Biochemistry Organic compounds Organic compounds Contain carbon, are covalently bonded, and are often large Contain carbon, are covalently bonded, and are often large Inorganic compounds Inorganic compounds Do not contain carbon Do not contain carbon Water, salts, and many acids and bases Water, salts, and many acids and bases Properties of Water High heat capacity absorbs and releases large amounts of heat before changing temperature High heat capacity absorbs and releases large amounts of heat before changing temperature High heat of vaporization changing from a liquid to a gas requires large amounts of heat High heat of vaporization changing from a liquid to a gas requires large amounts of heat Polar solvent properties dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the bodys major transport medium Polar solvent properties dissolves ionic substances, forms hydration layers around large charged molecules, and serves as the bodys major transport medium PLAY InterActive Physiology : Fluid, Electrolyte, and Acid/Base Balance: Introduction to Body Fluids Properties of Water Reactivity is an important part of hydrolysis and dehydration synthesis reactions Reactivity is an important part of hydrolysis and dehydration synthesis reactions Cushioning resilient cushion around certain body organs Cushioning resilient cushion around certain body organs Salts Inorganic compounds Inorganic compounds Contain cations other than H + and anions other than OH Contain cations other than H + and anions other than OH Are electrolytes; they conduct electrical currents Are electrolytes; they conduct electrical currents Acids and Bases Acids release H + and are therefore proton donors Acids release H + and are therefore proton donors HCl H + + Cl Bases release OH and are proton acceptors Bases release OH and are proton acceptors NaOH Na + + OH Acid-Base Concentration (pH) Acidic solutions have higher H + concentration and therefore a lower pH Acidic solutions have higher H + concentration and therefore a lower pH Alkaline solutions have lower H + concentration and therefore a higher pH Alkaline solutions have lower H + concentration and therefore a higher pH Neutral solutions have equal H + and OH concentrations Neutral solutions have equal H + and OH concentrations Acid-Base Concentration (pH) Acidic: pH 06.99 Acidic: pH 06.99 Basic: pH 7.0114 Basic: pH 7.0114 Neutral: pH 7.00 Neutral: pH 7.00 Figure 2.13 Buffers Systems that resist abrupt and large swings in the pH of body fluids Systems that resist abrupt and large swings in the pH of body fluids Carbonic acid-bicarbonate system Carbonic acid-bicarbonate system Carbonic acid dissociates, reversibly releasing bicarbonate ions and protons Carbonic acid dissociates, reversibly releasing bicarbonate ions and protons The chemical equilibrium between carbonic acid and bicarbonate resists pH changes in the blood The chemical equilibrium between carbonic acid and bicarbonate resists pH changes in the blood PLAY InterActive Physiology : Fluid, Electrolyte, and Acid/Base Balance: Acid/Base Homeostasis Organic Compounds Molecules unique to living systems contain carbon and hence are organic compounds Molecules unique to living systems contain carbon and hence are organic compounds They include: They include: Carbohydrates Carbohydrates Lipids Lipids Proteins Proteins Nucleic Acids Nucleic Acids Carbohydrates Contain carbon, hydrogen, and oxygen Contain carbon, hydrogen, and oxygen Their major function is to supply a source of cellular food Their major function is to supply a source of cellular food Examples: Examples: Monosaccharides or simple sugars Monosaccharides or simple sugars Figure 2.14a Carbohydrates Disaccharides or double sugars Disaccharides or double sugars Figure 2.14b PLAY Disaccharides Carbohydrates Polysaccharides or polymers of simple sugars Polysaccharides or polymers of simple sugars Figure 2.14c PLAY Polysaccharides Lipids Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates Contain C, H, and O, but the proportion of oxygen in lipids is less than in carbohydrates Examples: Examples: Neutral fats or triglycerides Neutral fats or triglycerides Phospholipids Phospholipids Steroids Steroids Eicosanoids Eicosanoids PLAY Fats Neutral Fats (Triglycerides) Composed of three fatty acids bonded to a glycerol molecule Composed of three fatty acids bonded to a glycerol molecule Figure 2.15a Other Lipids Phospholipids modified triglycerides with two fatty acid groups and a phosphorus group