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Bio 1107, Study guide for chapters 6-9

by: Monica Notetaker

Bio 1107, Study guide for chapters 6-9 BIO 1107

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Monica Notetaker
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These notes cover material from chapters 6-9 with a variety of charts, definitions, and explanations.
Intro to Biology
Dr. Brookshire
Study Guide
Cellular, Cellular Respiration, metabolism, Membranes
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This 12 page Study Guide was uploaded by Monica Notetaker on Saturday February 20, 2016. The Study Guide belongs to BIO 1107 at Kennesaw State University taught by Dr. Brookshire in Fall 2016. Since its upload, it has received 88 views. For similar materials see Intro to Biology in Biology at Kennesaw State University.


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Date Created: 02/20/16
Bio test 2 study guide Chapter 6: Tour of the Cell Microscopes:  Light microscope: light passes through specimen, then through a class lens; can’t see the specifics of a cell, but can see living cells  Electron Microscope: beam of electrons shot through specimen; resolves smaller structures  Scanning Electron Microscope: Studies the surface of a specimen; gold film and electron beam leads to 3-D looking image  Transmission Electron Microscope: Electron beam enters thin part of a specimen; studies internal cellular structures *All 3 electron microscopes can NOT be used to look at live cells*  Use Cell Fractionation to take apart cell and separate the organelles and subcellular structures to study Eukaryote Both Prokaryote Bigger than Prokaryotes Flagella and Cilia Smaller size Membrane-bound nucleus and Plasma Membrane Non membrane-bound nucleoid nucleolus Complex cilia and flagella Cell division Simple cilia and flagella Linear DNA Cytoplasm Circular DNA Membrane-bound organelles Ribosomes (free- floating) No membrane-bound organelles Membrane receptors Chromosomes No membrane receptors Mitosis and Meiosis Binary fission Simple cell wall when present Complex Cell wall Cytoskeleton No cytoskeleton Cell Size  As cell size increases, volume increases faster than SA increases.  Larger organisms tend to have more cells, not larger cells.  Microvilli are long, thin projections from the cell that increase SA without increasing volume Organelles  The Endomembrane System is composed of several different organelles and subcellular components that perform a variety of functions in order to regulate protein traffic and perform metabolic functions in the cell. ~ Tasks include synthesis of proteins, protein transport, metabolism, movement of lipids, and detoxifying poisons.  Glycoproteins are proteins bound to a carbohydrate that serve as ID molecules for the vesicles to know where to take the protein.  Nuclear envelope -> Rough ER -> Vesicles->Golgi->Vesicles-> Plasma Membrane, Lysosomes, or Vacuoles Endomembrane Organelle Structure Function Plasma Membrane Semi-fluid, phospholipid bilayer Selective barrier that allows the surround the cell passage of things in and out of the cell Nuclear Envelope Porous double-membrane Regulates passage of molecules enclosing the nucleus and particles (mRNA) Ribosomes Bound or free in the cytosol; Carries out protein sysnthesis composed of rRNA and protein; (builds proteins) large and small subunits; not membranous Rough Endoplasmic Reticulum Double-membrane of cisternae Creates membrane and (sacs) with ribosomes attached synthesizes proteins to be sent to surface; accounts for over off half the membrane of the cell + Smooth Endoplasmic Reticulum Double-membrane forming Stores Ca ions and processes cisternae toxins Transport Vesicles Pinched-off portions of Transports proteins and other membrane (sacs) containing molecules throughout the cell something in them Golgi Apparatus Composed of flattened Center of manufacturing, membranous sacs (cisternae); 2 warehousing, storing, and faces: cis and trans (proteins shipping proteins; produces modified from cis to trans face) glycolipids Lysosomes Sac of hydrolytic enzymes Recycles organelles and digests macromolecules Vacuoles Membrane-bound sac; large Maintains cell homeostasis and vesicle storage Eukaryotic Genetic Info  Nucleus contains most of the genes; some found in mitochondria and chloroplasts  Chromatin is a long DNA molecule associated with many proteins  rRNA (ribosomal) is synthesized into subunits, which pass through nuclear pores and combine to form ribosomes Genetic Assist Organelle Structure Function Nucleus Sphere-shaped structure Controls cell growth, surrounded by double- movement, reproduction, and membrane nuclear