Chapter 2: The Chemistry of Life PDF

Because learning changes everything. ® Chapter 02 The Chemistry of Life ANATOMY & PHYSIOLOGY The Unity of Form and Function TENTH EDITION KENNETH S. SALADIN © McGraw Hill LLC. All rights reserved. No reproduction or distribution without the prior written consent of McGraw...

Because learning changes everything. ® Chapter 02 The Chemistry of Life ANATOMY & PHYSIOLOGY The Unity of Form and Function TENTH EDITION KENNETH S. SALADIN © McGraw Hill LLC. All rights reserved. No reproduction or distribution without the prior written consent of McGraw Hill LLC.  2.1a The Chemical Elements A chemical element is the simplest form of matter to have unique chemical properties Each identified by an atomic number—number of protons in the nucleus Periodic table arranges elements (represented as 1-2 letter symbols) by atomic number 91 naturally occurring elements 24 play roles in humans; 6 are most abundant (98.5% body weight) Oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus Trace elements present in minute amounts, but play vital roles Some are minerals—inorganic elements extracted from soil by plant, passed up food chain to humans 4% of body weight, mostly calcium and phosphorus Body structure (bones, teeth), enzyme function, nerve/muscle cell functions © McGraw Hill, LLC 2  2.1b Atomic Structure Greek philosopher coined the term atom (“indivisible”) as the smallest unit of matter Neils Bohr proposed planetary model of atomic structure in 1913; useful as a schematic, but not accurate structure Nucleus—center of atom, composed of protons and neutrons Protons (p+) : single (+) charge; mass = 1 atomic mass unit (amu) Neutrons (n0) : no charge; mass = 1 amu Atomic mass is approx equal to total number of protons and neutrons Electrons (e- ) in concentric clouds (electron shells or energy levels) surrounding nucleus Have a single (−) charge, very low mass An atom is electrically neutral, as number of electrons equals number of protons Valence electrons in the outermost shell and determine chemical bonding properties of an atom © McGraw Hill, LLC 3  Models of Atomic Structure—Bohr Planetary Model Access the text alternative for slide images. Figure 2.1a,b © McGraw Hill, LLC 4  Models of Atomic Structure—Quantum Mechanical Model Access the text alternative for slide images. Figure 2.1c © McGraw Hill, LLC 5  2.1d Ions, Electrolytes, and Free Radicals 1 An ion is a charged particle (atom or molecule) with unequal number of protons and electrons Ionization—transfer of electrons from one atom to another Anion—particle that has a net negative charge due to gain of electrons Cation—particle that has a net positive charge due to loss of electrons Ions with opposite charges are attracted to each other © McGraw Hill, LLC 6  Ionization 1 Access the text alternative for slide images. Figure 2.4 © McGraw Hill, LLC 7  Ionization 2 Access the text alternative for slide images. Figure 2.4 © McGraw Hill, LLC 8  Ions, Electrolytes, and Free Radicals 2 Ions (continued) Salts—electrically neutral compounds of cations and anions; readily dissociate in water into ions and act as electrolytes Examples: Sodium chloride, calcium chloride Electrolytes—substances that ionize in water and form solutions capable of conducting electric current Functions of electrolytes: Chemical reactivity, osmotic effects, electrical excitability of nerve and muscle Electrolyte balance is one of the most important considerations in patient care (imbalances can lead to coma or cardiac arrest) © McGraw Hill, LLC 9  Ions, Electrolytes, and Free Radicals 3 Ions (continued) Free radicals—unstable, highly reactive particles with an unusual number of electrons Produced by normal metabolic reactions, radiation, certain chemicals Trigger reactions that destroy molecules, and can cause cancer, death of heart tissue, and aging Example: superoxide anion, O- 2 Antioxidants—chemicals that neutralize free radicals Example: superoxide dismutase (SOD) is an antioxidant enzyme that converts superoxide anion into oxygen and hydrogen peroxide Selenium, vitamin E, vitamin C, and carotenoids are antioxidants obtained through the diet © McGraw Hill, LLC 10  2.1e Molecules and Chemical Bonds 1 Atoms can combine to form molecules Molecule—particle composed of two or more atoms united by a chemical