Chapter 8: Energy and Metabolism

Chapter 8: Energy and Metabolism Why do organisms need energy? How do organisms manage their energy needs? Defining terms and issues: energy and thermodynamics metabolic reactions and energy transfers Harvesting and using energy ATP is the main energy currency in cells energy harvesting (redox reactions) Regulating reactions: Enzymes

Discuss energy conversions and the 1st and 2nd law of thermodynamics Be sure to use the terms work potential energy kinetic energy entropy What are Joules (J) and calories (cal)?

Energy and Thermodynamics energy for work: change in state or motion of matter

Energy and Thermodynamics energy for work: change in state or motion of matter expressed in Joules or calories 1 kcal = 4184 kj

Energy and Thermodynamics energy for work: change in state or motion of matter expressed in Joules or calories 1 kcal = 4184 kj energy conversion: energy form change potential / kinetic

Energy and Thermodynamics potential energy (capacity to do work)

Energy and Thermodynamics potential energy (capacity to do work) kinetic energy (energy of motion, actively performing work) chemical bonds: potential energy work is required for the processes of life

Discuss energy conversions and the 1st and 2nd law of thermodynamics Be sure to use the terms work potential energy kinetic energy entropy What are Joules (J) and calories (cal)?

Energy and Thermodynamics Laws of thermodynamics describe the constraints on energy usage

The laws of thermodynamics are sometimes stated as: In energy conversions, You can t win, and you can t break even Explain

Laws of Thermodynamics First law: the total amount of energy (+ matter) in a closed system remains constant

Laws of Thermodynamics First law: the total amount of energy (+ matter) in a closed system remains constant also called conservation of energy

Laws of Thermodynamics First law: the total amount of energy (+ matter) in a closed system remains constant also called conservation of energy note: the universe is a closed system living things are open systems

Laws of Thermodynamics Second law: in every energy conversion some energy is converted to heat energy heat energy is lost to the surroundings heat energy cannot be used for work

Laws of Thermodynamics Second law: in every energy conversion some energy is converted to heat energy heat energy is lost to the surroundings heat energy cannot be used for work energy converted to heat in the surroundings increases entropy (spreading of energy)

Laws of Thermodynamics Second law: Upshot: no energy conversion is 100% efficient You can t break even Just to maintain their current state, organisms must get a constant influx of energy because of energy lost in conversions

The laws of thermodynamics are sometimes stated as: In energy conversions, You can t win, and you can t break even Explain

Differentiate between: anabolism and catabolism exergonic and endergonic reactions

Metabolism: anabolism + catabolism metabolism divided into anabolism (anabolic reactions) anabolic reactions are processes that build complex molecules from simpler ones

Metabolism: anabolism + catabolism metabolism divided into anabolism (anabolic reactions) anabolic reactions are processes that build complex molecules from simpler ones catabolism (catabolic reactions) catabolic reactions are processes the break down complex molecules into simpler ones

Differentiate between: anabolism and catabolism exergonic and endergonic reactions

Chemical Reactions and Free Energy Chemical reactions involve changes in chemical bonds

Chemical Reactions and Free Energy Chemical reactions involve changes in chemical bonds changes in substance concentrations

Chemical Reactions and Free Energy Chemical reactions involve changes in chemical bonds changes in substance concentrations changes in free energy free energy = energy available to do work in a chemical reaction (such as: create a chemical bond) free energy changes depend on bond energies and concentrations of reactants and products bond energy = energy required to break a bond; value depends on the bond

Chemical Reactions and Free Energy left undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and products is correct forward and reverse reaction rates are equal; concentrations remain constant

Chemical Reactions and Free Energy exergonic reactions the products have less free energy than reactants the difference in energy is released and is available to do work

Chemical Reactions and Free Energy exergonic reactions the products have less free energy than reactants the difference in energy is released and is available to do work exergonic reactions are thermodynamically favored; thus, they are spontaneous, but not necessarily fast (more on activation energy later)

