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Chapter 6: Metabolism and Enzymes
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The sum total of an organism’s chemical reactions is called metabolism. The chemistry of life is organized into Metabolic Pathways
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Catabolic pathways release energy by breaking down complex molecules to simpler compounds Metabolic Pathways are made of: ATP
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Anabolic pathways consume energy to build complicated molecules from simpler compounds. Metabolic Pathways are made of: ATP
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Catabolic Pathways and Anabolic Pathways act in tandem Metabolic Pathways :
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Fig. 6.1 The inset shows the first two steps in the catabolic pathway that breaks down glucose.
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Chemical reactions can be classified as either exergonic or endergonic based on energy. An exergonic reaction proceeds with a net release of energy. Fig. 6.6a C 6 H 12 O 6 + 6O 2 -> 6CO 2 + 6H 2 O CATABOLIC PATHWAY Free energy of this reaction is negative ( G)
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An endergonic reaction is one that absorbs energy from its surroundings. –Endergonic reactions store energy ANABOLIC PATHWAY 6CO 2 + 6H 2 O -> C 6 H 12 O 6 + 6O 2 Free energy of this reaction is positive ( G)
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Exergonic Reactions and Endergonic Reactions are Coupled using ATP ATP (adenosine triphosphate) is a type of nucleotide ATP has the nitrogenous base adenine, the sugar ribose, and a chain of 3 phosphate groups ATP: Adenine Triphosphate
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Bonds between PO 4 groups can be broken to release energy This is a hydrolysis reaction ATP: Adenosine Triphosphate
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PO 4 released is tagged to a reactant Reactant is phosphorylated and now able to undergo the chemical reaction ATP can be regenerated ATP: High NRG PO 4 Bond Transfer
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Energy Facts Energy is used by the cell for: Mechanical Work (movement), Transport (of macromolecules into and out of cells), and Chemical Work (drive endergonic reactions in anabolic pathways) Plants transform light to chemical energy; they do not produce energy.
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Activation energy: Energy needed by reactants to make the products (NRG Barrier) Activation Energy is used to make transition state complexes whose bonds are strained. Then, products form from these transition state complxes by breaking and making new bonds.
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Activation energy: Enzymes lower the Activation Energy needed for a reaction Enzymes drive most chemical reactions in the body
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Activation energy: Enzymes lower the Activation Energy needed for a reaction Enzymes drive most chemical reactions in the body Lactose ----------------------------- > Glucose + Galactose Lactase (lactaid pills)
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ENZYMES Enzyme discovery to benefit homeland security Enzymes are Proteins (names end in ase)
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Enzymes:Are Substrate Specific Enzyme names have 2 parts: First part – which substrate it acts on/what product is formed Second part – what it does Malate Dehydrogenase Citrate synthase
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Enzymes:Are Substrate Specific 1. Oxidoreductases: Oxidation – reduction; (dehydrogenase, reductase, oxidase) 2. Transferases: Transfer functional groups; (transferase; phosphorylase) 3. Hydrolases: hydrolytic cleavage of C-O, C-N, C-C bonds (phosphatase; protease) 4. Lyases – cleave bonds (decarboxylase) 5. Isomerases - geometric or structural changes within a molecule (epimerase or isomerase) 6. Ligases - joining together of two molecules using ATP (synthetase; ligase) Skip details
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Enzymes: Active Site Enzymes act on Substrates (reactants) Active Site: is a pocket or groove on the surface of the enzyme into which the substrate fits (often active siteis a nonpolar environment) Substrate binds to active site by hydrogen bonding/weak forces to form an enzyme- substrate complex
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Enzymes: Active Sites Active Site binding helps the reaction by: Substrates are placed in the correct orientation for the reaction. Puts 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.
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Induced Fit Model For Enzyme Action: Substrate binding to active site causes a change in enzyme shape around active site The active site is molded into a tighter fit around the substrates Substrates are held in close contact; E A is lowered; products are formed and released Enzyme regains original shape; it is reused Enzymes: How do they work?
