Organic and Biological Molecules

Chapter 22

Chapter 22 PreviewOrganic and Biological Molecules

Alkanes: Saturated Hydrocarbons Isomerism, Nomenclature, Reactions of alkanes, Cyclic alkanes

Alkenes, Alkynes, and Aromatic Hydrocarbons Reaction of alkenes and alkynes

Hydrocarbon DerivativesAlcohols, Aldehydes and ketones, Carboxylic acids and esters, and amines

Polymers and Natural PolymersProperties of polymers, Types of polymers, plymers based on ethylene, Protein, Carbohydrates, and Nucleic Acids

Late 18th century:•Compounds from living organisms - Organic•Compounds from lifeless matter – Inorganic•Organic compounds thought to have ‘vital force’

Ammonium cyanate(from mineral sources)

‘Inorganic’

Urea(from urine)

‘Organic’

Wöhler 1800-1882 ∆

(Heat)

IntroductionWhat is Organic Chemistry?

It is defined as the study of hydrocarbons (compounds of hydrogen and carbon) and their derivatives

Organic chemicals are universal

OrganicOrganicChemicalsChemicals

Biological matter•Plants•Animals•Microbes

Geological matter•Fossil Fuels•Other

Atmosphericand

cosmic matter

Manufacturedproducts

22.1 Alkanes: Saturated HydrocarbonAlkanes CnH2n+2

consist of only carbon and hydrogen bonded by single covalent bonds single

HCH HH

HCH CH

HH

H

HCH CH

HC

H

HH

H

HCH CH

HC

H

HC

H

HH

H

CH3

HCH CH

HC

H

HC

H

HC

H

HH

H

methane ethane propane butane

CH3CH3 CH3CH2CH3 CH3CH2CH2CH3

pentane

CH3CH2CH2CH2CH3

Skeletal structure of only carbon atoms

propane

butane

pentane

C1 – C4 n-alkanes are all gasesMethane main component of natural gas

Propane and butane often stored as compressed gases

n

1

2

3

4

5

6

MolecularFormula

CH4

C2H6

C3H8

C4H10

C5H12

C6H14

Structuralformula

HCH

CCH

HH

H

HH

HCH

CH

HH

CH

HH

HCH

CCH

HC

H

HH

HCH

CCH

HC

H

HH

HCH

CCH

HC

H

HH

H

H

H

HH

H

HCH

HH

H

HCH

HCH

HH

Name

methane

ethane

propane

butane

pentane

hexane

Condensedstructural

formulaCH4

CH3CH3

CH3CH2CH3

CH3CH2CH2CH3

CH3CH2CH2CH2CH3

CH3CH2CH2CH2CH2CH3

Further members of the series

Heptane CH3CH2CH2CH2CH2CH2CH3

Octane CH3CH2CH2CH2CH2CH2CH2CH3

Nonane CH3CH2CH2CH2CH2CH2CH2CH2CH3

Decane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3

Undecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

Dodecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

Etc., etc.

Isomers are molecules that have the same molecular formula but different structures

Isomerism

Extent of structural isomerism in alkanes

Alkane No. of structural isomersMethane 1Ethane 1Propane 1Butane 2Pentane 3Hexane 5

Decane 75

Pentadecane 4347

Eicosane 366,319

Triacontane 44 x 109(C30H62)

All known

Pentane C5H12 3 structural isomers

CH3 CH2 CH2 CH2 CH3 CH3 CH2 CH CH3

CH3

CH3 C CH3

CH3

CH3

•No other arrangements of C5H12 possible •All of these based on tetrahedral (sp3 hybridised) Carbon

CH3 CH2 CHCH3

CH3 CH3 CH CH2 CH3CH3

CH3 CH2 CHCH3

CH3

= =

Note

etc.

How many structural isomers does pentane, C5H12, have?

