UNIT FOUR Chapters 6, 7, and 8. ENERGY AND METABOLISM Chapter 6.
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Transcript of UNIT FOUR Chapters 6, 7, and 8. ENERGY AND METABOLISM Chapter 6.
![Page 1: UNIT FOUR Chapters 6, 7, and 8. ENERGY AND METABOLISM Chapter 6.](https://reader030.fdocuments.in/reader030/viewer/2022020308/56649e905503460f94b94c32/html5/thumbnails/1.jpg)
UNIT FOURChapters 6, 7, and 8
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ENERGY AND METABOLISMChapter 6
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FIRST LAW OF THERMODYNAMICS
• Concerns the amount of energy in the universe
• States that energy can not be created or destroyed it can only change from one form to another
• The total amount of energy in the universe remains constant
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SECOND LAW OF THERMODYNAMICS
• Concerns the transformation of potential energy into heat or random molecular motion during an energy transaction
• Disorder, or entropy, is constantly increasing
• In general reactions spontaneously proceed to turn more ordered, less stable form into a less ordered more stable form
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FREE ENERGY
• Energy available to do work
• G = Gibbs free energy
• H = enthalpy, energy in the chemical bonds
• T = absolute temperature in Kelvin
• S = entropy, disorder of system
• G = H – TS
• ΔG = ΔH - TΔS
• Assumptions• Constant temperature• Constant pressure• Constant volume
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PREDICTING REACTIONS
Endergonic
• ΔG is positive
• Input of energy
Exergonic
• ΔG is negative
• Energy is released
• Spontaneously proceeding reactions
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ACTIVATION ENERGY
• Extra energy needed to destabilize chemical bonds
• Initiates the reaction
• Larger activation energy requirements tend to proceed more slowly
• Rate of reaction can be increased two ways• Increase the energy of the
reacting molecules• Lower activation energy
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CATALYSTS
• Process of influencing chemical bonds is called catalysis
• Catalysts affect the transition state of chemicals making them more stable and thus lowering the activation energy
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WHY RUN REACTIONS??
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ATP CYCLEMost cells don’t stockpile ATP
Cells keep a few seconds worth of ATP on hand
Constantly producing more from ADP and inorganic phosphate
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ENZYMES: BIOLOGICAL CATALYSTS
• The unique 3D shape of the enzyme is hugely important
• The enzyme creates a temporary association between the substrates
• Carbonic anhydrase example• CO2 + H2O H2CO3
• proceeds either direction, but huge activation energy• Under normal conditions perhaps 200 molecules per hour• When catalyzed 600,000 molecules can be produced per second
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ENZYME ACTIVE SITES
• Active site is a pocket for the substrate
• Once the substrate bonds the whole structure is called the enzyme-substrate complex
• The amino acid side chains of the substrate and enzyme interact to weaken bonds and thus lower activation energy
• Substrate binding changes the enzyme shape—induced fit
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MULTIENZYME COMPLEXES
• Pyruvate dehydrogenase has 60 sububnits
• Why have these?• Increase rate of reaction• Limits unwanted side reactions• All reactions can be controlled
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NONPROTEIN ENZYMES: RIBOZYMES
• Thomas R. Cech, University of Colorado, 1981
• Discovered that certain reactions seemed to be catalyzed by RNA rather than enzymes
• Extraordinary specificity
• Intramolecular catalysis—run reactions on themselves
• Intermolecular catalysis—run reactions on other molecules
• Ribosomal RNA plays a role in ribosome function, the ribosome is a ribozyme
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ENZYME SENSITIVITYConcentrations of enzyme and substrate
Temperature
pH
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TURNING ENZYMES ON AND OFF
Activator
• A substrate that binds and increases activity
Inhibitor
• A substrate that binds and decreases activity
• Many times the end product of a pathway is the inhibitor
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TYPES OF INHIBITORS
• Competitive—compete with the substrate for the active site
• Noncompetitive—bind the enzyme at a point other than the active site and cause a conformational shape change
• Many of the noncompetitive inhibitors bind at a place called the allosteric site, hence these are called allosteric inhibitors
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ENZYME COFACTORS AND COENZYMES
• Typically metal ions that are found in the active site and directly participate in the catalysis• Zinc, Molybdenum, and Manganese
• If the cofactor is a nonprotein organic molecule it is a coenzyme• B6 and B12
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WHAT’S THE POINT??
