1. Organic and Biological Molecules
Chapter 24
Organic and Biological Molecules

2. 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.
The study of the chemistry of living
matter

3. Hydrocarbons
compounds composed of carbon and hydrogen.
Saturated compounds (alkanes) have the maximum number of hydrogen atoms attached to each carbon atom

4. Unsaturated compounds have fewer hydrogen atoms attached to the carbon chain than alkanes
Unsaturated: They contain carbon-carbon multiple bonds (double or triple)

5. 22.1 Alkanes: Saturated hydrocarbons
Saturated hydrocarbons, CnH2n+2
“Saturated” because they can’t take any more hydrogen atoms
Normal straight chains (unbranched hydrocarbons)
H3C–(CH2)n–2–CH3
Waxes, oils, & fuel gases as n decreases.

6. Alkanes: Saturated Hydrocarbons
The C-H Bonds in Methane

7. The Lewis structure of ethane.

8. Propane

9. Butane

10. The First 10 “Normal” Alkanes
Name Formula M.P. B.P. # Structural Isomers
Methane CH
Ethane C2H
Propane C3H
Butane C4H
Pentane C5H
Hexane C6H
Heptane C7H
Octane C8H
Nonane C9H
Decane C10H
C1 - C4 are Gases
at Room Temperature
C5 - C16 are Liquids
at Room Temperature

11. IUPAC Rules for Naming Branched Alkanes
Find and name the parent chain in the hydrocarbon - this forms the root of the hydrocarbon name
Number the carbon atoms in the parent chain starting at the end closest to the branching
Name alkane branches by dropping the “ane” from the names and adding “yl”. A one-carbon branch is called “methyl”, a two-carbon branch is “ethyl”, etc…
When there are more than one type of branch (ethyl and methyl, for example), they are named alphabetically
Finally, use prefixes to indicate multiple branches

12. Rules for Naming Alkanes
1. For alkanes beyond butane, add -ane to the Greek root for the number of carbons.
C-C-C-C-C-C : hexane
2. Alkyl substituents: drop the -ane and add -yl
-C2H5 is ethyl

14. Rules for Naming Alkanes
3. Positions of substituent groups are specified by numbering the longest chain sequentially. C 
C-C-C-C-C-C
3-methylhexane
Start numbering at the end closest to the branching
4. Location and name are followed by root alkane name. Substituents are given in alphabetical order and use di-, tri-, etc.

15. Normal vs Branched Alkanes
Normal alkanes consist of continuous chains of carbon atoms
Alkanes that are NOT continuous chains of carbon atoms contain branches
The longest continuous chain of carbons is called the parent chain

16. Structural Isomerism
Structural isomers are molecules with the same chemical formulas but different molecular structures - different “connectivity”.
They arise because of the many ways to create branched hydrocarbons.
n-pentane, C5H12
2-methlbutane, C5H12

17. Example : Show the structural formula of 2,2-dimethylpentane
The parent chain is indicated by the ROOT of the name - “pentane”. This means there are 5 carbons in the parent chain. 1 2 3 4 5
“dimethyl” tells us that there are TWO methyl branches on the parent chain. A methyl branch is made of a single carbon atom.
“2,2-” tell us that BOTH methyl branches are on the second carbon atom in the parent chain.

18. Example: Structural formula of 3-ethyl-2,4-dimethylheptane?
The parent chain is indicated by the ROOT of the name - “heptane”. This means there are 7 carbons in the parent chain. 1 2 3 4 5 7 6
“2,4-dimethyl” tells us there are TWO methyl branches on the parent chain, at carbons #2 and #4.
“3-ethyl-” tell us there is an ethyl branch (2-carbon branch) on carbon #3 of the parent chain.

19. Example: 2,3,3-trimethyl-4-propyloctane
The parent chain is indicated by the ROOT of the name - “octane”. This means there are 8 carbons in the parent chain. 1 2 3 4 5 7 6 8
“2,3,3-trimethyl” tells us there are THREE methyl branches - one on carbon #2 and two on carbon #3.
“4-propyl-” tell us there is a propyl branch (3-carbon branch) on carbon #4 of the parent chain. 1 2 3 4 5 7 6 8

20. Example : Name the molecules shown
parent chain has 5 carbons - “pentane”
two methyl branches - start counting from the right - #2 and #3
2,3-dimethylpentane
parent chain has 8 carbons - “octane”
two methyl branches - start counting from the left - #3 and #4
one ethyl branch - #5
name branches alphabetically 5
5-ethyl-
3,4-dimethyl 4 3
octane

