BIOL 1020 – CHAPTER 8 LECTURE NOTES

Chapter 8: Energy and Metabolism

  1. Discuss energy conversions and the 1st and 2nd law of thermodynamics. Be sure to use the terms work, potential energy, kinetic energy, and entropy.
  1. What are Joules (J) and calories (cal)?
  1. The laws of thermodynamics are sometimes stated as: In energy conversions, “You can’t win, and you can’t break even.” Explain.
  1. Differentiate between:

anabolism and catabolism

exergonic and endergonic reactions

  1. 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?

  1. 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.
  1. 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
  1. What are the four main things that enzymes do to lower activation energy?
  1. How are enzymes named (what suffixes indicate an enzyme)?
  1. Explain the terms cofactor, apoenzyme, and coenzyme.
  1. Discuss the effects of temperature and pH on enzyme activity.
  1. What is a metabolic pathway?
  1. How do cells regulate enzyme activity? Include the terms inhibitors, activators, allosteric site, and feedback inhibition; also, differentiate between irreversible and reversible inhibition and between competitive and noncompetitive inhibition.

Chapter 8: Energy and Metabolism

Why do organisms need energy? How do organisms manage their energy needs?

  1. Energy and thermodynamics
  2. Living organisms require energy to do work, any change in state or motion of matter
  3. energy can be expressed in units of work (kJ) or heat energy (kcal); 1 kcal = 4.184 kJ
  4. energy can change forms (energy conversion)
  5. organisms carry out transformation in energy forms between potential energy (capacity to do work) and kinetic energy (energy of motion, actively performing work)
  6. organisms commonly use chemical bonds for storage and transfer of (potential) energy
  7. work is required for the processes of life
  8. Two laws of thermodynamics describe the constraints on energy usage
  9. First law: the total amount of energy (+ matter) in a closed system remains constant (principle of conservation of energy)
  10. The universe is a closed system
  11. Living things are open systems
  12. Second law: in every energy conversion, some energy is converted to heat energy that is lost to the surroundings, and thus cannot be used for work
  13. Also can be stated as: Every energy conversion increased the entropy of the universe.
  14. Energy converted to heat in the surroundings increases entropy (spreading of energy)
  15. Upshot: no energy conversion is 100% efficient
  16. Just to maintain their current state, organisms must get a constant influx of energy because of energy lost in conversions
  17. Metabolic reactions include anabolism and catabolism, and involve energy transfers
  18. Recall that metabolism is the sum of chemical activities in a organism
  19. Metabolism can be divided into anabolism (anabolic reactions) and catabolism (catabolic reactions)
  20. anabolic reactions are processes that build complex molecules from simpler ones
  21. catabolic reactions are processes the break down complex molecules into simpler ones
  22. Chemical reactions involve changes in chemical bonds and substance concentrations, along with changes in free energy
  23. free energy = energy available to do work in a chemical reaction (such as: create a chemical bond)
  24. free energy changes depend on bond energies and concentrations of reactants and products
  25. bond energy = energy required to break a bond; value depends on the bond
  26. left undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and products is correct
  27. forward and reverse reaction rates are equal; concentrations remain constant
  28. cells manipulate relative concentrations in many ways, so that equilibrium is rare for key reactions
  29. exergonic reactions – the products have less free energy than reactants
  30. the difference in energy is released and is available to do work
  31. exergonic reactions are thermodynamically favored; thus, they are spontaneous, but not necessarily fast (more on activation energy later)
  32. catabolic reactions are usually exergonic
  33. ATP + H2O  ADP + Pi is highly exergonic in cellular conditions
  34. endergonic reactions – the products have more free energy than the reactants
  35. the difference in free energy must be supplied (stored in chemical bonds)
  36. endergonic reactions are not thermodynamically favored, so they are not spontaneous
  37. an endergonic reaction is coupled with an exergonic reaction to provide the needed energy to drive an endergonic reaction
  38. together, the coupled reactions must have a net exergonic nature
  39. reaction coupling requires that the reactions share a common intermediate(s)

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 + H2O  ADP + Pi
  • anabolic reactions are usually endergonic

One way that organisms manage their energy needs is to use ATP as a ready energy source for many reactions.

