Biology Week 3 Notes
Biology Week 3 Notes Biology 101
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This 10 page Class Notes was uploaded by Bailey Wilhoit on Sunday October 2, 2016. The Class Notes belongs to Biology 101 at University of South Carolina - Columbia taught by Dr. Czako in Fall 2016. Since its upload, it has received 6 views. For similar materials see Biological Principles I in Science at University of South Carolina - Columbia.
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Date Created: 10/02/16
Biology Notes Week 3 7.2: Membrane structure results in selective permeability ● Cell has to exchange materials with surroundings ○ Controlled by plasma membrane ● Membranes are selectively permeable ● Permeability of lipid bilayer ○ Nonpolar (hydrophobic) molecules can dissolve in the bilayer and pass through quickly ○ Polar (hydrophilic) molecules no not cross easily ● Transport proteins ○ Specific for substance being moved ○ Allow hydrophilic molecules to pass across membrane ○ Channel proteins are types of transport proteins that certain molecules or ions can use as a tunnel to pass through ■ Called aquaporins (type of channel protein) facilitate the passage of water ○ Carrier proteins bind to molecules and change shape to allow them to pass through the membrane 7.3: Passive transport is diffusion of a substance across a membrane with no energy investment ● Diffusion:tendency for molecules to spread out evenly into the available space ● Each molecule moves randomly, but diffusion of a population of molecules may be directional ● Dynamic equilibrium: the same amount of molecules that cross the membrane one way, cross it the other way ● Substances diffuse down their concentration gradient ○ Region where the density of a chemical substance increases or decreases ○ Does not require work ○ Diffusion of substance across biological membrane is passive transport because no energy is needed by cell ● Effects of osmosis on water balance ○ The diffusion of water across a selectively permeable membrane is osmosis ○ Water diffuses from the lower concentration solute to the higher concentration solute until there is equilibrium ● Water balance of cells without cell walls ○ Tonicity: ability of a surrounding solution to cause a cell to gain or lose water ○ Isotonic solution: solute concentration is same as that inside the cell; no net water movement across membrane ○ Hypertonic solution: solute concentration is greater than the concentration inside the cell; cell loses water ○ Hypotonic solution: solute concentration is less than concentration inside cell; cell gains water ○ Hypotonic and hypertonic environments create problems ■ Osmoregulation: control of solute concentrations and water balance ● Necessary adaptation for life ○ EX: Paramecium (hypertonic) has contractile vacuole that acts as a pump ● Water balance of cell with a cell wall ○ Cell walls maintain water balance ○ Plant cells in hypotonic solutions swell until wall opposes uptake; cell is now turgid (firm) ○ If plant cell and its surroundings are isotonic there is no net movement and the cell becomes flaccid (limp) ○ In hypertonic environment, plant cells lose water ○ Membrane pulls away from cell wall, causing plant to wilt (plasmolysis) ● Facilitated DIffusion ○ Transport proteins speed up passive movement of molecules across membrane ■ Include channel proteins and carrier proteins ● Channel proteins provide tunnels that allow certain molecules to cross membrane ● Aquaporins facilitate water diffusion ● Carrier proteins go through subtle change in shape that moves the solute binding site across membrane ■ Ion channels facilitate ion diffusion ● Gated channels open/close in response to stimuli 7.4: Active transport uses energy to move solutes against their gradients ● Facilitated diffusion is passive because the solute moves down its concentration gradient (requires no energy) ● Some can move against their concentration gradients ● Active transport moves substances against their concentration gradients ○ Requires energy (usually ATP) ○ Performed by specific proteins embedded in the membranes ○ Allows cells to maintain concentration gradients that differ from surroundings ○ The sodium potassium pump is an active transport system ● Membrane potential is the voltage difference across a membrane ○ Voltage is created by differences is the distribution of positive and negative ions across a membrane ○ The electrochemical gradient drives the diffusion of ions across a membrane through the combination of two forces: ■ Chemical force= ions concentration gradient ■ Electrical force= effect of membrane potential on the ion’s movement ○ Electronegative pump: transport protein that generates voltage across membrane ■ Sodium potassium pump is the major electrogenic pump in animal cells ■ Proton pump is the main electrogenic pump of plants, fungi, and bacteria ■ Help store energy that can be used for work ■ Cotransport: coupled transport by membrane protein ● Occurs when active transport of a solute