2 C.1 ProteinsC.1.1: Explain the 4 levels of protein structure, indicating each level’s significanceC.1.2: Outline the differences between fibrous & globular proteins, with reference to two examples of each typeC.1.3: Explain the significance of polar and non-polar amino acidsC.1.4: State six functions of proteins, giving a named example of each
3 4 levels of Protein Structure PrimaryThe unique amino acid sequenceLike the order of letters in a very long wordSlight changes in primary structure greatly affect overall conformation and function
4 4 levels of Protein Structure SecondaryCoils and folds of the primary structure as a result of hydrogen bondingElectronegative O & N attract HE.g. – alpha helix, pleated sheet
5 4 levels of Protein Structure TertiaryContortions of molecule by bonding between R groups of amino acidsHydrophobic interactions importantCore versus outer partsMay be further reinforced by disulfide bonds
6 4 levels of Protein Structure Quartnerary2 or more polypeptide chains aggregated into functional unitCollagen – 3 proteins together, Hemoglobin 4 proteins togetherShape of subunits together specifies function
8 Fibrous vs. Globular Proteins Functional Quaternary proteins are either …Fibrous – long ropelike structuresCollagen – 40% of protein in human body, from skin, bone, tendons & ligamentsKeratin – hair, horns, skinGlobular –sphericalHemoglobin – oxygen binding protein in bloodLysozyme – immune enzyme in saliva, tears, sweat that targets bacterial surface proteins
9 Polar vs Nonpolar Polarity of amino acids influences protein behavior Membrane position (polar portions in or out of cells, nonpolar portions in membrane)Hydrophobic channel creationSpecificity of enzyme active site – complements properties of the substrate
10 Important Proteins Protein Function Keratin Casein Hemoglobin Actin InsulinLysozyme
11 Important Proteins Protein Function Keratin Support in hair, horns and feathersCaseinStorage of AA for babies in milkHemoglobinTransport of O2 by bloodActinMovement of muscle fibersInsulinHormone regulates sugar in bloodLysozymeDefense against foreign substances
12 C.2 EnzymesC.2.1: State that metabolic pathways consist of chains and cycles of enzyme catalyzed reactionsC.2.2: Describe the induced fit modelC.2.3: Explain that enzymes lower the activation energy of the chemical reactions which they catalyze.C.2.4: Explain the difference between competitive and non-competitive inhibition with reference to one example of each.C.2.5: Explain the role of allostery in the control of metabolic pathways by end-product inhibition
13 Chemical Reaction Types Exergonic reaction ENERGY OUTWARD: proceeds with the net release of free energyEndergonic reaction ENERGY INWARD: proceeds with the net absorbtion of energy from the surroundings
14 MetabolismMetabolism = The totality of an organisms chemical processes.Managing the material and energy resources of the cell.Metabolic Pathways consist of chains and cycles of enzyme catalyzed reactionsCatabolic pathways: break down molecules and release energyAnabolic pathways: build complex molecules and absorb energy
18 Models of enzyme function LOCK & KEY MODELEach enzyme fits exactly one substrateComplementary shapes like a lock and a keyINDUCED FIT MODELExtension of Lock and key modelSome enzymes can bond multiple substratesInteraction between enzyme and substrate induces change to fit
20 The induced fit model accounts for the broad specificity of some enzymes
21 Competitive vs. non-competitve Competitive – inhibiting molecule is structurally similar to substrate, binds to active site, prevents substrate bondingInhibition of butanedioic acid dehydrogenase by propanedoic acid in the Krebs cycleInhibition of folic acid synthesis in bacteria by sulfonamide protosil (an antibiotic)Non-competitive – inhibiting molecule binds to enzyme (not at A.S.) causing conformational change to active siteHg+2, Ag+, Cu+, inhibition of cytochrome oxidase by binding to –SH groups and breaking -S-S- linkages
23 Allosteric Regulation Form of non-competitive inhibitionInhibition is a natural mechanism of cell metabolic controlShape of allosteric enzymes can be altered by binding of end products at the allosteric siteMetabolites or end products can serve in negative feedback by binding to allosteric site and decreasing enzyme functionATP inhibition of phosphofructokinase in glycolysis
