1. Chapter 25 The Chemistry of Life: Organic and Biological Chemistry
CHEMISTRY The Central Science 9th Edition
Chapter 25 The Chemistry of Life: Organic and Biological Chemistry
David P. White
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2. Some General Characteristics of Organic Molecules
The Structures of Organic Molecules
Organic molecules exhibit three different types of hybridization at the carbon center:
sp3 hybridized carbons for tetrahedral geometries;
sp2 hybridized carbons for trigonal planar geometries; and
sp hybridized carbons for linear geometries.
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3. Some General Characteristics of Organic Molecules
The Structures of Organic Molecules
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4. Some General Characteristics of Organic Molecules
The Stabilities of Organic Molecules
Carbon forms very strong bonds between H, O, N, and halogens.
Carbon also forms strong bonds with itself.
Therefore, C can form stable long chain or ring structures.
Bond strength increases from single to double to triple bond.
Bond length decreases in the same direction.
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5. Some General Characteristics of Organic Molecules
The Stabilities of Organic Molecules
Carbon and hydrogen have very similar electronegativities, so the C-H bond is essentially non-polar.
Therefore, compounds containing C-C and C-H bonds are thermodynamically stable and kinetically inert.
Adding functional groups (e.g., C-O-H) introduces reactivity into organic molecules.
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6. Some General Characteristics of Organic Molecules
Solubility and Acid-Base Properties of Organic Substances
Compounds with only C-C or C-H bonds are nonpolar and are soluble in nonpolar solvents and not very soluble in water.
Water soluble organic molecules have polar functional groups.
Surfactants have long nonpolar portions of the molecule with a small ionic or polar tip.
The most important organic acids are carboxylic acids with the
-COOH functional group.
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7. Some General Characteristics of Organic Molecules
Solubility and Acid-Base Properties of Organic Substances
Basic organic molecules are usually amines, -NH2, -NHR, or -NR2 functional groups.
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8. Introduction to Hydrocarbons
Hydrocarbons are compounds with only C and H.
There are four classes:
alkanes (all  bonds and no  bonds);
alkenes (a mixture of  and  bonds, but no triple bonds);
alkynes (must contain triple bonds); and
aromatics (have planar, ring structures with alternating single and double bonds).
Saturated compounds have only  bonds.
Unsaturated compounds have both  and  bonds.
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10. Alkanes
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11. Alkanes
The name of alkanes varied according to the number of C atoms present in the chain.
Since the only intermolecular forces available to alkanes are London dispersion forces, the boiling points increase smoothly as the molar mass increases.
Methane to butane are gases at normal pressures.
Pentane to decane are liquids at normal pressures.
Each carbon in an alkane has 4 single bonds.
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12. Alkanes
In this table each member differs by one CH2 unit. This is called a homologous series.
Structures of Alkanes
VSEPR theory predicts each C atom is tetrahedral.
Therefore, each C atom has sp3 hybridized orbitals.
It is easy to rotate about the C-C bond in alkanes.
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14. Alkanes Structural Isomers
Straight chain hydrocarbons have each C atom joined in a continuous chain.
In a straight chain hydrocarbon no one C atom may be attached to more than two other C atoms.
Straight chain hydrocarbons are not linear. Each C atom is tetrahedral, so the chains are bent.
Branched chain hydrocarbons are possible for four or more C atoms, which give rise to structural isomers.
Structural isomers have different physical properties.
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16. Alkanes
Structural Isomers
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17. Alkanes Nomenclature of Alkanes
All organic molecule names have three parts:
Prefix, which tells the nature of the substituents;
Base, which gives the number of carbons; and the
Suffix, which gives the family (alkanes, etc.).
Rules for naming compounds are given by the International Union for Pure and Applied Chemistry (IUPAC).
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18. Alkanes Nomenclature of Alkanes To name alkanes:
Find the longest chain and use it as the name of the compound.
Number the carbon atoms starting with the end closest to the substituent.
