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Biology- Organisms Final Study Guide

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by: Lauren Maddox

Biology- Organisms Final Study Guide bio 114

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Final Study Guide for Biology 114
Biology of Organisms (Bio 114)
Dr. Oliver Hyman
Study Guide
Biology; Science; Organisms; Bio 114
50 ?




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"Clutch. So clutch. Thank you sooo much Lauren!!! Thanks so much for your help! Needed it bad lol"
Ansley Cartwright

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This 27 page Study Guide was uploaded by Lauren Maddox on Saturday March 12, 2016. The Study Guide belongs to bio 114 at James Madison University taught by Dr. Oliver Hyman in Spring 2016. Since its upload, it has received 28 views. For similar materials see Biology of Organisms (Bio 114) in Biology at James Madison University.


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Date Created: 03/12/16
Learning Objectives from Exam I Learning Objectives for Final from Exam I: Process of Science and Cell Theory; 1 Students should be able to list the five fundamental characteristics of life and use these characteristics to determine whether something is living or non-living. Blooms Level: Knowledge, Comprehension and Application 1. use energy 2. made of cells 3. process hereditary information 4. replicate 5. product evolution 2 Students should be able to distinguish between descriptive vs. non- experimental vs. experimental studies and how these different aspects of study design relate to determining “causality” Blooms Level: Knowledge Descriptive-observation, not testing hypothesis Non-experimental- measures IV and DV, correlation Experimental- manipulates IV and DV establishes causality 3 Students should be able to identify the elements of well-designed experiments (control, indep, dep. vars, etc). Blooms Level: Knowledge Chemical Evolution and Cell Membranes 1 Students will be able to sketch a relative time-line or concept map to show Oparin and Haldane's theory of chemical evolution from prebiotic Earth to a living cell. Blooms Level: Knowledge Energy from heat, sun, and lightning acting on very simple chemicals was captured in chemical bonds forming simple, small, reduced carbon-containing molecules The simple molecules made amino acids, nucleotides, sugars, and lipids These created macromolecules- proteins, polysaccharides, and nucleic acids Then one of these were able to replicate 2 Students will be able to incorporate the role of energy into their map in LO #1 . Blooms Level: Knowledge, Comprehension and Application Each step requires input of energy • Reactions tend to be spontaneous when the product molecules have lower potential energy than the reactants • In chemical evolution, reactions went from more oxidized, low potential energy to more reduced, higher potential energy • These reactions did not occur spontaneously • Chemical evolution o Relatively low-energy molecule à higher energy molecule (more reduced) • Sun (heat and radiation) changes energy levels in molecules because it was transformed into chemical energy allowing for formation of higher energy molecules o Sunlight on the reactant side balances the higher energy required for the formation of formaldehyde and water o Building larger, more complex molecules requires work to be done 3 Students will be able to list and identify distinguishing properties of the 4 basic macromolecules and the fundamental roles that these molecules play in a living cell. Blooms Level: Knowledge, Comprehension and Application Proteins-hemoglobin molecule in red blood cells that transport oxygen through your blood to different tissues. Can be antibodies-made by immune system cells that attack pathogen. Can be catalyst. Can be formed in simulations of early earth conditions. Conditions that simulate undersea vents have polymerized AAs into proteins. 4 different nucleotides: A, T, G, C, and U- dna-exists as a double strand, double helix, functions as set of instructions that controls what proteins get made. RNA- single stranded, uses U instead of T, contains ribose as its sugar. Structurally complex and variable. Central dogma—DNA to RNA to protein. Dna to RNA is transcriptions. The new sequence from this is used for dictating which amino acids are put together. Rna to protein- translation. Polysaccharides-storage, structural support and energy 4 Students will be able to identify the defining characteristics that distinguish life from non-life and provide examples of the characteristics in different groups of organisms. Blooms Level: Knowledge and Comprehension Defining feature is a cell membrane 5 Students will be able to provide evidence of RNA World Hypothesis based on the basic properties of macromolecules and the criteria for the first self-replicating molecule. Blooms Level: Knowledge and Comprehension In order for a molecule to self replicate—contain information, act as a template, and act as a catalyst. Can act as a catalyst because it contains ribosomes. • Self-replicating molecule must o Contain information § Protein, DNA, RNA o Act as a template (serve as a blueprint to make a copy) § DNA, RNA o Act as a catalyst during the assembly and polymerization of its copy (act as an enzyme) § RNA, protein § Would have to replicate itself without help from sophisticated enzymes § Must be able to catalyze the reactions involved in replication • Altman and Cech discovered the first ribozyme, an enzyme made of RNA o First solid evidence for the RNA world hypothesis • Belief that RNA was the first self-replicating molecule 6 Students will understand molecular characteristics that impact polarity and how polarity determines behavior of molecules. Blooms Level: Knowledge and Comprehension 7 Students will be able to sketch a phospholipid bilayer and identify the polar and non-polar regions and explain how phospholipid characteristics of length, saturation and temperature impact permeability of the membrane. Blooms Level: Knowledge and Comprehension • Polar head (hydrophilic) • Nonpolar tail (hydrophobic) • Phospholipid characteristics o Length § Longer- tougher to