Biochemistry Notes PDF

29 Nadine Dababseh Noor Hamadneh Nafez Abu Tarboush 1  Naming of Enzymes 1. General naming: the enzyme is named after the substrate and ends with a suffix –ase Example: ATPase is an enzyme that breaks down ATP, and ATP synthase is an enzyme...

29 Nadine Dababseh Noor Hamadneh Nafez Abu Tarboush 1  Naming of Enzymes 1. General naming: the enzyme is named after the substrate and ends with a suffix –ase Example: ATPase is an enzyme that breaks down ATP, and ATP synthase is an enzyme that synthesizes ATP 2. Common naming: a name that has no relation to the substrate of reaction and not ending with –ase Example: Trypsin which breaks down proteins in the small intestine 3. The EC (Enzyme Commission) number: gives a description of the substrate, enzyme and the reaction EC numbers do not specify enzymes, but enzyme catalyzed reactions A four-digit code separated by periods: Major Class (First digit): Defines the major class of enzymes based on the type of reaction they catalyze, there are 7 major classes. Minor Class (Second digit): Specifies the substrate or group of compounds the enzyme acts upon. Subclass (Third digit): Provides further refinement of the substrate or reaction type. Sub-classification (Fourth digit): Unique identifier for the enzyme, assigned to each enzyme within a given subclass. Example: EC 3: hydrolases EC 3.4: hydrolases that act on peptide bonds EC 3.4.11: hydrolases that cleave off the amino-terminal of the amino acid polypeptide EC 3.4.11.4: cleave off the amino-terminal end from a tripeptide Enzyme classification according to structure 1. Simple vs complex (conjugated) 2. Holoenzyme vs apoenzyme 2 Enzyme classification by Function Class (1st digit): Describes the general type of reaction the enzyme catalyzes. There are 7 major classes in order: 1: Oxidoreductases catalyze oxidation-reduction reactions 2: Transferases transfer of groups from one molecule to another 3: Hydrolases hydrolysis of various bonds (breaking down the substance by the addition of water) 4: Lyases breaking of double bonds by means other than hydrolysis or oxidation (addition of H2O, CO2, NH3) 5: Isomerases isomerization of molecules (some minor classes have mutase in their names) 6: Ligases joining two molecules with covalent bonds (needs energy) 7: translocases catalyze the movement of a molecule from one location to another (will be discussed further) Oxidoreductases (1) They facilitate the transfer of electrons from one molecule to another. Redox reactions (involves the transfer of hydrogen atoms, electrons or oxygen atoms) Requires coenzymes (heme) 3 Minor classes: Dehydrogenases: Transfer hydrogen ions or electrons from substrate to NAD+(most common acceptor). Example: lactate dehydrogenase Alcohol dehydrogenase Oxidases: Transfer electrons to oxygen producing hydrogen peroxide as a by- product Example: glucose oxidase Peroxidases: Use hydrogen peroxide as an electron acceptor (oxidizing agent) to oxidize two molecules of glutathione (GSH) which results in water Oxygenases: oxidation by oxygen and the reduced product is H2O not H2O2 Types of oxygenases: 1- Monooxygenases: transfer one oxygen atom to the substrate, and reduce the other oxygen atom to water 2- Dioxygenases: incorporate both atoms of molecular oxygen (O2) into the products of the reaction 4 Transferases (2) Transferases are enzymes that catalyze the transfer of functional groups (methyl, acetyl, sulfate or phosphate groups) from one molecule to another. Minor class: - Kinases: Transfer phosphate groups Example: glucokinase, phosphofructokinase Phosphofructokinase: Catalyzes the transfer of phosphate from ATP to fructose-6-phosphate giving fructose-1,6- bisphosphate in glycolysis (Most common donor of phosphate is ATP) - Transaminases (aminotransferases): Transfer amino groups from one amino acid to a keto acid, converting the amino acid to a keto acid and the keto acid to an amino acid Example: Alanine Pyruvic acid Glutamic acid Alpha ketoglutamic acid Aspartate Oxaloacetate 5 Hydrolases (3) Hydrolases are enzymes that catalyze hydrolysis reactions, which