Chapter 24. The Chemistry of Life: Organic and Biological
Chemistry
Media Resources
Figures and Tables in Transparency Pack: Section:
Figure 24.1 Carbon Geometries 24.1 General Characteristics of Organic Molecules
Table 24.1 The Four Hydrocarbon Types 24.2 Introduction to Hydrocarbons
Figure 24.15 The Two Enantiomeric Forms of 24.5 Chirality in Organic Chemistry
2-Bromopentane
Figure 24.18 The 20 Amino Acids Found in the 24.7 Proteins
Human Body
Figure 24.20 The Structure of Proteins 24.7 Proteins
Figure 24.21 Linear Structure of the Carbohydrates 24.8 Carbohydrates
Glucose and Fructose
Figure 24.22 Cyclic Glucose Has an Form and a 24.8 Carbohydrates
Activities: Section:
Boiling Point 24.2 Introduction to Hydrocarbons
Hydrocarbons
Animations: Section:
Movies: Section:
Testing for Unsaturated Hydrocarbons with Bromine 24.3 Alkenes, Alkynes, and Aromatic
Hydrocarbons
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3-D Models: Section:
Methane 24.1 General Characteristics of Organic Molecules
Acetonitrile 24.1 General Characteristics of Organic Molecules
Glucose 24.1 General Characteristics of Organic Molecules
Hydrocarbons
Hydrogen Chloride 24.3 Alkenes, Alkynes, and Aromatic
Hydrocarbons
Methanol 24.4 Organic Functional Groups
Ethanamine (ethylamine) 24.4 Organic Functional Groups
Ethanal (acetaldehyde) 24.4 Organic Functional Groups
Propanone (acetone) 24.4 Organic Functional Groups
Ethanoic Acid (acetic acid) 24.4 Organic Functional Groups
Other Resources
Further Readings: Section:
Alkanes: Abundant, Pervasive, Important, and 24.2 Introduction to Hydrocarbons
Essential
The IUPAC Rules for Naming Organic Molecules 24.2 Introduction to Hydrocarbons
Why Is ‘R’ Used to Symbolize Hydrocarbon 24.2 Introduction to Hydrocarbons
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Icie Macy Hoobler: Pioneer Woman Biochemist 24.6 Introduction to Biochemistry
Why Teach Biochemistry? 24.6 Introduction to Biochemistry
Chemistry of Dyeing of Eggs 24.7 Proteins
Reversible Oxygenation of Oxygen Transport 24.7 Proteins
Proteins
DNAmonic 24.10 Nucleic Acids
A Simple Demonstration of How Intermolecular 24.10 Nucleic Acids
Forces Make DNA Helical
The DNA Story 24.10 Nucleic Acids
Meeting the Matchmaker 24.10 Nucleic Acids
Live Demonstrations: Section:
Oxidation of Alcohol by Mn2O7 24.4 Organic Functional Groups
The Disappearing Coffee Cup 24.4 Organic Functional Groups
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Chapter 24. The Chemistry of Life: Organic and Biological
Chemistry
Common Student Misconceptions
• Students will often find the distinction between organic and inorganic molecules as somewhat vague.
As a rule of thumb, inorganic carbon is carbon that is not bound to hydrogen, for example, H2CO3.
Teaching Tips
• Students should be encouraged to follow the chapter links to review earlier material as they progress
Lecture Outline
24.1 General Characteristics of Organic Molecules
• Organic chemistry is the branch of chemistry that studies carbon compounds.
• Biochemistry, biological chemistry, or chemical biology is the study of the chemistry of living
things.
The Structures of Organic Molecules
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• The shapes of organic and biochemical molecules are important in determining their physical and
chemical properties.
• Consider the element carbon:
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• Carbon-carbon bonds for the backbone or skeleton of the molecule and the H atoms are on the surface
of the molecule.
The Stabilities of Organic Substances
• The stability of organic substances varies.
Solubility and Acid-Base Properties of Organic Substances
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• The most common bonds in organic substances are carbon-carbon bonds.
• This results in a low overall polarity of many organic molecules.
• Such molecules are soluble in nonpolar solvents.
24.2 Introduction to Hydrocarbons
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• The simplest class of organic molecules is the hydrocarbons.
• Hydrocarbons consist only of carbon and hydrogen.
• There are four major classes of hydrocarbons: alkanes, alkenes, alkynes, and aromatics.
