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Chapters 4-8 with textbook & lecture info

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York University
BIOL 1000
Tamara Kelly

Chapter 4: Light and Life Lectures: o Cell Surface receptors: Signal transduction: o A. Reception by a cell surface molecule  Receptors embedded in plasma membrane accept a signal molecule.  Signal transduction systems getting a message from call surface receptor o B. Signal Transduction o C. Response  Enzyme activation, turns on/off gene transcription o Signal Transduction pathways o Second messenger pathways/systems o Intracellular signaling pathways o All mean the same ^^^  Started by conformational change by receptor  Kinases: phosphorylates  Phosphates: dephosphorylate  Often sets off a cascade of events o Enzyme activation o Phosphorylation: common way to activate the enzyme o Protein Kinase (enzyme) o Phosphorylates proteins o Protein Phosphatases (enzyme) o Dephosphorylates proteins o Enzymes: o Act on substrates o Reusable o Act on several molecules to make lots of products o Intra: inside o Inter: between o 1. Reception: o Binding of signal o 1 messenger o 2. Transduction: o Second messenger  Cyclic AMP signal Transduction pathway  Cyclic adenosine monophosphate (cAMP)  G protein: couple receptor  Second messenger: o Small molecules o Diffuse faster within cell o Can be made quickly o Non proteins (increase concentration rapidly)  cAMP: ATP catalyzed by Adenylyl Cyclase o 3. Responder o Signal transduction + transcription control: o Protein kinase A phosphorylates CREB activating it o CREB binds to transcription factor on DNA o This binding to transcription factor initiates DNA transcription o CREB: substrate of kinase A, when activated, turns on specific genes o What activates a G protein? It binds with only GTP. o Effector Molecule: interacts with an activated G protein o If G protein was always bounded to GTP, transcription would NOT be controlled by the first messenger o Termination: o Phosphodiesterase  cAMP  AMP o G proteins  GTP  GDP o Phosphatases  dephosphorylates protein o Oncogenes: o Genes that code for an abnormal protein which stimulates cell division o Associated with cancer development o Photo-Oncogenes: normal version of an oncogene  Example: ras-oncogene o Free Energy: o Portion of a systems energy that is available to do work = G o Preforms the work of life o Reactants/products contain G o Change = Delta G o Exergonic/Catabolic: o G in products < reactants (Negative G) o Energy released o Systems begin in less stable space o Spontaneous o Doesn’t require ATP o Ex. Respiration o Endergonic/Anabolic: o G in products > reactants (Positive G) o Energy used o Systems are more stable – not spontaneous o Require ATP o Activated Carrier Molecules: o Generated by catabolic reactions o Delivered to anabolic o Examples: ATP, NADH, NADPH o Coupling Reactions: o Exergonic + endergonic o Glutamine synthetase: pulls ATP, holds glutamine o  these proteins are called Enzymes (increased rate of reaction) o Substrate: what enzyme works on (Reactants) o Substrate binds to active site o Substrate complex forms o Products released, enzymes ready to be reused o Enzymes CAN: o Lower AE o Increase rate of reaction o Facilitate an exergonic reaction o Recycle themselves o Enzymes CAN’T: o Provide E/ change G o Make endergonic reaction help spontaneously o Catalyze many different reactions o 3 mechanisms for lowering Ea. 1) Bring reactants together to react: reaction between 2 reactants wont happen if the two don’t meet 2) Creating an environment that promotes the reaction 3) Changing the shape of the substrate making it more reactive o Enzyme Cofactors: o Metals ex. Copper, zinc, iron o Non protein organic molecules: coenzymes ex: vitamins o Rate of reaction: based on substrate + enzyme concentration o Competitive inhibition: substrate competing with inhibitor for active site o Non-Competitive: inhibiting molecule binds to enzyme (not active site) causing a change in the active site  enzyme is considered inactive (ex. Poisons) o Irreversible inhibition: inhibiting molecule covalently binds to enzyme but not A.S. causing conformational change.  