cross, making membrane even denser § Shorter- easier to cross o Saturation § Unsaturated- kinks created by double bonds produce spaces • Reduce the strength of interactions, weakening barrier to solutes and making it easier for things to cross § Saturated- fewer spaces and stronger interactions o Temperature § Lower temperature- molecules move more slowly • Hydrophobic tails pack together more tightly, possibly solidify § Higher temperature- molecules increase in motion • Polarity of molecule o Small nonpolar molecules move across more quickly o Large molecules and charged substances cross slowly, if at all • Short and unsaturated- higher permeability and fluidity • Long and saturated- lower permeability and fluidity 8 Students will identify key characteristics and distinguish between passive diffusion, osmosis, facilitated transport and active transport as mechanisms of membrane transport. Blooms Level: Knowledge Passive diffusion Substances on one side of a lipid bilayer can move to the other side spontaneously Concentration gradient- difference in solute concentrations Net movement from high to low concentration Diffusion is a spontaneous process because it results in an increase of entropy Chemical equilibrium established Osmosis Occurs only when solutions are separated by a membrane that permits water to cross but holds back some or all of the solutes Selectively permeable membrane Only unbound water molecules are allowed to cross Flow from lower solute concentration to higher solute concentration Osmosis dilutes the higher concentration and equalizes the concentration on both sides Movement in spontaneous Can swell or shrink a vesicle Inside solution hypotonic to the outside (lower concentration) causes cells to shrink because net flow of water is out of the vesicle Inside solution hypertonic to the outside (higher concentration) causes cells to swell because net flow of water is into the vesicle Facilitated transport Ion channels- ions routinely cross membranes through specialized membrane proteins Move from high to low concentration Move from areas of like charge to unlike charge Ions move in response to a combined concentration and electrical gradient, called the electrochemical gradient Channel proteins Selective because their structure only permits a particular type of ion or small molecule to pass through it Aquaporin’s- channels that allow water to cross the plasma membrane faster than without Gated channels- open or close in response to a signal, such as the binding of a particular molecule or a change in the electrical voltage across the membrane Flow of ions and small molecules through membrane channels is carefully controlled Carrier proteins- specialized membrane proteins that change shape during the transport process Active transport Cells move molecules against their electrochemical gradient Requires input of energy 9 Students will be able to use their fundamental knowledge of molecule polarity (objective 7) phospholipid bilayers (objective 8) and membrane transport (objective 9) to predict relative levels of movement of different molecules with different phospholipid bilayer features in the context of a biological problem. Blooms Level: Knowledge, Comprehension and Application Learning Objectives: Glycolysis, Fermentation and Respiration 1 Students will be able to draw the equation showing how energy is generated from ATP hydrolysis (ATP à ADP + P) and know how long ATP can last for in the cell. Blooms Level: Knowledge ATP + H2O à ADP + P + Energy Cells contain only enough ATP to last from 30 seconds to a few minutes ATP is unstable and is not stored 2 Students will explain how energy for cells to do work is generated from sugar. To do this, students will be able to write the cell respiration equation linked to the equation for ATP hydrolysis. Blooms Level: Knowledge and Comprehension • ATP hydrolysis o ATP + H2O à ADP + P + energy • Endergonic reactions in cells a result of the energy released from the exergonic hydrolysis of ATP • Energy released used for phosphorylation • The ATP that is produced in cellular respiration can be hydrolyzed to release energy that can be used to drive endergonic reactions • ATP is then regenerated through phosphorylation 3 Using the equation for cell respiration (including glycolysis), students will be able to identify which steps the different reactants are used in and what they are converted to and which steps the different products are formed in. Blooms Level: Knowledge and Comprehension • Reactants o Glucose- glycolysis o Oxygen- needed for all other processes • Products o CO2- pyruvate processing, citric acid cycle o H2O- oxidative phosphorylation o ATP- glycolysis, citric acid cycle, and oxidative phosphorylation • Electrons from NADH and FADH2 are transferred to oxygen. NADH and FADH2 are oxidized to NAD+ and FAD, and oxygen is reduced to form water. 4 Students will be able to identify reduction and oxidation reactions that occur throughout glycolysis and cell respiration and identify which molecule of two is more reduced and how this relates to levels of energy in the molecule. Blooms Level: Knowledge, Comprehension and Application Cell respiration- sugar is oxidized to carbon dioxide In glycolysis- nad+ is reduced to NADH and glucose is oxidized to pyruvate 5 Students will know which organisms (Eukaryotes, Prokaryotes, Animals, Plants) need ATP and perform glycolysis and cell respiration, where the different stages of each these processes occurs in these different taxonomic groups, and how this relates to the evolutionary history of these processes (are they ancient ancestral traits or newly derived traits held in common?). Blooms Level: Knowledge All organisms need ATP and undergo cellular respiration Plants produce glucose needed to cellular respiration • Glycolysis- cytoplasm of eukaryotes and prokaryotes • TCA- mitochondrial matrix in eukaryotes, cytosol in prokaryotes • ETC- inner membrane of mitochondria in eukaryotes, plasma membrane in prokaryotes 6 Students will understand what conditions regulate the fate of pyruvate after glycolysis in the cell. Blooms Level: Knowledge and Comprehension When oxygen or another electron acceptor used by the ETC is present in a cell, the pyruvate produced by glycolysis enters the citric acid cycle and the electron transport system is active. If no electron acceptor is available to keep the ETC running, the pyruvate undergoes reactions known as fermentation. 