cells and metabolism big ideas. l.o. 1.15 – the student is able to describe specific examples of...

Cells and Metabolism Big Ideas

L.O. 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all living organisms.

Essential knowledge 2.A.1: All living systems require constant input of free energy. a. Life requires a highly ordered system. 1. Order is maintained by constant free energy input into the system. 2. Loss of order or free energy flow results in death. 3. Increased disorder and entropy are offset by biological processes that maintain or increase order. b. Living systems do not violate the second law of thermodynamics, which states that entropy increases over time. 1. Order is maintained by coupling cellular processes that increase entropy (and so have negative changes in free energy) with those that decrease entropy (and so have positive changes in free energy). 2. Energy input must exceed free energy lost to entropy to maintain order and power cellular processes. 3. Energetically favorable exergonic reactions, such as ATPADP, that have a negative change in free energy can be used to maintain or increase order in a system by being coupled with reactions that have a positive free energy change.

c. Energy-related pathways in biological systems are sequential and may be entered at multiple points in the pathway. [See also 2.A.2] Krebs cycle Glycolysis Calvin cycle Fermentation d. Organisms use free energy to maintain organization, grow and reproduce. 1. Organisms use various strategies to regulate body temperature and metabolism. Endothermy (the use of thermal energy generated bymetabolism to maintain homeostatic body temperatures. Ectothermy (the use of external thermal energy to help regulate and maintain body temperature) Elevated floral temperatures in some plant species 2. Reproduction and rearing of offspring require free energy beyond that used for maintenance and growth. Different organisms use various reproductive strategies in response to energy availability. Seasonal reproduction in animals and plants Life-history strategy (biennial plants, reproductive diapause) 3. There is a relationship between metabolic rate per unit body mass and the size of multicellular organisms generally, the smaller the organism, the higher the metabolic rate. 4. Excess acquired free energy versus required free energy expenditure results in energy storage or growth. 5. Insufficient acquired free energy versus required free energy expenditure results in loss of mass and, ultimately, the death of an organism

e. Changes in free energy availability can result in changes in population size. f. Changes in free energy availability can result in disruptions to an ecosystem. Change in the producer level can affect the number and size of other trophic levels. Change in energy resources levels such as sunlight can affect the number and size of the trophic levels. Learning Objectives: LO 2.1 The student is able to explain how biological systems use free energy based on empirical data that all organisms require constant energy input to maintain organization, to grow and to reproduce. [See SP 6.2] LO 2.2 The student is able to justify a scientific claim that free energy is required for living systems to maintain organization, to grow or to reproduce, but that multiple strategies exist in different living systems. [See SP 6.1] LO 2.3 The student is able to predict how changes in free energy availability affect organisms, populations and ecosystems. [See SP 6.4]

The Laws of Energy Transformation Thermodynamics is the study of energy transformations A isolated system, such as that approximated by liquid in a thermos, is isolated from its surroundings In an open system, energy and matter can be transferred between the system and its surroundings Organisms are open systems 2011 Pearson Education, Inc.

The First Law of Thermodynamics According to the first law of thermodynamics, the energy of the universe is constant Energy can be transferred and transformed, but it cannot be created or destroyed The first law is also called the principle of conservation of energy 2011 Pearson Education, Inc.

The Second Law of Thermodynamics During every energy transfer or transformation, some energy is unusable, and is often lost as heat According to the second law of thermodynamics Every energy transfer or transformation increases the entropy (disorder) of the universe 2011 Pearson Education, Inc.

Figure 8.3 (a) First law of thermodynamics (b) Second law of thermodynamics Chemical energy Heat

Free-Energy Change, G A living systems free energy is energy that can do work when temperature and pressure are uniform, as in a living cell The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously 2011 Pearson Education, Inc.

The change in free energy (G) during a process is related to the change in enthalpy, or change in total energy (H), change in entropy (S), and temperature in Kelvin (T) G = H TS Only processes with a negative G are spontaneous Spontaneous processes can be harnessed to perform work 2011 Pearson Education, Inc.

Free Energy, Stability, and Equilibrium Free energy is a measure of a systems instability, its tendency to change to a more stable state During a spontaneous change, free energy decreases and the stability of a system increases Equilibrium is a state of maximum stability A process is spontaneous and can perform work only when it is moving toward equilibrium 2011 Pearson Education, Inc.

Figure 8.5 More free energy (higher G) Less stable Greater work capacity In a spontaneous change The free energy of the system decreases ( G 0) The system becomes more stable The released free energy can be harnessed to do work Less free energy (lower G) More stable Less work capacity (a) Gravitational motion (b) Diffusion(c) Chemical reaction

Exergonic and Endergonic Reactions in Metabolism An exergonic reaction proceeds with a net release of free energy and is spontaneous An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous 2011 Pearson Education, Inc.

Figure 8.6 (a) Exergonic reaction: energy released, spontaneous (b) Endergonic reaction: energy required, nonspontaneous Reactants Energy Products Progress of the reaction Amount of energy released ( G 0) Reactants Energy Products Amount of energy required ( G 0) Progress of the reaction Free energy

Equilibrium and Metabolism Reactions in a closed system eventually reach equilibrium and then do no work Cells are not in equilibrium; they are open systems experiencing a constant flow of materials A defining feature of life is that metabolism is never at equilibrium A catabolic pathway in a cell releases free energy in a series of reactions Closed and open hydroelectric systems can serve as analogies 2011 Pearson Education, Inc.

Figure 8.7 (a) An isolated hydroelectric system (b) An open hydroelectric system (c) A multistep open hydroelectric system G 0 G 0

Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work Chemical Transport Mechanical To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one Most energy coupling in cells is mediated by ATP 2011 Pearson Education, Inc.

The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cells energy shuttle ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups 2011 Pearson Education, Inc.

Figure 8.8 (a) The structure of ATP Phosphate groups Adenine Ribose Adenosine triphosphate (ATP) Energy Inorganic phosphate Adenosine diphosphate (ADP) (b) The hydrolysis of ATP

How the Hydrolysis of ATP Performs Work The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic 2011 Pearson Education, Inc.

Figure 8.9 Glutamic acid Ammonia Glutamine (b) Conversion reaction coupled with ATP hydrolysis Glutamic acid conversion to glutamine (a) (c) Free-energy change for coupled reaction Glutamic acid Glutamine Phosphorylated intermediate Glu NH 3 NH 2 Glu G Glu = +3.4 kcal/mol ATP ADP NH 3 Glu P P i ADP Glu NH 2 G Glu = +3.4 kcal/mol Glu NH 3 NH 2 ATP G ATP = 7.3 kcal/mol G Glu = +3.4 kcal/mol + G ATP = 7.3 kcal/mol Net G = 3.9 kcal/mol 1 2

ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant The recipient molecule is now called a phosphorylated intermediate 2011 Pearson Education, Inc.

Figure 8.10 Transport protein Solute ATP P P i ADP P i ADP ATP Solute transported Vesicle Cytoskeletal track Motor proteinProtein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. (a) Transport work: ATP phosphorylates transport proteins.

The Regeneration of ATP ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) The energy to phosphorylate ADP comes from catabolic reactions in the cell The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways 2011 Pearson Education, Inc.

Free Energy Equations and Diagrams Delta G? Activation energy?