Enzyme is permanently inactive (ex. Poisons). o Allosteric Control: non-competitive site binding to allosteric site o Covalent Modification: Regulation  phosphorylation o Pi added to the molecule o Factors affecting enzyme activity: o Ph.  optimal specific pH for each enzyme o Temp  higher temperatures call for higher activation energy o Normal protein  increased temp/pH/salinity  denatured protein Textbook: Energy and Laws of Thermodynamics:  Capacity to do work o Kinetic: energy of motion o Potential: energy stored (ex. Niagara Falls: as water moves over the waterfall, potential energy is converted into kinetic energy) o Energy can be converted between potential and kinetic but cannot be created or destroyed  Thermodynamics: the study of energy flow between a system and its surroundings during chemical and physical reactions o Isolated system: A system doesn’t exchange energy or matter with its surroundings o Closed System: exchanged energy but not matter with its surroundings o Open System: exchanged both energy and matter with its surroundings  First law of thermodynamics: the total amount of energy in a system and its surroundings remains constant o Also called the principle of the conservation of energy. o Second law of thermodynamics: any process involving a spontaneous change from an initial to a final state, the total entropy (disorder) of the system and its surroundings always increase. o Each time energy is transformed from one form to another, some energy is lost and unavailable to do work.  This unused energy results in an increase in the disorder/randomness in the universe  entropy  Humans eat food to maintain low entropy o Life obeys the second law of thermodynamics. Life is maintained in a highly ordered state because it is an open system bringing energy in from the surroundings and in turn increasing the disorder of the surroundings. o But, life also goes against the second law because things don’t become more random in a living cell, they become more ordered (ex. Brain, flower, Photosystem II) nd o According to 2 law, entropy of a system and is surroundings is always supposed to increase  true in humans. During 1000s of reactions req. to generate order in the human body, living things give off heat and by products of CO2 that are much less ordered and increase the disorder/entropy o Living cells: thermodynamically open systems, exchanging energy and matter with their surroundings. Free Energy and Spontaneous Reactions  Spontaneous Reaction: occurs without the input of energy from the surroundings, releases free energy that is available to do work  Free energy equation G= H-T S states that free energy change in G, is influenced by two factors: change in enthalpy (potential energy in a system) and the change in entropy of the system as a reaction goes to completion.  Factors that oppose the completion of spontaneous reactions are the relative concentrations of reactants and products produce an equilibrium point at which reactants are converted to products and products are converted back to reactants at equal rates. When organisms reach equilibrium G=0, they die.  Reactions with a negative G are spontaneous: release free energy and are known as exergonic. Reactions with a positive G require free energy (ATP) and are known as endergonic reactions.  Metabolism is the biochemical modification and use of energy in the synthesis and break down of organic molecules.  Catabolic pathway: releases the potential energy of a molecule in breaking it down to a simpler molecule.  Anabolic pathway: uses energy to convert a simple molecule to a more complex molecule ( G is positive) Adenosine Triphosphate is the Energy Currency of the Cell  The hydrolysis of ATP releases free energy that can be used as a source of energy for the cell. o Results in ADP and an inorganic phosphate (Pi)  A cell can couple the exergonic reaction of ATP breakdown (not hydrolysis) to make otherwise endergonic reaction proceed spontaneously. Coupling requires enzymes o Energy coupling: requires an enzyme to bring ATP and the reactant molecule into close association o Coupling system works by joining an exergonic reaction, the hydrolysis of water, to the endergonic biosynthesis reaction producing an overall endergonic reaction  How do cells carry out this reaction? Harness energy released in ATP hydrolysis  The ATP used in coupling reactions is replenished by reactions that link ATP synthesis to catabolic reactions. ATP thus cycles between reactions that release free energy and reactions that require free energy. o Regenerated by recombining ADP and Pi Role of Enzymes in Biological Reactions  Enzymes are catalysts that speed the rate at which spontaneous reactions occur because they lower the activation energy (initial energy)  Enzymes are specific: catalyze reactions of only a single type of molecule  Catalysis occurs at the active site: enzyme binds to the substrate (reactant molecule). Once bound the enzyme is released unchanged when the reaction is complete.  