  1. ATP is the main energy currency in cells
  2. Recall ATP (adenosine triphosphate) is a nucleotide with adenine base, ribose sugar, and a chain of 3 phosphate groups
  3. The last two phosphate groups are joined to the phosphate group chain by unstable bonds; breaking these bonds is relatively easy, and releases energy; thus:
  4. hydrolysis of ATP to ADP and inorganic phosphate (Pi) releases energy

ATP + H2O  ADP + Pi

  1. the amount of energy released depends in part on concentrations of reactants and products, but is generally ~30 kJ/mol
  1. Intermediates are involved when ATP hydrolysis is coupled to a reaction to provide energy; often these involve phosphorylated compounds, with the inorganic phosphate removed from ATP transferred onto another compound rather than being immediately released

EXAMPLE:

glucose + fructose  sucrose + H2O (endergonic; requires ~27 kJ/mol)

ATP + H2O  ADP + Pi (provides ~30 kJ/mol)

coupled:glucose + fructose + ATP + H2O  sucrose + H2O + ADP + Pi

simplified:glucose + fructose + ATP  sucrose +ADP + Pi

with intermediates:glucose + fructose + ATP + H2O  glucose-P + fructose + ADP  sucrose + H2O + ADP + Pi

  1. Thus, energy transfer in cellular reactions is often accomplished through transfer of a phosphate group from ATP
  2. Making ATP involves an endergonic condensation reaction
  3. reverse of an exergonic reaction is always endergonic

ADP + Pi ATP + H2O (endergonic, usually requires more than ~30 kJ/mol)

  1. must be coupled with an exergonic reaction; typically from a catabolic pathway (more on that later)
  1. Overall, ATP is typically created in catabolic reactions and used in anabolic reactions, linking those aspects of metabolism
  2. Cells maintain high levels of ATP relative to ADP
  3. maximizes energy available from hydrolysis of ATP
  4. ratio typically greater than 10 ATP: 1 ADP
  5. Overall concentration of ATP still very low
  6. supply typically only enough for a few seconds at best
  7. instability prevents stockpiling
  8. must be constantly produced
  9. in a typical cell, the rate of use and production of ATP is about 10 million molecules per second
  10. resting human has less than 1 g of ATP at any given time but uses about 45 kg per day

Redox reactions are used to harvest energy from some chemicals; the acceptors of that energy typically cannot be used directly as energy currency.

  1. Redox reactions are also used for energy transfer
  2. Electrons can also be used for energy transfer
  3. Redox reactions: recall reduction, gain electrons; oxidation, lose electrons; both occur simultaneously in cells (generally no free electrons in cells)
  4. Typically, the oxidized substance gives up energy with the electron, the reduced substance gains energy with the electron
  5. Commonly occur as a chain of redox reactions or electron transfers (more on electron transport chains later)
  6. As the electron is transferred to an acceptor molecule, it releases free energy that can be used for other chemical reactions
  7. Typically, a proton is removed as well when an electron is removed from covalent molecules; thus, the equivalent of a hydrogen atom is transferred
  8. Catabolism typically involves removal of hydrogen atoms from nutrients (such as carbohydrates), and the transfer of the protons and electrons to intermediate electron acceptors
  9. One common intermediate acceptor is nicotinamide adenine dinucleotide (NAD+)
  10. Use XH2 to represent a nutrient molecule:

XH2 + NAD+ X + NADH + H+

  • Often, the reduced form is just called NADH
  • 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
  1. Other commonly used acceptors are NADP+, FAD, and cytochromes
  2. NADP+/NADPH – important in photosynthesis
  3. FAD/FADH2 – flavin adenine dinucleotide
  4. Cytochromes – small iron-containing proteins; iron serves as electron acceptor

Enzymes are a large part of the answer to how organisms manage their energy needs. Manipulation of reactions is essential to and largely defining of life, and enzymes manipulate the speed of reactions. Understanding life requires understanding how enzymes work.