Name and give the location of each substituent.
When two or more substituents are present list them in alphabetical order.
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19. Alkanes Cycloalkanes Alkanes that form rings are called cycloalkanes.
Cyclopropane and cyclobutanes are strained because the C-C-C bond angles in the ring are less than 109.5 required for the tetrahedral geometry.
Because of the strain in the ring, cyclopropane is very reactive.
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20. Alkanes
Cycloalkanes
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21. 2C2H6(g) + 7O2(g)  4CO2(g) + 6H2O(l) H = -2855 kJ
Alkanes
Reactions of Alkanes
The C-C and C-H bonds are very strong. Therefore, alkanes are very unreactive.
At room temperature alkanes do not react with acids, bases, or strong oxidizing agents.
Alkanes do combust in air (making them good fuels):
2C2H6(g) + 7O2(g)  4CO2(g) + 6H2O(l) H = kJ
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22. Unsaturated Hydrocarbons
Alkenes
Alkenes contain C, H atoms and single and double bonds.
The simplest alkenes are H2C=CH2 (ethene) and CH3CH=CH2 (propene):
their trivial names are ethylene and propylene.
Alkenes are named in the same way as alkanes with the suffix -ene replacing the -ane in alkanes.
The location of the double bond is indicated by a number.
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23. Unsaturated Hydrocarbons
Alkenes
Geometrical isomers are possible since there is no rotation about a C=C  bond.
Note the overlap between orbitals is above and below the plane of the  bonds.
As the C-C bond begins to rotate (moving from cis to trans) the overlap decreases.
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24. Unsaturated Hydrocarbons
Alkenes
At 90 the  bond breaks completely.
Therefore, there is no rotation about a  bond.
Therefore, cis and trans isomers do not readily interconvert.
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25. Unsaturated Hydrocarbons
Alkynes
Alkynes are hydrocarbons with one or more CC bond. Therefore, alkynes have one  and two  bonds between two C atoms.
Ethyne (acetylene) is a reactive alkyne: HCCH.
When acetylene is burned in the presence of oxygen (oxyacetylene torch) the temperature is about 3200 K.
Alkynes are named in the same way as alkenes with the suffix -yne replacing the -ene for alkenes.
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26. Unsaturated Hydrocarbons
Addition Reactions of Alkenes and Alkynes
The most dominant reaction for alkenes and alkynes involves the addition of something to the two atoms which form the double bond:
Note that the C-C  bond has been replaced by two C-Br  bonds.
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27. Unsaturated Hydrocarbons
Addition Reactions of Alkenes and Alkynes
A common addition reaction is hydrogenation:
CH3CH=CHCH3 + H2  CH3CH2CH2CH3
Hydrogenation requires high temperatures and pressures as well as the presence of a catalyst.
It is possible to cause hydrogen halides and water to add across  bonds:
CH2=CH2 + HBr  CH3CH2Br
CH2=CH2 + H2O  CH3CH2OH
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28. Unsaturated Hydrocarbons
Mechanism of Addition Reactions
Consider the reaction between 2-butene and HBr:
Careful kinetics experiments show the rate law to be
Therefore, both 2-butene and HBr must be involved in the rate determining step.
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29. Unsaturated Hydrocarbons
Mechanism of Addition Reactions
From the kinetics data, we can propose the following mechanism:
The p-electrons in the alkene attack the d+ H atom of the HBr to leave a positive charge on one carbon (slow step):
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30. Unsaturated Hydrocarbons
Mechanism of Addition Reactions
Then the pair of electrons on bromide attacks the carbon with a positive charge to give the product.
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31. Unsaturated Hydrocarbons
Aromatic Hydrocarbons
Aromatic structures are formally related to benzene.
The delocalized  electrons are usually represented as a circle in the center of the ring.
Benzene is a planar symmetrical molecule.
Benzene is not reactive because of the stability associated with the delocalized  electrons.
