Chapter 6 Membranes: Phospholipids and Water: ∙ When phospholipids come in contact with water: o Micelles: heads face water and tails face each other o Phospholipid bilayers: Cell membranes Phospholipid bilayer form when two sheets of phospholipids align. Hydrophilic heads in each layer face a surrounding solution while the hIf you want to learn more check out wis 2040 exam 2
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ydrophobic tails face one another inside the bilayer Phospholipid bilayer form spontaneously with no outside input of energy required Selective Permeability of Lipid Bilayers: ∙ The permeability of a structure is its tendency to allow a given substance to pass across it. ∙ Phospholipid bilayers have selective permeability. o Small or nonpolar molecules move across phospholipid bilayers quickly. o Charged or large polar substances cross slowly, if at all. Many Factors Affect Membrane Permeability: ∙ Many factors influence the behavior of the membrane: o Number of double bonds between the carbons in the phospholipid’s hydrophobic tail o Length of the tail o Number of cholesterol molecules in the membrane o Temperature Bond Saturation and Membrane Permeability: ∙ Double bonds between carbons in a hydrocarbon chain can cause a “kink” in the hydrocarbon chain, preventing the close packing of hydrocarbon tails, and reducing hydrophobic interactions. o Unsaturated hydrocarbon chains have at least one double bond. o Hydrocarbon chains without double bonds are termed saturated. ∙ Saturated fats have more chemical energy than unsaturated fats. ∙ Membranes with unsaturated phospholipid tails are much more permeable than those formed by phospholipids with saturated tails. Other Factors that Affect Permeability: ∙ Hydrophobic interactions become stronger as saturated hydrocarbon tails increase in length. o Membranes containing phospholipids with longer tails have reduced permeability.∙ Adding cholesterol (a steroid) to membranes increases the density of the hydrophobic section. o Cholesterol decreases membrane permeability. o Membrane fluidity decreases with temperature because molecules in the bilayer move more slowly. o Decreased membrane fluidity causes decreased permeability. Fluidity of the Membrane: ∙ Individual phospholipids can move laterally throughout the lipid bilayer. o They rarely flip between layers. ∙ How quickly molecules move within and across membranes is a function of temperature and the structure of the hydrocarbon tails in the bilayer. FluidMosaic Model of Membrane Structure: ∙ Although phospholipids provide the basic membrane structure, plasma membranes contain as much protein as phospholipids. ∙ The fluidmosaic model of membrane structure suggests that some proteins are inserted into the lipid bilayer, making the membrane a fluid, dynamic mosaic of phospholipids and proteins. Ch. 6 Active and Passive Transport Across Membranes: Diffusion Along a Concentration Gradient: ∙ A difference in solute concentrations creates a concentration gradient. ∙ Molecules and ions move randomly when a concentration gradient exists, but there is a net movement from high concentration regions to lowconcentration regions. Diffusion along a concentration gradient increases entropy and is thus spontaneous. ∙ Equilibrium is established once the molecules or ions are randomly distributed throughout a solution. o Molecules are still moving randomly but there is no more net movement. Osmosis: ∙ Water moves quickly across lipid bilayers. o The movement of water is a special case of diffusion called osmosis. ∙ Water moves from regions of low solute concentration to regions of high solute concentration. o This movement dilutes the higher concentration, thus equalizing the concentration on both sides of the bilayer. ∙ Osmosis only occurs across a selectively permeable membrane.Osmosis and Relative Solute Concentration: ∙ The concentration of a solution outside a cell may differ from the concentration inside the cell. o An outside solution with a higher concentration is said to be hypertonic to the inside of a cell. o A solution with a lower concentration is hypotonic to the cell. o If solute concentrations are equal on the outside and inside of a cell, solutions are isotonic to each other. Osmosis in Hypertonic, Hypotonic, and Isotonic Solutions: ∙ In a hypertonic solution, water will move out of the cell by osmosis and the cell will shrink. ∙ In a hypotonic solution, water will move into the cell by osmosis and the cell will swell. ∙ In an isotonic solution, there will be no net water movement and the cell size will remain the same. Membrane Proteins: ∙ Integral proteins are amphipathic and so can span a membrane, with segments facing both its interior and exterior surfaces. o Integral proteins that span the membrane are called transmembrane proteins. These proteins are involved in the transport of selected ions and molecules across the plasma membrane. Transmembrane proteins can therefore affect membrane permeability. ∙ Peripheral proteins are found only on one side of the membrane. o Often attached to integral proteins Membrane Proteins Affect Ions and Molecules: ∙ The transmembrane proteins that transport molecules are called transport proteins. There are three broad classes of transport proteins, each of which affects membrane permeability: 1. Channels 2. Carrier proteins or transporters 3. Pumps Ion Channels and the Electrochemical Gradient: ∙ Ion channels are specialized membrane proteins. o Ion channels circumvent the plasma membrane’s impermeability to small, charged compounds. ∙ When ions build up on one side of a plasma membrane, they establish both a concentration gradient and a charge gradient, collectively called the electrochemical gradient. ∙ Ions diffuse through channels down their electrochemical gradients. This passive transport decreases the charge and concentration differences between the cell’s exterior and interior. Facilitated Diffusion via Channel Proteins: ∙ Cells have many different types of channel proteins in their membranes, each featuring a structure that allows it to admit a particular type of ion or small molecule. ∙ These channels are responsible for facilitated diffusion: the passive transport of substances that would not otherwise cross the membrane. Facilitated Diffusion via Carrier Proteins: ∙ Facilitated diffusion can occur through channels or through carrier proteins, or transporters, which change shape during the transport process. ∙ Facilitated diffusion by transporters occurs only down a concentration gradient, reducing differences between solutions. ∙ Glucose is a building block for important macromolecules and a major energy source, but lipid bilayers are only moderately permeable to glucose o A glucose transporter named GLUT1 increases membrane permeability to glucose. Active Transport by Pumps: ∙ Cells can transport molecules or ions against an electrochemical gradient. o This process requires energy in the form of ATP and is called active transport. ∙ Pumps are membrane proteins that provide active transport of molecules across the membrane. o For example, the sodiumpotassium pump, Na+/K+ATPase, uses ATP to transport Na+ and K+ against their concentration gradients. Secondary Active Transport: ∙ In addition to moving materials against their concentration gradients, pumps set up electrochemical gradients. ∙ These gradients make it possible for cells to engage in secondary active transport, or cotransport. o The gradient provides the potential energy required to power the movement of a different molecule against its particular gradient. Summary of Memory Transport:∙ There are three mechanisms of membrane transport: 1. Diffusion 2. Facilitated diffusion 3. Active transport ∙ Diffusion and facilitated diffusion are forms of passive transport and thus move materials down their concentration gradient and do not require an input of energy. ∙ Active transport moves materials against their concentration gradient and requires energy provided by ATP or an electrochemical gradient. Plasma Membrane and the Intracellular Environment: ∙ The selective permeability of the lipid bilayer and the specificity of the proteins involved in passive transport and active transport enable cells to create an internal environment that is much different from the external one. Chapter 7 Inside the CellBasics: The Cell Theory: ∙ Every living thing has at least one cell 1. Nucleic acids: store and transmit information 2. Proteins: perform most of the cell’s functions, more than 50% of the dry mass of cells 3. Carbohydrates: chemical energy, carbon, support, identity 4. Plasma membrane: selectively permeable membrane barrier Grouping Cells: ∙ According to morphology, there are two broad groupings of life: 1. Prokaryotes, which lack a membranebound nucleus. 