Organic Chemistry

Chao-Tsen Chen

National Taiwan UniversityChemistry Department

Bioorganic Chemistry Lab.

IIIB IVB

9VB VIB VIIB

H He

VIIIBIB IIB

IA VIIIAIIA

IIIA IVA VA VIAVIIA

Li

Na

Rb

K

Cs

Fr

Ne

Kr

Rn

Ar

Xe

CSiPeriodic Table

Definition of Organic Definition of Organic ChemistryChemistry

Study of carbonStudy of carbon--containing compounds and containing compounds and their propertiestheir propertiesOriginally, organic substances are the products Originally, organic substances are the products produced by living systems.produced by living systems.In 1828, the experiment performed by German In 1828, the experiment performed by German chemist Friedrich chemist Friedrich WWööhlerhler revolutionizes the revolutionizes the concept of organic substances. concept of organic substances.

NH4OCNHeat

H2N CO

NH2

UreaAmmonium cyanate

Importance of Organic ChemistryImportance of Organic Chemistry

I) Understand living systems

II) Provide necessity in the modern life such as synthetic fibers, plastics, drug, and artificial sweeteners

III) Supply energy to power civilization Organic materials found in coal and petroleum

Contents :1. Alkanes: Saturated Hydrocarbons

H1s

H1s

H1s

H1ssp3 sp3

sp3

sp3

C

Contents :

2. Alkenes and Alkynes

C C

2p

H1s H1s

sp2

sp2

sp2sp2

sp2

sp2

3. Aromatic Hydrocarbons

Benzene Naphthalene Anthracene

Fullerene (C60)

4. Hydrocarbon Derivatives

Functional GroupC, H +

R OH

R O R'

R CO

H

R CO

O H

Alcohols

Ethers

Aldehydes

Carboxylic Acids

5. Polymers

α-amino acids polypeptide

Proteins

6. Natural PolymersMonomer Polymer

polymerization

DNA

1. Alkanes: Saturated Hydrocarbons

Methane Ethane Propane Butane

C CH

H H

H+ H2 H C

H

HCH

HH

Unsaturated Saturated

CH

HH H

C CH

HH

H

HH C

CC

H

HH

H HH

H HC

CC

CHH

H

H H

H H

HHH

sp3 hybridization

1. Alkanes: Saturated Hydrocarbons

Methane Ethane Propane Butane

109.5o

C CH

H H

H+ H2 H C

H

HCH

HH

Unsaturated Saturated

Not really straight but Zig-Zag

75174-30142C10H22Decane35151-54128C9H20Nonane18126-57114C8H18Octane998-91100C7H16Heptane568-9586C6H14Hexane336-13072C5H12Pentane20-13858C4H10Butane1-42-18744C3H8Propane 1-89-18330C2H6Ethane 1-162-18216CH4Methane

Number of Structural Isomers

Boiling Point (℃)

Melting Point (℃)

Molar MassFormulaName

Table 22.1 Selected Properties of the First Ten Normal Alkane

CH2 CH3CH3

General formula for alkanes:

nCnH2n+2 (normal; straight-chain; unbranched hydrocarbon)

Isomerism in Alkanes

CC

CCH

HH

H H

H H

HHH C

C

C C

H HH

HH

HHH

HH

n-butane isobutane

Structural/Constitutional Isomers

Different chemical and physical properties

Example 1.Draw the isomers of pentane

Penta = 5 n = 5 C5H(2x5)+2C5H12

n-Pentane Isopentane Neopentane

Nomenclature (IUPAC)1. The longest continuous chain of carbon

atoms determines the root name for the compound.

2. When alkane groups appear as substitue-nts, they are named by dropping the -ane and adding –yl.

3. The positions of substituent groups are specified by numbering the longest chainof carbon atoms sequentially, staring at the end closest to the branching.

4. The location and name of each substitue-nt are followed by the root alkane name.

The substituents are listed in alphabetical order.

