Organic Chemistry and Biochemistry

Organic Chemistry and Biochemistry
The study of carbon-containing compounds and their properties. The vast majority of organic compounds contain chains or rings of carbon atoms. Biochemistry The study of the chemistry of living things. Copyright © Cengage Learning. All rights reserved

The Bonding of Carbon Because carbon has four valence electrons, it can form four covalent bonds. Carbon forms single, double, and triple bonds to achieve a filled octet. A unique feature of carbon is its ability to bond with other carbons to form long chains or rings of various length. 2

Why is Carbon Unique? 1. Forms four covalent bonds
2. Bonds covalently to: H, O, N, P, S, and all other nonmetals (except noble gases) 3. Carbon atoms join to form: a. Chains and b. Rings

Common Elements in Organic Compounds

Examples of Organic Chemicals
Foods Carbohydrates Fats Proteins Clothing silk, linen, wool, cotton, Dacron, Nylon, Orlon, etc. Plastics Pharmaceuticals Detergents and Soaps Pesticides Gasoline and oils Water purification

Organic vs Inorganic: Differences
Bonding Covalent Ionic Physical State (room temp) Gas/liquid common Solids common Melting points Tend to be low Tend to be very high Sol. In water Tend to be insoluble Much higher percent soluble Conductivity Nonconductors Conduct in soln. and molten

Hydrocarbons The simplest organic compounds are hydrocarbons, compounds containing only carbon and hydrogen. The three main groups of hydrocarbons are: saturated hydrocarbons, hydrocarbons with only single bonds between the carbon atoms. unsaturated hydrocarbons, hydrocarbons that contain double or triple bonds between carbon atoms. 2

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Hydrocarbons Compounds composed of carbon and hydrogen. Saturated: C—C bonds are all single bonds. alkanes [CnH2n+2] Copyright © Cengage Learning. All rights reserved

Hydrocarbons Unsaturated: contains carbon–carbon multiple bonds.

Hydrocarbons The simplest organic compounds are hydrocarbons, compounds containing only carbon and hydrogen. The saturated and unsaturated hydrocarbons are often referred to as the aliphatic hydrocarbons. 2

Alkanes Alkanes have the general formula CnH2n+2 where n = 1,2,3,…
only single covalent bonds saturated hydrocarbons because they contain the maximum number of hydrogen atoms that can bond with the number of carbon atoms in the molecule CH4 C2H6 C3H8 methane ethane propane

Alkanes The alkanes are acyclic, saturated hydrocarbons that form a homologous series of compounds, with the general formula CnH2n+2. The simplest hydrocarbon is methane, CH4. molecular formula structural formula 2

Alkanes The structural formulas for the first four straight-chain (or normal) alkanes are shown below. methane ethane propane butane 2

Alkanes Chemists often use condensed structural formulas, where the bonds around each carbon atom are not explicitly written. methane ethane propane butane 2

Alkanes The alkanes constitute a homologous series of compounds in which one compound differs from a preceding one by a fixed group of atoms, in this case, a –CH2– group. Members of a homologous series have similar chemical properties, and their physical properties change throughout the series in a regular way. 2

Hydrocarbons: They are nonpolar molecules and consequently are not soluble in water but are soluble in typical nonpolar organic solvents like toluene or pentane.

Alkanes The alkanes constitute a homologous series of compounds in which one compound differs from a preceding one by a fixed group of atoms, in this case, a –CH2– group. Note that the melting and boiling points increase with an increase in the number of carbon atoms. 2

Constitutional Isomerism and Branched-Chain Alkanes
In addition to straight-chain alkanes, branched-chain alkanes are possible. For example, isobutane (or 2-methylpropane) has the structure or 2

Constitutional Isomerism and Branched-Chain Alkanes
In addition to straight-chain alkanes, branched-chain alkanes are possible. Note that isobutane, C4H10, has the same molecular formula as normal butane. Butane and isobutane are constitutional (or structural) isomers, compounds with the same molecular formula but different structural formulas. 2

Models of isobutane and butane.