7 Students will be able to explain the ultimate goal of fermentation for the cell and understand the relative levels of ATP generated in this process compared to the levels generated in cell respiration. Blooms Level: Knowledge and Comprehension • Regenerates NAD+ by oxidizing NADH • Allows glycolysis to keep producing ATP even when the ETC is shut down • Extremely inefficient compared to cell respiration o Produces just 2 molecules of ATP for each molecule of glucose metabolized o Cellular respiration produces 29 ATP • In organisms that usually use oxygen as an electron acceptor, fermentation is an alternative mode of ATP production when oxygen supplies temporarily run out 8 Students will understand the general difference between how ATP is generated from energy released in glycolysis and TCA cycle versus how it is generated from energy released during the ETC. Blooms Level: Knowledge and Comprehension Atp is produced from ADP For TCA—when energy is released by the oxidation of one molecule of acetyl CoA is used to produce either GTP or ATP. It is generated in muscle cells 9 Students will be able to write the equation for glycolysis and explain how the energy released from oxidation of glucose contributes to formation of two different energy containing molecules and how cells undergoing glycolysis use these two energy molecules differently. Blooms Level: Knowledge and Comprehension Students will understand the consequence of when cell respiration lacks an electron acceptor like oxygen. Blooms Level: Knowledge • Oxygen is the most efficient electron acceptor • Large difference between the potential energy of electrons in NADH and those in oxygen • ETC can therefore generate a large proton-motive force • Cells that do not use oxygen as an electron acceptor cannot generate such a large potential energy difference o Make less ATP from each glucose molecule o Aerobic organisms grow more slowly than anaerobic o When there is no terminal electron acceptor, the electrons in each of the complexes of the ETC have no place to go and the chain stops o NADH remains reduced o Concentration of NAD+ drops so there is none to drive glycolysis o NO ATP CAN BE PRODUCED Photosynthesis Students should be able to: 2 Describe the evolutionary significance of photosynthesis and list several ways in which photosynthesis benefits organisms on Earth. Photosynthesis first evolved in prokaryotes. In 2.7 bya. Cyanobacteria were the first to introduce oxygen into the atmosphere. They were just doing it on the membranes throughout cytosol. Diatoms-single celled protists. Produce half of organic C and O2 in oceans. Green algae does it. Terrestrial Eukaryotes-land plants. It happens in the chloroplast, primary producers for terrestrial food chains. You can outcompete organisms that can’t do photosynthesis. Oxygen accumulates in the atmosphere. Allows for evolution and diversification of organisms using O2 for cell respiration. Has formed the ozone layer-protects us from UV radiation. It has a key role in carbon cycling- takes carbon out of atmosphere and uses it to make photosynthesis. It removes anthropogenic CO2. It influences our temperature. Bacterial cells that evolved the ability to use it as an electron acceptor via cellular respiration. These organisms can use much more ATP. Enables cell respiration. 3 Identify how matter and energy are transformed during photosynthesis. Matter is conserved: matter on the left side balances the matter on the right side. It is a transfer of energy from light energy to chemical energy in reduced carbon molecule; sugar . Light-energy+ H2O + CO2--- à O2 + chemical energy in the many C -H bonds of sugar. The light energy is captured in a way that is transferred to chemical bonds - light energy from sun to chlorophyll to the primary reaction center to ATP. Called the antenna complex. Photo ns (light energy) strikes a pigment molecule in the antenna complex, the energy is absorbed and an electron is excited in response. This is known as resonance energy transfer. Only happens between pigments that absorb higher energy photons to those absorbin g lower energy photons. Once the energy is transferred, the original excited electron falls back to its ground state. Energy is transferred inside the antenna complex. Then it goes to the reaction center- its excited electron is transferred to an electron acceptor. Electromagnetic energy is transformed to chemical energy. 4 Write the equation for photosynthesis. Identify the stages of photosynthesis in which each reactant is used, each product is produced, where these reactions occur, and the major reduction and oxidation reactions within photosynthesis. 6CO2 + 6H20 à 6O2 + C6H12O6 The carbon in the CO2 and the sugar is reduced. The Oxygen in water and oxygen is oxidized. Light capturing reactions- occur in thylakoids in chloroplast, h20 to o2. Atp and NADPH is produced for the Calvin cycle. The Calvin cycle occurs in stroma-space outside of thylakoids. Atp and NADPH used to reduce co2 to sugar. Resulting sugar used in cellular respiration. It converts CE from light-capturing reactions into chemical energy in sugars. 2 Explain how the light reactions and Calvin Cycle are linked together and how this impacts the time of day that the light reactions and Calvin cycle take place in most plants. They both happen in the chloroplast. Calvin cycle can only use ATP available in the chloroplast from light reactions. Takes place in the day because that is when light reactions occur. 