Chapter 2 The Chemical Level of Organization Lecture

Chapter 2 The Chemical Level of Organization Lecture Presentation by Lee Ann Frederick University of Texas at Arlington

An Introduction to the Chemical Level of Organization • Learning Outcomes • 2 -1 Describe an atom and how atomic structure affects interactions between atoms. • 2 -2 Compare the ways in which atoms combine to form molecules and compounds. • 2 -3 Distinguish among the major types of chemical reactions that are important for studying physiology. • 2 -4 Describe the crucial role of enzymes in metabolism. © 2015 Pearson Education, Inc.

An Introduction to the Chemical Level of Organization • Learning Outcomes • 2 -5 Distinguish between organic and inorganic compounds. • 2 -6 Explain how the chemical properties of water make life possible. • 2 -7 Discuss the importance of p. H and the role of buffers in body fluids. • 2 -8 Describe the physiological roles of inorganic compounds. • 2 -9 Discuss the structures and functions of carbohydrates. © 2015 Pearson Education, Inc.

An Introduction to the Chemical Level of Organization • Learning Outcomes • 2 -10 Discuss the structures and functions of lipids. • 2 -11 Discuss the structures and functions of proteins. • 2 -12 Discuss the structures and functions of nucleic acids. • 2 -13 Discuss the structures and functions of high-energy compounds. • 2 -14 Explain the relationship between chemicals and cells. © 2015 Pearson Education, Inc.

An Introduction to the Chemical Level of Organization • Chemistry • Is the science of change • Topics of this chapter include: • The structure of atoms • The basic chemical building blocks • How atoms combine to form increasingly complex structures © 2015 Pearson Education, Inc.

2 -1 Atoms and Atomic Structure • Matter • Is made up of atoms • Atoms join together to form chemicals with different characteristics • Chemical characteristics determine physiology at the molecular and cellular levels © 2015 Pearson Education, Inc.

2 -1 Atoms and Atomic Structure • Subatomic Particles • Proton • Positive charge, 1 mass unit • Neutron • Neutral, 1 mass unit • Electron • Negative charge, low mass © 2015 Pearson Education, Inc.

2 -1 Atoms and Atomic Structure • Atomic number • Number of protons • Nucleus • Contains protons and neutrons • Electron cloud • Contains electrons © 2015 Pearson Education, Inc.

Figure 2 -1 The Structure of Hydrogen Atoms. Electron shell − e p+ Hydrogen-1 mass number: 1 a A typical hydrogen nucleus contains a proton and no neutrons. © 2015 Pearson Education, Inc. − e p+ n − n e p+ n Hydrogen-2, deuterium Hydrogen-3, tritium mass number: 2 mass number: 3 b A deuterium (2 H) nucleus contains a proton and a neutron. c A tritium (3 H) nucleus contains a proton and two neutrons.

Table 2 -1 Principal Elements in the Human Body © 2015 Pearson Education, Inc.

Table 2 -1 Principal Elements in the Human Body © 2015 Pearson Education, Inc.

2 -1 Atoms and Atomic Structure • Elements and Isotopes • Elements are determined by the atomic number of an atom • Remember, atomic number = number of protons • Elements are the most basic chemicals © 2015 Pearson Education, Inc.

2 -1 Atoms and Atomic Structure • Elements and Isotopes • Isotopes are the specific version of an element based on its mass number • Mass number = number of protons plus the number of neutrons • Only neutrons are different because the number of protons determines the element © 2015 Pearson Education, Inc.

2 -1 Atoms and Atomic Structure • Atomic Weight • Exact mass of all particles • Measured in moles • Average of the mass numbers of the isotopes © 2015 Pearson Education, Inc.

2 -1 Atoms and Atomic Structure • Electrons and Energy Levels • Electrons in the electron cloud determine the reactivity of an atom • The electron cloud contains shells, or energy levels, that hold a maximum number of electrons • Outermost shell is the valence shell, and it determines bonding • The number of electrons per shell corresponds to the number of atoms in that row of the periodic table © 2015 Pearson Education, Inc.

Figure 2 -2 The Arrangement of Electrons into Energy Levels. The first energy level can hold a maximum of two electrons. −e p+ Hydrogen, H Atomic number: 1 Mass number: 1 1 electron a Hydrogen (H). A typical hydrogen atom has one proton and one electron. The electron orbiting the nucleus occupies the first, or lowest, energy level, diagrammed as an electron shell. © 2015 Pearson Education, Inc. −e n p+ e− Helium, He Atomic number: 2 Mass number: 4 (2 protons + 2 neutrons) 2 electrons b Helium (He). An atom of helium has two protons, two neutrons, and two electrons. The two electrons orbit in the same energy level.

