BIO exam 3 study guide
BIO exam 3 study guide Bio 104
Kutztown University of Pennsylvania
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This 23 page Study Guide was uploaded by Ashlee Notetaker on Saturday April 2, 2016. The Study Guide belongs to Bio 104 at Kutztown University of Pennsylvania taught by Dr. Sacchi in Spring 2016. Since its upload, it has received 15 views. For similar materials see Principles of Biology in Biology at Kutztown University of Pennsylvania.
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Exam 3 Study Guide Chapter 5: membrane structure and function Components of the plasma membrane: Phospholipid bilayer. Protein components. Cholesterol (animal plasma membrane). o Related steroids are found in the plasma membrane of plants. o Cholesterol helps modify the fluidity of the membrane over a range of temperatures. Phospholipid Bilayer Amphipathic molecule, meaning it is both hydrophobic (waterfearing) and hydrophobic (waterloving). o Thus the bilayer that is formed when in water. o Hydrophobic polar heads associate with the polar molecules found on the outside and inside of the cell. o Hydrophobic nonpolar tails associate with hydrophobic nonpolar molecules. Integral Proteins: embedded in the plasma membrane. Hydrophobic core that associate with nonpolar core of the membrane. Hydrophilic ends of integral proteins protrude from both surfaces of the bilayer, interacting with polar H20 molecules. Integral proteins can be held in place by attachments to protein fibers of the cytoskeleton (inside) and givers of the extracellular matrix (outside). o Only animals of extracellular matrix – containing various protein fibers and large, complex carbohydrates. The extracellular matrix lends external support to the plasma membrane – assisting in cell communication. Peripheral Proteins: occur only on the cytoplasmic side of the membrane. One membrane is different from another by types of proteins integrated into the membrane. Cell membranes are highly similar in the types of molecules they contain, making them interchangeable and allow them to fuse together properly. FluidMosaic Model Membranes are flexible structures consisting of a variety of molecules, including phospholipids, cholesterol, and proteins. o Fluidmosaic model is used to describe the interactions between these components. Cells are flexible because the phospholipid bilayer is fluid. o At body temperature – the phospholipid bilayer has a consistency of olive oil. The greater the concentration of unsaturated fatty acids residues, the more fluid the bilayer. Cholesterol molecules prevent the plasma membrane from becoming too fluid at higher temperatures or too solid at lower temperatures. o At high temp: cholesterol stiffens the membrane – making it less fluid. o At low temp: cholesterol helps prevent membrane from freezing by not allowing contact between certain phospholipid tails. The presence of many proteins in the plasma membrane are what makes it mosaic. o Protein position can change over time – unless anchored to another structure (cytoskeleton or extracellular matrix). A membrane is asymmetrical – not identical sides. Glycoproteins and Glycolipids Phospholipids and proteins that have attached carbohydrate (sugar) chains called glycoproteins and glycolipids. o Carbohydrate chains are diverse (branched/unbranched, sequence and number of sugars) Because of the carbohydrate diversity, each cells has its own “fingerprint.” Thus, glycoproteins and glycolipids play an important role in cellular identification. o When transplanted tissues are rejected it is because the immune system is able to detect that the foreign tissues cells do not have the appropriate carbohydrate chains. o In humans carbohydrate chains are the basis for the A, B and O blood types. In animals the carbohydrate chain is a glycocalyx – protects cell, cellcell adhesion, reception of signaling molecules and celltocell recognition. Protein Functions Channel proteins: involved in passing molecules through the membrane. Carrier proteins: involved in passing molecules through the membrane. When substance is received, carrier proteins change their shape so the substance can move across the membrane. Cell recognition proteins: glycoproteins that help the cell recognize when it is being invaded by pathogens, so the immune response can occur. Receptor protein: a shape that allow only a specific molecule to bind to it. When a molecule binds the protein changes shapes and thereby bring about cellular response. Enzymatic protein: carry out metabolic reactions. Junction protein: forming junctions between animal cells signaling molecules that pass through gap junctions allow the cilia of cells that line the respiratory tract to beat in unison. Permeability of the Plasma Membrane The plasma membranes general job is to regulate what foes in and out of the cell. Selectively permeable allowing only certain substances into the cell while keeping others out. Molecules that can freely cross the membrane generally require no energy to do so. o Hydrophobic substances