1 Chapter 9 Introduction to Metabolism CHAPTER GLOSSARY Activation energy Active site Allosteric 異位 enzyme Anabolism 合成代謝 Apoenzyme 脢本體 Catabolism 分解代謝 Catalyst Coenzyme Denaturation Electron transport chain (ETC) Endergonic 吸收能量的 reaction Entropy 熵 ; 亂度 Enzyme Equilibrium Exergonic 釋出能量的 reaction Feedback inhibiton Free energy change Holoenzyme 全酵素 Metabolism Michaelis constant (K m ) Phosphorelay system Prosthetic group 輔基 Reducing power Reversible covalent modification Standard reduction potential

2 metabolism is the total of all chemical reactions in the cell and is divided into two parts  catabolism ( 分解代謝 )  anabolism ( 合成代謝 ) Figure 9.1 Overview of Metabolism

3 Catabolism ( 分解代謝 ) fueling 供給燃料 reactions energy-conserving 保存 reactions provide ready source or reducing power (electrons) generate precursors for biosynthesis Anabolism ( 合成代謝 ) the synthesis of complex organic molecules from simpler ones requires energy from fueling reactions

4 Microbial Metabolism have representatives in all five major nutritional types contribute to cycling of elements in ecosystems  some cycling reactions performed only by microbes

5 Microbial Cells Must Do Work chemical work  synthesis of complex molecules transport work  take up of nutrients, elimination of wastes, and maintenance of ion balances mechanical work  cell motility and movement of structures within cells

6 The Laws of Thermodynamics thermodynamics  a science that analyzes energy changes in a collection of matter called a system (e.g., a cell)  all other matter in the universe 宇宙 is called the surroundings 環境 First Law of Thermodynamics energy can be neither created nor destroyed total energy in universe remains constant  However, energy may be redistributed either within a system or between the system and its surroundings Second Law of Thermodynamics physical and chemical processes proceed in such a way that the disorder of the universe increases to the maximum possible entropy 熵  amount of disorder in a system Heat is released by one chemical reaction and absorbed by another

7 Energy Units calorie (cal)  amount of heat energy needed to raise 1 gram of water from 14.5 to 15.5°C joules (J)  units of work capable of being done by a unit of energy  1 cal of heat is equivalent to J of work

8 Free Energy and Reactions  G =  H - T  S expresses the change in energy that can occur in chemical reactions and other processes used to indicate if a reaction will proceed spontaneously  if  G is negative, reaction is spontaneous  if  G is positive, reaction is not spontaneous  G  free energy change  amount of energy available to do work  H  change in enthalpy (heat content; 焓, 熱含量 ) T  temperature in Kelvin  S  change in entropy 熵

9 Chemical equilibrium equilibrium A + B C + D  reaction is at equilibrium when rate of forward reaction = rate of reverse reaction equilibrium constant (K eq )  expresses the equilibrium concentrations of products and reactants to one another Standard free energy change (  G o ) free energy change defined at standard conditions of concentration, pressure, temperature, and pH  G o ´  standard free energy change at pH 7  directly related to K eq  G o ´ = RTlogK eq

10  G o and Equilibrium Exergonic reactions  G o ´ is negative (reaction proceeds spontaneously) Endergonic reactions  G o ´ is positive (reaction will not proceed spontaneously)

11 Energy Currency of the Cell Adenosine 5’-triphosphate (ATP)

12 Role of ATP in Metabolism The cell’s energy cycle high energy molecule exergonic breakdown of ATP is coupled with endergonic reactions to make them more favorable ATP +H 2 O ADP + P i + H +   G o ´ = kcal/mol guanosine 5 ˈ - triphosphate, cytosine 5 ˈ - triphosphate and uridine 5 ˈ - triphosphate also supply some energy

13 Oxidation-Reduction Reactions and Electron Carriers many metabolic processes involve oxidation-reduction reactions (electron transfers) electron carriers are often used to transfer electrons from an electron donor to an electron acceptor Oxidation-Reduction (Redox) Reactions transfer of electrons from a donor to an acceptor  can result in energy release, which can be conserved and used to form ATP  the more electrons a molecule has, the more energy rich it is Redox: Two Half Reactions one is electron donating (oxidizing reaction) one is electron accepting reaction (reducing reaction) acceptor and donor are conjugate redox pair acceptor + ne - donor reduction

14 Standard Reduction Potential (E 0 ) equilibrium constant for an oxidation- reduction reaction a measure of the tendency of the reducing agent to lose electrons more negative E 0  better electron donor more positive E 0  better electron acceptor