envelope; eating; contains genetic contains membrane material for proteins and cell chromosomes, nucleolus, and reproduction; directs protein cytoplasm synthesis via production of mRNA Nuclear envelope Double-membrane around Houses and protects nucleus; nucleus regulates molecular passage Nuclear Lamina Network of protein filaments in Maintains the shape of the the nucleus nucleus Nucleolus Dense fibers and granules in Adjoin chromatin in nucleus nucleus Chromosomes Organized DNA Carries genetic information Energy Organelles  Organelles convert energy into usable forms for work  Endosymbiont Theory suggests that an early, eukaryotic cell engulfed an oxygen-using, non- photosynthetic prokaryotic cell, to which it became endosymbiont with its host cell and eventually merged into one organism.  The non-host cell became an organelle of the host cell, known as the mitochondria. Energy Organelle Structure Function Mitochondria Convoluted, folded inner Site of cellular respiration; membrane (cristae); converts chemical energy to intermembrane space and ATP to do cellular work mitochondrial matrix (location of DNA, ribosomes, enzymes) Chloroplast (in cells that Double-membrane; innermost Converts sunlight energy into perform photosynthesis) is a fluid filled space called sugar for food and cellular stroma with thylakoids; stroma energy (photosynthesis) contains DNA, ribosomes, enzymes and chlorophyll Peroxisome Single-membrane containing Transfers a H to detoxify alcohol enzymes in the liver Cytoskeleton of the Cell  The cytoskeleton is dynamic.  Composed of various parts and 3 different fibers that complete tasks of movement in the cell. Cytoskeleton Organelle Structure Function Cytoskeleton Network of fibers Supports cell, provides anchorage for organelles and cytosolic enzymes, and maintains cell shape Microtubule Hollow rods constructed of Shapes and supports cell, tubulin provides track for motor proteins, responsible for beating of cilia and flagella Microfilaments (actin) Solid rods made of actin and has Bears tension, resists pulling the ability to branch forces in the cell, gives plasma membrane its unique, gel-like consistency Intermediate Filaments Built by same enzymes that Supports shape, specialized to make keratin; in between the bear tension, makes up “cage” size of microtubule and around the nucleus; most microfilament permanent filament in cell Basal Body Outer doublet with pairs of Anchors cilia and flagella to the large motor proteins (dymeins) cell spaced away in length, reaching toward other doublet Cilia Group of microtubules “oar-like” movement; cell sheathed by extension of motility plasma membrane (shorter; multiple) Flagella Group of microtubules Adulatory movement of cell; sheathed by extension of “squiggle”; cell movement plasma membrane (longer than cilia; only one usually) Unique Plant Organelles and Structures  Plant cells have both a plasma membrane and a cell wall.  Plant cell walls are attached to each other tightly and firmly through middle lamella, which is a thin layer of sticky polysaccharides (pectins) that glue cell walls together.  Plasmadesmata are channels in the cell wall that allows for communication between adjacent cells.  When a plant cell stops growing, it secretes a hardening substance to either strengthen its primary cell wall or create a secondary cell wall between the plasma membrane and the primary cell wall (wood is due to secondary cell walls). Plant Organelle Structure Function Chloroplast Double-membrane Carries out photosynthesis Cell Wall Microfibrils of cellulose Protects, maintains shape, prevents excess water loss, supports plant against gravity, and communicates between other plant cells. Central Vacuole Large, membrane-bound sac Storage, maintains structure, support, and pressure within a plant cell; disposes of by- products, stockpiles proteins and inorganic ions, holds pigments, stores defensive compounds Chlorophyll Pigment found in chloroplast Absorbs red and orange light while reflecting green; responsible for energy transferring in photosynthesis Intercellular Communication  Neighboring cells interact, communicate, and adhere via direct contact.  Animals have three main types of intercellular links Intercellular Linkage Structure Function Tight Junctions Membranes of adjacent cells Prevents leakage of are fused together, forming extracellular fluid continuous belt around the cell Desmosomes Reinforced by intermediate Anchorage of cells filaments; fasten cells together into strong sheets (like rivets) Gap Junctions Cytoplasmic channels between Communication of cells adjacent cells surrounded by special membrane proteins Chapter 7: Membrane Structure and Function Membrane Fluidity  Fluid Mosaic Model emphasizes the fluid structure of the membrane with a variety of proteins embedded in and around it.  