Structural isomers are molecules that have the same molecular formula but different structures

How many structural isomers does pentane, C5H12, have?
n-pentane C H CH3 2,2-dimethylpropane 2-methylbutane

Rules for Naming Alkanes
For alkanes beyond butane, add –ane to the Greek root for the number of carbons. CH3–CH2–CH2–CH2–CH2–CH3 = hexane Alkyl substituents: drop the –ane and add –yl. C2H6 is ethane C2H5 is ethyl Copyright © Cengage Learning. All rights reserved

Positions of substituent groups are specified by numbering the longest chain sequentially. The numbering is such that substituents are at lowest possible number along chain. CH3 CH3–CH2–CH–CH2–CH2–CH3 3-methylhexane Copyright © Cengage Learning. All rights reserved

Location and name are followed by root alkane name. Substituents in alphabetical order and use di–, tri–, etc. CH3 CH3 CH3–CH2–CH–CH–CH2–CH3 3,4-dimethylhexane Copyright © Cengage Learning. All rights reserved

Alkane Nomenclature The parent name of the hydrocarbon is that given to the longest continuous chain of carbon atoms in the molecule. CH3 CH2 CH 4-methylheptane 1 2 3 4 5 6 7 An alkane less one hydrogen atom is an alkyl group. CH4 methane CH3 methyl

First Ten Normal Alkanes
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Alkane Nomenclature When one or more hydrogen atoms are replaced by other groups, the name of the compound must indicate the locations of carbon atoms where replacements are made. Number in the direction that gives the smaller numbers for the locations of the branches. CH3 CH CH2 1 2 3 4 5 2-methylpentane CH3 CH2 CH 1 2 3 4 5 4-methylpentane

Alkane Nomenclature Use prefixes di-, tri-, tetra-, when there is more than one alkyl branch of the same kind. CH3 CH CH2 1 2 3 4 5 6 2,3-dimethylhexane CH3 CH C CH2 1 2 3 4 5 6 3,3-dimethylhexane

Alkane Nomenclature CH3 CH Br NO2 2-bromo-3-nitrobutane CH2 CH CH3 Br
Use previous rules for other types of substituents. When there are two or more different branches, the name of each branch, with its position number, precedes the base name. The branch names are placed in alphabetical order. CH3 CH Br 1 2 3 4 NO2 2-bromo-3-nitrobutane CH2 CH CH3 Br 1 2 3 4 NO2 1-bromo-3-nitrobutane

What is the IUPAC name of the following compound?
CH3 CH CH2 C2H5 1 2 3 4 5 6 7 8 4-ethyl-2-methyloctane What is the structure of 4-methyl-2-propylhexane? 1 2 3 4 5 6 CH3 CH CH2 C2H5

The Most Common Alkyl Substituents and Their Names

EXERCISE! a) b) 3,6-diethyl-3-methyloctane Name each of the following:
2,2,4,5-tetramethylhexane b) 3,6-diethyl-3-methyloctane a) 2,2,4,5-tetramethylhexane b) 3,6-diethyl-3-methyloctane Copyright © Cengage Learning. All rights reserved

Reactions of Alkanes With Oxygen
All hydrocarbons burn in an excess of O2 to produce carbon dioxide, water, and heat. For example, a propane gas grill uses the reaction 2

Substitution Reactions of Alkanes
Primarily where halogen atoms replace hydrogen atoms. Copyright © Cengage Learning. All rights reserved

Dehydrogenation Reactions of Alkanes
Hydrogen atoms are removed and the product is an unsaturated hydrocarbon. Copyright © Cengage Learning. All rights reserved

Cycloalkanes The cycloalkanes are cyclic, saturated hydrocarbons that form another homologous series with the general formula CnH2n in which the carbon atoms are joined in a ring. Below is the structure for cyclobutane. 2