bond Compound—molecule composed of two or more different elements Can be represented by a molecular formula, which identifies constituent elements and how many atoms of each are present Also can be represented by a structural formula, which identifies the location of each atom Isomers—molecules with identical molecular formulae but different arrangements of their atoms © McGraw Hill, LLC 11  Two Structural Isomers—Ethanol and Ethyl Ether Access the text alternative for slide images. Figure 2.5 © McGraw Hill, LLC 12  Molecules and Chemical Bonds 3 Chemical bonds hold atoms together within a molecule, or attract one molecule to another Ionic bonds—attraction of a cation to an anion Example: sodium and chloride ions bond to form sodium chloride Relatively easily broken by something more attractive, such as water Covalent bonds—atoms share one or more pairs of electrons Single covalent bond: nuclei share 1 pair of electrons Double covalent bond: nuclei share 2 pairs of electrons If electrons are shared equally, it’s a nonpolar covalent bond; example: carbon atoms bonding together If electrons shared unequally, it’s a polar covalent bond; example: hydrogen bonding with oxygen, electrons spend more time by oxygen © McGraw Hill, LLC 13  Single Covalent Bond Access the text alternative for slide images. Figure 2.6a © McGraw Hill, LLC 14  Double Covalent Bond Access the text alternative for slide images. Figure 2.6b © McGraw Hill, LLC 15  Nonpolar and Polar Covalent Bonds Access the text alternative for slide images. Figure 2.7 © McGraw Hill, LLC 16  Molecules and Chemical Bonds 4 A hydrogen bond is a weak attraction between a slightly positive hydrogen atom in one molecule and a slightly negative oxygen or nitrogen atom in another atom Relatively weak bonds, but very important to physiology Water molecules are attracted to each other by hydrogen bonds. Large molecules (DNA and proteins) are shaped in part by the formation of hydrogen bonds within them. © McGraw Hill, LLC 17  Hydrogen Bonding of Water Access the text alternative for slide images. Figure 2.8 © McGraw Hill, LLC 18  2.2 Introduction Body fluids are complex mixtures of chemicals Mixtures—consist of substances that are physically blended but not chemically combined; each substance retains its own chemical properties © McGraw Hill, LLC 19  2.2a Water 1 Most mixtures in our bodies consist of chemicals dissolved or suspended in water Water is 50 to 75% of body weight Polar covalent bonds and a V-shape give water a set of properties that account for its ability to support life Solvency Cohesion Adhesion Chemical reactivity Thermal stability © McGraw Hill, LLC 20  Water 2 Properties of water: Solvency—ability to dissolve other chemicals Water is the universal solvent because it dissolves more substances than any other solvent Metabolic reactions depend on solvency of water Hydrophilic substances dissolve in water; are polarized or charged Hydrophobic substances do not dissolve in water; are nonpolar or neutral To be soluble in water, molecule must be polarized or charged Example: attractions to water overpower ionic bond in NaCl © McGraw Hill, LLC 21  Water and Hydration Spheres Access the text alternative for slide images. Figure 2.9 © McGraw Hill, LLC 22  Water 3 Properties of water (continued): Adhesion—tendency of one substance to cling to another Water adheres to membranes reducing friction around organs Cohesion—tendency of molecules of the same substance to cling to each other Water is very cohesive due to its hydrogen bonds Surface film on surface of water is due to molecules being held together by surface tension Chemical reactivity—ability to participate in chemical reactions Water ionizes into H+ and OH- ; ionizes other chemicals (acids, salts); involved in hydrolysis and dehydration synthesis reactions © McGraw Hill, LLC 23  Water 4 Properties of water (continued): Thermal stability due to high heat capacity—amount of heat needed to raise the temperature of 1g of a substance by 1°C Calorie (cal) is the base unit of heat; 1 cal is the amount of heat to raise the temperature of 1g of water by 1°C Water stabilizes internal temperature; hydrogen bonds resist temperature increases by inhibiting molecular motion © McGraw Hill, LLC 24  2.2c Acids, Bases, and pH 1 Substances can be acids or bases depending