can cross the membrane with no energy cost because their hydrophobic nature is similar to that of the phospholipid center of the membrane. o Polar molecules are chemically incompatible with the center of the membrane and so require energy to drive their transport. In general, small, noncharged molecules, such as carbon dioxide, oxygen, glycerol, and alcohol, can freely cross the membrane. Passage of Molecules Into and Out of the Cell Diffusion: high to low concentration (lipidsoluble molecules, gases). Facilitated: high to low concentration (some sugars, amino acids). Channels or carrier and concentration gradient. Active: low to high concentration (sugars, amino acids, ions). Carrier plus energy. Bulk Transport: toward outside or inside (macromolecules). Vesicle utilization. Concentration Gradient: molecules that move from an area where their concentration is high to low. Oxygen concentration is higher outside of cell, lower inside of cell. o Thus, the oxygen moves across the membrane into the cell. Carbon dioxide concentration is higher inside of cell, lower outside of cell. o Thus, carbon dioxide flows from the inside of the cell to the outside of the cell. Aquaporins: allow H2O to cross membrane and allow cells to equalize water pressure differences between their interior and exterior environments. Ions and polar molecules (such as glucose and amino acids) can cross a membrane. Often assisted by carrier proteins, which recognize shape of ion/molecule and must combine with ion/molecule before changing its shape and transporting the molecule/ion across the membrane. Bulk Transport is a way that large particles can enter or exit a cell. Exocytosis: fusion of vesicle with the plasma membrane moves a particle to the outside of the membrane. Endocytosis: vesicle formation moves a particle to inside the plasma membrane. o Vesicle formation is reserved for movement of macromolecules or even something larger, such as a virus. Passive Transport across a Membrane Diffusion: movement of water from a high to lower concentration until equilibration is achieved and the molecule are distributed. Solution: contain both a solute (solid) and solvent (liquid). Solute and solvent must be equally distributed for equilibrium to be reached. Once reached there is no net movement. The plasma membrane allow only a few types of molecules to enter/exit the cell by diffusion. Influences on rate of diffusion Temperature Pressure Electrical currents Molecule size Osmosis: the diffusion of water across a selectively permeable membrane from high to low concentration. Osmotic Pressure: the pressure that develops in a system due to osmosis. Isotonic Solution: the solute concentration and water concentration both inside and outside the cell are equal. Hypotonic Solution: causes cells to swell, or even burst, due to the intake of water. When a plant is places in a hypotonic solution: the cytoplasm expands, because the large central vacuole gains water and the plasma membrane pushes against the rigid cell wall. Plant cells do not burst because no cell wall gives way. Organisms that live in freshwater have contractive vacuoles that help them avoid taking in too much water. o Freshwater fish have kidneys that excrete a large volume of dilute urine. Hypertonic Solution: cause the cell to shrink or shrivel, due to water loss. When a plant cell is placed in a hypertonic solution, the plasma membrane pulls away from the cell wall as the large central vacuole loses water. Facilitated Transport: explains how molecules such as glucose and amino acids are rapidly transported across the plasma membrane. H2O molecules move through channel protein. Glucose and amino acids move through by way of carrier proteins. Facilitated transport requires no energy because movement is with concertation gradient. Active Transport: requires energy because movement is against concentration gradient. Energy usually in the form of ATP. Carrier proteins and ATP needed to move molecules against their concertation gradient. o The ATP is needed in order for the molecule to combine with carrier. Sodiumpotassium pump: moves sodium ions (Na+) to the outside of the cell and potassium ions (K+) to the inside of the cell, through the same carrier protein. Animal cells 3 Na+ (sodium) ions are carried outward for every 2 potassium (K+) ions carried inward. Active transport Bulk Transport: membrane vesicles formed around macromolecules require an expenditure of cellular energy. Active transport Exocytosis: intracellular vesicle fuses with the plasma membrane as secretion occurs. Golgi body produces vesicle. The membrane of the vesicle becomes part of the plasma membrane because both are nonpolar – as substances exit the cell. Proteins released from vesicle may adhere to the cell surface or become incorporated into an extracellular matrix. Endocytosis: cells take in substances by moving vesicles around the material. Plasma membrane invaginates to envelope the substance, and then membrane pinches off to form an intracellular vesicle. Occurs in 3 different ways: o