Biochemistry PDF

Biochemistry Biochemistry can be defined as the science concerned with the chemical basis of life (Gk bios "life"). The cell is the structural unit of living systems. Thus, biochemistry can also be described as the science concerned with the chemical constituent...

Biochemistry Biochemistry can be defined as the science concerned with the chemical basis of life (Gk bios "life"). The cell is the structural unit of living systems. Thus, biochemistry can also be described as the science concerned with the chemical constituents of living cells and with the reactions and processes they undergo. By this definition, biochemistry encompasses large areas of cell biology, of molecular biology, and of molecular genetics. Because life depends on biochemical reactions, biochemistry has become the basic language of all biologic sciences. Biochemistry is concerned with the entire spectrum of life forms, from relatively simple viruses and bacteria to complex human beings. Metabolism  Metabolism En maceomole olecules Contalnien Metabolic pathways are series of consecutive enzymatic Proteins nutrients Polysaccharides Carbohydrates reactions that produce specific products. Their reactants, Lipids Nucleic acids Fats Proteins intermediates, and products are referred to as metabolites. Each reaction in the metabolic pathways is catalyzed by a distinct enzyme, of which there are 4000 known. DP+HPO NADY NADP The reaction pathways often divided into two categories: FAD 1. Catabolism, or degradation nutrients and cell Anabolism ATP Catabolism constituents are broken down exergonically to salvage NADH FADH. their components and/or to generate free energy. 2. Anabolism,or biosynthesis - biomolecules are synthesized Chemical energy from simpler components. The free energy released by catabolic processes is conserved Precursor molecules Energy. depleted through the synthesis of ATP from ADP and phosphate or Amino acids end products Sugars CO through the reduction of the coenzyme NADP to NADPH. Nirrogeous bases ATP and NADPH are the major free energy sources for anabolic pathways. Enerry relationships between catabolic and anabolic pathways  ATP and NADPH are the major free Overview of catabolism energy sources for anabolic pathways Proteins Carbohydrates Lipids Complex metabolltes Amino acids Chcese Glucose Fatty acids &Glycerol ADP + HPO NADP ADP ATP NAD Glycolysis NADH Degradation Biosynthesis Pyruvate Co, ATP Acety-CoA NADPH Simple products NH, Citric NAD Acid NADH -FAD -FADH Catabolism: Large numbers of diverse substances Cycle (carbohydrates, lipids, and proteins) to common intermediates (mainly acetyl-CoA). These intermediates CO, are then further metabolized in a central oxidative -NADH pathway that terminates in a few end products. NAD FAD Oxidative phosphortatlon FADH, Biosynthesis: Relatively few metabolites, mainly ADP pyruvate, acetyl-CoA, and the citric acid cycle intermediates, serve as starting materials fora host of H,0 varied biosynthetic products.  Enzymes Biocatalyst - a biological substance that initiates or increases the rate of a chemical reaction in a living organisms without itself being affected: proteins (enzymes) " in a few cases nucleic acids (ribozymes, Altman A and Cech TR, Nobel Price 1998)  Naming and classification of enzymes Enzymes names - traditionally end in "-ase" (Eg: amylase) - exceptions are proteolytic enzymes (Eg: Trypsin) Why classify enzymes?- Lack of consistency in the nomenclature Some names indicates the only the substrate; no nature of the reaction Eg: lactase and fumarase Some names explains only the nature of the reaction Eg: transcarboxylase Some enzymes make clear the substrate and nature of the reaction Eg: malate dehydrogenase Some enzymes known by more than one name International Union of Biochemistry appointed a commission to classify the enzymes in 1955 (Enzyme Commission). The first version was published in 1961. The current sixth edition, published in 1992, contains 3196 different enzymes.  The Enzyme Commission's (EC) system of classification First Enzyme class Type of reaction catalyzed digit Oxidation/Reduction reactions 1 Oxidoreductases Transfer of H atoms, O atoms or electrons from one substrate to another Transfer of an atom or group between two molecules (excluding 2 Transferases reactions in other classes) AX + B BX +A Hydrolysis reactions 3 Hydrolases A-X + H,0 X-0H + HA Lyases Removal of a group from substrate (not by hydrolysis) 5 Isomerases Isomerization reactions The synthetic joining of two molecules, coupled with the breakdown of ATP or other NTPS. 6 Ligases X+Y + ATP >X-Y + ADP + Pi X+ Y+ ATP >X-Y + AMP + PPi The EC assigned to each enzyme (1) a code number of four elements separated by dots. First number :The main class Second number :The subclass Third number : The Sub-subclass Fourth number: The arbitrarily assigned serial number in sub-subclass (2) a systematic name - includes the name of the substrate or substrates and a word ending'-ase' indicating the nature of the reaction. Example: Hexokinase Systematic name: ATP:glucose phosphotransferase - indicates catalyzes the transfer of a phosphoryl group from ATP to glucose. Classification number: EC 2.7.1.1. 