Figure 2 -2 The Arrangement of Electrons into Energy Levels. The second and third energy levels can each contain up to 8 electrons. −e −e n p+ e− −e −e c Lithium (Li). A lithium atom has three protons, three neutrons, and three electrons. The first energy level can hold only two electrons, so the third electron occupies a second energy level. © 2015 Pearson Education, Inc. e− − e e− n −e p+ −e Lithium, Li Atomic number: 3 Mass number: 6 (3 protons + 3 neutrons) 3 electrons e− −e e− Neon, Ne Atomic number: 10 Mass number: 20 (10 protons + 10 neutrons) 10 electrons d Neon (Ne). A neon atom has 10 protons, 10 neutrons, and 10 electrons. The second level can hold up to eight electrons; thus, both the first and second energy levels are filled.

2 -2 Molecules and Compounds • Chemical Bonds • Involve the sharing, gaining, and losing of electrons in the valence shell • Three major types of chemical bonds 1. Ionic bonds • Attraction between cations (electron donor) and anions (electron acceptor) 2. Covalent bonds • Strong electron bonds involving shared electrons 3. Hydrogen bonds • Weak polar bonds based on partial electrical attractions © 2015 Pearson Education, Inc.

2 -2 Molecules and Compounds • Chemical Bonds • Form molecules and/or compounds • Molecules • Two or more atoms joined by strong bonds • Compounds are all molecules, but not all molecules are compounds • H 2 = molecule only • H 2 O = molecule and compound © 2015 Pearson Education, Inc.

Figure 2 -3 Chemical Notation (Part 4 of 4). Ions A superscript plus or minus sign following the symbol of an element indicates an ion. A single plus sign indicates a cation with a charge of +1. (The original atom has lost one electron. ) A single minus sign indicates an anion with a charge of − 1. (The original atom has gained one electron. ) If more than one electron has been lost or gained, the charge on the ion is indicated by a number preceding the plus or minus sign. VISUAL REPRESENTATION Na+ Cl− Ca 2+ sodium ion chloride ion calcium ion the chlorine the sodium the calcium atom has lost atom has gained atom has lost one electron two electrons A sodium atom becomes a sodium ion Electron lost Na Sodium atom (Na) © 2015 Pearson Education, Inc. + Na+ Sodium ion (Na+) CHEMICAL NOTATION Na+ Cl− sodium chloride ion Ca 2+ calcium ion

2 -2 Molecules and Compounds • Covalent Bonds • Involve the sharing of pairs of electrons between atoms • Sharing one pair of electrons is a single covalent bond • Sharing two pairs of electrons is a double covalent bond • Sharing three pairs of electrons is a triple covalent bond © 2015 Pearson Education, Inc.

2 -2 Molecules and Compounds • Covalent Bonds • Nonpolar covalent bonds • Involve equal sharing of electrons because atoms • Polar covalent bonds • Involve the unequal sharing of electrons because one of the atoms involved in the bond has a disproportionately strong pull on the electrons © 2015 Pearson Education, Inc.

2 -2 Molecules and Compounds • Hydrogen Bonds • Bonds between adjacent molecules, not atoms • Hydrogen bonds between H 2 O molecules cause surface tension © 2015 Pearson Education, Inc.

2 -2 Molecules and Compounds • States of Matter • Solid • Constant volume and shape • Liquid • Constant volume but changes shape • Gas • Changes volume and shape © 2015 Pearson Education, Inc.

2 -3 Chemical Reactions • In a Chemical Reaction • Either new bonds are formed or existing bonds are broken • Reactants • Materials going into a reaction • Products • Materials coming out of a reaction • Metabolism • All of the reactions that are occurring at one time © 2015 Pearson Education, Inc.

2 -3 Chemical Reactions • Basic Energy Concepts • Energy • The power to do work • Work • A change in mass or distance • Kinetic energy • Energy of motion • Potential energy • Stored energy • Chemical energy • Potential energy stored in chemical bonds © 2015 Pearson Education, Inc.

2 -3 Chemical Reactions • Decomposition Reaction (Catabolism) • Breaks chemical bonds • AB A + B • Hydrolysis A-B + H 2 O A-H + HO-B • Synthesis Reaction (Anabolism) • Forms chemical bonds • A + B AB • Dehydration synthesis (condensation reaction) A-H + HO-B A-B + H 2 O © 2015 Pearson Education, Inc.