15 The greater the difference between the E 0 of the donor and the E 0 of the acceptor  the more negative the  G o ´

16 Electron Transport Chain (ETC) electron carriers organized into ETC with the first electron carrier having the most negative E’ o  as a result the potential energy stored in first redox couple is released and used to form ATP  first carrier is reduced and electrons moved to the next carrier and so on

17 Electron carriers NAD  nicotinamide adenine dinucleotide NADP  nicotinamide adenine dinucleotide phosphate located in plasma membranes of chemoorganotrophs in bacteria and archaeal cells located in internal mitochondrial membranes in eukaryotic cells examples of electron carriers include NAD, NADP, and others

18 Electron carriers FAD  flavin adenine dinucleotide FMN  flavin mononucleotide  riboflavin phosphate coenzyme Q (CoQ)  a quinone  also called ubiquinone

19 Electron carriers cytochromes  use iron to transfer electrons iron is part of a heme group nonheme iron proteins  e.g., ferrodoxin  use iron to transport electrons iron is not part of a heme group

20 Enzymes carry out reactions at physiological conditions so they proceed in a timely manner enzymes speed up the rate at which a reaction proceeds toward its final equilibrium

21 Structure and Classification of Enzymes some enzymes are composed solely of one or more polypeptides some enzymes are composed of one or more polypeptides and nonprotein components protein catalysts  have great specificity for the reaction catalyzed and the molecules acted on catalyst 催化劑  substance that increases the rate of a reaction without being permanently altered substrates  reacting molecules products  substances formed by reaction

22 Enzyme structure apoenzyme  protein component of an enzyme cofactor  nonprotein component of an enzyme prosthetic group – firmly attached coenzyme – loosely attached holoenzyme = apoenzyme + cofactor Coenzymes often act as carriers, transporting substances around the cell

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24 The Mechanism of Enzyme Reactions a typical exergonic reaction A + B  AB ‡  C + D transition-state complex – resembles both the substrates and the products activation energy – energy required to form transition- state complex enzyme speeds up reaction by lowering E a

25 How enzymes lower E a by increasing concentrations of substrates at active site of enzyme by orienting substrates properly with respect to each other in order to form the transition-state complex two models for enzyme-substrate interaction  lock and key and induced fit

26 Lock and Key Model of Enzyme Function The induced Fit Model of Enzyme Function

27 The Effect of Environment on Enzyme Activity enzyme activity is significantly impacted by substrate concentration, pH, and temperature Effect of [substrate] rate increases as [substrate] increases no further increase occurs after all enzyme molecules are saturated with substrate

28 Effect of pH and temperature each enzyme has specific pH and temperature optima denaturation  loss of enzyme’s structure and activity when temperature and pH rise too much above optima

29 Enzyme Inhibition Competitive Inhibition of Enzyme Activity competitive inhibitor  directly competes with binding of substrate to active site noncompetitive inhibitor  binds enzyme at site other than active site  changes enzyme’s shape so that it becomes less active

30 Ribozymes Thomas Cech and Sidney Altman discovered that some RNA molecules also can catalyze reactions examples  catalyze peptide bond formation  self-splicing  involved in self-replication

31 Regulation of Metabolism important for conservation of energy and materials maintenance of metabolic balance despite changes in environment three major mechanisms  metabolic channeling  regulation of the synthesis of a particular enzyme (transcriptional and translational)  direct stimulation or inhibition of the activity of a critical enzyme post-translational

32 Metabolic Channeling differential localization of enzymes and metabolites compartmentation  differential distribution of enzymes and metabolites among separate cell structures or organelles  can generate marked variations in metabolite concentrations Post-Translational Regulation of Enzyme Activity two important reversible control measures  allosteric regulation  covalent modification

33 Allosteric Regulation most regulatory enzymes activity altered by small molecule  allosteric effector binds non-covalently at regulatory site changes shape of enzyme and alters activity of catalytic site positive effector increases enzyme activity negative effector inhibits the enzyme

34 Covalent Modification of Enzymes reversible on and off switch addition or removal of a chemical group (phosphate, methyl, adenyl) advantages of this method  respond to more stimuli in varied and sophisticated ways  regulation on enzymes that catalyze covalent modification adds second level Regulation of glutamine synthetase activity by covalent modification

35 Feedback Inhibition also called end product inhibition inhibition of one or more critical enzymes in a pathway regulates entire pathway  pacemaker enzyme catalyzes the slowest or rate-limiting reaction in the pathway each end product regulates its own branch of the pathway each end product regulates the initial pacemaker enzyme isoenzymes – different enzymes that catalyze same reaction