Essential knowledge 2.A.2: Organisms capture and store free energy for use in biological processes. a. Autotrophs capture free energy from physical sources in the environment. 1. Photosynthetic organisms capture free energy present in sunlight. 2. Chemosynthetic organisms capture free energy from small inorganic molecules present in their environment, and this process can occur in the absence of oxygen. b. Heterotrophs capture free energy present in carbon compounds produced by other organisms. 1. Heterotrophs may metabolize carbohydrates, lipids and proteins by hydrolysis as sources of free energy. 2. Fermentation produces organic molecules, including alcohol and lactic acid, and it occurs in the absence of oxygen.

c. Different energy-capturing processes use different types of electron acceptors. NADP+ in photosynthesis Oxygen in cellular respiration d. The light-dependent reactions of photosynthesis in eukaryotes involve a series of coordinated reaction pathways that capture free energy present in light to yield ATP and NADPH, which power the production of organic molecules. 1. During photosynthesis, chlorophylls absorb free energy from light, boosting electrons to a higher energy level in Photosystems I and II. 2. Photosystems I and II are embedded in the internal membranes of chloroplasts (thylakoids) and are connected by the transfer of higher free energy electrons through an electron transport chain (ETC). [See also 4.A.2] 3. When electrons are transferred between molecules in a sequence of reactions as they pass through the ETC, an electrochemical gradient of hydrogen ions (protons) across the thykaloid membrane is established. 4. The formation of the proton gradient is a separate process, but it is linked to the synthesis of ATP from ADP and inorganic phosphate via ATP synthase. 5. The energy captured in the light reactions as ATP and NADPH powers the production of carbohydrates from carbon dioxide in the Calvin cycle, which occurs in the stroma of the chloroplast.

e. Photosynthesis first evolved in prokaryotic organisms; scientific evidence supports that prokaryotic (bacterial) photosynthesis was responsible for the production of an oxygenated atmosphere; prokaryotic photosynthetic pathways were the foundation of eukaryotic photosynthesis. f. Cellular respiration in eukaryotes involves a series of coordinated enzyme-catalyzed reactions that harvest free energy from simple carbohydrates. 1. Glycolysis rearranges the bonds in glucose molecules, releasing free energy to form ATP from ADP and inorganic phosphate, and resulting in the production of pyruvate. 2. Pyruvate is transported from the cytoplasm to the mitochondrion, where further oxidation occurs. [See also 4.A.2] 3. In the Krebs cycle, carbon dioxide is released from organic intermediates ATP is synthesized from ADP and inorganic phosphate via substrate level phosphorylation and electrons are captured by coenzymes. 4. Electrons that are extracted in the series of Krebs cycle reactions are carried by NADH and FADH2 to the electron transport chain.

g. The electron transport chain captures free energy from electrons in a series of coupled reactions that establish an electrochemical gradient across membranes. 1. Electron transport chain reactions occur in chloroplasts (photosynthesis), mitochondria (cellular respiration) and prokaryotic plasma membranes. 2. In cellular respiration, electrons delivered by NADH and FADH2 are passed to a series of electron acceptors as they move toward the terminal electron acceptor, oxygen. In photosynthesis, the terminal electron acceptor is NADP+. 3. The passage of electrons is accompanied by the formation of a proton gradient across the inner mitochondrial membrane or the thylakoid membrane of chloroplasts, with the membrane(s) separating a region of high proton concentration from a region of low proton concentration. In prokaryotes, the passage of electrons is accompanied by the outward movement of protons across the plasma membrane. 4. The flow of protons back through membrane-bound ATP synthase by chemiosmosis generates ATP from ADP and inorganic phosphate. 5. In cellular respiration, decoupling oxidative phosphorylation from electron transport is involved in thermoregulation. h. Free energy becomes available for metabolism by the conversion of ATPADP, which is coupled to many steps in metabolic pathways.

Learning Objectives: LO 2.4 The student is able to use representations to pose scientific questions about what mechanisms and structural features allow organisms to capture, store and use free energy. [See SP 1.4, 3.1] LO 2.5 The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store or use free energy. [See SP 6.2]

Figure 9.2 Light energy ECOSYSTEM Photosynthesis in chloroplasts Cellular respiration in mitochondria CO 2 H 2 O O 2 Organic molecules ATP powers most cellular work ATP Heat energy

Catabolic pathways yield energy by oxidizing organic fuels to produce ATP The breakdown of organic molecules is exergonic Fermentation is a partial degradation of sugars that occurs without O2 Aerobic respiration consumes organic molecules and O2 and yields ATP Anaerobic respiration is similar to aerobic respiration but consumes compounds other than O2 2011 Pearson Education, Inc.

Cellular respiration includes both aerobic and anaerobic respiration but is often used to refer to aerobic respiration Although carbohydrates, fats, and proteins are all consumed as fuel, it is helpful to trace cellular respiration with the sugar glucose C6H12O6 + 6 O2 6 CO2 + 6 H2O + Energy (ATP + heat) 2011 Pearson Education, Inc.

The Principle of Redox Chemical reactions that transfer electrons between reactants are called oxidation- reduction reactions, or redox reactions In oxidation, a substance loses electrons, or is oxidized In reduction, a substance gains electrons, or is reduced (the amount of positive charge is reduced) 2011 Pearson Education, Inc. becomes oxidized (loses electron) becomes reduced (gains electron)

Oxidation of Organic Fuel Molecules During Cellular Respiration During cellular respiration, the fuel (such as glucose) is oxidized, and O2 is reduced 2011 Pearson Education, Inc. becomes oxidized becomes reduced

Stepwise Energy Harvest via NAD+ and the Electron Transport Chain In cellular respiration, glucose and other organic molecules are broken down in a series of steps Electrons from organic compounds are usually first transferred to NAD+, a coenzyme As an electron acceptor, NAD+ functions as an oxidizing agent during cellular respiration Each NADH (the reduced form of NAD+) represents stored energy that is tapped to synthesize ATP 2011 Pearson Education, Inc.

Figure 9.4 Nicotinamide (oxidized form) NAD (from food) Dehydrogenase Reduction of NAD Oxidation of NADH Nicotinamide (reduced form) NADH Dehydrogenase

NADH passes the electrons to the electron transport chain Unlike an uncontrolled reaction, the electron transport chain passes electrons in a series of steps instead of one explosive reaction O2 pulls electrons down the chain in an energy-yielding tumble The energy yielded is used to regenerate ATP 2011 Pearson Education, Inc.

Figure 9.5 (a) Uncontrolled reaction (b) Cellular respiration Explosive release of heat and light energy Controlled release of energy for synthesis of ATP Free energy, G H 2 1 / 2 O 2 2 H 1 / 2 O 2 H2OH2O H2OH2O 2 H + 2 e 2 e 2 H + ATP Electron transport chain (from food via NADH)

Electron shuttles span membrane MITOCHONDRION 2 NADH 6 NADH 2 FADH 2 or 2 ATP about 26 or 28 ATP Glycolysis Glucose 2 Pyruvate Pyruvate oxidation 2 Acetyl CoA Citric acid cycle Oxidative phosphorylation: electron transport and chemiosmosis CYTOSOL Maximum per glucose: About 30 or 32 ATP Moving into matrix on your picture, point to matrix, cristae, inner mitochondrial membrane, and intermembrane space NADH from glycolysis 1.5 ATP vs. 2.5 ATP per NADH depending on which shuttle working

Electron shuttles span membrane MITOCHONDRION 2 NADH 6 NADH 2 FADH 2 or 2 ATP about 26 or 28 ATP Glycolysis Glucose 2 Pyruvate Pyruvate oxidation 2 Acetyl CoA Citric acid cycle Oxidative phosphorylation: electron transport and chemiosmosis CYTOSOL Maximum per glucose: About 30 or 32 ATP Now moving to the inner mitochondrial membrane 4. Electrons that are extracted in the series of Krebs cycle reactions are carried by NADH and FADH2 to the electron transport chain.

g. The electron transport chain captures free energy from electrons in a series of coupled reactions that establish an electrochemical gradient across membranes. 1. Electron transport chain reactions occur in chloroplasts (photosynthesis), mitochondria (cellular respiration) and prokaryotic plasma membranes.