2. Eukaryotes, which have membranebound nucleus ∙ According to phylogeny, or evolutionary history, there are three domains: 1. Bacteria—prokaryotic 2. Archaea—prokaryotic 3. Eukarya—eukaryotic Prokaryotic CellStructural Overview: ∙ All prokaryotes lack a membranebound nucleus., which means they don’t have a nucleus ∙ Structure is basic ∙ Recent advances in microscopy reveal complexity in prokaryotic structure. ∙ Archaeal cell structure is relatively poorly understood. ∙ Bacterial cells vary greatly in size and shape, but most bacteria contain several structural similarities:o Plasma membrane o A single chromosome, genetic information o Ribosomes, which synthesize proteins o o Stiff cell wall Prokaryotic CellGenetic Information: ∙ Most prokaryotic species have one supercoiled (tightly coiled) circular chromosome found in the nucleoid region of the cell. o The chromosome contains a long strand of DNA and a few supportive proteins. ∙ In addition to the large chromosome, many bacteria contain plasmids o Small, supercoiled, circular DNA molecules. o Plasmids usually contain genes that help the cell adapt to unusual environmental conditions. Can be transferred from one cell to another, a way to transfer some genetic information. Prokaryotic CellInternal Structure: ∙ In addition to the nucleoid chromosome and plasmids, other structures are contained within the cytoplasm: o All prokaryotic cells contain ribosomes, consisting of RNA molecules and protein, for protein synthesis. o Many prokaryotes have internal photosynthetic membranes, carry out photosynthesis across the membrane. o The inside of many prokaryotic cells is supported by a cytoskeleton of long, thin protein filaments. Bacterial Organelles: ∙ Recently, internal compartments in many bacterial species were discovered. o These compartments qualify as organelles (“little organs”). An organelle is a membranebound compartment inside the cell that contains enzymes or structures specialized for a particular function. Organelles are common in eukaryotic cells. o Each type of bacterial organelle is found in certain species. o Bacterial organelles perform an array of tasks Prokaryotic CellsExternal Structure: ∙ Some prokaryotes have taillike flagella on the cell surface that spin around to move the cell. ∙ Most prokaryotes have a cell wall. o Bacterial and archaeal cell walls are a tough, fibrous layer that surrounds the plasma membrane.∙ Many species have an additional layer outside the cell wall composed of glycolipids. ∙ Many prokaryotes have fimbriae o Are needlelike projections o Extend from the plasma membrane of some bacteria o Promote attachment to other cells or surfaces Introduction to Eukaryotes: ∙ Eukaryotes range from microscopic algae to 100metertall redwood trees ∙ Many eukaryotes are multicellular, others are unicellular. ∙ Most eukaryotic cells are larger than most prokaryotic cells. Eukaryotic Cells: ∙ The relatively large size of the eukaryotic cell makes it difficult for molecules to diffuse across the entire cell. o This problem is partially solved by breaking up the large cell volume into several smaller membranebound organelles. ∙ The compartmentalization of eukaryotic cells offers two primary advantages: 1. Separation of incompatible chemical reactions 2. Increasing the efficiency of chemical reactions Comparison of Eukaryotic and Prokaryotic Cells: ∙ Four key differences between eukaryotic and prokaryotic cells have been identified 1. Eukaryotic chromosomes are found inside a membranebound compartment called a nucleus 2. Eukaryotic cells are often much larger. By a factor of 1 3. Eukaryotic cells contain extensive amounts of internal membrane. 4. Eukaryotic cells feature a diverse and dynamic cytoskeleton The Nucleus: ∙ The nucleus is large and highly organized. ∙ STRUCTURE: o The nucleus is surrounded by a double plasma membrane nuclear envelope. o The nucleus has a darker distinct region called the nucleolus. o The nuclear envelope is studded with porelike openings, allows for easy transport of materials o The inside surface is linked to fibrous proteins They form a latticelike sheet called the nuclear lamina ∙ FUNCTION: o Information storage and processing Contains the cell’s chromosomeso Ribosomal RNA synthesis (in the nucleolus) Ribosomes: ∙ STRUCTURE: o Ribosomes are nonmembranous (they are not considered organelles). o Have large and small subunits, both containing RNA molecules and protein o Ribosomes can be attached to the rough ER or free in the cytosol, the fluid part of the cytoplasm. ∙ FUNCTION: Protein synthesis Rough Endoplasmic Reticulum: ∙ STRUCTURE: o The rough endoplasmic reticulum (rough ER, RER) is a network of membranebound tubes and sacs studded with ribosomes. The interior is called the lumen. o The rough ER is continuous with the nuclear envelope. ∙ FUNCTION: o Ribosomes associated with the rough ER synthesize proteins o New proteins are folded and processed in the rough ER lumen. Smooth Endoplasmic Reticulum: ∙ STRUCTURE: The smooth endoplasmic reticulum (smooth ER, SER) lacks the ribosomes associated with the rough ER. ∙ FUNCTION: o Enzymes within the smooth ER may synthesize fatty acids and phospholipids, or break down poisonous lipids. o Reservoir for Ca2+ ions Golgi Apparatus: ∙ STRUCTURE: o The Golgi apparatus is formed by a series of stacked flat membranous sacs called cisternae. o Has a distinct polarity cis surface is closest to nucleus trans surface faces the plasma membrane ∙ FUNCTION: o The Golgi apparatus processes, sorts, and ships proteins synthesized in the rough ER. o Membranous vesicles carry materials to and from the organelle. The Endomembrane System: ∙ The endomembrane system is composed of the smooth and rough ER and the Golgi apparatus, and is the primary system for protein and lipid synthesis. ∙ Ions, ATP, amino acids, and other small molecules diffuse randomly throughout the cell, but the movement of proteins and other large molecules is energy demanding and tightly regulated. Peroxisomes: ∙ STRUCTURE: Peroxisomes are globular organelles bound by a single membrane. ∙ FUNCTION: o Center of oxidation reactions o Specialized peroxisomes in plants called glyoxysomes are packed with enzymes that oxidize fats to form a compound that can be used to store energy for the cell. Lysosomes: ∙ STRUCTURE: o Lysosomes are singlemembranebound structures containing approximately 40 different digestive enzymes. o Lysosomes are found in animal cells. ∙ FUNCTION: Lysosomes are used for digestion and waste processing. How are Materials Delivered to the Lysosomes?: ∙ Materials are delivered to the lysosomes by three processes: o Phagocytosis (cell eating): 1. Detection 2. Phagosome formation 3. Delivery to lysosome and digestion 4. Release of particles into cytosol o Autophagy (self): 1. Organelle surrounded by membrane 2. Delivery to lysosome 3. Recycling o Receptormediated endocytosis: 1. Macromolecules bind to receptors 2. Early endosome forms 3. Processing 4. Digestive enzymes received 5. Mature lysosome ∙ Endocytosis is a process by which the cell membrane can pinch off a vesicle to bring outside material into the cell. o In addition to phagocytosis and receptormediated endocytosis, a third type of endocytosis called pinocytosis(cell drinking) brings fluid into the cell. Vacuoles: ∙ STRUCTURE: o Vacuoles are large membranebound structures