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University of California - Riverside

Lectures 8 and-9  Biological membranes: Structure and Function Campbell 8th Ed. Chapter 7, pages 125-130, 131-136, 138-139 1) Effects of Osmosis on Water Balance a) Water diffuses across the membrane from the region of lower solute concentration to that of higher solute concentration until the solute concentrations on both sides of the membrane are equal i) Osmosis = diffusion of water across a selectively permeable membrane b) Movement of water across cell membranes and the balance of water between the cell and its environment are crucial to organisms 2) Water Balance of Cells Without Walls a) When considering the behavior of a cell in a solution, both solute concentration and membrane permeability must be considered i) Tonicity = ability of a solution to cause a cell to gain or lose water (1) depends in part on its concentration of solutes that cannot cross the membrane (nonpenetrating solutes), relative to that inside the cell (a) If there is a higher concentration of nonpenetrating solutes in the surrounding solution, water will tend to leave the cell, and vice versa ii) Isotonic = referring to a solution that, when surrounding a cell, causes no net movement of water into or out of the cell (1) Water flows across the membrane, but at the same rate in both directions (2) The volume of an animal cell is stable iii) Hypertonic = referring to a solution that, when surrounding a cell, will cause the cell to lose water (1) Shrivel and die iv) Hypotonic = referring to a solution that, when surrounding a cell, will cause the cell to take up water. (1) Swell and burst/lyse b) Can tolerate neither excessive uptake nor excessive loss of water i) Osmoregulation = regulation of solute concentrations and water balance by a cell or organism 3) Water Balance of Cells with Walls a) cells of plants, prokaryotes, fungi and some protists have walls b) plant cell swells as water enters by osmosis i) Relatively inelastic wall will expand only so much before it exerts a back pressure on the cell that opposes further water uptake (1) Turgid = swollen or distended, as in plant cells c) Flaccid = limp, lacking turgor (stiffness or firmness), as in a plant cell in surroundings where there is a tendency for water to leave the cell d) A wall is of no advantage if the cell is immersed in a hypertonic environment, plant cell, will lose water to its surroundings and shrink; its plasma membrane pulls away from the wall i) Plasmolysis = causes the plant to wilt and can lead to plant death 4) Facilitated Diffusion: Passive Transport Aided by Proteins a) many polar molecules and ions impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane i) facilitated diffusion (1) channel proteins simply provide corridors that allow a specific molecule or ion to cross the membrane (a) ion channels = a transmembrane protein channel that allows a specific ion to diffuse across the membrane down its concentration or electrochemical gradient (2) carrier protein alternates between two shapes, moving a solute across the membrane during the shape change  7.4 Active transport uses energy to moves solutes against their gradients o facilitated diffusion  is considered passive transport because the solute is moving down its concentration gradient  Speeds transport of a solute by providing efficient passage through the membrane, but it does not alter the direction of transport o Some transport proteins, however, can move solutes against their concentration gradients, across the plasma membrane from the side where they are less concentrated (whether inside or outside) to the side where they are more concentrated 1) The Need for Energy in Active Transport a) To pump a solute across a membrane against its gradient requires work; the cell must expend energy i) Active transport (1) enables a cell to maintain internal concentrations of small solutes that differ from concentrations in its environment (2) ATP supplies the energy for most active transport (a) powers active transport by transferring its terminal phosphate group directly to the transport protein (i) can induce the protein to change its shape in a manner that translocates a solute bond to the protein across the membrane 1. Sodium-potassium pump = a transport protein in the plasma membrane of animal cells that actively transports sodium out of the cell and potassium into the cell 2) How Ion Pumps Maintain Membrane Potential a) All cells have voltages across their plasma membranes i) Membrane potential = the difference in electrical charge (voltage) across a cell’s plasma membrane due to the differential distribution of ions. Membrane potential affects the activity of excitable cells and the transmembrane movement of all charged substances (1) Inside of the cell is negative compared with the outside, the membrane potential favors the passive transport of cations into the cell and anions out the cell (a) Two forces drive the diffusion of ions across a membrane: a chemical force (the ion's concentration gradient) and an electrical force (the effect of the membrane potential on the ion's movement) (i) Electrochemical gradient ii) Electrogenic pump = transport protein that generates voltage across a membrane (1) Sodium-potassium pump of animal cells (2) Proton pump = an active transport protein in a cell