Figure 9.13 NADH FADH 2 2 H + 1 / 2 O 2 2 e H2OH2O NAD Multiprotein complexes (originally from NADH or FADH 2 ) I II III IV 50 40 30 20 10 0 Free energy (G) relative to O 2 (kcal/mol) FMN Fe S FAD Q Cyt b Cyt c 1 Cyt c Cyt a Cyt a 3 Fe S 2. In cellular respiration, electrons delivered by NADH and FADH2 are passed to a series of electron acceptors as they move toward the terminal electron acceptor, oxygen. The electrons carried by FADH2 have lower free energy and are added to a later point in the chain.

3. The passage of electrons is accompanied by the formation of a proton gradient across the inner mitochondrial membrane or the thylakoid membrane of chloroplasts, with the membrane(s) separating a region of high proton concentration from a region of low proton concentration. In prokaryotes, the passage of electrons is accompanied by the outward movement of protons across the plasma membrane.

Figure 9.15 Protein complex of electron carriers (carrying electrons from food) Electron transport chain Oxidative phosphorylation Chemiosmosis ATP synthase I II III IV Q Cyt c FAD FADH 2 NADH ADP P i NAD HH 2 H + 1 / 2 O 2 HH HH HH 21 HH H2OH2O ATP

4. The flow of protons back through membrane-bound ATP synthase by chemiosmosis generates ATP from ADP and inorganic phosphate. ATP synthase uses the exergonic flow of H + to drive phosphorylation of ATP This is an example of chemiosmosis, the use of energy in a H + gradient to drive cellular work The H + gradient is referred to as a proton-motive force, emphasizing its capacity to do work Figure 9.14 INTERMEMBRANE SPACE Rotor Stator HH Internal rod Catalytic knob ADP + P i ATP MITOCHONDRIAL MATRIX

Figure 9.16 Electron shuttles span membrane MITOCHONDRION 2 NADH 6 NADH 2 FADH 2 or 2 ATP about 26 or 28 ATP Glycolysis Glucose 2 Pyruvate Pyruvate oxidation 2 Acetyl CoA Citric acid cycle Oxidative phosphorylation: electron transport and chemiosmosis CYTOSOL Maximum per glucose: About 30 or 32 ATP

5. In cellular respiration, decoupling oxidative phosphorylation from electron transport is involved in thermoregulation. Used by hibernating mammals Brown fat, high in mitochondria, with ETC uncoupling protein Protein is activated during hibernation Allows protons to flow back down their gradient without making ATP (uncoupled) Ongoing oxidation of stored fuel generates heat to keep body temp warmer than environment If ATP were made, would build up to high levels that would shut down the cell respiration pathways

Temp regulation

Fermentation produces organic molecules, including alcohol and lactic acid, and it occurs in the absence of oxygen. See Ch. 9 slide 78 Animation

In alcohol fermentation, pyruvate is converted to ethanol in two steps. First, pyruvate is converted to a two-carbon compound, acetaldehyde by the removal of CO 2. Second, acetaldehyde is reduced by NADH to ethanol. Alcohol fermentation by yeast is used in brewing and winemaking. Fig. 9.17a

During lactic acid fermentation, pyruvate is reduced directly by NADH to form lactate (ionized form of lactic acid). Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt. Muscle cells switch from aerobic respiration to lactic acid fermentation to generate ATP when O 2 is scarce. The waste product, lactate, may cause muscle fatigue, but ultimately it is converted back to pyruvate in the liver. Fig. 9.17b

Some organisms (facultative anaerobes), including yeast and many bacteria, can survive using either fermentation or respiration. At a cellular level, human muscle cells can behave as facultative anaerobes, but nerve cells cannot. For facultative anaerobes, pyruvate is a fork in the metabolic road that leads to two alternative routes. Fig. 9.18

The Evolutionary Significance of Glycolysis Ancient prokaryotes are thought to have used glycolysis long before there was oxygen in the atmosphere Very little O 2 was available in the atmosphere until about 2.7 billion years ago, so early prokaryotes likely used only glycolysis to generate ATP Glycolysis is a very ancient process 2011 Pearson Education, Inc.

Control of catabolism is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway. One strategic point occurs in the third step of glycolysis, catalyzed by phosphofructokinase. Fig. 9.20

Carbohydrates, fats, and proteins can all be catabolized through the same pathways. Fig. 9.19

Chloroplasts: The Sites of Photosynthesis in Plants Leaves are the major locations of photosynthesis Their green color is from chlorophyll, the green pigment within chloroplasts Chloroplasts are found mainly in cells of the mesophyll, the interior tissue of the leaf Each mesophyll cell contains 3040 chloroplasts 2011 Pearson Education, Inc.

CO 2 enters and O 2 exits the leaf through microscopic pores called stomata The chlorophyll is in the membranes of thylakoids (connected sacs in the chloroplast); thylakoids may be stacked in columns called grana Chloroplasts also contain stroma, a dense interior fluid 2011 Pearson Education, Inc.

Figure 10.4 Mesophyll Leaf cross section Chloroplasts Vein Stomata Chloroplast Mesophyll cell CO 2 O2O2 20 m Outer membrane Intermembrane space Inner membrane 1 m Thylakoid space Thylakoid Granum Stroma Lets look at model

Photosynthesis as a Redox Process Photosynthesis reverses the direction of electron flow compared to respiration Photosynthesis is a redox process in which H 2 O is oxidized and CO 2 is reduced Photosynthesis is an endergonic process; the energy boost is provided by light 2011 Pearson Education, Inc. Energy 6 CO 2 6 H 2 O C 6 H 12 O 6 6 O 2 becomes reduced becomes oxidized

The Two Stages of Photosynthesis: A Preview Photosynthesis consists of the light reactions (the photo part) and Calvin cycle (the synthesis part) The light reactions (in the thylakoids) Split H 2 O Release O 2 Reduce NADP + to NADPH Generate ATP from ADP by photophosphorylation 2011 Pearson Education, Inc.

The Calvin cycle (in the stroma) forms sugar from CO 2, using ATP and NADPH The Calvin cycle begins with carbon fixation, incorporating CO 2 into organic molecules 2011 Pearson Education, Inc.

Light Light Reactions Calvin Cycle Chloroplast [CH 2 O] (sugar) ATP NADPH NADP ADP + P i H2OH2O CO 2 O2O2 Figure 10.6-4

While light travels as a wave, many of its properties are those of a discrete particle, the photon. Photons are not tangible objects, but they do have fixed quantities of energy and amount depends on wavelength.