found in plants and fungi. o Some contain digestive enzymes. ∙ FUNCTION: o Some vacuoles are specialized for digestion. o Most vacuoles are used for storage of water and/or ions to help the cell maintain its normal volume. Mitochondria: ∙ STRUCTURE: o Mitochondria have two membranes; the inner one is folded into a series of sac like cristae. The solution inside the cristae is called the mitochondrial matrix. o Mitochondria have their own DNA and manufacture their own ribosomes. ∙ FUNCTION: o ATP production is a mitochondrion’s core function. Chloroplasts: ∙ STRUCTURE: o Most plant and algal cells have chloroplasts that, like mitochondria, have a double membrane and contain their own DNA. o Chloroplasts contain membranebound, flattened vesicles called thylakoids, which are stacked into piles called grana. Outside the thylakoids is the solution called the stroma. ∙ FUNCTION: Chloroplasts convert light energy to chemical energy – in other words, they perform photosynthesis. Cell Wall: ∙ Fungi, algae, and plants have a stiff outer cell wall that protects the cell. o In plants and algae, the cell wall’s primary component is cellulose. o In fungi, the primary component is chitin. ∙ Some plant cells have a secondary cell wall containing lignin. See more in taller plants like trees, present so that they can stand tall Cytoskeleton: ∙ STRUCTURE: The cytoskeleton is composed of protein fibers and gives the cell shape and structural stability. ∙ FUNCTION: o The cytoskeleton organizes all of the organelles and other cellular structures into a cohesive whole.o Aids cell movement o Transports materials within the cell Structure and Function of the Entire Cell: ∙ An organelle’s membrane and its enzymes correlate with its function, and cell structure (e.g., the type, size, and number of organelles) correlates with cell function. ∙ Cells are dynamic living things with interacting parts and constantly moving molecules. Dynamic Eukaryotic Cells: ∙ Your body’s cells use, and synthesize, approximately 10 million ATP molecules per second. ∙ Cellular enzymes can catalyze >25,000 reactions per second. ∙ Each membrane phospholipid can travel the breadth of its organelle or cell in under a minute. ∙ The hundreds of trillions of mitochondria inside you are replaced about every 10 days, for as long as you live ∙ The fluid plasma membrane’s composition is constantly changing Ch. 7 Cytoskeleton, Flagella, and Cilia: Dynamic Cytoskeleton: ∙ The cytoskeleton is a complex network of fibers that helps maintain cell shape by providing structural support. The cytoskeleton is dynamic; it changes to alter the cell’s shape, to transport materials in the cell, or to move the cell itself. ∙ There are three types of cytoskeletal elements: o Actin filaments (microfilaments) o Intermediate filaments o Microtubules Actin Filaments: ∙ Actin filaments are the smallest cytoskeletal elements. ∙ Actin filaments form by polymerization of individual actin molecules. ∙ Actin filaments are grouped together into long bundles or dense networks that are usually found just inside the plasma membrane and help define the cell’s shape. ∙ Actin filaments have two distinct ends, the plus and minus ends.o The plus end grows faster than the minus end. ActinMyosin Interactions: ∙ Actin filaments can also be involved in movement by interacting with the motor protein myosin. ∙ Actinmyosin interactions can cause cell movements such as cell crawling, cytokinesis, and cytoplasmic streaming. Intermediate Filaments: ∙ Intermediate filaments are defined by size rather than composition. Many types of intermediate filaments exist, each consisting of a different protein. ∙ Intermediate filaments provide structural support for the cell. They are not involved in movement ∙ Intermediate filaments form a flexible skeleton that helps shape the cell surface and hold the nucleus in place. Microtubule Structure: ∙ Microtubules are large, hollow tubes made of tubulin dimers (twopart compounds). ∙ Microtubules have polarity, are dynamic, and usually grow at their plus ends. ∙ Microtubules originate from the microtubule organizing center and grow outward, radiating throughout the cell. ∙ Animal cells have just one microtubule organizing center called the centrosome. Centrosomes contain two bundles of microtubules called centrioles. Microtubule Function: ∙ Microtubules provide stability and are involved in movement; they may also provide a structural framework for organelles. o Microtubules can act as “railroad tracks”; transport vesicles move through the cell along these microtubule tracks in an energydependent process. ∙ Microtubules require ATP and kinesin for vesicle transport to occur. Kinesin is a motor protein that converts chemical energy in ATP into mechanical work. Cilia and FlagellaMoving Entire Cell: ∙ Flagella are long, hairlike projections from the cell surface that move cells. o Bacterial flagella are made of flagellin and rotate like a propeller. o Eukaryotic flagella are made of microtubules and wave back and forth. ∙ Closely related to eukaryotic flagella are cilia, which are short, filamentlike projections. ∙ Cells generally have just one or two flagella but may have many cilia Cilia and Flagella Structure:∙ The axoneme of cilia and flagella is a complex “9 + 2” arrangement of microtubules connected by links and spokes. ∙ The axoneme attaches to the cell at a structure called the basal body A Motor Protein in Axenome: ∙ The motor protein dynein forms the arms between doublets and changes shape when ATP is hydrolyzed to “walk” up the microtubule. ∙ When the dynein arms on just one side of the axoneme move, cilia and flagella bend instead of elongating because the links and bridges constrain movement of the microtubule doublets. Ch. 7Transport Within Cells: The Nuclear EnvelopeTransport Mechanism: ∙ Nuclear envelope: has 2 membranes, each has a lipid bilayer and is continuous with ER ∙ Nuclear lamina: fibrous proteins that form latticelike sheets o Stiffen membrane structure and maintain shape o Provide attachment points for each chromosome ∙ Contains thousands of openings called nuclear pores ∙ Function as doors into and out of nucleus How are Molecules Imported into the Nucleus?: ∙ Messenger RNAs and ribosomes are synthesized in the nucleus and exported to the cytoplasm. Materials such as proteins needed in the nucleus are imported into the nucleus. ∙ Movement of proteins and other large molecules into and out of the nucleus is an energy demanding process. ∙ Proteins destined for the nucleus have a molecular “zip code”—a 17aminoacidlong nuclear localization signal (NLS)—which allows them to enter the nucleus. The Secretory Pathway Hypothesis: ∙ The secretory pathway hypothesis proposes that proteins intended for secretion from the cell are synthesized and processed in a highly prescribed set of steps. ∙ Proteins are packaged into vesicles when they move from the RER to the Golgi apparatus and from the Golgi apparatus to the cell surface. o The RER and Golgi apparatus function as an integrated endomembrane system. The Signal Hypothesis: ∙ The signal hypothesis predicts that proteins bound for the endomembrane system have a “zip code” that directs the growing polypeptide to the ER. o This “zip code” is a 20aminoacidlong ER signal sequence. ∙ The ER signal sequence binds to a signal recognition particle (SRP) that then binds to a receptor in the ER membrane. ∙ In the RER lumen, proteins are folded and glycosylated. o Carbohydrates are attached to the protein. From ER to Golgi: ∙ Proteins are transported from the ER to the Golgi apparatus in vesicles that bud off the ER, then fuse with the Golgi apparatus membrane and deposit their contents inside. Inside the Golgi Apparatus: ∙ The Golgi apparatus’s composition is dynamic. o New cisternae form at the cis face. o Old cisternae break off from the trans face. ∙ Protein products enter the Golgi apparatus at the cis face and pass through cisternae containing enzymes for attaching specific carbohydrate chains, before exiting on the far side (trans face) of the Golgi. How Are Products Shipped from the Golgi?: ∙ Each protein that comes out of the Golgi apparatus has a molecular tag that places it in a particular type of transport vesicle. o Each type of transport vesicle also has a tag that allows it to be transported to the correct destination. ∙ Proteins produced in a cell have distinctive molecular address labels, which allow proteins to be shipped to the compartments where they function. Exocytosis: ∙ Some proteins are sent to the cell surface in vesicles that fuse with the plasma membrane, releasing their contents to the exterior of the cell in a process called exocytosis. Ch.8Energetic Coupling and ATP: Energetic Coupling: ∙ Energetic coupling between exergonic and endergonic reactions allows chemical energy released from one reaction to drive another reaction. Introducing ATP: ∙ ATP (adenosine triphosphate) is the cellular currency for energy – it provides the fuel for most cellular activities. ∙ ATP has high potential energy and allows cells to do work.