Enzymes: Core Concepts & Kinetics - BIOL5031 PDF

Chapter 8 Enzymes: Core Concepts & Kinetics Unit 8.1 Enzymes are Powerful & Highly Specific Catalysts BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 1 Outline of Chapter 8 8.1 En...

Chapter 8 Enzymes: Core Concepts & Kinetics Unit 8.1 Enzymes are Powerful & Highly Specific Catalysts BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 1 Outline of Chapter 8 8.1 Enzymes are powerful & highly specific catalysts 8.2 Free energy is a useful thermodynamic function for understanding enzymes 8.3 Enzymes accelerate reactions by facilitating the formation of the transition state 8.4 The Michaelis-Menten Model accounts for the kinetic properties of many enzymes 8.5 Enzymes can be inhibited by specific molecules 8.6 Vitamins are often precursors to coenzymes BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 2 Learning Outcomes o Recognize that nearly all enzymes are proteins o Illustrate that enzymes are highly specific and have great catalytic power o Explain how enzymes can enhance reaction rates by factors of 106 or more o Clarify that many enzymes require cofactors (metals or small organic molecules) for activity o Illustrate that enzymes can transform energy from one form to another o Distinguish function of enzymes from their names BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 3 Introduction BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 4 Enzymes are Remarkable Catalysts Enzymes: powerful biological catalysts. What is a catalyst? Made by all living organisms Dramatically enhance and control the rates of chemical reactions Almost all enzymes are proteins, why proteins? Proteins → highly effective catalysts → capacity to specifically bind a very wide range of molecules How do enzymes work? Enzymes bring substrates together in an optimal orientation → making and breaking chemical bonds Catalytically active RNA molecules → Ribozymes RNA was a biocatalyst early in evolution BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 5 Two Remarkable Properties of Enzymes 1. Speed Enzymes can accelerate reactions by factors of a billion or more! Most reactions do not take place at noticeable rates in the absence of enzymes BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 6 Power of Carbonic Anhydrase The transfer of CO2 from tissues → blood & then to air in alveolae of lungs would be less complete in absence of this enzyme Each molecule of carbonic anhydrase molecule → can hydrate 106 molecules of CO2/sec This catalyzed reaction is 107 times as fast as uncatalyzed one BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 7 Two Remarkable Properties of Enzymes 2. Specificity Enzymes are HIGHLY specific in: Reactions they catalyze Reactants they bind which are called ………………… An enzyme usually catalyzes a single chemical reaction or a set of closely related reactions E.g. Proteases catalyze proteolysis → hydrolysis of a …………… bond BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 8  Most proteolytic enzymes also catalyze a different but related reaction in vitro → hydrolysis of an ester bond Such reactions: ✓ Are more easily monitored than is proteolysis ✓ Useful in experimental investigations of these enzymes Enzymes can display a high degree of specificity, why? Due to the precise interaction of the enzyme and the substrate BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 9 Proteolytic Enzymes Differ in their Degree of Specificity Papain: is quite undiscriminating → cleaves any peptide bond with little regard to identity of the adjacent side chains Trypsin: is quite specific → catalyzes splitting of peptide bonds only on the carboxyl side of Lys and Arg residues Thrombin: is even more specific than trypsin → catalyzes hydrolysis of Arg-Gly bonds in particular peptide sequences only BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 10 Enzymes Classification Many enzymes have common names that provide little information about their function. E.g. trypsin, papain, thrombin Most other enzymes are named for their substrates and for reactions that they catalyze, with suffix “-ase" added Peptide hydrolase is an enzyme that hydrolyzes peptide bonds ATP synthase is an enzyme that synthesizes ATP ❖ Note: enzymes catalyze reaction in both forward & reverse directions, BUT only 1 direction is denoted in the name BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 11 Enzyme Nomenclature To bring some consistency to enzyme nomenclature→ a classification system for enzymes was established Reactions are divided into 6 MAJOR groups These groups are further subdivided A 4-number code preceded by the letters EC → identifies all enzymes BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 12 Enzyme Nomenclature Nucleoside monophosphate (NMP) kinase catalyzes the following reaction: ATP + NMP ADP + NDP NMP kinase transfers a P group from ATP to NMP to NDP and ADP i.e. it is a transferase, or member of group 2 Many groups such as sugars & carbon units can be transferred Transferases that shift a P group are designated → 2.7 Various functional groups can accept P group If a phosphate is the acceptor → transferase is designated 2.7.4 The final number designates the acceptor more precisely NMP kinase → a nucleoside monophosphate is the acceptor and enzyme's designation is EC 2.7.4.4 BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 13 Many Enzymes Require Cofactors for Activity The catalytic activity of many enzymes depends on presence of small molecules (cofactors) Although the precise role varies with the cofactor and enzyme These cofactors are able to execute chemical reactions that cannot be performed by the standard set of 20 amino acids An enzyme without its cofactor = an apoenzyme The complete catalytically active enzyme = a holoenzyme Apoenzyme + Cofactor = Holoenzyme BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 14 Many Enzymes Require Cofactors for Activity Cofactors can be subdivided into 2 groups: i. Metals ii. Coenzymes: (Small organic molecules) Coenzymes are often derived from vitamins Coenzymes can be either: Tightly bound coenzymes → prosthetic groups (catalytic and unchanged in the reaction) Loosely associated coenzymes → behave more like co- substrates, why? The use of the same coenzyme by a variety of enzymes sets coenzymes apart from normal substrates, however, as does their source in vitamins Enzymes that use the same coenzyme → usually perform catalysis by similar mechanisms BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 15 Enzyme Cofactors BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 16 The B Vitamins BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 17 Enzymes Can Transform Energy from One Form into Another In many biochemical reactions, the energy of the reactants is converted with high efficiency into a different form Photosynthesis: light energy → chemical-bond energy (through an ion gradient) Cellular respiration: free energy in small molecules→ free energy of an ion gradient → free energy of ATP How can enzymes use the chemical energy in ATP? Myosin enzyme: ATP → mechanical energy of contracting muscles Membrane pumps: use it to transport molecules/ions → creating chemical & electrical gradients BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 19 Summary o Nearly all enzymes are proteins o Enzymes are highly specific and have great catalytic power o Enzymes can enhance reaction rates by factors of 106 or more o Many enzymes require cofactors (metals or small organic molecules) for activity o Enzymes can transform energy from one form to another o Function of enzymes can be distinguished from their names BIOL5031 Enzyme Biochemistry Dr. Bahja Al Riyami 20