Phospholipids modified triglycerides with two fatty acid groups and a phosphorus group Figure 2.15b Other Lipids Steroids flat molecules with four interlocking hydrocarbon rings Steroids flat molecules with four interlocking hydrocarbon rings Eicosanoids 20-carbon fatty acids found in cell membranes Eicosanoids 20-carbon fatty acids found in cell membranes Figure 2.15c Representative Lipids Found in the Body Neutral fats found in subcutaneous tissue and around organs Neutral fats found in subcutaneous tissue and around organs Phospholipids chief component of cell membranes Phospholipids chief component of cell membranes Steroids cholesterol, bile salts, vitamin D, sex hormones, and adrenal cortical hormones Steroids cholesterol, bile salts, vitamin D, sex hormones, and adrenal cortical hormones Representative Lipids Found in the Body Fat-soluble vitamins vitamins A, E, and K Fat-soluble vitamins vitamins A, E, and K Eicosanoids prostaglandins, leukotrienes, and thromboxanes Eicosanoids prostaglandins, leukotrienes, and thromboxanes Lipoproteins transport fatty acids and cholesterol in the bloodstream Lipoproteins transport fatty acids and cholesterol in the bloodstream Amino Acids Building blocks of protein, containing an amino group and a carboxyl group Building blocks of protein, containing an amino group and a carboxyl group Amino group NH 2 Amino group NH 2 Carboxyl groups COOH Carboxyl groups COOH Amino Acids Figure 2.16ac Amino Acids Figure 2.16d, e Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Amino acid Dehydration synthesis Hydrolysis Dipeptide Peptide bond +N H H C R H O N H H C R CC H O H2OH2O H2OH2O N H H C R C H O N H C R C H O OH Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Amino acid +N H H C R H O N H H C R CC H O OH Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Amino acid Dehydration synthesis +N H H C R H O N H H C R CC H O H2OH2O OH Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Amino acid Dehydration synthesis Dipeptide Peptide bond +N H H C R H O N H H C R CC H O H2OH2O N H H C R C H O N H C R C H O OH Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Dipeptide Peptide bond N H H C R C H O N H C R C H O OH Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Hydrolysis Dipeptide Peptide bond H2OH2O N H H C R C H O N H C R C H O OH Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Amino acid Hydrolysis Dipeptide Peptide bond +N H H C R H O N H H C R CC H O H2OH2O N H H C R C H O N H C R C H O OH Protein Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Macromolecules composed of combinations of 20 types of amino acids bound together with peptide bonds Figure 2.17 Amino acid Dehydration synthesis Hydrolysis Dipeptide Peptide bond +N H H C R H O N H H C R CC H O H2OH2O H2OH2O N H H C R C H O N H C R C H O OH Structural Levels of Proteins Primary amino acid sequence Primary amino acid sequence Secondary alpha helices or beta pleated sheets Secondary alpha helices or beta pleated sheets PLAY Chemistry of Life: Proteins: Secondary Structure PLAY Chemistry of Life: Proteins: Primary Structure PLAY Chemistry of Life: Introduction to Protein Structure Structural Levels of Proteins Tertiary superimposed folding of secondary structures Tertiary superimposed folding of secondary structures Quaternary polypeptide chains linked together in a specific manner Quaternary polypeptide chains linked together in a specific manner PLAY Chemistry of Life: Proteins: Quaternary Structure PLAY Chemistry of Life: Proteins: Tertiary Structure Structural Levels of Proteins Figure 2.18ac Structural Levels of Proteins Figure 2.18b,d,e Fibrous and Globular Proteins Fibrous proteins Fibrous proteins Extended and strand-like proteins Extended and strand-like proteins Examples: keratin, elastin, collagen, and certain contractile fibers Examples: keratin, elastin, collagen, and certain contractile fibers Fibrous and Globular Proteins Globular proteins Globular proteins Compact, spherical proteins with tertiary and quaternary structures Compact, spherical proteins with tertiary and quaternary structures Examples: antibodies, hormones, and enzymes Examples: antibodies, hormones, and enzymes Protein Denuaturation Reversible unfolding of proteins due to drops in pH and/or increased temperature Reversible unfolding of proteins due to drops in pH and/or increased temperature Figure 2.19a Protein Denuaturation Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes Irreversibly denatured proteins cannot refold and are formed