chapter 22. organic and biological...

Chapter 22. Organic and Biological Molecules

Substances - Organic substances

- Inorganic substabces

Produced by living systems

1828 Friedrich Wöhler NH4OCN H2N C NH2

O

Heat

Ammonium Cyanate

Urea

Organic chemistry : The study of carbon-containing compounds and their properties.

Alkanes: Saturated Hydrocarbons

Hydrocarbons: compounds composed of carbon and hydrogen

Saturated hydrocarbon: carbon-carbon bonds are all single - alkanes

Unsaturated hydrocarbon: contains carbon-carbon multiple bonds - alkenes and alkynes.

CH C C

H

H

HH

H

CH C C

H

H

HC

H

C

H

H

HH

H

Alkanes

methane ethane

propane butaneC

H

H H

H

H

C

HH

H

C

H

C

H

C

HH

H H

H

H

C

H

C

H

C

HH

H C

H

H

H

H

H

C

H

C

H

H

HH

H

All C atoms have sp3 hybrides.

C

H

C

H

C

HH

H H

H

Hn

H3C CH2 CH3n≡

methylene

Alkanes: Saturated Hydrocarbons

AlkanesC

H

C

H

C

HH

H H

H

Hn

H3C CH2 CH3n≡

methylene

CnH2n+2

Alkanes: Saturated Hydrocarbons

Isomerism of Alkanes

Alkanes with more than 3 carbons (from butane) exhibit structural isomerism.

C

C CC

H

H

H

HH H

H

H

H

H

Butane≡ ≡

≡

≡ ≡ ≡

CH3

CH2

CH2

CH3CH3 CH2 CH2 CH3

CH3

CH

CH3

CH3CH3

CH CH3CH3

normal butane (n-butane)

isobutane

Pentane CH3 CH2 CH2 CH2 CH3

CH3 C CH3

CH3

CH3

CH2 CH CH3

CH3

CH3normal pentane (n-pentane)

isopentane

neopentane

H C C C C H

H

H

H

H

H

H

H

H

Alkanes: Saturated Hydrocarbons

Nomenclatures

1. For alkanes beyond butane, add -ane to the

Greek root for the number of carbons.

pentane hexane

heptane

2. For a branched hydrocarbon, longest continuous

chain of carbon atoms determines the root name.

CH3 CH2 CH CH2 CH3

CH2

CH2

CH3

six carbons => hexane

3. When alkane groups (alkyl) appears as substituents:

drop the -ane and add -yl.

4. Positions of substituent groups are specified by

numbering the longest chain sequentially. Location

and name of substituent are followed by root alkane

name.

CH2 CH2 CH CH2 CH3

C2H5

CH3

125 36 4

652 41 3

3-ethylhexane

5. For more than one substituents,

list substituents alphabetically.

And the prefix di-, tri-, .. are used

for multiple, identical substituents.

CH2 CH2 CH CH2 CH3

C2H5

CH3

C2H5

3,3-diethylhexane

Alkanes: Saturated Hydrocarbons

Nomenclatures

Ex) Draw the structural isomers for the alkane C6H14 and give the systematic name for each one.

hexane

2-methylpentane

3-methylpentane

2,3-dimethylbutane

2,2-dimethylbutane

Ex) Determine the structures of

a. 4-ethyl-3,5-dimethylnonane

b.4-tert-butylheptane

Alkanes: Saturated Hydrocarbons

Reaction of Alkanes

Alkanes are saturated so that they are not much reactive. => lubricating materials, plastics

Substitution reaction

CH4 + Cl2 → CH3Cl + HCl

CH3Cl + Cl2 → CH2Cl2 + HCl

CH2Cl2 + Cl2 → CHCl3 + HCl

CHCl3 + Cl2 → CCl4 + HCl

Chloromethane

Dichloromethane

Trichloromethane

(chloroform)

