BCH3033 Biochemistry 1 Chapter 6a - Florida Atlantic University - PDF

BCH3033: Biochemistry 1 Chapter 6a 02.16.2024 Donella Beckwith, Ph.D. [email protected] 1 Enzymes are powerful biological catalysts. Rate accelerations by enzymes are often far greater than those by synthetic or inorganic catalysts. Like all catalysts, enzymes increase reaction rates, lowering react...

BCH3033: Biochemistry 1 Chapter 6a 02.16.2024 Donella Beckwith, Ph.D. [email protected] 1 Enzymes are powerful biological catalysts. Rate accelerations by enzymes are often far greater than those by synthetic or inorganic catalysts. Like all catalysts, enzymes increase reaction rates, lowering reaction activation barriers. Enzymes do not affect the equilibria of reactions. 2 Enzymes exhibit a very high degree of specificity. Each enzyme catalyzes only one chemical reaction, or sometimes a few closely related reactions. Reaction activation barriers are thus lowered selectively. 3 Active Site Enzymatic reactions occur in specialized pockets called active sites. These pockets are similar to ligand binding sites, except that a reaction occurs there—the conversion of a substrate (a molecule that is acted on by an enzyme) to a product. 4 Catalytic Power Two concepts explain the catalytic power of enzymes: 1st: enzymes bind most tightly to the transition state of the catalyzed reaction, using binding energy to lower the activation barrier. 2nd: enzyme active sites are organized by evolution to facilitate multiple mechanisms of chemical catalysis simultaneously. 5 Enzyme Regulation Many enzymes are regulated. Regulatory mechanisms include – reversible covalent modification – binding of allosteric modulators – proteolytic activation – noncovalent binding to regulatory proteins – elaborate regulatory cascades Enzymes are often subject to multiple methods of regulation, which allows for exquisite control of every chemical process that occurs in a cell. 6 Most Enzymes Are Proteins Can be prosthetic groups catalytic activity depends on the integrity of the native protein conformation molecular weight = ranges from 12,000 to >1 million some enzyme require additional chemical components: – Cofactor: non-protein compound 1+ inorganic ions (such as Fe2+, Mg2+, Mn2+, or Zn2+) Coenzyme: complex organic or metalloorganic molecule that act as transient carriers of specific functional groups inactive enzyme biologically active 7 Question Enzymes: A. are proteins (with few exceptions). B. can be denatured and still retain full activity. C. have names always ending in “-ase.” D. are also referred to as “coenzymes.” 8 Inorganic Ions as Cofactors Table 6-1 Some Inorganic Ions That Serve as Cofactors for Enzymes Ions Enzymes Cu2+ Cytochrome oxidase Fe2+ or Fe3+ Cytochrome oxidase, catalase, peroxidase K+ Pyruvate kinase Mg2+ Hexokinase, glucose 6-phosphatase, pyruvate kinase Mn2+ Arginase, ribonucleotide reductase Mo Dinitrogenase Ni2+ Urease Zn2+ Carbonic anhydrase, alcohol dehydrogenase, carboxypeptidases A and B 9 Question In enzymes, which inorganic ion does NOT serve as a cofactor? Zn2+ A. B. Cu2+ C. Ca2+ D. Mg2+ Ions Enzymes Cu2+ Cytochrome oxidase Fe2+ or Fe3+ Cytochrome oxidase, catalase, peroxidase K+ Pyruvate kinase Mg2+ Hexokinase, glucose 6phosphatase, pyruvate kinase Mn2+ Arginase, ribonucleotide reductase Mo Dinitrogenase Ni2+ Urease Zn2+ Carbonic anhydrase, alcohol dehydrogenase, carboxypeptidases A and B 10 Coenzymes as Transient Carriers of Atoms or Functional Groups Table 6-2 Some Coenzymes That Serve as Transient Carriers of Specific Atoms or Functional Groups Coenzyme Examples of chemical groups transferred Dietary precursor in mammals Biocytin CO2 Biotin (vitamin B7) Coenzyme A Acyl groups Pantothenic acid (vitamin B5) and other compounds 5′-Deoxyadenosylcobalamin (coenzyme B12) H atoms and alkyl groups Vitamin B12 Flavin adenine dinucleotide Electrons Riboflavin (vitamin B2) Lipoate Electrons and acyl groups Not required in diet Nicotinamide adenine dinucleotide Hydride ion (:H–) Nicotinic acid (niacin, vitamin B3) Pyridoxal phosphate Amino groups Pyridoxine (vitamin B6) Tetrahydrofolate One-carbon groups Folate (vitamin B9) Thiamine pyrophosphate Aldehydes Thiamine (vitamin B1) 11 Describing Enzymes and Their Additional Chemical Components prosthetic group = coenzyme or metal ion that is very tightly or covalently bound to the enzyme protein holoenzyme = complete catalytically active enzyme together with its bound coenzyme and/or metal ions apoenzyme or apoprotein = the protein part of a holoenzyme inactive enzyme biologically active 12 Question An apoenzyme: A. is the nonprotein component of a holoenzyme. B. always requires an inorganic ion for its activity. C. requires a cofactor for its activity. D. is an enzyme consisting of RNA rather than protein. 