Biochem Review Session PDF

MODULE 5 INTRODUCTION TO ENZYMOLOGY OVERVIEW 4.1 Regarding Enzymes 4.2 Enzymes Increase Reaction Rates 4.3 The Mechanism Of An Enzyme Can Be Deduced From Structural, Kinetic, and Spectral Data 4.4Examples of Enzyme Regulation 4.1 DEFINITIONS Enzyme: Catalysts involved in biochemical reactions...

MODULE 5 INTRODUCTION TO ENZYMOLOGY OVERVIEW 4.1 Regarding Enzymes 4.2 Enzymes Increase Reaction Rates 4.3 The Mechanism Of An Enzyme Can Be Deduced From Structural, Kinetic, and Spectral Data 4.4Examples of Enzyme Regulation 4.1 DEFINITIONS Enzyme: Catalysts involved in biochemical reactions Substrate: Molecules that act as reactants in enzymatic reactions Active Site: Location on an enzyme where the substrate binds Allosteric Site: Location on an enzyme that allows substances to bind in order to activate or inhibit enzymatic activity 2 ENZYME-SUBSTRATE BINDING MODELS Lock and Key Enzyme is conformationally static and substrate must be EXACT fit in order for catalyzation to occur Induced Fit Enzyme binds substrate “loosely” and once bound both enzyme and substrate undergo slight conformational change to achieve a perfect fit ENZYME REGULATION Competitive Inhibition Other substances directly bind to active site: now the active site is blocked and desired substrate cannot bind. Therefore catalytic activity is inhibited Noncompetitive Regulation Molecules bind to the allosteric site of an enzyme in order to change the conformation of the enzyme: either to allow substrate binding, or to inhibit substrate binding ENZYME CLASSIFICATIONS 4.1 1 Oxidoreductase Catalyze reactions involving gaining or losing electrons 4 Lyase Break double bonds using means excluding oxidation or hydrolysis 2 Transferase Transfer one group to another 5 Isomerase Catalyze a rearrangement of the molecule 3 Hydrolase Cleave a bond with water 6 Ligase Join two molecules 4.2 ENZYMES INCREASE REACTION RATES Enzymes increase reaction rates by increasing stability of intermediates therefore lowering the activation energy needed for a reaction to take place 4.2 CENTRAL EQUATIONS FOR ENZYME KINETICS Vo = Initial Velocity Vmax= maximum catalytic velocity of an enzyme at a given substrate Concentration [S] = Substrate Concentration Km= Michaelis Constant 4.2 WHAT HAPPENS WHEN ENZYMES ARE SATURATED WITH SUBSTRATE? Once all enzymes are saturated, the reaction rate becomes steady as it infinitely tends towards Vmax. 4.2 LINEWEAVER-BURKE PLOT Double reciprocal of Michaelis Menten equation Easier method to interpret graphical data 4.2 COMPETITIVE INHIBITORS 4.2 NON-COMPETITIVE INHIBITORS 4.2 MIXED INHIBITORS 4.3 TYPES OF ENZYME CATALYSTS General Acid Base Catalyst Metal Ion Catalysis Covalent Catalysis Amino acid side chains donate or accept protons Active site metal ion can act as a redox active center Nucleophilic or electrophilic attack on an atom results in a covalent intermediate Polar and charged amino acids play an important role Metal Ions are found in one third of all enzymes Involves Ser, Asp, Cys, Lys, Tyr, and several cofactors 4.3 DEFINITIONS Proteases: Enzymes that degrade proteins. Ie. Serine protease (Chymotrypsin) WAYS TO REGULATE ENZYMES 4.4 1. Altering gene expression 2. Isolating enzymes in certain parts of the cell and/or body 3. Limit enzyme-substrate interaction COVALENT MODIFICATION 4.4 Definition: Covalent addition or removal of groups from proteins. Proteolytic Cleavage - Example of enzyme activation An inactive enzyme becomes activated after cleavage Zymogens - Inactive enzyme precursors that require proteolytic activation Phosphorylation - Type of enzyme activation Facilitated by protein kinases - Add phosphate groups to hydroxyl groups of serine, threonine, or tyrosine - Phosphatases remove phosphate groups ALLOSTERIC REGULATION 4.4 - Inhibits or activates enzyme by binding to allosteric site MODULE 6 CARBOHYDRATES OVERVIEW 6.1 Monosaccharides 6.2 Complex Carbohydrates 6.3 Glycolysis 6.4 Gluconeogenesis 6.5 The Fates of Pyruvate MONOSACCHARIDE CLASSIFICATION Number of Carbons # of carbons name 3 triose 4 tetrose Aldehydes or Ketones If the carbonyl group is an: Aldehyde = aldose Ketone = ketose Stereochemistry Penultimate carbon - Anomeric carbon - 5 pentose 6 hexose - 7 heptos e determines D or L D: Hydroxyl on right L: Hydroxyl on left Most common aldoses - Glucose, mannose, galactose, ribose , glyceraldehyde Most common ketoses - Fructose, xylulose, dihydroxyacetone Former carbonyl carbon (C1) from the hemiacetal/hemiketal α-OH on bottom face β-OH on top face Mutarotation - Converting from one anomeric form to the next Epimers - Differ at one stereocenter MONOSACCHARIDE MODIFICATIONS - Amino sugars - - Acylation - - - - Xylitol Carbonyl group reduced to alcohol Sugar acid - - - N-acetylglucosamine (acetyl derivative of glucosamine) Addition of acyl group Sugar alcohols (no ring = low calorie) - - Hydroxyl group replaced by amine Glucosamine Glucuronic acid C6 oxidized to COOH Deoxy sugars - Formed by removal of hydroxyl moieties on one or more carbons 2-deoxyribose COMPLEX CARBOHYDRATES Polysaccharides Defined - Polysaccharides are polymers of monosaccharides Polysaccharides are dependent on α or β linkages and number of carbons involved in the linkage Common Disaccharides Common Disaccharides - Lactose: consists of glucose and galactose - Sucrose: consists