3 Identify all the “forms” (ex. Carbon in sugar or protein or anothe2 CO molecule) that a carbon atom from a CO 2molecule in the atmosphere can assume when moving through the carbon cycle (ex. Sugar/starch/cellulose within a plant, CO2 in atmosphere, or sugar/protein/glycogen in a chemoheterotroph. Identify the processes that drive these transformations (cellular respiration, photosynthesis, biosynthesis, storage, etc.). See cycle you did in class and try to draw your own and see how many carbon transfer steps you can come up with). Process Plants Animals Cell respiration C from sugar made by C from consumed plant to C in CO2 sugar converted to C in CO2 photosynthesis C from CO2 converted NA to C in sugar biosynthesis C from CO2 converted C from consumed to C in amino acids, sugar converted to C nucleotides and fats, in amino acids, etc. nucleotides, fats, etc storage C from CO2 converted C from consumed to C in starch, sugar to C in eventually to C in glycogen, eventually CO2 to C in CO2 Decomposition C from sugar, amino same acids, nucleotides, fats, starch, glycogen in dead animals and plants converted to C in CO2 by respiration of decomposers 5 Predict the impact that changes in photosynthesis and cell respiration have on the mass of a plant and the CO2levels in the plant’s environment and why (see problem you did in class) 6 Photosynthesis makes them gain mass, respiration makes them lose. Plants take in more CO2 than they release. They have a net uptake of carbon. 7 In light- co2 is less 8 In dark- co2 is greater, mass is lost 5 Identify similarities and differences between photosynthesis and respiration in terms of the molecules produced and consumed and their energy levels (reduced vs. oxidized) 6 Both produce ATP. Different reactants—opposite. Photosynthesis can only occur in sunlight, in respiration sunlight isn’t required. In CR- oxygen is absorbed and co2 is released. In Photo- co2 is absorbed and oxygen is produced. In CR- releases energy, photo requires it. Both use electron transport chain. 7 8 Photosynthesis is an endergonic suite of redox reactions that produce sugars from carbon dioxide and light energy. Cellular respiration is an exergonic suite of redox reactions that produces carbon dioxide and ATP from sugars. Evolution by Natural Selection 6 Explain the relationship between the terms “evolution” and “natural selection”. Individuals are naturally selected. Populations evolve. All organisms distant from a common ancestor, all organisms evolve through natural selection. List Darwin’s criteria for natural selection and identify these criteria in an example/story of natural selection Individual organisms that make a population vary in traits, some of the trait differences are heritable (coded for in DNA), more offspring are produced than can reproduce so some will reproduce more than others, those that survive best and reproduce most are not a random sample from the population. Natural selection occurs when individuals with certain heritable traits produce more offspring than individuals without those traits. Dot organisms—1. All circles, but different colors living in same area. 2. Purple give birth to purple, blue give birth to blue. 3/4. nd nd 2 generation before reproducing run into predator, the 2 generation is all blue, and they reproduce blue. 8 Recognize common misconceptions that people have about evolution and natural selection and explain why they are wrong. 9 Misconception Correction Example Evolutionary change Natural selection Selection doesn’t occurs in organisms just sorts existing cause neck length variants in to increase in organisms; it individual giraffes, doesn’t change only in populations them. Evolutionary change occurs only in populations. Acclimatization doesn’t equal adaptation Adaptations occur Mutation, the Tapeworms are not because organisms source of new lower than their need or want them alleles, occurs by human hosts, just chance. Evolution adapted to a is not goal directed different or progressive. environment There is no such thing as a higher or lower organisms Organisms sacrifice Individual with Lemmings do not themselves for the alleles that cause jump off cliffs into good of the species self-sacrificing the sea to save the behavior die and do species not produce offspring, so these alleles are eliminated from the population Evolution perfects Some traits are Finch beaks cannot organisms nonadaptive. Some be both deep and traits cannot be narrow, due to optimized due to genetic fitness trade-offs. constraints. Some traits are limited by genetic or historical constraints. 10 9 Define and list examples of analogous characteristics that arise through convergent evolution and homologous characteristics. Homologous characteristics- trait shared by 2+ taxa that was inherited by common ancestor (backbones). Analogous characteristics are shared but not from common ancestor. Convergent evolution- similar adaptations that evolve independently. Wings in birds and bats. 10 Recognize clues that suggest that the similarities in two species are due to convergent evolution and not inheritance from a common ancestor. List examples of atavisms, vestigial traits and developmental homologies and explain how these examples support the theory that all organisms are related. Vestigial traits- a reduced or incompletely developed structure that has no function or reduced function, but is clearly similar to functioning organs or structures in closely related species. Atavism- genetically silenced over time, but for a twist of fate it can be brought up (webbed fate). Developmental homologies- gill pouch Phylogeny 3 Identify the parts of a phylogenetic tree 4 Correctly read and interpret a phylogenetic tree 5 Identify homologies, analogies, synapomorphies (and which monophyletic group they belong to), common ancestors (with identification of which lived most recently), parsimony, and different monophyletic groups on a phylogenetic tree. 6 Draw a tree of life for the 3 domains eukarya, archaea, and bacteria. Archaea is more closely related to eukarya. 7 Explain why homologous characteristics should only be placed on a tree once (parsimony). Want the simplest tree 8 Describe the experiments done by Carl Woese that resulted in our current tree of life with 3 domains. 9 Correctly place molecular and morphological characteristics of bacteria, archaea, and eukaryotes on the tree of life. 10He compared nucleotide sequences in ribosomal RNA to study relationships. 111. Fundamental division NOT between prokaryotes and eukaryotes. 122. archaea and eukarya share a more recent common ancestor than archaea and bacteria. This common ancestor was likely a prokaryote with a complex RNA polymerase and histones. 