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“Glucose” 3-D Model from Instructor’s Resource CD/DVD
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“Sodium Stearate” 3-D Model from Instructor’s Resource CD/DVD
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Table 24.1 from Transparency Pack
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“Ethane” 3–D Model from Instructor’s Resource CD/DVD
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• Aromatic hydrocarbons have carbon atoms connected in a planar ring structure.
• The carbons are linked by both and bonds.
• The best known example is benzene (C6H6).
• Alkenes, alkynes, and aromatic hydrocarbons are all examples of unsaturated hydrocarbons.
• The name of the alkane varies according to the number of C atoms present in the chain.
Structures of Alkanes
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• VSEPR theory predicts each C atom is tetrahedral.
• Therefore, each C atom has sp3-hybridized orbitals.
• Rotation about the C–C bond in alkanes is relatively easy.
Structural Isomers
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• In straight-chain hydrocarbons, the C atoms are joined in a continuous chain.
• In a straight-chain hydrocarbon, no one C atom may be attached to more than two other C atoms.
Nomenclature of Alkanes
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• Organic compounds are named according to rules established by the International Union for Pure and
Applied Chemistry (IUPAC).
• To name alkanes:
• Find the longest chain and use it as the base name of the compound.
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Figure 24.3 from Transparency Pack
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Figure 24.4 from Transparency Pack
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• Groups attached to the main chain are called substituents.
• Number the carbon atoms in the longest chain starting with the end closest to a substituent.
Cycloalkanes
• Alkanes that form rings are called cycloalkanes.
• Cyclopropane and cyclobutane are strained because the C–C–C bond angles in the ring are less than
the 109.5° required for a tetrahedral geometry.
• Because of the strain in the ring, cyclopropane is very reactive.
24.3 Alkenes, Alkynes, and Aromatic Hydrocarbons
• Alkanes contain the largest possible number of hydrogen atoms per carbon atom; they are called
saturated hydrocarbons.
• Alkenes, alkynes, and aromatic hydrocarbons contain less hydrogens than an alkane with the same
number of carbon atoms.
• They are called unsaturated hydrocarbons.
• They tend to be more reactive than unsaturated hydrocarbons.
Alkenes
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• Alkenes are unsaturated hydrocarbons that contain C and H atoms and at least one C-C double bond.
• The simplest alkenes are H2C=CH2 (ethene) and CH3CH=CH2 (propene).
• Their common names are ethylene and propylene.
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• The triple bond has one and two bonds between two C atoms.
• Ethyne (acetylene) is the simplest alkyne: HC≡CH.
• Alkynes are named in the same way as alkenes with the suffix –yne replacing the –ene for alkenes.
Addition Reactions of Alkenes and Alkynes
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• The dominant reactions for alkenes and alkynes are addition reactions.
• They involve the addition of something to the two atoms that form the double or triple bond.
• Example: The addition of a halogen (bromine) to ethylene:
Aromatic Hydrocarbons
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• Aromatic structures are formally related to benzene (C6H6).
• Many aromatic compounds are given common names (e.g., naphthalene, toluene, anthracene).
Stabilization of Electrons by Delocalization
• Benzene is a planar symmetrical molecule.
• The delocalized electrons are usually represented as a circle in the center of the ring.
Substitution Reactions
• Benzene is not reactive because of the stability associated with the delocalized electrons.
• Even though they contain bonds, aromatic hydrocarbons undergo substitution reactions more
readily than addition reactions.
chloride (catalyst).
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“Addition Reactions of Alkenes” Activity from Instructor’s Resource CD/DVD
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“Surface Reaction–Hydrogenation” Animation from Instructor’s Resource CD/DVD
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“Testing for Unsaturated Hydrocarbons with Bromine” Movie from Instructor’s Resource CD/DVD
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24.4 Organic Functional Groups
• Hydrocarbons are relatively unreactive.
• For an organic molecule to be reactive it needs something additional.
Alcohols
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• Alcohols are derived from hydrocarbons and contain –OH (hydroxyl or alcohol) groups.
• The names are derived from the hydrocarbon name with –ol replacing the –ane suffix.
• Example: ethane becomes ethanol.
• Because the O–H bond is polar and can participate in hydrogen bonding, alcohols are more water
soluble than alkanes.
Ethers
• Compounds in which two hydrocarbons are linked by an oxygen are called ethers.
• Ethers can be formed by a dehydration reaction:
CH3CH2–OH + H–OCH2CH3 → CH3CH2–O–CH2CH3 + H2O
• This condensation reaction involves the removal of a water molecule from two molecules of
alcohol.
• Ethers are commonly used as solvents.