Chemical Reactions and Free Energy catabolic reactions are usually exergonic ATP + H 2 O ADP + P i is highly exergonic

Chemical Reactions and Free Energy endergonic reactions the products have more free energy than the reactants the difference in free energy must be supplied (stored in chemical bonds)

Chemical Reactions and Free Energy endergonic reactions the products have more free energy than the reactants the difference in free energy must be supplied (stored in chemical bonds) endergonic reactions are not thermodynamically favored, so they are not spontaneous

Chemical Reactions and Free Energy

Chemical Reactions and Free Energy How to get energy for an endergonic reaction?

Chemical Reactions and Free Energy How to get energy for an endergonic reaction? couple with an exergonic one!

Chemical Reactions and Free Energy How to get energy for an endergonic reaction? couple with an exergonic one! together, the coupled reactions must have a net exergonic nature

Chemical Reactions and Free Energy How to get energy for an endergonic reaction? couple with an exergonic one! together, the coupled reactions must have a net exergonic nature reaction coupling requires that the reactions share a common intermediate(s)

Chemical Reactions and Free Energy EXAMPLE: A B (exergonic) C D (endergonic)

Chemical Reactions and Free Energy EXAMPLE: A B (exergonic) C D (endergonic) Coupled: A + C B + D (overall exergonic)

Chemical Reactions and Free Energy EXAMPLE: A B (exergonic) C D (endergonic) Coupled: A + C B + D (overall exergonic) Actually: A + C I B + D

Chemical Reactions and Free Energy EXAMPLE: A B (exergonic) C D (endergonic) Coupled: A + C B + D (overall exergonic) Actually: A + C I B + D typically, the exergonic reaction in the couple is ATP + H 2 O ADP + P i anabolic reactions are usually endergonic

Why is ATP so darned important? What is a phosphorylated intermediate? How much ATP is in a cell at any given time? Why must cells keep a high ATP/ADP ratio?

ATP is the main energy currency in cells One way that organisms manage their energy needs is to use ATP as a ready energy source for many reactions

ATP is the main energy currency in cells ATP nucleotide with adenine base, ribose sugar, and a chain of 3 phosphate groups

ATP is the main energy currency in cells last two phosphate groups are joined to the chain by unstable bonds; breaking these bonds is relatively easy and releases energy; thus:

ATP is the main energy currency in cells hydrolysis of ATP to ADP and inorganic phosphate (P i ) releases energy ATP + H 2 O ADP + P i

ATP is the main energy currency in cells hydrolysis of ATP to ADP and inorganic phosphate (P i ) releases energy ATP + H 2 O ADP + P i the amount of energy released depends in part on concentrations of reactants and products is generally ~30 kj/mol

ATP is the main energy currency in cells Intermediates when ATP hydrolysis is coupled to a reaction to provide energy

ATP is the main energy currency in cells Intermediates when ATP hydrolysis is coupled to a reaction to provide energy often phosphorylated compounds glucose glucose-6-phosphate

ATP is the main energy currency in cells Intermediates when ATP hydrolysis is coupled to a reaction to provide energy often phosphorylated compounds the inorganic phosphate is transferred onto another compound rather than being immediately released glucose glucose-6-phosphate

ATP is the main energy currency in cells EXAMPLE of a coupled reaction: glucose + fructose sucrose + H 2 O (endergonic; requires ~27 kj/mol) ATP + H 2 O ADP + P i (exergonic; provides ~30 kj/mol) coupled: glucose + fructose + ATP + H 2 O sucrose + H 2 O + ADP + P i simplified: glucose + fructose + ATP sucrose +ADP + P i with intermediates: glucose + fructose + ATP + H 2 O glucose-p + fructose + ADP sucrose + H 2 O + ADP + P i (net exergonic, releases ~3 kj/mol)