133. Fungi more closely related to animals than plants 144. Microorganisms are way more diverse than we thought 155. trees are always a work in progress. Prokaryotes: Archaea and Bacteria 10 Explain how prokaryotes have been able to introduce so much diversity into their population fast rate of reproduction, ability to exchange DNA 2 Explain the connection between metabolic and habitat diversity Sugar- e-donor. O2- e acceptor. It allows them to live in an environment where other organisms cannot, which lowers competition for resources. Co-exist with other prokaryotic species by cleaning up each other’s mess and again not competing for resources. 3 Sketch the nitrogen cycle and describe the role that different species of bacteria have in this cycle. 4 Provide examples of adaptations of psychrophiles and thermophiles and explain how these adaptations enable survival in extreme temperatures. Psychrophiles <15 C, death over 25 C. found mostly in cold ocean bottoms. Specialized membranes and proteins. Thermophiles- 50 C – 130 C. found in compost piles, hot springs, ocean hydrothermal vents, artificial hot water areas. They have internal temps. 5 Predict the properties of bacteria isolated from various extreme environments They have specialized cell membranes, and specialized proteins and DNA. Membranes are more permeable at high temps and less permeable at low temps. Thermophiles would have long, saturated phospholipids while psychrophiles would have short, unsaturated ones. At high temps, proteins and DNA denature- unfold. To prevent this- thermophiles have higher % of GC than AT in Non- Coding region of DNA. Their proteins have more charged amino acids. Resulting in more ionic bonds, which are stronger than H-bonds. 6 Explain the mechanisms by which variation is introduced into prokaryote populations (conjugation, etc) and how this differs from mechanisms in other populations such as eukaryotes (sex, etc). Transformation, transduction, conjugation Transformation-takes up free DNA from environment Transduction- virus’s can take up DNA by accident and give it to other bacteria Conjugation-bridge forms and the DNA passes from one to another. 7 Describe binary fission and its consequences with regards to genetic variation. The specific type of asexual reproduction carried out by prokaryotes. Means divide in half. Chromosome attaches to cell membrane, chromosome (DNA) is replicated, cell membrane pinches in “invaginates). Results in two daughter cells, which are identical to each other and the original parent cell. Low error rate, no genetic variation. Distinguish between the 4 general methods for obtaining E and C-C bonds (auto/hetero and photo/chemo) Phototrophs- light feeders. Chemotrophs-chemical feeders. Autotrophs- self-synthesized (using simple molecules like CO2, CH4). Heterotrophs- other feeders, from molecules produced by other organisms (sugar, fat, protein, etc). Photoautotrophs-plants Chemoheterotrophs-animals Evolution of Eukaryotes Students should be able to: 3 List key traits that define eukaryotes and the relative time line for when these traits arose they have very diverse lineage, diverse morphology, uni and multicellular, tiny to huge size, diverse reproduction- asexually by mitosis and sexually by meiosis. They have a membrane bound DNA (nucleus) and organelles (mitochondria. They have linear chromosomes they first appeared 2 bya. It took so long because st chemical evolution, then 1 prokaryotic cell, then diversification of prokaryotes. They have nuclear envelopes-has to do with surface area. How does SA: V relate to cellular processes? Volume dictates energy needs and waste production. Bigger cells need to add SA without adding volume = infoldings. If cells can infold, they can increase volume without decreasing sa:v ATP takes place in cell membranes, therefore more ATP is made. 4 List key events in the evolution of eukaryotic cells including evolution of the nucleus, mitochondria and chloroplasts. o Mitochondria: Mitochondria are about the size of an average a- proteobacterium o They replicate by fission, like bacterial cells. Duplication of mitochondria takes place independently of division by the host cell. o Mitochondria have own ribosomes and manufacture some of their own proteins, closely resemble bacterial ribosomes in size and composition and are poisoned by antibiotics that inhibit bacterial ribosomes o They have double membranes o Have their own genomes, organized as circular molecules-like the bacterial chromosome o Chloroplasts: Chloroplasts have the same list of bacteria-like characteristics presented earlier for mitochondria o Examples of endosymbiotic cyanobacteria are living inside the cells of protists or animals today o Chloroplasts contain a circular dna molecule containing genes like similar cyanobacterial genes o The photosynthetic organelle of one group of protists, has an outer layer containing the same constituent found in the cell walls of cyanobacteria Nucleus- infoldings of the plasma membrane occur in some bacteria living today, and the nuclear envelope and er of today’s eukaryotes are continuous 5 List current theories for how the traits in 1 and 2 arose 6 Endosymbiosis Theory- mitochondria originated when a bacterial cell took up residence inside another cell 2bya. 7 The relationship between the archaeal host and the engulfed bacterial cell was presumed to be stable because a mutual advantage existed between them: the host supplied the bacterium with protection and carbon compounds from its prey, while the bacterium produced much more atp than the host cell could synthesize on its on. The leading hypothesis to explain the origin of the nuclear envelope is based on infoldings of the plasma membrane 3 List the selective advantage(s) that the characteristics listed in 1 and 2 provide eukaryotes For the nucleus- it separated transcription and translation. RNA transcripts are processed inside the nucleus but translated outside the nucleus. With a simple nuclear envelope in place, alternative splicing and other forms of rna processing could occur-giving the early eukaryotes a new way to manage and process gene information Mitochondria- mitochondrial genomes typically encode less than 50 genes, whereas genomes from the endosymbiotic bacterium could encode about 1500 genes. These genes moved into the nuclear genome in the lateral gene transfer. Many still encode proteins that are synthesized by cytosolic ribosomes and imported into mitochondria. 