Some movement of molecules within the membrane, like large membrane proteins drifting along, and some are anchored into the cytoskeleton or matrix and cannot move.  Membrane fluidity is influenced by temperature; as membrane cools, goes from fluid to solid as phospholipids pack tighter together, as membrane warms, cholesterol restrains movement of phospholipids by wedging in between them to reduce fluidity.  Cholesterol acts as a membrane “buffer” by resisting change in membrane fluidity when temperature shifts.  Asymmetrical arrangement of membrane determined as ER and Golgi build the membrane.  Transmembrane proteins, glycolipids, and secretory proteins are transported in vesicles to the plasma membrane and fuse together, releasing vesicle components into membrane while vesicle becomes part of the membrane *Molecules originating on inside face of ER end up on outside face of plasma membrane* Major Membrane Proteins Structure Function Integral Proteins Penetrate the hydrophobic There are 6 major functions of interior of the bilayer, spanning these membrane proteins the entire membrane (transmembrane protein); have hydrophobic and hydrophilic region Peripheral Proteins Loosely bound to membrane Attachments provide strong surface of integral protein; not framework for the animal cell embedded in bilayer; attached (along with 6 major functions) to either cytoskeleton or ECM fibers Carrier Protein Composed of a specific shape Binds to molecules that alters and receptors across the span shape of protein and shuttles it of the membrane across the membrane Aquaporin Channel proteins in the Facilitate fast passage of water membrane across membrane Channel Protein Channel lined with ions or Allows specific ions and polar hydrophilic corridors spanning molecules to flow through the the membrane membrane into the cell Six Major Functions of Plasma Membrane Proteins 1. Transport solutes in and out of cell - Membrane is selectively permeable, so only allows certain things in and out of the cell. - Nonpolar molecules pass easily through bilayer, while ions and polar molecules need assistance from membrane proteins (channels and carriers) to move quickly 2. Enzymatic Activity 3. Signal Transduction (relaying hormonal messages to the cell) 4. Cell-Cell Recognition - Allows proteins to attach cells together - Use ID tags (glycoproteins or glycolipids) on outside part of membrane to identify a cell and interact accordingly. - Basis for recognizing foreign cells by immune system 5. Intercellular Joining of Adjacent Cells (Gap junctions, Tight junctions) 6. Attachment to cytoskeleton and ECM - Maintains cell shape and location of certain membrane proteins Passive Transport  Diffusion is the result of thermal motion of the movement of molecules randomly spreading out over space. Diffusion is at equal rates both ways.  Facilitated Diffusion is the passive movement of molecules down their concentration gradients with help from transport proteins.  Passive Transport is a spontaneous process in which energy is not required to complete. Substances naturally diffuse from areas of high concentration to areas of lower concentration.  Osmosis is the passive transport of water, where solute concentration and membrane permeability affect tonicity, or the ability of a surrounding solution to cause a cell to gain or lose water.  A hypertonic solution contains non-penetrating solutes, causing the cell to lose water to the environment, and it shrivels up and dies.  A hypotonic solution causes water to enter the cell faster than it can leave, causing the cell to swell and lyse (burst).  Cells that don’t have cell walls have osmoregulation to control water balance in and outside of the cell to maintain an isotonic (equal) balance.  Plant cells with cell walls tend to want to have a hypotonic solution, where the cell is turgid and swollen, which contributes to the mechanical support of the plant.  Ion channels usually function as gated channels, where a chemical, electrical, or physical stimulus opens and closes the channel. Active Transport  Active Transport requires energy to move solutes against their concentration gradients while maintaining concentration of small, diffusible molecules in the cell.  Sodium/Potassium Pump employs active transport in maintaining a higher concentration of potassium in the cell and a higher concentration of sodium outside of the cell. The pump moves potassium in against its gradient and sodium out against its gradient, maintaining the concentrations needed for stability both in and out of the cell. This pump is an example of an electrogenic pump, generating a voltage gradient across the membrane and store energy that can be used for cellular work.  