∙ ATP works by phosphorylating (transferring a phosphate group to) target molecules. Structure and Function of ATP: ∙ The electrons in ATP have high potential energy because the four negative charges in its three phosphate groups repel each other. ∙ Hydrolysis (requires water) of the bond between the two outermost phosphate groups results in formation of ADP and Pi (inorganic phosphate, H2PO4−) in a highly exergonic reaction. o the released phosphate group is transferred to a protein. (phosphorylation) ATP Hydrolysis and Protein Phosphorylation: ∙ Hydrolysis of ATP is exergonic because the entropy of the product molecules is much higher than that of the reactants. ∙ Energy released during ATP hydrolysis is transferred to a protein during phosphorylation. o This phosphorylation usually causes a change in the protein’s shape. How Does ATP Drive Endergonic Reactions?: ∙ When a protein is phosphorylated, the exergonic phosphorylation reaction is paired with an endergonic reaction by energetic coupling. ∙ In cells, endergonic reactions become exergonic when the substrates or enzymes involved are phosphorylated. Chapter 8Energy and Chemical Reactions: Energy: ∙ Two types of energy exist 1. Kinetic energy o energy of motion o at the molecular level is thermal energy 2. Potential energy o energy of position or configuration o at the molecular level chemical energy is stored ∙ The free energy of a reaction is the amount of energy available to do work Nature of Chemical Energy: ∙ In cells, electrons are the most important source of chemical potential energy o the amount of potential energy in an electron is based on its position relative to positive and negative charges Electrons closer to negative charges and farther from positive charges have higher potential energy ∙ Molecular potential energy is a function of electron configuration and positionFirst Law of Thermodynamics: ∙ Energy is conserved o Energy cannot be created or destroyed o Energy can only be transferred and transformed ∙ Enthalpy (H) includes o The potential energy of the molecule (heat content) o Effect of the molecule on surrounding pressure and volume o Changes in enthalpy are represented by ΔH o Difference in heat content Enthalpy: ∙ Exothermic reaction o releases heat energy (heat pack) o ΔH < 0 o products have less potential energy than reactants ∙ Endothermic reaction (cold pack) o Heat energy is taken up o ΔH > 0 o products have higher potential energy than reactants Entropy: ∙ A measure of the amount of disorder ∙ Entropy increases when the products of a chemical reaction become less ordered than the reactant molecules o ΔS > 0 ∙ Second law of thermodynamics o the entropy of the universe always increases (universe is becoming more and more disordered) o total entropy always increases in isolated systems Gibbs Free Energy Change: ∙ Determines whether a reaction is spontaneous or requires added energy to proceed o ΔG = ΔH – TΔS ΔG = Gibbs free energy change ΔH = change in enthalpy a measure of chemical potential energy ΔS = change in entropy a measure of disorder T = temperature in degrees Kelvin (molecules either move faster or slow down) What makes a chemical reaction spontaneous?∙ ΔG < 0 = a spontaneous reaction (an exergonic reaction) ∙ ΔG > 0 = a reaction that requires energy input to occur and is not spontaneous (an endergonic reaction) ∙ ΔG = 0 = a reaction that is at equilibrium, no change in free energy Temperature and concentration affect concentration rates: ∙ For most reactions to proceed, one or more chemical bonds have to break and others have to form. ∙ Substances must collide in a specific orientation that brings the electrons involved near each other o when the concentration of reactants is high, more collisions should occur therefore reactions should proceed more quickly o when the temperature is high, molecules are moving faster, so more collisions should occur therefore reactions should proceed more quickly Ch. 8Enzymes: An Intro to Catalysis: ∙ Catalysis may be the most fundamental of protein functions. Enzymes carry out this catalysis. ∙ Reactions take place when: o Reactants collide in precise orientation o Reactants have enough kinetic energy to overcome repulsion between the electrons that come in contact during bond formation o Reactions don’t happen unless these conditions are met ∙ Enzymes perform two functions: 1. Bring substrates (bind to the enzymes) together in precise orientation so that the electrons involved in the reaction can interact 2. Decrease the amount of kinetic energy reactants must have for the reaction to proceed Activation Energy and Rates of Reaction: ∙ The activation energy (Ea) of a reaction is the amount of free energy required to reach the intermediate condition, or transition state. Catalyst and Free Energy: ∙ A catalyst is a substance that lowers the activation energy of a reaction and increases the rate of the reaction. Not changed in the reaction, nor are they consumed. ∙ Catalysts lower the activation energy of a reaction by lowering the free energy of the transition state. ∙ Catalysts do not change the free energy (ΔG) and are not consumed in the reaction Enzymes:∙ Enzymes are protein catalysts and typically catalyze only one reaction. ∙ Most biological chemical reactions occur at meaningful rates only in the presence of an enzyme. ∙ Enzymes: 1. Bring reactants together in precise orientations 2. Stabilize transition states ∙ Protein catalysts are important because they speed up the chemical reactions that are required for life. Otherwise, they would not happen at all. How do Enzymes Work?: ∙ Enzymes bring substrates together in specific positions that facilitate reactions, and are very specific in which reactions they catalyze. ∙ Substrates bind to the enzyme’s active site. ∙ Many enzymes undergo a conformational change when the substrates are bound to the active site; this change is called an induced fit. ∙ Interactions between the enzyme and the substrate stabilize the transition state and lower the activation energy required for the reaction to proceed. Do Enzymes Act Alone?: ∙ They do not act alone ∙ Most enzymes are regulated by molecules that are not part of the enzyme itself. o Some enzymes require cofactors to function normally. These are either metal ions or small organic molecules called coenzymes. cofactors are inorganic ions such as the metal ions ions Zn2+, Mg2+, and Fe2+ that reversibly interact with enzymes coenzymes are organic molecules that interact with enzymes such as the electron carriers NADH or FADH2 o Some enzymes have prosthetic groups, which are nonamino acid atoms and molecules that are permanently attached to proteins Enzyme Regulation: ∙ Competitive inhibition occurs when a molecule similar in size and shape to the substrate competes with the substrate for access to the active site. A Competition basically. ∙ Allosteric regulation occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site. o Allosteric regulation can activate or deactivate the enzyme. What Limits the Rate of Catalysis?: ∙ Enzymes are saturable; in other words, the rate of a reaction is limited by the amounts of substrate present and available enzyme.