1	Chapter 25 Organic Chemistry
2	Organic Chemistry Chemistry of living substances Basically the chemistry of hydrocarbons and their derivatives. Biochemistry: chemistry of biological processes.
3	Hydrocarbons Carbon is a very versatile element. It forms fairy stable single, double, and triple bonds. Singly bonded carbon: sp³ hybridized. Doubly bonded carbon: sp² hybridized. Triply bonded carbon: sp hybridized It can form very long chains of bonded atoms (catenation).
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5	Hydrocarbons Alkanes Contain only single bonds between the carbons. Also called saturated hydrocarbons. Generic formula: C_nH_2n+2 Alkenes Contain at least one carbon-carbon double bond. Also called olefins. Generic formula: C_nH_2n
6	Hydrocarbons Alkynes Contain at least one carbon-carbon triple bond. Generic formula: C_nH_2n-2 Aromatic hydrocarbons Contain a six-membered benzene ring or fused benzene rings.
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9	Alkanes Singly bonded carbon atoms sp³ hybridized, tetrahedral geometries, 109.5° bond angles
10	Alkanes CH₄: methane C₂H₆: ethane C₃H₈: propane C₄H₁₀: butane C₅H₁₂: pentane C_nH_2n+2
11	Structural Isomers Have the same formula but different structures. The atoms are connected in a different fashion. Structural isomers have different physical properties.
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13	Nomenclature IUPAC (International Union of Pure and Applied Chemistry) Decides upon the system of naming chemical compounds. In organic compounds, the name consists of three parts: a prefix, a root (or base) name, and a suffix.
14	Nomenclature The number of carbons in the longest continuous chain of carbon atoms in the structure determines the root or base name: 1: meth- 6: hex- 2: eth- 7: hept- 3: prop- 8: oct- 4: but- 9: non- 5: pent- 10: dec-
15	Nomenclature For alkanes, the suffix is –ane 1: methane 6: hexane 2: ethane 7: heptane 3: propane 8: octane 4: butane 9: nonane 5: pentane 10: decane
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17	Nomenclature The red colored groups are called substituents. They consist of groups that are not part of the continuous chain of carbon atoms. The substituent names consist of the base name for the number of carbons in the group with the suffix “-yl”
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19	Nomenclature The substituents are named in the prefix in alphabetical order, with the number of each type of substituents denoted by the prefixes: di-, tri-, tetra-, penta-, etc. The carbon number of the continuous chain to which the substituent is attached to is denoted before the substituent’s name. Count from the end that results in the lowest number in the name.
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25	Cycloalkanes Sometimes bonded carbon atoms combine to form a ring. For singly bonded carbons, these hydrocarbons are called cycloalkanes. Formula is different than non-cyclic alkanes Cyclopropane: C₃H₆ Cyclobutane: C₄H₈ Cyclopentane: C₅H₁₀ Cyclohexane: C₆H₁₂
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27	Reactivity of alkanes Generally quite unreactive compounds. Most important class of reactions for alkanes are combustion reactions.
28	Alkenes Any hydrocarbon with at least one multiple bond is called unsaturated. Alkenes contain at least one C=C bond. In the naming of alkenes, the suffix is “–ene.” C₂H₄: ethene or ethylene C₃H₆: propene or propylene C_nH_2n
29	C₄H₈: butene
30	Geometric Isomers Same formula but different placement of atoms. Comes from restricted rotation about double bonds.
31	C₅H₁₀
32	Alkynes Contain at least one carbon-carbon triple bond. Suffix is “-yne.” C₂H₂ethyne or acetylene C₃H₄ propyne C_nH_2n-2
33	Reactions of alkenes and alkynes Much more reactive than alkanes. Small molecules can add across the double bond in what is called an addition reaction.
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35	Addition Reactions Other small molecules such as HBr, HCl, F₂, H₂O, and H₂ may add across a multiple bond. The addition reaction of H₂ is called hydrogenation.
36	Aromatic hydrocarbons Consist of benzene, substituted benzene and fused benzene rings. These compounds undergo resonance and are extra stable.
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38	Aromatic compounds Unreactive compared to other unsaturated hydrocarbons. They generally do no undergo addition reactions. They do undergo substitution reactions for the H atoms. Electrophilic Aromatic Substitution.
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41	Isomers Benzene rings have ortho-, meta-, and para- isomers when they have two of the same kind of substituents on the ring.
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43	Functional Groups Organic compounds are classified into functional groups. A functional group is a collection of a small number of atoms in a particular structure. The functional group plays a big role in determining the chemistry of the organic compound. Organic compounds are classified by functional groups.
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45	Alcohol
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47	Ethers R, R’: hydrocarbon groups, R’ means it is usually a different hydrocarbon than R. Ethers are formed by the reaction of two alcohols joining together with the production of water in a reaction called a condensation reaction.
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49	Ethers Tend to be fairly volatile liquids. Used as organic solvents.