Cytoplasm is negatively charged compared to the ECM.  All cells maintain a voltage (electrical potential resulting from separation of opposite charges) across their plasma membranes. The membrane potential acts as a battery, favoring cation transport into the cell and anion transport out of the cell.  Electrical force based on membrane potential and chemical force based on ion’s concentration gradient drives the diffusion of ions across a membrane.  Proton pumps are found in plants, bacteria, and fungi, and they actively transport H ions out of the cell.  Cotransport provides an indirect influence from one ATP-powered pump to power the active transport of other solutes to prevent the transport of molecules back into the cell that were just removed. Exo and Endocytosis  Large molecules cross membranes in vesicles, which requires energy.  During exocytosis, a transport vesicle budded off from the golgi is moved by the cytoskeleton to the plasma membrane, where the two membranes fuse and the contents are spilt outside the cell.  During endocytosis, a small area of the plasma membrane sinks in to form a pocket and deepens to form a vesicle around the material from outside the cell to bring it inside the cell. 1. Phagocytosis: cellular eating 2. Pinocytosis: cellular drinking 3. Receptor-mediated endocytosis: enables cell to acquire bulk quantities of something low in concentration in the environment. Chapter 8: Metabolism Metabolism and Energy Transformations  Metabolism is the sum total of an organism’s chemical reactions, and is an emergent property.  Metabolic pathways begin with a single molecule, then altered in a series of defined steps to form a specific product.  Catabolic Pathways release energy by breaking down complex molecules into simpler compounds (i.e, cellular respiration), while anabolic pathways consume energy to build complicated molecules from simpler compounds (proteins from amino acids).  Energy from catabolic reactions is used to drive anabolic reactions.  All systems in biology are open systems, meaning matter and energy can be exchanged between the system and its surroundings.  Laws of Thermodynamics: 1. First Law: energy cannot be created or destroyed, but it can be transformed. 2. Second Law: every energy transfer or transformation increases the entropy of the universe. - Increase in entropy in the form of increased heat - Entropy of system will decrease as long as the total universal entropy increases Free Energy  Free Energy (G) is a portion of a system’s energy that can perform work when pressure and temperature are uniform throughout the system.  Delta G is the change in free energy; DG= DH-TdS= Gfinal-Ginitial  When dG is negative, the reaction is spontaneous (energy can be harvested to do work). When dG is positive, the reaction is non-spontaneous.  When dG=0, the system is in equilibrium and cannot do work.  Exergonic Reactions are spontaneous (-dG) and release energy to do work (i.e., cellular respiration). The magnitude of dG is the maximum amount of work that reaction can perform; greater decrease in free energy means more work can be done.  Endergonic Reactions are non-spontaneous (+dG) and absorbs free energy from the surrounding (i.e., photosynthesis); quantity of dG is the amount of energy required for this reaction to occur.  Cells maintain a disequilibrium in order for them to continue to do work and live. ATP  Cells do 3 main types of work: 1. Chemical work (pushing endergonic reactions) 2. Transport work (pumping substances in and out) 3. Mechanical work (movement and contractions)  Energy Coupling uses exergonic processes to drive endergonic process; energy in the form of ATP (nucleotide triphosphate with ribose sugar, adenine base, and 3 phosphate groups) supplies the energy needed to do cellular work.  Bonds between phosphate groups (usually the terminal phosphate group) can be broken by hydrolysis, turning ATP to ADP+P.iEnergy does not come from breaking of weak covalent bonds, but from the instability of this region of the molecule due to repulsion forces between the 3 negatively charged phosphate groups.  ATP is renewable; generated by adding a phosphate group to ADP (ATP cycle shuttling inorganic phosphate and energy)- endergonic process Enzymes  Enzymes are proteins that act as a catalyst to speed up chemical reactions by reducing the activation energy. Enzymes are NOT consumed in the reaction and do not change dG.  Activation Energy is the initial investment of energy for starting a reaction; amount of energy needed to change reactants to products. Reactants will reach a transition state, where the reactants have absorbed enough energy to break bonds and are very unstable.  