Most aromatic rings are given common names.
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33. Unsaturated Hydrocarbons
Aromatic Hydrocarbons
Even though they contain  bonds, aromatic hydrocarbons undergo substitution more readily than addition.
Example: if benzene is treated with nitric acid in the presence of sulfuric acid (catalyst), nitrobenzene is produced.
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34. Functional Groups: Alcohols and Ethers
To get reactivity out of an organic molecule, functional groups have to be added.
Functional groups control how a molecule functions.
More complicated functional groups contain elements other than C or H (heteroatoms).
Functional group containing molecules can either be saturated (alcohols, ethers, amines etc.) or unsaturated (carboxylic acids, esters, amides, etc.).
We usually use R to represent alkyl groups.
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37. Functional Groups: Alcohols and Ethers
Alcohols (R-OH)
Alcohols are derived from hydrocarbons and contain -OH groups.
The names are derived from the hydrocarbon name with -ol replacing the -ane suffix. Example: ethane becomes ethanol.
Since the O-H bond is polar, alcohols are more water soluble than alkanes.
CH3OH, methanol, is used as a gasoline additive and a fuel.
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38. Functional Groups: Alcohols and Ethers
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39. Functional Groups: Alcohols and Ethers
Alcohols (R-OH)
Methanol is produced by the reaction of CO with hydrogen under high pressure ( atm) and high temperature (400C):
CO(g) + 2H2(g)  CH3OH(g)
Ethanol is produced by fermenting carbohydrates.
Ethanol is the alcohol found in alcoholic beverages.
Polyhydroxy alcohols (polyols) contain more than one OH group per molecule (e.g. ethylene glycol used as antifreeze).
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40. Functional Groups: Alcohols and Ethers
Alcohols (R-OH)
Aromatic alcohols can also be formed (e.g. phenol).
Note that aromatic alcohols are weak acids.
The only biochemically important alcohol is cholesterol.
Ethers (R-O-R′)
Compounds in which two hydrocarbons linked by an oxygen are called ethers.
Ethers are commonly used as solvents.
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41. Compounds with a Carbonyl Group
Aldehydes and Ketones
The carbonyl functional group is C=O.
Aldehydes must have at least one H atom attached to the carbonyl group:
Ketones must have two C atoms attached to the carbonyl group:
Aldehydes and ketones are prepared from the oxidation of alcohols.
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42. Compounds with a Carbonyl Group
Carboxylic Acids
Carboxylic acids contain a carbonyl group with an -OH attached.
The carboxyl functional group is -COOH:
Carboxylic acids are weak acids.
Typical carboxylic acids are spinach, vinegar, cleaners, vitamin C, aspirin, and citrus fruits.
Carboxylic acids are also used to make polymers for fibers, paints, and films.
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43. Compounds with a Carbonyl Group
Carboxylic Acids
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44. Compounds with a Carbonyl Group
Carboxylic Acids
Trivial names of carboxylic acids reflect their origins (e.g. formic acid was first extracted from ants, the Latin formica means “ant”).
Carboxylic acids can be prepared by oxidizing alcohols which contain a -CH2OH group.
Acetic acid can be prepared by reacting methanol with CO in the presence of a Rh catalyst. This sort of reaction is called carbonylation.
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45. Compounds with a Carbonyl Group
Esters
Some common esters are: benzocaine (in sun burn lotions), ethyl acetate (nail polish remover), vegetable oils, polyester thread, and aspirin.
Esters contain -COOR groups:
Esters can be prepared by reacting a carboxylic acid with an alcohol and eliminating water:
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46. Compounds with a Carbonyl Group
Esters
Esters are named first using the alcohol part and then the acid part (in the above example: ethyl from ethanol and acetate from acetic acid).
In the presence of base, ester hydrolyze (molecule split into acid and alcohol).
Saponification is the hydrolysis of an ester in the presence of a base.
Esters tend to have characteristic odors and are used as food flavorings and scents.