2 -3 Chemical Reactions • Exchange Reaction • Involves decomposition first, then synthesis • AB + CD AD + CB © 2015 Pearson Education, Inc.

2 -3 Chemical Reactions • Reversible Reaction • A + B ↔ AB • At equilibrium the amounts of chemicals do not change even though the reactions are still occurring © 2015 Pearson Education, Inc.

2 -4 Enzymes • Chemical Reactions • In cells, cannot start without help • Activation energy is the amount of energy needed to get a reaction started • Enzymes are protein catalysts that lower the activation energy of reactions © 2015 Pearson Education, Inc.

2 -4 Enzymes • Exergonic (Exothermic) Reactions • Produce more energy than they use • Endergonic (Endothermic) Reactions • Use more energy than they produce © 2015 Pearson Education, Inc.

2 -5 Inorganic and Organic Compounds • Nutrients • Essential molecules obtained from food • Metabolites • Molecules made or broken down in the body • Inorganic Compounds • Molecules not based on carbon and hydrogen • Carbon dioxide, oxygen, water, and inorganic acids, bases, and salts • Organic Compounds • Molecules based on carbon and hydrogen • Carbohydrates, proteins, lipids, and nucleic acids © 2015 Pearson Education, Inc.

2 -6 Properties of Water • The Properties of Aqueous Solutions • Electrolytes are inorganic ions that conduct electricity in solution • Electrolyte imbalance seriously disturbs vital body functions • Water accounts for up to two-thirds of your total body weight © 2015 Pearson Education, Inc.

2 -6 Properties of Water • The Properties of Aqueous Solutions • Hydrophilic and hydrophobic compounds • Hydrophilic • hydro- = water, philos = loving • Interacts with water • Includes ions and polar molecules • Hydrophobic • phobos = fear • Does NOT interact with water • Includes nonpolar molecules, fats, and oils © 2015 Pearson Education, Inc.

2 -6 Properties of Water • Colloids and Suspensions • Colloid • A solution of very large organic molecules • For example, blood plasma • Suspension • A solution in which particles settle (sediment) • For example, whole blood • Concentration • The amount of solute in a solvent (mol/L, mg/m. L) © 2015 Pearson Education, Inc.

2 -7 p. H and Homeostasis • p. H • The concentration of hydrogen ions (H+) in a solution • Neutral p. H • A balance of H+ and OH • Pure water = 7. 0 © 2015 Pearson Education, Inc.

2 -7 p. H and Homeostasis • Acidic p. H Lower Than 7. 0 • High H+ concentration • Low OH concentration • Basic (or alkaline) p. H Higher Than 7. 0 • Low H+ concentration • High OH concentration • p. H of Human Blood • Ranges from 7. 35 to 7. 45 © 2015 Pearson Education, Inc.

2 -7 p. H and Homeostasis • p. H Scale • Has an inverse relationship with H+ concentration • More H+ ions means lower p. H, fewer H+ ions means higher p. H © 2015 Pearson Education, Inc.

Figure 2 -10 The p. H Scale Indicates Hydrogen Ion Concentration. 1 mol/L hydrochloric acid Beer, vinegar, wine, Tomatoes, pickles grapes Stomach acid Extremely acidic p. H 0 [H+] 100 (mol/L) 1 10− 1 Urine Saliva, milk Increasing concentration of H+ 2 10− 2 © 2015 Pearson Education, Inc. 3 10− 3 4 10− 4 5 10− 5 6 10− 6 Blood Ocean Pure Eggswater Neutral 7 10− 7 Household bleach Household ammonia Increasing concentration of OH− 8 10− 8 9 10− 9 10 10− 10 11 10− 11 12 10− 12 1 mol/L sodium hydroxide Oven cleaner Extremely basic 13 10− 13 14 10− 14

2 -8 Inorganic Compounds • Buffers • Weak acid/salt compounds • Neutralize either strong acid or strong base • Antacids • Basic compounds that neutralize acid and form a salt • Alka-Seltzer, Tums, Rolaids, etc. • Salts • Solutes that dissociate into cations and anions other than hydrogen ions and hydroxide ions © 2015 Pearson Education, Inc.

2 -9 Carbohydrates • Organic Molecules • Contain H, C, and usually O • Are covalently bonded • • Carbohydrates Lipids Proteins (or amino acids) Nucleic acids © 2015 Pearson Education, Inc.

Table 2 -3 Important Functional Groups of Organic Compounds. © 2015 Pearson Education, Inc.