  1. Enzymes regulate chemical reactions in living organisms
  2. An enzyme is an organic molecule (typically a protein) that acts as a catalyst
  3. catalyst – substance that increases the rate of a chemical reaction without being consumed in the reaction (the catalyst recycles back to its original state)
  4. enzymes (catalysts) only alter reaction rate; thermodynamics still governs whether the reaction can occur – thus, enzymes only catalyze reactions that are occurring anyway
  5. Enzymes (catalysts) work by lowering the activation energy of a reaction
  6. all reactions have a required energy of activation (the energy required to break existing bonds) that must be supplied in some way before the reaction can proceed; also, reactants must come together
  7. catalysts greatly reduce the activation energy requirement, making it easier for a reaction to occur
  8. often, this reduction in activation energy is due to in part to the enzyme holding reactants (substrates) close together, which also reduces the reliance on random collisions
  9. Enzymes lower activation energy by forming a complex with the substrate(s)
  10. the ability to form an enzyme-substrate complex is highly dependent on the shape of the enzyme
  11. the site where the substrate(s) binds to the enzyme is called the active site
  12. when the enzyme-substrate complex forms, there are typically shape changes in the enzyme and substrate(s) – this is called induced fit
  13. the enzyme-substrate complex is typically very unstable and short-lived; it breaks down into released product(s) and a free enzyme that is ready to be reused
  14. overall:

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

  1. the reduction in activation energy is due primarily to four things:
  2. an enzyme holds reactants (substrates) close together in the right orientation for the reaction, which reduces the reliance on random collisions
  3. an enzyme may put a “strain” on existing bonds, making them easier to break
  4. an enzyme provides a “microenvironment” that is more chemically suited to the reaction
  5. sometimes the active site of the enzyme itself is directly involved in the reaction during the transition states
  6. Enzyme names
  7. many names give some indication of substrate
  8. most enzyme names end in –ase (example: sucrase)
  9. some end in –zyme (example: lysozyme)
  10. some traditional names are less indicative of enzyme function (example: pepsin)
  11. Enzymes are generally highly specific
  12. overall shape as well as spatial arrangements in the active site limit what enzyme-substrate complexes can readily form
  13. the amount of specificity depends on the particular enzyme
  14. example of high specificity: sucrase splits sucrose, not other disaccharides
  15. example of low specificity: lipase splits variety of fatty acids from glycerol
  16. enzymes are classified by the kind of reaction they catalyze
  17. Many enzymes require cofactors to function
  18. apoenzyme + cofactor  active enzyme (bound together)
  19. alone, an apoenzyme or a cofactor has little if any catalytic activity
  20. cofactors may or may not be changed by the reaction
  21. cofactors can be organic or inorganic
  22. organic examples (coenzymes):
  23. ATP, NADH, NADPH, FADH2
  24. typically changed by the catalyzed reaction
  25. inorganic examples
  26. metal ions like Ca2+, Mg2+, Fe3+, etc.
  27. typically not changed by the catalyzed reaction
  28. most vitamins are coenzymes or part of coenzymes, or are used for making coenzymes
  29. Enzymes are most active under optimal conditions
  30. each enzyme has an optimal temperature
  31. most effective as a catalyst at the optimal temperature
  32. rate of drop-off in effectiveness away from optimal temperature depends on the enzyme
  33. high temperatures tend to denature enzymes
  34. human enzymes have temperature optima near human body temperature (37°C)
  35. each enzyme has an optimal pH
  36. again, most effective at the optimum; drop-off varies
  37. extremes of pH tend to denature enzymes
  38. 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
  39. Metabolic pathways use organized “teams” of enzymes
  40. the products of one reaction often serve as substrates for the next reaction
  41. removing products (by having them participate the “next reaction”) improves reaction rate
  42. multiple metabolic pathways exit in cells, overlapping in some areas and diverging in others
  43. Cells can regulate enzyme activity to control reactions
  44. increase substrate amount  increase reaction rate (up to saturation of available enzyme molecules)
  45. increase enzyme amount  increase reaction rate (as long as substrate amount > enzyme amount)
  46. compartmentation of the enzyme, substrate, and products can help control reaction rate
  47. inhibitors and activators of enzymes
  48. inhibitors reduce or eliminate catalytic activity
  49. activators allow or enhance catalytic activity
  50. sometime, this uses an allosteric site – a receptor site on an enzyme where an inhibitor or activator can bind
  51. a common example of allosteric control is feedback inhibition, where 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) and inhibits activity of the enzyme
  52. irreversible inhibition – enzyme is permanently inactivated or destroyed; includes many drugs and toxins
  53. reversible inhibition – if inhibitor is removed, the enzyme activity can be recovered
  54. competitive inhibition – inhibitor is similar in structure to a substrate; competes with substrate for binding to the active site
  55. noncompetitive inhibition – binds at allosteric site, alters enzyme shape to make active site unavailable

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