Tetrachloromethane

(carbon tetrachloride)

hn

hn

hn

hn

Cl2 → Cl· + Cl·hn

Combustion reaction

2C4H10(g) + 13O2(g) → 8CO2(g) + 10H2O(g)

butane

propane

Dehydrogenation reaction

CH3CH3 → CH2=CH2 + H2

Cr2O3

500 oC

Alkanes: Saturated Hydrocarbons

Cyclic Alkanes

Carbon atoms can form rings containing only carbon-carbon single bonds

cyclopropane

60o 88o

cyclopropane cyclobutane

weak and strained : reactive

cyclopentane cyclohexane

tetrahedral angles: stablecyclohexane

more stable

12

5 3

6

4

1-isopropyl-3-methylcyclohexane 1-ethyl-2-propylcyclobutane13

4 2

substituents: alphabetical order

Alkenes and Alkynes

Alkenes: hydrocarbons that contain at least one carbon-carbon double bond.

H

C C

H

H

H

ethene ethane

1. Root hydrocarbon name ends in -ene

Nomenclatures

2. With more than 3 carbons, double bond is indicated by the lowest numbered carbon atom in the bond.

C C

CH3

H

H

H

propene

C C

H

H

CH2

H

CH3

1-butene cis-2-butene trans-2-butene

Alkenes and Alkynes

Alkynes: hydrocarbons that contain at least one carbon-carbon triple bond.

C C HH

ethyne

(acetylene)

1. Root hydrocarbon name ends in -yne

Nomenclatures

2. With more than 3 carbons, triple bond is indicated by the lowest numbered carbon atom in the bond.

HC C CH3 HC C CH2 CH3 H3C C C CH3

propyne 1-butyne 2-butyne

CH3

CH CH

CH3

CHC2H5

CH3

C C CH

CH2 CH3

CH2 CH3

CH2

CH3

cyclohexene 4-methylecyclopentene 4-methyl-trans-2-hexene 5-ethyl-3-heptyne

Alkenes and Alkynes

Reactions of Alkenes and Alkynes

Unsaturated hydrocarbons => addition reaction in which (weaker) p bonds are broken and

new (stronger) s bonds are formed to atoms being added

Hydrogenation reaction

CH2=CHCH3 + H2 → CH3CH2CH3

Catalyst/Pt, Pd, Ni

1. Adsorption and activation of the reactants.

2. Migration of the adsorbed reactants on the surface.

3. Reaction of the adsorbed substances.

4. Escape, or desorption, of the products.

Step for heterogeneous catalysis weakening the H-H bond,

or reducing the activation

energy

Halogenation reaction

CH2=CHCH2CH2CH3 + Br2 → CH2BrCHBrCH2CH2CH3

Chapter 12.

Polymerization

Aromatic Hydrocarbons

Aromatic hydrocarbons: a special class of cyclic unsaturated hydrocarbons.

Benzene (C6H6)

Reactions: No addition reaction but substitution reaction

+ Cl2 →

Cl

+ HCl

+ HNO3 →

+ CH3Cl →

NO2

CH3

+ H2O

+ HCl

Chlorobenzene

Nitrobenzene

Toluene

Aromatic HydrocarbonsNomemclatures

12

5 3

6

4

1,2-dichlorobenzene

Cl

Cl

Cl

Cl

o = ortho

m = meta

p = parao

m m

o

p

o-dichlorobenzene

Hydrocarbon DerivativesHydrocarbon derivatives : Hydrocarbons having additional atoms or groups of atoms,

called functional groups.

Hydrocarbon DerivativesAlcohols

Functional group : -OH R C

H

H

OH C

R

R'

H

OH C

R

R'

R"

OH

primary alcohol secondary alcohol tertiary alcohol

Nomenclature : -ol

CO + 2H2 → CH3OH

400oC

ZnO/Cr2O3

(methanol : wood alcohol, starting material for higher order organic compounds)

C6H12O6 → 2CH3CH2OH + 2CO2

yeast

glucose ethanol

Hydrocarbon DerivativesAlcohols

C6H12O6 → 2CH3CH2OH + 2CO2

yeast

glucose

CH2=CH2 + H2O → CH3CH2OH

catalyst

1,2-ethanediol (ethylene glycol)

HO-CH2-CH2-OH

Polyhydroxyl (poly-ol)

Aromatic alcohol

OH

phenol

OH

Ex) name and primary, secondary, tertiary ?