membrane that uses ATP to transport hydrogen ions out of a cell against their concentration gradient, generating a membrane potential in the process 3) Cotransport: Coupled Transport by a Membrane Protien a) Cotransport = a single ATP-powered pump that transports a specific solute can indirectly drive the active transport of several other solutes in a mechanism i) Substance that has been pumped across a membrane can do work as it moves back across the membrane by diffusion, analogous to water that has been pumped uphill and performs work as it flows back down ii) A carrier protein such as this sucrose-H constransport is able to use the diffusion of + H down its electrochemical gradient into the cell to drive the uptake of sucrose. The H gradient is maintained by an ATP-driven proton pump that concentrates H + outside the cell, thus storing potential energy that can be used for active transport, in this case of sucrose. Thus ATP is indirectly providing the energy necessary for cotransport  7.5 Bulk transport across the plasma membrane occurs by exocytosis and endocytosis o Water and small solutes enter and leave the cell by diffusing through the lipid bilayer of the plasma membrane or by being pumped or carried across the membrane by transport proteins 1) Exocytosis a) Exocytosis = cell secretes certain biological molecules by the fusion of vesicles with the plasma membrane i) Secretory cells use this to export products (1) Some cells in the pancreas make insulin and secrete it into the extracellular fluid by exocytosis (2) The neuron (nerve cell), which uses exocytosis to release neurotransmitters that signal other neurons or muscle cells 2) Endocytosis a) Endocytosis = cell takes in biological molecules and particulate matter by forming new vesicles from the plasma membrane i) Small area of the plasma membrane sinks inward to form a pocket, as the pocket deepens, it pinches in, forming a vesicle containing material that had been outside the cell ii) Phagocytosis = cellular eating iii) Pinocytosis = cellular drinking iv) Receptor-mediated endocytosis = the movement of specific molecules into a cell by the inward budding of vesicles containing proteins with receptor sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances b) Ligands = a molecule that binds specifically to another molecule, usually a larger one  M ovement through Membranes Campbell 8th Edition: Chapter 7, pages 131-137; Chapter 8 pages 142-146; Chapter 8 pages 148-150 The Energy of Life  8.1 An organim’s metabolism transforms matter and energy, subject to the laws of thermodynamics o Metabolism = the totality of an organism’s chemical reactions  Emergent property of life that arises from interactions between molecules within the orderly environment of the cell 1) Organization of the Chemistry of Life into Metabolic Pathways a) Metabolic pathway = a series of chemical reactions that either builds a complex molecule (anabolic pathway) or breaks down a complex molecule to simpler molecules (catabolic pathway) i) Catabolic pathways = a metabolic pathway that releases energy by breaking down complex molecules to simpler molecules (1) Major pathway is cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water ii) Anabolic pathways = a metabolic pathway that consumes energy to synthesize a complex molecule from simpler molecules iii) Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways b) Metabolism as a wholes manages the material and energy resources of the cell c) Bioenergetics = the study of how energy flows through living organisms 2) Forms of Energy a) Energy = is the capacity to cause change i) Exists in various forms, and the work of life depends on the ability of cells to transform energy from one form into another b) Kinetic energy = energy that is associated with the relative motion of objects c) Heat/thermal energy = kinetic energy associated with the random movement of atoms or molecules d) Potential energy = energy that matter possesses because of its location or structure e) Chemical energy = potential energy available for release in chemical reaction 3) The Law of Energy Transformation a) Thermodynamics = the study of energy transformation that occur in a collection of matter 4) The First Law of Thermodynamics a) First law of thermodynamics = energy can be transferred or transformed but neither created nor destroyed 5) The Second Law of Thermodynamics a) Second law of Thermodynamics = Every energy transfer or transformation increases the disorder (entropy) of the universe b) Entropy = measure of disorder or randomness i) The more randomly arranged a collection of matter is, the greater its entropy c) Spontaneous, process that can occur without an input of energy i) For a process to occur spontaneously it must increase the entropy of the universe d) Nonspontaneous, process that cannot occur on its own 6) Biological Order and Disorder  8.