Location + substituent + root alkane name

International UnionPure and Applied Chemistry

Structure NameCH3

CH2CH3

CH2CH2CH3

CHCH3CH3

CH2CH2CH2CH3

CHCH2CH3CH3

HC CH3CH3

H2C

CH3C CH3CH3

Methyl

Ethyl

Propyl

Isopropyl

Butyl

sec-Butyl

Isobutyl

tert-Butyl

CH3CH2CH2CHH2C CH2H3C CH3

six carbon

five carbon

H3C CH2 CHCH3

CH2 CH2 CH31 2 3 4 5 6

123456Correct

Incorrect

H3C CH CHCl

CH2 CH2 CH3

CH3

1 2 3 4 5 63-chloro-2-methylhexane

H3C CH CHCH3

CH CH2 CH3

CH3

1 2 3 4 5 6

CH3

2,3,4-trimethylhexane

Example 2.Draw the isomers for C6H14 and give the systematicName for each one.

12

2

2

2

211

11

3

3

3 3

34

4

4

44

5

5

56

Hexane

2

methyl

pentane2-Methyl

3

pentane

methyl

3-Methyl

butane2,3-Dimethyl

32

butane2,2-Dimethyl

2

CH4 + Cl2 CH3Cl + HCl

CHCl3 + Cl2 CCl4 + HCl

CH3Cl + Cl2 CH2Cl2 + HCl

CH2Cl2 + Cl2 CHCl3 + HCl

Reactions of Alkanes1. Combustion reactions

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

2. Substitution reactionshv

hv

hv

hv

Chloromethane

Dichloromethane

Trichloromethane(chloroform)

Tetrachloromethane(carbon tetrachloride)

Cl2 Cl Clhv

Free radical

(methylene chloride)

FreonsFreons

CFCFxxClCl44--x x chlorofluorocarbons (CFCs)chlorofluorocarbons (CFCs)

Unreactive

Coolant fluids in refrigerators and air conditioners

Environment Threats (Ozone layer damage)

3. Dehydrogenation reactions

+ H2CH2CH2CH3CH3Ethylene

Cr2O3

500oC

Cyclic Alkanes CnH2n

Cyclopropane Cyclobutane Cyclopentane Cyclohexane

very unstable!quite reactive!

stable!

C C

C

60o

109.5o

No "head-on"overlap of atomic orbitals

H HHH

These two Hatoms repeleach other

Boat

(Chair form)

Cyclic Alkanes CnH2n

Cyclopropane Cyclobutane Cyclopentane

Nomenclature for Nomenclature for cycloalkanecycloalkane

CH CH3H3C

CH3

1-isopropyl-3-methylcyclhexane

not 1-methyl-3-isopropylcyclohexanenot 3-methyl-1-isopropylcyclohexane

not 1-isopropyl-5-methylcyclohexane

1 2345

61

2

34

56

CH2CH3

CH2CH2CH3

1-ethyl-2-propylcyclobutane

23 14

Alkenes and Alkynes

C CH

H H

H

CnH2n CnH2n-2

C CH H

Ethylene (C2H4) Ethyne (C2H2) (acetylene)

CH2 CH CH3CH2 CH CH2CH3CH2 CH CH2CH2CH3CH2 CH CH2CH2CH2CH3

propenebutene

pentenehexene

propynebutyne

CH C CH3CH C CH2CH3CH C CH2CH2CH3CH C CH2CH2CH2CH3

pentynehexyne

C C

2p

H1s H1s

sp2

sp2

sp2sp2sp2

sp2 C CH H

sp 2p

2p sp

2p2p

sp

2p2p

2pH1s H1s2p

Stereoisomers of alkenes

cis-2-buteneCH3

H3C H

H

H3C CH3

H Htrans-2-butene

Cyclic alkenes(1)-Cyclohexene 4-Methyl-(1)-cyclopentene

12

34

5

Nomenclature for alkenes and Nomenclature for alkenes and alkynealkyne

H CH3

HCHCH3

H3CH2C

1

23456

4-methyl-trans-2-hexene

C CH3CH2C CHCH2CH3CH2CH3

1 2 3 4 5 6 7

1234567

5-methyl-3-heptyne or 5-methyl-hept-3-ynenot 3-methyl-4-heptyne

Alkene

Alkyne

CH2

CH2BrCHBrCH2CH2CH3

CHCH2CH2CH3 + Br21 2 3 4 5

1 2 3 4 5

Reactions of Alkenes and Alkynes

Addition reactions :I. Hydrogenation reactions

II. Halogenation reactions

CH2 CHCH3 + H2 CH2CHCH3

H H1-Propene

Catalyst

Propane

1-Pentene

1,2-Dibromopentane

(Pt or Pd or Ni)

III. Polymerization

Aromatic HydrocarbonsBenzene

C

CC

C

CC

H

H

H

H

H

H120O120O

120O

Reactions of Aromatic HydrocarbonsCl

+ Cl2 + HCl

NO2

+ HNO3 + H2O

FeCl3

H2SO4

Nitrobenzene

Chlorobenzene

CH3

+ CH3Cl + HCl

more like substitutionreaction!!