ATP is the main energy currency in cells EXAMPLE of a coupled reaction: glucose + fructose sucrose + H 2 O (endergonic; requires ~27 kj/mol) ATP + H 2 O ADP + P i (exergonic; provides ~30 kj/mol)

ATP is the main energy currency in cells Thus, energy transfer in cellular reactions is often accomplished through transfer of a phosphate group from ATP

ATP is the main energy currency in cells Making ATP involves an endergonic condensation reaction reverse of an exergonic reaction is always endergonic ADP + P i ATP + H 2 O

ATP is the main energy currency in cells Making ATP involves an endergonic condensation reaction reverse of an exergonic reaction is always endergonic ADP + P i ATP + H 2 O endergonic, usually requires more than ~30 kj/mol must be coupled with an exergonic reaction; typically from a catabolic pathway (more on that later)

ATP is the main energy currency in cells Overall, ATP is typically created in catabolic reactions and used in anabolic reactions, linking those aspects of metabolism

ATP is the main energy currency in cells Cells maintain high levels of ATP relative to ADP maximizes energy available from hydrolysis of ATP

ATP is the main energy currency in cells Cells maintain high levels of ATP relative to ADP maximizes energy available from hydrolysis of ATP ratio typically greater than 10 ATP: 1 ADP

ATP is the main energy currency in cells Overall concentration of ATP still very low supply typically only enough for a few seconds at best

ATP is the main energy currency in cells Overall concentration of ATP still very low supply typically only enough for a few seconds at best instability prevents stockpiling

ATP is the main energy currency in cells Overall concentration of ATP still very low supply typically only enough for a few seconds at best instability prevents stockpiling must be constantly produced in a typical cell, the rate of use and production of ATP is about 10 million molecules per second resting human has less than 1 g of ATP at any given time but uses about 45 kg per day

Why is ATP so darned important? What is a phosphorylated intermediate? How much ATP is in a cell at any given time? Why must cells keep a high ATP/ADP ratio?

What are redox reactions used for in cells? How (generally) can you tell which of two similar compounds is reduced and which is oxidized? Give some examples of compounds commonly used in redox reactions in cells

Redox reactions are also used for energy transfer Redox reactions are used to harvest energy from some chemicals The acceptors of that energy typically cannot be used directly as energy currency

Redox reactions are also used for energy transfer Redox reactions are used to harvest energy from some chemicals The acceptors of that energy typically cannot be used directly as energy currency Electrons can also be used for energy transfer Redox reactions: recall reduction, gain electrons; oxidation, lose electrons; both occur simultaneously in cells (generally no free electrons in cells)

0804 Redox Reactions Slide number: 6 Loss of electron (oxidation) o o e + _ A + B A B A* B* Gain of electron (reduction) Low energy High energy Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display

Redox reactions are also used for energy transfer chain of redox reactions / electron transfers common more on electron transport chains later

Redox reactions are also used for energy transfer chain of redox reactions / electron transfers common more on electron transport chains later each electron transfer releases free energy free energy can be used for other chemical reactions

Redox reactions are also used for energy transfer Catabolism typically involves: removal of hydrogen atoms from nutrients (such as carbohydrates) transfer of the protons and electrons to intermediate electron acceptors

Redox reactions are also used for energy transfer intermediate acceptor example: nicotinamide adenine dinucleotide (NAD + )

Redox reactions are also used for energy transfer intermediate acceptor example: nicotinamide adenine dinucleotide (NAD + ) Use XH 2 to represent a nutrient molecule: XH 2 + NAD + X + NADH + H +

Redox reactions are also used for energy transfer intermediate acceptor example: nicotinamide adenine dinucleotide (NAD + ) Use XH 2 to represent a nutrient molecule: XH 2 + NAD + X + NADH + H + Often, the reduced form is just called NADH

Redox reactions are also used for energy transfer Reduced state stores energy, which is partially released as free energy when NADH is oxidized