of glucose and fructose - Maltose: consists of two glucose molecules COMPLEX CARBOHYDRATES cont. Common Polysaccharides Polysaccharides for energy storage - Raffinose: trisaccharide consisting of galactose, glucose and fructose - Inulin: oligosaccharide consisting of fructose polymers - Amylose: linear polymer of thousands of glucose monomers - Amylopectin: branched polymer of thousands of glucose monomers - Glycogen: storage form of a carbohydrate Structural Polysaccharides - Cellulose: linear glucose polymers - Chitin: structural carbohydrate - Alginate: copolymer of glucuronate and mannuronate Which polysaccharide is it? Which polysaccharide is it? Which polysaccharide is it? GLYCOLYSIS Overview of Glycolysis - One molecule of glucose is converted into two pyruvate molecules - Provides energy via ATP and NADH/H⁺ Reactions of Glycolysis Energy investment stage - First five steps - Two ATP are invested Energy yielding stage - Last five steps - Two ATP are produced SUMMARY OF GLYCOLYSIS - One molecule of glucose ( six carbons) is catabolized into two pyruvates (three carbons) - Ten step anaerobic process - Two net ATP and two net NADH/H⁺ molecules are generated - Provides entry points for other molecules such as fructose and glycerol - Pyruvate can be oxidized to acetyl-CoA and can go into the citric acid cycle GLUCONEOGENESIS Overview - Synthesis of glucose - - Can be made from pyruvate, lactate, glycerol, and several amino acids Requires 6 ATP Regulation - Occurs through compartmentalization - Allosteric regulation - Phosphorylation - Changes in gene expression Control - Reciprocal with glycolysis control - Energetic level of the cell is low = gluconeogenesis inhibited Plasma glucose is low = glycolysis inhibited FATES OF PYRUVATE - Pyruvate has distinct fates depending on the type of cell (or organ) and the metabolic state of the organism. - Aerobic conditions: Pyruvate → Acetyl-CoA - Anaerobic conditions: Pyruvate → Lactate Pyruvate → Acetaldehyde → Ethanol - Microbes can decarboxylate pyruvate into ethanol. MODULE 7 LIPIDS AND MEMBRANES OVERVIEW 9.1 Lipid molecules 9.4 Ketone body metabolism 9.5 Steroid metabolism WHY ARE LIPIDS UNIQUE? Lipids do not share common structure, but do share chemical properties ● ● ● All lipids are hydrophobic or amphiphilic ○ all are insoluble in water Lipids do not contain monomers They are classified based on their structures FATTY ACIDS Properties and Functions - Amphiphatic - Unbranched long-chain carboxylic acids - Even number of carbon atoms - Serve to insulate organs Nomenclature Saturated Fatty Acids - No double bonds Unsaturated - Trans configuration - Hydrogenated - Hydrogens in opposite directions - Cis configuration - Naturally occurring - Hydrogens in same direction PHOSPHOLIPIDS Amphiphilic molecules that contain a phosphate moiety, and form membranes. Divided into: Glycerophospholipids - Glycerol backbone, TWO fatty acyl chains, and a phosphoalcohol Sphingolipids - Sphingosine backbone, ONE fatty acyl chain, and a phospoalcohol TRIACYLGLYCEROLS Structure - Neutral lipid (does not have charged group) - Three fatty acids esterified to a glycerol molecule - The unsaturated fatty acid is attached to carbon 2 in glycerol Function - Store lipids in our bodies - Solid under physiological conditions To use the stored energy, cholesterol related molecules are required WHAT IS CHOLESTEROL Cholesterol Defined - Cholesterol is essential for synthesis of important molecules - Cholesterol is a common steroid - Maintains membrane fluidity - Has multiple functions including - Transport across the membrane - Diffusion of proteins within the membrane - Membrane integrity -cholesterol related molecules include lipoproteins such as VLDL, LDL, and HDL Cholesteryl Esters Defined - - Fatty acids esterified to cholesterol Form a large group of plaque in the arteries, which can lead to heart disease Can be stored in the body as a cholesterol reserve Bile Salts Defined - - Detergents synthesized from cholesterol by the liver and stored in the gallbladder Used to solubilize dietary lipids in the small intestines; increases the surface area and facilitates the enzymatic degradation of lipids STEROID BODY METABOLISM Steroids Defined - - Group of lipids with diverse functions but a common skeleton consisting of four fused rings Examples includes hormones Steroid Hormones - Made from cholesterol Critical for sexual development, reproduction, and regulation of mineral balance in higher organisms KETONE BODY METABOLISM What Are Ketone Bodies - - - Small soluble molecules that are made in the liver in times of energetic scarcity They provide energy to tissues such as the brain when glucose is not available Can permeate the blood brain barrier Examples of Ketone Bodies GLYCOCONJUGATES Types - - - - Glycoproteins: Proteins with some amount of carbohydrate modification Glycolipids: Membrane phospholipids with a carbohydrate moiety Proteoglycans: Polysaccharide mesh nets joined to fibrous proteins Peptidoglycans: Long polysaccharide chains cross-linked by peptides Some Examples - - - - ABO Blood group antigens (immune system identification) GPI anchors (anchor proteins to outer plasma membrane leaflet Keratin sulfate (structural component of bone, horn and cornea) Important component of bacterial cell wall structure THE END Good Luck on Midterm #2 :)