Activation energy is usually high, and transition state is hard to reach. Heat can speed up reactions, but eventually enough heat denatures proteins and kills the cell.  Enzymes lower the activation energy to selective reactions so more reactants can go to products more quickly. Substrates, the reactant that the enzyme acts on, binds to the enzyme’s active site (specific space for substrate), forming an enzyme-substrate complex.  Enzyme specificity is due to the fit between the active site and the substrate, consequence to the weak interactions (H bonds and ionic) between them. Binding substrate to an active site causes the enzyme to change shape, catalyzing via the R groups on the amino acids the substrate to product, then releases it.  Variety of mechanisms by enzymes to speed up reaction: 1. More than one reactant: active site brings substrates together in correct orientation for the reaction to proceed. 2. Stretch substrates into transition state 3. Create a microenvironment conductive to a specific reaction 4. Briefly bind to substrate to restore active site to original state  At low substrate concentration, increasing substrate speeds binding to available active sites  At high concentrations, all active sites are engaged; speed dependent on enzyme’s ability to convert substrate to product.  Enzyme activity affected by temperature and pH; increase temp, increase collisions, increase reaction rate, but high temps can denature enzyme. Optimal pH to maintain conformation of enzyme as well.  Cofactors are non-protein helpers for catalytic activity; bind permanently or reversibly to an enzyme. Most vitamins are coenzymes (organic cofactor).  Competitive Inhibitors resemble the substrate and bind irreversibly (covalently) to an enzyme’s active site, but can be overcome by increasing substrate concentration. Noncompetitive inhibitors impede on the enzyme’s reactions by binding to another part of the enzyme, which changes it shape and makes the active site less effective.  Selective inhibition is crucial to controlling metabolism. Enzyme Activity and Metabolism  Allosteric regulation is the effect of binding a regulatory molecule to a different site (regulatory site) of the enzyme, which affects the enzyme’s function. Molecules that regulate enzymatic activity act as noncompetitive inhibitors.  Allosteric molecules have an inactive shape and an active shape; when bound to regulate, it changes the enzyme’s shape and stops the reaction. When condition shifts, it will become inactive and the enzyme will start binding to substrates again. They tend to bind to enzymes at low affinity, and are all very distinct.  ATP acts as an allosteric regulator to reduce the enzyme’s affinity for substrate, while ADP functions as an activator to control the rates of the reactions and the amount of product formed.  Cooperativity in enzymes is the result of multiple active sites, where a molecule will bind to one of the active sites and change the shape of all the subunits in the enzyme, affecting the catalysis of all sites on the enzyme.  Feedback Inhibition is an early step in a metabolic pathway of a multienzyme complex that is turned off by the inhibitory binding of the pathway’s final product to an enzyme acting early in the pathway, controlling the amount of product being created. Chapter 9: Cellular Respiration and Fermentation Cellular Respiration  Cellular Respiration is a series of catabolic pathways which work together to generate ATP through redox reactions.  Redox Reactions involve the transfer of electrons from one reactant to another. Reduction is the addition of an electron, while oxidation is the loss of an electron.  Energy must be added to pull off an electron from an atom; higher electronegativity makes it harder to pull off that electron, so it requires more energy to do so. Redox reactions that relocate electrons closer to oxygen releases chemical energy that can do work.  Electrons lose potential energy when it goes from a less electronegative atom to a more electronegative atom. Oxidation of Glucose  As hydrogen is transferred from glucose to oxygen, electron energy state changes to a lower state of energy that releases energy used for ATP synthesis.  Carbohydrates and fats are reservoirs of electrons associated with hydrogen because of their activation energy barrier making them stable due to enzymes lowering the activation energy.  At key steps, electrons are stripped from glucose and electrons are transferred with H. H is passed to coenzyme NAD before reaching oxygen. +  NAD is an electron carrier that can cycle easily between oxidized and reduced (NADH) states. It functions as an oxidizing agent in respiration.  