(b) Action spectrum (a) Absorption spectra Engelmanns experiment (c) Chloro- phyll a Chlorophyll b Carotenoids Wavelength of light (nm) Absorption of light by chloroplast pigments Rate of photosynthesis (measured by O 2 release) Aerobic bacteria Filament of alga 400 500600700 400 500600700 400 500600700 RESULTS Figure 10.10

Chlorophyll a is the main photosynthetic pigment Accessory pigments, such as chlorophyll b, broaden the spectrum used for photosynthesis Accessory pigments called carotenoids absorb excessive light that would damage chlorophyll 2011 Pearson Education, Inc.

Excited electrons are unstable. Generally, they drop to their ground state in a billionth of a second, releasing heat energy. Some pigments, including chlorophyll, release a photon of light, in a process called fluorescence, as well as heat. Fig. 10.10

Fig. 10.9

Figure 10.18 STROMA (low H concentration) THYLAKOID SPACE (high H concentration) Light Photosystem II Cytochrome complex Photosystem I Light NADP reductase NADP + H To Calvin Cycle ATP synthase Thylakoid membrane 2 13 NADPH Fd Pc Pq 4 H + +2 H + H+H+ ADP + P i ATP 1/21/2 H2OH2O O2O2

A Photosystem: A Reaction-Center Complex Associated with Light- Harvesting Complexes A photosystem consists of a reaction-center complex (a type of protein complex) surrounded by light-harvesting complexes The light-harvesting complexes (pigment molecules bound to proteins) transfer the energy of photons to the reaction center 2011 Pearson Education, Inc.

Figure 10.13 (b) Structure of photosystem II (a) How a photosystem harvests light Thylakoid membrane Photon Photosystem STROMA Light- harvesting complexes Reaction- center complex Primary electron acceptor Transfer of energy Special pair of chlorophyll a molecules Pigment molecules THYLAKOID SPACE (INTERIOR OF THYLAKOID) Chlorophyll STROMA Protein subunits THYLAKOID SPACE ee Each photosystem consists of chlorophylls, accessory pigments, and proteins. The black arrows represent photons being passed like a wave to reaction center chlorophylls that actually donate their electrons.

Figure 10.14-5 Cytochrome complex Primary acceptor H2OH2O O2O2 2 H + 1/21/2 P680 Light Pigment molecules Photosystem II (PS II ) Photosystem I (PS I ) Pq Pc ATP 1 235 6 7 8 Electron transport chain P700 Light + H NADP NADPH NADP reductase Fd ee ee ee ee 4 ee ee Linear Electron Flow

Photosystem II Photosystem I Mill makes ATP ATP NADPH ee ee ee ee ee ee ee Photon Figure 10.15

Lets watch animation of Phase I http://www.mhhe.com/biosci/genbio/biolink /j_explorations/ch09expl.htmhttp://www.mhhe.com/biosci/genbio/biolink /j_explorations/ch09expl.htm

A Comparison of Chemiosmosis in Chloroplasts and Mitochondria Chloroplasts and mitochondria generate ATP by chemiosmosis, but use different sources of energy Mitochondria transfer chemical energy from food to ATP; chloroplasts transform light energy into the chemical energy of ATP Spatial organization of chemiosmosis differs between chloroplasts and mitochondria but also shows similarities 2011 Pearson Education, Inc.

In mitochondria, protons are pumped to the intermembrane space and drive ATP synthesis as they diffuse back into the mitochondrial matrix In chloroplasts, protons are pumped into the thylakoid space and drive ATP synthesis as they diffuse back into the stroma 2011 Pearson Education, Inc.

Mitochondrion Chloroplast MITOCHONDRION STRUCTURE CHLOROPLAST STRUCTURE Intermembrane space Inner membrane Matrix Thylakoid space Thylakoid membrane Stroma Electron transport chain HH Diffusion ATP synthase HH ADP P i KeyHigher [H ] Lower [H ] ATP Figure 10.17

ATP and NADPH are produced on the side facing the stroma, where the Calvin cycle takes place In summary, light reactions generate ATP and increase the potential energy of electrons by moving them from H 2 O to NADPH 2011 Pearson Education, Inc.

Input 3 (Entering one at a time) CO 2 Phase 1: Carbon fixation Rubisco 3PP P6 Short-lived intermediate 3-Phosphoglycerate 6 6 ADP ATP 6PP 1,3-Bisphosphoglycerate Calvin Cycle 6 NADPH 6 NADP 6 P i6 P i 6P Phase 2: Reduction Glyceraldehyde 3-phosphate (G3P) P 5 G3P ATP 3 ADP Phase 3: Regeneration of the CO 2 acceptor (RuBP) 3P P Ribulose bisphosphate (RuBP) 1P G3P (a sugar) Output Glucose and other organic compounds 3 Figure 10.19-3 For every one net G3P, requires 9 ATP and 6 NADPH from the light reaction. Calvin Cycle

Cyclic Electron Flow Cyclic electron flow uses only photosystem I and produces ATP, but not NADPH No oxygen is released Cyclic electron flow generates surplus ATP, satisfying the higher demand in the Calvin cycle 2011 Pearson Education, Inc.

Figure 10.16 Photosystem I Primary acceptor Cytochrome complex Fd Pc ATP Primary acceptor Pq Fd NADPH NADP reductase NADP + H Photosystem II

In photosynthesis, the energy that enters the chloroplasts as sunlight becomes stored as chemical energy in organic compounds. Photosynthesis is the biospheres metabolic foundation - About 50% of the organic material made is consumed as fuel for cellular respiration in plant mitochondria. Rest is stored or used to build other organic compounds.

On a global scale, photosynthesis is the most important process to the welfare of life on Earth. Each year photosynthesis synthesizes 160 billion metric tons of carbohydrate per year.

Essential knowledge 2.B.1: Cell membranes are selectively permeable due to their structure. a.Cell membranes separate the internal environment of the cell from the external environment. b. Selective permeability is a direct consequence of membrane structure, as described by the fluid mosaic model. [See also 4.A.1] 1. Cell membranes consist of a structural framework of phospholipid molecules, embedded proteins, cholesterol, glycoproteins and glycolipids. 2. Phospholipids give the membrane both hydrophilic and hydrophobic properties. The hydrophilic phosphate portions of the phospholipids are oriented toward the aqueous external or internal environments, while the hydrophobic fatty acid portions face each other within the interior of the membrane itself. 3. Embedded proteins can be hydrophilic, with charged and polar side groups, or hydrophobic, with nonpolar side groups. 4. Small, uncharged polar molecules and small nonpolar molecules, such as N2, freely pass across the membrane. Hydrophilic substances such as large polar molecules and ions move across the membrane through embedded channel and transport proteins. Water moves across membranes and through channel proteins called aquaporins.

c. Cell walls provide a structural boundary, as well as a permeability barrier for some substances to the internal environments. 1. Plant cell walls are made of cellulose and are external to the cell membrane. 2. Other examples are cells walls of prokaryotes and fungi. Learning Objectives: LO 2.10 The student is able to use representations and models to pose scientific questions about the properties of cell membranes and selective permeability based on molecular structure. [See SP 1.4, 3.1] LO 2.11 The student is able to construct models that connect the movement of molecules across membranes with membrane structure and function. [See SP 1.1, 7.1, 7.2]

