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255 Cards in this Set
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A property of biological membranes that allows some substances to cross more easily than others.
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Selective permeability
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A molecule that has both a hydrophilic region and a hydrophobic region.
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Amphipathic molecule
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The currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of individually inserted protein molecules drifting laterally in a fluid bilayer of phospholipids.
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Fluid mosaic model
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A lipid covalently attached to a carbohydrate.
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Glycolipid
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A protein covalently attached to a carbohydrate.
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Glycoprotein
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Typically a transmembrane protein with hydrophobic regions that completely spans the hydrophobic interior of the membrane.
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Integral protein
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A protein appendage loosely bound to the surface of a membrane and not embedded in the lipid bilayer.
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Peripheral protein
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An increase or decrease in the density of a chemical substance in an area. Cells often maintain concentration gradients of ions across their membranes. When a gradient exists, the ions or other chemical substances involved tend to move from where they are more concentrated to where they are less concentrated.
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Concentration gradient
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The spontaneous tendency of a substance to move down its concentration gradient from a more concentrated to a less concentrated area.
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Diffusion
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Limp. A walled cell is flaccid in surroundings where there is no tendency for water to enter.
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Flaccid
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A protein channel in a cell membrane that opens or closes in response to a particular stimulus.
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Gated channel
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In comparing two solutions, referring to the one with the greater solute concentration.
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Hypertonic
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In comparing two solutions, referring to the one with the lower solute concentration.
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Hypotonic
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Protein channel in a cell membrane that allows passage of a specific ion down its concentration gradient.
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Ion channel
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Having the same solute concentration as another solution.
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Isotonic
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The regulation of solute and water concentrations in body fluids by organisms living in hyperosmotic, hypoosmotic, and terrestrial environments.
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Osmoregulation
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The diffusion of water across a selectively permeable membrane.
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Osmosis
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The diffusion of a substance across a biological membrane.
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Passive transport
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A phenomenon in walled cells in which the cytoplasm shrivels and the plasma membrane pulls away from the cell wall when the cell loses water to a hypertonic environment.
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Plasmolysis
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The ability of a solution to cause a cell within it to gain or lose water.
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Tonicity
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Very firm. A walled cell become turgid if it has a greater solute concentration than its surroundings, resulting in entry of water.
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Turgid
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The movement of a substance across a biological membrane against its concentration or electrochemical gradient with the help of energy input and specific transport proteins.
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Active transport
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The coupling of the downhill diffusion of one substance to the uphill transport of another against its own concentration gradient.
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Cotransport
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The diffusion gradient of an ion, representing a type of potential energy that accounts for both the concentration different of the ion across a membrane and its tendency to move relative to the membrane potential.
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Electrochemical gradient
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An ion transport protein that generates voltage across a membrane.
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Electrogenic pump
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The charge between a cell's cytoplasm and the extracellular fluid, due to the differential distribution of ions. Membrane potential affects the activity of excitable cells and the transmembrane movement of all charged substances.
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Membrane potential
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An active transport mechanism in cell membranes that uses ATP to force hydrogen ions out of a cell, generating a membrane potential in the process.
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Proton pump
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A special transport protein in the plasma membrane of animal cells that transports sodium out of the cell and potassium into the cell against their concentration gradients.
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Sodium-potassium pump
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The cellular uptake of macromolecules and particulate substances by localized regions of the plasma membrane that surround the substance and pinch off to form an intracellular vesicle.
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Endocytosis
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The cellular secretion of macromolecules by the fusion of vesicles with the plasma membrane.
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Exocytosis
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A molecule that binds specifically to a receptor site of another molecule.
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Ligand
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A type of endocytosis involving large, particulate substances, accomplished mainly by macrophages, neutrophils, and dendritic cells.
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Phagocytosis
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A type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes.
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Pinocytosis
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The movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances.
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Receptor-mediated endocytosis
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An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydolyzed. This energy is used to drive endergonic reactions in cells.
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ATP (adenosine triphosphate)
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In cellular metabolism, the use of energy to drive endergonic reactions in cells.
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Energy coupling
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Referring to a molecule that has been the recipient of a phosphate group.
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Phosphorylated
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The specific portion of an enzyme that attaches to the substrate by means of weak chemical bonds.
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Active site
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A chemical agent that changes the rate of reaction without being consumed by the reaction.
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Catalyst
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An organic molecule serving as a cofactor. Most vitamins function as coenzymes in important metabolic reactions.
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Coenzyme
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Any non-protein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.
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Cofactor
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A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics.
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Competitive inhibitor
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A protein serving as a catalyst, a chemical agent that changes the rate of a reaction without being consumed by the reaction.
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Enzyme
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A temporary complex formed when an enzyme binds to its substrate molecule(s).
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Enzyme-substrate complex
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The amount of energy that reactants must absorb before a chemical reaction will start; also called activation energy.
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Free-energy of activation
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The change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substance.
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Induced-fit
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A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate.
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Non-competitive inhibitor
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The reactant on which an enzyme works.
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Substrate
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The binding of a molecule to a protein that affects the function of the protein at a different site.
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Allosteric regulation
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An interaction of the constituent subunits of a protein whereby a conformational change in one subunit is transmitted to all the others.
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Cooperativity
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A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within the pathway.
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Feedback inhibition
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What is meant by membrane fluidity and how does it relate to the different types of molecules found in membranes? What are integral and peripheral membrane proteins?
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The molecules of the membrane are thought to be in constant motion. The lipid bilayers can slide in opposite directions. Proteins embedded on or in the membrane can move to different locations. Integral proteins are proteins that extend through the membrane. Peripheral proteins are oppressed to either side of a membrane but do not extend through it.
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Define diffusion, selectively permeable membrane and osmosis.
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Diffusion - net movement of proteins from areas of high concentration to areas of low concentration. Selectively permeable membrane - membrane that permits some but not all molecules to pass through it. Osmosis - movement of water through a selectively permeable membrane. Osmosis is movement of water from a hypotonic to a hypertonic solution
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The concentration of solutes in a cell can be 200 mM (total number of moles of solute per liter of cell solution). Use the terms hypotonic, isotonic and hypertonic to answer the following questions. The cell is put in a beaker with a sucrose concentration of 100 mM. Which term applies to the solution in the beaker? Which term applies to the solution in the cell?
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The solution in the beaker (100 mM) is hypotonic relative to the concentration in the cell which is hypertonic (200 mM).
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Would you expect a typical, healthy plant cell to be hypertonic, hypotonic or isotonic relative to its environment? Why? What about a typical animal cell? Why?
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A healthy plant cell is normally hypertonic relative to its environment. Therefore water moves into the plant cell and the cell develops turgor because of the strength of the cell wall. A healthy animal cell is isotonic with its environment because it maximizes the amount of water in the cell without leading to membrane destruction.
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Define facilitated diffusion and give two models that explain how facilitated diffusion occurs.
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Facilitated diffusion is diffusion across a membrane through integral membrane proteins. The molecules move passively from high to low concentration. Model one is movement through a channel or pore protein. These proteins act somewhat like pipes for the molecules to move through. By structure, proteins have specificity for solutes and can be gated or have open and closed positions. The second model is a carrier protein that transports a molecule by binding it on one side of the membrane and then transporting it to the other side due to a change protein conformation or structure.
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Define active transport. What is an ATPase? How does it relate to active transport? What is an electrogenic pump
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Active transport- transport of solutes across a membrane against a concentration gradient with the help of energy input and transport proteins. An ATPase is an enzyme that hydrolyzes ATP to release energy. This energy is used to drive active transport. An electrogenic pump is a protein that actively transports charged molecules or ions. The most common electrogenic pump is a proton pump.
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Explain how the transport of sucrose, an uncharged molecule can also be "coupled" to the transport of protons.
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An electrogenic (proton) pump produces an excess of protons on the outside of a cell and an electrochemical gradient favoring proton transport back into the cell. In the presence of a separate membrane protein, a sucrose transporter, the transport of protons back into the cell is coupled to the transport of sucrose. The protons are moving in response to both a difference in concentration and a difference in charge.
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What is the difference between endergonic and exergonic reactions? Illustrate how and endergonic and exergonic reaction can be coupled with the formation of glutamine from glutamic acid.
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An endergonic reaction absorbs energy from its surroundings while an exergonic reaction releases energy. (See figure in lecture notes.) The hydrolysis of ATP (an exergonic reaction) releases more energy than is needed to drive the bonding of glutamic acid to a second amino group producing glutamine. Thus ATP breakdown drives the formation of glutamine.
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What is a catalyst? How do enzymes catalyze reactions in an energetic sense?
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A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction. Enzymes reduce the activation energy required to start a reaction.
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What is the "active site" of an enzyme and how does it relate to the induced-fit model of enzyme function?
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An active site is a location on an enzyme that binds to a specific substrate. The interactions between chemical groups on the enzyme and the substrate results in the enzyme changing shape at least slightly to better fit the substrate. The close fit of chemical groups on the enzyme and the substrate facilitates the catalysis of the chemical reaction.
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How is enzyme activity related to temperature and pH?
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Most enzymes have a temperature optimum for temperature and pH. The optima produce the best chemical configuration for the enzyme to act as a catalyst.
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Define the term cofactor in relation to enzyme activity.
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A cofactor is a nonprotein molecule that increases the activity of an enzyme. Cofactors can be tightly bound to an enzyme or loosely associated with the enzyme.