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47. Compounds with a Carbonyl Group
Amines and Amides
Amines are organic bases.
Just as alcohols can be thought of organic forms of water, amines can be thought of organic forms of ammonia.
Amides are composites of carbonyl and amine functionalities:
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48. Chirality in Organic Chemistry
A molecule that exists as a pair of nonsuperimposable mirror images is called chiral.
Organic compounds that contain one carbon atom that is attached to four different atoms or groups are chiral.
The carbon atom attached to the four different moieties is called a stereogenic carbon.
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49. Chirality in Organic Chemistry
Consider *CHBr(CH3)(CH2CH2CH3). The *C is attached to: (i) H, (ii) Br, (iii) CH3, and (iv) CH2CH2CH3:
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50. Chirality in Organic Chemistry
Chiral molecules exist as a pair of enantiomers.
The enantiomers are nonsuperimposable mirror images.
Organic chemists label enantiomers as R and S.
If two enantiomers are placed in a solution in equal amounts, then the mixture is called racemic.
If one molecule contains two stereogenic centers, one R and one S, then the molecule shows no optical activity.
Many pharmaceuticals are chiral molecules.
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51. S-ibuprofen:

52. Introduction to Biochemistry
The chemistry of living organisms is called biochemistry.
Biochemical molecules tend to be very large and difficult to synthesize.
Living organisms are highly ordered. Therefore, living organisms have very low entropy.
Most biologically important molecules are polymers, called biopolymers.
Biopolymers fall into three classes: proteins, polysaccharides (carbohydrates), and nucleic acids.
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53. Proteins
Amino Acids
Proteins are large molecules present in all cells.
They are made up of -amino acids.
There are two forms of an amino acid: one that is neutral (with -NH2 and -OH groups) and one that is zwitterionic (with -NH3+ and -O- groups).
A zwitterion has both positive and negative charge in one molecule.
There are about 20 amino acids found in most proteins.
Each amino acid is assigned a three-letter abbreviation.
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55. Proteins Amino Acids Our bodies can synthesize about 10 amino acids.
Essential amino acids are the other 10 amino acids, which have to be ingested.
The -carbon in all amino acids except glycine is chiral (has 4 different groups attached to it).
Chiral molecules exist as two nonsuperimposable mirror images.
The two mirror images are called enantiomers.
Chiral molecules can rotate the plane of polarized light.
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56. Proteins
Amino Acids
The enantiomer that rotates the plane of polarized light to the left is called L- (laevus = “left”) and the other enantiomer is called D- (dexter = right).
Enantiomers have identical physical and chemical properties. They only differ in their interaction with other enantiomers.
Most amino acids in proteins exist in the L-form.
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57. Proteins
Amino Acids

58. Proteins Polypeptides and Proteins Proteins are polyamides.
When formed by amino acids, each amide group is called a peptide bond.
Peptides are formed by condensation of the -COOH group of one amino acid and the NH group of another amino acid.
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59. Proteins Polypeptides and Proteins
The acid forming the peptide bond is named first. Example: if a dipeptide is formed from alanine and glycine so that the COOH group of glycine reacts with the NH group of alanine, then the dipeptide is called glycylalanine.
Glycylalanine is abbreviated gly-ala.
Polypeptides are formed with a large number of amino acids (usually result in proteins with molecular weights between 6000 and 50 million amu).
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60. Proteins Protein Structure
Primary structure is the sequence of the amino acids in the protein.
A change in one amino acid can alter the biochemical behavior of the protein.
Secondary structure is the regular arrangement of segments of protein.
One common secondary structure is the -helix.
Hydrogen bonds between N-H bonds and carbonyl groups hold the helix in place.
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61. Pitch is the distance between coils.
Protein Structure
Pitch is the distance between coils.
The pitch and diameter ensure no bond angles are strained and the N-H and carbonyl functional groups are optimized for H-bonding.
