Enzyme 2024 汪敏 PDF

Enzyme What are enzymes? Enzymes are powerful and highly specific biocatalysts produced by living cells which increase the rates of chemical reactions in tissues, which catalyze the conversion of one or more compounds (substrates) into one or more different compounds (products)。 Are all enzymes...

Enzyme What are enzymes? Enzymes are powerful and highly specific biocatalysts produced by living cells which increase the rates of chemical reactions in tissues, which catalyze the conversion of one or more compounds (substrates) into one or more different compounds (products)。 Are all enzymes proteins? It depends on how you define "enzyme". Wiktionary says: an enzyme is a globular protein that catalyses a biological chemical reaction. Wikipedia says: Enzymes are macromolecular biological catalysts.  Enzyme Living Cells: Thousands of chemical reactions are proceeding very rapidly All reactions are catalyzed by special biocatalysts, enzymes —protein and occasionally RNA or DNA (ribozymes) Reactions in cells are different from general chemical reactions: easily, rapidly regulated and controlled Enzymes are highly effective and extremely specific catalysts  Main topics Structure and Function of Enzyme Property and Catalytic Mechanisms of Enzymes Kinetics of Enzyme-Catalyzed Reaction Regulatory Enzymes Nomenclature and Classification of Enzymes Clinical Application of Enzymes  Part one Structure and Function of Enzyme  1. Structure of enzyme Composition of Enzyme Molecules simple enzyme: all proteins conjugate enzyme: protein and non-protein conponents protein components ：apoenzyme holoenzyme determine reaction specificity nonprotein components : cofactors determine reaction type Inorganic ions: metal ions Small organic molecules Cofactors play an important role in comjugate Enzymes Prosthetic groups: tight bound to the protein portion by covalent bond Cofactors Coenzyme: bound loosely Simple dialysis can separate it from its protein partner. Many Coenzymes & Prosthetic Groups are Derivatives of B Vitamins Coenzymes: serve as substrate shuttles or group transfer agent e.g. folate (methyl), coenzyme A (acyl), NADH and NADPH (H and electron) Metal ions: cofactors in ~2/3 of enzymes Metalloenzymes (metal as prosthetic groups) roughly 1/3 of Prosthetic groups Metal-activated enzymes  Function of Metal ions Participate in redox reactions ,transport electron Facilitate the binding and orientation of substrates Facilitate the formation of covalent bonds Interact with substrates to render them more electrophilic (electro-poor) or nucleophilic (electro-rich) Cofactors of enzymes  Vitamins Vitamins are a group of organic compounds required in small quantities for a variety of biochemical functions and which, generally, cannot be synthesized by the body and must be supplied in the diet. Deficiency of any vitamin will lead to a specific disease Classification of the vitamins Non-B-Complex: Ascorbic acid (vit.C) Water-soluble B-Complex: Thiamine(Vit.B1),Riboflavin(Vit.B2) Niacin(Vit.B3),Biotin,Pantothenic acid,Folic acid, Vit.B12, Pyridoxine(Vit.B6) Fat-soluble : Vit. A, D, E, K  Vitamins Vitamin B1. (thiamin). – Active form: Thymine pyrophosphate (TPP) acts as a coenzyme in oxidative decarboxylation of alpha keto acids. Vitamin B 2. (riboflavin) - Active form: Flavin mononucleotide(FMN) and Flavin adenine dinucleotide (FAD) accept two hydrogen atoms reversibly forming FMNH2 or FADH2. FMN and FAD are bound to oxidoreductases(flavoenzymes)  Vitamin B3 (vitamin PP, nicotinamide) NADP+ nicotinamide adenine dinucleotide phosphate NAD+ nicotinamide adenine dinucleotide Coenzyme in oxidation and reduction reactions. NAD+ and NADP+ ( Oxidized forms) accept a hydride ion (a hydrogen atom plus one electron) to produce NADH and NADPH ( Reduced forms). Structure of NAD+ and NADP+. For NAD+, R = H. For NADP+, R = PO3 2− Different components of Enzymes monomeric enzyme: only possess a tertiary structure oligomeric enzyme: two or more polypeptide chains ssociated by non- covalent interactions and never by peptide bonds multienzyme complex: a structurally distinct and ordered collection of enz ymes, often catalyzing successive steps in a metabolic pathway multifunctional enzyme or tandem enzyme: different enzymic activities that are resident in the same polypeptide chain  multienzyme complex pyruvate dehydrogenase complex  2. Active center of enzyme Active site / active center The region of an enzyme where substrate molecules bind and undergo a chemical reaction. Essential group The amino acid residues drawn from diverse portions of the polypeptide chain of the enzyme, which are essential to the enzyme activity. Binding groups Catalytic groups Essential groups outside of the active Structure of chymotrypsin site  Substrate Essential groups outside active site Catalytic site Essential groups in active site Active site Binding site  The active site of lysozyme  The active site of lysozyme can attach six hexosyl residues（NAG6, A， B，C，D，E，F).  