Reduce the activation energy by inducing the transition state of the reaction, from which the reaction can move in the direction or either products or reactions  3 Major mechanisms that bring enzymatic catalysis by reducing activation energy: o Enzymes bring reaction molecules together o Enzymes expose reactant molecules to alter charges that promote catalysis o Enzymes change shape of the substrate molecules Conditions and Factors that Affect Enzyme Activity:  The rate of reaction is proportional to the amount of enzymes. The rate of reaction increases with substrate concentration until the enzyme becomes saturated with reactants. At that point, increases in substrate concentration do not increase the rate of reaction Inhibitors: nonsubstrate molecules regulate enzymes o Competitive inhibitors: interfere with reaction rates by combining with the active site of an enzyme o Non-competitive inhibitors combine with sites elsewhere on the enzyme Allosteric Regulation: o Noncompetitive inhibition except that regulatory molecules may increase or decrease enzyme activity. Carried feedback inhibition which a product of an enzyme-catalyzed pathway acts as an allosteric inhibitor of the first enzyme in the pathway o Allosteric Site controls two alternate conformations  High Affinity State- enzyme binds strongly to its substrate  Low Affinity State- enzyme binds weakly or not at all Feedback Inhibition: o Allosteric inhibitors are a product of the metabolic pathway they regulate o If the product accumulated in excess, an allosteric inhibitor automatically slows/stops the enzyme reaction producing it o If the product becomes too scarce, the inhibition is reduced o Prevents cellular resources from being wasted in the synthesis of molecules made at intermediate steps of pathways  Key enzymes are regulated by chemical modification by substances such as ions and certain function groups. The modifications change enzyme conformation resulting in increased of decreases activity  Enzymes have optimal activity at a certain pH and a certain temperature. pH levels and Temperature before and after optimal reduce the rate of reaction Chapter 5: Cell Membranes and Signaling Lectures: Functions: 1) Semi-Permeable Barrier • Intra v Extracellular Environments • Inside organelle vs. cytosol 2. Maintain Ion Gradients • For energy conservation, signaling, energy and metabolism • Regulated transport in/out organelle/cell 3. Involved in Signaling Metabolism • Relay signals from in/outside cell *Lipid -> hydrophobic -> Non-Polar Components of Membrane: 1. Lipid -> Plant membrane contains cholesterol 2. Protein -> integral (embedded), peripheral (on surface) 3. Carbohydrates -> linked to lipids (glycolipids) and proteins (glycoproteins) Fluid Mosaic Model • referring to the lipid bilayer/membrane • Fluid: free to move • Mosaic: made of different components Sources of Diversity: 1. Lipid Composition • Differing: amount/types of lipids, levels of saturated/unsaturated fats, amounts of cholesterol • Cholesterol alters membrane properties • Phospholipids differ for each monolayer • Different phospholipids required for different functions • Neuron: protective myelin sheath, high in lipid 2. Proteins + Carbohydrates • different types and amounts of glycolipid (carb on outer side) • inner/outer layers of bilayer vary in composition • Fluid membrane: ◦ Too fluid --> melts/disrupts structure --> Unsaturated ◦ Too viscous --> affects enzyme function, disrupts movement/permeability - To increase fluidity: increase unsaturated fatty acids/temperature - To decrease fluidity: increase saturated fatty acids/decrease temperature o Things that affect fluidity:  Saturated/unsaturated fatty acid tales  Temperature  Cholesterol (buffer) o Regulation of fluidity  Saturated/unsaturated fatty acids  Cholesterol levels  Role of denaturize enzymes • Cholesterol: serves as a fluid buffer in membrane  Ion channel rates o Up to 100 million ions/second  Transport o Passive  No protein  Proteins  Channel protein  Carrier protein o Active  Tonicity: the relative difference in solute concentration  Cytosol: inside the cell  Water movements across the plasma membrane: o Simple/facilitated o Aquaporin o Billion molecules o Structure creates specifity  Active Transport: o Requires energy o Always against c-gradient o Important for creating/maintaining C-gradient o 1. Primary: powered by ATP  Moves cations across membranes to create C-gradient  ATP required  Examples: H+ pump, CA+ pump. NA/K pump o 2. Secondary: indirectly powered by ATP, using C-gradient  Energy for transport comes from ion c-gradient  Symport: ion + molecule move in same direction  Antiport: ion moves one direction, molecule moves in another  Na/Glucose Symport: binding of Na causes conformation change that increases binding affinity for glucose (cooperative binding) o Transporting large molecules:  Endocytosis (IN)  Pinocytosis + phagocytosis  Exocytosis (OUT)  Membrane Proteins: o Functions: Transport, Enzymatic Activity, Signal Transduction, Attachment/recognition o Primary Structure: Amino sequence o Secondary Structure: hydrogen bonding between backbone