on their tendency to release or bind H+ ions An acid is a proton donor; releases H+ ions in water A base is a proton acceptor; accepts H+ ions or releases OH- ions in water Acidity is measured by pH scale Derived from the molarity of H+ pH of 7.0 is neutral (H+ OH- ) pH of less than 7 is acidic (H+  OH- ) pH of greater than 7 is basic (OH-  H+ ) Maintaining normal (slightly basic) pH of blood is crucial for physiological functions Buffers are chemical solutions that resist changes in pH © McGraw Hill, LLC 25  Acids, Bases, and pH 2 pH (continued) pH is the negative logarithm of hydrogen ion molarity ph =  log  H+  Example: if  H+  10  3 , then pH  log  10  3  3     A change of one number on the pH scale represents a tenfold change in H+ concentration pH 4.0 is 10 times as acidic as pH 5.0 © McGraw Hill, LLC 26  The pH Scale (Acids, pH7) Access the text alternative for slide images. Figure 2.11 © McGraw Hill, LLC 28  2.3a Energy and Work Energy is the capacity to do work To do work means to move something, such as a muscle or a molecule Potential energy—energy stored in an object, but not currently doing work; example: water behind a dam Chemical energy—potential energy in molecular bonds Free energy—potential energy available in a system to do work Kinetic energy—energy of motion, energy doing work © McGraw Hill, LLC 29  2.3b Classes of Chemical Reactions 1 A chemical reaction is a process in which a covalent or ionic bond is formed or broken A chemical equation symbolizes the course of a chemical reaction Reactants (on left) → products (on right) Classes of chemical reactions include: Decomposition reactions Synthesis reactions Exchange reactions © McGraw Hill, LLC 30  Classes of Chemical Reactions 2 Classes of chemical reactions (continued) Decomposition reactions Large molecule breaks down into two or more smaller ones AB → A + B Synthesis reactions Two or more small molecules combine to form a larger one A + B → AB Exchange reactions Two molecules exchange atoms or group of atoms AB + CD → AC + BD Example: stomach acid (HCl) and sodium bicarbonate (NaHCO3) from the pancreas combine to form NaCl and H2C O3 © McGraw Hill, LLC 31  Decomposition Reaction Access the text alternative for slide images. Figure 2.12a © McGraw Hill, LLC 32  Synthesis Reaction Access the text alternative for slide images. Figure 2.12b © McGraw Hill, LLC 33  Exchange Reaction Access the text alternative for slide images. Figure 2.12c © McGraw Hill, LLC 34  Classes of Chemical Reactions 3 Reversible reactions can proceed in either direction under different circumstances Symbolized with double-headed arrow Example: CO2  H2O  H2CO3  HCO3-  H+ An important reaction in respiratory, urinary, and digestive physiology © McGraw Hill, LLC 35  2.3d Metabolism, Oxidation, and Reduction 1 Metabolism—all chemical reactions of the body; two divisions: Catabolism Energy-releasing (exergonic) decomposition reactions Breaks covalent bonds Produces smaller molecules Anabolism Energy-storing (endergonic) synthesis reactions Requires energy input Example: production of protein or fat Catabolism and anabolism are inseparably linked Anabolism is driven by energy released by catabolism © McGraw Hill, LLC 36  Metabolism, Oxidation, and Reduction 2 Metabolism (continued) Oxidation A chemical reaction in which a molecule gives up electrons and releases energy Molecule is oxidized when it loses electrons The oxidizing agent is the electron acceptor (often oxygen) Reduction Any chemical reaction in which a molecule gains electrons and energy Molecule is reduced when it accepts electrons The reducing agent is the molecule that donates electrons Oxidation of one molecule is always accompanied by reduction of another; called oxidation-reduction (redox) reactions © McGraw Hill, LLC 37  2.4a Carbon Compounds and Functional Groups 1 Organic chemistry is the study of compounds containing carbon Four categories: Carbohydrates Lipids Proteins Nucleic acids © McGraw Hill, LLC 38  2.4b Monomers and Polymers 1 Macromolecules are large organic molecules with high molecular weights Most macromolecules are polymers Molecules made of a repetitive series of identical or similar subunits called monomers Monomers may be identical or different Examples: starch is a polymer of about 3,000 identical glucose monomers; DNA is a