Chapter 2: The Chemistry of Life PDF

11/09/2023 Chapter 2 Matter The Chemistry of Life ▪ Matter—anything that occupies space and has...

11/09/2023 Chapter 2 Matter The Chemistry of Life ▪ Matter—anything that occupies space and has mass ▪ Matter may exist as one of three states ▪ Solid: definite shape and volume ▪ Liquid: definite volume; shape of container ▪ Gaseous: neither a definite shape nor volume © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 1 2 Matter Composition of Matter ▪ Matter may be changed ▪ Elements—fundamental units of matter ▪ Physically ▪ 96 percent of the body is made from four elements: ▪ Changes do not alter the basic nature of a substance 1. Oxygen (O)—most common; 65% of the body’s mass ▪ Examples include changes in the state of matter (solid, 2. Carbon (C) liquid, or gas) 3. Hydrogen (H) ▪ Chemically 4. Nitrogen (N) ▪ Changes alter the chemical composition of a substance ▪ Periodic table contains a complete listing of elements © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 3 4 Table 2.1 Common Elements Making Up the Human Body (1 of 3) Composition of Matter ▪ Atoms ▪ Building blocks of elements ▪ Atomic symbol is chemical shorthand for each element © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 5 6 1  11/09/2023 Table 2.2 Subatomic Particles The Basic Atomic Subparticles ▪ Protons (p+) are positively charged ▪ Neutrons (n0) are uncharged or neutral ▪ Electrons (e–) are negatively charged © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 7 8 The Basic Atomic Subparticles Planetary and Orbital Models of an Atom ▪ All atoms are electrically neutral ▪ Number of protons equals numbers of electrons in an atom ▪ Positive and negative charges cancel each other out © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 9 10 Figure 2.1a The structure of an atom. Figure 2.1b The structure of an atom. Nucleus Nucleus Helium atom Helium atom 2 protons (p+) 2 protons (p+) 2 neutrons (n0) 2 neutrons (n0) 2 electrons (e−) 2 electrons (e−) (a) Planetary model (b) Orbital model KEY: KEY: Proton Electron Proton Neutron Neutron Electron cloud © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 11 12 2  11/09/2023 Planetary and Orbital Models of an Atom Identifying Elements ▪ Electrons determine an atom’s chemical behavior ▪ To identify an element, we need to know the: and bonding properties ▪ Atomic number ▪ Atomic mass number ▪ Atomic weight © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 13 14 Figure 2.2 Atomic structure of the three smallest atoms. Identifying Elements ▪ Atomic number—equal to the number of protons that the atom contains KEY: ▪ Unique to atoms of a particular element Proton ▪ Indirectly tells the number of electrons in an atom Neutron Electron ▪ Atomic mass number—sum of the protons and neutrons contained in an atom’s nucleus (a) Hydrogen (H) (b) Helium (He) (c) Lithium (Li) (1p+; 0n0; 1e−) (2p+; 2n0; 2e−) (3p+; 4n0; 3e−) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 15 16 Figure 2.3 Isotopes of hydrogen. Atomic Weight and Isotopes ▪ Isotopes ▪ Atoms that have the same number of protons and KEY: electrons but vary in the number of neutrons Proton ▪ Isotopes have the same atomic number but different Neutron atomic masses Electron Hydrogen (1H) Deuterium (2H) Tritium (3H) (1p+; 0n0; 1e−) (1p+; 1n0; 1e−) (1p+; 2n0; 1e−) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 17 18 3  11/09/2023 Molecules and Compounds Molecules and Compounds ▪ Molecule—two or more atoms of the same ▪ Compound—two or more atoms of different elements combined chemically elements combined chemically to form a ▪ Example of a chemical reaction, shown as a molecule of a compound chemical equation, resulting in a molecule: ▪ Example of a chemical reaction resulting in a H (atom) + H (atom) → H2 (molecule) compound: ▪ The reactants are the atoms on the left 4H + C → CH4 (methane) ▪ The product is the molecule on the right, represented by a molecular formula © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 19 20 Figure 2.4 Properties of a compound differ from those of its atoms. Chemical Bonds and Chemical Reactions ▪ Chemical reactions occur when atoms combine with or dissociate from other atoms ▪ Chemical bonds are energy relationships involving interactions among the electrons of reacting atoms Sodium (silvery metal) Chlorine (poisonous gas) Sodium chloride (table salt) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 21 22 Role of Electrons Role of Electrons ▪ Electrons occupy energy levels called electron ▪ Each electron shell has distinct properties shells (or energy levels) ▪ How to fill the atom’s electrons shells ▪ Electrons closest to the nucleus are most strongly ▪ Shell 1 can hold a maximum of 2 electrons attracted to its positive charge ▪ Shell 2 can hold a maximum of 8 electrons ▪ Distant electrons further from the nucleus are ▪ Shell 3 can hold a maximum of 18 electrons likely to interact with other atoms ▪ Subsequent shells can hold more electrons ▪ Bonding involves interactions only between electrons in the outermost (valence) shell ▪ Atoms with full valence shells do not form bonds © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 23 24 4  11/09/2023 Figure 2.5a Chemically inert and reactive elements. Figure 2.5b Chemically inert and reactive elements. (b) Chemically reactive elements Outermost energy level (valence shell) incomplete (a) Chemically inert elements 4e Outermost energy level (valence shell) complete 1e 2e H C 8e 2e 2e Hydrogen (H) Carbon (C) He Ne (1p+; 0n0; 1e−) (6p+; 6n0; 6e−) 1e 6e 8e 2e 2e O Na Helium (He) Neon (Ne) (2p+; 2n0; 2e−) (10p+; 10n0; 10e−) Oxygen (O) (8p+; 8n0; 8e−) Sodium (Na) (11p+; 12n0; 11e−) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 25 26 Types of Chemical Bonds Types of Chemical Bonds ▪ Ionic bonds ▪ Ions ▪ Form when electrons are completely transferred from ▪ Result from the loss or gain of electrons one atom to another ▪ Anions have negative charge due to gain of electron(s) ▪ Allow atoms to achieve stability through the transfer of ▪ Cations have positive charge due to loss of electron(s) electrons ▪ Tend to stay close together because opposite charges attract © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 27 28 Figure 2.6 Formation of an ionic bond. Types of Chemical Bonds ▪ Covalent bonds + − ▪ Atoms become stable through shared electrons ▪ Electrons are shared in pairs ▪ Single covalent bonds share one pair of electrons Na Cl Na Cl ▪ Double covalent bonds share two pairs of electrons Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl−) (11p+; 12n0; 11e−) (17p+; 18n0; 17e−) Sodium chloride (NaCl) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 29 30 5  11/09/2023 Figure 2.7a Formation of covalent bonds. Figure 2.7b Formation of covalent bonds. Reacting atoms Resulting molecules Reacting atoms Resulting molecules H H H H or O O O O or Hydrogen Hydrogen Molecule of atom atom hydrogen gas (H2) Oxygen atom Oxygen atom Molecule of oxygen gas (O2) (a) Formation of a single covalent bond (b) Formation of a double covalent bond © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 31 32 Figure 2.7c Formation of covalent bonds. Types of Chemical Bonds Reacting atoms Resulting molecules ▪ Covalent bonds can be described as either H H nonpolar or polar ▪ Nonpolar covalent bonds H ▪ Electrons are shared equally between the atoms of the C H C H or molecule H ▪ Electrically neutral as a molecule ▪ Example: carbon dioxide H H Hydrogen atoms Carbon atom Molecule of methane gas (CH4) (c) Formation of four single covalent bonds © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 33 34 Figure 2.8a Molecular models illustrating the three-dimensional structure of carbon dioxide and water molecules. (a) Carbon dioxide (CO2) © 2018 Pearson Education, Ltd. 35 36 6  11/09/2023 Figure 2.8b Molecular models illustrating the three-dimensional structure of carbon dioxide and water molecules. Types of Chemical Bonds ▪ Covalent bonds can be described as either nonpolar or polar (continued) ▪ Polar covalent bonds δ− ▪ Electrons are not shared equally between the atoms of the molecule ▪ Molecule has a positive and negative side, or pole δ+ δ+ ▪ Example: water (b) Water (H2O) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 37 38 Types of Chemical Bonds ▪ Hydrogen bonds ▪ Extremely weak chemical bonds ▪ Formed when a hydrogen atom is attracted to the negative portion, such as an oxygen or nitrogen atom, of another molecule ▪ Responsible for the surface tension of water ▪ Important for forming intramolecular bonds, as in protein structure © 2018 Pearson Education, Ltd. 39 40 © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 41 42 7  11/09/2023 Figure 2.9 Hydrogen bonding between polar water molecules. Patterns of Chemical Reactions δ+ H H O ▪ Synthesis reaction (dehydration) (A + B → AB) δ− ▪ Atoms or molecules combine to form a larger, more Hydrogen bonds complex molecule δ+ ▪ Energy is absorbed for bond formation δ+ ▪ Underlies all anabolic (building) activities in the body δ− δ− δ− H ▪ Decomposition reaction (hydrolysis) (AB → A + B) H O O δ+ δ+ H H ▪ Molecule is broken down into smaller molecules H O δ+ ▪ Chemical energy is released H δ− ▪ Underlies all catabolic (destructive) activities in the (a) (b) body © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 43 44 Figure 2.10a Patterns of chemical reactions. Figure 2.10b Patterns of chemical reactions. (a) Synthesis reactions (b) Decomposition reactions Smaller particles are Bonds are broken in larger bonded together to form molecules, resulting in larger, more complex smaller, less complex molecules. molecules. Example Example Amino acids are joined Glycogen is broken down to together to form a protein release glucose units. molecule. Amino acid Glycogen molecules Protein molecule Glucose molecules © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 45 46 Figure 2.10c Patterns of chemical reactions. (c) Exchange reactions Patterns of Chemical Reactions Bonds are both made and broken. ▪ Exchange reaction Example AB + C → AC + B ATP transfers its terminal phosphate group to glucose to form glucose- phosphate. and AB + CD → AD + CB P P P ▪ Involves simultaneous synthesis and decomposition Glucose Adenosine triphosphate reactions as bonds are both made and broken (ATP) ▪ Switch is made between molecule parts, and different molecules are made P P P Glucose- Adenosine diphosphate phosphate (ADP) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 47 48 8  11/09/2023 Table 2.4 Factors Increasing the Rate of Chemical Reactions Patterns of Chemical Reactions ▪ Most chemical reactions are reversible ▪ Factors influencing the rate of chemical reactions are shown in Table 2.4 © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 49 50 Biochemistry: The Chemical Composition of Inorganic Compounds Living Matter ▪ Inorganic compounds ▪ Water ▪ Most lack carbon, or lacks carbon-hydrogen bond ▪ Most abundant inorganic compound in the body ▪ Tend to be small, simple molecules ▪ Accounts for two-thirds of the body’s weight ▪ Include water, salts, and many (not all) acids and ▪ Vital properties include: bases ▪ High heat capacity (slowly changes temperature) ▪ Organic compounds ▪ Solvent properties ▪ Chemical reactivity ▪ Contain carbon excluding carbonates and oxides ▪ Cushioning/lubricant ▪ All are large, covalent molecules ▪ Include carbohydrates, lipids, proteins, and nucleic acids © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 51 52 Inorganic Compounds Inorganic Compounds ▪ High heat capacity ▪ Solvent properties ▪ Water absorbs and releases a large amount of heat ▪ Water is often called the “universal solvent” before it changes temperature ▪ Prevents sudden changes in body temperature © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 53 54 9  11/09/2023 Inorganic Compounds Inorganic Compounds ▪ Chemical reactivity ▪ Cushioning ▪ Water is an important reactant in some chemical ▪ Water serves a protective function reactions ▪ Examples: cerebrospinal fluid protects the brain from ▪ Reactions that require water are known as hydrolysis physical trauma, and amniotic fluid protects a reactions developing fetus ▪ Example: water helps digest food or break down biological molecules © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 55 56 Inorganic Compounds Inorganic Compounds ▪ Water Compartments ▪ Salts ▪ Intracellular Fluid / ICF (65% of the total body water) ▪ Ionic compound ▪ Extracellular Fluid / ECF (35% of the total body water) ▪ Easily dissociate (break apart) into ions in the presence ▪ Plasma of water ▪ Lymph ▪ Vital to many body functions ▪ Tissue Fluid or Interstitial fluid ▪ Example: sodium and potassium ions are essential for ▪ Specialized fluids (synovial, CSF, aqueous humor in the nerve impulses eyes) ▪ All salts are electrolytes ▪ Electrolytes are ions that conduct electrical currents © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 57 58 Figure 2.11 