Essential knowledge 2.B.2: Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes. a. Passive transport does not require the input of metabolic energy; the net movement of molecules is from high concentration to low concentration. 1. Passive transport plays a primary role in the import of resources and the export of wastes. 2. Membrane proteins play a role in facilitated diffusion of charged and polar molecules through a membrane. Glucose transport Na+/K+ transport 3. External environments can be hypotonic, hypertonic or isotonic to internal environments of cells. b. Active transport requires free energy to move molecules from regions of low concentration to regions of high concentration. 1. Active transport is a process where free energy (often provided by ATP) is used by proteins embedded in the membrane to move molecules and/or ions across the membrane and to establish and maintain concentration gradients. 2. Membrane proteins are necessary for active transport.

c. The processes of endocytosis and exocytosis move large molecules from the external environment to the internal environment and vice versa, respectively. 1. In exocytosis, internal vesicles fuse with the plasma membrane to secrete large macromolecules out of the cell. 2. In endocytosis, the cell takes in macromolecules and particulate matter by forming new vesicles derived from the plasma membrane. Learning Objective LO 2.12 The student is able to use representations and models to analyze situations or solve problems qualitatively and quantitatively to investigate whether dynamic homeostasis is maintained by the active movement of molecules across membranes. [See SP1.4]

Concept 7.1: Cellular membranes are fluid mosaics of lipids and proteins Phospholipids are the most abundant lipid in the plasma membrane Phospholipids are amphipathic molecules, containing hydrophobic and hydrophilic regions The fluid mosaic model states that a membrane is a fluid structure with a mosaic of various proteins embedded in it 2011 Pearson Education, Inc.

Figure 7.2 Hydrophilic head Hydrophobic tail WATER

Figure 7.3 Phospholipid bilayer Hydrophobic regions of protein Hydrophilic regions of protein

Figure 7.5 Glyco- protein Carbohydrate Glycolipid Microfilaments of cytoskeleton EXTRACELLULAR SIDE OF MEMBRANE CYTOPLASMIC SIDE OF MEMBRANE Integral protein Peripheral proteins Cholesterol Fibers of extracellular matrix (ECM)

Figure 7.6 Lateral movement occurs 10 7 times per second. Flip-flopping across the membrane is rare ( once per month).

Figure 7.7 Membrane proteins Mouse cell Human cell Hybrid cell Mixed proteins after 1 hour RESULTS

As temperatures cool, membranes switch from a fluid state to a solid state The temperature at which a membrane solidifies depends on the types of lipids Membranes rich in unsaturated fatty acids are more fluid than those rich in saturated fatty acids Membranes must be fluid to work properly; they are usually about as fluid as salad oil 2011 Pearson Education, Inc.

The steroid cholesterol has different effects on membrane fluidity at different temperatures At warm temperatures (such as 37C), cholesterol restrains movement of phospholipids At cool temperatures, it maintains fluidity by preventing tight packing 2011 Pearson Education, Inc.

Figure 7.8 Fluid Unsaturated hydrocarbon tails Viscous Saturated hydrocarbon tails (a) Unsaturated versus saturated hydrocarbon tails (b) Cholesterol within the animal cell membrane Cholesterol

Evolution of Differences in Membrane Lipid Composition Variations in lipid composition of cell membranes of many species appear to be adaptations to specific environmental conditions Ability to change the lipid compositions in response to temperature changes has evolved in organisms that live where temperatures vary 2011 Pearson Education, Inc.

Peripheral proteins are bound to the surface of the membrane Integral proteins penetrate the hydrophobic core Integral proteins that span the membrane are called transmembrane proteins The hydrophobic regions of an integral protein consist of one or more stretches of nonpolar amino acids, often coiled into alpha helices 2011 Pearson Education, Inc.

Figure 7.9 N-terminus helix C-terminus EXTRACELLULAR SIDE CYTOPLASMIC SIDE

Figure 7.10 Enzymes Signaling molecule Receptor Signal transduction Glyco- protein ATP (a) Transport (b) Enzymatic activity (c) Signal transduction (d) Cell-cell recognition (e) Intercellular joining (f) Attachment to the cytoskeleton and extracellular matrix (ECM)

The Role of Membrane Carbohydrates in Cell-Cell Recognition Cells recognize each other by binding to surface molecules, often containing carbohydrates, on the extracellular surface of the plasma membrane Membrane carbohydrates may be covalently bonded to lipids (forming glycolipids) or more commonly to proteins (forming glycoproteins) Carbohydrates on the external side of the plasma membrane vary among species, individuals, and even cell types in an individual 2011 Pearson Education, Inc.

Figure 7.11 Receptor (CD4) Co-receptor (CCR5) HIV Receptor (CD4) but no CCR5 Plasma membrane HIV can infect a cell that has CCR5 on its surface, as in most people. HIV cannot infect a cell lacking CCR5 on its surface, as in resistant individuals.

Concept 7.2: Membrane structure results in selective permeability A cell must exchange materials with its surroundings, a process controlled by the plasma membrane Plasma membranes are selectively permeable, regulating the cells molecular traffic Hydrophobic (nonpolar) molecules, such as hydrocarbons, can dissolve in the lipid bilayer and pass through the membrane rapidly Polar molecules, such as sugars, do not cross the membrane easily 2011 Pearson Education, Inc.

Transport Proteins Transport proteins allow passage of hydrophilic substances across the membrane Some transport proteins, called channel proteins, have a hydrophilic channel that certain molecules or ions can use as a tunnel Channel proteins called aquaporins facilitate the passage of water Other transport proteins, called carrier proteins, bind to molecules and change shape to shuttle them across the membrane A transport protein is specific for the substance it moves 2011 Pearson Education, Inc.

Figure 7.17 EXTRACELLULAR FLUID CYTOPLASM Channel protein Solute Carrier protein (a) A channel protein (b) A carrier protein

Facilitated Diffusion: Passive Transport Aided by Proteins In facilitated diffusion, transport proteins speed the passive movement of molecules across the plasma membrane Channel proteins provide corridors that allow a specific molecule or ion to cross the membrane Channel proteins include Aquaporins, for facilitated diffusion of water Ion channels that open or close in response to a stimulus (gated channels) 2011 Pearson Education, Inc.

Concept 7.4: Active transport uses energy to move solutes against their gradients Facilitated diffusion is still passive because the solute moves down its concentration gradient, and the transport requires no energy Some transport proteins, however, can move solutes against their concentration gradients 2011 Pearson Education, Inc.

The Need for Energy in Active Transport Active transport moves substances against their concentration gradients Active transport requires energy, usually in the form of ATP Active transport is performed by specific proteins embedded in the membranes 2011 Pearson Education, Inc.

Animation: Active Transport Right-click slide / select Play

Active transport allows cells to maintain concentration gradients that differ from their surroundings The sodium-potassium pump is one type of active transport system 2011 Pearson Education, Inc.

Figure 7.18-6 EXTRACELLULAR FLUID [Na ] high [K ] low [Na ] low [K ] high CYTOPLASM Na 123456 KK KK KK KK KK KK P P P P i ATP ADP

Figure 7.19 Passive transportActive transport DiffusionFacilitated diffusion ATP

How Ion Pumps Maintain Membrane Potential Membrane potential is the voltage difference across a membrane Voltage is created by differences in the distribution of positive and negative ions across a membrane 2011 Pearson Education, Inc.

Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane A chemical force (the ions concentration gradient) An electrical force (the effect of the membrane potential on the ions movement) 2011 Pearson Education, Inc.

An electrogenic pump is a transport protein that generates voltage across a membrane The sodium-potassium pump is the major electrogenic pump of animal cells The main electrogenic pump of plants, fungi, and bacteria is a proton pump Electrogenic pumps help store energy that can be used for cellular work 2011 Pearson Education, Inc.

Figure 7.20 CYTOPLASM ATP EXTRACELLULAR FLUID Proton pump HH HH HH HH HH HH

Cotransport: Coupled Transport by a Membrane Protein Cotransport occurs when active transport of a solute indirectly drives transport of other solutes Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive active transport of nutrients into the cell 2011 Pearson Education, Inc.

Figure 7.21 ATP HH HH HH HH HH HH HH HH Proton pump Sucrose-H cotransporter Sucrose Diffusion of H

Concept 7.5: Bulk transport across the plasma membrane occurs by exocytosis and endocytosis Small molecules and water enter or leave the cell through the lipid bilayer or via transport proteins Large molecules, such as polysaccharides and proteins, cross the membrane in bulk via vesicles Bulk transport requires energy 2011 Pearson Education, Inc.

Animation: Exocytosis and Endocytosis Introduction Right-click slide / select Play

Exocytosis In exocytosis, transport vesicles migrate to the membrane, fuse with it, and release their contents Many secretory cells use exocytosis to export their products 2011 Pearson Education, Inc.

Animation: Exocytosis Right-click slide / select Play

Endocytosis In endocytosis, the cell takes in macromolecules by forming vesicles from the plasma membrane Endocytosis is a reversal of exocytosis, involving different proteins There are three types of endocytosis Phagocytosis (cellular eating) Pinocytosis (cellular drinking) Receptor-mediated endocytosis 2011 Pearson Education, Inc.

Animation: Phagocytosis Right-click slide / select Play In phagocytosis a cell engulfs a particle in a vacuole The vacuole fuses with a lysosome to digest the particle

2011 Pearson Education, Inc. Animation: Pinocytosis Right-click slide / select Play In pinocytosis, molecules are taken up when extracellular fluid is gulped into tiny vesicles

2011 Pearson Education, Inc. Animation: Receptor-Mediated Endocytosis Right-click slide / select Play In receptor- mediated endocytosis, binding of ligands to receptors triggers vesicle formation A ligand is any molecule that binds specifically to a receptor site of another molecule

Figure 7.22 Solutes Pseudopodium Food or other particle Food vacuole CYTOPLASM Plasma membrane Vesicle Receptor Ligand Coat proteins Coated pit Coated vesicle EXTRACELLULAR FLUID Phagocytosis Pinocytosis Receptor-Mediated Endocytosis

L.0. 2.12

Enduring understanding 2.B: Growth, reproduction and dynamic homeostasis require that cells create and maintain internal environments that are different from their external environments. Essential knowledge 2.B.3: Eukaryotic cells maintain internal membranes that partition the cell into specialized regions. a. Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing surface area where reactions can occur. b. Membranes and membrane-bound organelles in eukaryotic cells localize (compartmentalize) intracellular metabolic processes and specific enzymatic reactions. [See also 4.A.2] Endoplasmic reticulum Mitochondria Chloroplasts Golgi Nuclear envelope c. Archaea and Bacteria generally lack internal membranes and organelles and have a cell wall.

2.B.3 Learning Objectives LO 2.13 The student is able to explain how internal membranes and organelles contribute to cell functions. [See SP 6.2] LO 2.14 The student is able to use representations and models to describe differences in prokaryotic and eukaryotic cells. [See SP1.4]

Fimbriae Bacterial chromosome A typical rod-shaped bacterium (a) Nucleoid Ribosomes Plasma membrane Cell wall Capsule Flagella A thin section through the bacterium Bacillus coagulans (TEM) (b) 0.5 m Figure 6.5

Eukaryotic cells are characterized by having DNA in a nucleus that is bounded by a membranous nuclear envelope Membrane-bound organelles Cytoplasm in the region between the plasma membrane and nucleus Eukaryotic cells are generally much larger than prokaryotic cells 2011 Pearson Education, Inc.

Figure 6.8a ENDOPLASMIC RETICULUM (ER) Rough ER Smooth ER Nuclear envelope Nucleolus Chromatin Plasma membrane Ribosomes Golgi apparatus Lysosome Mitochondrion Peroxisome Microvilli Microtubules Intermediate filaments Microfilaments Centrosome CYTOSKELETON: Flagellum NUCLEUS

Nuclear envelope Nucleolus Chromatin Golgi apparatus Mitochondrion Peroxisome Plasma membrane Cell wall Wall of adjacent cell Plasmodesmata Chloroplast Microtubules Intermediate filaments Microfilaments CYTOSKELETON Central vacuole Ribosomes Smooth endoplasmic reticulum Rough endoplasmic reticulum Figure 6.8c

Essential knowledge 4.A.2: The structure and function of subcellular components, and their interactions, provide essential cellular processes. a. Ribosomes are small, universal structures comprised of two interacting parts: ribosomal RNA and protein. In a sequential manner, these cellular components interact to become the site of protein synthesis where the translation of the genetic instructions yields specific polypeptides. [See also 2.B.3] b. Endoplasmic reticulum (ER) occurs in two forms: smooth and rough. [See also 2.B.3] 1. Rough endoplasmic reticulum functions to compartmentalize the cell, serves as mechanical support, provides site-specific protein synthesis with membrane-bound ribosomes and plays a role in intracellular transport. 2. In most cases, smooth ER synthesizes lipids.

c. The Golgi complex is a membrane-bound structure that consists of a series of flattened membrane sacs (cisternae). [See also 2.B.3] 1. Functions of the Golgi include synthesis and packaging of materials (small molecules) for transport (in vesicles), and production of lysosomes. d. Mitochondria specialize in energy capture and transformation. [See also 2.A.2, 2.B.3] 1. Mitochondria have a double membrane that allows compartmentalization within the mitochondria and is important to its function. 2. The outer membrane is smooth, but the inner membrane is highly convoluted, forming folds called cristae. 3. Cristae contain enzymes important to ATP production; cristae also increase the surface area for ATP production.

e. Lysosomes are membrane-enclosed sacs that contain hydrolytic enzymes, which are important in intracellular digestion, the recycling of a cells organic materials and programmed cell death (apoptosis). Lysosomes carry out intracellular digestion in a variety of ways. [See also 2.B.3] f. A vacuole is a membrane-bound sac that plays roles in intracellular digestion and the release of cellular waste products. In plants, a large vacuole serves many functions, from storage of pigments orpoisonous substances to a role in cell growth. In addition, a large central vacuole allows for a large surface area to volume ratio. [See also 2.A.3, 2.B.3] g. Chloroplasts are specialized organelles found in algae and higher plants that capture energy through photosynthesis. [See also 2.A.2, 2 B.3] 1. The structure and function relationship in the chloroplast allows cells to capture the energy available in sunlight and convert it to chemical bond energy via photosynthesis. 2. Chloroplasts contain chlorophylls, which are responsible for the green color of a plant and are the key light-trapping molecules in photosynthesis. There are several types of chlorophyll, but the predominant form in plants is chlorophyll a. 3. Chloroplasts have a double outer membrane that creates a compartmentalized structure, which supports its function. Within the chloroplasts are membrane-bound structures called thylakoids. Energy- capturing reactions housed in the thylakoids are organized in stacks, called grana, to produce ATP and NADPH2, which fuel carbon-fixing reactions in the Calvin-Benson cycle. Carbon fixation occurs in the stroma, where molecules of CO2 are converted to carbohydrates.