Phagocytosis: transports large substances into the cell. o Pinocytosis: transports liquid or very small particles into cell. o Receptormediated endocytosis: form of pinocytosis that uses a receptor protein to recognize compatible molecules and take them into the cell. Modification of Cell Surfaces Cell Surfaces in Animals: Extracellular Matrix: meshwork of proteins and polysaccharides in close association with the cell that produced them. The extracellular matrix and cytoskeleton play a role in cell signaling, and influence the shape and cell activity. Proteoglycan: polysaccharides that attach to a protein in the extracellular matrix. Resists compression of extracellular matrix, and assist in cell signaling when they regulate passage of molecules. Junctions between cells: Adhesion junctions: mechanically attach adjacent cells. o Most common between skin cells. Tight junctions: connect plasma membrane between adjacent cells together. o Tissues that serve as barriers are held together by tight junctions. Gap junctions: allow cell’s to communicate – formed by two identical plasma membrane channels joining. o Lend strength and allow small molecules to pass through. Plant cell walls – in addition to the plasma membrane, plant cells are surrounded by a porous cell wall. Primary cell wall: all plant cells have, containing cellulose fibrils, microfibrils are held together by noncellulose substances. Secondary cell wall: forms inside the primary cell wall. o Greater cellulose fibrils (quantity). o Common in woody plants. Plasmodesmata: connects cytoplasm in living cells of a plant. Chapter 6: Metabolism: energy and enzymes Cells and the Flow of Energy Energy: the ability to do work or bring about a change. Forms of energy: Kinetic energy: energy of motion. Potential energy: stored energy. o Food is a form of potential energy called chemical energy, because it is composed of organic molecules. o When a moose walks it turns chemical energy into a type of kinetic energy called mechanical energy. Laws of thermodynamics: explain why energy flows through an ecosystem and through cells. First law: the law of conservation of energy – energy cannot be created nor destroyed, but it can be changed from one form to another. o When leaf cells photosynthesize, solar energy is used to form carbohydrate molecules from carbon dioxide gas and water. Carbohydrates have bonds that store energy, making them energyrich molecules. Carbon dioxide and water are energypoor molecules. o Plants capture only a small portion of solar energy, much of it is lost as heat (which is also a form of energy). Energy exchange produces heat. Second law: applies to living systems – energy cannot be change from one form to another without a loss of useable energy. o When heat dissipates into the environment it is no longer usable – not available to do work. o No process requiring a conversion of energy is ever 100% efficient. Cells are capable of about 40% efficiency, the rest is lost as heat. Cells and Entropy Entropy: the relative amount of disorganization. Every energy transformation makes the universe less organized, or structured, and more disordered, or chaotic. The second law of thermodynamics that each cellular process makes less energy available to do useful work in the future. Metabolic Reactions and Energy Transformations Metabolism: sum of all chemical reactions that occur in a cell. Includes both spontaneous and energy requiring reactions. Reactants: substances that participate in that reaction. Products: form as a result of reaction. A reaction will occur spontaneously if it increases the entropy if the universe. o Spontaneous reactions occur without an input of energy. Free energy: amount of energy left to do work after a chemical reaction has occurred. Change in free energy = subtracting free energy of the reactants from that of the products. A negative result means that the products have less free energy than the reactants, and the reaction will occur spontaneously. Exergonic reaction: spontaneous and release energy. Endergonic reaction: require an input of energy to occur. Protein and carbohydrate synthesis are endergonic. Must be coupled with exergonic reaction. ATP is an energy carrier between exergonic and endergonic reactions. ATP Energy for Cells ATP (adenosine triphosphate) is the energy currency of cells. The more active an organism – the greater demand for ATP. ATP is regenerate by ADP (adenosine diphosphate) and inorganic phosphate. o The cycle is powered by the breakdown of glucose and other biomolecules during cellular respiration. o About 40% of the free energy stored in chemical bonds of a glucose molecule is transformed to ATP; the rest is lost as heat. o ATP breakdown can be coupled to endergonic reactions – minimizing energy loss. Structure of ATP ATP is a nucleotide composed of a nitrogen containing base adenine and the 5carbon sugar ribose (together called adenosine) and 3 phosphate groups (phosphate groups repel each other, creating instability and potential energy). ATP is high energy because its phosphate