Dehydrogenase enzyme strips two H’s from glucose, passing 2 electrons and 1 H to NAD (other + proton released to surroundings). NAD is neutralized when it is reduced to NADH.  Electrons carried by NADH lose very little potential energy; each NADH is “stored energy” used for other reactions. Glycolysis  First process in cellular respiration; occurs in cytosol and does not require oxygen to occur (anaerobic).  Glucose is first split into 2, 3-carbon sugars called glucose 6-phosphate, then are rearranged into 2 pyruvate molecules (ionized form of pyruvic acid).  10 steps catalyzed by different enzymes  Energy investment phase using ATP and energy pay off phase where ATP is produced by substrate-level phosphorylation, addition of a phosphate group to pyruvate and aerobic oxidation when oxygen is present (loss of electrons) of pyruvate to release energy.  NAD is reduced to NADH from the electrons released by glucose oxidation.  Net yield: 2 ATP, 2 NADH per glucose  More than ¾ of the original energy from glucose is still present in the pyruvate molecules. Citric Acid Cycle  Takes place in mitochondria  If oxygen is present, pyruvate enters the mitochondria via active transport and citric acid enzymes complete the oxidation to CO . 2  Pyruvate is converted into acetyl coA by undergoing 3 reactions 1. Carboxyl group is removed from CO2, fully oxidized with little energy. 2. Remaining 2 carbon fragment is oxidized to form acetate, and enzymes transfer electrons to NAD to form NADH. 3. Acetate+CoA-> acetyl CoA; very reactive.  Then, feeds its acetyl group into the citric acid cycle to be further oxidized by combining with oxaloacetate to form citrate.  Next 7 steps regenerates oxaloacetate from citrate, making this a cycle.  For each acetyl group that enters the cycle, 3 NAD goes to NADH.  In one step, electron carrier FAD accepts 2 electrons and 2 protons to become FADH . 2  Total yield per glucose: 6 NADH, 2 FADH ,22 ATP, 6 CO2 Electron Transport Chain  Electron Transport Chain (ETC) is a collection of molecules embedded in the folds of the mitochondria (larger SA in the cristae).  NADH and FADH bri2g electrons to the ETC, and when they release them, the electrons travel down the chain. NADH drops electrons off at the beginning of the chain, and FADH dro2s them off somewhere down the chain because it has lower energy level.  Electrons drop in free energy as they drop down the chain, and the electron carriers alternate between oxidized and reduced states as they accept and lose electrons.  Electronegativity increases moving down the chain until the electrons reach oxygen, the final most electronegative acceptor.  The ETC produces a total of 32 ATP molecules.  The main function of the ETC is to establish the energy gradient to power ATP synthesis. Chemiosmosis  From the existing ion gradient from the ETC, chemiosmosis utilizes the energy stored in the form of a H+ gradient across the membrane to drive cellular processes.  This energy is used by ATP synthase to turn ADP+Pi to ATP through ATP synthesis.  Through chemiosmosis, the exergonic flow of H+ used by the enzyme to make ATP couples redox reactions of ETC and ATP synthesis.  Certain ETC members take up H+ with electrons, and release H+ in the surrounding solution, and deposited into intermembrane space.  The resulting H+ gradient is a proton motive force, a gradient with the capacity to do work. Cellular Respiration Efficiency  35% efficiency for cellular respiration  Complete oxidation of glucose releases 686 kcal/mol. Fermentation  Fermentation occurs when there is no oxygen present, and allows generation of ATP by substrate-level phosphorylation.  In alcohol fermentation, pyruvate is converted into ethanol in 2 steps: 1. CO2 is removed from Pyruvate to form acetalhyde 2. Acetalhyde is reduced by NADH to ethanol and regenerates NAD needed to continue glycolysis.  During lactate acid fermentation, pyruvate is directly reduced by NADH to form lactate without releasing CO2. Excess lactate is taken to liver cells via blood to be converted back into pyruvate.  In fermentation, pyruvate or acetalhyde are final electron acceptors, not oxygen. Glycolysis and Krebs Connectivity  Major intersections of various catabolic and anabolic pathways.  Can convert one molecule into another that is needed  Phosphofuctokinase is an allosteric enzyme that is inhibited by ATP and stimulated by ADP; regulates cellular respiration; synchronizes the rates of Krebs and Glycolysis.  Proteins and fats can also enter respiratory pathways used by carbohydrates


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