C C C C C

H H H H H

H

HHHHH

H

C C C C

H CH3 H H

H

HHHH

H

C C C

H CH3 H

H

HH

H

CH3

n-pentane

2-methylbutane

2,2-dimethylpropane

1. The parent name of the hydrocarbon is that given to the longest continuous chain of carbon atoms in the molecule.

CH3 CH2 CH2 CH CH2 CH2 CH3

CH3

1 2 3 4 5 6 74-methylheptane

2. An alkane minus one hydrogen atom is called an Alkyl group

CH4

CH3

methane

methyl

Common Alkyl Groups

Nomenclature

3. 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 CH2 CH3

CH3

1 2 3 4 5

2-methylpentane

CH3 CH2 CH2 CH CH3

CH3

1 2 3 4 5

4-methylpentane

Nomenclature

4. Use prefixes di-, tri-, tetra-, when there is more than one alkyl branch of the same kind.

CH3 CH CH CH2 CH2 CH3

CH3

1 2 3 4 5 6

CH3

2,3-dimethylhexane

CH3 CH CH CH2 CH2 CH3

CH31 2 3 4 5 6

CH3

3,3-dimethylhexane

Nomenclature

5. Use previous rules for other types of substituents.

CH3 CH CH CH3

Br

1 2 3 4

NO2

2-bromo-3-nitrobutane

CH2 CH CH CH3

Br

1 2 3 4

NO2

1-bromo-3-nitrobutane

Names of Common Groups

Nomenclature

NomenclatureRules for Naming Alkanes:

1. Names after butane are obtained by adding the suffix –ane to the Greek root for the nyumber of carbon atoms (pent- for five, hex- for six …)

2. For a branched carbon hydrocarbons, the name is given for the longest continuous chain

3. When they are substituents, the –ane is replaced with -yl

4. The positions of substituent groups are specified by numbering the longest chain starting from the closest end.

5. The location and names of each substituent are followed by the root alkane name and they have to be listed in alphabetical order, and the prifix di-, tri- … for multiple.

CH3 CH2 CCH3

HCH2 CH2 C

CH3

CH2

CH2 CH3CH2 CH3

CH3 CCH3

CH3

CH2 CCH3

HCH3

2,2,4-Trimethylpentane

CH3 CH2 CCH3

CH2

CH2 CCH3

CH3CH3 H

1

23456

2,4-dimethyl-4-ethylhexane

What is the IUPAC name of the following compound?

1 2 3 4 5 6 7 8CH3 CH CH2 CH CH2 CH2 CH3

C2H5

CH2

CH3

Questions

What is the structure of 2-propyl-4-methylhexane?

Alkane Reactions

CH4 (g) + 2O2 (g) CO2 (g) + 2H2O (l) ∆H0 = -890.4 kJ

Alkanes are fairly uncreative, but at sufficient high temperature react vigorously and exothermically with oxygen

CH4 (g) + Cl2 (g) CH3Cl (g) + HCl (g)light

Cl2 + energy Cl• + Cl•

Cl• + C HH

H

H

C H

H

H

• + HCl

CH

H

H

• + Cl Cl C ClH

H

H

+ Cl•

Combustion reaction

Substitution reaction

Freons CFxCl4-x

Substitution reactionFormation of unsaturated hydrocarbons

CH3CH3 CH2=CH2+H2Using Cr2O3 at high temperature

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

22.2 Alkene and AlkyneAlkene have the general formula CnH2n where n = 2,3,…

• contain at least one carbon-carbon double bond and the systematic names are ethene, propene, …..

CH2 CH CH2 CH3

1-butene

CH3 CH CH CH3

2-butene

C C

Cl Cl

H H

C C

Cl H

H Clcis-dichloroethylene trans-dichloroethylene

• have restricted rotation around the double bond to produce cis-trans isomerisms

Alkyne

Alkyne have the general formula CnH2n-2 where n = 2,3,4,…

• contain at least one carbon-carbon triple bond and the systematic names are ethyne, propyne, …..

1-butyne 2-butyneCH C CH2 CH3 CH3 C C CH3

Reactions of alkenes and alkynes

Halogenation ReactionsCH2 CH2 (g) + Br2 (g) CH2Br CH2Br (g)

HydrogenationCH CH (g) + H2 (g) CH2 CH2 (g)

PolymerizationSmall molecules are joined together to form large molecules

22.3 Aromatic Hydrocarbons

C

CC

CC

C

H

H

H

H

H

H

C

CC

CC

C

H

H

H

H

H

H

A special class of cyclic unsaturated hydrocarbons

•Benzene is the simplest

•The delocalized p-electronsmake it different thanthe other unsaturated hydrocarbons

•Benzene does not present the addition reactions

Aromatic Compound Nomenclature

CH2CH3

ethylbenzeneCl

chlorobenzene

NH2

aminobenzeneNO2

nitrobenzene

12

34

5

6

Br

Br

1,2-dibromobenzene

Br

Br

1,3-dibromobenzene

Aromatic Compound Reactions

H

H

H

H

HH

Br

H

H

H

HH

+ HBr+ Br2FeBr3

catalyst

H

H

H

H

HH

CH2CH3H

H

H

HH

+ HCl+ CH3CH2ClAlCl3

catalyst

Substitution reaction

Polycyclic Aromatic Hydrocarbons

22.4 Hydrocarbon Derivatives

Hydrocarbons that have additional atoms or groups different than Carbon and hydrogen (functional group)

The common functional groups are….