∙ All enzymes show this type of saturation kinetics. o At some point, active sites, become full, cannot accept substrates any faster, no matter how large the concentration of substrates gets Physical Conditions Affect Enzyme Function: ∙ Enzymes function best at some particular temperature and pH o Temperature (kinetic energy )affects the movement of the substrates and enzyme o pH affects the enzyme’s shape and reactivity. o Could have denaturing of the enzyme if you affect the temperature or the ph too much Rate of EnzymeCatalyzed Reactions: ∙ The rate of an enzymecatalyzed reaction depends on: o Substrate concentration, the higher, the faster o The enzyme’s intrinsic affinity for the substrate o Temperature o pH Metabolic Pathways: ∙ Enzymes work together in metabolic pathways: series of reactions catalyzed by different enzymes that can be used to build biological molecules Ch. 8Redox Reactions: Redox: ∙ Reduction–oxidation reactions (redox reactions) are chemical reactions that involve electron transfer. o Redox reactions drive ATP formation. ∙ When an atom or molecule gains an electron, it is reduced ∙ When an atom or molecule loses an electron, it is oxidized. ∙ Oxidation and reduction events are always coupled—if one atom loses an electron, another has to gain it. o Electron donors are always paired with electron acceptors Electrons Are Accompanied by Protons: ∙ Each electron transferred from one molecule to another during a redox reaction is usually accompanied by a proton (H+). o The reduced molecule gains a proton and has higher potential energy. o The oxidized molecule loses a proton and has lower potential energy. o Electron=negative, proton=positive ∙ Nicotinamide adenine dinucleotide (NAD+) is reduced to form NADH.o NADH readily donates electrons to other molecules and is thus called an electron carrier and has “reducing power. Ch. 9 Cellular Respiration and FermentationAerobic Cellular Respiration: What Happens When Glucose is Oxidized?: ∙ The carbon atoms of glucose are oxidized to form carbon dioxide, and the oxygen atoms in oxygen are reduced to form water: o C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy ∙ In cells, glucose is oxidized through a long series of carefully controlled redox reactions. The resulting change in free energy is used to synthesize ATP from ADP and Pi. Together, these reactions comprise cellular respiration. An Overview of Cellular Respiration: ∙ All organisms use glucose to build fats, carbohydrates, and other compounds; cells recover glucose by breaking down these molecules. o Glucose is used to make ATP through either cellular respiration or fermentation. ∙ Cellular respiration produces ATP from a molecule with high potential energy – usually glucose. Each of the four steps of cellular respiration consists of a series of chemical reactions, and a distinctive starting molecule and characteristic set of products Steps of Cellular Respiration: ∙ Cellular respiration is any suite of reactions that produces ATP in an electron transport chain. ∙ Cellular respiration has four steps: 1. Glycolysis – glucose is broken down to pyruvate. 2. Pyruvate processing – pyruvate is oxidized to form acetyl CoA. 3. Citric acid cycle – acetyl CoA is oxidized to CO2. 4. Electron transport and chemiosmosis – compounds that were reduced in steps 1–3 are oxidized in reactions leading to ATP production. Glycolysis: ∙ Glycolysis, a series of 10 chemical reactions, is the first step in glucose oxidation. ∙ All of the enzymes needed for glycolysis are found in the cytosol. ∙ In glycolysis, glucose is broken down into two 3carbon molecules of pyruvate, and the potential energy released is used to phosphorylate ADP to form ATP. Glycolysis Reactions: ∙ Glycolysis consists of an energy investment phase and an energy payoff phase.∙ In the energy investment phase, two molecules of ATP are consumed, and glucose is phosphorylated twice, forming fructose1,6bisphosphate. ∙ In the energy payoff phase: o Sugar is split to form two pyruvate molecules. o Two molecules of NAD+ are reduced to NADH. o Four molecules of ATP are formed by substratelevel phosphorylation (net gain of 2 ATP). The remaining reactions occur in the mitochondria: ∙ Pyruvate produced during glycolysis is transported from the cytosol into the mitochondria. ∙ Mitochondria have both inner and outer membranes. ∙ Layers of saclike structures called cristae fill the interior of the mitochondria, and are connected to the inner membrane by short tubes. ∙ The mitochondrial matrix is inside the inner membrane but outside the cristae. Pyruvate Processing: ∙ Pyruvate processing is the second step in glucose oxidation. It is catalyzed by the enzyme pyruvate dehydrogenase in the mitochondrial matrix. ∙ In the presence of O2, pyruvate undergoes a series of reactions that results in the product molecule acetyl coenzyme A (acetyl CoA) o During these reactions, another molecule of NADH is synthesized, and one of the carbon atoms in pyruvate is oxidized to CO2. The Citric Acid Cycle: ∙ During the third step of glucose oxidation, the acetyl CoA produced by pyruvate processing enters the citric acid cycle (also known as the Krebs cycle or tricarboxylic acid or TCA cycle), located in the mitochondrial matrix. o Each acetyl CoA is oxidized to two molecules of CO2. ∙ Some of the potential energy released is used to 1. Reduce NAD+ to NADH. 2. Reduce flavin adenine dinucleotide (FAD) to FADH2 (another electron carrier). 3. Phosphorylate GDP to form GTP (later converted to ATP). Substrates of Citric Acid Cycle: ∙ A series of carboxylic acids is oxidized and recycled in the citric acid cycle. ∙ Citrate (the first molecule in the cycle) is formed from acetylCoA and oxaloacetate (the last molecule in the cycle). ∙ The citric acid cycle completes glucose oxidation. The energy released by the oxidation of one acetyl CoA molecule is used to produce 3 NADH, 1 FADH2, and 1 GTP, which is then converted to ATP.Glucose Oxidation Summary: ∙ Glucose oxidation produces ATP, NADH, FADH2, and CO2. High energy electron carriers ∙ Glucose is completely oxidized to carbon dioxide via glycolysis, the subsequent oxidation of pyruvate, and then the citric acid cycle. ∙ In eukaryotes, glycolysis occurs in the cytosol; pyruvate oxidation and the citric acid cycle take place in the mitochondrial matrix. The Electron Transport Chain: ∙ During the fourth step in cellular respiration, the high potential energy of the electrons carried by NADH and FADH2 is gradually decreased as they move through a series of redox reactions. ∙ The proteins involved in these reactions make up what is called an electron transport chain (ETC). Also known as the electron transport system ∙ O2 is the final electron acceptor. The transfer of electrons (along with protons) to oxygen forms water. Electron Transport and Chemiosmosis: ∙ Most of the ETC molecules are proteins containing chemical groups that facilitate redox reactions. All but one of these proteins are embedded in the inner mitochondrial membrane. o In contrast, the lipidsoluble ubiquinone (Q) can move throughout the membrane. ∙ During electron transport, NADH donates electrons to a flavincontaining protein at the top of the chain, but FADH2 donates electrons to an ironsulfur protein that passes electrons directly to Q. How is ETC Organized?: ∙ ETC proteins are organized into four multiprotein complexes (IIV) and cofactors. Protons pump into intermembrane space from mitochondrial matrix by complexes I & IV ∙ Q & cytochrome c transfer electrons between complexes o Q also carriers protons across membranes Chemiosmosis Hypothesis: ∙ The ETC pumps protons from the mitochondrial matrix to the intermembrane space. The protonmotive force from this electrochemical gradient can be used to make ATP in a process known as chemiosmosis.ATP Synthase Structure: ∙ ATP synthase is an enzyme complex consisting of two components: 1. ATP synthesizing portion (F1 subunit) 2. Membranespanning, protontransporting base (F0 subunit) ∙ Units connected by rotor and stator ∙ Protons following through F0 subunit causes portion of F0 subunit to spin as well as rotor ∙ Part of F0 subunit and rotor spins, there is a conformational change in F1 subunit which catalyzes phosphorylation of ADP to ATP ATP yield from cellular respiration: ∙ The vast majority of the “payoff” from glucose oxidation occurs via oxidative phosphorylation; ATP synthase produces estimated 25 of the estimated net 29 ATP molecules produced per glucose molecule during cell respiration. Ch. 9ATP & the Regulation of Cellular Respiration: Methods of Producing ATP: ∙ Substratelevel phosphorylation occurs when ATP is produced by the enzyme catalyzed transfer of a phosphate group from an intermediate substrate to ADP. o This is how ATP is produced in glycolysis and the citric acid cycle. ∙ In an electron transport chain a proton gradient provides energy for ATP production; the membrane protein ATP synthase uses this energy to phosphorylate ADP to form ATP. This process is called oxidative phosphorylation. Oxidative Phosphorylation: ∙ The energy released as electrons move through the ETC is used to pump protons across the plasma membrane into the intermembrane space, forming a strong electrochemical gradient. ∙ The protons then move through the enzyme ATP synthase, driving the production of ATP from ADP and Pi. ∙ Because this mode of ATP production links the phosphorylation of ADP with NADH and FADH2 oxidation, it is called oxidative phosphorylation. Feedback Inhibition: ∙ Feedback inhibition occurs when an enzyme in a pathway is inhibited by the product of that pathway. o Cells that are able to stop glycolytic reactions when ATP is abundant can conserve their stores of glucose for times when ATP is scarce. Feedback Inhibition Regulates Glycolysis:∙ During glycolysis, high levels of ATP inhibit the enzyme phosphofructokinase, which catalyzes one of the early reactions. ∙ Phosphofructokinase has two binding sites for ATP: 1. The active site, where ATP phosphorylates fructose6phosphate, resulting in the synthesis of fructose1,6bisphosphate 2. A regulatory site ∙ High ATP concentrations cause ATP to bind at the regulatory site (what type of regulation is this?), changing the enzyme’s shape and dramatically decreasing the reaction rate at the active site. Pyruvate Processing Regulation: ∙ Pyruvate processing is under both positive and negative control. Abundant ATP reserves as well as a large amounts of AcetylCoA or NADH inhibit the enzyme complex; large supplies of reactants and low supplies of products stimulate it. Citric Acid cycle summary: ∙ The citric acid cycle can be turned off at multiple points, via several different mechanisms of feedback inhibition. ∙ To summarize, the citric acid cycle starts with acetyl CoA and ends with CO2. The potential energy that is released is used to produce NADH, FADH2, and ATP. When energy supplies are high, the cycle slows down. Ch. 9Energy Considerations: Free Energy Changes: ∙ For each glucose molecule that is oxidized to 6 CO2, the cell reduces 10 molecules of NAD+ to NADH and 2 molecules of FAD to FADH2, and produces 4 molecules of ATP by substratelevel phosphorylation. ∙ The ATP can be used directly for cellular work. ∙ However, most of glucose’s original energy is contained in the electrons transferred to NADH and FADH2. Electron Transport Chain: ∙ During the electron transport chain in cellular respiration, the high potential energy of the electrons carried by NADH and FADH2 is gradually decreased as they move through a series of redox reactions. ∙ O2 is the final electron acceptor. The transfer of electrons (along with protons) to oxygen forms water.Oxidative Phosphorylation: ∙ The energy released as electrons move through the ETC is used to pump protons across the plasma membrane into the intermembrane space, forming a strong electrochemical gradient. ∙ The protons then move through the enzyme ATP synthase, driving the production of ATP from ADP and Pi. Cellular Respiration and Metabolic pathways: ∙ Energy and carbon are cells’ two fundamental requirements. o They need highenergy electrons for generating chemical energy in the form of ATP, and a source of carboncontaining molecules for synthesizing macromolecules. ∙ Metabolism includes thousands of different chemical reactions. o Catabolic pathways involve the breakdown of molecules and the production of ATP. o Anabolic pathways result in the synthesis of larger molecules from smaller components. Processing proteins and fats as fuel: ∙ Proteins, carbohydrates, and fats can all furnish substrates for cellular respiration. o Enzymes routinely break down fats to form glycerol, which enters the glycolytic pathway, and acetyl CoA, which enters the citric acid cycle. o Enzymes remove the amino groups from proteins; the remaining carbon compounds are intermediates in glycolysis and the citric acid cycle. ∙ For ATP production, cells first use carbohydrates, then fats, and finally proteins. Anabolic Pathways Synthesize key molecules: ∙ Molecules found in carbohydrate metabolism are used to synthesize macromolecules such as RNA, DNA, glycogen or starch, amino acids, fatty acids, and other cell components. Ch. 9Fermentation: Aerobic and Anaerobic Respiration: ∙ All eukaryotes and many prokaryotes use oxygen as the final electron acceptor of electron transport chains in the process of aerobic respiration. ∙ Some prokaryotes, especially those in oxygenpoor environments, use other electron acceptors in the process of anaerobic respiration. Oxygen as final electron acceptor:∙ Oxygen is the most effective electron acceptor because it is highly electronegative. There is a large difference between the potential energy of NADH and O2 electrons which allows the generation of a large protonmotive force for ATP production. ∙ Cells that do not use oxygen as an electron acceptor cannot generate such a large potential energy difference. Thus, they make less ATP than cells that use aerobic respiration. Fermentation: ∙ In most organisms, cellular respiration cannot occur without oxygen. Fermentation, a metabolic pathway that regenerates NAD+ from stockpiles of NADH, allows glycolysis to continue producing ATP in the absence of oxygen. ∙ Fermentation occurs when pyruvate or a molecule derived from pyruvate accepts electrons from NADH. ∙ This transfer of electrons oxidizes NADH to NAD+. o With NAD+ present, glycolysis can continue to produce ATP via substratelevel phosphorylation Different Fermentation Pathways: ∙ In lactic acid fermentation, pyruvate produced by glycolysis accepts electrons from NADH. Lactate and NAD+ are produced. o Lactic acid fermentation occurs in muscle cells. ∙ In alcohol fermentation, pyruvate is enzymatically converted to acetaldehyde and CO2. Acetaldehyde accepts electrons from NADH. Ethanol and NAD+ are produced o Alcohol fermentation occurs in yeast. Fermentation and Cellular Respiration Efficiency: ∙ Fermentation is extremely inefficient compared with cellular respiration. o Fermentation produces just two ATP molecules per glucose molecule, compared with about 29 ATP molecules per glucose molecule in cellular respiration. o Consequently, organisms never use fermentation if an appropriate electron acceptor is available for cellular respiration. Chapter 10PhotosynthesisThe Basics: An Overview of Photosynthesis: ∙ Photosynthesis is the process of using sunlight to produce carbohydrate. This process requires sunlight, carbon dioxide, and water, and produces oxygen as a byproduct. The overall reaction when glucose is the carbohydrate can be written as: 6 CO2 + 6 H2O + light energy →→→ C6H12O6 + 6 O2 ∙ Photosynthesis contrasts with cellular respiration. o Photosynthesis is endergonic. Reduces CO2 to sugar o Cellular respiration is exergonic. Oxidizes sugar to CO2 Photosynthesis: Two linked sets of reactions: ∙ Photosynthesis consists of two linked sets of reactions: lightdependent reactions produce O2 from H2O, and the Calvin cycle or lightindependent reactions produce sugar from CO2. ∙ The reactions are linked by electrons, which are released