2 -9 Carbohydrates • Carbohydrates contain carbon, hydrogen, and oxygen in a 1: 2: 1 ratio • Monosaccharide — simple sugar 3 to 7 carbon atoms, glucose, fructose, galactose • Disaccharide — two sugars condensed by dehydration synthesis , sucrose, maltose • Polysaccharide — many sugars condensed by dehydration synthesis, glycogen, starch, cellulose © 2015 Pearson Education, Inc.

Table 2 -4 Carbohydrates in the Body. © 2015 Pearson Education, Inc.

2 -10 Lipids • Mainly hydrophobic molecules such as fats, oils, and waxes • Made mostly of carbon and hydrogen atoms • Include: • • • Fatty acids Eicosanoids Glycerides Steroids Phospholipids and glycolipids © 2015 Pearson Education, Inc.

2 -10 Lipids • Fatty Acids • Long chains of carbon and hydrogen with a carboxyl group (COOH) at one end • Are relatively nonpolar, except the carboxyl group • Fatty acids may be: • Saturated with hydrogen (no covalent bonds) • Unsaturated (one or more double bonds) • Monounsaturated = one double bond • Polyunsaturated = two or more double bonds © 2015 Pearson Education, Inc.

Figure 2 -14 b Fatty Acids. Saturated Unsaturated b © 2015 Pearson Education, Inc. A fatty acid is either saturated (has single covalent bonds only) or unsaturated (has one or more double covalent bonds). The presence of a double bond causes a sharp bend in the molecule.

2 -10 Lipids • Glycerides • Fatty acids attached to a glycerol molecule • Triglycerides are three fatty-acid tails • Also called triacylglycerols or neutral fats • Have three important functions 1. Energy source 2. Insulation 3. Protection © 2015 Pearson Education, Inc.

2 -10 Lipids • Steroids • Four rings of carbon and hydrogen with an assortment of functional groups • Types of steroids • Cholesterol • Component of plasma (cell) membranes • Estrogens and testosterone • Sex hormones • Corticosteroids and calcitriol • Metabolic regulation • Bile salts • Derived from steroids © 2015 Pearson Education, Inc.

Figure 2 -17 Steroids Have a Complex Four-Ring Structure. a Cholesterol b Estrogen © 2015 Pearson Education, Inc. c Testosterone

2 -10 Lipids • Phospholipids and Glycolipids • Diglycerides attached to either a phosphate group (phospholipid) or a sugar (glycolipid) • Generally, both have hydrophilic heads and hydrophobic tails and are structural lipids, components of plasma (cell) membranes © 2015 Pearson Education, Inc.

Figure 2 -18 b Phospholipids and Glycolipids. Carbohydrate Glycerol Fatty acids b © 2015 Pearson Education, Inc. In a glycolipid, a carbohydrate is attached to a diglyceride.

Figure 2 -18 c Phospholipids and Glycolipids. Hydrophilic heads c In large numbers, phospholipids and glycolipids form Hydrophobic tails micelles, with the hydrophilic heads facing the water molecules, and the hydrophobic tails on the inside of each droplet. Glycolipid Phospholipid WATER © 2015 Pearson Education, Inc.

Table 2 -5 Representative Lipids and Their Functions in the Body. © 2015 Pearson Education, Inc.

2 -11 Proteins • Are the most abundant and important organic molecules • Contain basic elements • Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) • Basic building blocks • 20 amino acids © 2015 Pearson Education, Inc.

2 -11 Proteins • Seven Major Protein Functions 1. Support • Structural proteins 2. Movement • Contractile proteins 3. Transport • Transport (carrier) proteins 4. Buffering • Regulation of p. H 5. Metabolic Regulation • Enzymes 6. Coordination and Control • Hormones 7. Defense • Antibodies © 2015 Pearson Education, Inc.

Figure 2 -19 Amino Acids. Structure of an Amino Acid Amino group Central carbon Carboxyl group R group (variable side chain of one or more atoms) © 2015 Pearson Education, Inc.

2 -11 Proteins • Protein Shape • Primary structure • The sequence of amino acids along a polypeptide • Secondary structure • Hydrogen bonds form spirals or pleats • Tertiary structure • Secondary structure folds into a unique shape • Quaternary structure • Final protein shape — several tertiary structures together © 2015 Pearson Education, Inc.