Tertiary structure is the three dimensional structure of the protein.
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62. Carbohydrates Carbohydrates have empirical formula Cx(H2O)y.
Carbohydrate means hydrate of carbon.
Most abundant carbohydrate is glucose, C6H12O6.
Carbohydrates are polyhydroxy aldehydes and ketones.
Glucose is a 6 carbon aldehyde sugar and fructose 6 carbon ketone sugar.
The alcohol side of glucose can react with the aldehyde side to form a six-membered ring.
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63. Carbohydrates Most glucose molecules are in the ring form.
Note the six-membered rings are not planar.
Focus on carbon atoms 1 and 5: if the OH groups are on opposite sides of the ring, then we have -glucose; if they are on the same side of the ring, then we have -glucose.
The - and - forms of glucose form very different compounds.
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66. Carbohydrates Disaccharides Glucose and fructose are monosaccharides.
Monosaccharides: simple sugars that cannot be broken down by hydrolysis with aqueous acids.
Disaccharides are sugars formed by the condensation of two monosaccharides. Examples: sucrose (table sugar) and lactose (milk sugar).
Sucrose is formed by the condensation of -glucose and fructose.
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67. Carbohydrates Disaccharides
Lactose is formed from galactose and -glucose.
Sucrose is about six times sweeter than lactose, a little sweeter than glucose and about half as sweet as fructose.
Disaccharides can be converted into monosaccharides by treatment with acid in aqueous solution.
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68. Carbohydrates Polysaccharides
Polysaccharides are formed by condensation of several monosaccharide units.
There are several different types. Example: starches can be derived from corn, potatoes, wheat or rice.
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69. Carbohydrates Polysaccharides Starch is not a pure substance.
Enzymes catalyze the conversion of starch to glucose.
Starch is poly -glucose whereas cellulose is poly -glucose.
Enzymes that hydrolyze starch do not hydrolyze cellulose because of the different shapes of the polymers.
Ingested cellulose is recovered unmetabolized.
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70. Carbohydrates Polysaccharides
Bacteria in the stomach of animals contain cellulases, which are enzymes that enable animals to use cellulose for food.
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72. Nucleic Acids Nucleic acids carry genetic information.
DNA (deoxyribonucleic acids) have molecular weights around  106 amu and are found inside the nucleus of the cell.
RNA (ribonucleic acids) have molecular weights around 20,000 to 40,000 amu and are found in the cytoplasm outside the nucleus of the cell.
Nucleic acids are made up of nucleotides.
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73. Nucleic Acids There are three important parts to a nucleic acid:
phosphoric acid unit,
five carbon sugar (e.g. deoxyribose), and
nitrogen containing organic base (e.g. adenine).
DNA and RNA have different sugars (dexoyribose vs. ribose).
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75. Nucleic Acids There are only five bases found in DNA and RNA:
adenine (A),
guanine (G),
cytosine (C),
thymine (T found in DNA only), and
uracil (U found in RNA only).
Nucleic acids are formed by condensing two nucleotides (the phosphoric acid condenses with the O-H group of the sugar).
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76. Nucleic Acids
DNA consists of two deoxyribonucleic acid strands wound together in a double helix.
The phosphate chains are wrapped around the outside of the DNA molecule.
Complementary base pairs are formed from bases which optimize H-bonding: T and A or C and G.
The complementary base pairs are held together by hydrogen bonding.
During cell division, the DNA double helix unwinds.

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78. Nucleic Acids
A new strand is formed when bases attach to each strand of the unwinding double helix.
Because of the optimized hydrogen bonding, there is only one location for each base.
Therefore, the order of bases in the new strand is the same as the order of bases in the original strand.
This is how genetic information is preserved during cell division.
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79. Nucleic Acids
DNA structure provides us with the understanding of how protein synthesis occurs, how viruses infect cells, and other biological problems occur.
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81. End of Chapter 25 The Chemistry of Life: Organic and Biological Chemistry
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