involve the breaking of a bond in a molecule by the addition of water. Breaks down complex polymers like proteins, lipids and carbohydrates (macromolecules) Minor classes: o Proteases (Peptidases): Break down proteins (proteolytic enzymes differ in their degree of substrate specificity) o Trypsin catalyzes the splitting of peptide bonds only on the carboxyl side of lysine and arginine o Thrombin catalyzes the hydrolysis of Arg-Gly bonds in particular peptide sequences only o Lipases: Hydrolyze ester bonds in lipids o Amylases: Hydrolyze starch into simpler sugars Lyases (4) Catalyze the addition or removal of functional groups from their Substrates with the associated formation or removal of double bonds between C-C, C-O and C-N. Note:- the use of water not as hydrolysis (break down molecule), it plays a role by hydration and dehydration (Breaking down or build up for double bond) Decarboxylazes are an example of lyases Minor classes o Aldolases: Catalyze the cleavage of carbon-carbon bonds (fructose-1,6- bisphosphate aldolase). o Enolase: interconverts phosphoenolpyruvate and 2- phosphoglycerate by formation and removal of double bonds 6 Isomerases (5) catalyze the conversion of a molecule to its isomer (a compound with the same chemical formula but a different arrangement of atoms). These enzymes do not change the number of atoms but rearrange the structure. Glucose-6-phosphate isomerase isomerizes glucose6- phosphate to fructose-6- phosphate Phosphoglycerate mutase transfers a phosphate group from carbon number 3 to carbon number 2 of phosphorylated glycerate (BPG intermediate) Ligases (6) Ligases catalyze the joining of two molecules (usually with the input of energy, ATP). They form new covalent bonds between two substrates, and release a by-product Example: pyruvate carboxylase 7 Functional groups in catalysis Functional groups on amino acid side chains: almost all polar amino acids (Ser, Cys, Lys, & His) can catalyze covalently Histidine can do pKa, physiological pH & acid-base catalysis Coenzymes in Catalysis (organic molecules): usually synthesized from vitamins and they are specific for a type of reaction 1. Activation-transfer coenzymes 2. Oxidation–reduction coenzymes Activation-Transfer coenzymes 2 mains groups Functional group: forms covalent bonds Binding group: binds to the enzyme Dependence on the enzyme for additional specificity of substrate & additional catalytic power 1-TPP Inactive Active Functional Function Reactions group thiamine Thiamine Reactive carbon thiamine carbon pyruvate Pyrophosphate atom forms a covalent dehydrogenase (Vitamin B1) (TPP) bond with a substrate keto α- group while ketoglutarate cleaving the dehydrogenase 8  adjacent carbon (carbon bond) Converted to the active form in the brain and liver Pyrophosphate: 2 phosphate groups linked together o Provides negatively charged oxygen atoms o Chelate Mg+2 (tight bonding) Decarboxylases need TPP to work Deficiency of vitamin B1 results in accumulation of the substrate and decrease in the product 2-coenzyme A (Co-A) Inactive Active Functional Function Binding group group pantothenate CoA sulfhydryl group Attacks carbonyl adenosine (Vitamin B5) (nucleophile) groups 3’,5’- bisphosphate Formation of acyl thioesters Acyl multiple carbons Acetyl 3 carbons Co-As structure includes Adenine, ribose with phosphate, pantothenic acid (vitamin B5) and a modified cysteine NAD+ and other coenzymes NAD+ is considered a coenzyme because it is synthesized from vitamins, common in many reactions and has a constant amount (in cells) and the original is regenerated 3- Biotin Inactive Active Deficiencies Function Reactions Biotin (vitamin B7) Biocytin (covalently Long course of carboxylation Pyruvate bound to Lys) antibiotic treatment reactions covalently carboxylase bound to Lys Consumption of AcetylCo raw eggs: egg white carboxylase 9  protein (avidin) has fatty acid high affinity to synthesis biotin Source: food and intestinal bacteria Helps carboxylases to function ‫تمت كتابة هذا الشيت عن روح والدة زميلنا عمرو رائد من دفعة تيجان‬ ‫دعواتكم لها بالرحمة والمغفرة‬ Thank you 10