• Metabolism is totally based on biochemical pathways, proteins, and enzyme function
• Anabolism—building
• Catabolism—breaking
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FEEDBACK INHIBITIONEnd product many times binds the allosteric site
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CELLULAR RESPIRATIONChapter 7
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ENERGY HARVESTING
Heterotrophs
• Live on organic compounds
• “fed by others”
Autotrophs
• Produce organic compounds
• “self-feeders”
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CELLS OXIDIZE ORGANIC COMPOUNDS
• The reactions we will examine are oxidation reactions
• Transfer of electrons
• Dehydrogenations reactions—loss of hydrogen protons
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THREE POSSIBLE OUTCOMES
• Aerobic respiration—the final electron acceptor is oxygen
• Anaerobic respiration—the final electron acceptor is an inorganic molecule other than oxygen
• Fermentation—final electron acceptor is an organic molecule
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“BURNING” CARBS
• C6H12O6 + 6O2 6CO2 + 6H2O + energy (heat and ATP)
• Change in energy is -686 kcal/mol at STP
• In a cell the change in energy can be -720 kcal/mol
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HOW DO WE COMPLETE THE REACTION?
• Electron movement is critical
• If the electrons were given directly to O2 it would be a combustion reaction
• Why don’t we burst into flames?
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INTERMEDIATE ELECTRON CARRIER
• NAD+ is a very important electron carrier
• Made of two nucleotides• Nicotinamide monophosphate,
active portion of molecule• Adenosine monophosphate, shape
recognition portion of molecule
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STAGES OF METABOLISM
• Glycolysis
• Oxidation of pyruvate (sometimes called intermediary metabolism)
• Krebs cycle
• Electron transport chain
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WHAT BINDS THE STAGES TOGETHER?ATP
It is the molecule that drives endergonic reactions
7kcal of energy in ATP, activation energy
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AN OVERVIEW
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GLYCOLYSISLiterally means “sugar splitting”
ATP needs be fed into the reaction to get it started—priming reactions
The glucose needs to be split—cleavage
NADH and ATP are formed—oxidation
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GOTTA KEEP PROCESSES GOING
• Three things happened in glycolysis• Glucose is converted to 2 molecules of pyruvate• 2 molecules of ADP are converted to ATP using substrate level
phosphorylation• 2 molecules of NAD+ are reduced to NADH
• Problem!• Energy still locked in pyruvate molecules• Need NAD+ to continue glycolysis
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RECYCLING NADH—NEED ANOTHER ELECTRON ACCEPTOR
Aerobic Respiration
• Oxygen will ultimately accept the electrons
• NADH can go back to NAD+
Fermentation
• Organic molecules can accept the electrons
• NADH can go back to NAD+
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OXIDATION OF PYRUVATEDecarboxylation reaction
The carbon that is cleaved is converted to CO2
The remaining acetyl group attaches to coenzyme A
Acetyl Co-A is the new molecule
Pyruvate dehydrogenase—60 unit multienzyme
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KREBS CYCLE
• The 2-carbon acetyl Co-A gets converted to 2 molecules of CO2
• Oxidation reactions
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WHAT DO I DO WITH THE NADH AND FADH2?Electron transport chain and cash them in for ATP
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CHEMIOSMOSIS
• The relative difference in electrical potential cause molecules to move from high concentration to low concentration
• ATP is made from ADP and Pi in the process
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ATP SYNTHASERotary motor
F0 complex is membrane bound
F1 complex is the stalk, knob, and head
Movement cause changes in conformation, which causes enzymatic reaction
Result is oxidative phosphorylation
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MOLECULAR ACCOUNTING
• How much ATP do we end up with?
• Each NADH is worth 2.5 ATP
• Each FADH2 is worth 1.5 ATP
• Retrace the steps, how much of everything was produced?
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IS 30 OR 32 ATP GOOD?
• Each ATP is worth 7.3 kcal/mol
• One glucose is 686 kcal/mol
• (30 x 7.3)/686 = 32%
• Is that good?
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WHAT INHIBITS AEROBIC RESPIRATION?