indirectly drives transport of other substances ● Plants use gradient oh hydrogen ions generated by proton pumps to drive active transport of nutrients to cell 7.5: Bulk transport across the plasma membrane occurs by exocytosis and endocytosis ● Small molecules and water enter or leave call through lipid bilayer or via transport proteins ● Large molecules, such as polysaccharides and proteins cross membrane in bulk via vesicles ○ Requires energy ● Exocytosis: ○ Transport vesicles migrate to the membrane, fuse, and releases contents outside cell ● Endocytosis: ○ Cell takes in macromolecules by forming vesicles from plasma membrane ○ Endocytosis is the reverse of exocytosis ○ Three types: ■ Phagocytosis (cellular eating) ● Cell engulfs a particle in vacuole ● Vacuole fuses with lysosome to digest particle ■ Pinocytosis (cellular drinking) ● Molecules dissolved in droplets are taken up when extracellular fluid is gulped into vesicles ■ Receptormediated endocytosis ● Binding of ligands to receptors triggers vesicle formation ● Ligand is a molecule that binds only to a receptor site of another molecule 8.1: An Organism’s Metabolism Transforms Matter and Energy, Subject to the Laws of Thermodynamics ● Metabolism: totality of an organism’s chemical reactions ● Organization of the Chemistry of Life into Metabolic Pathways ○ Metabolic pathways begin with a specific molecule that is altered, ending with a certain product ■ Each step of the pathway is catalyzed by a different enzyme ○ Manages the material and energy resources of cell ○ Catabolic pathways: ■ The process by which some metabolic pathways create energy by breaking down complex molecules into simpler compounds ■ Energy that was stored in the organic molecules become available to do work ■ Ex: cellular respiration ○ Anabolic pathways (biosynthetic) ■ Process of consuming energy to build complicated molecules from simpler substances ■ Ex: synthesis of amino acids from simpler molecules ○ Energy released from catabolic pathway reactions can be used to fuel anabolic pathway reactions ○ Bioenergetics: study of how energy flows through living organisms ● Forms of Energy ○ Energy is associated with the relative motion of objects (kinetic energy) ○ Moving objects can perform work by causing other objects to move ■ Ex: water from a dam turns a turbine ○ Thermal energy: kinetic energy associated with random movement of atoms of molecules ■ Thermal energy in transfer from one object to another is called heat ○ Potential energy: energy matter has because of its location of structure ■ Ex: water behind a dam has potential energy because of its high altitude ○ Chemical energy: potential energy available for release in chemical reaction ■ Catabolic pathways break down high energy complex molecules. The breakdown and release of energy result in lowerenergy breakdown products ● Laws of Energy Transformation ○ Thermodynamics: study of energy transformations that occur in a collection of matter ○ “System” refers to the matter under study ○ “Surroundings” refers to all other matter around the system ○ An isolated system is unable to share energy with surroundings ○ An open system is able to share energy with surroundings ● First Law of Thermodynamics (principle of conservation of energy) ○ Energy of the universe is constant ■ Energy can be transferred and transformed, but not created or destroyed ● Second Law of Thermodynamics ○ Every energy transfer or transformation increases the entropy of the universe ■ During every energy transfer/transformation some energy becomes unavailable to do work ■ Most is lost as heat ■ Living cells unavoidably convert some energy to heat ● System can only use heat as energy if there is a temperature difference resulting in the thermal energy flowing as heat from a warmer location to a cooler one ■ Each energy transfer/transformation makes the universe more disordered, measured by scientists as entropy ● The more randomly arranged a collection of matter is, the greater its entropy is ■ Entropy helps us to understand why some processes are more favorable ● If a process increases entropy naturally, it can proceed without an energy input. This is called a spontaneous process ○ Ex: water flows downhill naturally, but only moves uphill when energy is applied ● A process that naturally decreases entropy is nonspontaneous. It will only happen if energy is supplied ● Biological Order and Disorder ○ Living systems increase entropy and cells create structures from less organized starting material ■ Ex: simple structures make up amino acids, and amino acids are ordered into polypeptides ○ Organisms also take in organized forms of matter from surroundings and replaces them with simpler substances ■ Ex: organisms get starch, protein, etc. from the food it eats. They break it down for energy, and release carbon dioxide and water 8.2: The FreeEnergy Change of a Reaction tells us Whether or not the Reaction Occurs Spontaneously ● Free Energy Change ????G ○ 1878 J. Williard Gibbs defined the Gibbs free energy of a system (referred to as free energy) ○ Free energy: portion of a system’s energy that can perform work when temperature and pressure are uniform ○ The change in free energy, ????G, can be calculated: ■ ????G= ????H T????S ■ ????H is the change in the system’s enthalpy ■ ????S is the change is system’s entropy ■ T is absolute temperature in K ○ If we know ????G we can predict whether the process will be spontaneous (energetically favorable) ○ Only process with a negative ????G are spontaneous ■ For ????G to be negative, ????H must be negative (system gives up entropy) or T????S must be positive (system gives up order and S increases), or both ■ Every spontaneous process decreases a system’s free energy ● Free Energy, Stability, and Equilibrium ○ ????G can also be represented as ■ ????G= G G Final Stateinitial state ■ ????G can be negative only when the process involves a loss of free energy from final state to initial state. Because there is less free energy, the system in the final state is more stable ○ Think of free energy as a measure of instability (tendency to change to a more stable state) ○ Unstable systems tend to change to more stable systems ■ Ex: a diver on a platform is more likely to fall (more unstable) than when floating in the water (stable) ○ Equilibrium describes state of maximum stability ■ Equilibrium is where forward and backward reactions occur at the same rate, no further net change in the concentration of products and reactants ■ As reaction moves toward equilibrium, the free energy of the mix of reactants and products decreases ■ G is at its lowest possible value. Any change in equilibrium will result in a positive ????G change and will not be spontaneous ○ A process is spontaneous and can perform work only when it is moving toward equilibrium ● Free Energy and Metabolism ○ Exergonic and Endergonic Reactions in Metabolism ■ Based on freeenergy changes, chemical reactions are either ● Exergonic (energy outward) ○ Net release of free energy ○ ????G is negative because the chemical mixture loses free energy, therefore exergonic reactions are spontaneous ○ Magnitude of ????G represents the maximum amount of work that can be done. The greater decrease in energy, the more work that can be done ● Endergonic (energy inward) ○ Absorbs free energy from surroundings ○ ????G is positive because this reaction stores energy ○ Nonspontaneous ○ Magnitude of ????G is amount of energy required to drive reaction ○ Equilibrium and Metabolism ■ In an isolated system, equilibrium is reached and no work can be done ■ A cell that has reached metabolic equilibrium is dead ■ Constant flow of materials in and out of a living cell keeps it from reaching equilibrium ■ Key to maintaining lack of equilibrium is the product of a reaction does not build up, but becomes the reactant in the next step 8.3: ATP Powers Cellular Work by Coupling Exergonic Reactions to Endergonic Reactions ● A cell does three main kinds of work: ○ Chemical work: pushing of endergonic reactions that don’t occur spontaneously ○ Transport work: pumping substances across membranes against direction of spontaneous movement ○ Mechanical work: like beating of cilia, contraction of muscles cells ● Energy coupling is a key feature in the way cells manage energy resources ○ Uses exergonic process to drive an endergonic one ○ ATP is responsible for most energy coupling in cells; in most cases it acts as immediate source of energy that powers the work ● Structure and Hydrolysis of ATP ○ ATP contains sugar ribose, with nitrogenous base and a chain of three phosphate groups ○ ATP is one of the nucleoside triphosphates that makes up RNA ○ Hydrolysis breaks the bonds between the phosphate groups ■ When the terminal phosphate bond is broken, a molecule of inorganic phosphate leaves the ATP and becomes ADP ■ Phosphate bonds of ATP are considered high energy because their hydrolysis releases energy ● The bonds themselves are not strong, the reactants just have a high energy (ATP and water) compared to the energy of the products (ADP and inorganic phosphate). The energy comes from the chemical change of system ■ Hydrolysis of ATP releases so much energy because all the phosphate groups are negatively charged, they repel each other, making ATP unstable. The triphosphate tail is like a spring. ● How the Hydrolysis of ATP Performs Work ○ When ATP is hydrolyzed in a test tube, the released free energy just heats the water ○ This would be inefficient or dangerous in an organism, so cell proteins harvest the released energy to perform the three types of work (chemical, mechanical, transport) ■ Ex: enzymes help the cell use the released energy to drive chemical reactions that would normally be endergonic ● If the free energy change of an endergonic reaction is less than theht amount of energy released by ATP hydrolysis, the two reactions can be coupled so that the reactions are exergonic. ● The key to coupling exergonic and endergonic reactions is the formation of a phosphorylated intermediate ○ Phosphorylated intermediate ■ Transfer of phosphate group from ATP to other molecule (process is called phosphorylation) ■ The recipient molecule is the phosphorylated intermediate (covalent bond) ○ This phosphorylated intermediate is more reactive ○ Transport and mechanical work are almost always done by ATP hydrolysis ■ ATP hydrolysis leads to change in protein shape and ability to bind to other molecules ● In some cases this occurs via phosphorylated intermediate ● In mechanical work involving motor proteins (walk) along cytoskeletal elements ○ ATP is first noncovalently bound to motor protein ○ ATP is hydrolyzed, releasing the ADP and inorganic phosphate ○ Another ATP molecule can bind ○ at each stage the protein changes shape and ability to bind to cytoskeleton, moving it along cytoskeletal track ● Regeneration of ATP ○ ATP can be regenerated by adding a phosphate to an ADP ○ The free energy required to turn ADP to ATP comes from exergonic breakdown reactions in cell ○ ATP Cycle: shuttling of inorganic phosphate and energy ■ Couples cell’s energyyielding (exergonic) processes to energy consuming (endergonic) processes ○ ATP formation from ADP is not spontaneous, so free energy must be spent ■ Catabolic pathways provide this energy 8.4: Enzymes Speed up Metabolic Reactions by Lowering Energy Barriers ● A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction ● Enzymes are catalytic proteins ● Activation Energy Barrier ○ Every chemical reaction involves bond breaking and forming ○ The initial energy needed to start a mechanical reaction is called the free energy of activation (activation energy) ■ This is supplied in form of thermal energy that the reactant molecules absorb from surroundings ● How Enzymes Speed up Reactions ○ Lowering EA barrier ○ Enzymes don’t affect change in free energy. They just quicken reactions that would occur naturally; without a catalyst it would require much higher temperature to speed up reaction ● Substrate Specificity of Enzymes ○ Reactant that an enzyme acts on is called the enzyme substrate ○ Enzymesubstrate complex: when the enzyme binds to the substrate ■ The enzymes only bind to specific substrates ○ Active site: region on the enzyme where the substrate binds ○ Induced fit of substrate brings chemical groups of the active site into positions that enhance their ability to catalyze reaction ● Catalysis in the Enzyme’s Active Site ○ In reaction, substrate binds to active site ○ The active site can lower E barrier by A ■ Orienting substrates correctly ■ Straining substrates bonds ■ Providing favorable microenvironment ■ Covalently bonding to substrate ● Effects of Local Conditions on Enzyme Activity ○ Enzyme’s activity can be affected by ■ General factors: temperature and pH ■ Chemicals that influence enzyme ● Effects of Temperature and pH ○ Every enzyme has an optimum temperature where it can function ■ They denature at temperatures that are too high ○ Every enzyme also has an optimum pH ● Cofactors ○ Nonprotein enzyme helpers ○ May be inorganic or organic ■ Organic cofactors are called coenzymes ● Includes vitamins ● Enzyme Inhibitors ○ Competitive inhibitors: bind to active site of an enzyme, competing with substrate ○ Noncompetitive Inhibitors: bind to another part of an enzyme, changing the enzyme’s shape and leaving the enzyme less effective ■ Ex: toxins, poisons, pesticides ● Evolution of Enzymes ○ Proteins are encoded by genes ○ Changes (mutations) in genes can lead to changes in proteins (amino acid composition of an enzyme) ○ These altered enzymes can result in altered substrate specificity ○ In new environment, a novel form of an enzyme might be favored 8.5: Regulation of Enzyme Activity Helps Control Metabolism ● If metabolic pathways were not tightly regulated, there would be chaos ● Cell regulates these pathways by switching on/off the genes that encode certain enzymes or regulating the enzyme activity ● Allosteric Regulation ○ Can inhibit or stimulate an enzyme’s activity ○ Occurs when regulatory molecule binds to protein at one site and affects protein function at another site ● Allosteric Activation and Inhibition ○ Most allosterically regulated enzymes are made from polypeptides ○ Each enzyme has active and inactive forms ○ Binding of activator stabilizes the active form ○ Binding of inhibitor stabilizes inactive form ○ Cooperativity: form of allosteric regulation that can amplify enzyme activity ■ One substrate molecule gets an enzyme ready to act on additional substrate molecules ■ Cooperativity is allosteric because binding by substrate to one active site affects a different active site ● Feedback inhibition ○ End product of a pathway shuts down the pathway ○ Prevents cell from wasting chemical resources by synthesizing more product than what is needed ● Localization of Enzymes Within Cell ○ Structures within cell help bring order to pathways ○ Some enzymes act as structural components of membranes ○ In eukaryotic cells, some enzymes reside in specific organelles ○ Cells can control enzyme activity by when and where enzyme is produced