OH

Br

Cl OH

2-butanol (seconary alcohol)

6-bromo-2-methyl-2-hexanol (tertiary)

3-chloro-1-propanol (primary)

Hydrocarbon DerivativesAldehydes and Ketons

Synthesis : oxidation of alcohol

OH

ox

H

O

primary aldehyde

ox

OOH

secondary ketone

CH

O

O

CH3

OH

CH CH

CH

O

Vanillin

Cinnamaldehyde

Functional group :

Nomenclature : -al -one

R

C

H

O

R

C

R'

OCarbonyl group

pleasant or unpleasant odor

(aldehyde)

Hydrocarbon DerivativesCarboxylic Acids and Esters

Functional group :

Nomenclature : -ic acid -ate

Carboxyl group

R

C

O

OH R

C

O

O

R'

Synthesis of carboxylic acids :

oxidation of primary alcohol with

strong oxidant

OH

O

OH

KMnO4(aq)

Synthesis of esters : carboxylic acid + alcohol

O

OH H O O

O

ethyl acetate

+ H2O

O

OH

OHOH

O

+ H2O

O

OH

O

O

salicylic acid aspirin

O

O

n-amyl acetate (n-pentyl acetate)

O

O

n-octyl acetate

sweet odor

(ester)

Hydrocarbon DerivativesAmines

Functional group : -NR2 (R=H, R, R')

R C

H

H

OH C

R

R'

H

OH C

R

R'

R"

OH

primary alcohol secondary alcohol tertiary alcohol

Nomenclature : amine.

For complex molecules amino

as a substituent

NH2

2-aminobutane

Bad "really bad" odor (amine)

F F

PolymersPolymers: large, usually chainlike molecules that are built from small molecules called monomers.

polyester

nylon

N CH2 N C

H H O

CH2 C

O

n6 4

Natural Polymers

The Characteristics of living Organisms

• Structurally complicated and highly organized -Intricate internal structure

• Extract, transform, and use energy from their environments

• The capacity for precise self replication and self assembly

Molecular logic of life

• Diverse living organisms share common chemical features.

• The same basic structural units (cells)

• The same kinds of macromolecules (DNA, RNA, proteins)

• Made up of the same kinds of monomeric subunits (nucleotides, amino acids)

Nucleaic Acids

Natural Polymers

Carbohydrates

Proteins

The players of life

The playground

Natural PolymersProteins: Natural polymers made up of a-amino acids (molecular weight from 6000 to >1,000,000 g/mol

Fibrous Proteins: provide structural integrity and strength to muscle, hair and cartilage

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

H

N

H

C

H

R OH

O

a-carbon

side chain

Amino acids

carboxyl groupamino group

H

N

H

C

H

R OH

O H

N

H

C

H

R' OH

O

H2N C

H

R

C

O

N

H

C

R'

H

COOH

+ H2O

dipeptide

peptide linkage

polypeptide

protein

Natural Polymers

Amino acidsProteins

a-helix

Natural PolymersProteins

1 2 3 4 5 6

H2N COOHLevels of protein structures

Primary: Sequence of amino acids in the protein chain.

C O H N

Secondary: Highly regular sub-structures- a-helix and strands of b-sheet. Secondary structures are locally defined,

meaning that there can be many different secondary motifs present in one single protein molecule (hydrogen

bonding determines this).

b-turnrandom-coil arrangement

b-sheet

Natural PolymersProteins

Levels of protein structures

Tertiary: The overall shape of the protein (determined by hydrogen-bonding, dipole-dipole interactions,

ionic bonds, covalent bonds and London forces).

ionic hydrogen covalent London dipole-dipole

Quaternary structure: complex of several protein molecules or

polypeptide chains, usually called protein subunits in this context, which

function as part of the larger assembly or protein complex.