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OXIDATION WITHOUT O2
Methanogens
• CO2 is the electron acceptor
• CO2 is reduced to CH4
• Found in soil
• Found in cows digestive system
Sulfur bacteria
• SO4 is the electron acceptor
• SO4 is reduced to H2S
• Hot springs and hydrothermal vents
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FERMENTATIONEthanol fermentation
some bacteria and yeasts
Lactic acid fermentation
humans when exercising
commercially to produce cheese and yogurt
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PROTEIN AND FAT CATBOLISM
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PHOTOSYNTHESISChapter 8
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TWO TYPES OF PHOTOSYNTHESIS
Anoxygenic
• Purple bacteria
• Green sulfur bacteria
• Green nonsulfur bacteria
• Heliobacteria
Oxygenic
• Cyanobacteria
• Seven groups of algae
• Essentially all land plants
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THREE STAGES OF PHOTOSYNTHESIS
• Capture sunlight
• Use the sunlight to make ATP and NADPH
• Use the ATP and NADPH to synthesize organic molecules from CO2
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6CO2 + 12H20 + LIGHT C6H12O6 + 6H2O + 6O2
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LEAF STRUCTUREMesophyll cells
Stoma
Chloroplast
Thylakoids
Grana
Stroma
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OVERVIEW
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PIGMENTS AND LIGHTAny molecule that absorbs light in the visible range is a pigment
Light can act as a wave or a photon, a discrete packet of energy
Short wavelength light is high energy
Long wavelength light is low energy
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PHOTOELECTRIC EFFECT
• A beam of light is able to remove electrons from molecules creating a current
• Chloroplasts are photoelectric devices
• Different molecules have different absorption spectra
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CHLOROPHYLLChlorophyll a is the main light conversion pigment in cyanobacteria and green plants
Chlorophyll b is an accessory pigment that helps chlorophyll a absorb more light
Porphyrin ring, alternating double and single bonds, magnesium in the middle
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PHOTOSYSTEMS
• Experiments on photosynthesis show that output increases linearly at low light intensities
• At high light intensity saturation is reached
• Investigators used single-celled algae Chlorella
• One molecule of O2 per 2500 chlorophyll molecules
• Chlorophyll works in clusters called photosystems
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PHOTOSYSTEM STRUCTURE
Saturation Antenna Complex
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REACTION CENTER
• Transmembrane protein-pigment complex
• Passes an electron to a neighbor
• Chlorophyll transfers electron to quinone, the primary acceptor
• Electron replaced with low energy electron from splitting of water
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LIGHT DEPENDENT REACTIONS
• Primary photoevent• Photon is captured by pigment• Electron in the pigment is excited
• Charge separation• Excitation energy transferred to
reaction center• Electron moves to acceptor
molecule• Electron transport initiated
• Electron transport• Electrons move through proteins
embedded in thylakoid membrane• Protons move across the
membrane to create a gradient• NADPH produced
• Chemiosmosis• Protons flow through ATP synthase
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BACTERIA AND SINGLE PHOTOSYSTEMS
• Cyclic photophosphorylation
• Anoxygenic process
• Absorbed electrons are not at a high enough excitation level to produce NADPH
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COUPLED, NONCYCLIC PHOTOSYSTEMS
• Photosystem I passes electrons to NADP+ to make NADPH
• Photosystem II can oxidize water to restore electrons to the whole process
• Known as noncyclic photophosphorylation
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ENHANCEMENT EFFECTThe two photosystems work in series to enhance the output of each other
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CARBON FIXATION: THE CALVIN CYCLE
• Energy to drive the cycle comes from the ATP made in the light dependent reactions
• Protons and electrons needed to build chemical bonds comes from BADPH produced in light dependent reactions
• Enzyme-catalyzed cycle similar to Krebs, but building molecules instead of breaking them down
• C3 photosynthesis because the first intermediate compound has 3 carbons
• CO2 attached to ribulose 1,5-bisphosphate (RuBP) by rubulose bisphophate carboxylase/oxygenase (rubisco)
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PHOTORESPIRATION
• Rubisco will pick up oxygen and send that into the Calvin cycle
• Why would this be a problem? What wouldn’t you make?
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FIGHTING PHOTORESPIRATION
• C3 plants fix carbon using the Calvin cycle directly
• C4 plants use and enzyme PEP carboxylase to make a four carbon compound malate—physical separation
• CAM plants open stomata at night, make oxaloacetate, store it, use the compounds during the day to run Calvin cycle—temporal separation
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C4Physical separation yields higher levels of CO2 entering the Calvin cycle
Examples: corn, crabgrass, sugarcane
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CAM PLANTSTemporal separation yields higher levels of CO2 entering the Calvin cycle
Examples: cactuses, pineapple, agave, many orchids