Chapter 2Chemical Principles I. Chemistry. a. Chemistry is the study of the interactions between atoms and molecules. b.

The atom is the smallest unit of an element of matter. c. Matterwhat is it? i. Has mass and takes up space. ii. Is composed of one or more elements. iii. Elementsubstance that cant be decomposed into substances with different properties. iv. Element vs. compound (NaCl). d. Atoms interact to form molecules. e. Atoms are composed of: Fig. 1. i. Electrons: negatively charged particles. ii. Protons: positively charged particles. iii. Neutrons: uncharged particles. f. Protons and neutrons reside in the nucleus. g. Electrons move around the nucleus. i. Typically, the number of electrons = the number of protons, so there is no net charge on the atom. v. Atomic number = the number of protons. 8O. vi. Mass number (atomic weight) = the number of protons + the number of neutrons. 16O. Chemical Elements. Table 1. [Students should memorize the names and symbols of these elements]. a. Each chemical element has a different number of protons in its nucleus. b. Isotopean atom of an element having more or fewer neutrons than typical. c. Isotopes of oxygen are: vii. 168O. 16 = Mass number (atomic weight) = the number of protons + the number of neutrons. 8 = Atomic number = the number of protons. How many neutrons? 8. i. 178O. 17 protons + neutrons. 8 protons. How many neutrons? 9. ii. 188O. 18 protons + neutrons. 8 protons. How many neutrons? 10. iii. 12C vs. 14C. d. The mass number the atomic number = the number of neutrons. e. Radioisotope: 14C decays to 14N by emitting energy and particles. i. Half-life of 5730 years. f. Moleculea combination of two or more atoms. g. Compounda combination of two or more elements. h. Molecular compoundthe smallest unit of a compound that retains all the properties of that compound (H2O). i. Organic compoundcontains carbon. j. Mixturetwo or more elements (or compounds) mingling without any chemical bonding. Electronic Configurations and Chemical Bonds. Table 2. b. Electrons orbit the nucleus of an atom in orbitals of increasing energy levels, or shells. i. Orbitals arent necessarily circular as the shell model suggests. In reality, the orbitals are clouds of various shapes. ii. Each orbital can only hold so many electrons. iii. A single shell can have multiple orbitals of different shapes. iv. There can be a maximum of 2 electrons in the first shell, 8 electrons in the second, 8 in the third c. Having a filled outer shell is most stable. d. The number of missing or extra electrons in the outer shell is called the valence number. e. Most atoms dont have filled outer shells, which then form chemical bonds with other atoms in order to fill their outer shells.

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f. A chemical bond is a union between the electrons of different atoms. i. The forces holding atoms together in a compound are called chemical bonds. g. Ionic Bonds. Fig. 2. i. Ions are atoms that have gained or lost electrons and are therefore charged. ii. Ionic bonds are attractions between ions of opposite charge. One atom loses electrons and another gains electrons. h. Covalent Bonds. Fig. 3. i. Covalent bonds form when two atoms share one or more pairs of electrons, without the electrons leaving their orbitals. ii. Covalent bond structural formulas: 1. H2 H-H : two atoms sharing one pair of electrons. 2. O2 O=O: two atoms sharing two pairs of electrons. 3. N2 NN: two atoms sharing three pairs of electrons. iii. Non polar covalent bondelectrons are shared equally between the atoms. iv. Polar covalent bondelectrons are not shared equally among the atoms, resulting in slight opposite charges on portions of the molecule, but there is no net charge. (H2O). i. Hydrogen Bonds. Fig. 4. i. Common in water. Occurs when a hydrogen atom that is already part of a polar covalent bond interacts weakly with a highly electronegative atom (Like O or N). Molecular Weight and Moles. a. The sum of the atomic weights in a molecule is the molecular weight. b. One mole of a substance is its molecular weight in grams. i. Example: Glucose (C6H12O6) 1. Molecular weight of C = 12; H = 1; O = 16. 2. Total molecular weight for glucose = (12 x 6) + (1 x 12) + (16 x 6) = 180 3. Put 180 grams of glucose in a container, and add enough water so that you have one liter of solution. 4. You have now made a one molar glucose solution. Chemical Reactions. a. Energy is required for a chemical reaction to occur. [Activation energy]. In cells, enzymes are also required. b. Chemical reactions involve the making or breaking of bonds between atoms. c. A change in chemical energy occurs during a chemical reaction. d. All chemical reactions are reversible in theory. e. Endergonic reactions absorb more energy than they release. f. Exergonic reactions release more energy than they absorb. g. Synthesis Reactions. i. Occur when atoms, ions, or molecules combine to form new, larger molecules: ii. A + B AB iii. Anabolism is the synthesis of molecules in a cell. 1. Condensation (dehydration) reactionwhere a H+ is removed from one molecule, OH- is removed from another, and the two molecules joinleaving H2O as a byproduct. [Monomers to polymers]. a. H+ = a proton. h. Decomposition Reactions. i. Occur when a molecule is split into smaller molecules, ions, or atoms: ii. AB A + B iii. Catabolic reactions are the decomposition reactions in a cell. = Catabolism. 1. Cleavage (hydrolysis)where a molecule is split in two, while simultaneously, H+ and OH- (from water) become attached to the newly exposed sites on the molecule. [Polymers to monomers].