4 List multiple lines of evidence that support the theory of endosymbiosis and the origin of the nucleus. Mitochondria all have their own circular genome. Mitochondria have 2 cell membranes. Mitochondria replicate by binary fission (just like other prokaryotes) and do so independently of the eukaryotic cell. Cr in prokaryotes and eukaryotes is almost exactly the same. infoldings of the plasma membrane occur in some bacteria living today, and the nuclear envelope and er of today’s eukaryotes are continuous 9 Explain how the evidence in 5 is supportive (for example; not just that “mitochondria have their own circular genome” but also that “this supports the hypothesis that mitochondria and chloroplasts were once prokaryotic cells as they also have a circular genome yet circular genomes are found no where else in eukaryotic cells”). 9 Describe how SA:V relates to cell size, energy production, nutrient acquisition, waste excretion, and the evolution of the nucleus. 10 Volume dictates energy needs and waste production. Smaller- needs less energy, makes less waster. Bigger- needs more energy, makes more water. As cells increase in size, energy needs to increase. Cell takes in food and let out wastes through the cell membrane. More infoldings- cell lose wastes more quickly per unit volume. Creates more ATP with higher sa:v. The smaller they are the higher the ratio is 7 Explain why the mechanisms of photosynthesis and cellular respiration are so similar in prokaryotes and eukaryotes hey are traits that are laterally transferred across branches on the tree of life. Eukaryotic reproduction: Mitosis and Meiosis Students should be able to: 7 List the fundamental and specific differences between meiosis and mitosis, in terms of the ploidy, genetic diversity, and general stages/alignment of chromosomes during the production of daughter cells/gametes 8 Mitosis-Produces genetically identical cells. Chromosomes contain all the organisms’ genetic info. Divides into daughter cells, with genes located at specific locations on chromosomes. All somatic cells. Does reproduction of a single cell- eukaryotes reproduce asexually by mitosis-1 mitotic division= new generation of identical organism. Multicellular eukaryotic cells undergo mitosis for growth, replacement of gen. identical cells. Multicellular eukaryotic cells undergo mitosis for: asexual reproduction (where multiple mitotic divisions make a new, genetically identical organisms. 9 Steps of Mitosis- prior to mitosis: each chromosome needs to be copied (DNA replication). After all chromosomes are replicated, sister chromatids align in the center of the cell, order is random. Sister chromatids separate. Single file alignment of sister chromatids is essential for ensuring each daughter cell gets each chromosome. 10 Mitosis is good for asexual reproduction- some eukaryotes reproduce a whole new organism by mitosis. Eukaryotes undergo mitosis for growth of organism, when new cells are needed to replace old and damaged cell, 11 Meiosis- produces genetically unique cells, complicated process, nothing like it in prokaryotes. For animals-reproduction by meiosis. Sexual reproduction- uses haploid cells- egg and sperm made through meiosis-lots of genetic variation introduced. Cell division resulting in chromosome reduction by half. Typically produces haploid n cells. All DNA copied in 2n but the resulting cells are haploid and not identical to each other or the parent cell because of how chromosomes line up and cell divides twice to make 4 haploid cells. 12 13 Differences: mitosis-stister chromatids separate. Meiosis- homologous pairs 1 separate, then sister chromatids separate. Mitosis is all diploid. Meiosis is diploid until anaphase I. 14 Mitosis Meiosis # of cell divisions 1 2 # of chromosomes in Same Half daughter cells compared to parent cells Separation of No Yes homologous pairs Are daughter cells No Yes (so much genetic genetically different variation is introduced from one another by meiosis *sex) 15 11 Determine the ploidy and chromosome number (n) of a cell. Ploidy is the number of unique copies of each chromosome. Chromosome number is the haploid number, which is the distinct types of chromosomes in a given cell. The ploidy 2n is given to diploid cells, two chromosomes of each type is given. For humans: there are 23 pairs of chromosomes so the chromosome number is 23. Humans are diploid so they are 2n=46. 10 Identify and describe sister chromatids, chromosomes, homologs, gametes, daughter cells, parent cells, and fertilization Sister chromatids-the two identical chromatid copies in a replicated chromosome. Chromosome is a structure made up of DNA and proteins; carries the cell’s hereditary information. Homologous pairs of chromosomes- pairs of sister chromatids, one set from mom, one set from dad, both the same chromosome number. They are similar in size, shape, and gene content. Gametes are sex chromosomes (egg and sperm). Daughter cells come from mitosis division, has the same genetic makeup as the parent cells. Parent cells- the original cells. • Explain how asexual reproduction by mitosis, self-fertilizing sexual reproduction, and cross-fertilizing sexual reproduction differ in the amount of genetic variation they produce. Asexual doesn’t produce a lot of variation because it’s the same cell. Clones. Least genetic variation. Only source of variation is random mutation. Sexual (self- fertilization) 1 individual produces sperm and eggs and fertilizes itself, more genetic variation. Source- independent assortment, crossing over and mutation Self fertilization- when gametes from the same individual fuse together, can still cause genetic variation, called hermaphrodites- contain both male and female sex organs. st Crossing over- early in meiosis (before 1 alignment) homologous chromosome pairs come together. Non-sister chromatids can swap pieces of chromosome. It creates new combinations of genes that were not present in either parent. 