Redox reactions are also used for energy transfer Reduced state stores energy, which is partially released as free energy when NADH is oxidized The free energy usually winds up being used to make ATP

Redox reactions are also used for energy transfer Other commonly used acceptors are NADP +, FAD, and cytochromes NADP + /NADPH important in photosynthesis FAD/FADH 2 flavin adenine dinucleotide Cytochromes small iron-containing proteins; iron serves as electron acceptor

What do enzymes do for cells, and how do they do it? Be sure to use the following terms: catalyst (or catalyze) activation energy enzyme-substrate complex active site induced fit

Enzymes Manipulation of reactions is essential to and largely defining of life

Enzymes Manipulation of reactions is essential to and largely defining of life Organisms use enzymes to manipulate the speed of reactions

Enzymes Manipulation of reactions is essential to and largely defining of life Organisms use enzymes to manipulate the speed of reactions Understanding life requires understanding how enzymes work

Enzymes Enzymes regulate chemical reactions in living organisms An enzyme is an organic molecule (typically a protein) that acts as a catalyst

Enzymes Enzymes regulate chemical reactions in living organisms An enzyme is an organic molecule (typically a protein) that acts as a catalyst catalyst increases the rate of a chemical reaction without being consumed in the reaction (the catalyst recycles back to its original state)

Fig 89 (TEArt) Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display 1 Bond Active site The substrate, sucrose, consists of glucose and fructose bonded together Enzyme 2 The substrate binds to the enzyme, forming an enzymesubstrate complex H 2 O 3 4 The binding of the substrate and enzyme places stress on the glucosefructose bond, and the bond breaks Glucose Fructose Products are released, and the enzyme is free to bind other substrates

0809 Enzyme Catalytic Cycle Slide number: 2 1 The substrate, sucrose, consists of glucose and fructose bonded together Bond Active site Enzyme Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display

0809 Enzyme Catalytic Cycle Slide number: 3 1 The substrate, sucrose, consists of glucose and fructose bonded together Bond Active site Enzyme Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display

0809 Enzyme Catalytic Cycle Slide number: 4 Bond 1 The substrate, sucrose, consists of glucose and fructose bonded together 2 The substrate binds to the enzyme, forming an enzymesubstrate complex Active site Enzyme Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display

0809 Enzyme Catalytic Cycle Slide number: 5 Bond 1 The substrate, sucrose, consists of glucose and fructose bonded together 2 The substrate binds to the enzyme, forming an enzymesubstrate complex H 2 O Active site Enzyme 3 The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display

0809 Enzyme Catalytic Cycle Slide number: 6 Bond Active site 1 The substrate, sucrose, consists Glucose of glucose and fructose bonded together 2 The substrate binds to the enzyme, forming an enzymesubstrate complex Enzyme 3 H 2 O The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks 4 Fructose Products are released, and the enzyme is free to bind other substrates Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display

Enzymes work by lowering activation energy of a reaction all reactions have a required energy of activation

Enzymes work by lowering activation energy of a reaction all reactions have a required energy of activation energy required to break existing bonds and bring reactants together

Enzymes work by lowering activation energy of a reaction all reactions have a required energy of activation energy required to break existing bonds and bring reactants together must be supplied in some way before the reaction can proceed

activation energy Enzymes catalysts greatly reduce the activation energy requirement, making it easier for a reaction to occur

Enzymes Enzymes lower activation energy by forming a complex with the substrate(s) the ability to form an enzyme-substrate complex is highly dependent on the shape of the enzyme

Enzymes Enzymes lower activation energy by forming a complex with the substrate(s) the ability to form an enzyme-substrate complex is highly dependent on the shape of the enzyme the site where the substrate(s) binds to the enzyme is called the active site when the enzyme-substrate complex forms, there are typically shape changes in the enzyme and substrate(s) called induced fit

Enzymes ES complex typically very unstable

Enzymes ES complex typically very unstable short-lived

Enzymes ES complex typically very unstable short-lived breaks down into released product(s) and a free enzyme that is ready to be reused

Enzymes ES complex typically very unstable short-lived breaks down into released product(s) and a free enzyme that is ready to be reused overall: enzyme + substrate(s) ES complex enzyme + product(s)

What do enzymes do for cells, and how do they do it? Be sure to use the following terms: catalyst (or catalyze) activation energy enzyme-substrate complex active site induced fit

What are the four main things that enzymes do to lower activation energy?

