Lecture Outline - Chapter 2

2.1. Elements and Atoms (Fig. 2.1) (p. 20)

1. Atoms are smallest units of matter involved in chemical reactions.
2. Six elements (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur) make up 98% of weight of organisms.
3. Parts of an atom: (Figs. 2.2, 2.3)
   • a. Nucleus: central portion composed of protons and neutrons.
     • i. Proton has one positive unit of charge, has an atomic weight of one.
     • ii. Neutron carries no charge, has an one atomic weight of one.
     • iii. Atomic number equals the number of protons.
     • iv. Atomic weight equals the number of protons plus number of neutrons. (Table 2.1)
   • b. Electron has one negative unit of charge and almost no weight.
     • i. In an electrically neutral atom, the number of protons is equal to number of electrons.
     • ii. Electrons with greatest amount of energy are located in shells farthest from nucleus.
     • iii. First shell contains up to 2 electrons; thereafter up to 8 electrons.
4. An element is any substance that contains just one type of atom; see simplified periodic table. Horizontal rows are arranged by atomic number and weight; vertical columns are arranged by number of electrons in outermost shell.
5. Isotopes: When Atomic Weights Vary
   • a. Isotopes are atoms with same number of protons and electrons but differing in number of neutrons and therefore weight; for example: ¹⁴C is an isotope of ¹²C.
   • b. Radioactive isotopes are unstable; as they decay, they emit radiation detected by a special counter or scanner. They are widely used in biological research and medical diagnostic procedures.

1. A molecule consists of two or more atoms (same kind or different) bonded together.
2. A compound is a molecule made of at least two different atoms.
3. Ionic Bonds Where Atoms Gain or Lose Electrons
   • a. Atoms (except hydrogen which has only one electron) react with other atoms to achieve eight electrons in their outer shell.
   • b. Ions are atoms that carry a charge as a result of giving or taking electrons; for example a sodium atom becomes sodium ion (Na⁺) when it gives up an electron; a chlorine atom becomes a chloride ion (Cl^-) when it receives an electron. (Fig. 2.4)
   • c. Ionic bonds form when oppositely charged ions are attracted to each other; for example, Na⁺ and Cl^- form NaCl. Ionic bonds are typically found in inorganic compounds. (Fig. 2.5)
   • d. There are many important ions in human body. (Table 2.2)
4. Covalent Reactions Where Atoms Share Electrons
   • a. Covalent bonds occur when electrons are shared so that each atom will have a complete outer shell; this is typically found in organic compounds. (Fig. 2.6)
   • b. Covalent bond representations can be achieved by:
     • i. Electron-dot structures.
     • ii. Structural formulas where a straight line is used between atoms to represent a pair of shared electrons.
     • iii. Molecular formula showing only the number of each type of atom making up molecule. (Fig. 2.7)
5. Double and Triple Bonds
   Two pairs of electrons are shared between atoms in a double bond. Atoms with triple bonds share three pairs of electrons between them.
6. Oxidation Loses, Reduction Gains
   • a. For ionic reactions, oxidation refers to loss of electrons: Na --> Na⁺.
   • b. For some covalent reactions, oxidation refers to loss of hydrogen atoms.
   • c. For ionic reactions, reduction refers to gain of electrons: Cl --> Cl^-.
   • d. For some covalent reactions, reduction refers to gain of hydrogen atoms.
   • e. Both processes occur concurrently in oxidation-reduction reactions.

1. Water
   • a. Water is a polar molecule with a slight positive charge on the hydrogen atoms and slight negative charge on the oxygen atom. (Fig. 2.8)
   • b. Water molecules are held together by hydrogen bonds, weak bonds found between a covalently bonded hydrogen and a negatively charged distant atom; this hydrogen bonding establishes the boiling and freezing points of water.
   • c. Water is a major solvent of both living and nonliving systems.
   • d. Cohesive water molecules dissolve polar substances and provide excellent liquid transport of nutrients and wastes.
   • e. Water requires much heat energy to raise its temperature, and releases heat slowly; this helps maintain a constant body temperature. (Fig. 2.9)
   • f. Water loses much heat when changed to vapor; sweating therefore cools animals rapidly.
   • g. Liquid water is more dense than ice (ice therefore floats); this insulates aquatic environment from dramatic temperature changes.
   • h. Dissociation of polar water molecules causes water to ionize to form H⁺ and OH^-.
2. Acids (H⁺ Up); Bases (H⁺ Down) (Fig. 2.10)
   • a. Water dissociates into equal numbers of hydrogen ions and hydroxyl ions.
     Example: H₂O --> H⁺ + OH^-

     b. Acids are molecules that dissociate in water and release hydrogen ions (protons).

     Example: HCl --> H⁺ + Cl^- (Fig. 2.11)

     c. Bases are molecules that either take up hydrogen ions or release hydroxyl ions.

     Example: NaOH --> Na⁺ + OH^- (Fig. 2.12)
3. pH Scale
   • a. Indicate acidity or basicity of a solution.
   • b. Defined as negative logarithm of the hydrogen ion concentration; neutral water dissociates into 10^-7 moles/liter of hydrogen ions.
   • c. Under pH 7 is acidic (more hydrogen ions, less hydroxyl ions).
   • d. Over pH 7 is basic (less hydrogen ions, more hydroxyl ions).
   • e. The pH scale ranges from 0 to 14; being a logarithmic scale, each pH unit is a 10-fold difference in H⁺ concentration. (Fig. 2.13)
4. Buffers Keep pH Steady
   • a. Buffers are chemicals or combinations of chemicals that take up excess hydrogen ions or hydroxyl ions and keep the pH constant. For example, carbonic acid and the bicarbonate ion prevent any changes in the blood pH when an acid or base is added.
   • b. Acid rain, much originating from power plants, damages trees and lakes when there is a shortage of limestone to buffer the acid.