21. Reactions of alkanes 2C4H10 + 13 O2 8CO2 + 10 H2O(g)
Combustion reactions
2C4H O CO H2O(g)
Substitution Reactions
CH4 + Cl CH3Cl + HCl
CH3Cl + Cl CH2Cl2 + HCl
CH2Cl2 + Cl CH Cl3 + HCl
CHCl3 + Cl C Cl4

22. Dehydrogenation Reactions
CH3CH CH CH2
Ethylene

23. Cyclic alkanes CnH2n
A cycloalkane is made of a hydrocarbon chain that has been joined to make a “ring”.
Note that two hydrogen atoms were lost in forming the ring

24. Ring Structures

25. Cyclohexane - Boat & Chair Conformations
Cyclohexane is NOT a planar molecule. To achieve its 109.5° bond angles and reduce angle strain, it adopts several different conformations.
The BOAT and CHAIR (99%) are two conformations
Boat
chair

26. 22.2 Alkenes and Alkynes
Alkenes: hydrocarbons that contain a carbon-carbon double bond. [CnH2n]
C=C Ethene
CC=C propene
Alkynes: hydrocarbons containing a carbon-carbon triple bond. [CnH2n-2]
C ΞC Ethyne
CCC Ξ CC pentyne

27. Alkenes & Alkynes
The suffix for the parent alkane chains are changed from “ane” to “ene” and “yne”
e.g. ethene, ethyne
Where it is ambiguous, the BONDS are numbered like branches so that the location of the multiple bond may be indicated
Alkenes are hydrocarbons that contain at least one carbon-carbon double bond
Alkynes are hydrocarbons that contain at least one carbon-carbon triple bond

28. Alkenes, CnH2n
Cycle formation isn’t the only possible result of dehydrogenation.
Adjacent C’s can double bond, C=C, making an (unsaturated) alkene.
Sp2

29. Nomenclature for Alkenes
1. Parent hydrocarbon name ends in -ene
C2H4; CH2=CH is ethene
2. With more than 3 carbons, double bond is indicated by the lowest numbered carbon atom in the bond.
C=C-C-C is 1-butene

30. Nomenclature alkenes and alkynes

31. Cis and Trans Isomers
Double bond is fixed (rotation around the double bond is restricted)
Cis/trans Isomers are possible
CH3 CH CH3
CH = CH CH = CH
cis trans CH3

32. Reactions of alkenes and alkynes
1. Addition Reactions
in which (weaker)  bonds are broken and new (stronger)  bonds are formed to atoms being added.

33. Hydrogenation reaction
Adds a hydrogen atom to each carbon atom of a double bond
H H H H
catalyst
H–C=C–H + H H–C–C–H
H H
Ethene Ethane
CH3-CH3

34. Halogenation reaction
Adds a halogen atom to each carbon atom of a double bond
H H H H
catalyst
H–C=C–H + Cl H–C–C–H
Cl Cl
Ethene Dichloro ethane

35. Halogenation Reactions
CH CHCH2CH2CH2 + Br2
CH2Br CHBrCH2CH2CH2
1,2-dibromopentane

36. Alkynes, CnH2n–2 Carbon-carbon triple bonds Names end in -yne
sp triple bonding makes a rigid 180° segment in a hydrocarbon.
Carbon-carbon triple bonds
Names end in -yne
HCCH ethyne(acetylene)
HCC-CH3 propyne

37. The Bonding in Acetylene

38. Naming Alkenes and Alkynes
When the carbon chain has 4 or more C atoms, number the chain to give the lowest number to the double or triple bond.
CH2=CHCH2CH3 1-butene
CH3CH=CHCH3 2-butene
CH3CHCHCH3 2-butyne

39. Question
Write the IUPAC name for each of the following unsaturated compounds:
A. CH3CH2CCCH3
CH3
B. CH3C=CHCH3 C.
2-pentyne
2-methyl-2-butene
3-methylcyclopentene

40. Name the following compound
Question
Name the following compound
5-ethyl-3-heptyne

41. Additions reactions:Hydrogenation and Halogenation
Hydrogens and halogens also add to the triple bond of an alkyne.

42. 22.3 Aromatic hydrocarbons Unsaturated Cyclic hydrocarbons
Alternating single/double bond
cycles occur in many organic molecules
This class is called “aromatic” (by virtue of their aroma).
Delocalized  bonds
possess a great stability
thus benzene does not
react like unsaturated
hydrocarbons