Cycloalkanes Alkanes whose carbon atoms are joined in rings are called cycloalkanes. They have the general formula CnH2n where n = 3,4,…

Cycloalkanes

CH3–CH2–CΞC–CH3 2–pentyne
Hydrocarbons Alkenes: hydrocarbons that contain at least one carbon–carbon double bond. [CnH2n] CH3–CH=CH propene Alkynes: hydrocarbons containing at least one carbon–carbon triple bond. [CnHn] CH3–CH2–CΞC–CH –pentyne

Alkenes and Alkynes The alkenes and alkynes are unsaturated hydrocarbons (cyclic or acyclic) that contain carbon-carbon double or triple bonds. Under proper conditions, molecular hydrogen can be added to an alkene or an alkyne to produce a saturated compound in a process called catalytic hydrogenation. 2

Alkenes and Geometric Isomers
Alkenes are hydrocarbons with the general formula CnH2n and contain a carbon-carbon double bond. (also called olefins) The simplest alkene is ethylene. 2

Alkenes are hydrocarbons with the general formula CnH2n and contain a carbon-carbon double bond. (also called olefins) Geometric isomers are isomers in which some atoms occupy different relative positions in space. 2

achiral chiral

Alkenes are hydrocarbons with the general formula CnH2n and contain a carbon-carbon double bond. (also called olefins) For example, 2-butene has two geometric isomers, called cis-2-butene and trans-2-butene. cis-2-butene trans-2-butene 2

Alkenes Alkenes have the general formula CnH2n where n = 2,3,…
contain at least one carbon-carbon double bond also called olefins CH2 CH CH3 CH3 CH 1-butene 2-butene C Cl H C Cl H cis-dichloroethylene trans-dichloroethylene

Cis-Trans Isomerization in the Vision Process

Oxidation Reactions of Alkenes
Because alkenes are hydrocarbons, they undergo complete combustion reactions with oxygen. Unsaturated hydrocarbons can also be partially oxidized under relatively mild conditions. For example, when aqueous potassium permanganate is added to an alkene (or alkyne), the purple color of KMnO4 fades as a brown precipitate of MnO2 forms. 2

Test for unsaturation using KMnO4(aq) solution.

Addition Reactions of Alkenes
Alkenes are more reactive than alkanes because many reactants add to the double bond. An addition reaction is a reaction in which parts of a reactant are added to each carbon atom of a carbon-carbon double bond which converts to a carbon-carbon single bond. 2

Addition Reactions of Alkenes
Alkenes are more reactive than alkanes because many reactants add to the double bond. A simple example is the addition of a halogen, such as Br2, to propene. + Br2 2

Alkene Reactions Cracking C2H6 (g) CH2 CH2 (g) + H2 (g)
Pt catalyst Addition Reactions CH2 CH2 (g) + HBr (g) CH3 CH2Br (g) CH2 CH2 (g) + Br2 (g) CH2Br CH2Br (g)

Alkynes Alkynes are unsaturated hydrocarbons containing a carbon-carbon triple bond. The general formula is CnH2n-2. The simplest alkyne is acetylene (ethyne). 2

Alkynes Alkynes have the general formula CnH2n-2 where n = 2,3,4,…
contain at least one carbon-carbon triple bond CH C CH2 CH3 CH3 C 1-butyne 2-butyne Production of acetylene CaC2 (s) + 2H2O (l) C2H2 (g) + Ca(OH)2 (aq)

Alkyne Reactions Hydrogenation CH CH (g) + H2 (g) CH2 CH2 (g)
Addition Reactions CH CH (g) + HBr (g) CH2 CHBr (g) CH CH (g) + Br2 (g) CHBr CHBr (g) CH CH (g) + 2Br2 (g) CHBr2 CHBr2 (g)