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In terms of cell function, why is it important that enzyme activity (and reactions) be regulated? Explain how competitive and non competitive inhibitors of the activity of an enzyme are thought to work.
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Regulation of enzyme activity limits reactions to those that are needed by the cell at any one time. This conserves energy and resources for the cell. Competitive inhibitors compete with substrates for the active sites of membranes. Therefore enzyme activity is directly related to the concentration of inhibitor. Non competitive inhibitors bind at a site other than the active site which generally changes the protein shape of the enzyme and reduces its ability to catalyze reactions.
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What is a metabolic pathway? Give an example.
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A metabolic pathway is a series of reactions that produces a specific product. In biological systems, each reaction in a pathway is catalyzed by a specific enzyme. An example from class was the synthesis of isoleucine from threonine.
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Define allosteric regulation. How can the rate of a reaction be increased or decreased by allosteric regulation?
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In allosteric regulation, a compound binds with an enzyme at a location other than the active site on the enzyme. Binding of the compound changes the structure of the enzyme (quaternary protein structure). If the compound causes the enzyme to be in its active form, the compound is classified as a positive regulator. If the compound causes the enzyme to be in its inactive form, the compound is classified as a negative regulator.
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What is feedback inhibition? How does feedback inhibition regulate the metabolic pathway that produces isoleucine in a cell?
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The switching off of a metabolic pathway by the inhibitory binding of its end product to an enzyme early in the metabolic pathway. Isoleucine is produced by a four step pathway starting with threonine. Isoleucine is a negative allosteric inhibitor of threonine deaminase which catalyzes the conversion of threonine to an intermediate compound. High concentrations of isoleucine inhibits the first step in the pathway slowing isoleucine production.
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What is the principal product of cellular respiration? Why is this product important to cells? How is respiration related to photosynthesis in the grand scheme of life on earth?
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The principal product of cellular respiration is ATP. ATP provides energy to run a myriad of reactions in the cell. ATP is produced by the breakdown of glucose into CO2 with the release of energy. Photosynthesis acts in basically the opposite manner. CO2 and Light energy are used in photosynthesis to make sugars.
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To what general class of molecules does adenosine triphosphate belong to (for example, carbohydrate, nucleic acid, etc)? This type of molecule is composed of three general components. What are they?
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Adenosine triphosphate (ATP) is a nucleotide derivative. Like all nucleotides it is made up of a ribose sugar, a nitrogenous base, and a phosphate.
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What happens when a molecule is oxidized? Reduced? What are the abbreviations for the reduced and oxidized forms of nicotinamide adenine dinucleotide? What are the abbreviations for the reduced and oxidized forms of flavin adenine dinucleotide?
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A molecule is oxidized when it gives up electrons and reduced when it takes up electrons. NAD+ is the oxidized form of nicotinamide adenine nucleotide while NADH is the reduced form. FAD is the oxidized form and FADH2 is the reduced form.
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Starting with a glucose molecule and 2 ATP, what are the carbon and energy outputs from glycolysis? What are the inputs into and outputs from the Citric Acid Cycle? What are the inputs into and outputs from the electron transport chain? Overall, approximately how many ATP are formed for each glucose molecule broken down in aerobic cellular respiration?
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The carbon outputs from glycolysis are 2 molecules of pyruvate and the energy outputs are 2 net ATP and 2 NADH. Before the Citric Acid Cycle, the 2 molecules of pyruvate are converted to 2 molecules of acetyl CoA with the production of 2 molecules of CO2 and 2 molecules of NADH. Input into the Citric acid cycle is two molecules of acetyl CoA and the output is 4 molecules of CO2 2 ATP, 6 molecules of NADH and 2 molecules of FADH2. The inputs into the electron transport system are 10 molecules of NADH, 2 molecules of FADH2, and 6 oxygen molecules. The output from the electron transport system is 32 to 34 ATP. Approximately 36 to 38 ATP can be formed from a single molecule of glucose.
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Draw a mitochondrion and identify the outer membrane, inner membrane, the intermembrane space, the matrix and cristae. Identify the location of glycolysis, the Citric Acid Cycle and Electron Transport Chain on your diagram.
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See Fig. 6.17 for drawing. Glycolysis occurs in the cytoplasm, outside the mitochondrion. The citric acid cycle takes place in the matrix and the electron transport system is located in the inner mitochondrial membrane.
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Why is ATP required to start glycolysis? What are the general features of a triose phosphate? How are triose phosphates formed in glycolysis? How are triose phosphates converted to pyruvate?
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ATP is needed to provide energy and phosphate for the formation of a six carbon molecule with a phosphate on each end. A triose phosphate is a 3 carbon monosaccharide with a phosphate attached. A six carbon compound with phosphates on each end is split in two to produce two 3 carbon phosphates. Pyruvate is produced by removing the phosphates from a 3 carbon compound with phosphates on each end.
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What is required for the transport of pyruvate into the mitochondrial matrix? What are the three steps that occur in the “Glycolysis-Citric Acid Cycle Junction”? Starting with a glucose molecule, how many NADH and CO2 molecules are there produced in the “Glycolysis-Citric Acid Cycle Junction”?
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A transport protein on the inner mitochondrial membrane. First, a CO2 is cleaved from pyruvate, second a molecule of NAD+ is reduced to produce a molecule of NADH and third a molecule of Coenzyme A is attached to the two carbons that remain from the original pyruvate. For every glucose molecule, 2 molecules of CO2 and 2 molecules NADH are formed.
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Where is respiratory acetyl CoA formed in the cell? How many carbon atoms does a molecule of acetyl CoA contribute to the Citric Acid Cycle?
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Respiratory acetyl CoA is formed in the mitochondrial matrix. Each aceytl CoA molecule contributes 2 carbon atoms to the Citric Acid Cycle.
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The Citric Acid Cycle is a cycle because the starting substrate (oxaloacetate) is regenerated. Briefly describe how oxaloacetate changes during the Citric Acid Cycle. If we start respiration (at glycolysis) with one glucose molecule, how many NADH, FADH2 and ATP molecules are there produced in the Citric Acid Cycle? How many CO2 molecules?
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Oxaloacetate is a 4 carbon compound and it first combines with an acetyl CoA molecule to form a 6 carbon molecule (citrate). The 6 carbon molecule is altered slightly and then a CO2 is cleaved from the molecule to form a 5 carbon molecule (alpha ketoglutarate). The 6 carbon molecule is oxidized and a molecule of NADH is formed in the process. Another CO2 is cleaved from the 5 carbon molecule producing a 4 carbon molecule (succinyl CoA) in the process another NADH is formed. The 4 carbon molecule is converted to another 4 carbon molecule (succinate) and in the process a molecule of ATP is formed. Succinate is converted to another 4 carbon molecule (malate) and in the process an FADH2 is formed. Malate (4C) is then converted back to oxaloacetate and in the process another NADH is formed. For each acetyl CoA input into the Citric Acid cycle we obtain 3 NADH, 1 FADH2, 1 ATP and 2 CO2 molecules. Since each glucose would produce 2 acetyl CoA molecules, the totals for starting with a glucose molecule would be 6 NADH, 2 FADH2, 2 ATP and 4 CO2 molecules.
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Functionally, how are the molecules that make up the Electron Transport System (E.T.S.) similar? What are the names of some of the molecules that make up the E.T.S.? Where in the mitochondrion is the E.T.S. found? Why does the E.T.S. stop when there is no oxygen present? Without oxygen, the citric acid cycle also stops. Why? Approximately how many ATP are made for every NADH? How many ATP for every FADH2? Why is there a difference?
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All of the molecules in the ETS system can be oxidized and reduced and they usually contain a metal such as iron or copper. Flavoprotein, iron-sulfur proteins, ubiquinone, cytochromes. The ETS is embedded in the inner mitochondrial membrane. Without oxygen present, all of the components of the ETS become reduced and electron transport stops. Oxidation of an NADH should produce 3 ATP and oxidation of an FADH2 should produce 2 ATP. ATP formation is dependent on a H+ gradient and since FADH2 contributes electrons to complex II and NADH contributes electrons to Complex I, fewer H+ are transported across the membrane per FADH2.
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In an active mitochondrion, would the intermembrane space or the matrix have a lower pH (be more acidic)? What is chemiosmosis? In general, how does the formation of ATP in the mitochondrion compare with the concept of "coupled transport" as it refers to membrane transport?
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The intermembrane space would have a lower pH because electron transport moves protons from the matrix to the intermembrane space across the inner mitochondrial membrane. Chemiosmosis is a mechanism by which energy in a proton (hydrogen ion) gradient is used to make ATP. In a general sense ATP formation and coupled transport are like the reverse of one another. In ATP formation, electron transport causes the formation of a hydrogen ion gradient and the potential energy of this gradient is used to make ATP. In "coupled transport", ATP is used to provide energy to produce an hydrogen ion gradient which provides the force to transport other molecules such as sucrose.
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How many ATP can be produced from a molecule of glucose? What are the relative contributions of glycolysis, the citric acid cycle and the Electron Transport Chain to this process? Why is there variability among cells in the amount of ATP produced per molecule of glucose?
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A molecule of glucose produces 36-38 ATP. Glycolysis - 2 ATP, Citric acid cycle- 2 ATP, ETS - 32-34 ATP.
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What type of metabolism can occur in cells that lack oxygen? What are the products of this process? How efficient is this process at producing energy as compared to aerobic respiration? What are two examples of anaerobic respiration in eukaryotic cells?