2 : Transferase (main class) 7 : Phosphotransferase (subclass) 1 : Phosphotransferase with a hydroxyl group as acceptor (sub-subclass) 1 : Arbitrarily assigned serial number  Isoenzymes in EC classification In EC classification, isoenzymes (different enzymes catalyzing the same reactions) will have the same four number code. Eg: Five different isoenzymes of lactate dehydrogenase will have same identical code EC 1.1.1.27. Full EC classification can be found at: https://iubmb.qmul.ac.uk/  Enzyme synthesis and structure Double-strand DNA Enzyme synthesis and structure ATGTGCTGGCGGCATTAT TAA 5 3' Antisense strand Amino acids 3 5' Sense strand Peptide bonds TAC ACGACOGCOGTAATA ATT " Transcription Transortgion - Translation mRNA - Post-translational modifications AUG UGCUGGCGGCAUUAU-.-UAA 4 Transation T Tv4RNA Start Stop codon codon Tyr-tANA AMP2 P Protein Met Cys- Trp Arg- His Tyr NH; COO  Cofactors Enzymes catalyze a wide variety of chemical Substrate reactions. Their functional groups of polypeptide can Coenzyme " facilely participate in acid-base reactions, form certain types of transient covalent bonds, and take part in charge-charge interactions. Apoenzyme Cofactor Holoenzyme They are less suitable for catalyzing oxidation (protein (nonprotein (whole portion), portion), enzyme), reduction reactions and many types of group Inactive actlvator active transfer processes. Enzymes catalyze these reactions in association with small molecule cofactors, which essentially act as the enzymes' "chemical teeth."  Inorganic metal ions like Fe2 Mg?", or Mn? Cofactors Coenzymes- organic or metalloorganic molecule like biotin coenzyme A, PLP Some Inorganic Elements That Serve as Cofactors Prosthetic group: A coenzyme or Cu?+ Cytochrome oxidase metal lon that is very tightly or even Fe? or Fe Cytochrome oxidase, catalase, peroxidase covalently bound to the enzyme K Pyruvate kinase protein. Mg?+ Hexokinase, glucose 6-phosphatase, pyruvate kinase Mn Arginase, ribonucleotide reductase Some enzymes require both Mo Dinitrogenase coenzyme and one or more metal N¡?+ Urease ions for activity. Se Glutathione peroxidase Zn? Carbonic anhydrase, alcohol dehydrogenase, carboxypeptidases A and B  Many vitamins are coenzyme precursors Coenzyme Reaction Mediated Precursor in mammals Biotin Carboxylation Biotin (vitamin B,) Cobalamin (B,,) coenzymes Alkylation Vitamin B12 Coenzyme A Acyl transfer Pantothenic acid (vitamin B,) Flavin coenzymes Oxidation-reduction Riboflavin (vitamin B,) Lipolc acid Acyl transfer Not required in diet Nicotinamide coenzymes Oxidation-reduction Nicotinic acid (niacin, Vit B,) Pyridoxal phosphate Amino group transfer Pyridoxine (vitamin B) Tetrahydrofolate One-carbon group transfer Folate (vitamin B,) Thiamine pyrophosphate Aldehyde transfer Thiamine (vitamin B,)  The active site Binding sites link to specific groups in the substrate, ensuring that the enzyme and substrate molecules are held in a fixed orientation with respect to each other, with the reacting group or groups in the vicinity of catalytic sites. Catalytic site catalyzes the reaction. The region which contains the binding and catalytic site is termed the active site, or active centre, of the enzyme. Tyr 248 Arg 145 GIu 270 MEnhalian zin Carboxypeptidase A metaloendopeptidase The active site comprises only a small proportion of the total volume of the enzyme is usually at or near the surface it must be accessible to substrate molecules in some cases, a clearly-defined pocket or cleft into which the whole or part of the substrate can fit often includes both polar and non-polar amino acid residues, creating an arrangement of hydrophilic and hydrophobic microenvironments not found elsewhere on an enzyme molecule The binding and catalytic sites must be either amino acids or cofactors. Substrate binding involves a variety of weak non-covalent interactions. The amino acid residues in the active site which do not have a binding or catalytic function may nevertheless contribute to the specificity of the enzyme.  Specificity of enzyme action Enzymes are specific in action, exhibit both substrate and product specificity. Group specificity These enzymes act on several different, though closely related, substrates to catalyze a reaction involvinga particular chemical group. Example: Alcohol dehydrogenase catalyzes the oxidation of a variety of alcohols. Hexokinase catalyzes the transfer of phosphate from ATP to several different hexose sugars. Absolute specificity These enzymes act only on one particular substrate. Example: Glucokinase catalyzes the transfer of phosphate from ATP to glucose and not to other sugar.  