25 Allosteric Reactionsare and example offeedback inhibition
26 C.3 RespirationC.3.1: State that oxidation involves the loss of electrons from an element whereas reduction involves the gain of electrons, and that oxidation frequently involves gaining oxygen or losing hydrogen, while reduction involves losing oxygen or gaining hydrogenC.3.2: Outline the process of glycolysis including phosphorylation, lysis, oxidation, and ATP formationC.3.3: Draw the structure of a mitochondrion as seen in electron micrographs.C.3.4: Explain aerobic respiration including oxidative decarboxylation of pyruvate, the krebs cycle, NADH+ + H+, the electron transport chain, and the role of oxygen
27 C.3 RespirationC.3.5: Explain oxidative phosphorylation in terms of chemiosmosisC.3.6: Explain the relationship between the structure of the mitochondrion and its function.C.3.7: Describe the central role of acetyl CoA in carbohydrate and fat metabolismC.3.8: Analyze data relating to respiration
28 Overall Process Organic compounds + Oxygen Carbon dioxide + Water + EnergyFor convenience we usually start with glucose, but can use lipids, proteins and other carbohydrates.C6H12O6 + 6 O CO2 + H2O + EnergyGlucose is oxidized and oxygen is reduced
29 Oxidation-Reduction Always coupled Chemical reactions which involve a partial or complete transfer of electrons from one reactant to another.Oxidation: partial or complete loss of e- from a substance; e- donor is the reducing agent.Reduction: partial or complete addition of e- to another substance; e- acceptor is an oxidizing agent.
30 Comparison of Oxidation and Reduction Addition of oxygen atomsRemoval of H atomsLoss of e- from a substanceReductionRemoval of oxygen atomsAddition of H atomsAddition of e- to a substance
32 3. Cell Respiration: a)Glycolysis Catalyzed by enzymes in the cytoplasmGlucose is partially oxidized and a small amount of ATP is producedAccomplished without the use of oxygenIs part of both aerobic and anaerobic respiration
34 Energy investment phase: 2 phosphate groups from ATP are added to a molecule of glucose (hexose sugar) to form a hexose biphosphate.Lysis: The hexose biphosphate is split to form two molecules of triose phosphate.Oxidation: 2 molecules of NAD+ are reduced to 2NADH + 2H+; so the triose phosphate is oxidized. The energy is used to add another phosphate group to each triose.NADH can enter the electron transport chain in the mitochondria and be used to produce more ATP in the process called oxidative phosphorylation4. ATP Formation: Two phosphate groups are removed from the two trioses and passed to ADP to form ATP.So 4 ATPs are generated for a net gain of 2 ATPs.ATP is produced by a process called substrate-level phosphorylation because an enzyme transfers a phosphate group from a substrate (organic molecule generated by the sequential breakdown of glucose) to ADP
35 The End of GlycolysisA 6 Carbon compound has been turned into 2 3 Carbon compounds called pyruvate (A.K.A. oxopropanoate).Glucose has been oxidizedNet gain 2 ATP, 2NADH + 2H+ATP made through substrate level phosphorlyationGlycolysis also yields 2 water molecules for each glucose.
36 Aerobic respiration Each pyruvate must be decarboxylated (CO2 removed) Remaining 2 carbon molecule (acetyl group) reacts with reduced coenzyme ADuring in the process NADH + H+ are formed
38 Summary of One Turn of the Krebs Cycle 1. Acetyl CoA (2C) enters the cycle & joins a 4C molecule.2. In a series of steps, the remaining H and high energy electrons are removed from the Acetyl CoA.3. Three NAD+ are converted into 3 NADH & 3H+.4. One FAD is converted into 1 FADH2.5. One ATP is made (by substrate phosphorylation).6. Two CO2 are released.7. At the end of the cycle, nothing remains of the original glucose molecule
41 Krebs cycle results per glucose 2 molecules of pyruvate are oxidized2 ATPs by substrate level phosphorylation6 NADH and 2 FADH2Starting material is regeneratedElectron transport chain couples electron flow down the chain to ATP synthesis.