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i. Exchange Reactions. i. Are part synthesis and part decomposition. ii. NaOH + HCl NaCl + H2O iii. Reversible Reactions. iv. Can readily go in either direction. v. Each direction may need special conditions. Important Biological Molecules. a. Organic compounds always contain carbon and hydrogen. b. Inorganic compounds typically lack carbon. c. Inorganic compounds: Water. Fig. 4. i. Water is a polar molecule. 1. The polarity of water allows the formation of hydrogen bonds with other polar molecules, such as sugar. ii. Water is a good solvent. Fig. 5. 1. All polar molecules and ions are attracted to (dissolve in) water. 2. Polar substances dissociate, forming solutes. 3. Polar molecules are said to be hydrophilic. 4. Non polar molecules are repelled by water, and are said to be hydrophobic. (Fats, oils). iii. Water can break into H+ and OH-. H+ and OH participate in chemical reactions. iv. Hydrogen bonding between water molecules makes water a temperature buffer. 1. Water can absorb a lot of heat before it becomes heated or evaporates, because of all the hydrogen bonds. 2. As the hydrogen bonds are broken, water evaporates, taking heat with it. v. [Density of water as a liquid vs. solid]. Acids, Bases, and Salts. Fig. 6. a. An acid is a substance that dissociates, giving up one or more H+. i. HCl H+ + Cl b. A base is a substance that dissociates, giving up one or more OH. i. NaOH Na+ + OH c. A salt is a substance that dissociates into cations (+) and anions (-), neither of which are H+ or OH. i. NaCl Na+ + Cl d. Electrolytessubstances that dissociate into ions in solution, and can conduct electricity. e. The amount of [H+] in a solution is expressed as pH. Fig. 7. i. pH = log[H+] ii. Increasing [H+] increases acidity. (Lower pH) iii. Increasing [OH] increases alkalinity. (Higher pH) iv. Acidic solutions contain more H+ than OH- and alkaline (basic) solutions contain more OH- than H+. 1. Each whole number pH value is either ten times more/less strong than the previous/following whole number. a. pH 0 = most acidic. b. pH 7 = neutral. c. pH 14 = most basic. v. Most organisms grow best between pH 6.5 and 8.5. Organic Compounds. a. By definition, organic compounds contain carbon (and hydrogen). b. They also contain many other elements, all held together by covalent bonds. c. Carbon can bond with up to four other atoms covalently. d. Carbon atoms are often found bonded together into chains and rings.

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e. Hydrocarbons are made of carbon and hydrogen only. Examples: i. methane CH4 ii. ethane C2H6 iii. propane C3H8 iv. butane C4H10 f. The chain of carbon atoms in an organic molecule is the carbon skeleton/backbone. g. Functional groups are clusters of atoms that also bond to a carbon backbone and influence the chemical behavior of organic compounds. Functional groups are responsible for most of the chemical properties of a particular organic compound. Table 3. h. Small organic molecules can combine into large macromolecules. i. Macromolecules are polymers consisting of many small repeating molecules. ii. The smaller molecules are called monomers. iii. Monomers join by condensation (dehydration) synthesis reactions to form polymers. iv. Polymers are broken apart by hydrolysis reactions to form monomers. Carbohydrates. a. Simple sugars or strings of simple sugars linked together. Ratio of C:H:O is 1:2:1. (CH2O)n b. Are important for structure and as energy sources. c. Monosaccharides are simple sugars with 3 to 7 carbon atoms. i. Usually only five or six carbons long, and often arranged into a ring. ii. Taste sweet, and dissolve in water. d. Disaccharides are formed when 2 monosaccharides are joined by dehydration synthesis. Fig. 8. e. Disaccharides can be broken down by hydrolysis. i. Lactose, sucrose, maltose. f. Oligosaccharides consist of 2 to 20 monosaccharides. g. Polysaccharides consist of straight or branched chains tens to hundreds of monosaccharides long joined together through dehydration synthesis. i. Starch, glycogen, and cellulose are polymers of glucose that are covalently bonded together differently. 1. Glycogensugar storage form used in animals, mostly found in the liver and skeletal muscles. 2. Starchsugar storage form used in plants. 3. Cellulosestructural carbohydrate used in plants. ii. Chitin is a polymer of two sugars repeating many times. Lipids. Fig. 9. i. Are the primary components of cell membranes. ii. Consist of C, H, and O. iii. Are nonpolar and insoluble in water (hydrophobic). 1. Fatty acidshave backbones of up to 36 carbons, a carboxyl group (COOH) at one end, and hydrogen atoms at nearly all other locations. a. Unsaturated fatty acids have one or more double bonds in the fatty acids. 2. Triglycerides contain glycerol and 3 fatty acids; formed by dehydration synthesis. a. Most common dietary lipid and the bodys richest energy source, it is stored as adipose in animals. [Oil vs. lard]. 3. Complex lipids. Fig. 10. a. Contain C, H, and O as well as P, N, or S. b. Phospholipidsmade of two fatty acids attached to a glycerol molecule, which is also attached to a phosphate group and another polar group. Primary component of cell membranes. c. Waxestightly packed molecules that are firm and repel water. (Earwax). 4. Sterols & Steroids. Fig. 11.

