Lecture 1.1 Introduction to Biochemistry and Water PDF

Internal Use Introduction to Biochemistry Internal Use Biochemistry The study of Molecular Basis of Life. 2 Internal Use Principles of Living Organisms Highly organized c...

Internal Use Introduction to Biochemistry Internal Use Biochemistry The study of Molecular Basis of Life. 2 Internal Use Principles of Living Organisms Highly organized cells Constant source of energy Regulated Chemical Reactions to maintain life. Fundamental Pathways found in many organisms. Certain molecules seen in all organisms (carbohydrates, lipids, proteins, and nucleic acid). “Instructions” for life encoded by the nucleic acids. Reproduction is inherent for all organisms. 3 Internal Use Biomolecules Water is the most important molecule in life. Molecules containing C, H, O, N, P, and S are also important Carbon being the central atom for most biomolecules because of its ability to form a tetravalent or 4 bonds. 4 Internal Use Hydrocarbons Polymers, long chains of organic molecules, which contain carbons and hydrogens only. Relatively inert. Precursor for most biomolecules. Non-polar due to similar electronegativity of C and H. Hydrophobic or insoluble in water. Example: Natural gas, Fossil Fuels, Coal 5 Internal Use Functional Groups Replacement of hydrogen gives rise to molecular functionality. Replacement of one hydrogen in methane with a hydroxyl group gives methanol. 6 Internal Use Functional Groups 7 Internal Use Biochemical Reactions Nucleophilic Substitution Hydrolysis Reaction Elimination Reaction Addition Reaction Isomerization Reaction RedOx Reactions Oxidation Reactions 8 Internal Use Metabolic Pathways Anabolic Pathways Synthesis of larger molecules from small molecules. Requires energy. Catabolic Pathways Breakdown of larger molecules to smaller molecules. Gives energy. 9 Internal Use Water The water molecules is a polar molecule which also creates hydrogen bonds between water molecules. 10 Internal Use Hydrogen bonding in water There is constant breakage and formation of hydrogen bonds in water. Water: 2.3 H-bonds Ice: 4 H-bonds 11 Internal Use Non-covalent Interactions Ionic Bonds (+) and (-) molecules Electrostatic Interactions (+) and (-) ions Hydration of Ions in Solution 12 Internal Use Non-covalent Bonding Hydrogen bonds Water, Amines, Alcohols, Carboxylic Acids Van der Waals forces Unequal distribution of electrons Hydrophobic interactions Occurs only in aqueous environment and tendency for hydrophobic molecules to coalesce 13 Internal Use Water: the universal solvent Ionic compounds Polar compound Amphipathic molecules Micelles 14 Internal Use Properties of water Liquid at normal temperature High Boiling Point and Melting point High heats of fusion and vaporization High heat capacity Surface tension 15 Internal Use Acids and Bases Acids: proton donor Base: proton acceptor Strong Acids and Bases Weak acids and bases; conjugates 16 Internal Use Buffers Solution of weak acid (HA) and conjugate base (A-) Resist a large change in pH of a solution The acid “absorbs” base. The base “absorbs” acid. 17 Internal Use Buffer Capacity Molar concentration of acid and base Ratio of acid and base Effective when pH = -+ 1 unit of pKa 18 Internal Use Henderson-Hasselbach Equation Equation for determining several aspects of any given buffer. 19 Internal Use Biological Buffers Bicarbonate: Blood pKa = 6.37, pH of blood = ~7.4 Blood pH controlled by respiration and kidneys. 20 Internal Use Biological Buffers Phosphate: intracellular pKa = 7.2 Important for phosphorylation Proteins: both intracellular and blood (hemoglobin) 21 Internal Use Control of Blood pH Lungs and Kidneys Lungs excrete carbon dioxide Kidneys excrete H+ by two major routes: 1. Ammonia 2. Phosphate *most bicarbonate is reabsorbed 22 Internal Use pH Conditions pH < 7.35, Acidosis pH > 7.45 Alkalosis 23 Internal Use Respiratory Acidosis Depression of respiratory rate Increases CO2 in blood Increases bicarbonate retention in kidney Lowers pH Hyperventilation Lowers CO2 in blood Lowers protons for kidney excretion Lowers reabsorption of bicarbonate and sodium Increases pH 24 Internal Use Respiratory Acidosis Depression of respiratory rate Increases CO2 in blood Increases bicarbonate retention in kidney Lowers pH Hyperventilation Lowers CO2 in blood Lowers protons for kidney excretion Lowers reabsorption of bicarbonate and sodium Increases pH 25 Internal Use Metabolic Acidosis Something causes the lowering of plasma bicarbonate Increased metabolism acids (e.g. lactic acid – during intense workout) Increased ketone bodies Loss of bicarbonate (diarrhea) Kidney failure resulting to low proton excretion 26 Internal Use Metabolic Alkalosis Something causes the increase in plasma bicarbonate Often a result of excessive vomiting Excessive excretion of protons 27 Internal Use 28