Dissociation of salt in water. δ+ H Inorganic Compounds δ − O H δ+ Water molecule ▪ Acids ▪ Electrolytes that dissociate (ionize) in water and release hydrogen ions (H+) ▪ Example: HCl → H+ + Cl– Na+ ▪ Weak acids ionize incompletely Na+ Cl− Cl− Salt Ions in crystal solution © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 59 60 10  11/09/2023 Inorganic Compounds Inorganic Compounds ▪ Bases (Alkaline) ▪ pH ▪ Electrolytes that dissociate (ionize) in water and ▪ pH measures relative concentration of hydrogen (and release hydroxyl ions (OH–) hydroxide) ions in body fluids ▪ Example: NaOH → Na+ + OH– ▪ pH scale is based on the number of protons in a solution ▪ pH scale runs from 0 to 14 ▪ Each successive change of 1 pH unit represents a tenfold change in H+ concentration © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 61 62 Inorganic Compounds ▪ pH (continued) ▪ Neutral ▪ 7 is neutral ▪ Neutral means that the number of hydrogen ions exactly equals the number of hydroxyl ions ▪ Acidic solutions have a pH below 7 ▪ More H+ than OH– ▪ Basic solutions have a pH above 7 ▪ Fewer H+ than OH– ▪ Buffers—chemicals that can regulate pH change © 2018 Pearson Education, Ltd. 63 64 Organic Compounds Organic Compounds ▪ Carbohydrates ▪ Monosaccharides—simple sugars ▪ Contain carbon, hydrogen, and oxygen ▪ Single-chain or single-ring structures ▪ Include sugars and starches ▪ Contain three to seven carbon atoms ▪ Classified according to size and solubility in water ▪ Examples: glucose (blood sugar), fructose, galactose, ▪ Monosaccharides—simple sugars and the structural ribose, deoxyribose units of the carbohydrate group ▪ Disaccharides—two simple sugars joined by dehydration synthesis ▪ Polysaccharides—long-branching chains of linked simple sugars © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 65 66 11  11/09/2023 Figure 2.14a Carbohydrates. Organic Compounds ▪ Disaccharides—two simple sugars joined by dehydration synthesis ▪ Examples include sucrose, lactose, and maltose ▪ Too large to pass through cell membranes (a) Simple sugar (monosaccharide) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 67 68 Figure 2.14b Carbohydrates. Figure 2.14c Carbohydrates. Dehydration synthesis H2O Hydrolysis Glucose Fructose Sucrose Water (b) Double sugar (disaccharide) (c) Dehydration synthesis and hydrolysis of a molecule of sucrose © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 69 70 Figure 2.14d Carbohydrates. Organic Compounds ▪ Polysaccharides: long, branching chains of linked simple sugars ▪ Large, insoluble molecules ▪ Function as storage products ▪ Examples include starch and glycogen (d) Starch (polysaccharide) © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 71 72 12  11/09/2023 Table 2.5 Representative Lipids Found in the Body (1 of 2) Organic Compounds ▪ Lipids ▪ Most abundant are the triglycerides, phospholipids, and steroids ▪ Contain carbon, hydrogen, and oxygen ▪ Carbon and hydrogen outnumber oxygen ▪ Insoluble in water, but soluble in other lipids © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 73 74 Figure 2.16a Examples of saturated and unsaturated fats and fatty acids. Organic Compounds ▪ Triglycerides, or neutral fats Structural formula of a saturated fat molecule ▪ Found in fat deposits ▪ Source of stored energy ▪ Composed of two types of building blocks—fatty acids and one glycerol molecule ▪ Saturated fatty acids ▪ Unsaturated fatty acids (a) Saturated fat. At room temperature, the molecules of a saturated fat such as this butter are packed closely together, forming a solid. © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 75 76 Figure 2.16a Examples of saturated and unsaturated fats and fatty acids. Figure 2.16b Examples of saturated and unsaturated fats and fatty acids. Structural formula of an Structural formula of a unsaturated fat molecule saturated fat molecule (b) Unsaturated fat. At room temperature, the (a) Saturated fat. At room temperature, the molecules of an unsaturated fat such as this molecules of a saturated fat such as this butter olive oil cannot pack together closely enough are packed closely together, forming a solid. to solidify because of the kinks in some of their fatty acid chains. © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 77 78 13  11/09/2023 Organic Compounds Organic Compounds ▪ Trans fats ▪ Phospholipids ▪ Oils that have been solidified by the addition of ▪ Contain two fatty acids chains rather than three; they hydrogen atoms at double bond sites are hydrophobic (“water fearing”) ▪ Increase risk of heart disease ▪ Phosphorus-containing polar “head” carries an electrical charge and is hydrophilic (“water loving”) ▪ Omega-3 fatty acids ▪ Charged “head” region interacts with water and ions ▪ Found in cold-water fish and plant sources, including while the fatty acid chains (“tails”) do not flax, pumpkin, and chia seeds; walnuts and soy foods ▪ Form cell membranes ▪ Appear to decrease risk of heart disease © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 79 80 Figure 2.15b Lipids. Organic Compounds ▪ Steroids Polar “head” ▪ Formed of four interlocking rings ▪ Include cholesterol, bile salts, vitamin D, and some Nonpolar “tail” hormones (schematic phospholipid) ▪ Some cholesterol is ingested from animal products; the liver also makes cholesterol Phosphorus-containing Glycerol 2 fatty acid chains group (polar head) backbone (nonpolar tail) ▪ Cholesterol is the basis for all steroids made in the (b) Typical structure of a phospholipid molecule (phosphatidylcholine). Two fatty acid chains and body a phosphorous-containing group are attached to a glycerol backbone. © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 81 82 Figure 2.15c Lipids. Organic Compounds ▪ Proteins ▪ Account for over half of the body’s organic matter ▪ Provide for construction materials for body tissues ▪ Play a vital role in cell function ▪ Act as enzymes, hormones, and antibodies ▪ Contain carbon, oxygen, hydrogen, nitrogen, and sometimes sulfur (c) Cholesterol. Simplified structure ▪ Built from building blocks called amino acids of cholesterol, a steroid, formed by four interlocking carbon rings. © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 83 84 14  11/09/2023 Table 2.6 Representative Classes of Functional Proteins Organic Compounds ▪ Protein structure ▪ Polypeptides contain fewer than 50 amino acids ▪ Proteins contain more than 50 amino acids ▪ Large, complex proteins contain 50 to thousands of amino acids ▪ Sequence of amino acids produces a variety of proteins © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 85 86 Organic Compounds Organic Compounds ▪ Enzymes ▪ Nucleic acids ▪ Act as biological catalysts ▪ Form genes ▪ Increase the rate of chemical reactions ▪ Composed of carbon, oxygen, hydrogen, nitrogen, and ▪ Can be recognized by their –ase suffix phosphorus atoms ▪ Hydrolase ▪ Largest biological molecules in the body ▪ Oxidase ▪ Two major kinds: ▪ DNA ▪ RNA © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 87 88 Figure 2.21ab Structure of DNA. Organic Compounds ▪ Nucleic acids are built from building blocks called nucleotides Pentose Nitrogen- Phosphate sugar: containing base: ▪ Nucleotides contain three parts group Deoxyribose Adenine (A) 1. A nitrogenous base ▪ A = Adenine ▪ G = Guanine ▪ C = Cytosine (b) Adenine nucleotide (Diagrammatic representation) ▪ T = Thymine ▪ U = Uracil (a) Adenine nucleotide (Chemical structure) 2. Pentose (five-carbon) sugar 3. A phosphate group © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 89 90 15  11/09/2023 Figure 2.21c Structure of DNA. Organic Compounds ▪ Deoxyribonucleic acid (DNA) ▪ The genetic material found within the cell’s nucleus ▪ Provides instructions for every protein in the body ▪ Contains the sugar deoxyribose and the bases adenine, thymine, cytosine, and guanine ▪ Replicates before cell division (c) Computer-generated image of a DNA molecule © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 91 92 Figure 2.21d Structure of DNA. Hydrogen bonds KEY: Organic Compounds Thymine (T) Adenine (A) Cytosine (C) ▪ Ribonucleic acid (RNA) Deoxyribose sugar Guanine (G) ▪ Carries out DNA’s instructions for protein synthesis Phosphate ▪ Created from a template of DNA ▪ Contains the sugar ribose and the bases adenine, uracil, cytosine, and guanine Sugar-phosphate backbone (d) Diagram of a DNA molecule © 2018 Pearson Education, Ltd. © 2018 Pearson Education, Ltd. 93 94 Organic Compounds ▪ Adenosine triphosphate (ATP) ▪ Composed of a nucleotide built from ribose sugar, adenine base, and three phosphate groups ▪ Chemical energy used by all cell © 2018 Pearson Education, Ltd. 95 16