polymer of 4 different nucleotide monomers Polymers formed by polymerization—the joining of monomers © McGraw Hill, LLC 39  Monomers and Polymers 2 Polymerization (continued) Monomers covalently linked together by dehydration synthesis (condensation) reactions A hydroxyl (-OH) group is removed from one monomer, and a hydrogen (-H) from another; water produced as a by-product Hydrolysis is the opposite of dehydration synthesis Splitting a polymer in monomers by the addition of water Enzyme helps break the covalent bond that links two monomers together A water molecule ionizes into OH and H+ OH- is added to one monomer H+ is added to the other monomer © McGraw Hill, LLC 40  Dehydration Synthesis and Hydrolysis Reactions Access the text alternative for slide images. Figure 2.14 © McGraw Hill, LLC 41  2.4c Carbohydrates 1 Carbohydrates are hydrophilic organic molecules General formula: (CH2O)n , n = number of carbon atoms Glucose, n = 6, so formula is C6H12O6 2:1 ratio of hydrogen to oxygen Examples: sugars and starches © McGraw Hill, LLC 42  Carbohydrates 2 Monosaccharides are the simplest carbohydrates Monomers of larger carbohydrates Three important monomers are glucose, galactose, and fructose Produced by digestion of more complex carbohydrates Glucose is blood sugar All three have the same molecular formula: C6H12O6 Isomers of each other Ribose and deoxyribose are also monomers Part of RNA and DNA, respectively © McGraw Hill, LLC 43  The Three Major Monosaccharides Access the text alternative for slide images. Figure 2.15 © McGraw Hill, LLC 44  Carbohydrates 3 Disaccharides are sugars made of two covalently bonded monosaccharides Three important disaccharides: Sucrose (table sugar)—glucose + fructose Lactose (milk sugar)—glucose + galactose Maltose (sugar in grain products)—glucose + glucose © McGraw Hill, LLC 45  Carbohydrates 4 Polysaccharides are long chains of monosaccharides (~50 or more, up to thousands) Three important polysaccharides: Glycogen—energy storage in cells of liver, muscle, brain, uterus, vagina Starch—energy storage in plants that is digestible by humans Cellulose—structural molecule in plants that is important for human dietary fiber (but indigestible to us) © McGraw Hill, LLC 46  Glycogen Access the text alternative for slide images. Figure 2.17 © McGraw Hill, LLC 47  Carbohydrates 5 Functions of carbohydrates: Quickly mobilized source of energy All digested carbohydrates converted to glucose Often conjugated (bound) to lipids and proteins Example: lipids, proteins of cell membrane have chains of up to 12 sugars attached to form glycolipids and glycoproteins, respectively Glycoproteins are a major component of mucus Proteoglycans—macromolecules that are more carbohydrate than protein Form gels that hold cells and tissues together; fill umbilical cord and eye Joint lubrication; responsible for the rubbery texture of cartilage © McGraw Hill, LLC 48  2.4d Lipids 1 Lipids are hydrophobic organic molecules with a high ratio of hydrogen to oxygen More calories per gram than carbohydrates Five primary types of lipids in the human body: Fatty acids Triglycerides Phospholipids Eicosanoids Steroids © McGraw Hill, LLC 49  Lipids 2 Types of lipids (continued) Fatty acids—chains of 4–24 carbon atoms with carboxyl group on one end and methyl group on the other Essential fatty acids must be obtained from food Fatty acids are classified as saturated or unsaturated Saturated fatty acid—carbon atoms linked by single covalent bonds Molecule contains as much hydrogen as possible (“saturated” with hydrogen) Unsaturated fatty acids—contain some double bonds between carbons Molecule has potential to add hydrogen Polyunsaturated fatty acids have multiple double bonds between carbons © McGraw Hill, LLC 50  Triglyceride (Fat) Synthesis 1 Access the text alternative for slide images. Figure 2.18a © McGraw Hill, LLC 51  Lipids 3 Types of lipids (continued) Triglycerides—three fatty acids linked to glycerol Formed by dehydration synthesis; broken down by hydrolysis Primary function is energy storage; also help with insulation and shock absorption (adipose tissue) Also called neutral fats because once formed, fatty acid is no longer acidic Dietary oils and fats are triglycerides Oils are usually liquid at room or body temperature Example: plant-derived polyunsaturated