by extreme pH or temperature changes Figure 2.19b Molecular Chaperones (Chaperonins) Help other proteins to achieve their functional three-dimensional shape Help other proteins to achieve their functional three-dimensional shape Maintain folding integrity Maintain folding integrity Assist in translocation of proteins across membranes Assist in translocation of proteins across membranes Promote the breakdown of damaged or denatured proteins Promote the breakdown of damaged or denatured proteins Characteristics of Enzymes Most are globular proteins that act as biological catalysts Most are globular proteins that act as biological catalysts Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion) Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion) Enzymes are chemically specific Enzymes are chemically specific Characteristics of Enzymes Frequently named for the type of reaction they catalyze Frequently named for the type of reaction they catalyze Enzyme names usually end in -ase Enzyme names usually end in -ase Lower activation energy Lower activation energy Characteristics of Enzymes Figure 2.20 Mechanism of Enzyme Action Enzyme binds with substrate Enzyme binds with substrate Product is formed at a lower activation energy Product is formed at a lower activation energy Product is released Product is released PLAY How Enzymes Work Figure 2.21 Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S) Internal rearrangements leading to catalysis Dipeptide product (P) Free enzyme (E) Substrates (S) Peptide bond H2OH2O + Figure 2.21 Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S) Substrates (S) H2OH2O + Figure 2.21 Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S) Internal rearrangements leading to catalysis Substrates (S) H2OH2O + Figure 2.21 Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S) Internal rearrangements leading to catalysis Dipeptide product (P) Free enzyme (E) Substrates (S) Peptide bond H2OH2O + Nucleic Acids Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus Composed of carbon, oxygen, hydrogen, nitrogen, and phosphorus Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group Nucleic Acids Five nitrogen bases contribute to nucleotide structure adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) Five nitrogen bases contribute to nucleotide structure adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) Two major classes DNA and RNA Two major classes DNA and RNA Deoxyribonucleic Acid (DNA) Double-stranded helical molecule found in the nucleus of the cell Double-stranded helical molecule found in the nucleus of the cell Replicates itself before the cell divides, ensuring genetic continuity Replicates itself before the cell divides, ensuring genetic continuity Provides instructions for protein synthesis Provides instructions for protein synthesis Structure of DNA Figure 2.22a Structure of DNA Figure 2.22b Ribonucleic Acid (RNA) Single-stranded molecule found in both the nucleus and the cytoplasm of a cell Single-stranded molecule found in both the nucleus and the cytoplasm of a cell Uses the nitrogenous base uracil instead of thymine Uses the nitrogenous base uracil instead of thymine Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA Three varieties of RNA: messenger RNA, transfer RNA, and ribosomal RNA Adenosine Triphosphate (ATP) Source of immediately usable energy for the cell Source of immediately usable energy for the cell Adenine-containing RNA nucleotide with three phosphate groups Adenine-containing RNA nucleotide with three phosphate groups Adenosine Triphosphate (ATP) Figure 2.23 Figure 2.24 Solute Solute transported Contracted smooth muscle cell Product made Relaxed smooth muscle cell Reactants Membrane protein P PiPi ATP PXX Y Y + (a) Transport work (b) Mechanical work (c) Chemical work PiPi PiPi + ADP Figure 2.24 Solute Membrane protein P ATP (a) Transport work Figure 2.24 Solute Solute transported Membrane protein P PiPi ATP (a) Transport work PiPi + ADP Figure 2.24 Relaxed smooth muscle cell ATP (b) Mechanical work Figure 2.24 Contracted smooth muscle cell Relaxed smooth muscle cell ATP (b) Mechanical work PiPi + ADP Figure 2.24 Reactants ATP PX Y+ (c) Chemical work Figure 2.24 Product madeReactants ATP PXX Y Y + (c) Chemical work PiPi PiPi + ADP Figure 2.24 Solute Solute transported Contracted smooth muscle cell Product made Relaxed smooth muscle cell Reactants Membrane protein P PiPi ATP PXX Y Y + (a) Transport work (b) Mechanical work (c) Chemical work PiPi PiPi + ADP