1. Organic molecules are generally associated with living organisms.
2. Organic molecules always contain carbon (C) and hydrogen (H).
3. Monomers are the building blocks for larger molecules called macromolecules or polymers. (Figs. 2.14 - 2.16)

1. Supply quick and short-term energy; also play structural role when joined with other molecules.
2. Atomic grouping of CH2O with 2:1 ratio of hydrogen to oxygen atoms.
3. The term carbohydrate means hydrates of carbon.
4. Simple carbohydrates.
   • a. Monosaccharides are simple sugars with 3 - 7 carbon atoms; examples include fructose in fruits, galactose in milk, and glucose--all with the same molecular formula C₆H₁₂O₆ but differing in arrangement of atoms; glucose is primary energy source for cells. (Fig. 2.17)
   • b. Disaccharides have two monosaccharide units joined together with water removed, a condensation reaction. (Fig. 2.18)
   • c. Maltose consists of two glucose molecules joined together.
   • d. Sucrose (table sugar) has a glucose and a fructose molecule joined together.
5. Complex Carbohydrates
   • a. Starch is a storage form of glucose in plants. (Fig. 2.19)
   • b. Glycogen is a storage form of glucose in animals. (Fig. 2.20)
   • c. Both are polysaccharides or polymers formed from the glucose monomer.
6. Cellulose is a polysaccharide found in plant cell walls to provide strength. Humans are unable to digest cellulose but it is used as fiber, or roughage. (Fig. 2.21)
7. During dehydration synthesis, monomers join together as water is formed. During hydrolysis, a polymer is broken down into monomers as water is broken down.

1. Functions include: long-term energy storage, insulation against heat loss, cushion organs.
2. Formed by one glycerol reacting with three fatty acid molecules; product is triglyceride and is non-polar. (Fig. 2.22)
3. Fats (lard, butter) are solid, oils (corn oil, soybean oil) are liquid at room temperature.
4. Fatty acids are hydrocarbon chains usually containing 16 - 18 carbons and ending with an acid group. Fatty acids are saturated (no double bonds) or unsaturated (has double bonds) which accounts for the liquid nature of vegetable oils. (Fig. 2.23)
5. Soaps
   • a. Not considered a lipid, soaps are salts formed from a fatty acid and an inorganic base.
   • b. When added to oils, soaps cause oil to mix with the water (a process called emulsification) because the nonpolar ends of the soap project into the fat droplet and the polar ends project outward.
   • c. Bile salts stored in gall bladder are important in digesting fats.
6. Phospholipids
   • a. Formed by two fatty acids (nonpolar groups) plus either a phosphate group (polar group) or both a phosphate and nitrogen attached to glycerol.
   • b. Important as basic structure of cell membranes.
7. Steroids
   • a. A lipid differing from fats.
   • b. Have backbone of four fused carbon rings with different functional groups.
   • c. Includes cholesterol, aldosterone (a hormone that regulates sodium in blood), and sex hormones such as testosterone. (Fig. 2.24)

1. Proteins function for structure: keratin in hair and nails, collagen in connective tissue, muscle proteins, etc.
2. Proteins serve as enzymes to speed chemical reactions.
3. Amino acids are monomers for protein.
   • a. Peptide bonds join two amino acids in a dipeptide.
   • b A polypeptide is a chain of amino acids joined by peptide bonds.
   • c. A protein consists of one or more polypeptides.
   • d. Amino acids differ by their "R group," the remainder group not bonded to a hydrogen or acidic group. (Fig. 2.25)
4. Dipeptides to Proteins.
   • i. Condensation reaction between two amino acids forms a dipeptide and water.
   • ii. Peptide bond is polar due to oxygen with partial negative and hydrogen with partial positive charges. (Fig. 2.26)
5. Levels of Protein Organization (Fig. 2.27a - c)
   • a. Primary structure is linear sequence of amino acids joined together by peptide bonds; there are 20 amino acids essential for building human proteins.
   • b. Secondary structure is formed by orientation of a certain polypeptide chain; for example, alpha helix is stabilized by hydrogen bonding between amino acids.
   • c. Tertiary structure is final three-dimensional shape; may be helical or globular.
   • d. Quaternary structure occurs when there is more than one polypeptide chain present; for example, clear albumin (egg white) is denatured (an irreversible change in molecular shape) when heated to fried egg white.

1. Function in reproduction of cells and code for production of proteins.
2. Nucleotides (Fig. 2.28)
   • a. Nucleotides are made of a phosphate, a pentose sugar, and a nitrogenous base.
3. DNA (Deoxyribonucleic acid)
   • a. DNA forms genes that regulate growth and reproduction of cells.
   • b. DNA is double stranded helix held together by hydrogen bonds and has a deoxyribose sugar.
4. RNA (Ribonucleic acid)
   • a. RNA works with DNA for protein synthesis.
   • b. RNA is a single-stranded molecule and has a ribose sugar.
5. ATP
   • a. ATP (adenosine triphosphate) is a nucleotide.
   • b. ATP functions as an energy carrier in cells due to energy stored in phosphate bonds.
   • c. ATP is composed of adenine, a ribose sugar, and three phosphate groups.