43. Benzene C6H6
The  structure is often preserved in benzene chemical reactions
Aromatic rings do not add, they substitute instead
sp2

44. Shorthand notation for benzene rings
The bonding in the benzene ring is a combination of different Lewis structures

45. Aromatic Hydrocarbons
Substitution reaction
Nitroobenzene
Chlorobenzene
-NO2
-CH3
+ Cl2
HNO3
Toluene
HNO3
benzene
CH3Cl
+ HCl
+H2O
+HCl

47. Nomenclature of benzene derivatives

48. More Complex Aromatic Systems

49. 22.4 Hydrocarbon Derivatives (Functional Groups)
Molecules that are fundamentally hydrocarbons but have additional atoms or group of atoms called functional groups
Part of an organic molecule where chemical reactions take place
Replace an H in the corresponding alkane
Provide a way to classify organic compounds

50. The Common Functional Groups
Class General Formula
Halohydrocarbons RX
Alcohols ROH
Ethers ROR
Aldehydes

51. Class General Formula
Ketones
Carboxylic Acids
Esters
Amines

52. Some Types of Functional Groups
Haloalkane -F, -Cl, -Br CH3Cl
Alcohol -OH CH3OH
Ether -O- CH3-O-CH3
Aldehyde
Ketone

53. More Functional Groups
Carboxylic acid -COOH CH3COOH
Ester COO- CH3COOCH3
Amine NH2 CH3NH2
Amide -CONH2 CH3CONH2

55. Haloahydrocarbons
An alkane in which one or more H atoms is replaced with a halogen (F, Cl, Br, or I)
CH3Br bromomethane
Br (methyl bromide)
CH3CH2CHCH3 2-bromobutane Cl
chlorocyclobutane

56. 1,3-dichlorocyclohexane
Name the following:
bromocyclopentane
1,3-dichlorocyclohexane 1 2 3

57. Substituents List other attached atoms or groups in alphabetical order
Br = bromo, Cl = chloro
Cl Br
CH3CHCH2CHCH2CH2CH3
4-bromo-2-chloroheptane 5 1 2 3 4

58. Nomenclature The name of this compound is: Cl CH3 CH3CH2CHCH2CHCH3
4-chloro-2-methylhexane

59. The –OH makes alcohol polar enough to hydrogen bonding
Alcohols: R–OH
The –OH makes alcohol polar enough to hydrogen bonding
Thus, they are water soluble
Ethanol is produced by the fermentation of glucose
C6H12O6
Glucose
2CH3CH2OH
Ethanol
yeast
+ 2 CO2
Methanol is produced industrially by hydrogenation
of carbon monoxide
CO + 2H2O CH3OH
Methanol

60. Uses of alcohols
Methanol is used to synthesize adhesives, fibers, plastics and recently as motor fuel
It is toxic to human and can lead to blindness and death
Ethanol can be added to gasoline to form gasohol and used in industry as solvent
Commercial production of ethanol:
CH2=CH2 + H2O CH3CH2OH

61. Classes of alcohols
Alcohols can be classified according to the number of hydrocarbon fragments bonded to the carbon where the –OH group is attached

62. Naming Alcohols
In IUPAC name, the -e in alkane name is replaced with -ol.
CH4 methane
CH3OH methanol (methyl alcohol)
CH3CH3 ethane
CH3CH2OH ethanol (ethyl alcohol)

63. Phenol
(Aromatic alcohol)

64. Some Typical Alcohols “Rubbing alcohol” CH3CHCH3
2-propanol (isopropyl alcohol)
Antifreeze HO-CH2-CH2-OH
1,2-ethanediol (ethylene glycol)

65. Naming Alcohols
IUPAC names for longer chains number the chain from the end nearest the -OH group.
CH3CH2CH2OH 1-propanol OH
CH3CHCH3 2-propanol
CH OH
CH3CHCH2CH2CHCH3 5-methyl-2-hexanol 5 2

66. Example Name the following alcohols: OH CH3CHCHCH2CH3 CH3
3-methyl-2-pentanol

67. Aldehydes and Ketones O carbonyl group
In an aldehyde, an H atom is attached to a carbonyl group
O carbonyl group 
CH3-C-H
In a ketone, two carbon groups are attached to a carbonyl group
CH3-C-CH3

68. Naming Aldehydes IUPAC name: Replace the -e in the alkane name by -al
Common Add aldehyde to the prefixes form (1C), acet (2C), propion(3), and butry(4C)
O O O
  