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously 1) Free-Energy Change, ∆𝐺 a) Free energy = portion of a system’s energy that can perform work when temperature and pressure are uniform through the system, as in a living cell b) The change is free energy, ∆𝐺, can be calculated for a chemical reaction with the following formula: ∆𝐺 = ∆𝐻 − 𝑇∆𝑆 2) Free Energy, Stability, and Equilibrium a) ∆𝐺 = 𝐺 𝑓𝑖𝑛𝑎𝑙 𝑠𝑡𝑎𝑡𝑒 𝐺 𝑖𝑛𝑖𝑡𝑖𝑎𝑙 𝑠𝑡𝑎𝑡𝑒 3) Exergonic and Endergonic Reactions in Metabolism a) Exergonic reaction = proceeds with a net release of free energy and is spontaneous b) Endergonic reaction = absorbs free energy from its surroundings and is nonspontaneous 4) Equilibrium and Metabolism a) Systems at equilibrium are at a minimum of G and can do no work, a cell that has reached metabolic equilibrium is dead  8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions o Cell does three kinds of works  Chemical work, the pushing of endergonic reactions, which would not occur spontaneously, such as the synthesis of polymers from monomers  Transport work, the pumping of substances across membranes against the direction of spontaneous movement  Mechanical work, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction o Energy coupling = in cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction  ATP is responsible for mediating most energy coupling in cells 1) The Structure and Hydrolysis of ATP a) ATP (adenosine triphosphate) = an adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. This energy is used to drive endergonic reactions in cells i) Contains the sugar ribose, with the nitrogenous base adenine and chain of three phosphate groups bonded to it ii) One of the nucleoside triphosphates used to make RNA b) The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis, energy is released from ATP when the terminal phosphate bond is broken, this release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves c) The hydrolysis of ATP: the reaction of ATP and water yields inorganic phosphate (P) i and ADP and releases energy 2) How ATP Performs Work a) The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP b) In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction c) If the ∆𝐺 of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that, overall, the coupled reactions are exergonic d) ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant e) Phosphorylated = recipient of the phosphate group f) How ATP drives transport and mechanical work: ATP hydrolysis causes changes in the shapes and binding affinities of proteins i) Directly, by phosphorylation, as shown for membrane proteins involved in active transport of solutes ii) Indirectly, via noncovalent binding of ATP and its hydrolytic products, as in the case for motor proteins that move vesicles (and organelles) along cytoskeletal “tracks” in the cell 3) The Regeneration of ATP a) ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) b) The energy to phosphorylate ADP comes from catabolic reactions in the cell c) The chemical potential energy temporarily stored in ATP drives most cellular work d) ATP formation from ADP and Pi is not spontaneous, free energy must be spent to make it occur  Cell structureCampbell 8th Ed. - Chapter 6, pages 98-109  6.2 Eukaryotic cells have internal membranes that compartmentalize their functions o basic structural and functional unit of every organism is one of two types of cells  prokaryotic  only organisms of the domains of Bacteria and Archaea  eukaryotic  protists  fungi  plants 1) Comparing Prokaryotic and Eukaryotic Cells a) Basic features of all cells: i) Bounded by a selective barrier, plasma membrane ii) Cytosol = semifluid substance iii) Contain chromosomes, which carry genes in the form of DNA iv) Have ribosomes, tiny complexes that make proteins according to instruction from the genes b) Prokaryotic cell i) No nucleus ii) Nucleoid = DNA in an unbound region iii) No membrane-bound organelles iv) Cytoplasm = interior of prokaryotic cell, also used for the region between the nucleus and the plasma membrane of a eukaryotic cell c) Eukaryotic cell i) DNA in a nucleus that is bounded by a double membrane ii) Membrane-bound organelles iii) Cytoplasm in the region between the plasma membrane and nucleus iv) Generally much larger then prokaryotic cells d) Plasma membrane = selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell i) Consists of a double layer (bilayer) of phospholipids with various proteins attached to or embedded in it (1) Interior of a membrane, the phospholipid tails are hydrophobic, as are the interior portions of membrane proteins in contact with them (2) Phospholipid heads are hydrophilic, as are proteins or parts of proteins in contact with the aqueous solution on either side of the membrane (3) Carbohydrate side chains are found only attached to proteins or lipids on the outer surface of the plasma membrane e) The logistics of carrying out cellular metabolism sets limits on the size of cells f) The smaller the object, the greater its ratio of surface area to volume g) Large organisms do not generally have larger cells than smaller organism – simply more cells h) Microvilli, increase surface area without an appreciable increase in volume 2) A Panoramic View of the Eukaryotic Cell a) A eukaryotic cell has internal membranes that partition the cell into organelles i) These membranes participate directly in the cell’s metabolism ii) The cell’s compartments provide different local environments that facilitate specific metabolic functions, so incompatible processes can go on simultaneously inside the same cell b) Biological membranes consist of a double layer of phospholipids and other lipids i) Embedded in this lipid bilayer or attached to its surfaces are diverse proteins c) Plant and animal cells have most of the same organelles  