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A single molecule of enzyme can catalyze 1000’s of reactions per second
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Enzymes can catalyze both forward and backward reactions Direction of a reaction depends on accumulation/removal of product Enzymes: How do they work? Malate Dehydrogenase
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Substrate Concentration Temperature pH Cofactors Coenzymes Competitive Inhibitors Non-competitiveInhibitor Allosteric Regulation and Co-operativity Feedback Inhibition Enzymes: Factors affecting their function (nine of them! - know these)
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Enzymes: Factors affecting their function The environment of the cell affects the structure of enzymes (proteins) at the secondary/tertiary/quarternary levels The effect is perceived as a change in reaction rate (rate of formation of product)
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1) Substrate Concentration Enzymes: Factors affecting their function Low [S]: an increase in substrate speeds binding to available active sites ([E] >>>> [S]) High [S]: Enzyme is SATURATED (all active sites are occupied) (([S] >>>> [E]) At High [S]: To increase reaction rate, increase [E]
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2) Temperature Enzymes: Factors affecting their function Low Temp: insufficient collisions between active site and substrates High Temp: Enzyme can denature and the folding can unravel, damaging functionality Optimal temp: Human enzymes – 37.5 o c
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3) pH – determines state of acidic/basic functional ‘R’ groups on amino acids, and hydrogen bonding Enzymes: Factors affecting their function Low/High pH: changes the above interactions and alters folding of enzyme protein/active site Optimal pH: Human enzymes – pH 6-8
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4) Cofactors –inorganic helpers. B ind permanently or reversibly to enzyme. What’s the biochemical reason? Examples: zinc, iron, and copper. Enzymes: Factors affecting their function Photosystem I multienzyme complexes
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5) Coenzymes – organic helpers (same idea as cofactors). Bind reversibly to enzymes - can be re-used. Examples:vitamins. Enzymes: Factors affecting their function
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Inhibitors: 6) Competitive Inhibitors: Active Site Directed Inhibitors - bind to active site and inhibit binding of substrate Enzymes: Factors affecting their function
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Inhibitors: 7) NonCompetitive Inhibitors: Bind to a different site on enzyme called Allosteric Site - diminishes bindng of substrate to active site Enzymes: Factors affecting their function Minimata Bay – Japan (Mercury Poisoning) Nerve Gas Used on Kurds by Iraq - 1993
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8) Allosteric Regulation: Enzyme has several subunits - hangs around in “active” or “inactive” state Effect of binding of regulator (inhibitor/activator) to one subunit is translated to other subunits (cooperativity) Enzymes: Factors affecting their function
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9) Feedback Inhibition - a metabolic pathway is turned off by its end product. End product becomes a inhibitor for a very early step enzyme. Very common! Enzymes: Factors affecting their function
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Rate of a Reaction Reaction Rate- the change in the concentration of a reactant or product with time. (M/s) General equation for a reaction: –A → B –Reactant → Product In order to monitor a reaction’s speed or rate, we can look at one of two things: –Decrease in [ reactant ] –Increase in [ product ] –Can be represented as: rate = - Δ [A] / Δ tor rate = Δ [B] / Δ t
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Rate of a Reaction
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Rate Calculations How do we calculate the rate of a reaction? –We first need this information: Time (s) [reactant] Or [product] [ ] means concentration Decrease in [reactant]/time OR Increase in [product]/time Calculate the slope of your graph - X axis - time; Y axis - you choose (Y2-Y1)/(x2-x1)
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Reaction rate calculation Initial Stage of Reaction: [Substrate] is: [Enzyme] is: Number of Active Sites available to catalyze this reaction is: Calculation of Initial Reaction rate: R i =( y 2 -y 1 )/(x 2 -x 1 ) => Rise/Run
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Reaction rate calculation Final Stage of Reaction: [Substrate] is: [Enzyme] is: Number of Active Sites available to catalyze this reaction is: Calculation of Final Reaction rate: R f =( y 2 -y 1 )/(x 2 -x 1 ) = Maximum Velocity: Vmax
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