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Fermentation occurs in cells that lack oxygen. Fermentation has two different carbon products: lactic acid or ethanol. Fermentation allows production of 2 ATP per glucose molecule and recycles NADH back to NAD+. This process is much less efficient than aerobic respiration since only 2 ATP are formed as opposed to 36-38 ATP per glucose for aerobic respiration. Plants growing in flooded conditions undergo fermentation because oxygen is consumed faster than it can be replaced by diffusion. The primary product in many roots is ethanol. Continuous use of muscles such as when we run more than 3 miles also produces anaerobic conditions. Oxygen is again consumed faster that it can be replaced in active muscle cells and they produce lactic acid.
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How can the breakdown of proteins and lipids (particularly fats) contribute to cellular respiration? How can proteins and fats be synthesized?
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Proteins are broken down into amino acids and then the amino group is removed. The remaining carbon skeletons are converted into various glycolytic and Citric Acid Cycle intermediates which feed into these locations in Glycolysis and the Citric Acid Cycle and produce energy. Fats are broken down into glycerol and fatty acids. The glycerol is converted to a triose- phosphate which feeds into glycolysis. The fatty acids are broken down to 2 carbon units and converted into acetyl-CoA which feeds into the citric acid cycle. Starting with carbon molecules produced in glycolysis and the citric acid cycle, proteins and fats can be synthesized by a reverse of the breakdown process.
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What are the two major components of photosynthesis? What are the major inputs and outputs for each component?
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The two major components of photosynthesis are the light reactions and the Calvin Cycle. The inputs into the light reactions are NADP+, ADP + Pi, light, and water. The outputs from the light reactions are ATP, NADPH, and oxygen. Inputs into the Calvin Cycle are ATP, NADPH, and carbon dioxide. The outputs are sugars, ADP + Pi, NADP+.
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Water loss from leaves is called an "necessary evil". Why is this water loss required for CO2 absorption?
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Carbon dioxide is absorbed by mesophyll cells that contain chloroplasts. The mesophyll cells have a wet surface and therefore water evaporates as carbon dioxide is absorbed. This water vapor leaves the plant through the stomates, reducing the leaf's water content. Therefore plants have to lose water vapor to take up carbon dioxide which is needed for photosynthesis.
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Draw a chloroplast. Identify the following structures or locations in the chloroplast: stroma, outer and inner membranes, thylakoid membranes, thylakoid space. Where is the light reactions located? Where is the Calvin cycle located?
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See Fig. 10.3 in the text. The chloroplast is surrounded by two membranes, the inner and outer membrane. Inside the inner membrane is an area that contains solution that is called the stroma. Interspersed throughout the stroma is the thylakoid membrane system. The thylakoid membranes are folded over and enclose the thylakoid membrane space. This space is separated from the stroma by the thylakoid membranes. The light reactions are embedded in the thylakoid membranes. The Calvin Cycle occurs in the stroma.
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What are two major parts of photosynthesis? What are the major inputs and outputs for each component?
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The two major components of photosynthesis are the light reactions and the Calvin Cycle. The inputs into the light reactions are NADP+, ADP + Pi, light, and water. The outputs from the light reactions are ATP, NADPH, and oxygen. Inputs into the Calvin Cycle are ATP, NADPH, and carbon dioxide. The outputs are sugars, ADP + Pi, NADP+.
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Draw cross section of a leaf and be able to identify epidermal and mesophyll cells in your drawing. What are the functions of epidermal cells and mesophyll cells? What are stomates and guard cells and where are they found. Why do terrestrial plants need stomates? Why must plants lose water to take up CO2?
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See diagram of a leaf section in the Study Guide (Lecture 17) or Fig. 10.3 from the text. The outer layers of the leaf (top and bottom) are the epidermal layers with epidermal cells and they surround the mesophyll cells which contain chloroplasts. Epidermal cells protect the leaf from losing water and serve as barriers to insect and pathogen attack. Mesophyll cells are the site of photosynthesis. Stomates are openings in the epidermal layers and each opening is surrounded by two guard cells which can regulate the size of the stomate. Photosynthesis occurs in the chloroplasts in the mesophyll cells. Stomates regulate the movement of carbon dioxide into the leaf and amount of water vapor that escapes the leaf. Carbon dioxide must be absorbed across a wet cell surface. Therefore water is constantly evaporating from the surface of mesophyll cells when carbon dioxide is being absorbed.
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Draw a chloroplast. Identify the following structures or locations in the chloroplast: stroma, outer and inner membranes, thylakoid membranes, thylakoid space. Where is the light reactions located? Where is the Calvin cycle located?
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See Fig. 10.3 in the text. The chloroplast is surrounded by two membranes, the inner and outer membrane. Inside the inner membrane is an area that contains solution that is called the stroma. Interspersed throughout the stroma is the thylakoid membrane system. The thylakoid membranes are folded over and enclose the thylakoid membrane space. This space is separated from the stroma by the thylakoid membranes. The light reactions are embedded in the thylakoid membranes. The Calvin Cycle occurs in the stroma.
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Name three types of pigments that play a role in photosynthesis. What is the difference between a primary and an accessory pigment?
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Three types of photosynthetic pigments are chlorophyll a, chlorophyll b, and carotenoids. In chlorophyll a, the primary acceptor, electrons change energy levels when the molecule absorbs enough light energy. Accessory pigments also absorb energy but this does not produce a change in electron energy level, the energy is transferred to chlorophyll a molecules.
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How is electron excitation produced in a chlorophyll molecule? What are three things that can happen to excited electrons in a chlorophyll a molecule? What are five major components of a photosystem? How is energy transferred in a photosystem and where do electrons end up in a given photosystem?
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Electron excitation is produced by absorption of enough energy to cause electrons in a chlorophyll a molecule to move to a higher orbital. Excited electrons in a chlorophyll a molecule can 1) drive electron transport, 2) return to a lower orbital and energy state with the release of energy as heat, 3) return to a lower orbital and energy state by re-radiating radiation in a process called flourescence. Five components of a photosystem are: pigment molecules, special chlorophyll a molecules, light-harvesting complexes, reaction center, primary electron acceptor. The steps in energy transfer in a photosystem are: absorption of light energy by all pigment molecules, transfer of energy to special chlorophyll a molecules, electron excitation in the special chlorophyll a molecules when they have absorbed enough energy, electron transfer from chlorophyll a molecule to primary electron acceptor molecule.
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What are P680 and P700 molecules and how are they associated with the photosystems? Where in the chloroplast would you find the electron transport components? What is the pathway of noncylic electron flow relative to the photosystems? In noncyclic electron flow, where do electrons end up?
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P680 and P700 are the "special" chlorophyll a molecules that can produce excited electron states. P680 is in the reaction center of PS II while P700 is in the reaction center of PSI. The electron transport components are found in the thylakoid membrane. The pathway: a P680 molecule absorbs enough light energy to cause electron excitation and those electrons reduce the primary electron acceptor of PSII. The electrons lost from the P680 are replaced by electrons produced from the splitting of a water molecule. The the primary electron acceptor of PSII then reduces plasotoquinone (PQ) to form PQH2 which in turn leads to reduction of cytochrome components in the cytochrome complex which leads to reduction of plastocyanin. At almost the same time, light energy leads to the excitation of electrons in P700 and those electrons reduce the primary electron acceptor of PSI. The electrons lost from P700 are replaced by electrons from the oxidation of plastocyanin. The primary electron acceptor of PSI then reduces ferredoxin which in turn reduces NADP+ to NADPH completing electron transport. Electron transport ends with the production of NADPH.
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What specific events during electron transport in the chloroplast produce an imbalance in H+ across the thylakoid membrane? On which side of the membrane does the H+ concentration accumulate in the light? How does this gradient in H+ drive the formation of ATP? Compare ATP formation in the chloroplast with that in the mitochondrion (Figs. 9.15 and 10.17) with regards to location, electron transport components, and final products.
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The H+ gradient across the thylakoid membrane is caused by 1) the splitting of water in the thylakoid space (one of the products is H+) and 2) the shuttling of H+ from the stroma to the thylakoid space every time plastoquinone (PQ) is reduced then oxidized. Therefore, H+ accumulates in the thylakoid lumen, reducing the pH relative to the pH of the stroma. The build up of H+ in the lumen produces a chemical potential gradient that favors transport back into the stroma. The potential energy stored in this gradient is harvested by ATP synthase proteins which use the energy to produce ATP. ATP formation in the mitochondrion depends on an electron transport chain that is embedded in the inner mitochondrial membrane while ATP formation in the chloroplast depends on an electron transport chain that is embedded in the thylakoid membrane. Components of both the mitochondrial and chloroplastic electron transport chains are similar in that they are both made up of molecules that mostly contain a metal atom and they are all easily reduced and oxidized. The final product for the mitochondrial ATP formation is water and from chloroplastic ATP formation is NADPH.
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What are the three phases of the Calvin Cycle? Describe briefly what happens in each phase. What are the substrates that are needed to produce 3-phosphoglycerate in the Calvin Cycle? What is the name of the enzyme that catalyzes this reaction? How is glyceraldehyde 3-phosphate, produced from 3-phosphoglycerate? How is the starting substrate for the Calvin Cycle regenerated? Why do we start the Calvin cycle with 3 molecules of substrate?