atoms:  Alpha coils  Beta sheets o Tertiary Structure: Folding due to R group interactions  Ionic  Hydrogen  Hydrophobic  Covalent: disulfide bridges o Quaternary Structure: more than mole polypeptide  Selective Permeability of Membrane: o 1. Nonpolar/hydrophobic: O2, CO2 o 2. Small, uncharged Polar: H20 o 3.Large, uncharged polar molecules: Glucose, Sucrose o 4. Ions: Na+, Cl- Textbook: Structure of Membrane:  Fluid mosaic model proposes that the membrane consists of a fluid lipid bilayer in which proteins are embedded and float freely  Membranes are asymmetrical. Lipid Fabric of a Membrane:  Lipid bilayer forms the structural framework of membranes and serves as a barrier preventing the passage of most water soluble molecules  Fluid phospholipid bilayer in which the polar regions of phospholipid molecules lie at the surface of the bilayer and their nonpolar tails associated together in the interior.  Saturated fatty acids contain the maximum number of hydrogen atoms and are linear molecules. Unsaturated fatty acids contain one or more double bonds, which cause the fatty acids to kink.  Unsaturated fatty acids are produced during fatty acid biosynthesis using organisms can adjust the fatty acid composition of membrane lipids to maintain proper fluidity through the action of a group of enzymes called desaturases. Membrane Proteins:  Membrane Proteins: o Transport: Protein provides a hydrophilic channel that allows movement of a specific compound. o Enzymatic Activity: Enzymes associated with the respiratory and photosynthetic ETC. o Signal Transduction: Receptor proteins on the outer surface of the membrane that bind to specific chemicals such as hormones. o Attachment/Recognition: Proteins exposed to bot the internal and external membrane surfaces act as attachment points for a range of cytoskeleton elements, as well as components involved in cell recognition.  Proteins embedded in the phospholipid bilayer carry out most membrane functions, including transport of selected hydrophilic substances, enzymatic activity, recognition and signal reception. o Integral membrane proteins interact with the hydrophobic core of the membrane bilayer. o A subset of integral proteins that transverse the entire lipid bilayer  trans-membrane proteins o Trans membrane proteins: integral, domains that span the membrane numerous times and are dominated by nonpolar amino acids o Peripheral membrane proteins associate with membrane hydrophilic surfaces. o Positioned on the surface of the membrane and do not interact with the hydrophobic core of the membrane, held by covalent bonds (hydrogen bonds and ionic bonds) o Many are fond on the cytoplasmic side of the plasma membrane and form part of the cytoskeleton. Passive Membrane Transport:  Depends on diffusion, the net movement of molecules from a region of higher concentration to a region of lower concentration. Passive transport doesn’t require cells to expend energy. o Driving force of diffusion: entropy  Proceeds to a dynamic equilibrium  Low to high entropy; high to low energy  Simple Diffusion: passive transport of small substances across a membrane  Facilitated Diffusion: diffusion of molecules across membranes by the use of specific membrane proteins: channel proteins and carrier proteins. o Carried out by two types of Transport proteins: channel + carrier  Channel Proteins: form hydrophilic pathways in the membrane through which molecules can pass.  Aquaporins: water specific transport proteins that diffuse water. Very narrow and allows for single-file movement of a billion water molecules/second.  Gated channel proteins: transporters that can switch between open, closed and intermediate states and are critical for the movement on ions.  Carrier Proteins: binds to a single specific solute, such as a sugar molecule or an amino acid, and transports it across the lipid bilayer. Because it’s a single solute being transported, it is referred to as uniport transport.  In preforming this step, the carrier protein undergoes conformational changes that progressively move the solute binding sire from one side of the membrane to the other. o Transport Proteins display a high degree of substrate specificity.  