Enzymes reduction in activation energy is due primarily to four things:

Enzymes reduction in activation energy is due primarily to four things: an enzyme holds reactants (substrates) close together in the right orientation for the reaction, which reduces the reliance on random collisions an enzyme may put a strain on existing bonds, making them easier to break an enzyme provides a microenvironment that is more chemically suited to the reaction

Enzymes enzyme + substrate(s) ES complex enzyme + product(s)

What are the four main things that enzymes do to lower activation energy?

How are enzymes named (what suffixes indicate an enzyme)?

Enzyme names Enzymes many names give some indication of substrate

Enzyme names Enzymes many names give some indication of substrate most enzyme names end in ase (example: sucrase)

Enzyme names Enzymes many names give some indication of substrate most enzyme names end in ase (example: sucrase) some end in zyme (example: lysozyme)

Enzyme names Enzymes many names give some indication of substrate most enzyme names end in ase (example: sucrase) some end in zyme (example: lysozyme) some traditional names are less indicative of enzyme function (examples: pepsin, trypsin)

Enzymes Enzymes are generally highly specific overall shape as well as spatial arrangements in the active site limit what enzyme-substrate complexes can readily form

Enzymes the amount of specificity depends on the particular enzyme example of high specificity: sucrase splits sucrose, not other disaccharides

Enzymes the amount of specificity depends on the particular enzyme example of high specificity: sucrase splits sucrose, not other disaccharides example of low specificity: lipase splits variety of fatty acids from glycerol

Enzymes enzymes are classified by the kind of reaction they catalyze The International Union of Biochemistry and Molecular Biology has developed a nomenclature for enzymes; the top-level classification is Oxidoreductases: catalyze oxidation/reduction reactions Transferases: transfer a functional group (eg a methyl or phosphate group) Hydrolases: catalyze the hydrolysis of various bonds Lyases: cleave various bonds by means other than hydrolysis and oxidation Isomerases: catalyze isomerization changes within a single molecule Ligases: join two molecules with covalent bonds The complete nomenclature can be browsed at http://wwwchemqmulacuk/iubmb/enzyme/

How are enzymes named (what suffixes indicate an enzyme)?

Explain the terms cofactor, apoenzyme, and coenzyme

Enzymes Many enzymes require additional chemical components (cofactors) to function

Enzymes Many enzymes require additional chemical components (cofactors) to function apoenzyme + cofactor active enzyme (bound together)

Enzymes Many enzymes require additional chemical components (cofactors) to function apoenzyme + cofactor active enzyme (bound together) alone, an apoenzyme or a cofactor has little if any catalytic activity

Enzymes cofactors can be organic or inorganic organic examples (coenzymes): ADP, NAD +, NADP +, FAD typically changed by the catalyzed reaction

Enzymes cofactors can be organic or inorganic organic examples (coenzymes): ADP, NAD +, NADP +, FAD typically changed by the catalyzed reaction inorganic examples: metal ions like Ca 2+, Mg 2+, Fe 3+, etc typically not changed by the catalyzed reaction

Fig 83 (TEArt) Copyright The McGraw-Hill Companies, Inc Permission required for reproduction or display Enzyme Energy-rich molecule H H NAD + NAD + NAD + H NAD H Product 1 Enzymes that harvest hydrogen atoms have a binding site for NAD + located near another binding site NAD + and an energy-rich molecule bind to the enzyme 2 In an oxidationreduction reaction, a hydrogen atom is transferred to NAD +, forming NADH NAD H 3 NADH then diffuses away and is available to other molecules

