organisms from multiple domains is because of the imperfect nature of DNA in the process of replicating and repairing. Usually an error in DNA occurs in one base pair for every one billion base pairs per replication cycle but the numbers add up quickly. What stops DNA polymerase, which reads from the 3’ -> 5’ end of the DNA strand, from creating more mutations in the DNA replication process is its ability to proofread information. There can also be a repair mishap where the Base-pair or Short-patch excision repair don’t occur correctly. Another reason that organisms from multiple domains have genetic variation is because of horizontal acquisitions of genetic information, usually in prokaryotes, through transformation, transduction, conjugation and transposition. Transformation is when a prokaryote uptakes naked DNA and incorporates it into its own DNA, transduction is when a virus injects genetic information from its previous host and transfers it to a new cell to which it injects its viral and previous host cell information into the new cell, conjugation is when two cells create a mating bridge and the replication of a plasmid occurs and is delivered to the recipient cell from the donor cell, and transposition is the movement of DNA around the chromosomes from one gene to another part of the genome through the function of transposable elements. Eukaryotes maintain their genetic variation through gamete formation. This includes crossing over which occurs in Prophase 1 where homologous chromosomes line up, cross a section of their chromatid and exchange portions of DNA, Independent assortment results from Anaphase 1 when the homologous chromosomes separate due to the contraction of spindles, and fertilization serves to increase variation because the mothers egg is a haploid, has half of the genetic information, and the sperm has the other half of the genetic variation. Multiple Choice: Which of the following is the least likely to contribute to genetic diversity in Eukaryotic cells. A. Crossing Over in Prophase 1 of meiosis B. The fertilization of the ovum by a gamete creating a zygote. C. Conjugation caused by a mating bridge forming and the donor cell transferring plasmid information to the recipient cell D.DNA polymerase adding the wrong base pairs to DNA during replication or repair of a DNA strand FRQ: Genetic variation is maintained by prokaryotic cells even though they do not undergo basic gamete formation like their Eukaryotic counterparts. Describe how conjugation in prokaryotic cells can increase their genetic variation. Draw a diagram and label the steps that you described in your description.

50. Multiple Choice: Which of the following is the least likely to contribute to genetic diversity in Eukaryotic cells. A. Crossing Over in Prophase 1 of meiosis B. The fertilization of the ovum by a gamete creating a zygote. C. Conjugation caused by a mating bridge forming and the donor cell transferring plasmid information to the recipient cell D.DNA polymerase adding the wrong base pairs to DNA during replication or repair of a DNA strand Multiple Choice Explanation: Crossing over increases genetic diversity in Eukaryotic cells by having Non-sister chromatids from homologous chromosomes exchange genetic information. This allows the combination of alleles form all the genes on the chromosome changes every generation. Fertilization occurs after meiosis where genetically varied gametes have half the chromosomes as the parent organism. When fertilization occurs, a random sperm and egg will fuse and create a zygote with the same number of chromosomes as the parent organisms. The resulting organism is a variation of the parental egg and sperm combination. Conjugation is most common in prokaryotic cells. This happens when a mating bridge is created between to cells and then the donor cells replicates its plasmid DNA and transfers it toe the recipient cell where crossing over can take place with the recipient cells DNA and the donor’s plasmid. Usually an error in DNA occurs in one base pair for every one billion base pairs per replication cycle but the numbers add up quickly. Although this number does not seem like a lot, there are 1 base pair mutation in one billion base pairs per replication cycle. Although this doesn’t sound like many mistakes, the numbers do accumulate at a very high rate. FRQ: Genetic variation is maintained by prokaryotic cells even though they do not undergo basic gamete formation like their Eukaryotic counterparts. Describe how conjugation in prokaryotic cells can increase their genetic variation. Draw a diagram and label the steps that you described in your description. Also add an example of how conjugation could be used in scientific research. Sample Drawing FRQ Answer: In the first part of conjugation there is an F+ plasmid cell, which will be the donor cell, and the F- cell, which is the recipient cell. The F+ cell has a pilus and it attaches it to the F- cell to create a mating bridge. Then the plasmid from the F+ cell is replicated and sent across the mating bridge. After the replication is complete, although the mating bridge usually breaks before the full replication of the plasmid, the donor plasmid will then be in the recipient cell and the connection between the cells is broken. This will then create to two F+ cells because both will have a plasmid. Now the previous recipient cell is now capable of transferring the plasmid DNA to other recipient cells. Conjugation can be used in research by having cells with plasmids donate their antibody resistant genes to other cells so that only the cells with the antibody resistant gene will survive in a petri dish with a petri dish with the antibody. Picture Source: http://academic.pgcc.edu/~kroberts/Lecture/Chapter%207/horizontal.html