Osmosis: net diffusion of water molecules across a selectively permeable membrane in response to differences in concentration of solute molecules o Movement of water by osmosis is dictated by solute concentration. o Tonicity: measure of osmotic pressure  Hypotonic: Solution surrounding cell has a lower concentration then that of the inside (cell swells)  Hypertonic: Solution surrounding cell has higher concentration then that of the inside (cell shrinks/shrivels)  Isotonic: solution concentration is equal inside/outside cell  ideal for animals/humans Active Membrane Transport:  Moves substances against concentration gradients and requires energy. Depends in membrane proteins, specific for certain substances and becomes saturated at high concentrations of the transported substance  Main functions for active transport: o Uptake of essential nutrients from the fluid surrounding cells even when their concentrations are lower than in cells o Removal of secretory waste materials from cells/ organelles even when the concentration of those is higher outside the cells/organelles. o Maintenance of essentially constant intracellular concentrations of ions  Proteins are either primary transport pumps: directly use ATP as energy, or Secondary transport pumps: favorable concentration gradients of positively charged ions, set up by primary transport pumps as their energy source for transport. o Sodium Potassium Pump: located in the plasma membrane of animals, pushed 3 NA+ ions out of cell and 2 K+ into the cell. As a result, positive charges accumulate in excess outside membrane, and inside of the cell become negatively charged with respect to the outside. In sum, we have both a concentration difference (of the ions) and an electrical charge difference on the two sides of a membrane  electro chemical gradient (stores energy used for other transport mechanisms)  Secondary active transport: o Can occur by Symport: transported substances moves in the same direction as the concentration gradient used as the energy source o Antiport: transported substances moves against the concentration gradient used as the energy source Exocytosis and Endocytosis:  The largest molecules transported through cellular membranes in active/passive transport are the size of amino acids or monosaccharide’s.  Large molecules and particles are moved out of and into cells by exocytosis and endocytosis. Allows substance to leave and enter cells without directly passing through the plasma membrane. o Exocytosis: vesicle carrying secreted materials contacts and fuses with the plasma membrane on its cytoplasmic side. The fusion introduces the vesicle membrane into the plasma membrane and releases the vesicle contents to the cell exterior. o Endocytosis: materials on the cell exterior are enclosed in a segment of the plasma membrane that pockets inward and pinches off the cytoplasmic side as an endocytic vesicle. Takes place in 1 of 2 distinct but related pathways: o Bulk phase endocytosis (aka pinocytosis): extracellular water taken in along with any molecules that happen to be in the solution of water. No binding by surface receptors takes place. o Receptor mediated endocytosis: receptors, which are integral proteins on plasma membrane, recognize only certain molecules and bind, primarily proteins or molecules carried by proteins.  Some cells, such as certain white blood cells (phagocytes) or protists, can take in large aggregated of molecules, cell parts, or even whole cells by a process related to RME, called phagocytosis. Cytoplasmic Roles of Membranes in Cell Signaling  1. Direct Channels o Gap Junctions (Animals) o Plasmodesmata (Plants)  2. Specific cell contacts: surface molecules binding to other cells  3. Intercellular Chemical Messengers: o Controlling/signaling cell: makes and secrets signal molecule (ligand) o Signaling Molecule: binds to target cell o Target cell: binds signaling molecules via Receptors and responds  Forms a ligand-receptor complex  Based on surface receptors have 3 components: o Extracellular signal molecules o Can act via short distance (neurotransmitters) or long distance (hormones)  Example: acetylcholine releasing from nerve cell, then binding to receptor on muscle cell, and then receptor binding leading to muscle contraction.  Long distance Signaling: o Endocrine cell: cell that releases a hormone o Hormone:  Released into the blood  Carried throughout the body  Billions of cells exposed to the hormone  Initiates responses with a receptor o Surface receptors: receive the signals. Integral membrane proteins that extend through the plasma membrane. Binding a signal molecules induces a molecular change in the receptor that activates its cytoplasmic end o Internal response pathways triggered when receptors bind a signal o Cellular response pathways operate by activating protein kinases, which adds phosphate groups that stimulate the activities of the target proteins bringing about the cellular response. Protein phosphatases that remove phosphate groups from target proteins revers the response. Receptors are removed by endocytosis when signal transduction has run its course. o Each step of a response pathway catalyzed by an enzyme is amplified because each enzyme can activate hundreds or thousands of proteins that enter the next step in the pathway. Thr
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