Natural PolymersProteins

The tremendous flexibility in the various levels of protein structure alls the tailoring of proteins for a wide

range of specific functions. Proteins are the "work-horse" molecules of living orgams.

Denaturation: Breaking-down of three dimensional structure of a protein

Heat

UV

X-ray

Nuclear radio acivity

Natural PolymersCarbohydrates

Food source for most organisms and structural material for plants

Empirical formula = CH2O

containing the functional groups of ketone at 2 position (or aldehyde at 1 position) and alcohols

Monosaccharides (simple sugars) :

Triose (3 carbons), Tetrose (4 carbons), Pentose (5 carbons), Hexose (6 carbons).......

enantiomers

chiral center

CHO

C OHH

C OHH

C OHH

CH2OH

CHO

C OHH

C OHH

C OHH

CH2OH

three chiral carbons => 8 optical isomers

CH2OH

C O

C OHH

C OHH

CH2OH

C

C OH

C OHH

C OHH

CH2OH

O

H

H

aldopentoseketopentose

CHO

C OHH

C OHH

C OHH

CH2OH

Ex) How many chiral carbon in the following aldopentose?

ketopentose => two chiral catbons => 4 optical isomers

pentose => two structural isomers (aldo and keto) => 12 optical isomers

Cyclization of D-fructose

Cyclization of D-glucose →

Natural PolymersCarbohydrates

C5H10O5

C6H12O6

Cyclization of Monosaccharides: monosaccharides

usually form a ring structure in aqueous soultion

Natural PolymersCarbohydrates

Dimerization of Monosaccharides: disaccharides

+H2O

-H2O

Polymerization of Monosaccharides: polyisaccharides

a-D-Glucose

=>

b-D-Glucose

=>

Starch

Cellulose

amylose (chain)

amylopectin

(branch)

Natural PolymersNucleic Acids

DNA (deoxyribonucleic acid): stores and transmits genetic information, responsible (with RNA) for protein synthesis. (Molar mass = several billion)

RNA (ribonucleic acid): helps in protein synthesis. (Molecular weight = 20,000 to 40,000)

Monomeric unit of nucleic acids: nucleotides

3. Phosporic acids (H3PO4)

2. N-containing Organic bases

Ribose (a pentose)

1. Deoxyribose for DNA and ribose for RNA

Polymerization of Nucleotides

Forming of Nucleotides

nucleoside

nucleotide

Nucleic Acids

CH2

CH2

Base

O

HO

HH

HH

O

PO

OH

OH

Base

O

HOH

HH

HH

O

PO

OH

OH

H

Dimerization of Nucleotides

H2O

Base

O

HO

HH

H

CH2

H

O

PO

OH

OH

Base

O

HOH

HH

H

CH2

H

O

PO OH

Natural Polymers

Natural PolymersNucleic Acids

Structure of DNA: Double-helical structure with complimentary based on the two strands

Cell division and transmission of genetic information

Natural PolymersNucleic Acids

Synthesis of proteins

mRNA (messenger RNA)

rRNA (ribosomal RNA)

Ribosome = complex of rRNA and proteins

Gene : A part of DNA which will be

expressed into a protein.

Natural PolymersNucleic Acids

Synthesis of proteinstRNA (transfer RNA)

김성호

1970's

Natural PolymersNucleic Acids

Synthesis of proteins2006 Nobel Prize in Chemistry

Roger Kornberg (2006)Arthur Kornberg (1959)

ChemistryPhysiology and Medicine

Why do we have to study Chemistry?

Chemical Bonding

Diversity in the Universe

creates

Chemical Bonding

Why do we have to study Chemistry?

We

Diversity in the Universe

understand

Why do we have to study Chemistry?

We

Diversity in the Universe

create

Why do we have to study Chemistry?

For Better Life

Good Luck for Your Finals !