in the lightdependent reactions when water is split to form oxygen gas and then transferred to the electron carrier NADP+, forming NADPH. ∙ The Calvin cycle then uses these electrons and the potential energy in ATP to reduce CO2 to make sugars. The structure of the chloroplasts: ∙ Photosynthesis occurs in the chloroplasts of green plants, algae, and other photosynthetic organisms. ∙ Chloroplasts are surrounded by two membranes. ∙ The internal membranes of chloroplasts form flattened, vesiclelike structures called thylakoids, some of which form stacks called grana. o Thylakoid membranes contain large quantities of pigments. The most common pigment is chlorophyll. ∙ The fluidfilled space between the thylakoids and the inner membrane is the stroma. Light energy: ∙ Electromagnetic radiation is a form of energy. ∙ Light is a type of energy electromagnetic radiation that acts both particlelike and wave like. o As a particle, light exists in discrete packets called photons. o As a wave, light can be characterized by its wavelength – the distance between two successive wave crests. Electromagnetic spectrum: ∙ The electromagnetic spectrum is the range of wavelengths of electromagnetic radiation. ∙ Electromagnetic radiation that humans can see is called visible light. ∙ Each photon and wavelength has a specific amount of energy. The energy of a photon of light is inversely proportional to its wavelength. o Shorter wavelengths such as ultraviolet light have more energy than longer wavelengths such as infrared light. Photosynthetic pigments absorb light:∙ Photons may be absorbed, transmitted, or reflected when they strike an object. ∙ Pigments are molecules that absorb only certain wavelengths of light. ∙ There are two major classes of pigment in plant leaves: chlorophylls and carotenoids. o The chlorophylls (chlorophyll a and chlorophyll b) absorb red and blue light and reflect and transmit green light. o The carotenoids absorb blue and green light and reflect and transmit yellow, orange, and red light. Absorption spectrum: ∙ Biologists use a graph called an absorption spectrum to study pigments. This spectrum plots the wavelength of light absorbed by pigment molecules. ∙ An action spectrum shows the rate of photosynthesis vs. wavelength. o Pigments that absorb blue and red photons are the most effective at driving photosynthesis. Because the chlorophylls absorb these wavelengths, they are most likely the main photosynthetic pigments. Role of Carotenoids and Other Accessory Pigments: ∙ Carotenoids are accessory pigments that absorb light and pass the energy on to chlorophyll. ∙ Carotenoids absorb wavelengths of light not absorbed by chlorophyll, thus extending the range of wavelengths that can drive photosynthesis. ∙ Carotenoids also stabilize free radicals, protecting chlorophylls from damage. Structure of Chlorophyll: ∙ Chlorophyll a and b are similar in structure and absorption spectra. ∙ Chlorophylls have a long “tail” made of isoprene subunits, and a “head” consisting of a large ring structure with a magnesium atom in the middle (a porphyrin ring). o The tail keeps the molecule embedded in the thylakoid membrane. o Light is absorbed in the head. Electrons Become Excited When Light is Absorbed: ∙ When a photon strikes chlorophyll, its energy can be transferred to an electron in the chlorophyll head. o The electron becomes excited, raised to a higher energy state. Fluorescence:∙ Fluorescence occurs when a pigment absorbs a photon and the electron gets excited, but then falls back to its ground state. Some of the absorbed energy is released as heat and the rest is released as electromagnetic radiation (light). ∙ Only approximately 2% of red and blue photons produce fluorescence. The remaining 98% drive photosynthesis. Photosystems: ∙ Chlorophyll molecules work together in groups, forming a complex called a photosystem. ∙ A photosystem consists of two major elements, an antenna complex and a reaction center, as well as proteins that capture and process excited electrons. The antenna complex: ∙ The photosystem’s antenna complex is composed of accessory pigment molecules. ∙ When a red or blue photon strikes a pigment molecule in the antenna complex, the energy is absorbed and an electron excited. This energy is passed to another chlorophyll molecule, exciting another electron. o This phenomenon is called resonance. ∙ Energy is transferred inside the antenna complex, from one molecule to the next, until it reaches the reaction center Reaction Center: ∙ At the reaction center, excited electrons are transferred to a specialized chlorophyll molecule that acts as an electron acceptor. ∙ When this electron acceptor becomes reduced, the electromagnetic energy is transformed to chemical energy. What Happens to Excited Electrons?: ∙ Excited electrons in chloroplasts may 1. drop back down to a low energy state, causing fluorescence 2. excite an electron in a nearby pigment, inducing resonance. 3. be transferred to an electron acceptor in a redox reaction. Nature of Chemical Energy and Redox Reactions: ∙ In cells, electrons are the most important source of chemical potential energy. ∙ The amount of potential energy in an electron is based on its position relative to positive and negative charges. o Electrons closer to negative charges (from other electrons) and farther from positive charges (in nuclei of nearby atoms), have higher potential energy. ∙ In general, a molecule’s potential energy is a function of its electrons’ configuration and position. Electrons Accompanied by Protons: ∙ The reduced molecule gains a proton and has higher potential energy. ∙ The oxidized molecule loses a proton and has lower potential energy Ch. 10PhotosynthesisThe Process: Photosystems: ∙ There are two types of reaction centers: photosystem I and photosystem II. Photosystem II: ∙ When energy reaches the reaction center of the photosystem, the reaction center chlorophyll is oxidized when a highenergy electron is donated to the electron acceptor pheophytin, a pigment molecule structurally similar to chlorophyll. ∙ The electron is passed to an electron transport chain (ETC) in the thylakoid membrane, producing a proton gradient and driving ATP production via ATP synthase. This ETC is similar in structure and function to the ETC in mitochondria. ∙ The ETC includes plastoquinone (PQ), which shuttles electrons from pheophytin across the thylakoid membrane to a cytochrome complex. ∙ Photosystem II triggers chemiosmosis and ATP synthesis in the chloroplast. Electrons Participate in Redox Reactions: ∙ Electrons in the electron transport chain participate in redox reactions and are gradually stepped down in potential energy. ∙ These redox reactions result in protons being pumped from one side of the membrane to the other. o Proton concentration inside the thylakoid increases 1000fold. Chemiosmosis and photophosphorylation: ∙ As in the mitochondria, protons diffuse down their electrochemical gradient. ∙ Chemiosmosis results when the flow of protons through ATP synthase causes a change in its shape, driving the phosphorylation of ADP. ∙ The capture of light energy by photosystem II to produce ATP is called photophosphorylation. Photosystem II Obtain Electrons ∙ Photosystem II oxidizes water to replace electrons used during the light reactions.