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Lecture 4: Energetics and Enzymatics
Bio 219:Dr. Adam Ross
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Energy
• Most (essentially all) energy on the planet comes from the sun
• Plants harness this energy with chlorophyll
• Animals get energy from plants or other animals• Some animals also use photosynthesis (algae, some nematodes)
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First Law of Thermodynamics
• Energy can never be created or destroyed, only transfered
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Second Law of Thermodynamics
• Isolated systems will tend toward disorder• Earth is not an isolated system
• Organisms are not isolated systems
• Isolated systems are unable to exchange energy or matter with surrounding systems/ environments
• Energy can be used to fight entropy (disorder)
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Gibbs free energy
• In biological systems energy and entropy change together
• Desribed by Gibbs free energy (G) equation:
• If ΔG is negative, reaction can occur spontaneously
• If ΔG is positive, the reaction is non spontaneous
𝑮 = 𝑯 − 𝑻𝑺𝐻 = 𝑒𝑛𝑡ℎ𝑎𝑙𝑝𝑦 𝑗𝑜𝑢𝑙𝑒𝑠
𝑇 = 𝑇𝑒𝑚𝑝𝑒𝑟𝑎𝑡𝑢𝑟𝑒 𝑘𝑒𝑙𝑣𝑖𝑛
𝑆 = 𝑒𝑛𝑡𝑟𝑜𝑝𝑦 ( 𝑗𝑜𝑢𝑙𝑒𝑘𝑒𝑙𝑣𝑖𝑛)
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Implications of Gibbs
• Favorable (negative ΔG) reactions can be used to give energy to unfavorable reactions (positive ΔG )
• Allows for coupling of reactions inside the cell.
• Decreases energy wasting in cellular processes.
• Just because a reaction is energetically favorable, does not mean it will happen rapidly, sometimes activation energy is very high• Enzymes can lower activation energy
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Metabolism
• Sum of all the chemical reactions that take place in the body• Some consume energy (endergonic)
• Some produce energy (exergonic)
• Some break things down (catabolic)
• Some build things up (anabolic)
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Major classes of metabolic reactions
• Dehyrdation/ Hydrolysis• Dehydration synthesis/ Hydrolytic cleavage
• Phosphorylation/ de-phosphorylation• Kinase/ phosphatase
• Oxidation/ Reduction (Redox)• Addition (reduction) or subtraction (oxidation) of electrons
• Oxidation Is Loss Reduction Is Gain (OIL RIG)
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Hydrolysis
• Water added to break bonds between monomers
• Catabolic reaction
• A–B + H2O → A–OH + H–B• Sucrose + H2O = glucose + fructose
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Dehydration (condensation)
• Removal of water to join monomers
• Anabolic reaction
• A–OH + H–B → A–B + H2O • Peptide bond formation, sugars
• AA1 + AA2 → AA1—AA2 + H2O
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Phosphorylation and Dephosphorylation
• Phosphorylation = addition of phosphate group
• Dephosphorylation = removal of phosphate group
• C + Pi → C–P + H2O
• ATP synthesis; • ADP + Pi + energy → ATP + H2O
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Redox• Oxidation
• Major energy source of cells: Oxidation of sugars, fatty acids and amino acids
• Redox reactions are coupled• For every oxidation there is a reduction
• Redox rxns usually involve transfer of H atoms not H+ ions
• coenzymes act as temporary carriers of H atoms and their electrons
NAD+ + 2 H → NADH + H+ FAD + 2 H → FADH2
oxidized reduced oxidized reduced
• - oxygen is the ultimate electron acceptor in cellular respiration: ½ O2 + 2 H → H2O
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Energy Metabolism
• Cells use chemical energy to drive biological processes:• Movement, synthesis, transport
• Energy is released in exergonic reactions• Convert high energy to low energy molecules
• Oxidation of glucose C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy
(high energy) (lower energy)
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Enzymes
• Biochemical catalysts• Speed up reactions by lowering activation energy
• Most are proteins
• Name of enzyme denotes function (usually end in –ase)• Phosphatase removes phosphate
• Kinase adds phosphate
• Helicase unwinds DNA
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Basic enzymatic reaction
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Properties of enzymes
• Substrate specificity:• Enzymes only bind specific substrates
• Specific fit: enzyme active site fit together in native state
• Induced fit: enzyme pulls on chemical bonds of substrate to change shape
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Properties of enzymes
• Enzymes are conserved after the reaction• The enzymatic protein is not used during the reaction, and is not altered in
such a way that it cannot perform the reaction again and again.
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Properties of enzymes
• Sensitive to temperature, pH, and salt concentration• These things affect the tertiary structure of proteins
• Cause change in shape of enzyme and substrate which decreases substrate binding to active site
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Saturation kinetics
• Reaction rate is non-linear• Depends on substrate [S] concentration
• Low [S]- low reaction rate, will increase with additional [S]
• High [S]- high reaction rate, reaction will not increase as much with additional [S]
• Saturated [S]- highest reaction rate, additional [S] will not increase reaction rate, all active sites are occupied by substrate.
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Michaelis-Menten kinetics
• Named after German biochemist Leonor Michaelis and Canadian physician Maud Menten
• Relates reaction rate (v) to substrate concentration [S]
•𝑣 = 𝑑[𝑃]𝑑𝑡 = 𝑉𝑚𝑎𝑥[𝑆]
𝐾𝑚+[𝑆]
• Vmax = maximum rate allowed by system (number of active sites)
• Km = Michaelis constant; [S] that gives ½ Vmax
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Michaelis-Menten
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So what?
• Enzyme kinetics is important-• Helps explain how enzymes work (what they do and how fast they do it)
• Helps predict how enzymes behave in living organisms
• Km and Vmax are attempts at how enzymes work together to control metabolism
• Can incorporate kinetic data with gene expression data
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Intermediates
• Often times reactions are not as simple as A+B=C
• Intermediates can be used and steps between original substrate and desired product• Glycolysis and most metabolic pathways behave this way.
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Regulation of enzyme activity
• Covalent regulation• Regulates enzyme activity by covalent addition of a chemical group
• Usually involves addition of phosphate group which activates enzyme
• Protein kinases are a class of enzymes that phosphorylate proteins in specific spots (Ser/Thr, Tyr)
• Changes shape of enzyme, which allows active site to interact with substrate
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Allosteric regulation
• Regulation by a non-covalent binding of a modulator to a regulatory site of the enzyme• Can be inhibition or activation
• Depends on concentration of substrate(s) and modulator(s)
• Homotropic• Substrate is also regulatory molecule
• Heterotropic• Another molecule (not substrate) is regulatory molecule
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Allosteric regulation
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Allosteric kinetics
Courtesy: Tim Vickers, Wikimedia commons
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Competitive inhibition
• Enzymes can be inhibited by non-substrates binding to the active site
Courtesy: Jeremy Crimson Mann via Wikimedia commons
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Feedback inhibition
• Product of reaction or pathway can inhibit an enzyme in an earlier step via allostery,