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The three phases of the Calvin cycle are: carbon fixation, reduction and regeneration. In carbon fixation, CO2 is combined with a 5 carbon bisphosphate to produce 2 molecules of 3 carbon phosphates, In the reduction phase, the 3 carbon phosphate is reduced by NADPH and ATP to for a triose phosphate, glyceraldehyde 3-P (G3P). In the regeneration phase, G3P molecules are combined in such a way as to produce ribulose bisphosphate, the original reactant. Ribulose bisphosphate (RuBP) and carbon dioxide are the reactants that produce 3 phosphoglycerate in the carbon fixation phase of the Calvin Cycle. Carbon fixation is catalyzed by the enzyme ribulose bisphosphate carboxylase/oxygenase (rubisco). In the reduction phase, 3 phosphoglycerate is phosphorylated by a substrate level phosphorylation from the breakdown of ATP to produce bisphosphoglycerate. The bisphosphoglycerate is reduced by NADPH to produce G3P molecules. The starting substrate, ribulose bisphosphate, is regenerated by re-arranging G3P molecules. Three molecules of CO2 must be fixed to produce 1 new molecule of the triose phosphate G3P. Each molecule of CO2 requires one molecule of RuBP (see the carbon fixation reaction, above).
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The important product of the Calvin cycle is a triose phosphate sugar (glyceraldehyde 3-phosphate; G3P). What storage product is formed in the chloroplast (stroma) from triose phosphates? What are two things that can happen to triose phosphates when transported into the cytoplasm?
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In the chloroplast stroma, triose phosphates can be used to build starch molecules. Triose phosphates can be transported into the cytoplasm where they can be used to produce energy in aerobic respiration (insertion into glycolysis) or used as building blocks for production of sucrose, the disaccharide that is used for carbohydrate transport throughout higher plants.
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In the Calvin Cycle, how many ATP and NADPH molecules are required to produce one molecule of glyceraldehyde-3-phosphate (G3P, a triose phosphate)? How many ATP and NADPH would be required to produce a glucose molecule?
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The production of a new triose phosphate by the Calvin Cycle requires 9ATP (6 during the reduction phase and 3 during the regeneration phase) and 6 NADPH molecules. Nominally, a glucose molecule would require twice as much as a triose phosphate, 18 ATP and 12 NADPH.
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What does rubisco stand for and why is it considered the most abundant protein on earth? What is the difference between rubisco and ribulose bisphosphate? Under what conditions did rubisco evolve on the earth?
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Rubisco stands for ribulose bisphosphate carboxylase/oxygenase. There is tremendous amount of plant biomass on the earth and in green cells, 30-50% of the soluble protein is rubisco. Rubisco is a complex protein structure that functions as an enzyme that catalyzes the carbon fixation reaction of the Calvin Cycle. In this reaction a carbon dioxide is added to a five carbon sugar, ribulose bisphosphate: ribulose bisphosphate is the substrate and rubisco is the enzyme that leads to the carboxylation of ribulose bisphosphate. Rubisco evolved on the early earth when there was a reducing atmosphere characterized by high concentrations of carbon dioxide and virtually no oxygen.
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What are the "good" and the "bad" reactions that involve rubisco and ribulose bisphosphate? Why is the "good" reaction favored at high CO2 concentrations [CO2] and why is the “bad” reaction favored under hot and dry conditions?
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In the "good" reaction catalyzed by rubisco, ribulose bisphosphate combines with carbon dioxide to produce 2 molecules of phosphoglycerate, thus we start with 5 carbons per reaction and end up with 6 carbons. In the "bad" reaction catalyzed by rubisco, ribulose bisphosphate combines with oxygen to produce one molecule of phosphoglycerate and on molecule of phosphoglycolate, a 2 carbon compound. Therefore the "bad" reaction starts with 5 carbons and ends up with 5 carbons, no carbons are added. At atmospheric carbon dioxide concentrations, the "good" reaction is limited by [CO2]. Therefore, raising the [CO2] increases the reaction rate and the production of triose phosphates. Under hot, dry conditions, stomates close to conserve water and the [CO2] decreases as it is used up by photosynthesis and the reaction rate declines.
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The majority of plants are categorized as C3 while a small number of plants are either C4 or CAM. What features of photosynthesis do all of these plants have in common? What is the origin of the names C3, C4 and CAM? In general, how does photosynthesis in C4 and CAM plants differ from that in C3 plants like tomatoes and oak trees? How is C4 different from CAM metabolism? Give some examples of C4 and CAM plants.
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C3, C4 and CAM plants all possess the light reactions and the Calvin Cycle. C3 plants are so named because they only fix CO2 in the Calvin Cycle where the first product is phosphoglycerate, a 3 carbon sugar. C4 plants possess an extra CO2 fixation reaction where carbon dioxide is fixed into a four carbon organic acid. CAM stands for crassulacean acid metabolism, a name that is derived from the discovery of this type of photosynthesis in plants from the genus Crassula. Both C4 and CAM plants first fix CO2 into a C4 acid which is shuttled to rubisco at the site of the Calvin Cycle. There the C4 acid is broken down, CO2 is released and it can then be fixed in the Calvin Cycle. C3 plants only possess the Calvin Cycle so they cannot produce C4 acids. In C4 plants, photosynthesis occurs during the day and carbon dioxide is first fixed into C4 acids in leaf mesophyll cells. The C4 acids are shuttled to special bundle sheath cells where the Calvin Cycle occurs. At night, CO2 enters the leaves of CAM plants through open stomates and is fixed into C4 acids During the day CAM stomates are closed and the C4 acids breakdown and release CO2 which is used to drive the Calvin Cycle. C4 plants: corn, and sugar cane. CAM: pineapple and most cacti.
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On the large scale, give two reasons why photosynthesis is fundamental to life on earth?
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Photosynthesis is the of source of energy for all organisms on the earth. Oxygen concentrations are stable on the earth because it is constantly being produced by photosynthesis
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Define Mitosis and cytokinesis. What are three important functions of cell division in eukaryotic organisms? Give examples of cells that illustrate each function.
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Mitosis is the division of genetic information and the nucleus during cell division. Cytokinesis is the division of a cell's cytoplasm during cell division. The three important functions are reproduction, growth and development and tissue renewal (repair). Examples, Single-cell amoeba reproduction, growth of a sand dollar embryo, and dividing bone marrow cells, respectively (see. Fig. 12.2).
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The mitotic cell cycle consists of two major phases, Interphase and the Mitotic phase. What are the names of the "subphases" that occur in each of these phases? Briefly, what happens in each of these subphases?
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The two phases are interphase and mitotic phases. Interphase - subphases are G1 (gap 1), S (synthesis), and G2 (gap 2). There is growth by production of proteins and cellular organelles in G1. In the S phase, DNA is duplicated. In G2 there is more growth by production of proteins and cellular organelles. Mitotic phase - subphases are mitosis and cytokinesis. In mitosis, the nucleus is divided and specifically duplicated chromosomes are separated. In cytokinesis, the cell cytoplasm is divided.
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What would be the typical time it would take for a human cell to complete a complete cell cycle? What would be the length of the different subphases of Interphase? Which subphase is the most variable in cells? How long would it take for the Mitotic phase?
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It takes about 24 hrs for a typical human cell to complete a cell cycle. The longest subphase is the S subphase of interphase which normally would take 10-12 hrs. The G1 and G2 subphases would take normally take 4-6 hrs and 5-6 hrs respectively. The G1 is typically the most variable. The Mitotic phase would normally take about 1 hr.
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What types of molecules make up a chromosome from a eukaryotic cell? Define the terms chromatid and centromere. Draw a chromosome to illustrate sister chromatids and the position of a centromere. When during the cell cycle is DNA duplicated?
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Eukaryotic cell chromosomes are made up of DNA and protein. When the chromosome is duplicated the chromosome is composed of two duplicate chromatids. The two chromatids are joined together by a centrome. See figure 12.4 for the structure of a duplicated chromosome and the placement of a centromere. DNA is duplicated during the S subphase of interphase, not during the mitosis phase.
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Starting with a single cell, how many cell products (daughter cells) are produced in mitosis? How does the chromosome makeup in each of the products compare to that in the original cell?
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In mitosis, each cell gives rise to two identical daughter cells. The daughter cells will possess identical sets of chromosomes and therefore the same number of chromosomes with the same genetic information.
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In mitosis, what characteristics mark prophase, prometaphase, metaphase, anaphase and telophase? Define or characterize these terms in relation to mitosis: centriole pairs, mitotic spindle, spindle pole, centromere, chromatin, kinetochore, kinetochore microtubules.
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In prophase some of the major events include: condensation of chromosomes in the nucleus, formation of the mitotic spindle (from microtubules) in the cytoplasm and disappearance of nucleoli. In prometaphase, major events include: Fragmentation of the nuclear membrane, microtubules from the spindle apparatus attach to sister chromatids at the kinetechore on each chromatid, and chromosomes migrate toward the center of the cell/nuclear region (the metaphase plate).
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What is the function of a cleavage furrow and what is the mechanism by which it is formed in cells? What is the function of a cell plate and what is the mechanism by which it is formed in cells? In what types of cells would you expect to find formation of cleavage furrows and cell plates?
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The cleavage furrow divides a mother cell into two daughter cells at the end of cytokinesis. Microfilaments stretch across the cell at the location of the metaphase plate and then tighten to pinch the cell. The cell plate also divides a mother cell into two daughter cells at the end of cytokinesis. Vesicles containing cell wall material and arising from the Golgi apparatus travel along microtubules to the metaphase plate where they fuse with one another. Cleavage furrows are formed in dividing animal cells and cell plates are formed in dividing plant cells.