• Common examples are diethyl ether and tetrahydrofuran (a cyclic ether).
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R–COR’
• Aldehydes and ketones are prepared by the oxidation of alcohols.
• Ketones are less reactive than aldehydes and are used as solvents.
• Two common examples of ketones are acetone and methyl ethyl ketone (MEK).
• Other examples of molecules that contain aldehydes or ketones are vanilla and cinnamon flavorings.
The ketones carvone and camphor are responsible for the flavors of spearmint and caraway,
respectively.
Carboxylic Acids and Esters
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• Carboxylic acids contain a carbonyl group with an –OH attached.
• The carboxyl functional group is –COOH: R–COOH
• Esters are named using the alcohol part first and then the acid part.
• Example: The ester formed from ethanol and acetic acid is ethyl acetate.
• Esters tend to have very pleasant characteristic odors and are often used as food flavorings and scents.
• Some common esters are benzocaine (used in some sunburn lotions), ethyl acetate (a component
of some nail polish removers), vegetable oils, polyester thread, and aspirin.
• In the presence of a base, esters hydrolyze (the molecule splits into acid and alcohol).
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“A Miracle Drug” from Further Readings
40
“Ester, What’s in My Food?” from Further Readings
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24.5 Chirality in Organic Chemistry
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• Recall that molecules whose mirror images are nonsuperimposable are chiral.
• Compounds containing carbon atoms with four different attached groups are inherently chiral.
• Chemists use the labels R– and S– to distinguish between these enantiomers.
24.6 Introduction of Biochemistry
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• The biosphere is the part of the Earth containing living organisms.
• Biochemical molecules tend to be very large and difficult to synthesize.
24.7 Proteins
Amino Acids
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“The World’s First ‘Pastarimeter’: An Analogous Demonstration of Polarimetry Using Pasta Fusilli”
from Live Demonstrations
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“Chirality” Animation from Instructor’s Resource CD/DVD
49
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• Proteins are macromolecules present in all cells.
• They are made up of building blocks called –amino acids.
• At normal physiological pH, amino acids are present in aqueous solution as the doubly ionized forms
called zwitterions.
Polypeptides and Proteins
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• Proteins are polyamides.
• When formed from amino acids, each amide group is called a peptide bond.
• Peptides are formed by condensation of the –COOH group of one amino acid with the –NH2 group of
another amino acid.
• Proteins are polypeptides with molecular weights between 6000 and 50 million amu.
Protein Structure
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• The arrangement or sequence of amino acids along a protein chain is called the protein’s primary
structure or primary sequence.
• A change in one amino acid can alter the biochemical behavior of the protein.
• An example of such a change is found in the disease sickle-cell anemia.
• This disease results from a single amino acid substitution on two of the subunits of
hemoglobin.
• Secondary structure refers to the regular arrangement of segments of the protein chain.
• One common secondary structure is the -helix.
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Figure 24.18 from Transparency Pack
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“Chemistry in the Dyeing of Eggs: from Further Readings
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• Tertiary structure is the three-dimensional structure of the protein.
• There are two broad categories of tertiary structure:
• Globular proteins: proteins that fold into a compact, roughly spherical shape, are soluble
in water and mobile in cells.
• Globular proteins generally have nonstructural functions (e.g., enzymes).
24.8 Carbohydrates
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• Carbohydrates have the empirical formula Cx(H2O)y.
• Carbohydrate means “hydrate of carbon.”
• The most abundant carbohydrate is glucose, C6H12O6.
• Carbohydrates are polyhydroxy aldehydes and ketones.
• Glucose is a six-carbon aldehyde sugar (aldose); fructose is a six-carbon ketone sugar (ketose).
• One of the alcohol groups of glucose can react with the aldehyde group to form a six-membered
ring.
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Figure 24.21 from Transparency Pack
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“An Easy Way to Convert a Fischer Projection into a Zigzag Representation” from Further Readings
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Figure 24.22 from Transparency Pack
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Disaccharides
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• Glucose and fructose are monosaccharides, simple sugars that cannot be broken down by hydrolysis
with aqueous acids.
Polysaccharides
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• Polysaccharides are formed by condensation of several monosaccharide units.
• There are many different types.
• Examples of polysaccharides based on glucose are starch, glycogen, and cellulose.
• The term starch refers to a group of polysaccharides found in plants (e.g., corn, potatoes, wheat,
24.9 Lipids
• Lipids are another important class of biomolecule.
• Lipids are used for energy storage (fats, oils) and as elements of biological structures such as cell
membranes (phospholipids, cholesterol).