∙ When excited electrons leave photosystem II and enter the ETC, the photosystem becomes so electronegative that enzymes can remove electrons from water, leaving protons and oxygen. Oxygenic and Anoxygenic photosynthesis: ∙ Photosystem II “splits” water to replace its lost electrons and in the process produces oxygen: 2 H2O → 4 H+ + 4 e– + O2 o This process is called oxygenic photosynthesis. ∙ Photosystem II is the only known protein complex able to oxidize water in this way. ∙ Purple nonsulfur and purple sulfur bacteria have a single photosystem and cannot oxidize water; thus they perform anoxygenic photosynthesis. Importance of Oxygenic Photosynthesis: ∙ The oxygen released from oxygenic photosynthesis was critical to the evolution of life as we know it. o O2 was almost nonexistent on Earth before enzymes evolved that could catalyze the oxidation of water. Photosystem I: ∙ As with photosystem II, pigments in the antenna complex absorb photons and pass the energy to the reaction center. ∙ Excited electrons from the reaction center of photosystem I are passed down an ETC of iron and sulfurcontaining proteins to ferredoxin. ∙ The enzyme NADP+ reductase transfers a proton and two electrons from ferredoxin to NADP+, forming NADPH. ∙ The photosystem itself and NADP+ reductase are anchored in the thylakoid membrane. NADPH is an Electron Carrier: ∙ Photosystem I produces NADPH, which is similar in function to the NADH and FADH2 produced by the citric acid cycle. NADPH is an electron carrier that can donate electrons to other compounds and thus reduce them. Summary of the photosystems: ∙ Photosystem II produces a proton gradient that drives the synthesis of ATP. ∙ Photosystem I yields reducing power in the form of NADPH. ∙ Although several groups of bacteria have just one of the two photosystems, the cyanobacteria, algae, and plants have both Z scheme: ∙ The Z scheme is a model of how photosystems I and II interact.∙ First, a photon excites an electron in the pigment molecules of photosystem II’s antenna complex, and resonance occurs until the energy reaches the reaction center. o The electrons of photosystem II will be replaced by electrons stripped from water, producing oxygen gas as a byproduct. ∙ A special pair of reactioncenter chlorophyll molecules named P680 passes the excited electron to pheophytin. ∙ From pheophytin, the potential energy of the electron is gradually stepped down through redox reactions in an electron transport chain. ∙ Plastoquinone uses the released energy to transport protons across the thylakoid membrane, building up a proton electrochemical gradient. ∙ ATP synthase uses this force to phosphorylate ADP, producing ATP. ∙ At the end of photosystem II’s ETC, the electron is passed to a protein called plastocyanin. ∙ Plastocyanin carries the electron back across the thylakoid membrane and donates it to photosystem I, thus physically linking the two photosystems. ∙ Electrons from PC replace electrons from the P700 pair of chlorophyll molecules in the photosystem I reaction center. ∙ These electrons enter an ETC, then are eventually passed to ferredoxin and used to reduce NADP+ to NADPH. Enhancement effect: ∙ The Z scheme explains the enhancement effect: o Photosynthesis is more efficient when both 680nm and 700nm wavelengths are available (hence the names of the pairs of reactioncenter chlorophyll molecules), allowing both photosystems to run at maximum rates. ∙ Photosystem I occasionally transfers electrons to photosystem II’s electron transport chain to increase ATP production, instead of using them to reduce NADP+. o This cyclic photophosphorylation coexists with the Z scheme and produces additional ATP Calvin cycle and carbon fixation: ∙ The energy transformation of the lightdependent reactions and the carbon dioxide reduction of the Calvin cycle are two separate but linked processes in photosynthesis. ∙ ATP and NADPH are produced by photosystems I and II in the presence of light. ∙ The reactions that produce sugar from carbon dioxide in the Calvin cycle are light independent. o These reactions require the ATP and NADPH produced by the lightdependent reactions. Calvin cycle: ∙ The Calvin cycle has three phases:1. Fixation: CO2 reacts with ribulose bisphosphate (RuBP), producing two 3phosphoglycerate molecules. o The attachment of CO2 to an organic compound is called carbon fixation. 2. Reduction: The 3phosphoglycerate molecules are phosphorylated by ATP and reduced by NADPH to produce glyceraldehyde 3phosphate (G3P). 3. Regeneration: The remaining G3P is used in reactions that regenerate RuBP. ∙ This cycle of reactions occurs in the chloroplast’s stroma. ∙ One turn of the Calvin cycle fixes one molecule of CO2. Therefore, three turns of the Calvin cycle are required to produce one molecule of G3P. ∙ The discovery of the Calvin cycle clarified how the ATP and NADPH produced by light capturing reactions allow cells to reduce CO2 to carbohydrate. Ch. 10PhotosynthesisThe Rest of the Story: Importance of Rubisco: ∙ The CO2fixing enzyme is called ribulose 1,5bisphosphate carboxylase/oxygenase (rubisco). ∙ Rubisco is found in all photosynthetic organisms that use the Calvin cycle to fix carbon, and is thought to be the most abundant enzyme on Earth. ∙ Rubisco is inefficient because although it does catalyze the addition of CO2 to RuBP, it also catalyzes the addition of O2 to RuBP. Photorespiration: ∙ Oxygen and carbon dioxide compete at the enzyme’s active sites, which slows the rate of CO2 reduction. ∙ When O2 and RuBP react in rubisco’s active site, one of the products undergoes a process called photorespiration o Photorespiration “undoes” photosynthesis because it consumes energy and releases fixed CO2. ∙ When photorespiration occurs, the rate of photosynthesis declines drastically. ∙ Carbon fixation is favored over photorespiration when a cell’s CO2 concentration is high and O2 concentration is low. Co2 Enters & Leaves Through Stomata: ∙ Stomata are leaf structures where gas exchange occurs. They consist of two guard cells that change shape to open or close. ∙ When a leaf’s CO2 concentration is low during photosynthesis, stomata open to allow atmospheric CO2 to diffuse into the leaf and its cells’ chloroplasts. ∙ A strong concentration gradient favoring entry of CO2 is maintained by the Calvin cycle, which constantly uses up the CO2 in chloroplasts.Plants Balance Water Preservation and CO2 Delivery: ∙ Stomata are normally open during the day and closed at night. ∙ On hot, dry days, leaf cells may lose a great deal of water to evaporation through their stomata. When this occurs, they must either close the openings and halt photosynthesis or risk death from dehydration. ∙ Closing the stomata causes CO2 delivery, and thus photosynthesis, to stop. ∙ In addition, the rate of photorespiration increases Mechanism for Increasing co2 concentration: ∙ The C4 pathway, which occurs mostly in plants from hot, dry habitats, limits the damaging effects of photorespiration by spatially separating carbon fixation and the Calvin cycle. o During carbon fixation, C4 plants incorporate CO2 into 4carbon (C4) organic acids instead of 3phosphoglycerate (performed by C3 plants). ∙ In crassulacean acid metabolism (CAM) plants, carbon fixation and the Calvin cycle are separated in time. These plants, which also live in hot, dry habitats, keep their stomata closed all day and open them only at night. C4 photosynthesis: ∙ In C4 plants, which perform C4 photosynthesis, carbon fixation and the Calvin cycle occur in separate types of cells. This occurs in a threestep process: 1. PEP carboxylase fixes CO2 in mesophyll cells. 2. The 4carbon organic acids produced travel to bundlesheath cells 3. The fourcarbon organic acids release a CO2 molecule, which rubisco uses to form 3phosphoglycerate, thus initiating the Calvin cycle. CAM plants: ∙ During the night, CAM plants take in CO2 and temporarily fix it into organic acids. ∙ During the day, CO2 is released from the stored organic acids and used by the Calvin cycle, thus minimizing the effects of photorespiration. Regulation of Photosynthesis: ∙ The rate of photosynthesis is finely tuned, to reflect changes in environmental conditions and use resources efficiently. ∙ For example, light triggers synthesis of photosynthetic proteins, and high sugar levels inhibit synthesis of photosynthetic proteins and stimulate production of proteins required for sugar processing and storage. Fate of sugar produced by photosynthesis:∙ G3P molecules produced by the Calvin cycle are often used to make glucose and fructose, which can be combined to form sucrose. ∙ In rapidly photosynthesizing cells where sucrose is abundant, glucose is temporarily stored in the chloroplast as starch. ∙ Because starch is not water soluble, it is broken down at night and used to make more sucrose for transport throughout the plant.