groups can easily be removed. Couple Reactions Through coupled reactions, ATP drives forward the energetically unfavorable processes that must occur. A cell has two main ways to couple ATP hydrolysis to an energy requiring reaction: ATP is used to energize a reactant or ATP is used to change the shape of a reactant. o Both are achieved by transferring a phosphate group to the reaction. Usually the energyreleasing reaction (exergonic) is the hydrolysis of ATP – because ATP’s phosphate groups release more energy than the amount consumed by the energy requiring reaction. ATP breakdown is couple to the energyrequiring reaction (endergonic). Function of ATP in Cells Chemical work: ATP supplies the energy needed to synthesize macromolecules (anabolism) that makes up the cell, and therefore the organism. Transport work: ATP supplies the energy needed to pump substances across the plasma membrane. Mechanical work: ATP supplies the energy needed to permit muscles to contract, cilia and flagella to beat, and chromosomes to move. Metabolic Pathways and Enzymes Enzyme: protein molecule that speeds a chemical reaction without itself being affected by the reaction. Allow reactions to occur under mild conditions. Regulate metabolism, by eliminating side reactions. Ribozymes: made of RNA (instead of proteins), can serve as biological catalyst. Ribozymes are involved in RNA synthesis and the synthesis of proteins at ribosomes. Metabolic Pathway: a series of linked reactions. Begin with a particular reactant and end with a final product. Each step in a metabolic pathway is a chemical reaction catalyzed by an enzyme. Substrates: reactants in a chemical reaction. In a metabolic pathway the substrates for the first reaction are converted into products, and those products then serve as the substrate for the next enzymecatalyzed reaction. o Different pathways can interact because of common molecule. o Metabolic pathways are useful for capturing/releasing small increments of molecular energy. o Enzymes in metabolic pathways allow cells to regulate and respond to changing environments. EnzymeSubstrate Complex Active site: part of enzyme that reacts with substrate. Induced fit model: enzyme undergoes slight shape change to achieve optimum fit of the substrate. The change in shape of the active site facilitates the reaction that now occurs. The products are then released, and the active site returns to its original shape ready to bind to another substrate molecule. Because enzymes bind with their substrates, they are sometimes names for their substrates and usually end in –ase. Degradation: the substrate is broken down to smaller products. Synthesis: the substrates are combined to produce a larger product. Certain enzymes carry out degradation or synthesis. Energy of Activation: energy must be added to cause molecules to react. Keeps molecules from spontaneously degrading within a cell. Reducing the energy of activation increases the rate at which the reaction may occur. o The presence of any enzyme does just that – which is why enzymes are considered biological catalyst for chemical reactions. The energy of activation will be higher when an enzyme is not present. Factors that Affect Enzyme Speed Increasing enzyme and substrate increase reaction time. pH, temp. or an inhibitor that can change the shape of an enzyme, called denaturation. o Causes decrease in reaction rate and doesn’t allow substrate to sufficiently fit in enzyme. Cofactors: molecules that help speed the rate of reaction, because they help bind the substrate to the active site, or participate in the reaction at the active site. Substrate Concentration Enzyme activity increases as substrate activity increases. o As more substrates fill active sites, more products result per unit of time. Optimal pH Each enzyme has an optimal pH where reaction rate is the highest. A change in pH can cause an enzyme to denature, and under extreme pH conditions an enzyme can lose its shape and become inactive. Temperature As temperature increases, enzyme activity increases. Enzyme Cofactors and Coenzymes Cofactor: ion or molecule (inorganic ions and organic proteins). Sometimes needed at active site for proper enzymatic function. Coenzymes: nonprotein organic molecule. Vitamins are components of coenzymes. Enzyme Inhibition: when a molecule (the inhibitor) binds to an enzyme and decreases its activity. Can be useful/beneficial by means of conserving raw materials and energy. Noncompetitive Inhibition: the inhibitor binds to the enzyme at a location other than the active site. This site is called an allosteric site. When an inhibitor is at the allosteric site, the active site of an enzyme changes shape, which in turn changes its function. Competitive Inhibition: an inhibitor and the substrate compete for the active site of an enzyme. Product forms only when substrate, not inhibitor – is at the active site. OxidationReduction Reactions and Metabolism Oxidation: loss of electrons Reduction: gain of electrons Because both go handinhand, the entire reaction is called redox reaction. Apply