triglycerides (polyunsaturated fats) such as corn and olive oils Saturated fats are solid at room or body temperature Example: animal-derived saturated triglycerides (for example, animal fat) © McGraw Hill, LLC 52  Triglyceride (Fat) Synthesis 2 Access the text alternative for slide images. Figure 2.18b © McGraw Hill, LLC 53  Lipids 4 Types of lipids (continued) Phospholipids—similar to triglycerides, but one fatty acid is replaced by a phosphate group Phospholipids are amphipathic Fatty acid “tails” are hydrophobic Phosphate “head” is hydrophilic Structural foundation of cell membrane © McGraw Hill, LLC 54  Lecithin, a Representative Phospholipid Access the text alternative for slide images. Figure 2.20 © McGraw Hill, LLC 55  Lipids 5 Types of lipids (continued) Eicosanoids—20-carbon compounds derived from a fatty acid called arachidonic acid Hormone-like chemical signals between cells Includes prostaglandins Function in inflammation, blood clotting, hormone action, labor contractions, blood vessel diameter Prostaglandin Figure 2.21 © McGraw Hill, LLC 56  Lipids 6 Types of lipids (continued) Steroids—lipid with 17 carbon atoms in four rings Cholesterol is the “parent” steroid from which other steroids are synthesized Important for nervous system function and structural integrity of all cell membranes 15% of our cholesterol comes from diet 85% is internally synthesized (mostly in liver) Other steroids include cortisol, progesterone, estrogens, testosterone, and bile acids © McGraw Hill, LLC 57  Cholesterol Access the text alternative for slide images. Figure 2.22 © McGraw Hill, LLC 58  “Good” and “Bad” Cholesterol There is only one kind of cholesterol “Good” and “bad” cholesterol refer to droplets of lipoprotein in the blood that are complexes of cholesterol, fat, phospholipid, and protein HDL (high-density lipoprotein) = “good cholesterol” Lower ratio of lipid to protein May help to prevent cardiovascular disease LDL (low-density lipoprotein) = “bad cholesterol” High ratio of lipid to protein Contributes to cardiovascular disease © McGraw Hill, LLC 59  2.4e Proteins 1 A protein is a polymer of amino acids Amino acids have a central carbon with three attachments Amino group (-NH2) Carboxyl group (–COOH) R (radical) group 20 amino acids used to make the proteins are identical except for the radical (R) group Properties of each amino acid determined by the R group © McGraw Hill, LLC 60  Amino Acids and Peptides 1 Access the text alternative for slide images. Figure 2.23a © McGraw Hill, LLC 61  Proteins 2 A peptide is composed of two or more amino acids joined by peptide bonds Peptide bond Formed by dehydration synthesis Peptides are named for the number of amino acids they contain Dipeptides (2 amino acids) Tripeptides (3 amino acids) Oligopeptides (fewer than 10 to15 amino acids) Polypeptides (larger than 15 amino acids) © McGraw Hill, LLC 62  Amino Acids and Peptides 2 Access the text alternative for slide images. Figure 2.23b © McGraw Hill, LLC 63  Protein Structure 1 Proteins have a complex three-dimensional shape referred to as their conformation Unique; crucial to function Proteins can reversibly change conformation to affect function Important examples seen in muscle contraction, enzyme catalysis, membrane channel opening, and so on Denaturation—extreme conformational change that destroys function Extreme heat or pH may cause permanent (irreversible) denaturation Example: cooked egg white becomes opaque and stiff © McGraw Hill, LLC 64  Protein Structure 2 Proteins have three to four levels of complexity: Primary structure Sequence of amino acids within protein molecule Primary structure is encoded by genes Secondary structure Coiled or folded shape held together by hydrogen bonds Most common secondary structures: Alpha helix has a springlike shape Beta sheet (beta-pleated sheet) has a folded, ribbonlike shape © McGraw Hill, LLC 65  Four Levels of Protein Structure 1 Access the text alternative for slide images. Figure 2.24 © McGraw Hill, LLC 66  Protein Structure 3 Protein levels of complexity (continued) Tertiary structure Further bending and folding of proteins into globular and fibrous shapes Globular proteins Compact tertiary structure for proteins within cell membrane and proteins that move freely in body fluids Fibrous proteins Slender