They exhibit characteristic chemistry

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

C6H12O6 (aq) 2CH3CH2OH (aq) + 2CO2 (g)enzyme

CH2 CH2 (g) + H2O (g) CH3CH2OH (g)H2SO4

Biological production of ethanol

Commercial production of ethanol

Metabolic oxidation of ethanol

CH3CH2OH CH3CHO + H2alcohol dehydrogenase

The systematic name is obtained from parent alkane by removing the final letter –e and adding –ol.

Aldehyde and KetonesThey contain carbonyl functional group.

R C H

O

• Aldehyde have the general formula

R C R’

O

• Ketone have the general formula

H C H

O

H C

O

CH3 C

O

CH3H3C___________ ___________ ___________

The systematic name of aldehyde is obtained from parent alkane by removing the final letter –e and adding –al, and for ketone also by removing the final letter –e and adding –one.

Carboxylic acids and Estersthey contain the carboxyl functional group.

The systematic name is obtained from parent alkane by removing the final letter –e and adding –oic.

CH3COOH + HOCH2CH3 CH3 C O CH2CH3 + H2O

O

ethyl acetate

The esters are formed, if carboxylic acid reacts with alcohol:

The systematic name is obtained from parent alkane by removing the final letter –oic and adding –oate of the acid, e.g., ethyl ethanoate.

AminesThey are organic bases with the general formula RNH2

CH3NH2 + H2O RNH3+ + OH-

CH3CH2NH2 + HCl CH3CH2NH3+Cl-

The common names are often used for simple amines, and the systematic name is obtained by using the name amino for each –NH2 group, e.g., 2-aminobutane

They are used for making dyes and their main reaction is acid-base:

A polymer is a high molar mass molecular compound made up of many repeating chemical units.

Naturally occurring polymers

•Proteins

•Nucleic acids

•Cellulose

•Rubber

Synthetic polymers

•Nylon

•Dacron

•Lucite

22.5 Polymers

The simple repeating unit of a polymer is the monomer.

Homopolymer is a polymer made up of only one type of monomer

( CF2 CF2 )n

Teflon

( CH2 CH2 )n

Polyethylene

( CH2 CH )n

Cl

PVC

R groups on same side of chain

Isotactic

R groups alternate from side to sideSyndiotactic

R groups disposed at random

Atactic

Stereoisomers of Polymers

22.2

Proteins

Amino acids are the basic structural units of proteins. An amino acid is a compound that contains at least one amino group (-NH2) and at least one carboxyl group (-COOH)

+H3N C C N C C O- + H2O

H

R1

H

R2

O O

H

+H3N C C O- + +H3N C C O-H

R1

H

R2

O O

Peptide bond

22.3

22.3

Protein Structure

22.3

Carbon

Nitrogen

Oxygen

R group

Hydrogen

The structure is held in position by intramolecularhydrogen bonds (………)

Protein Structure

22.3

Protein Structure

22.3

Intermolecular Forces in a Protein Molecule

ionic forces

ionic forces

hydrogenbonds dispersion

forces

dispersionforces

dispersionforces

dipole-dipoleforces

Hydrogen Bonds in Parallel and Antiparallel β-pleated Sheets

22.3

Protein Structure

22.3

The structural changes that occur when oxygen binds to the heme group in hemoglobin.

Nucleic Acids

Nucleic acids are high molar mass polymers that play an essential role in protein synthesis.

1. Deoxyribonucleic acid (DNA)

2. Ribonucleic acid (RNA)

DNA molecule has 2 helical strands. Each strand is made up of nucleotides.

22.4

The Components of the Nucleic Acids DNA and RNA

22.4

Base-Pair Formation by Adenine and Thymine and by Cytosine and Guanine

22.4

Chemistry In Action: DNA Fingerprinting

22.4