11 List the processes that produce genetic variation (independent assortment, crossing over, mixing of genomes, and mutation) and recall which of these processes occur in the modes of reproduction listed in 4. Independent assortment- random aligning of homologous chromosomes during Meiosis I. leads to variation in the genetic make up of the gametes. This arrangement of homologs is random. Crossing over- homologous chromosomes during Meiosis results in even more variation. Early in Meiosis homologous chromosome pairs come together. Non sister chromatids can swap pieces of chromosome (crossing over). These are new combinations of genes that were not present in either parent. Independent assortment and crossing over and mutation- sexual (self- fertilization). Random mutation is asexual (mitosis) Sexual (cross-fertilization)- independent assortment, crossing over, mutation, and mixing of genes from different individuals. 2 4 Explain how the processes listed in 5 create genetic diversity and magnitude of diversity they are capable of producing 5 Independent assortment allows for random alignments, which leads to variation in the genetic make up of the gametes. Crossing over has the most genetic variation-combinations of genes were not present in either parent. 6 Asexual (mitosis)- least genetic variation, only source of variation is random mutation 7 Sexual (self-fertilization)- more genetic variation, source: independent assortment, crossing over, and mutation 8 Sexual (cross-fertilization)- most genetic variation. Source: independent assortment, crossing over, mutation, and mixing of genes from different individuals. 5 Identify cells that show correct (or incorrect) alignment during the alignment phases of mitosis and meiosis. 6 Identify which process (mitosis vs. meiosis) is used in various types of eukaryotic reproduction and how this influences the genetic diversity of the resulting cells/organisms for asexual reproduction, eukaryotes use mitosis. It doesn’t have any variation. It is used for growth and replacing cells. For sexual reproduction: meiosis is used. It uses haploid cells (egg and sperm) made through meiosis. Lots of genetic variation used. 7 Explain the advantages and disadvantages of sexual reproduction. 8 Sexual reproduction doesn’t multiply as efficiently as asexual organisms. The purifying selection hypothesis- sex removes bad genes. It says that mitosis has exact genetic replicas, which could be bad, so all offspring or asexual parents will inherit these bad mutations or genes. If there are bad genes in meiosis, these are not inherited by all offspring. Another hypothesis for why sex exists is the changing-environment hypothesis. It says that offspring that are genetic clones of their parents are unlikely to thrive if the environment changes. 9 Suggestion: Make two columns: mitosis and meiosis, list the similarities and differences between the two processes. For example; homologous chromosomes separate in meiosis but not mitosis, sister chromatids separate in both (include drawing), any info about the how the ploidy changes throughout the process, etc. Then list how these stages are used by different groups of organisms we talked about; specifically plasmodium, plants (but also compared to animals). For example; animals use meiosis to make gametes, plasmodium and plants use mitosis to make gametes. Add as much organism specific information as you can to this mitosis/meiosis chart. Protists Students should be able to: 8 List the characteristics that define protists and their phylogenetic relationships to each other and other groups (eukaryotes, prokaryotes, etc). Students should understand the phylogeny of protists in the context of all eukaryotes. A protest is any eukaryote that is not a plant, animal or fungus. They are the most diverse group of eukaryotes, uni or multicellular, diverse life-cycles, diverse metabolisms (hetero and photo), and mobility. They all have a common feature of tending to live in environments surrounded by water (wet soil, water, and other organisms. They are a paraphyletic group-represent some, not all of the descendant of a single common ancestor. 9 List some common examples of protists phytoplankton, amoeba, dinoflagellates, nori, diatoms 16 Recall the general placement of plantae, green plants, land plants, green algae, protists (as a group), fungi and animals on a phylogenetic tree. Explain why climate change scientists (think CO 2), public health professionals, farmers and aquatic ecosystem scientists should all be interested in protists. Phytoplankton serve as bottom of food chain for aquatic ecosystem, they generate much of the oceans organic carbon (sugar) to feed other organisms, and they supply much of the oceans oxygen. Protists take in as much CO2 as all land plants combined. Co2 is fixed from the air, eventually carbon in organisms derived from fixed co2 sinks to ocean floor. The carbon is trapped forming rock, or petroleum. Stops co2 from leaking back into atmosphere. They can wipe out crops- in 1846 they wiped out entire potato crop in one week, people starved to death. They are the causes of 1 of 3 major world disease crises. Teach us about eukaryotic evolution 11 3 Distinguish between diploid dominant and haploid dominant life-cycles using specific examples of each. Diploid dominant- spend most time multicellular- humans. Haploid dominant- spend majority of their life in the haploid phase-protists, green algae 4 Sketch the life cycle of plasmodium, including the human, the mosquito, the plasmodium, where meiosis, mitosis, and fertilization occur, and the haploid and diploid stages of plasmodium. 