to covalent reactions in cells. When there is a loss of a hydrogen atom, there is an electron loss. When there is a gain of a hydrogen atom, there is an electron gain. In photosynthesis: carbon dioxide is reduced and water is oxidized. In mitochondria and cellular respiration: mitochondria oxidize carbohydrates and use the energy to build ATP molecules. In cellular respiration glucose has lost hydrogen atoms (oxidized) and oxygen gains (reduction). Chapter 7: Photosynthesis Photosynthetic Organisms Photosynthesis: converts solar energy into the chemical energy of a carbohydrate. Photosynthetic organisms (plants, algae, cyanobacteria) are called autotrophs, because they produce food. Photosynthetic organisms harness the energy from the sun and provide gases and nutrients for heterotrophs. o Heterotrophs generate chemical energy and produce carbon dioxide and water. Producers (autotrophs) feed themselves and consumers (heterotrophs). Both producers and consumers use organic molecules produced by photosynthesis as a source of building blocks for growth and repair, and as a source of chemical energy for cellular work. Photosynthesis produce O2 as a byproduct. o Oxygen is required for cellular respiration. o Oxygen forms an ozone in the atmosphere that shields ultraviolet radiation and makes terrestrial life possible. Fossil Fuels: the energy within oil and coal was originally captured from the sun by plants and algae. Fermentation of plants produces ethanol. Photosynthesis in Flowering Plants Mesophyll: tissue, in which cells are specialized for photosynthesis. Raw materials for photosynthesis: H2O and carbon dioxide. The root of a plant absorb water, water then travels to vascular tissue up the stem to a leaf – entering into leaf veins. Carbon dioxide in the air enters a leaf through small openings called stomata. After entering a leaf, CO2 and H2O diffuse into chloroplasts (inside the mesophyll), the organelles that carry on photosynthesis. o Chloroplasts provide tremendous surface area for photosynthesis to occur. Stroma: a double membrane surrounds a chloroplast, and its semifluid interior is called stroma. The stroma contains an enzymerich solution, where CO2 is first attached to an organic compound and then reduced to a carbohydrate. o Carbohydrate in glucose form is a source of chemical energy for most organisms. A different membrane inside the stroma forms flattened sacs called thylakoids. o When thylakoids are stacked they form a grana. o Inner compartments of individual thylakoid is called thylakoid space. o Thylakoid membranes contain chlorophyll (green) and other pigments that are capable of absorbing the solar energy that drives photosynthesis. The Process of Photosynthesis 6CO2 + 12H2O + Solar Energy C6H12O6 + 6H2O + 6O2 Reactants: carbon dioxide and water Products: carbohydrate, water and oxygen Photosynthesis involves oxidation – reduction (redox) and the movement of electrons from one molecule to another. Solar energy is used to generate the ATP needed to reduce carbon dioxide to a carbohydrate. The Role of NADP+/NADPH NADP+ is the coenzyme of redox, active during photosynthesis. When NADP+ is reduced, it had accepted two electrons and one hydrogen atom, and when NADPH is oxidized, it gives up its electrons. NADP+ + 2e + H+ NADPH During photosynthesis when H2O splits, oxygen is released and the hydrogen atoms are taken up by NADP+. Later, NADPH reduces carbon dioxide to a carbohydrate. Two sets of Reactions The process of photosynthesis can be divided into two stages: 1. The light reactions: take place on thylakoids (day). 2. Calvin cycle reactions: take place in the stroma (day and night). The Light Reactions: solar energy (sun) is converted to chemical energy (ATP, NADPH). The green pigment chlorophyll, present in thylakoid membranes, is responsible for absorbing the solar energy that drives photosynthesis. Solar energy energizes electrons, which move down the electron transport chain. As electrons move down the electron transport chain, energy is released and captured to produce ATP molecules. Energized electrons are also taken up by NADP+, which is reduced and becomes NADPH. Calvin Cycle Reactions: ATP, NADPH Carbohydrate The enzymes needed to speed the reduction of carbon dioxide during both day and night are located in the semifluid substance of the chloroplast stroma. Carbon dioxide is taken up and converted (reduced) to a carbohydrate that can later be converted to glucose. The ATP and NADPH formed during light reactions are used to reduce carbon dioxide. o Once ATP and NADPH are used, ADP + P and NADP+ return back to light reaction to be utilized again. Plants Convert Solar Energy Short Wavelength: gamma rays Longest Wavelength: radio waves Higherenergy wavelengths are screened out by the ozone layer in the atmosphere before they reach the earth’s surface. Lowerenergy wavelengths are screens out by water vapor and carbon dioxide. Visible light is the most prevalent – organisms have evolved using these. Pigment and Photosynthesis Pigment molecules absorb wavelengths