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In what type of cells does Binary Fission occur? Describe what happens in Binary Fission. What are two ways that Binary Fission is similar to the Mitotic Cell Cycle. What are two ways that Binary Fission differs from the Mitotic Cell Cycle?
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Binary Fission occurs in prokaryotic cells. In a prokaryotic cell the circular chromosome undergoes replication starting at a point on the chromosome called the origin of replication. The two origins of replication move toward opposite sides of the cell, presumably by interactions with the cell membrane, while replication of the chromosome continues. As chromosome duplication continues, the cell elongates between the two origins of replication. When replication of the chromosome finishes, the plasma membrane at the boundary between the two chromosomes begins to grow inward to the center of the cell and new cell wall is deposited on both sides of the new membrane material, eventually leading to the formation of two daughter cells. In both Binary Fission and Mitotic Cell Division, the chromosomes contain genetic information in the sequence of nucleotides; during division two copies of each type of chromosome move apart and one copy ends up in each of two daughter cells. In Binary Fission the chromosome is arranged in a circle while in the Mitotic Cell cycle, chromosomes are linear; movement of chromosomes in Binary Fission is associated with the cell membrane while movement in the Mitotic Cell Cycle depends on microtubules in the spindle apparatus.
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Why is it particularly important that the cell cycle be closely regulated in multicellular eukaryotic organisms? What is a kinase? What is a cyclin dependent kinase and a cyclin? What is an MPF and what does an MPF do?
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Normal growth and development of multicellular organisms is dependent on the timing and rate of cell division which must be closely regulated. A kinase is a type of enzyme that works by phosphorylating a protein. Cyclin dependent kinases are kinase enzymes that are important in the cell cycle and to be active they must be attached to specific proteins called cyclins. MPF which stands for "maturation-promoting factor", is a cyclin dependent kinase that must be at some threshold concentration in a cell for the cell to move from G2 to the mitotic phase of the cell cycle.
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What are "density dependent inhibition" and "anchorage dependence" in animal cells? How are cancer cells related to the cell cycle?
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Crowding of animal cells apparently is a physical signal that causes stoppage of cell division and this is referred to as "density dependent inhibition". Most animal cells must be attached to some sort of substrate (culture vessel in vitro, extracellular matrix in vivo) to divide and this is referred to as "anchorage dependence". Cancer cells are cells freed of cell cycle controls and they continually divide producing potentially catastrophic results.
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What type of cell division produces asexual reproduction. What is "budding" and how is it related to asexual reproduction?
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Asexual reproduction is produced by mitotic cell division so that the mother and daughter cells are genetically identical. Budding -in some multicellular organisms, a small mass of cells divide mitotically and then separate from the "parent".
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What are homologous chromosomes? Differentiate between autosomes and sex chromosomes; somatic cells and sex cells (gametes); haploid and diploid. How many products are formed from a single (mother) cell by meiosis? How does this compare with mitosis?
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Homologous chromosomes - chromosomes that are similar both physically and genetically. Sex chromosomes - chromosomes that determine the sex of an individual, autosomes - chromosomes that code for non-sexual characteristics. Sex cells (gametes) - a reproductive cell, autosome - normal cell that is not involved in reproduction. Diploid - term used to describe the genetic makeup of a cell; diploid cells have two sets of homologous chromosomes and this is the normal condition of somatic cells. Haploid - term used to describe the genetic makeup of a cell; haploid cells have a single set of chromosomes (none of the chromosomes are homologous) and this is the normal state of gamete cells. In meiosis a mother cell gives rise to four products, each with half the number of chromosomes found in the mother cell. In mitosis each mother cell produces two daughter cells with the same genetic makeup.
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Somatic cells of alligators are thought to be 2n=32. What does that symbolism mean? Alligators form gametes which further become modified to become sperm and egg cells. How many chromosomes would you find in an alligator sperm cell?
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2n=32 means the cells are diploid (2n) and in a diploid cell are 32 chromosomes, 2 sets of 16 homologous chromosomes. An alligator sperm cell would possess 16 chromosomes since it should be haploid. (n=16).
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What are the roles of mitosis and meiosis in the human life cycle and where do these types of cell division occur in the human body? Are humans predominantly haploid or diploid?
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In the human life cycle, mitosis is the prominent type of cell division and normal growth, development and repair of cells occurs by this type of cell division throughout the human body. Meiosis produces gametes or sex cells and this only occurs in specialized cells, in the ovary in females and the testis in males. Humans are predominantly diploid.
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What happens to homologous chromosomes in prophase I of meiosis? Be sure to include an explanation of the term synapsis and define chiasmata.
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In prophase I of meiosis, replicated, homologous chromosomes physically pair up in the cell. The pairing of homologous chromosomes is termed synapsis. In synapsis, two chromatids, one from each homologous chromosome can come in contact and if they physically cross one another they form a chiasma (plural chiasmata). In synapsis there can be crossing over or a physical exchange of genetic material between non-sister chromatids.
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Assume a cell is diploid with four chromosomes (2n = 4). Describe the arrangement of the chromosomes at metaphase I of meiosis I. Describe the chromosome arrangement for the same cell if it were at metaphase of mitosis as opposed to metaphase I of meiosis I.
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For 2n=4 there would be two pairs of homologous chromosomes straddling the metaphase plate. At metaphase of mitosis, however, four chromosomes would be lined up independently on the metaphase plate.
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What happens to paired chromosomes as telophase I of meiosis I begins? How many cells are there normally produced at the end of meiosis I? How many chromosomes are there in each of these products as compared to the starting mother cell?
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As telophase I begins, the paired, replicated chromosomes separate and move towards opposite poles of the cell. At the end of meiosis I there are two products. Each product has half as many chromosomes as the original cell so in the example from the previous question, each product would have 2 chromosomes (and the DNA in each chromosome would be replicated or consist of two sister chromatids).
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Using the same example as in the previous two questions (2n=4), how are the chromosomes arranged at metaphase II of meiosis II? Specifically describe the differences in appearance among metaphase I and metaphase II of meiosis and metaphase of mitosis for this cell.
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In metaphase II, the replicated chromosomes would line up randomly on the metaphase plate and be unpaired. In each cell there would be two replicated chromosomes, independent of one another, lying on the metaphase plate. In metaphase I of meiosis 2 pairs of replicated chromosome would be lined up on the metaphase plate. In metaphase II there would be two unpaired, replicated chromosomes lying on the metaphase plate. In metaphase of mitosis, there would be 4 unpaired and replicated chromosomes lined up on the metaphase plate.
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How many daughter cells are there produced in meiosis and mitosis? Relative to the starting mother cell, how many chromosomes are there in the daughter cells produced by meiosis and by mitosis? What is the major function of meiosis?
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Mitosis produces 2 daughter cells and meiosis produces 4 daughter cells. The daughter cells produced in mitosis have the same number of chromosomes as in the mother cell. The daughter cells produced in meiosis have half as many chromosomes as the original mother cell. The major function of meiosis is to produce sex cells or gametes with half the number of chromosomes found in somatic cells.
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What is meant by membrane fluidity and how does it relate to the different types of molecules found in membranes? What are integral and peripheral membrane proteins?
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Membrane fluidity is due to the kinks in the unsaturated hydrocarbon tails. It keeps the molecules from packing together. Integral proteins - penetrate the hydrophobic core of the lipid bilayer. In essence, they are "integrated" into the membrane. Peripheral proteins - not embedded in the lipid bilayer at all, they are appendages loosely bound to the surface of the membrane, often to the exposed parts of the integral proteins. The lipid bilayers slide relative to each other and the proteins move like floats in the bilayer.
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Define diffusions, selectively permeable membrane, and osmosis.
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Diffusion - the tendency for molecules of any substance to spread out evenly into the available space; Selectively permeable membrane - membrane that controls the transportation into and out of the cell; osmosis - the diffusion of water across a selectively permeable membrane.
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The concentration of solutes in a cell can be 200mM (total number of moles of solute per liter of cell solution). Use the terms hypotonic, isotonic, and hypertonic to answer the following question. The cell is put in a beaker with a sucrose concentration of 100mM. Which term applies to the solution in the beaker? Which term applies to the solution in the cell?
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The beaker is hypotonic and the cell is hypertonic. The fluid moves from the beaker to the cell.
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Would you expect a typical, healthy plant cell to be hypertonic, hypotonic, or isotonic relative to its environment? Why? What about a typical animal cell? Why?
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I would expect a typical plant cell to be hypertonic because water is constantly moving into the cell and gives it turgor. A typical animal cell would need to be isotonic because it could not handle either extreme. It would either burst or shrivel up and die.
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Define facilitated diffusion and give two models that are thought to explain how facilitated diffusions occur.
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Facilitated diffusion - passive transport across a membrane. Channel protein - allows substance to flow right through it. Carrier protein - carrier substances across membrane.
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Define active transport. What is an ATPase? How does it relate to active transport? What is an electrogenic pump?
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Active transport - transport of solutes across a membrane against a concentration gradient with the help of energy input and transport proteins. ATPase means an enzyme that catalyzes the breakdown of ATP (and release of energy).
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Explain how the transport of sucrose, an uncharged molecule can also be "coupled" to the transport of protons. What is symport?