50	Carbonyl group Many functional groups contain a C=O bond. This is called a carbonyl group. It is not an organic functional group. It is a part of several organic functional groups.
51	Aldehydes Carbonyl group has at least 1 “H” atom attached to the carbon atom. R = “H” formaldehyde (methanal) Vanilla, cinnamon flavoring are aldehydes.
52	Ketones With hydrocarbons attached at both ends, the functional group is ketone. Acetone, spearmint, caraway seeds. Ketones are less reactive than aldehydes. Acetone used as a solvent.
53	Carboxylic Acids Organic acids. RCOOH
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55	Esters Formed by the condensation reaction of an alcohol with a carboxylic acid. Generally have very pleasant odors. Banana smell, may perfumes.
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57	Ester reactions In the presence of a base, an ester breaks up in a reaction called saponification to produce a soap.
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59	Amines Nitrogen containing hydrocarbon. Organic bases.
60	Amides Formed by a condensation reaction between a carboxylic acid and an amine. Nitrogen containing compound with the nitrogen next to a carbonyl group.
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62	Chirality A molecule that is not superimposable on its mirror image is called chiral. Compounds containing carbon atoms with four different attached groups are a chiral center.
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64	Enantiomers Non-superimposable mirror images are called optical isomers or enantiomers. Enantiomers have identical physical properies. They behave identically with non-chiral reagents. They react differently with chiral reagents. Chirality or stereochemistry plays an important role in organic chemistry.
65	Biochemistry Biopolymers: large molecules that consist of a regular repeating unit. Proteins Polysaccharides Nucleic Acids
66	Proteins 50% of your body’s dry weight is made of proteins. Very large molecules consisting of long chains of compounds called amino acids.
67	Amino Acids Generic formula written below. There are 20 amino acids generally found in the body. Usually the form in which the amine group is protonated and the carboxylic acid is deprotonated, called the zwitterion predominates at neutral pH
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69	Polypeptides Two amino acids can connect to each other in a condensation reaction to form a dipeptide. The amine group of one amino acid reacts with the carboxylic acid of the other amino acid to from a dipeptide and water.
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71	Polypeptides Large numbers of amino acids linked by peptide linkages. Proteins consist of chains of polypeptide. Molecular weights 6000-over 50 million amu.
72	Structure of Proteins Primary structure Sequence of amino acids in the protein chain. Secondary structure How the segments of the protein chain are oriented. a-helix Random coil
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75	Protein structure Tertiary structure Overall shape of the protein Globular protein Protein chains fold into a roughly spherical shape. Tend to be water soluble. Fibrous protein Protein chains align themselves to form long, water insoluble fibers.
76	Enzymes Biochemical catalysts Consist of protein molecules. Tertiary structure plays a very important role in determining which molecules the enzyme works on.
77	Carbohydrates Hydrate of carbon: C_n(H₂O)_n Glucose, Fructose: C₆H₁₂O₆ Actually carbohydrates are polyhydroxy aldehydes or ketones. Structures can be represented by a linear chain or by a cyclic structure. Glucose and fructose are called monosaccharides.
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80	Glucose The cyclic structure of glucose has two different orientations depending on the direction in which the –OH group on the last carbon points. Leads to a and b forms.
81	Fructose Forms a 5-membered cyclic ring.
82	Disaccharide Monosaccharides can combine in a condensation reaction to form disaccharides.
83	Polysaccharides Many monosaccharides can combine in condensation reactions to form polysaccharides. Important polysaccharides are starch, glycogen, and cellulose. All consist of repeating glucose units. Glycogen and starch have a-linkages. Cellulose has b-linkages.
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86	Glycogen and Starch a-linkages are easily digested by plants and animals. Glycogen is used by animals for quick energy storage. Starch is used by plants for quick energy storgage.
87	Cellulose b-linkages are not digested by most animals Cellulose used by plants for structural integrity. (wood) Animals that graze have bacteria in their digestive system that digest part of the cellulose.
88	Nucleic Acids Carries genetic material and transports the genetic information to the production centers of the cell. Deoxyribonucleic acid (DNA) Very large molecules 6-16 million amu molecular weight Carries the genetic information for the cell in the nucleus. Ribonucleic acid (RNA) Smaller molecules 20,000-40,000 amu Transports the information contained in DNA from the nucleus out to the production centers of the cell.
89	Nucleotide Building blocks of nucleic acid. Consists of 3 parts A phosphoric acid molecule, H₃PO₄ A five carbon sugar A nitrogen containing base.
90	5 carbon sugar Ribose in RNA, deoxyribose in DNA
91	Nitrogen containing base
92	Nucleotide The 3 parts combine in condensation reactions.
93	Formation of Nucleic Acid Nucleotides link up via sugar-phosphate- sugar linkages to from chains
94	Nucleic Acid In DNA, two chains wrap in a double helix with the two chains held together by hydrogen bonds between the bases.
95	Nucleic acids Only particular bases pair up in hydrogen bonding linkages