Stereochemical specificity R enantiomer Senantiomer If a substrate exist in two stereochemical forms, only one of the isomers will undergo reaction as a result of a catalysis by a particular enzyme. Example: L-amino acid oxidase mediates the oxidation of L-amino acids to oxo acids. binding site of the receptor D-amino acid oxidase mediates the oxidation of D binding site of the receptor amino acids to oXO acids. COO CO0 The only enzymes which act on both stereoisomeric forms are those function is to interconvert L- and D CH, CH, isomers. D-Alanine L-Alanine Eg: Alanine racemase which catalyzes: L-Alanine 4 D-Alanine  Monomeric enzymes Consist only a single polypeptide chain Can not be dissociated into smaller units Very few monomeric enzymes are known All of these catalyze hydrolysis reactions In general, they contain 100-300 amino acids (M.Wt. 13-35 kDa) So Some are associated with a metal ion (eg. SpeccY Carboxypeptidase A) N Most are act without any cofactor. Gly 216 Examples: A number of proteases are monomeric enzymes Tyr 172 (serine proteases, pepsin A, rennin, papain, L2 exopeptidases like carboxy peptidase Aand B). X-ray structure of bovine trypsin in covalent Other enzymes include ribonuclease and complex with its inhibitor leupeptin lysozyme.  Oligomeric enzymes Oligomeric enzymes consists of two or more polypeptide chains which are usually linked to each other by non-covalent interactions and never by peptide bonds. C=0 The component polypeptide chains are termed sub-units and may be identical to or different from each other. CH, Pyruvate The molecular weight is usually in excess of 35 kDa. ToNADH The vast majority of known enzymes are oligomeric enzymes. lactate dehydrogenase For example, all of the enzymes involved in glycolysis possess either two or four NAD subunits. HO-(-H CH, L-Lactate Lactate dehydrogenase  Free energy: The indicator of spontaneity Free energy: The amount of energy free' for work under the given conditions. J. Willard Gibbs defined the free energy content of any closed system as: G=H-TS H=Enthalpy, reflecting the number and kinds of bonds S= Entropy T=The absolute temperature (in Kelvin) When a chemical reaction occurs at constant temperature, the free-energy change, AG, is AG= AH -TAS Aprocess tends to occur spontaneously only if AG is negative. The standard Gibbs free energy (AG): Change of free energy that acCompanies the formation of 1 mole of substance from its component elements, at their standard states (the most stable form of the element at 25°C and 100 kPa) AG (kJ" mol) ATP + H,0 ADP + P, -30.5 The AG of a reaction varies with the total concentrations of its reactants and products and thus with their ionic states. So, ATP hydrolysis under physiological conditions has AG 50 kJ mol rather than the -30.5 kJ mol: of its AGO.  Energy-coupling links the reactions in biology Cell function depends largely on molecules, such as proteins Reaction 2: and nucleic acids, for which the free energy of formation ATPADP +P, Reaction 3: positive. Gluense giucone AT ADP Reaction l: To carry out these thermodynamically unfavorable, energy Glucoe. gucose 6phauphate requiring (endergonic) reactions, cells couple them to other AG reactions that liberate free energy (exergonic reactions), so that the overall process is exergonic: the sum of the free energy changes is negative. The coupling of exergonic and endergonic reactions by enzymes Reaction coordinate is absolutely central to the energy exchanges in living systems. (a) AGO' (kJ " mol) Endergonic half-reaction 1 P + glucose glucose-6-P + H,0 +13.8 Exergonic half-reaction 2 ATP + H,0 ADP + P. -30.5 Overall coupled reaction ATP + glucose ADP + glucose-6-P -16.7 23 Enzyme kinetics  Chemical reactions The collision theory Molecules can react only if they come into contact with each other. Any factor which increases the collisions will increase the reaction rate. e.g. increased concentration of the reactants or increased temperature. However, not all colliding molecules will react, since, not all colliding molecules possess between them suficient energy to undergo reaction. Activation energy and transition state theory Not all colliding molecules will react, since, not all colliding molecules possess between them sufficient energy to undergo reaction. The energy of an individual molecule will depend on, for example on what collisions that molecule has recently been involved in. In order for a reaction to take place, colliding molecules must have sufficient energy to overcome a potential-barrier known as the energy of activation. This is true even of energetically favorable reactions. The requirement of the activation energy is explained by transition state theory (Henry Eyring): Every chemical reaction proceeds via the formation of an unstable intermediate between reactants and products. transition-state free energy R'COR t H,0 + R'OH activation energy E" OC O-C + R"OH initial state overall free OR" energy change final state course of reaction