42 ETC / Oxidative Phosphorlyation The purpose of the Electron Transport Chain is to receive the high energy electrons carried by the coenzymes NADH &FADH2 and use the energy from these electrons to pump protons out of the matrix. A high concentration of protons results. As the protons diffuse back to the matrix, their energy is used by the ATP synthase to create 32 ATP.Oxidative phosphorylation (electron transport) - The creation of ATP via chemiosmosis as a result of electron transport.
43 Electron transport a) Occurs at cristae (Inner membranes) b) NADH & FADH2 deliver H+ and e- to cristae.c) Electrons "transport" along cristae through electron acceptors, provide energy to pump H+ from matrix to outer compartment.d) Concentration of H+ is now higher in outer compartment. H+ pass through ATP synthetases in cristae back to matrix. 32 ATP are made. This is known as chemiosmosis.e) Last step involves H+ & e- added to oxygen. This frees NAD+ to return to glycolysis & Krebs Cycle to pick up more H+ & e-.
47 Chemiosmosis is the process where protons diffuse from the outer compartment (high concentration) through ATP Synthase in the Cristae to the Matrix (low H+ Concentration). The energy in the protons as they pass is used by ATP synthase to create 32 ATP.
48 XIV: Mitochondria and Chloroplasts Main energy transformers of cells; transduce energy acquired from the surroundings into forms usable for cellular work.BOTH:a) enclosed by double membranes which are NOT part of endomembrane systemb) contain ribosomes and some DNA that programs a small portion of their own protein synthesisc) are semiautonomous organelles that grow and reproduce within the cell (see Ch. 26 for a discussion of the origins of eukaryotic cells from symbiotic consortiums of prokaryotic cells; Dr. Lynn Margulis’ endosymbiotic theory.
49 MitochondriaSites of cellular respiration (catabolic oxygen-requiring process that uses energy extracted from organic macromolecules to produce ATP).Found in nearly all eukaryotic cells; number directly correlates with cell’s metabolic activity.]1 um in diameter; 1-10 um in lengthCan move, change shape and divide
51 Mitochondria Structure BE ABLE TO DRAW AND LABELEnclosed by two membranes: smooth outer membrane and convoluted inner membrane which contains embedded enzymes involved in cellular respiration.Infoldings or cristae increase surface areaMembranes divide mitochondrion into 2 internal compartments:a) intermembrane space: same solute composition of cytosol.b) mitochondrial matrix: contains enzymes that catalyze many steps of cell respiration (Krebs cycle)
52 The Role of acetyl CoAAcetyl CoA is an intermediate in carbohydrate metabolismIn lipid metabolism, the oxidation of fatty acid chains results in the formation of carbon fragments with 2C each2 carbon fragments are acetyl fragmentsThey pass into Krebs cycle
53 Proteins and fats in cell respiration: Central role of Acetyl CoA
54 C.4 PhotosynthesisC.4.1: Draw the structure of a chloroplast as seen in electron micrographsC.4.2: State that photosynthesis consists of light-dependent and light-independent reactions.C.4.3: Explain the light dependent reactionsC.4.4: Explain phosphorylation in terms of chemiosmosisC.4.5: Explain the light independent reactions
55 C.4 PhotosynthesisC.4.6: Explain the relationship between the structure of the chloroplast and its functionC.4.7: Draw the action spectrum for photosynthesisC.4.8: Explain the relationship between the action spectrum and the absorption spectrum of photosynthetic pigments in green plantsC.4.9: Explain the concept of limiting factors with reference to light intensity, temperature and concentration of carbondioxide.C.4.10: Analyze data relating to photosynthesis
57 B. Chloroplasts BE ABLE TO DRAW AND LABEL One of a group of plant and algal membrane-bound organellesChloroplasts divided into 3 functional compartments by a system of membranes.1. Intermembrane space: space between the double chloroplast membrane.2. Stroma: viscous fluid outside the grana (stacks of thylakoids); light-independent chemical reactions take place here. Carbon dioxide converted to sugar.3. Thylakoids: flattened membranous sacs inside chloroplast; chlorophyll is found in membranes; function in the light-dependent chemical reactions.4. Thylakoid space: space inside the thylakoids.