Fig 8A

Explain the terms cofactor, apoenzyme, and coenzyme

Discuss the effects of temperature and ph on enzyme activity

Enzymes are most active under optimal conditions each enzyme has an optimal temperature most effective as a catalyst at the optimal temperature

Enzymes are most active under optimal conditions each enzyme has an optimal temperature most effective as a catalyst at the optimal temperature rate of drop-off in effectiveness away from optimal temperature depends on the enzyme high temperatures tend to denature enzymes

Enzymes are most active under optimal conditions each enzyme has an optimal ph again, most effective at the optimum; drop-off varies

Enzymes are most active under optimal conditions each enzyme has an optimal ph again, most effective at the optimum; drop-off varies extremes of ph tend to denature enzymes

Enzymes are most active under optimal conditions each enzyme has an optimal ph again, most effective at the optimum; drop-off varies extremes of ph tend to denature enzymes a particular organism shows more variety in enzyme ph optima than in temperature optima, but most of its enzymes will still be optimal at the ph normally found in the cytosol of its cells

Discuss the effects of temperature and ph on enzyme activity

What is a metabolic pathway?

Enzymes Metabolic pathways use organized teams of enzymes the products of one reaction often serve as substrates for the next reaction

Enzymes Metabolic pathways use organized teams of enzymes the products of one reaction often serve as substrates for the next reaction removing products (by having them participate the next reaction ) improves reaction rate (avoids equilibrium)

Fig 815

What is a metabolic pathway?

How do cells regulate enzyme activity? Include the terms: inhibitors activators allosteric site feedback inhibition Also, differentiate between: irreversible and reversible inhibition competitive and noncompetitive inhibition

Enzymes Cells can regulate enzyme activity to control reactions increase substrate amount increase reaction rate (up to saturation of available enzyme molecules)

Enzymes Cells can regulate enzyme activity to control reactions increase substrate amount increase reaction rate (up to saturation of available enzyme molecules) increase enzyme amount increase reaction rate (as long as substrate amount > enzyme amount)

Rate of reaction Rate of reaction When substrate concentration >> enzyme concentration Enzyme concentration Substrate concentration (a) (b)

Cells can regulate enzyme activity to control reactions inhibitors and activators of enzymes activators allow or enhance catalytic activity

Cells can regulate enzyme activity to control reactions inhibitors and activators of enzymes activators allow or enhance catalytic activity inhibitors reduce or eliminate catalytic activity

Cells can regulate enzyme activity to control reactions inhibitors and activators of enzymes activators allow or enhance catalytic activity inhibitors reduce or eliminate catalytic activity sometime, this uses an allosteric site a receptor site on an enzyme where an inhibitor or activator can bind

Cells can regulate enzyme activity to control reactions a common example of allosteric control is feedback inhibition the last product in a metabolic pathway binds to an allosteric site of an enzyme in an early step of the pathway (often the first) this product inhibits activity of the enzyme

Enzyme #1 (Threonine deaminase) Enzyme #2 Threonine -Ketobutyrate -Aceto- -hydroxybutyrate Enzyme #3,b-Dihydroxy-b-methylvalerate Feedback inhibition (Isoleucine inhibits enzyme #1) Enzyme #4 -Keto-b-methylvalerate Enzyme #5 Isoleucine

Fig 920

Cells can regulate enzyme activity to control reactions irreversible inhibition enzyme is permanently inactivated or destroyed; includes many drugs and toxins

Cells can regulate enzyme activity to control reactions irreversible inhibition enzyme is permanently inactivated or destroyed; includes many drugs and toxins reversible inhibition if inhibitor is removed, the enzyme activity can be recovered

Cells can regulate enzyme activity to control reactions reversible inhibition if inhibitor is removed, the enzyme activity can be recovered competitive inhibition inhibitor is similar in structure to a substrate; competes with substrate for binding to the active site