• Fats and oils are derived from glycerol and long-chain carboxylic acids called fatty acids.
• Fats tend to be solid at room temperature and are enriched in saturated fatty acids.
• Saturated fatty acids have R groups that are alkanes (no double bonds).
• Oils tend to be liquid at room temperature and are enriched in unsaturated fatty acids.
• Unsaturated fatty acids have R groups that are alkenes (at least one double bond).
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• Glycerol phospholipids also contain glycerol and fatty acid components.
• Their structure, however, also includes a charged phosphate-containing group linked to the
glycerol.
• In an aqueous environment, phospholipids cluster together with their charged polar head groups
facing the water and their nonpolar tails facing inward.
• Thus, phospholipids form bilayers that are key components of cellular membranes.
24.10 Nucleic Acids
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• Nucleic acids carry genetic information.
• DNA (deoxyribonucleic acids) have molecular weights around 6 – 16 x 106 amu.
• RNA (ribonucleic acids) have molecular weights around 20,000 to 40,000 amu.
• Nucleic acids are made up of monomers called nucleotides.
• a phosphoric acid unit
• Nucleic acids form by the condensation of nucleotides (the phosphoric acid condenses with the O–H
group of the sugar).
• DNA consists of two deoxyribonucleic acid strands wound together in a double helix.
• The sugar-phosphate chains are wrapped around the outside of the DNA molecule.
• Complementary base pairs are formed between bases on each chain.
• The complementary base pairs are held together by London-dispersion forces and hydrogen
bonding.
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• The structures of T and A make them ideal hydrogen-bonding partners.
• Two hydrogen bonds form between T and A.
• The same is true for C and G.
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Further Readings:
1. Raymond B. Seymour, “Alkanes: Abundant, Pervasive, Important, and Essential,” J. Chem. Educ.,
Vol. 66, 1989, 59–63.
5. William B. Jensen, “The Origins of the Ortho-, Meta-, and Para- Prefixes in Chemical Nomenclature,”
J. Chem. Educ., Vol. 83, 2006, 356.
6. Michele Clarke, Ann Brown, Dianne N. Epp, Mary Gallup, Jeffrey R. Wilson, and Judith A.
Wuerthele, “Ester, What’s in My Food?” J. Chem. Educ., Vol. 63, 1986, 1050–1051.
10. Gil Downs, “Why Teach Biochemistry?” J. Chem. Educ., Vol. 64, 1987, 339.
11. Robert C. Mebane and Thomas R. Rybolt, “Chemistry in the Dyeing of Eggs,” J. Chem. Educ., Vol.
64, 1987, 291–293.
12. C. M. Drain and Barry B. Corden, “Reversible Oxygenation of Oxygen Transport Proteins,” J. Chem.
Educ., Vol. 64, 1987, 441–443.
13. Sandra Signorella and Luis F. Sala, “An Easy Way to Convert a Fischer Projection into a Zigzag
Representation,” J. Chem. Educ., Vol. 68, 1991, 105–106.
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18. Philip S. Beauchamp, “‘Absolutely’ Simple Stereochemistry,” J. Chem. Educ., Vol. 61, 1984, 666–
667.
21. Maureen M. Julian, “Rosalind Franklin: From Coal to DNA to Plant Viruses,” J. Chem. Educ., Vol.
60, 1983, 660–662.
22. A. B. Wolbarst, “DNAmonic,” J. Chem. Educ., Vol. 56, 1979, 733. A mnemonic device for base-
pairing in DNA is suggested: Pure Silver Taxi (purine: Ag; T=A, G=C).
Live Demonstrations:
1. Lee R. Summerlin and James L. Ealy, Jr., “Oxidation of Alcohol by Mn2O7,” Chemical
Demonstrations, A Sourcebook for Teachers (Washington: American Chemical Society, 1985), pp. 103–
104.
2. Lee. R. Summerlin,, Christie L. Borgford, and Julie B. Ealy, “The Disappearing Coffee Cup,” Chemical
Demonstrations, A Sourcebook for Teachers, Volume 2 (Washington: American Chemical Society, 1988),
p. 96. A polystyrene coffee cup is “melted” in a pool of acetone.
Fusilli,” J. Chem. Educ., Vol. 79, 2002, 1214–1216.
5. Gretchen L. Anderson, “Demonstration of Enantiomer Specificity of Proteins and Drugs,” J. Chem.
Educ., Vol. 81, 2004, 971–974. A classroom exercise to illustrate the properties of enantiomers.