5 Explain the roles of mitosis and meiosis in the plasmodium life cycle, and how this would relate to developing targets for anti-malarial treatments (What are the benefits of targeting life stages in humans vs. mosquitos? What are the benefits of targeting mitosis vs. meiosis?) Mitosis increases the number of malaria parasites in the human blood stream. Meiosis introduces more genetic variation into the malaria population than mitosis. Higher rates of mitosis will increase the chances of malaria being transferred from humans to mosquitos and vice versa. Higher rates of meiosis will increase the odds of a malaria parasite evolving a trait that enables it to avoid treatments. Evolution of Land Plants and Land Plant Diversity Students should be able to: 1. List the main groups of land plants, provide common examples of each, and be able to identify the most visible life stages of these common examples as sporophytes (2n) or gametophytes (n) nonvascular plants- liverworts, mosses, hornworts-gametophytes Vascular- seedless-ferns (sporophyte) and seed plants- gymnosperms-pines (sporophyte) and angiosperms-anthophyta (sporophyte) 7 Explain the advantage(s) of moving onto dry land for plants and list characteristics required for this transition (i.e. cuticle, stomata, pollen, etc.) 2. Explain the transition from completely submerged aquatic plants to aquatic plants that can survive periods of dryness at edges of water to plants that can survive completely “on land” to plants that can survive not just on land but on dryer parts of land with no dependence on being in high moisture environments. In this explanation, include the adaptations that evolved at each transition and the selective advantage these adaptations provided for life in on land. oceans are getting crowded so have to compete for sunlight, O2, CO2, inorganic nutrients. No multicellular life on the land yet, so didn’t have to compete for those things. They have a higher rate of photosynthesis because the water absorbs the light. They now have flavonoid that occurred by chance and can absorb uv light, and it protects dna from damage. • CO2 is more abundant in the atmosphere and diffuses more readily in the atmosphere than in water. They adapted the cuticle watertight sealant that covers the aboveground parts of plants gives them the ability to survive in dry environments. Random mutations brought this about. Cuticle won’t allow co2 inside. The stoma or stomata was the solution to this. The stoma consists of an opening surrounded by specialized guard cells. The opening called the pore, opens or closes as the guard cells change shape. • When guard cells lose water, they become limp and the stomata closes. Pores are closed at night to prevent water loss from the plant when co2 uptake isn’t needed. • They could also grow taller- Lignin is a complex polymer built from 6- carbon rings. Very strong, effective in resisting compressing forces such as gravity. • Lignin is cell walls of water conducting cells is considered the defining feature of vascular tissue. The evolution of vascular tissue allowed early plants to support erect stems and transport waster from roots to aboveground tissues. To reproduce on land: gametes produced in complex, multicellular structures, and the embryo was retained on the mother plant and was nourished by it. To fertilze plants- pollen 4 In line with #2 above, students should be able to draw a phylogenetic tree that shows The different groups of green plants in the correct location Synapomorphies (with correct location) of green algae and land plants Synapomorphies (with correct location) of only but all land plants Synapomorphies of vascular plants Synapomorphies of seed plants Explain the important roles that vascular tissue/lignin play in enabling plants to survive on land vascular tissue- a way to get water from soil to parts of plant not in direct contact with water. A way to get sugar from sites of photosynthesis to other parts of plant. Stronger structural support. Vascular tissue- transports water and sugar through taller plant. Lignin- strongest part of vascular tissue, provides structural support. Vascular tissue is found in bundles running through roots, stems, and leaves. 5 6 Explain similarities and differences in the roles of xylem and phloem Suggestion: Make a two column chart and address: what moves through the tissue, direction of movement, is energy required for movement through the tissue, etc.) Xylem phloem What moves through Water and dissolved Sugars and other the tissue nutrients substances What is the direction of From soil/roots up to Carries down from movement rest of plant source to sink Is energy required no yes What causes the pull Transpiration- warm Concentration arm causes water to gradients of sugar evaporate out of between different cells stomata in leaves at play a role (facilitated top at plant. Results in and active transport a lower pressure at the across cell top of the plant. Water membranes) moves from high to low pressure. Only works bc of cohesive and adhesive properties of water. Result of transpiration: delivery of water and dissolved minerals from roots to leaves. Cools the plant. Driven by sun’s energy and cohesive properties of water 7 Sketch a simple alternation of generations life cycle for each major land plant group and be able identify the following; gametophyte, sporophyte, spores, gametes (sperm/egg), zygote, pollen, mitosis, meiosis, fertilization, single-celled vs. multicellular stages, haploid vs. diploid stages, whether the life cycle is sporophyte or gametophyte dominant, heterosporous or homosporous, is water dependent or independent for fertilization, and whether life stages (gametetophyte/sporophyte) are dependent or independent of each other Suggestion: Fill out the table I gave you. When studying the table, quiz yourself by covering up the answers. It’s important that you spend enough time looking at it that you are not just memorizing the chart. The chart is designed to help you organize the info and compartmentalize it in your head. For example when you get to “pollen” go through why pollen is an important adaptation, what stage of the life-cycle pollen is, what stage of the life cycle gives rise to pollen, etc. If you study the chart this way, I think that it will sink in more than just memorization of words in certain boxes. 8 Describe the various mechanisms that plants have of dispersal, which groups have these traits, and why dispersal is important (spores, pollen, seeds, fruits). 9. Predict the types of adaptations a plant might (modes of dispersal, mode of fertilization, other adaptations like cuticle, etc.) have according to the water availability of its habitat.


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