of light. o Not all wavelengths, they reflect or transmit some. The pigments in chloroplast (chlorophyll) that are capable of absorbing various portions of visible light is called their absorption spectrum. Green light is transmitted and reflected by chlorophyll, which is why plants appear green. Photosynthetic organisms differ in the type of chlorophyll they contain. o Chlorophyll A (green) o Chlorophyll B (green) o Both absorb violet, blue and red. Carotenoids: pigments of plants and algae that is often yellow or orange in color (fall colors). Spectrophotometer: measures the amount of light that passes through the sample, and from this it is possible to calculate how much was absorbed. Electrons Flow in the Light Reactions Light reactions utilize two systems (in this order): Photosystem II Photosystem I Photosystem II: Electrons flow a noncyclic pathway that begins with photosystem II. Solar energy strikes the pigment complex (molecules of either chlorophyll A, chlorophyll B or carotenoids). Solar energy is passed from one pigment to the other until it is concentrated in a particular pair of chlorophyll a molecules, called reaction center. Electrons in the reaction center become energized, leave the reaction center and move to nearby electron acceptor molecules. Electrons are replaced where they had left. o Electrons are removed from water, which splits, releasing oxygen into the atmosphere. o The oxygen released typically gets used in mitochondria to make ATP. o The hydrogen ions stay in the thylakoid space and contribute to the formation of a hydrogen ion gradient. An electron acceptor molecule sends energized electrons, received from the reaction center, down an electron transport chain. o Electron transport chain: a series of carriers that pass electrons from one to another. As electrons are passed from one carrier to the next, energy is captured and stored in the form of hydrogen ion gradient. o ATP that is produced here will be used by the Calvin cycle (stroma) to reduce CO2 to a carbohydrate. Photosystem I: Solar energy is absorbed by pigment complex. Energized electrons leave the reaction center and are captured by electron acceptors. o Lowenergy electrons from the ETC replace those lost in PSI. The electron acceptor molecule pass their electrons to NADP+ molecules. o NADP+ accepts 2 e and 1 H to become reduced and form NADPH. o NADPH is then used in the Calvin cycle, along with ATP to reduce CO2 to a carbohydrate. End of photosystem II, and I ATP and NADPH are not made in equal amounts during the light reactions. More ATP is required during the Calvin cycle. Extra ATP comes from cyclic pathway in photosystem I, an electron can be rerouted back to an earlier point in the ETC – yielding more ATP. As electrons are traveling down the electron transport chain, H+ is being pumped from the stroma into the thylakoid space. When H+ flow back out of the space into the stroma through an ATP synthase complex, ATP is produce from ADP + P. This method of ATP synthesis is called chemiosmosis, because ATP production is tied to the establishment of H+ gradient. Plants Fix Carbon Dioxide The Calvin cycle: will use ATP and NADPH for carbon dioxide fixation. Light independent reaction, inside stroma. 3 steps of Calvin cycle: 1. Carbon dioxide fixation 2. Carbon dioxide reduction 3. Regeneration of RuBP Step 1: carbon dioxide fixation A molecule of carbon dioxide from the atmosphere is attached to RuBP, a 5carbon molecule. The result is one 6carbon molecule, which splits into two 3carbon molecules (3PG). The enzyme that speeds this reaction is RuBP carboxylase. Step 2: Carbon dioxide reduction Each of the two 3PG (3carbon molecules) undergoes reduction to G3P. Done by adding ATP and NADPH. G3P has more electrons, and now more chemically able to store energy and form larger organic molecules. Step 3: regeneration of RuBP It takes three turns of the Calvin cycle to allow one G3P to exit. For every three turns, 5 molecules of G3P are used to reform 3 molecules of RuBP. Done by adding 3 ATP molecules. The Importance of the Calvin Cycle G3P can be converted into other molecules a plant needs: o Glucose o Starting point for various carbohydrates to be produced o Fatty acid synthesis, amino acid synthesis Other Types of Photosynthesis C3 Plants: use the enzyme RuBP carboxylase to fix CO2 to RuBP in mesophyll (photosynthetic) cells. Stomata: H2O can leave and CO2 can enter. o If the weather is hot and dry the stomata close (conserving water) and cause CO2 decrease and O2 increase. o O2 will combine with RuBP rather than CO2, resulting in one molecule of 3PG and the eventual release of CO2. This is called photorespiration. C4 Plants: fix CO2 to PEP (a 3carbon molecule) using the enzyme PEP carboxylase. The result = oxaloacetate (4carbon molecule). Higher photosynthetic rate because they can avoid photorespiration. PEP carboxylase does not combine with O2 – even when stomata are closed, CO2 is delivered to the Calvin cycle in the bundle sheeth cells. When the weather is moderate C3 plants have the advantage. When