4.A.2 Learning Objectives LO 4.4 The student is able to make a prediction about the interactions of subcellular organelles. [See SP 6.4] LO 4.5 The student is able to construct explanations based on scientific evidence as to how interactions of subcellular structures provide essential functions. [See SP 6.2] LO 4.6 The student is able to use representations and models to analyze situations qualitatively to describe how interactions of subcellular structures, which possess specialized functions, provide essential functions. [See SP 1.4]

Concept 6.4: The endomembrane system regulates protein traffic and performs metabolic functions in the cell Components of the endomembrane system Nuclear envelope Endoplasmic reticulum Golgi apparatus Lysosomes Vacuoles Plasma membrane These components are either continuous or connected via transfer by vesicles 2011 Pearson Education, Inc. X

The Endoplasmic Reticulum: Biosynthetic Factory The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells The ER membrane is continuous with the nuclear envelope There are two distinct regions of ER Smooth ER, which lacks ribosomes Rough ER, surface is studded with ribosomes 2011 Pearson Education, Inc.

Figure 6.11 Smooth ER Rough ER ER lumen Cisternae Ribosomes Smooth ER Transport vesicle Transitional ER Rough ER 200 nm Nuclear envelope X

Functions of Smooth ER The smooth ER Synthesizes lipids Metabolizes carbohydrates Detoxifies drugs and poisons Stores calcium ions 2011 Pearson Education, Inc.

Functions of Rough ER The rough ER Has bound ribosomes, which secrete glycoproteins (proteins covalently bonded to carbohydrates) Distributes transport vesicles, proteins surrounded by membranes Is a membrane factory for the cell 2011 Pearson Education, Inc.

The Golgi apparatus consists of flattened membranous sacs called cisternae Functions of the Golgi apparatus Modifies products of the ER Manufactures certain macromolecules Sorts and packages materials into transport vesicles The Golgi Apparatus: Shipping and Receiving Center 2011 Pearson Education, Inc.

Figure 6.12 cis face (receiving side of Golgi apparatus) trans face (shipping side of Golgi apparatus) 0.1 m TEM of Golgi apparatus Cisternae

Lysosomes: Digestive Compartments A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids Lysosomal enzymes work best in the acidic environment inside the lysosome 2011 Pearson Education, Inc. X

Animation: Lysosome Formation Right-click slide / select Play X

Some types of cell can engulf another cell by phagocytosis; this forms a food vacuole A lysosome fuses with the food vacuole and digests the molecules Lysosomes also use enzymes to recycle the cells own organelles and macromolecules, a process called autophagy 2011 Pearson Education, Inc.

Figure 6.13 Nucleus Lysosome 1 m Digestive enzymes Digestion Food vacuole Lysosome Plasma membrane (a) Phagocytosis Vesicle containing two damaged organelles 1 m Mitochondrion fragment Peroxisome fragment (b) Autophagy Peroxisome Vesicle Mitochondrion Lysosome Digestion X

Vacuoles: Diverse Maintenance Compartments A plant cell or fungal cell may have one or several vacuoles, derived from endoplasmic reticulum and Golgi apparatus 2011 Pearson Education, Inc. Food vacuoles are formed by phagocytosis Contractile vacuoles, found in many freshwater protists, pump excess water out of cells Central vacuoles, found in many mature plant cells, hold organic compounds and water

Figure 6.15-1 Smooth ER Nucleus Rough ER Plasma membrane X ENDOMEMBRANE SYSTEM MUST KNOW!

Figure 6.15-2 Smooth ER Nucleus Rough ER Plasma membrane cis Golgi trans Golgi X

Figure 6.15-3 Smooth ER Nucleus Rough ER Plasma membrane cis Golgi trans Golgi X

Peroxisomes: Oxidation Peroxisomes are specialized metabolic compartments bounded by a single membrane Peroxisomes produce hydrogen peroxide and convert it to water Peroxisomes perform reactions with many different functions How peroxisomes are related to other organelles is still unknown 2011 Pearson Education, Inc.

Figure 6.UN01 Nucleus (ER) (Nuclear envelope)

Roles of the Cytoskeleton: Support and Motility The cytoskeleton helps to support the cell and maintain its shape It interacts with motor proteins to produce motility Inside the cell, vesicles can travel along monorails provided by the cytoskeleton Recent evidence suggests that the cytoskeleton may help regulate biochemical activities 2011 Pearson Education, Inc. X

Figure 6.21 ATP Vesicle (a) Motor protein (ATP powered) Microtubule of cytoskeleton Receptor for motor protein 0.25 m Vesicles Microtubule (b) X

Enduring understanding 4.B: Competition and cooperation are important aspects of biological systems. Essential knowledge 4.B.1: Interactions between molecules affect their structure and function. a. Change in the structure of a molecular system may result in a change of the function of the system. [See also 3.D.3] b. The shape of enzymes, active sites and interaction with specific molecules are essential for basic functioning of the enzyme 1. For an enzyme-mediated chemical reaction to occur, the substrate must be complementary to the surface properties (shape and charge) of the active site. In other words, the substrate must fit into the enzymes active site. 2. Cofactors and coenzymes affect enzyme function; this interaction relates to a structural change that alters the activity rate of the enzyme. The enzyme may only become active when all the appropriate cofactors or coenzymes are present and bind to the appropriate sites on the enzyme.

c. Other molecules and the environment in which the enzyme acts can enhance or inhibit enzyme activity. Molecules can bind reversibly or irreversibly to the active or allosteric sites, changing the activity of the enzyme. d. The change in function of an enzyme can be interpreted from data regarding the concentrations of product or substrate as a function of time. These representations demonstrate the relationship between an enzymes activity, the disappearance of substrate, and/or presence of a competitive inhibitor. Learning Objective: LO 4.17 The student is able to analyze data to identify how molecular interactions affect structure and function. [See SP 5.1]

Concept 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 An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction 2011 Pearson Education, Inc. Sucrase Sucrose (C 12 H 22 O 11 ) Glucose (C 6 H 12 O 6 ) Fructose (C 6 H 12 O 6 )

Enzyme speed reactions by lowering E A. The transition state can then be reached even at moderate temperatures. Enzymes do not change delta G. It hastens reactions that would occur eventually. Because enzymes are so selective, they determine which chemical processes will occur at any time. Fig. 6.13

A substrate is a reactant which binds to an enzyme. When a substrate or substrates binds to an enzyme, the enzyme catalyzes the conversion of the substrate to the product. Sucrase is an enzyme that binds to sucrose and breaks the disaccharide into fructose and glucose. 2. Enzymes are substrate specific

The active site of an enzymes is typically a pocket or groove on the surface of the protein into which the substrate fits. The specificity of an enzyme is due to the fit between the active site and that of the substrate. As the substrate binds, the enzyme changes shape leading to a tighter induced fit, bringing chemical groups in position to catalyze the reaction. Fig. 6.14

In most cases substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds. R groups of a few amino acids on the active site catalyze the conversion of substrate to product. 3. The active site is an enzymes catalytic center