a. Sterolsall have a rigid four-ring backbone, but lack fatty acid tails. Includes cholesterol, and are components of vitamin D, bile salts, cell membranes, and steroid hormones. XI. Proteins. i. ii. iii. iv. v. vi. Are essential in cell structure and function. Enzymes are proteins that speed chemical reactions. Transporter proteins move chemicals across membranes. Flagella are made of proteins. Some bacterial toxins are proteins. Consist of monomer subunits called amino acids. Fig. 12. 1. Amino acidorganic compound made up of an amino group, a carboxyl group, a hydrogen atom, and an R group, all attached to a central carbon atom. Many amino acids linked together form proteins. [20 different amino acids]. Table 4. 2. Exist in either of two stereoisomers, D or L. Fig. 13. 3. L-forms are most often found in nature. vii. Peptide Bonds. Fig. 14. 1. Peptide bonds between amino acids are formed by dehydration synthesis. viii. Levels of Protein Structure. Fig. 15. 1. Primary structure of proteins, and protein synthesis. a. Proteins form when individual amino acids are covalently linked together forming peptide bonds. (-N-C-C-N-C-C-N-C-C-). This is called a polypeptide chain and forms the primary structure of the protein. b. A specific protein will have a specific sequence of amino acids. This specific sequence is the proteins primary structure. 2. 3-D structure of proteins. a. Secondary structurethe coils, loops, bends, etc. of a polypeptide chain as it interacts with other portions of itself or other chains nearby. i. Results in the formation of hydrogen bonds and allows R groups to interact. ii. Coiled chains (alpha helix) and (beta) sheets are examples of secondary structure. b. Tertiary structure is the overall structural arrangement of the entire protein. The tertiary structure occurs when the protein folds irregularly, forming disulfide bonds, hydrogen bonds, and ionic bonds between amino acids in the chain. c. Quaternary structure arises when proteins made up of multiple polypeptide chains are held together by hydrogen bonds and other weak forces. Hemoglobin, insulin, keratin, collagen. ix. Proteins may be: 1. Structural proteinsfound in bone, muscle, hair. 2. Transport proteinstransport substances across cell membranes or in blood. 3. Regulatory proteinshormones. 4. Enzymesreduce activation energy of chemical reactions, so the reactions go faster, without a great input of energy. x. Proteins may be globular, as is hemoglobin, or fibrous like collagen. xi. Lipoproteins form when certain proteins combine with lipids. xii. Glycoproteins form when oligosaccharides are bonded to certain proteins. xiii. Breaking the weak bonds (hydrogen bonds) of a protein disrupts its 3-D shape. The protein is then said to be denatured, and can no longer function. Nucleotides and nucleic acids. Fig. 16. a. Nucleotides are made up of a pentose (five-carbon) sugar (ribose or deoxyribose), a phosphate group, and a nitrogen-containing (purine or pyrimidine) base.

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b. In nucleic acids, four kinds of nucleotides are bonded together in different long chain sequences. c. DNA (deoxyribonucleic acid) is a double strand nucleic acid. i. Has deoxyribose as the pentose sugar. ii. Exists as a double helix. iii. Contains the following nucleotides: 1. Thymine (T) [a pyrimidine] 2. Adenine (A) [a purine] 3. Cytosine (C) [a pyrimidine] 4. Guanine (G) [a purine] iv. (A) hydrogen bonds with (T). [purine + pyrimidine] v. (G) hydrogen bonds with (C). [purine + pyrimidine] d. RNA (ribonucleic acid) is a single strand nucleic acid. i. Has ribose as the pentose sugar. ii. Is single-stranded. iii. Contains the following nucleotides: 1. Uracil (U) [a pyrimidine] instead of Thymine 2. Adenine (A) 3. Cytosine (C) 4. Guanine (G) iv. (A) hydrogen bonds with Uracil (U). [purine + pyrimidine] Fig. 17. v. (G) hydrogen bonds with (C). [purine + pyrimidine] e. ATP (adenosine triphosphate) is a nucleotide with three phosphate groups attached to it. It is the primary energy source for cellular activities. Fig. 18. i. Has ribose, adenine, and 3 phosphate groups. ii. Is made by dehydration synthesis. iii. Is broken by hydrolysis to liberate useful energy for the cells metabolism.