the weather is hot/dry C4 plants have the advantage. CAM Plant: Fix CO2 at night (open stomata), forming a 4carbon molecule that is released to the Calvin cycle during the day. Chapter 8: Cellular Respiration Cellular respiration: process by which cells acquire energy by breaking down nutrient molecules produced by photosynthesizes. Require oxygen and gives off CO2 (opposite of photosynthesis). Cellular respiration involves the complete breakdown of glucose to carbon dioxide and water (H2O). C6H12O6 + 6O2 6CO2 + 6H20 + Energy Cellular respiration breaks down glucose (high energy) to CO2 and H20 (low energy), thus energy is released. o The energy that is released is used to make ATP. The cell carries out cellular respiration in order to build ATP molecules. Energy within glucose is released slowly, so ATP production can gradually occur. o 3638 ATP molecules after complete breakdown. o 3940% of the energy that was available from glucose. NAD+ and FAD NAD+: coenzyme of oxidationreduction. NAD+ + 2E + H NADH The electrons received by NAD+ are high energy electrons that are carried to the ETC. Only a small amount of NAD+ needs to be present, because it can be used over and over. FAD: coenzyme of oxidation – reduction. FAD + 2E + 2H FADH2 Phases of Cellular Respiration: 1. Glycolysis (anaerobic) 2. The preparatory reaction (aerobic) 3. The citric acid cycle (aerobic) 4. The electron transport chain (aerobic) Glycolysis takes place outside the mitochondria, in the cytoplasm and does not require the presence of oxygen. The other three phases occur inside mitochondria, where oxygen is the final acceptor of electrons. Glycolysis: takes place in the cytoplasm, breakdown of 6carbon molecule glucose to two 3 carbon pyruvate molecules. Two steps of glycolysis: 1. Energy – investment: ATP is used to “jumpstart” glycolysis. 2. Energy – harvesting: 4 total ATP made, producing two net overall. Energyinvestment Two ATP are used to activate glucose by adding phosphate. Glucose eventually split into two G3P molecules (3carbon). o Each G3P phosphate group is acquired from one ATP molecule. o From this point on – each G3P molecule undergoes the same series of reactions. Energy – harvesting Oxidation of G3P now occurs by the removal of electrons, accompanied by hydrogen ions. Electrons are picked up by coenzyme NAD+: per G3P molecule. When O2 is available, each NADH molecule carries two highenergy electrons to the ETC and becomes NAD+ again. A phosphate group is added to each 3carbon molecule. o Used to synthesize 2 ATP in later steps of glycolysis. o This is called substratelevel ATP synthesis because an enzyme passes high energy phosphate to ADP, and ATP results. o Coupled reaction o The adding of a phosphate yields: G3P BPG Now: 2 molecules of 3PG (3carbons + P) Oxidation occurs again, but by the removal of H2O. Substratelevel ATP synthesis occurs again per 3carbon molecule (P). o Two molecules of pyruvate results (3carbon). o When O2 is available pyruvate enters mitochondria, where it is metabolized. Subtracting the two ATP that were used to get started, from the four produced overall, there is a net gain of two ATP from glycolysis. Glycolysis is a series of ten steps – each catalyzed by an enzyme. Outside the Mitochondria: Fermentation Fermentation: anaerobic process that produces a limited amount of ATP in the absence of oxygen. In human/animal cells pyruvate is reduced by NADH to lactate. Depending on their enzyme, bacteria vary as to whether they produce an organic acid (like lactate) or an alcohol and CO2. When two (3carbon) molecules of pyruvate are not available to O2: Animals and Bacteria: (2) 3carbon lactate Plants and Yeast: (2) CO2 molecules given off, (2) CO2 alcohol Fermentation is beneficial because the cell still needs energy when oxygen is absent. Fermentation regenerates NAD+ so it can be used again. 2 ATP result from fermentation: 2.1% of the total breakdown of glucose Inside the Mitochondria Mitochondrion has a double membrane with an intermembrane space (between the outer and inner membrane). Cristae are folds of inner membrane that jut into the matrix, the inner most compartment, filled with gellike fluid. The prep reaction, citric acid cycle and ETC are all located in the mitochondria. o Oxygen must be present. o The enzymes that speed the prep reaction and citric acid cycle are in the matrix. The ETC is located in the cristae. Mitochondria is considered the powerhouse of the cell because most of the ATP is produced here. The Preparatory Reaction: converts products from glycolysis into products that enter the citric acid cycle. One prep reaction occurs per pyruvate molecule (twice). 3carbon pyruvate is converted to a 2carbon acetyl group and CO2 is given off. o This is oxidation reaction in which electrons are removed from pyruvate by NAD+ and NADH is formed. o NADH carries highenergy electrons to the ETC. o CO2 diffuses into cells. 