Fig. 6.15

1) Enzymes are unaffected by the reaction and are reusable in fact, a single enzyme molecule can catalyze thousands or more reactions a second. 2)Very specific only bind one substrate 3)Dont change the reaction equilibrium 4) Metabolic enzymes can catalyze a reaction in both the forward and reverse direction. The actual direction depends on the relative concentrations of products and reactants. Enzymes catalyze reactions in the direction of equilibrium. Characteristics of Enzymes

Enzymes use a variety of mechanisms to lower activation energy and speed a reaction. The active site orients substrates in the correct orientation for the reaction. As the active site binds the substrate, it may put stress on bonds that must be broken, making it easier to reach the transition state. R groups at the active site may create a conducive microenvironment for a specific reaction. Enzymes may even bind covalently to substrates in an intermediate step before returning to normal. How Enzymes Lower Activation Energy

The three-dimensional structures of enzymes (almost all proteins) depend on environmental conditions. Changes in shape influence the reaction rate. Some conditions lead to the most active conformation and lead to optimal rate of reaction. A cells physical and chemical environment affects enzyme activity

1 ) The rate that a specific number of enzymes converts substrates to products depends in part on substrate concentrations. As add substrate, speeds up until a certain point = enzyme saturation. At low substrate concentrations, an increase in substrate speeds binding to available active sites. However, there is a limit to how fast a reaction can occur. At some substrate concentrations, the active sites on all enzymes are engaged, called enzyme saturation. 2) Enzyme concentration Things that Influence Reaction Rates

3) Temperature has a major impact on reaction rate. As temperature increases, collisions between substrates and active sites occur more frequently as molecules move faster. However, at some point thermal agitation begins to disrupt the weak bonds that stabilize the proteins active conformation and the protein denatures. Each enzyme has an optimal temperature. Fig. 6.16a

4) Because pH also influences shape and therefore reaction rate, each enzyme has an optimal pH too. This falls between pH 6 - 8 for most enzymes. However, digestive enzymes in the stomach are designed to work best at pH 2 while those in the intestine are optimal at pH 8, both matching their working environments. Fig. 6.16b

5) Ion concentration salts and other ions their charges may disrupt charged R-groups that determine shape of proteins active site 6) Many enzymes require nonprotein helpers, cofactors, for catalytic activity. They bind permanently to the enzyme or reversibly. Some inorganic cofactors include zinc, iron, and copper. Organic cofactors, coenzymes, include vitamins or molecules derived from vitamins. The manners by which cofactors assist catalysis are diverse.

7) Binding by some molecules, inhibitors, prevent enzymes from catalyzing reactions. If binding involves covalent bonds, then inhibition is often irreversible. If binding is weak, inhibition may be reversible. If the inhibitor binds to the same site as the substrate, then it blocks substrate binding via competitive inhibition. Fig. 6.17a, b

If the inhibitor binds somewhere other than the active site, it blocks substrate binding via noncompetitive inhibition. Binding by the inhibitor causes the enzyme to change shape, rendering the active site unreceptive at worst or less effective at catalyzing the reaction. Reversible inhibition of enzymes is a natural part of the regulation of metabolism. Fig. 6.17c

Lets look at a model enzyme-catalyzed reaction http://www.kscience.co.uk/animations/model.swf Setup each and then record trend: 1) control E(5), S(20), T(40), pH(7) vol(300) 2) increase enzyme (15) 3) increase substrate (40) 4) non-optimal temp (0 and 60) 5) non-optimal pH (10) Note: this particular model uses an enzyme that favors acid pH Then try E(10), S(60) and rest as for control notice how rate of reaction slows

In general More enzyme = faster reaction rate More substrate up to a certain point = faster reaction rate Too high/too low temp = slower reaction rate Too high/too low pH = slower reaction rate With inhibitors= slower reaction rate

Regulation of enzyme activity helps control metabolism Chemical chaos would result if a cells metabolic pathways were not tightly regulated A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes 2011 Pearson Education, Inc.

Allosteric Regulation of Enzymes Allosteric regulation may either inhibit or stimulate an enzymes activity Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the proteins function at another site 2011 Pearson Education, Inc.

Figure 8.19 Regulatory site (one of four) (a) Allosteric activators and inhibitors Allosteric enzyme with four subunits Active site (one of four) Active form Activator Stabilized active form Oscillation Non- functional active site Inactive form Inhibitor Stabilized inactive form Inactive form Substrate Stabilized active form (b) Cooperativity: another type of allosteric activation

Cooperativity is a form of allosteric regulation that can amplify enzyme activity One substrate molecule primes an enzyme to act on additional substrate molecules more readily Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site 2011 Pearson Education, Inc.

Identification of Allosteric Regulators Allosteric regulators are attractive drug candidates for enzyme regulation because of their specificity Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses 2011 Pearson Education, Inc.

Figure 8.20 Caspase 1 Active site Substrate SH Known active form Active form can bind substrate Allosteric binding site Allosteric inhibitor Hypothesis: allosteric inhibitor locks enzyme in inactive form Caspase 1 Active formAllosterically inhibited form Inhibitor Inactive form EXPERIMENT RESULTS Known inactive form

Feedback Inhibition In feedback inhibition, the end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed 2011 Pearson Education, Inc.

Figure 8.21 Active site available Isoleucine used up by cell Feedback inhibition Active site of enzyme 1 is no longer able to catalyze the conversion of threonine to intermediate A; pathway is switched off. Isoleucine binds to allosteric site. Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Intermediate A Intermediate B Intermediate C Intermediate D Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 End product (isoleucine)

L.O. 4.17

Essential knowledge 4.B.2: Cooperative interactions within organisms promote efficiency in the use of energy and matter. a. Organisms have areas or compartments that perform a subset of functions related to energy and matter, and these parts contribute to the whole. [See also 2.A.2, 4.A.2] 1. At the cellular level, the plasma membrane, cytoplasm and,for eukaryotes, the organelles contribute to the overall specialization and functioning of the cell. 2. Within multicellular organisms, specialization of organs contributes to the overall functioning of the organism. Exchange of gases Circulation of fluids Digestion of food Excretion of wastes 3. Interactions among cells of a population of unicellular organisms can be similar to those of multicellular organisms, and these interactions lead to increased efficiency and utilization of energy and matter. Learning Objective: LO 4.18 The student is able to use representations and models to analyze how cooperative interactions within organisms promote efficiency in the use of energy and matter. [See SP 1.4]

Enduring understanding 4.C: Naturally occurring diversity among and between components within biological systems affects interactions with the environment. Essential knowledge 4.C.1: Variation in molecular units provides cells with a wider range of functions. a. Variations within molecular classes provide cells and organisms with a wider range of functions. [See also 2.B.1, 3.A.1, 4.A.1, 4.A.2] Different types of phospholipids in cell membranes Different types of hemoglobin MHC proteins Chlorophylls Molecular diversity of antibodies in response to an antigen b. Multiple copies of alleles or genes (gene duplication) may provide new phenotypes. [See also 3.A.4, 3.C.1] 1. A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses.

2. Gene duplication creates a situation in which one copy of the gene maintains its original function, while the duplicate may evolve a new function. The antifreeze gene in fish Learning Objective: LO 4.22 The student is able to construct explanations based on evidence of how variation in molecular units provides cells with a wider range of functions. [See SP 6.2]