filaments suited for roles in muscle contraction and strengthening of skin and hair © McGraw Hill, LLC 67  Protein Structure 4 Protein levels of complexity (continued) Quaternary structure Associations of two or more polypeptide chains due to ionic bonds and hydrophobic–hydrophilic interactions Occurs only in some proteins Example: hemoglobin has four peptide subunits © McGraw Hill, LLC 68  Four Levels of Protein Structure 2 Access the text alternative for slide images. Figure 2.24 © McGraw Hill, LLC 69  Protein Functions 1 Proteins have more diverse functions than other macromolecules Structure Keratin—tough structural protein of hair, nails, skin surface Collagen—contained in deeper layers of skin, bones, cartilage, and teeth Communication Neurotransmitters, some hormones, and other signaling molecules are proteins Signaling molecules that exert their effects by reversibly binding to a receptor molecule are called ligands The receptors to which the signaling molecules bind are also proteins © McGraw Hill, LLC 70  Protein Functions 2 Protein functions (continued) Membrane transport Channels allow hydrophilic substances to diffuse across cell membranes Carriers help solutes cross cell membranes via active or passive transport Catalysis The enzymes that catalyze physiological reactions are usually globular proteins Recognition and protection Glycoproteins are important for immune recognition Antibodies are proteins © McGraw Hill, LLC 71  Protein Functions 3 Protein functions (continued) Movement Molecular motors (motor proteins) are molecules with the ability to change shape repeatedly Cell adhesion Proteins bind cells together © McGraw Hill, LLC 72  2.4f Enzymes and Metabolism Enzymes are proteins that function as biological catalysts Enzymes act on one or more substrates Speed up chemical reaction by lowering the activation energy—the energy needed to get a reaction started Permit reactions to occur rapidly at body temperature Enzyme naming convention: Named for substrate with -ase as the suffix Examples: amylase catalyzes the hydrolysis of amylose (starch); lactase catalyzes the hydrolysis of lactose (milk sugar) © McGraw Hill, LLC 73  Effect of an Enzyme on Activation Energy Access the text alternative for slide images. Figure 2.26 © McGraw Hill, LLC 74  Enzyme Structure and Action 1 Enzyme action: 1. Substrate binds to pocket on enzyme called the active site 2. Formation of enzyme–substrate complex Enzyme–substrate specificity is like a lock and key 3. Enzyme releases reaction products Enzyme unchanged and can repeat process Example: the substrate sucrose is hydrolyzed by sucrase into the reaction products glucose and fructose © McGraw Hill, LLC 75  The Three Steps of an Enzymatic Reaction Access the text alternative for slide images. Figure 2.27 © McGraw Hill, LLC 76  Enzyme Structure and Action 2 Temperature, pH and other factors can change enzyme shape and function Can alter ability of enzyme to bind to substrate Enzymes vary in optimum pH Salivary amylase works best at pH 7.0 Pepsin in stomach works best at pH 2.0 Temperature optimum for human enzymes is usually near body temperature (37°C) © McGraw Hill, LLC 77  2.4g ATP, Other Nucleotides, and Nucleic Acids Nucleotides—organic compounds with three components: Nitrogenous base (single or double carbon–nitrogen ring) Sugar (monosaccharide) One or more phosphate groups © McGraw Hill, LLC 78  Adenosine Triphosphate (ATP) Access the text alternative for slide images. Figure 2.29a © McGraw Hill, LLC 79  Adenosine Triphosphate 1 Adenosine triphosphate (ATP) is the body’s most important energy-transfer molecule Stores energy gained from exergonic reactions Releases it within seconds for physiological work Holds energy in covalent bonds between phosphates Second and third phosphate groups have high energy bonds (~) Most energy transfers to and from ATP involve adding or removing the third phosphate group © McGraw Hill, LLC 80  Nucleic Acids Nucleic acids are polymers of nucleotides DNA (deoxyribonucleic acid) Contains millions of nucleotides Constitutes genes, the instructions for synthesizing proteins RNA (ribonucleic acid) 70 to 10,000 nucleotides long Carries out genetic instruction (encoded in DNA) for synthesizing proteins Assembles amino acids in right order to produce proteins © McGraw Hill, LLC 81