Nomenclature of Alkenes and Alkynes
The following four IUPAC rules are applied in naming the branched-chain alkenes and alkynes. The rules are essentially the same as those for alkanes, except that names end in –ene for alkenes and –yne for alkynes. The position of the double (or triple) bond is indicated in the name by bond position number. 2

The following four IUPAC rules are applied in naming the branched-chain alkenes and alkynes. 3-methyl-1-pentene 2

The following four IUPAC rules are applied in naming the branched-chain alkenes and alkynes. Recall that alkenes also exhibit cis and trans isomerism and so either cis or trans must be included in the name. 2

EXERCISE! Name each of the following: a) 2,3,5-trimethyl-2-hexene b) 6-ethyl-3-methyl-3-octene a) 2,3,5-trimethyl-2-hexene b) 6-ethyl-3-methyl-3-octene Copyright © Cengage Learning. All rights reserved

A special class of cyclic unsaturated hydrocarbons. Simplest of these is benzene (C6H6). The delocalization of the electrons makes the benzene ring behave differently from a typical unsaturated hydrocarbon. Copyright © Cengage Learning. All rights reserved

Aromatic Hydrocarbons
Aromatic hydrocarbons usually contain benzene rings-six membered rings of carbon atoms with alternating C-C single and C=C double bonds. The structure of benzene is 2

Aromatic hydrocarbons usually contain benzene rings-six membered rings of carbon atoms with alternating C-C single and C=C double bonds. . Aromatic compounds are found everywhere from pain relievers to flavoring agents. 2

Aromatic Compound Nomenclature
CH2CH3 ethylbenzene NH2 aminobenzene Cl chlorobenzene NO2 nitrobenzene Br Br 1 2 3 4 5 6 1,2-dibromobenzene 1,3-dibromobenzene

Aromatic Compound Reactions
Substitution reaction H Br + HBr + Br2 FeBr3 catalyst H CH2CH3 + HCl + CH3CH2Cl AlCl3 catalyst

Polycyclic Aromatic Hydrocarbons

Classification of Hydrocarbons

Derivatives of Hydrocarbons
A functional group is a reactive portion of a molecule that undergoes predictable reactions. In the previous sections we discussed the hydrocarbons and their reactions. All other organic compounds can be considered to be derivatives of hydrocarbons. 2

Organic Compounds Containing Oxygen
An alcohol is a compound obtained by substituting a hydroxyl group (-OH) for an –H atom on a carbon atom of a hydrocarbon group. Some examples are methanol ethanol 2-propanol 2

Functional Group Chemistry
Alcohols contain the hydroxyl functional group and have the general formula R-OH.

Biological production of ethanol
C6H12O6 (aq) CH3CH2OH (aq) + 2CO2 (g) enzyme Commercial production of ethanol CH2 CH2 (g) + H2O (g) CH3CH2OH (g) H2SO4 Metabolic oxidation of ethanol CH3CH2OH CH3CHO + H2 alcohol dehydrogenase

An ether is a compound with an oxygen “bridge” between two alkyl groups. An example is diethyl ether This is the most common ether, often called simply ether, used as an anesthetic. 2

Ethers have the general formula R-O-R’. Condensation Reaction CH3OH + HOCH CH3OCH3 + H2O H2SO4 catalyst

An aldehyde is a compound containing a carbonyl group with at least one H atom attached to it. An example is ethanal 2

A ketone is a compound containing a carbonyl group with two hydrocarbon groups attached to it. An example is 2-butanone 2

Aldehydes and ketones contain the carbonyl ( ) functional group. O C R C H O aldehydes have the general formula R C R’ O ketones have the general formula H C H O H C O CH3 C O CH3 H3C formaldehyde acetaldehyde acetone

A carboxylic acid is a compound containing the carboxyl group, -COOH. An example is ethanoic acid 2

Carboxylic acids contain the carboxyl ( -COOH ) functional group.