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The transport of sucrose can be coupled to the transport of proteins by the use of a cotransporter and an H+ molecule. Symport is cotransport where two things are moved in the same direction across a membrane.
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What is the difference between endergonic and exergonic reactions?
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Endergonic - requires energy. Exergonic - releases energy.
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Explain why enzymes are termed biological catalysts. How do enzymes "speed up" reactions in an energetic sense?
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Enzymes are termed biological catalysts because they speed up reactions by lowering the activation energy required to start the reaction.
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What is the "active site" of an enzyme and how does it relate to the induced-fit model of enzyme function?
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An active site is the place on a protein where the reactant bonds to it. It relates to the induced fit model because the active site is the grove in the proteins.
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How is enzyme activity related to temperature and pH? Define the term cofactor in relation to enzyme activity.
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When pH or temperature are changed, the enzymes tend not to function. Cofactor is a nonprotein helper that is required for protein activity.
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In terms of cell function, why is it important that enzyme activity (and reactions) be regulated? Explain how competitive and noncompetitive inhibitors of the activity of an enzyme are thought to work.
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It is important that enzyme activity be regulated because if not, chemical chaos would occur. Competitive inhibitors block the reactants from the protein while noncompetitive inhibitors change of the shape of the protein.
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What are metabolic pathways?
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Metabolic pathways - series of reactions that produce product.
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Define allosteric regulation. How can the rate of a reaction be increased or decreased by allosteric regulation?
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Allosteric regulation - a protein's function at one site is affected by the binding of a regulatory molecule to a separate site.
The rate of the reaction can be increased if an allosteric activator stabilizes the active form. It can be decreased if an allosteric inhibitor stabilizes inactive form. |
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What is feedback inhibition? How does feedback inhibition regulate the metabolic pathway that produces isoleucine in a cell?
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Feedback inhibition is when a metabolic pathway is switched off by the inhibitory binding of its end products and enzyme that acts early in the pathway.
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What is the principal product of cellular respiration? Why is this product important to cells? How is respiration related to photosynthesis in the grand scheme of life on earth?
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The principal product of cellular respiration is ATP. This product is important to cells because it provides them with energy. Respiration is related to photosynthesis in the grand scheme of earth because the products of respirations are the reactants of photosynthesis.
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To what general class of molecules does adenosine triphosphate belong to (for example, carbohydrate, nucleic acid, etc)? This type of molecule is composed of three general components. What are they?
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Adenosine triphosphate belongs to the nucleic acid group. It consists of 3 phosphates and 2 nucleotides.
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What happens when a molecule is oxidized? Reduced? What are the abbreviations for the reduced and oxidized forms of nicotinamide adenine dinucleotide? What are the abbreviations for the reduced and oxidized forms of flavin adenine dinucleotide?
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When a molecule is oxidized, it loses electrons. When a molecule is reduced, it gains electrons. Nicotinamide - NAD, NADH, and Flavin - FAD, FADH2.
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Starting with a glucose molecule and 2 ATP, what are the carbon and energy outputs from glycolysis? What are the inputs into and outputs from the Citric Acid Cycle? What are the inputs into and outputs from the electron transport chain? Overall, approximately how many ATP are formed for each glucose molecule broken down in aerobic cellular respiration?
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The carbon output of glycolysis is 2 Pyruvate and the energy output is 2 ATP. The inputs of the Citric Acid Cycle are 2 acetyl CoA and the produce are 6 CO2, 8 NADH, 2 FADH2, and 2 ATP. The inputs of the electron transport chain are 10 NADH, 2 FADH2, and 6O2. The output of the electron transport chain is 32~34 ATP and 6H2O.
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Identify the location of glycolysis, the Citric Acid Cycle, and Electron Transport Chain.
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Glycolysis takes place in the cytoplasm, the Citric Acid Cycle takes place in the inner membrane space, and the electron transport chain takes place in the intermembrane space.
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Why is ATP required to start glycolysis? What are the general features of a triose phosphate? How are triose phosphates formed in glycolysis? How are triose phosphates coverted to pyruvate?
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ATP is required to start glycolysis because it needs energy to perform its function. The general features of the triose phosphate are 3 carbons and 1 phosphate. Triose phosphates are formed in glycolysis by breaking down the glucose molecule and adding 2 phosphates. The phosphates are then converted to pyruvate by reducing NAD+ to NADH and by producing a net gain of 2 ATP.
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What is required for the transport of pyruvate into the mitochondrial matrix? What are the three steps that occur in the "Glycolysis-Citric Acid Cycle Junction"? Starting with a glucose molecule, how many NADH and CO2 molecules are there produced in the "Glycolysis-Citric Acid Cycle Junction"?
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A transport protein is required for the transport of pyruvate into the mitochondrial matrix. The first step that occurs in the Glycolysis-Citric Acid Cycle Junction is the removal of a carbon dioxide. The second step that occurs in the Glycolysis-Citric Acid Cycle Junction is the reduction of NAD+ to NADH. The third step is the attachment of CoA to the acetate by an unstable bond. 2 CO2 and 2 NADH are produced from this process.
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What is acetyl Coenzyme A (acetyl CoA). HOw many carbon molecules does acetyl CoA contribute to Citric Acid Cycle?
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Acetyl CoA is the end product of the Citric Acid Cycle. It contains an acetate and a CoA. Acetyl CoA contributes 2 carbons per Coenzyme.
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The Citric Acid Cycle is a cycle because the starting substrate (oxeloacetate) is regenerated. Briefly describe how oxaloacetate changes during the Citric Acid Cycle. Again, if we started respiration with one glucose molecule, how many NADH, FADH2, and ATP molecules are there produced in the Citric Acid Cycle? How many CO2 molecules?
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Acetyl CoA adds its 2 carbons acetate to oxaloacetate to produce citrate.
Citrate is converted into its isomer isocitrate by removing water then adding another. Isocitrate loses a carbon dioxide and then an NAD+ is reduced to NADH to form Ketogluterate. Ketogluterate loses another carbon dioxide and the resulting compound is oxidized reducing NAD+ to NADH. The remaining molecule is then attached to CoA by an unstable bond to form Succinyl CoA. Succinyl CoA is displaced by a phosphate group which is then transformed to GDP to form GTP and then ADP to form ATP. The end result is succinate. Succinate is oxidized and changes FAD+ to FADH2 which produces Fumarate. Fumarate then has water added to it to form Malate. Malate is then oxidized reducing NAD+ to NADH which regenerates oxaloacetate. The end result would produce 8 NADH, 2 FADH2, 2 ATP, and 6 CO2. |
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In an active mitochondrion, would the intermembrane space or the matrix have a lower pH (be more acidic)? How does the ETS generate this difference in pH? What is chemiosmosis? For thought: how does the formation of ATP compare with the concept of "coupled transport" as it refers to membrane transport?
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In an active mitochondria, the intermembrane space would have a lower pH. The Electron transport system generates this difference in pH by moving electron to the intermembrane space through oxidation reactions. Chemiosmosis is the process in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work such as the synthesis of ATP.
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How many ATP can be produced from a molecule of glucose? What are the relative contribution of glycolysis, the Citric Acid Cycle, and the Electron Transport Chain to this process? Why is there variability among cells in the amount of ATP produced per molecule of glucose?
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34 ATP can be produced from one molecule of glucose. The relative contri. There is variability among cell in the amount of ATP produces per Molecule of glucose because not all of the NADH produced in the outer membrane space is always able to make it into the mitochondria.
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When does fermentation occur? What are the products of this process? How efficient is this process at producing energy as compared to aerobic respiration? What are two examples of anaerobic respiration in eukaryotic cells?
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Fermentation occurs when there is no oxygen available to produce ATP. The products of this process are 2 ATP and lactic acid or ethanol. It is not very efficient when compared to aerobic respiration. Two examples of anaerobic respiration in eukaryotic cells are plant roots and muscle cells.
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How can the breakdown of proteins and lipids contribute to cellular respiration? How can proteins and fats be synthesized?
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Proteins and lipids can all be used as fuel for cellular respiration. They enter glycolysis or the citric acid cycle at various points. Proteins and fats can be syntehsized through the consumption of ATP.
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What are the two major components of photosynthesis? What are the major inputs and outputs for each component?
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The two major components of photosynthesis are light energy and CO2. The major inputs for light energy are energy and the output is ATP and the major input for CO2 is carbon. The major output is oxygen.
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How is electromagnetic radiation energy related to its wavelength? How is visible light defined and what wavelengths does it include?
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Energy is related to the wavelength because the smaller the wavelength, the greater the energy and the longer the wavelength, the less energy. Visible light is defined as various colors detected by the human eye. It ranges from 380nm to 750nm.
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What type of pigments are most closely associated with photosynthesis? What are the wavelengths of light that are absorbed by this pigment? Why do leaves appear green and not red or blue?
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Blue and red pigments are most closely associated with photosynthesis.
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How is the formation of ATP in the light reaction similar to the formation of ATP in mitochondria?
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They both used NAD+ in their processes.
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How is light energy related to electron excitation in a chlorphyll molecule? What are three things that can happen to excited electrons in a chlorophyll molecule? What are the major components of a photosystem? How is energy transferred in a photosystem and where do electrons end up in a given photosystem?
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When light energy enters the chlorophyll molecule, it excites the electrons. Three things that can happen to excited electrons in a chlorophyll molecule: it can release heat, drive photosynthesis, or be reradiated at longer wavelengths to produce fluorescence.