The residues containing essential groups in the active site are numbered as 35, 52, 62, 63, 101 and 108. Glu35 and Asp52 are catalytic sites,  Asp101 and Trp108 are binding sites.  3. Isoenzymes Isoenzymes have different amino acid sequences but catalyze the same reaction. Isoenymes may exhibit subtle differences in properties such as sensitivity to particular regulatory factors or substrate affinity that adapt them to specific tissues or circumstances. * Lactate dehydrogenase (LDH1～ LDH5) H H H H H H H M M M H H H M M M M M M M LDH1 LDH2 LDH3 LDH4 LDH5 (H4) (H3M) (H2M2) (HM3) (M4) Heart, Reticuloendothelial Lung Kidney, Liver, Red blood system Placenta, Striated cells Pancreas muscle Each LDH molecule is composed of four polypeptide chains , There are two types of polypeptide chains in LDH called muscle subunits (M) and heart subunits (H) which can be combined into the LDH tetramer in 5 different ways.  Lactate LDH Pyruvate CH3CHOCOOH CH3COCOOH NAD+ NADH+H+ The M4 froms of the isozyme seem to have a higher affinity for pyruvate compared with the H4 form Following a myocardial infarction ,the LDH1 (H4) rises and reaches a peak appoximately 24h later.  Part two Property and Catalytic Mechanisms of Enzymes  Like all catalysts, enzymes are neither consumed nor permanently altered as a consequence of their participation in a reaction.  Only catalyze the thermodynamically favorable reactions.  Speeds the reaction rate, but can not alter the equilibrium of the reaction. 1. Properties of enzyme catalyzed reactions. Highly catalytic efficiency:  Enzyme display enormous catalytic power, accelerating reaction rates as much as 1016 over uncatalyzed levels.  Milder reaction conditions (T 60 years Atrophic gastritis: chronic inflammation of the stomach inadequate HCL production B12 is not released from protein binding it Can’t be absorbed  B12 Deficiency Pernicious anemia – characterized by large, immature red blood cells and damage to nervous system Other symptoms include: – smooth tongue – fatigue – damaged nerve sheaths  creeping paralysis  general malfunction of nerves and muscles – nerve damage is serious and irreversible  Sources of B12 Only in foods of animal origin Serious problem for strict vegetarians or vegans – need to eat B12 fortified foods OR take supplements  Final Word on B Vitamins Small amounts needed but play crucial role – Roles of B vitamins are closely interrelated – Deficiency of one often influences role of another Toxicity is more likely to result from over use of supplements, not food intake  Vitamin C Ascorbic Acid – means “no scurvy” acid  Vitamin C Role as an antioxidant – protects water soluble compounds from oxygen damage – protects iron from oxidation & thus promotes its absorption Role as cofactor in production & maintenance of collagen  Collagen Protein that forms the base for all connective tissues in body – bones, skin, teeth, tendons Also important for: – scar tissue of wound healing – reinforcing structure to repair bone fractures – supporting material of capillaries that prevents bruising  Vitamin C Enhances immune system and protects against infection Important for thyroxin production – hormone that regulates basal metabolic rate and body temperature Involved in release of stress hormones from adrenal gland  Vitamin C Deficiency Scurvy Symptoms : – loss of appetite – growth cessation – tenderness to touch – weakness – bleeding gums & loose teeth – tiny red spots/bruises on skin – anemia  Vitamin C Deficiency Although Vit C intake may be low in certain groups, scurvy is seldom seen in China But may be seen in: – infants fed only cow’s milk – the elderly – alcoholics Vitamin C and the Common Cold Linus Pauling in 1960’s: massive doses of Vit C could protect against & cure the common cold Studies have since discredited this theory Evidence that Vit C may lessen severity of symptoms but nothing can prevent or cure the common cold  Vitamin C Supplements Widespread use re: to preventing or curing colds and cancer Possible toxic effects from very high doses taken over long period of time. Adverse effects include: – nausea, abdominal cramps, diarrhea – can interfere with test used to detect diabetes – can interfere with some medications  Vitamin C Sources Fruits and vegetables Citrus fruits Broccoli, green pepper, cantaloupe, strawberries, cauliflower Potato -- as a staple Vitamin C enriched juices (e.g. apple) Vitamin is destroyed by oxidation, high heat, and loss in water  Lipoic Acid Acts as an acyl group carrier involved in carbohydrate metabolism. Functions in resisting fatty liver and decreasing concentration of cholesterol in blood. In humans, deficiency is not reported  People most likely to need vitamin supplements Women preparing for conception, pregnant People with low energy intake (1200 kcal) Vegans (Vit B 12) Newborns need Vit K People with limited milk intake and limited sun exposure (Vit D) People with certain medical conditions Smokers & excess alcohol consumers Calcium, phosphorus and their metabolism  Calcium is one of the most abundant inorganic elements in the human body, with an adult content of about 30mol (1200g/70kg body weight), second only to carbon, hydrogen, oxygen, and nitrogen. Phosphorus content is approximately 19.4mol (600g) for an adult. Calcium and phosphorus are not only important components of bone, but also have many other important physiological functions  Distribution and function of calcium and phosphorus in the body Calcium is both the main component of bone and plays an important regulatory role. - Calcium is the main component of bones and teeth, playing a supportive and protective role. - Cytoplasmic calcium plays many important physiological roles as a second messenger in signal transduction.  Distribution and function of calcium and phosphorus in the body Phosphorus is a component of many important biomolecules in the body. Phosphorus, in addition to constituting bone salts and participating in osteogenesis, is also a component of important biomolecules such as nucleic acids, nucleotides, phospholipids, and coenzymes, playing their respective important physiological functions  Distribution and function of calcium and phosphorus in the body Disruption of calcium and phosphorus metabolism can cause various diseases Vitamin D deficiency can cause calcium absorption disorders, leading to rickets in children and osteomalacia in adults. Bone matrix loss and progressive bone desalination can lead to osteoporosis in middle-aged and elderly individuals. Hyperphosphatemia is common in patients with chronic kidney disease and is closely related to serious cardiovascular complications such as coronary artery and heart valve calcification. Calcium and phosphorus metabolism and dynamic balance in the human body The metabolism of calcium and phosphorus in the bone is the main component of calcium and phosphorus metabolism in the body bone Calcium phosphorus kindney blood vessel intestine urinary excretion Fecal excretion Calcium and phosphorus metabolism are regulated by three hormones Main regulatory hormones: 1,25-(OH)2-VitD3（active form of vitamin D3） parathyroid hormone (PTH) calcitonin (CT) Main regulatory target organs: Small intestine, kidney bone  Q: Quiz 1 Of the six curves labeled in the Lineweaver-Burk graph below, three represent the effects of 0mM, 5mM, and 15 mM of a competitive inhibitor on a hypothetical enzyme. Which of the curves most likely represents the 15-mM concentration of the competitive inhibitor. A X 1/V B C D A E 1/[S]  Q: A noncompetitive inhibitor of an enzyme a. Increase Km with no or little change in Vmax b. Decrease Km and decrease Vmax c. Decrease Vmax d. Increase Vmax e. Increase Km and increase Vmax A: c  Q: The Km is: a. Numerically equal to 1/2 Vmax b. Dependent on the enzyme concentration c. Independent on pH d. Numerically equal to the substrate concentration that gives 1/2 Vmax e. Increased in the presence of a noncompetitive inhibitor  A: d  Km does not depend on the concentration of enzyme, but can vary with pH.  A noncompetitive inhibitor decreases Vmax, but does not alter Km Quiz 2 Q: Which of the following statements correctly describes allosteric enzymes? a. Effectors may enhance or inhibit substrate binding b. They are not usually controlled by feedback inhibition c. The regulatory site may be the catalytic site d. Michaelis-Menten kinetics describe their activity Quiz 2 A: a Hint: b. Many allosteric enzymes are often placed at the first step of a metabolic pathway. The end product of the pathway then act as a negative effector of the enzyme.This is called feedback inhibition. c. When a modifier binds at the allosteric site, it affects the active site by altering Vmax and Km. d. All allosteric enzyme doesnot obey Michaelis- Menten kinetics.