58 Absorbance Peaks in: Red & Blue Minimum in Green Figure Evidence that chloroplast pigments participate in photosynthesis: absorption and action spectra for photosynthesis in an algaAbsorbancePeaks in:Red & BlueMinimum inGreen
59 Photosynthesis consists of the light dependent and light independent reactions
60 2 step process Light Dependent Reactions = photo Light Independent Reactions (Calvin cycle) = synthesisLight dependent reactions are in the thylakoid, light independent reactions in the stromaTransforming light energy into chemical energy of ATP and NADPHCreation of Sugars from inorganic compounds
61 PhotosystemsIn thylakoid membrane chlorophyll organized with other molecules in photosystems“Antenna array” of Chlor. A, B, & carotenoid pigments, clustered around a reaction centerReaction center is a single Chlorophyl A associated with the “primary electron acceptor” (PEA)Chlorophyl A passes electrons to the PEAPEA traps excited electrons before they fall back to ground state
63 Photosystems2 types of photosystems in thylakoid membrane cooperate in light reactionsCalled Photosystem I & II – different PEAPhotosystem I – P700 best absorbance at 700 nm wavelength (red)Photosystem II – P680 also in redIdentical chlorophyll but different protein association
64 Electron flow Light drives synthesis of ATP and NADPH Energy transformation based on flow of electronsTwo routes of electron flowNoncyclic electron Flow = predominates during light reactions – ejected electrons don’t cycle back to ground stateCyclic electron Flow = uses Photosystem I not PS II – no production of NADPH or O2
65 Figure How noncyclic electron flow during the light reactions generates ATP and NADPH (Layer 5)
66 Light dependent reactions use solar power to produce ATP and NADPH to fuel sugar production in the Calvin cycle
67 Cyclic electron FlowCyclic electron Flow = uses Photosystem I not PS II – no production of NADPH or O2Short circuit back into electron transport chainDoes produce ATP cyclic phosphorylationLight independent reaction consumes more ATP than NADPH, Cyclic electron flow makes up the difference in ATP required
69 Review of chemiosmosis Mechanism of generating ATPElectron transport chain pumps protons across the membrane while electrons are shuttled through different carriersProtons pumped to the inside of thylakoidsProtons accumulate, pH and charge increase move out to stroma through channelsMovement through channels in ATP synthase drives production of ATP
70 Figure 10.15 Comparison of chemiosmosis in mitochondria and chloroplasts
71 Figure 10.16 The light reactions and chemiosmosis: the organization of the thylakoid membrane
72 The Light Independent Reactions: Synthesis of sugars Takes place in the StromaCarbon enters as CO2 and leaves as sugarATP is the energy sourceNADPH provides reducing power for adding high energy electronsDirect product of Calvin cycle is glyceraldehyde-3-phosphate (G3P)3 cycles to make this productActually fixing three molecules of CO2
76 Limiting FactorsCertain factors in the environment can effect how photosynthesis occursMain limiting factors are Temperature, Light intensity, and CO2 concentrationOther factors include nutrient availability, such as nitrogen, phosphorous and ironDifferent factors limit plant growth in different areas
77 Effects of Light Intensity & Temperature on Photosynthesis
78 As light intensity increases the rate of photosynthesis increases and Plateau once photosynthetic machinery is operating at peak capacityPhotoinhibition: sunburn for plants, occurs when too much light overloads photosynthetic machineryFor a given light intensity, Higher temperature Increased rate of photosynthesis
79 A = at low light intensities light is a limiting factor and temperature has no effect B = at higher light intensities, temperature is a limiting factor, warmer higher rate of photosynthesis
80 Effects of Carbon Dioxide on Photosynthetic Rate