An ester is a compound formed from a carboxylic acid, RCOOH, and an alcohol, R’OH. The general structure is 2

Esters have the general formula R’COOR, where R is a hydrocarbon group. CH3COOH + HOCH2CH CH3 C O CH2CH3 + H2O O ethyl acetate

Organic Compounds Containing Nitrogen
Most organic bases are amines, which are compounds that are structurally derived by replacing one or more hydrogen atoms of ammonia with hydrocarbon groups. primary amine secondary amine tertiary amine 2

Amines are organic bases with the general formula R3N. CH3NH2 + H2O RNH3+ + OH- CH3CH2NH2 + HCl CH3CH2NH3+Cl-

Most organic bases are amines, which are compounds that are structurally derived by replacing one or more hydrogen atoms of ammonia with hydrocarbon groups. 2

Amides are compounds derived from the reaction of ammonia, or of a primary or secondary amine, with a carboxylic acid. The general formula for a common amide is 2

The Common Functional Groups

Sources and Uses of Alkanes and Cycloalkanes
Fossil fuels are the principal source of all types of organic compounds. Because fossil fuels are mixtures of hydrocarbons, it is usually necessary to separate these mixtures by distillation. 2

Chemistry In Action: The Petroleum Industry
Crude Oil

Sources and Uses of Alkanes and Cycloalkanes
The alkanes serve as the starting point for most plastics and pharmaceuticals. 2

Common Synthetic Polymers and their Monomers and Applications

Types of Polymerization
Addition Polymerization Monomers “add together” to form the polymer, with no other products. (Teflon®)

Proteins Natural polymers made up of -amino acids with molar masses: ~ 6000 to > 1,000,000 g/mol Fibrous Proteins: provide structural integrity and strength to muscle, hair and cartilage. Copyright © Cengage Learning. All rights reserved

Proteins Globular Proteins: Roughly spherical shape Transport and store oxygen and nutrients Act as catalysts Fight invasion by foreign objects Participate in the body’s regulatory system Transport electrons in metabolism Copyright © Cengage Learning. All rights reserved

Levels of Structure in Proteins
Primary: Sequence of amino acids in the protein chain. Secondary: The arrangement of the protein chain in the long molecule (hydrogen bonding determines this). Tertiary: The overall shape of the protein (determined by hydrogen-bonding, dipole-dipole interactions, ionic bonds, covalent bonds and London forces). Copyright © Cengage Learning. All rights reserved

Hydrogen Bonding in α-Helical Arrangement of a Protein Chain

Carbohydrates Food source for most organisms and structural material for plants. Empirical formula = CH2O Monosaccharides (simple sugars) pentoses – ribose, arabinose hexoses – fructose, glucose Copyright © Cengage Learning. All rights reserved

Some Important Monosaccharides

Carbohydrates Disaccharides (formed from 2 monosaccharides joined by a glycoside linkage, a C—O—C bond between the rings): sucrose (glucose + fructose) Polysaccharides (many monosaccharide units): starch, cellulose Copyright © Cengage Learning. All rights reserved

The Disaccharide Sucrose is Formed From α-D-glucose and Fructose

Nucleic Acids DNA (deoxyribonucleic acid): stores and transmits genetic information, responsible (with RNA) for protein synthesis. (Molar masses = several billion) RNA (ribonucleic acid): helps in protein synthesis. (Molar masses from 20,000 to 40,000 g/mol) Copyright © Cengage Learning. All rights reserved

Nucleotides Monomers of the nucleic acids. Three distinct parts: A five–carbon sugar, deoxyribose in DNA and ribose in RNA. A nitrogen–containing organic base. A phosphoric acid molecule (H3PO4). Copyright © Cengage Learning. All rights reserved

Deoxyribose (in DNA) and Ribose (in RNA)

The Organic Bases Found in DNA and RNA

Hydrogen Bonding in DNA

Organic Chemistry and Biochemistry

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