13 Question Some enzymes require an inorganic ion for catalytic function. When this inorganic ion is very tightly or covalently bound by the enzyme it is called a(n): A. apoenzyme. B. prosthetic group. C. holoenzyme. D. catalyst. 14 Enzymes Are Classified by the Reactions They Catalyze enzymes are divided into seven classes, each with subclasses, based on the type of reaction catalyzed each enzyme has a four-part Enzyme Commission number (E.C. number) and a systematic name most enzymes have trivial names Table 6-3 International Classification of Enzymes Class number Class name Type of reaction catalyzed 1 Oxidoreductases Transfer of electrons (hydride ions or H atoms) 2 Transferases Group transfer 3 Hydrolases Hydrolysis (transfer of functional groups to water) 4 Lyases Cleavage of C—C, C—O, C—N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds 5 Isomerases Transfer of groups within molecules to yield isomeric forms 6 Ligases Formation of C—C, C—S, C—O, and C—N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor 7 Translocases Movement of molecules or ions across membranes or their separation within membranes 15 Translocases 7.x.x.x: 16 Translocases 17 Question ________ is NOT an E.C. class name for enzymes. A. Transferases B. Polymerases C. Lyases D. Isomerases 18 Enzyme-Catalyzed Reactions Take Place within the Active Site active site = provides a specific environment in which a given reaction can occur more rapidly substrate = the molecule that is bound to the active site and is acted upon by the enzyme 19 Enzymes Reactions simple enzymatic reactions can be written as E + S ⇌ ES ⇌ EP ⇌ E + P (6-1) where E, S, and P represent the enzyme, substrate, and product and ES and EP are transient complexes of the enzyme 20 Enzymes Affect Reaction Rates, Not Equilibria simple enzymatic reactions can be written as E + S ⇌ ES ⇌ EP ⇌ E + P (6-1) where E, S, and P represent the enzyme, substrate, and product and ES and EP are transient complexes of the enzyme 21 Ground State and Transition State ground state = starting point for either the forward or reverse reaction transition state (‡) = the point at which decay to substrate or product are equally likely 22 Energy Changes in a Reaction Coordinate Diagram biochemical standard freeenergy change = ∆G′° = the standard free-energy change at pH 7.0 activation energy (∆G‡) = difference between the ground state energy level and the transition state energy level 23 Question What is the free-energy starting point for a reverse reaction designated as? A. transition state (‡) B. ground state C. biochemical standard free energy D. activation energy (∆G‡) 24 Catalysts Lower the Activation Energy and Increase the Reaction Rate Activation energy 25 Catalysts Do Not Affect Reaction Equilibria any enzyme that catalyzes the reaction S → P also catalyzes the reaction P → S enzymes accelerate the interconversion of S and P enzymes are not used up in the process the equilibrium point is unaffected 26 Reaction Intermediates reaction intermediate = any species on the reaction pathway that has a finite chemical lifetime – example: ES and EP complexes E + S ⇌ ES ⇌ EP ⇌ E + P 27 Rate-Limiting Steps rate-limiting step = the step in a reaction with the highest activation energy that determines the overall rate of the reaction activation energies are barriers to chemical reactions 28 Question The conversion of sucrose to CO2 and water has a very large and negative ∆G′°. Why is the conversion NOT spontaneous? A. Only some reactions have a negative ∆G′°. B. Conversion requires heat and O2. C. Conversion requires the presence of cofactors. D. There is a very large activation energy barrier. 