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What are the three phases of the Calvin Cycle? Describe briefly what happens in each phase. In which of the three parts of the Calvin Cycle do you find these molecules: ribulous bisphosphate, glyceraldehyde 3-P, 3-phosphoglycerate, and 1, 3-bisphosphoglycerate? Why do we start the Calvin Cycle with 3 molecules of substrate?
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The three phrases of the calvin cycle are carbon fixation, reduction, and regeneration. You find ribulose bisphosphate in the fixation/regeneration phase. You find glyceraldehydes 3-P in the reduction phase. You find 3-phosphoglycerate in the fixation and the reduction phase. You find 1, 3-biphosphoglycerate in the reduction phase. We start the Calcin cycle in with 3 molecules of substrate because _____________________.
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The important product of the Calvin cycle is a triose phosphate sugar (glyceraldehyde 3-P = G3P). What storage product is formed in the chloroplast (stroma) from triose phosphate? What are two things that can happen to triose phosphates when transported into the cytoplasm?
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Starch is formed in the stroma from the triose phosphates. When transported to the cytoplast, the triose phosphates can either enter glycolysis to produce ATP or drive sucrose synthesis for transport throughout the plant.
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What does rubisco stand for and why is it considered the most abundant protein on earth? What is the difference between rubisco and ribulose biphosphate? Under what conditions did rubisco evolve on the earth? What are the "good" and the "bad" reactions that involve rubisco and ribulose? Why is the "good" reaction favored at high CO2 concentrations and why is the "bad" reaction favored under hot and dry conditions?
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Rubisco stands for ribulose carboxylase. It is considered the most abundant protein on earth because it is found in all chloroplasts and it is also the most abundant protein in them. Rubisco is a protein and ribulose bisphosphate is a 5 carbon sugar. Rubisco evolved under reducing conditions (high CO2 and no O2). The good reaction is when there is CO2 available. The bad reaction is when there are low amounts of CO2 and th reaction has to use O2. Because the good reactions have the components needed and the bad reactions have a substitute reactant.
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While photosynthesis in most plants like tomatoes and oaks trees (C3 plants) do poorly under hot and dry conditions, C4 and CAM plants have special photosynthetic adaptations to these conditions. In general, how doe photosynthesis in C4 and CAM plants differ from that in C3 plants like tomatoes and oak trees? How is C4 different from CAM metabolism? Give some examples of C4 and CAM plants.
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C4 plants produce C4 acid in the mesophyll cells, and the calvin cycle occurs in the bundle sheath cells (vein). C4 - corn, sugar cane. CAM - pineapple, cactus.
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Why is photosynthesis important for life on earth?
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Photosynthesis is important for life on earth, because it produces 150 billion metric tons of carbohydrates per year...enough to provide an energy source for all organisms. Also O2 concentration is the atmosphere is maintained at approximately 22% by photosynthesis.
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What are three important functions of cell division in eukaryotic organisms? Give examples of cells that illustrate each function.
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Three important functions of cell division in eukaryotic organisms are reproduction (amoeba), growth and development (sand dollar embryo), and tissue renewal/repair (bone marrow cells).
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The mitotic cell cycle consists of two major phases, Interphase and the Mitotic phase. What are the names of the "subphases" that occur in each of these phases? Briefly, what happens in the cell in these subphases?
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Interphase - G1 (Gap 1), S (DNA synthesis), G2 (Gap 2)
Mitotic - Mitosis (nuclear division), Cytokinesis (cytoplasmic division). |
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What types of molecules make up a chromosome from a eukaryotic cell? Define the terms chromatid and centromere. Draw a chromosome to illustrate sister chromatids and the position of a centromere. When during the cell cycle is DNA replicated?
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The chromosome is made up of a centromere and sister chromatids.
Chromatid - contains DNA molecules Centromere - the narrow waist where the two chromatids are attached DNA is replicated in the S phase. |
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Starting with a single cell, how many cell products (daughter cells) are produced in mitosis? How does the chromosome makeup in each of the products compare to that in the original cell?
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Starting with a single cell, two identical daughter cells are produced in mitosis. The chromosome makeup is identical to that in the original cell.
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In mitosis, what characteristics mark prophase, prometaphase, metaphase, anaphase, and telophase? Define or characterize these terms in relation to mitosis: centriole pairs, mitotic spindle, spindle pole, centromere, chromatin, kinetochore, kinetochore microtubules.
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Prophase - chromosomes condense, mitotic spindle forms, nucleoli disappear.
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What happens in Prometaphase?
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Prometaphase - nuclear membrane breaks down, chromosomes begin to migrate towards the metaphase plate, kinetochore microtubules of the spindle apparatus attach to the kinetichore on each chromatid.
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What happens in Metaphase?
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Metaphase - chromosomes align themselves on the metaphase plate.
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What happens in Anaphase?
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Anaphase - chromatids separate at centromeres, where microtubules are attached to kinetichore, separated chromatids migrate towards opposite poles as kinetichore microtubules shorten.
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What happens in Telophase?
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Telophase - beings when migrating chromatids arrives at spindle poles, nuclear membranes form at each pole.
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What are centriole pairs?
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Centriole pairs - inside of centromeres; only found in animals.
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What are mitotic spindles?
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Mitotic spindle - assemblage of microtubules and associated proteins involved in mitosis.
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What are spindle poles?
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Spindle pole - two mitotic spindles on opposite sides of the cell.
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What are centromeres?
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Centromere - point of connection between two chromatids.
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What are chromatids?
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Chromatid - DNA and proteins that make up a eukaryotic chromosome.
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What are kinetichores?
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Kinetichore - specialized region on the centromere that links each sister chromatid to mitotic spindle.
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What are kinetichore microtubules?
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Kinetichore microtubules - connected to mitotic spindle.
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What is cytokinesis? What is the difference between a cleavage furrow and cell plate? How do they relate to cell division and in what kind of organisms would you find each?
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Cytokinesis - cytoplasmic division.
A cleavage furrow is in animal cells and a cell plate is in plant cells. They relate to cell division because they are actually what divides the cell. |
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Why is it particularly important that the cell cycle by closely regulated in multicellular eukaryotic organisms? What is a cyclin dependent kinase and a cyclin? What does MPF stand for? How are these types of molecules thought to regulate mitosis and the cell cycle? HOw is cell cycle regulation related to cancer?
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It is important that the cell cycle be closely regulated in multicellular organisms so only the right amount is produced.
Cyclin dependent kinase - enzyme that activates proteins by phosphorilation. Cyclin - proteins that activate kinase. MPF - maturation promoting factor - they regulate mitosis and the cell cycle because when these are in abundance, the major parts of the cell's cycle happen. If the cell isn't regulated, cancer cells start to grow wildly. |
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What is binary fission? In what types of cells in this process found? How does binary fission different from the Mitotic cell cycle?
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Binary fission - prokaryotic cell division.
Binary fission - is a lot simpler and faster than mitotic cell division. |
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What type of cell division produces asexual reproduction. What is "budding" and how is it related to asexual reproduction?
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Mitosis produces asexual reproduction specifically through budding. Budding is when a part of the organism starts to copy itself and put it in a part of itself that will break off.
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Define the terms somatic cell, autosome, homologous chromosomes, sex chromosomes, gamete, haploid, and diploid. How many products are formed from a single (mother) cell by meiosis? How does this compare with mitosis?
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Somatic cell - any cell in a multicellular organism except a sperm or egg cell.
Autosome - chromosome that is not directly involved in determining sex. Homologous chromosome - chromosomes of the same length, centromere position, and staining pattern. Sex chromosomes - one pair of chromosomes responsible for determining the sex of an individual. Gamete - a haploid cell; unite during reproduction to produce diploid zygote. Haploid - cell containing only one set of chromosomes. Diploid - a cell containing 2 sets of chromosomes, one for each parent. |
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Somatic cells of alligators are thought be 2n=32. What does that symbolism mean? Alligators form gametes which further become modified to become sperm and egg cells. How many chromosomes would you find in an alligator sperm cell?
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The 2n means 2 pairs of chromosomes. You would find 16 chromosomes in an alligator sperm cell.
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What are the roles of mitosis and meiosis in the human life cycle? Are human cells predominately haploid or diploid?
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The roles of mitosis are growth, reproduction, and repairs. Meiosis is the transfer genetics. Human cells are primarily diploid.
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What occurs in prophase of meiosis I?
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Prophase I - pairing of homologous chromosomes, rearranging of chromosomes during crossing over of chiasmata.
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What occurs in metaphase of meiosis I?
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Metaphase I - pair chromosomes align on metaphase plate, pairing is independent.
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What occurs in anaphase of meiosis I?
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Anaphase I - homologous chromosomes separate, chromosomes migrate towards the poles.
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What occurs in telophase of meiosis I?
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Telophase I - chromosomes reach poles and 2 nuclei form.
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What is meant by independent assortment of chromosomes? What is synapsis? What is crossing over and how does it relate to chiasmata? How does crossing over affect genetic variability?
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Independent assortment of chromosomes means there is no set pattern to how the chromosomes will mix. Synapsis is pairing of the homologous chromosomes. Crossing over is when part of a chromosome switches with part of a different chromosome. The point they switch at is called the chiasmata. Crossing over allows for many variations of genetics.
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A cell with a solute concentration of 200mM is placed in a bathing solution with a solute concentration of 150mM. Relative to the bathing solution, the cell solution is best described as __________.