2carbon acetyl group is combined with a molecule known as CoA. o CoA carries each acetyl group to the citric acid cycle. The Citric Acid Cycle: Krebs cycle 2carbon acetyl group joins with 4carbon molecule, and 6carbon citrate results. Oxidation occurs – NAD+ is reduced to NADH and CO2 is released. Now, a 5carbon molecule ketoglutarate. Again, NAD+ is reduced to NADH and CO2 is released. ATP is produced – ADP + P. Now, a 4carbon molecule succinate. FAD is reduced to FADH2. Now, 4carbon molecule fumarate. NAD+ is reduced to NADH. Now, 4carbon molecule oxaloacetate. The cycle terns twice per glucose molecule. Production of CO2 6carbon atoms originally in glucose have now become CO2. The prep reactions produces 2 and the citric acid cycle produces 4. Electron Transport Chain Located in cristae of mitochondria and the plasma membrane of aerobic prokaryotes, is a series of carriers that pass electrons from one to another. The high energy electrons that enter are carried by NADH and FADH2. When both NADH and FADH2 give up their highenergy electrons they become oxidized and return back to NAD+ and FAD. Many of the redox carriers are cytochrome molecules. Cytochrome is a protein, with a central atom of iron. As electrons travel down the ETC, energy is captured and eventually used to form ATP molecules. Oxygen is the final acceptor of electrons from the ETC: after receiving electrons, oxygen combines with hydrogen ions and water forms. Cycling of Carriers When NADH delivers electrons to ETC – 3 ATP When FADH2 delivers electrons to ETC – 2 ATP Coenzymes are then recycled – reused. The ETC Pumps Hydrogen Ions The H+ ions flow down a gradient from the intermembrane space into the matrix, the enzyme ATP synthase synthesizes ATP from ADP + P. Chemiosmosis: ATP production is tied to the establishment of an H+ gradient. ATP then moved out of the mitochondria and is used to preform cellular work, during which it breaks down to ADP + P. ATP Totals Substratelevel ATP synthesis: Per glucose molecule there is a net gain of two ATP from glycolysis (in cytoplasm). The citric acid cycle (matrix of mitochondria) accounts for two ATP per glucose molecule. ETC yields 3234 ATP molecules. Grand total: 3638 ATP molecules. Metabolic Pool Catabolism: break down molecules – must be balanced with constructive reactions (anabolism). This balance is essential to optimal cellular function. Chapter 9: the cell cycle and cellular respiration Cell cycle is a set of stages that takes place between the time a eukaryotic cell divides and the times the resulting daughter cells also divide. Interphase: time when cell preforms its normal functions. Most of the cell cycle is spent in interphase. G1 stage: cell grows in size and increases the number of organelles, and accumulates materials needed for DNA synthesis. G0 stage: rested cells – continue normal functions but do not prepare for cell division. S stage: DNA replication occurs – two identical DNA double helix molecules. Chromatid: one single double helix molecule. Sister chromatids: two identical DNA double helix molecules – remain attached until mitosis where they are separated. G2 stage: the cell synthesizes the proteins needed for cell division. Apoptosis: programmed cell death. Cell division increases and apoptosis decreases the number of somatic (body) cells. The eukaryotic chromosome: contains a single double helix molecule. DNA wraps around a histone protein. Euchromatin: loosely coiled, represents the active chromatin containing genes that are being transcribed. Heterchromatin: highly compacted – inactive chromatin. Chromosome Numbers Diploid (2N): total number of chromosomes found in all cells of an individual. Haploid (N): one chromosome of each kind (half diploid number). Chromosome Duplication Before nuclear division, DNA replicates, duplicating the chromosomes in the parent cell. o Occurs during S stage of interphase. Each new chromosome has two identical chromatids (double helical molecules). o New identical chromatids are called sister chromatids. Sister chromatids are restricted and attached to each other at a region called centrosome. Protein complexes called kinetochores develop on each side. o Kinetochores attach to spindle fibers in mitotic stage. Division of the Centrosome The centrosome divides before mitosis begins. In animal cells each centrosome contains a pair of barrel shaped organelles called centrioles. Phases of Mitosis: Prophase: nucleolus disappears and the nuclear envelope fragments. Spindle fibers begin to assemble as the two centrosomes migrate away from one another. Premetaphase (late prophase): kinetochores appear on each side of centromere, and these attach sister chromatids to the kinetochore spindle fibers. Metaphase: chromosome (each consisting of two sister chromatids) are at the metaphase plate (center of fully formed spindle). Anaphase: daughter chromosomes (each consisting of one chromatid) are moving toward the poles of the spindle. Telophase: daughter cells are forming as nuclear envelopes and nucleoli appear. Chromosomes will become indistinct chromatin. Cytokinesis: two cell formation Animal cells: cleavage furrow Plant cells: cell plate
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