29 Enzymes Lower Activation Energies Selectively enzymes have developed to lower activation energies selectively to increase rates for reactions needed for cell survival 30 Question What does an enzyme change relative to an uncatalyzed reaction? A. the equilibrium constant B. the rate of the reaction C. the pH D. the free energy change of the reaction 31 Reaction Rates and Equilibria Have Precise Thermodynamic Definitions reaction equilibria are linked to the standard freeenergy change for the reaction, ∆G′° reaction rates are linked to the activation energy, ∆G‡ 32 Thermodynamics Relates Keq and ∆G ° equilibrium constant, Keq = describes an equilibrium such as S ⇌ P under standard conditions used to compare biochemical process: [P] K′eq = [S] from thermodynamics: ∆G′° = −RT ln K′eq (6-2) (6-3) 33 The Relationship between K eq and ∆G ° Table 6-4 Relationship between K′eq and ∆G′° K′eq ∆G′° (kJ/mol) 10–6 34.2 10–5 28.5 10–4 22.8 10–3 17.1 10–2 11.4 10–1 5.7 1 0.0 101 –5.7 102 –11.4 103 –17.1 34 Question Which statement is true regarding the relationship between biochemical standard free-energy change and the equilibrium constant Keq? ∆G′° = –RT ln K′eq A. The relationship between free-energy change and equilibrium is exponential. B. A decrease in Keq translates into a more negative free energy. C. The higher the temperature, the less the reaction favors product formation. D. Small changes in free energy can lead to large changes in equilibria. 35 Rate Constants and Rate Equations the rate of any reaction is determined by the concentration of reactant(s) and the rate constant, k for the unimolecular reaction S → P, a rate equation expresses the rate of the reaction V = k[S] (6-4) where V is the velocity or rate of the reaction and [S] is the concentration of the substrate 36 First-Order Reactions first-order reaction = rate depends only on the concentration of S k has units of reciprocal time, such as s–1 37 Question If a first-order reaction for the unimolar reaction S → P has a rate constant k of 0.05 s–1, how is this interpreted qualitatively? A. 0.05% of the available S will be converted to P in 1 second. B. 5% of the available S will be converted to P in 1 second. C. 0.05% of the available P will be converted to S in 1 second. D. 5% of the available P will be converted to S in 1 second. V = k[S] 38 Second-Order Reactions second-order reaction = rate depends on the concentration of two different compounds or the reaction is between two molecules of the same compound k has units of M–1s–1 the rate equation becomes V = k[S1][S2] (6-5) 39 The Relationship between Rate Constants and Activation Energy from transition-state theory k= kT –∆G‡/RT e h (6-6) R = 8.315 J/mol·K where k is the Boltzmann constant and h is Planck’s constant the relationship between the rate constant k and the activation energy ∆G‡ is inverse and exponential 40 A Few Principles Explain the Catalytic Power and Specificity of Enzymes enzymes enhance rates in the range of 5 to 17 orders of magnitude Table 6-5 Some Rate Enhancements Produced by Enzymes Cyclophilin 105 Carbonic anhydrase 107 Triose phosphate isomerase 109 Carboxypeptidase A 1011 Phosphoglucomutase 1012 Succinyl-CoA transferase 1013 Urease 1014 Orotidine monophosphate decarboxylase 1017 41 Interactions between Enzymes and Substrates binding energy, ∆GB = energy derived from noncovalent enzyme-substrate interaction – mediated by hydrogen bonds, ionic interactions, and the hydrophobic effect – major source of free energy used by enzymes to lower the activation energy covalent interactions between enzyme and substrate lower the activation energy 42 The Role of Binding Energy in Catalysis the sum of the unfavorable activation energy ∆G‡ and the favorable binding energy ∆GB results in a lower net activation energy weak binding interactions between the enzyme and the substrate drive enzymatic catalysis optimized binding energy in the transition state is accomplished by positioning a substrate in a cavity (the active site) 43 Noncovalent Interactions between Enzyme and Substrate Are Optimized in the Transition State “lock and key” hypothesis = enzymes are structurally complementary to their substrates 44 Enzymes Must Be Complementary to the Reaction Transition State the full complement of interactions between substrate and enzyme is formed only when the substrate reaches the transition state 45 Question Binding energy is defined as the: A. energy derived from noncovalent enzyme-substrate interaction. B. energy derived from release of the product and release from the EP interaction. C. energy released from the conversion of ES to EP. D. difference in the uncatalyzed activation energy and catalyzed activation energy. 46