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Hypertonic
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A molecule becomes more oxidized when it ___________.
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Loses an electron
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Plants that fix CO2 into C4 acids at night when stomates are open and carry out the Calvin Cycle during the day when stomates are closed are called _________.
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CAM plants
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Electrons needed by photosystem II originate from ___________?
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Water
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The stage of the cell cycle when DNA is replicated is ______________.
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S phase
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The concentration of solutes in a cell is 200mM and cell is placed in a bathing solution with a solute concentration of 150mM. At first, there would be a net movement of water _________.
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from the bathing solution into the cell
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In a eukaryotic cell, reactions of the citric acid cycle occur _____________.
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In the mitochondrial matrix
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Complete oxidation of glucose in aerobic respiration produces ____________ molecules of ATP.
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36-38
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The mitotic spindle is composed of _____________.
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Microtubules
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The following sequence correctly describes the synthesis of ATP associated with electron transport in mitochondria?
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NADH, electron transport, proton gradient, chemiosmosis
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How many CO2 molecules are needed to make one triose phosphate molecule in photosynthesis?
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Three
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Isoleucine is produced from threonine in five enzymatically driven steps. When present in significant concentrations, threonine blocks the first step that converts isoleucine into an intermediate compound. This is best described as an example of ________________.
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Feedback inhibition
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The Citric Acid Cycle start with the input of ______________.
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Acetyl co-A
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The most prevalent and efficient catabolic pathway for the production of ATp, in which oxygen is consumed as a reactant along with the organic fuel.
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Cellular respiration
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A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules to carbon dioxide; occurs within the mitochondrion; the second major stage in cellular respiration.
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Citric Acid Cycle
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A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.
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Electron Transport Chain
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A catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces a characteristic end product, such as ethyl alcohol or lactic acid.
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Fermentation
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The splitting of glucose into pyruvate. Glycolysis is the one metabolic pathway that occurs in all living cells, serving as the starting point for fermentation or aerobic respiration.
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Glycolysis
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Nicotinamide adenine dinucleotide, a coenzyme present in all cells that helps enzymes transfer electrons during the redox reactions of metabolism.
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NAD+
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The loss of electrons from a substance involved in redox reaction.
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Oxidation
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The production of ATP using energy derived from the redox reactions of an electron transport chain.
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Oxidative phosphorylation
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The electron acceptor in a redox reaction.
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Oxidizing agent
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A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction.
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Reducing agent
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The addition of electrons to a substance involved in a redox reaction.
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Reduction
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The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism.
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Substrate-level phosphorylation
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A cluster of several membrane proteins found in the mitochondrial crista (and bacterial plasma membrane) that function in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen ion concentration gradient to make ATP. ATP synthases provide a port through which hydrogen ions diffuse into the matrix of a mitochondrion.
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ATP synthase
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An energy-coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across a membrane to drive cellular work, such as the synthesis of ATP. Most ATP synthesis in cells occurs by this.
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Chemiosmosis
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An iron-containing protein, a component of electron transport chains in the mitochondria and chloroplasts.
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Cytochrome
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The potential energy stored in the form of an electrochemical gradient, generated by the pumping of hydrogen ions across the biological membranes during chemiosmosis.
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Proton-motive force
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Containing oxygen; referring to an organism, environment, or cellular process that requires oxygen.
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Aerobic
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The conversion of pyruvate to carbon dioxide and ethyl alcohol.
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Alcohol fermentation
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Lacking oxygen; referring to an organism, environment, or cellular process that lacks oxygen and may be poisoned by it.
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Anaerobic
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An organism that makes ATP by aerobic respiration if oxygen is present but that switches to fermentation under anaerobic conditions.
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Facultative anaerobe
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The conversion of pyruvate to lactate with no release of carbon dioxide
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Lactic acid fermentation
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An organism that obtains organic food molecules without eating other organisms or substances derived from other organisms. Autotrophs use energy from the sun or from the oxidation of inorganic substances to make organic molecules from inorganic ones.
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Autotrophs
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The second of the two major stages in photosynthesis (following light reactions), involving atmospheric CO2 fixation and reduction of the fixed carbon into carbohydrate.
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Calvin cycle
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The incorporation of carbon from CO2 into an organic compound by an autotrophic organism (a plant, another photosynthetic organism, or a chemoautotropic baterium).
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Carbon fixation
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A green pigment located within the chloroplasts of plants. Chlorophyll can participate directly in the light reactions, which convert solar enery to chemical energy.
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Chlorophyll
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An organism that obtains organic food molecules by eating other organisms or their by-products.
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Heterotroph
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The steps in photosynthesis that occur on the thlykoid membranes of the chloroplast and that convert solar energy to the chemical energy of ATP and NADPH, evolving oxygen in the process.
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Light reactions
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The ground tissue of a leaf, sandwiched between the upper and lower epidermis and specialized for photosynthesis.
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Mesophyll
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Nicotinamide adenine dinucleotide phosphate, an acceptor that temporarily stores energized electrons produced during the light reactions.
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NADP+
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The process of generating ATP from ADP and phosphate by means of proton-motive force generated by the thylakoid membrane of the chloroplast during the light reactions of photosynthesis.
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Photophosphorylation
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The conversion of light energy to chemical energy that is stored in glucose or other organic compounds; occurs in plants, algae, and certain prokaryotes.
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Photosynthesis
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A microscopic pore surrounding by guard cells in the epidermic of leaves and stems that allows gas exchange between the environment and the interior of the plant.
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Stoma
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The fluid of the choloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water.
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Stroma
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A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy.
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Thylakoid
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The range of a pigment's ability to absorb various wavelengths of light.
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Absorption spectrum
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A graph that depicts the relative effectiveness of different wavelengths of radiation in driving a particular process.
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Action spectrum
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An accessory pigment, either yellow or orange, in the chloroplasts of plants. By absorbing wavelengths of light that chlorophyll cannot, cartenoids broaden the spectrum of colors that drive photosynthesis.
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Carotenoid
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A type of blue-green photosynthetic pigment that participates directly in the light reactions.
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Chlorophyll a
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A type of yellow-green accessory photosynthetic pigment that transfers energy to chlophyll a.
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Chlorophyll b
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A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and that produces ATP but not NADPH or oxygen.
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Cyclin electron flow
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The entire spectrum of radiation in wavelength from less than a nanometer to more than a kilometer.
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Electromagnetic spectrum
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Complex of proteins associated with pigment molecules (including chlorophyll a, chlorophyll b, and carotenoids) that captures light energy and transfers it to reaction-outer pigments in a photosystem.
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Light-harvesting complex
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A route of electron flow during the light reactions of photosynthesis that involves both photosystems and produces ATP, NADPH, and oxygen. The net electron flow is from water to NADP+.
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Non-cyclin electron flow
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A quantum, or discrete amount, of light energy
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Photon
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Light-capturing unit located in the thylakoid membrane of the chloroplast, consisting of a reaction center surrounded by numerous light-harvesting complexes. There are two types of photosystems, I and II; they absorb light best at different wavelengths.
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Photosystem
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One of two light-capturing units in a chloroplast's thylakoid membrane; it has two molecules of P700 chlorophyll a at its reaction center.
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Photosystem I
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One of two light-capture units in a chloroplast's thylakoid membrane; it has two molecules of P680 chlorophyll a at its reaction center.
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Photosystem II
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A specialized molecule sharing the reaction center with the pair of reaction-center chlorophyll a molecules; it accepts an electron from one of these two chlorophylls.
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Primary electron acceptor
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Complex of proteins associated with two special chlorophyll a molecules and a primary electron acceptor. Located centrally in a photosystem, this complex triggers that light reaction of photosynthesis. Excited by light energy, one of the chlorophylls donates an electron to the primary electron acceptor, which passes an electron to an electron transport chain.
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Reaction center
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An instrument that measure the proportions of light of different wavelengths absorbed and transmitted by a pigment solution.
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Spectrophotometer
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That portion of the electromagnetic spectrum detected as various colors by the human eye; randing in wavelength from about 380 nm to about 750 nm.
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Visible light
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The distance between crests of waves, such as those of the electromagnetic spectrum.
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Wavelength
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A type of photosynthetic cell arranged into tightly packed sheaths around the veins of a leaf.
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Bundle-sheath cell
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A plant that uses the Calvin cycle for the initial steps that incorporate CO2 into organic material, forming a three-carbon compound as the first stable intermediate.
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C3 plant
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A plant that uses crassulacean acid metabolism, an adaptation for photosynthesis in arid conditions, first discovered in the family of Crassulaceae. Carbon dioxide entering open stomata during the night is converted into organic acids, which release CO2 for the Calvin cycle during the day, when stomata are closed.
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CAM plant
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A type of metabolism in which carbon dioxide is taken in at night and incorporated into a variety of organic acids.
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Crassulacean acid metabolism (CAM)
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A loosely arranged photosynthetic cell located between the bundle sheath and the leaf surface.
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Mesophyll cell
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An enzyme that adds carbon dioxide to phosphoenolypyruvate (PEP) to form oxaloacetate.
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PEP carboxylase
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A metabolic pathway that consumes oxygen, releases carbon dioxide, generates no ATP, and decreases photosynthetic output; generally occurs on hot, dry, bright days, when stomata is closed and the oxygen concentration in the leaf exceeds that of carbon dioxide.
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Photorespiration
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