6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes o The nucleus contains most of the DNA in a eukaryotic cell o Ribosomes use the information from the DNA to make proteins 1) The Nucleus: Information Central a) Nucleus = chromosome-containing organelle of a eukaryotic cell i) Generally the most conspicuous organelle in a eukaryotic cell b) Nuclear envelope = membrane in eukaryotes that encloses the nucleus, separating it from the cytoplasm i) Double membrane ii) A lipid bilayer with associated proteins iii) Envelope is perforated by pores (1) Protein structure called a pore complex lines each pore and regulates the entry and exit of certain large macromolecule and particles (2) Nuclear lamina = a netlike array of protein filaments that maintains the shape of the nucleus c) Nuclear matrix, framework of fibers extending throughout the nuclear interior d) Chromosomes = threadlike, gene-carrying structure found in the nucleus, each consisting of one very long DNA molecule and associated proteins i) Chromatin = complex of DNA and proteins that makes up a eukaryotic chromosome, when the cell is not dividing, it exists as a mass of very long, thin fibers that are not visible a light microscope e) Nucleolus = specialized structure in the nucleus, formed from various chromosomes and active in the synthesis of ribosomes f) Proteins imported from the cytoplasm are assembled with rRNA into large and small ribosomal subunits in the nucleolus g) The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA) according to instructions provided by the DNA. The mRNA is then transported to the cytoplasm via the nuclear pores. Once an mRNA molecule reaches the cytoplasm, ribosomes translate the mRNA′s genetic message into the primary structure of a specific polypeptide. 2) Ribosomes: Protein Factories a) Ribosomes = complexes made up of ribosomal RNA and protein, are the cellular components that carry out protein synthesis i) In the cytosol (free ribosomes) (1) Function with cytosol ii) On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes) (1) Bound ribosomes generally make proteins that are destined either for insertion into membranes, for packaging within certain organelles such as lysosomes, or for export from the cell (secretion) b) Bound and free ribosomes are structurally identical and can alternate between the two roles  6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell o Endomembrane system = collection of membranes inside and around a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles.  Synthesis of proteins  Transport into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons  Nuclear envelope  Endoplasmic reticulum  Golgi apparatus  Lysosomes  Vacuoles  Plasma membrane o Vesicles = sac made of membrane inside of cells 1) The Endoplasmic Reticulum: Biosynthetic Factory a) Endoplasmic reticulum (ER) = an extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome–studded (rough) and ribosome–free (smooth) regions i) Accounts for more than half of the total membrane in many eukaryotic cells ii) Consists of a network of membranous tubules and sacs called cisternae iii) Continuous with the nuclear envelope iv) Two distinct regions: (1) Smooth ER = portion of the endoplasmic reticulum that is free of ribosomes (2) Rough ER = portion of the endoplasmic reticulum studded with ribosomes 2) Functions of Smooth ER a) Functions: i) Synthesizes lipids (1) Oils (2) Phospholipids (3) steroids ii) Metabolizes carbohydrates iii) Detoxifies poison iv) Stores calcium b) Other enzymes help detoxify drugs and poisons, especially in liver cells i) Detoxification usually involves adding hydroxyl groups to drugs, making them more soluble and easier to flush from the body 3) Functions of Rough ER a) Rough ER i) Glycoproteins = protein covalently attached to a carbohydrate ii) Transport vesicles = tiny membranous sac in a cell’s cytoplasm carrying molecules produced by the cell iii) Is a membrane factory for the cell iv) Makes own membrane phospholipids 4) The Golgi Apparatus: Shipping and Receiving Center a) Golgi apparatus = organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum i) Especially extensive in cells specialized for secretion ii) A golgi stack has a distinct polarity (1) The two poles are referred to as the cis face and the trans faces; these act, respectively, as the receiving and shipping departments of the golgi apparatus (a) Cis face located near ER (receiving side) (b) Trans face gives rise to vesicles, which pinch off and travel to other sites (shipping side) iii) Manufactures certain macromolecules by itself iv) Modifies products of the ER v) Sorts and packages materials into transport vesicles b) Products of the ER are usually modified during their transit from the cis region to the trans region of the Golgi c) Golgi products that will be secreted depart from the trans face of the Golgi inside transport vesicles that eventually fuse with the plasma membrane d) Cisternal maturation model, cisternae of the Golgi actually progress forward from the cis to the trans face of the Golgi, carrying and modifying their protein cargo as they move 5) Lysosomes: Digestive Compartments a) Lysosomes = membranous sac of hydrolytic enzymes that an animal cell uses to digest macromolecules i) Excessive leakage from a large number of lysosomes can destroy a cell by autodigestion b) Proteins of the inner surface of the