Figure 2 -21 Protein Structure. A 1 A 2 A 3 A 4 A 5 A 6 A 7 A 8 A 9 Linear chain of amino acids a Primary structure. The primary structure of a polypeptide is the sequence of amino acids (A 1, A 2, A 3, and so on) along its length. a A 1 A 10 A 6 A 3 A 5 A 3 A 4 A 5 Hydrogen bond A 2 A 7 OR A 9 A 8 A 7 A 6 A 11 A 12 A 13 A 14 Alpha helix Beta sheet b Secondary structure is primarily the result of hydrogen Alpha helix bonding along the length of the polypeptide chain. Such bonding often produces a simple spiral, called an alpha helix (α helix) or a flattened arrangement known as a beta sheet (β sheet). OR Heme units c Tertiary structure is the coiling and folding of a polypeptide. Within the cylindrical segments of this globular protein, the polypeptide chain is arranged in an alpha helix. Hemoglobin (globular protein) Collagen (fibrous protein) d Quaternary structure develops when separate © 2015 Pearson Education, Inc. polypeptide subunits interact to form a larger molecule. A single hemoglobin molecule contains four globular subunits. Hemoglobin transports oxygen in the blood; the oxygen binds reversibly to the heme units. In collagen, three helical polypeptide subunits intertwine. Collagen is the principal extracellular protein in most organs.

2 -11 Proteins • Fibrous Proteins • Structural sheets or strands • Globular Proteins • Soluble spheres with active functions • Protein function is based on shape • Shape is based on sequence of amino acids © 2015 Pearson Education, Inc.

2 -11 Proteins • Enzyme Function • Enzymes are catalysts • Proteins that lower the activation energy of a chemical reaction • Cofactor • An ion or molecule that binds to an enzyme before substrates can bind • Coenzyme • Nonprotein organic cofactors (vitamins) • Isozymes • Two enzymes that can catalyze the same reaction © 2015 Pearson Education, Inc.

2 -12 Nucleic Acids • Are large organic molecules, found in the nucleus, which store and process information at the molecular level • Deoxyribonucleic acid (DNA) • • Determines inherited characteristics Directs protein synthesis Controls enzyme production Controls metabolism • Ribonucleic acid (RNA) • Controls intermediate steps in protein synthesis © 2015 Pearson Education, Inc.

2 -12 Nucleic Acids • Structure of Nucleic Acids • DNA and RNA are strings of nucleotides • Nucleotides • Are the building blocks of DNA and RNA • Have three molecular parts 1. 2. 3. © 2015 Pearson Education, Inc. A pentose sugar (deoxyribose or ribose) Phosphate group Nitrogenous base (A, G, T, C, or U)

Figure 2 -23 a Nucleotides and Nitrogenous Bases. a Nucleotide structure The nitrogenous base may be a purine or a pyrimidine. Phosphate group Sugar Nitrogenous base © 2015 Pearson Education, Inc.

2 -12 Nucleic Acids • DNA and RNA • DNA is double stranded, and the bases form hydrogen bonds to hold the DNA together • RNA is usually a single strand • DNA forms a twisting double helix • Complementary base pairs • Purines pair with pyrimidines • DNA • Adenine (A) and thymine (T) • Cytosine (C) and guanine (G) • RNA • Uracil (U) replaces thymine (T) © 2015 Pearson Education, Inc.

Figure 2 -24 The Structure of Nucleic Acids. Phosphate group Deoxyribose Adenine Thymine Hydrogen bond DNA strand 1 DNA strand 2 a RNA molecule. An RNA molecule has a single nucleotide chain. Its shape is determined by the sequence of nucleotides and by the interactions among them. Cytosine Guanine b DNA molecule. A DNA molecule © 2015 Pearson Education, Inc. has a pair of nucleotide chains linked by hydrogen bonding between complementary base pairs.

2 -12 Nucleic Acids • Types of RNA • Messenger RNA (m. RNA) • Transfer RNA (t. RNA) • Ribosomal RNA (r. RNA) © 2015 Pearson Education, Inc.

Table 2 -6 Comparison of RNA with DNA. © 2015 Pearson Education, Inc.

2 -13 High-Energy Compounds • Nucleotides Can Be Used to Store Energy • Adenosine diphosphate (ADP) • Two phosphate groups; di- = 2 • Adenosine triphosphate (ATP) • Three phosphate groups; tri- = 3 © 2015 Pearson Education, Inc.

2 -14 Chemicals and Cells • Biochemical building blocks form functional units called cells • Metabolic turnover lets your body grow, change, and adapt to new conditions and activities • Your body recycles and renews all of its chemical components at intervals ranging from minutes to years © 2015 Pearson Education, Inc.

Table 2 -7 Classes of Inorganic and Organic Compounds. © 2015 Pearson Education, Inc.

Table 2 -8 Turnover Times. © 2015 Pearson Education, Inc.