H-C-H CH3-C-H CH3CH2C-H
methanal ethanal propanal
(formaldehyde) (acetaldehyde) (propionaldehyde)
methane
propane
ethane

69. Aldehydes as Flavorings

70. Naming Ketones O O   CH3 -C-CH3 CH3-C-CH2-CH3 2-Propanone 2-Butanone
IUPAC name: the -e in the alkane name is replaced with –one and a number to indicate the position of carbonyl group when needed.
In the common name, add the word ketone
after naming the alkyl groups attached to the
carbonyl group
O O
 
CH3 -C-CH3 CH3-C-CH2-CH3
2-Propanone Butanone
(Dimethyl ketone) (Ethyl methyl ketone)
butane
propane
cyclohexane
Acetone

71. Name the following compounds
A. CH3CH2CCH B.
2-butanone (ethyl methyl ketone)
CH3 O
C. CH3-C-CH2CH
cyclohexanone
CH3
3,3-dimethylbutanal

72. Draw the structural formulas for each of the following compounds
A. 3-Methylpentanal CH3CH2CHCH2CH
Br O 
B. 2,3-Dibromopropanal Br-CH2CHCH O
C. 3-Methyl-2-butanone CH3CHCCH3
CH3

73. Preparation of aldehydes and Ketones
They are produced by oxidation of alcohols:
CH3CH2OH
Oxidation
acetaldehyde
ethanal
Primary alcohol
Oxidation
acetone
propanone
Secondary alcohol

74. Carboxylic Acids and Esters
Carboxylic acids contain the carboxyl group as carbon 1. O
R 
CH3 — C—OH CH3—COOH
carboxyl group
General formula R—COOH

75. Nomenclature of Carboxylic Acids
Formula IUPAC Common
alkan -oic acid prefix – ic acid
HCOOH methanoic acid formic acid
CH3COOH ethanoic acid acetic acid
CH3CH2COOH propanoic acid propionic acid
CH3CH2CH2COOH butanoic acid butyric acid

76. IUPAC nomenclature for Carboxylic acids
Identify longest chain
Number carboxyl carbon as 1
CH3 |
CH3 — CH—CH2 —COOH
3-methylbutanoic acid 4 1 3 2

77. CH3 |
CH3CHCOOH
2-methylpropanoic acid;

78. Reaction of carboxylic acid with alcohol
Esterification
Alcohol
Carboxylic acid
Ester

79. Esters Esters give fruity odors
In ester, the H in the carboxyl group is replaced with an alkyl group O 
CH3 — C—O —CH CH3—COO —CH3
ester group
Esters give fruity odors

80. Naming Esters The parent alcohol is named first with a –yl ending
Change the –oic ending of the parent acid to –ate
acid alcohol O
 methyl
CH3 — C—O —CH3
Ethanoate methyl ethanoate (IUPAC)
(acetate) methyl acetate (common)

81. Amines one N-C two N-C three N-C bond bonds bonds
Organic compounds of nitrogen N; derivatives of ammonia
Classified as primary, secondary, tertiary
CH CH3
 
CH3—NH2 CH3—NH CH3—N — CH3
Primary Secondary Tertiary
one N-C two N-C three N-C
bond bonds bonds

82. Naming Amines IUPAC aminoalkane Common alkylamine CH3CH2NH2
aminoethane
(ethylamine)
NH2 |
CH3CHCH3
2-aminopropane Aniline
(isopropylamine)

83. 22.5 Polymers Poly= many; mers=parts
Polymers are large, usually chainlike molecules that are built from small molecules called monomers joined by covalent bonds
Monomer Polymer
Ethylene Polyethylene
Vinyl chloride Polyvinyl chloride
Tetrafluoroethylene Teflon

84. Some common synthetic polymers, their monomers and applications

85. Types of Polymerization
Addition Polymerization: monomers “add together” to form the polymer, with no other products. ( Polyethylene and Teflon)
Condensation Polymerization: A small molecule, such as water, is formed for each extension of the polymer chain. (Nylon)

86. Addition Polymerization
A species with
an unpaired
electron such as
hydroxyl free radical
The polymerization process
Is initiated by a free radical
Free radical attacks and break
The  bond of ethylene molecule
To form a new free radical
Repetition of the process thousands of times creates a long chain
polymer
The process is terminated when two radicals react to form a bond;
thus there will be no free radical is available for further repetitions.

87. Condensation Polymerization Formation of Nylon
Dicarboxylic acid
Diamine
Dimer
Small molecule such as H2O is formed
from each extension of the polymer chain
both ends are free to react

88. Nylon