lysosomal membrane and the digestive enzymes themselves are thought to be spared from destruction by having three–dimensional conformations that protect vulnerable bonds from enzymatic attack c) Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids d) Phagocytosis = type of endocytosis in which large particulate substances or small organisms are taken up by a cell. It is carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils, and dendritic cells) e) Lysosome fuses with the food vacuole and digests the molecules f) Lysosomes also use enzymes to recycle the cell’s own organelles and macromolecules, a process call autophagy i) During autophagy, a damaged organelle or small amount of cytosol becomes surrounded by a membrane, and a lysosome fuses with this vesicle 6) Vacuoles: Diverse Maintenance Compartments a) A plant cell or fungal cell may have one or several vacuoles b) Food vacuoles = membranous sac formed by phagocytosis c) Contractile vacuoles = membranous sac that helps move excess water out of certain cells i) Pump excess water out of the cell, thereby maintaining the appropriate concentration of salts and other molecules d) Central vacuoles = membranous sac in a mature plant cell with diverse roles in reproduction, growth, and development i) Develops by the coalescence of smaller vacuoles, themselves derived from endoplasmic reticulum and golgi apparatus e) Vacuole has a major role in the growth of plant cells, which enlarge as their vacuoles absorb water, enabling the cell to become larger with a minima investment in new cytoplasm 7) The Endomembrane System: A Review a) The endomembrane system is a complex and dynamic player in the cell’s compartmental organization  6.5 Mitochondria and chloroplasts change energy from one from to another o Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work  Mitochondria = an organelle in eukaryotic cells that serves as the site of cellular respiration  Chloroplast = an organelle found only in plants and photosynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water o Mitochondria and chloroplasts are enclosed by membranes, they are not part of the endomembrane system  Each of these organelles has at least two membranes separating the innermost space from the cytosol  Their membrane proteins are made by free ribosomes in the cytosol and by ribosomes contained within these organelles themselves  Contain DNA  This DNA programs the synthesis of the proteins made on the organelle′s own ribosomes  Semiautonomous organelles that grow and reproduce within the cell o Peroxisome = microbody containing enzymes that transfer hydrogen from various substrates to oxygen, producing and then degrading hydrogen peroxide 1) Mitochondria: Chemical Energy Conversion a) Mitochondria are in nearly all eukaryotic cells b) The mitochondrion is enclosed by two membranes, each a phospholipid bilayer with a unique collection of embedded proteins i) Cristae = infolding of the inner membrane of a mitochondrion that houses the electron transport chain and the enzyme catalyzing the synthesis of ATP (1) Intermembrane space, narrow region between the inner and outer membranes (2) Mitochondrial matrix, enclosed by the inner membrane (a) Contains many different enzymes as well as the mitochondrial DNA and ribosomes (b) Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix (3) Present a large surface area for enzymes that synthesize ATP  Finish cell structure; redox reactions and enzymes; glycolysis and cellular respirationCampbell 8th edition: Chapter 7, pages 138-139; Chapter 8 pages 147-156; Chapter 9 pages 162-178.  8.4 Enzymes speed up metabolic reactions by lowering energy barriers o Catalyst = chemical agent that speeds up a reaction without being consumed by the reaction o Enzyme = catalytic protein o Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction 1) The Activation Energy Barrier a) Every chemical reaction between molecules involves bond breaking and bond forming b) Free energy of activation/activation energy (E ) =ainitial energy needed to start a chemical reaction i) Often supplied in the form of heat from the surroundings ii) The amount of energy needed to push the reactants over an energy barrier, or hill, so that the “downhill” part of the reaction can begin iii) If the reaction is exergonic, a will be repaid with dividends, as the formation of new bonds releases more energy than was invested in the breaking of old bonds iv) In most cases, however, E isaso high and the transition state is reached so rarely that the reaction will hardly proceed at all 2) How Enzymes Lower the E Barriea a) Heat speeds a reaction by allowing reactants to attain the transition state more often, but this solution would be inappropriate for biological systems i) First, high temperature denatures proteins and kills cells ii) Second, heat would speed up all reactions, not just those that are necessary iii) Organisms therefore use an alternative: catalysis b) Enzymes catalyze reactions by lowering the E barriar c) Enzymes do not affect the change in free energy (∆𝐺); instead, they hasten reactions that would occur eventually 3) Substrate Specificity of Enzymes a) Substrate = reactant on which an enzyme works b) Enzyme-substrate complex = a temporary complex formed when an enzyme binds to its substrate molecules(s) i) React
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