AlCl3

Nomenclature of Benzene DerivativesNomenclature of Benzene Derivatives

Benzene

Br1

2

34

5

6

(1)-Bromobenzene

12

34

5

6

CH3

(1)-Methylbenzene (Toluene)

Disubstituted1,2-disbustituted: Ortho-1,3-disbustituted: Meta-1,4-disbustituted: Para-

123

45

6

BrBr

1,2-dibromobenzne(o-dibromobenzene)

1

45

6 2

3

Br

Br

1,3-dibromobenzne(m-dibromobenzene)

1

45

6 2

3

Br

Br1,4-dibromobenzne(p-dibromobenzene)

3-Iodotoluene(m-Iodotoluene)

123

45

6

CH3

I

12

3

45

6

NO2

Cl

3-Chloronitrobenzene(m-nitrobenzene)

Nomenclature of Benzene Nomenclature of Benzene DerivativesDerivatives

CHCH2CHCH2CH32 3 4 5 61

H3C

Cl23456 1

Phenyl 4-Chloro-2-phenylhexane not 3-Chloro-5-phenylhexane

Nomenclature of Nomenclature of PolyaromaticsPolyaromatics

Naphthalene Anthracene Phenanthrene

Pyrene3,4-Benzpyrene

Polyaromatic Hydrocarbon (PAH): Carcinogen

Hydrocarbon DerivativesThe Common Functional Groups

CH3NH2 Aminomethane(methylamine)

Amines

CH3COOCH2CH3 Ethyl acetateEsters

CH3COOH Ethanoic acid(acetic acid)

Carboxylic acids

CH3COCH3 Propanone(dimethyl ketone)

Ketones

CH2O Methanal(formaldehyde)

Aldehydes

CH3OCH3 Dimethyl etherEthers

CH3OH Methanol(methyl alcohol)

Alcohols

CH3I Iodomenthane(methyl Iodide)

Halohydrocarbons X(F, Cl, Br, I)

OH

O

CO

H

CO

C OHO

CO

O

NH2

R OH

R O R'

R CO

H

R CO

R'

R CO

OH

R CO

O R'

R NH2

R X

(hydroxyl)

(amino)

(carboxyl)

Nomenclature for AlcoholsNomenclature for Alcohols

H3C CHCH2CH3OH

1 2 3 4

1234

ClCH2CH2CH2OH123

1 2 3

CH3CCH2CH2CH2CH2BrCH3

OH

1 2 3 4 5 6

123456

2-Butanol

3-Chloropropan-(1)-ol

6-Bromo-2-methyl-2-hexanolOr 6-Bromo-2-methyl-hexan-2-olNot 1-Bromo-5-methyl-5-hexanol

Not (1)-chloro-3-propanolNot (1)-chloro-propan-3-ol

RH2C CH2OH12 CHOH

R

R'R' COH

R

R''Primary alcohol (1o)(one R group)

Secondary alcohol (2o)(two R groups) Tertiary alcohol (3o)

(three R groups)

Alcohols (higher boiling and melting points)

CO + 2H2 CH3OH

C6H12O6 2CH3CH2OH + 2CO2

CH2 CH2 + H2O CH3CH2OH

400oC

ZnO/Cr2O3

Yeast

Glucose Ethanol

AcidCatalyst

Polyhydroxyl

H2C OHH2C OH

1,2-ethanediol (ethylene glycol)

OH

phenol

Aromatic Alcohols

Methanol (wood alcohol)

Preparation

Aldehydes and Ketones

R CO

H R CO

R'CO

CO

Aldehyde Ketone

CarbonylGroup

CH3CH2OH CH3CO

HPrimary alcohol

Oxidation Aldehyde

CH3CHCH3OH

CH3CCH3

O

Oxidation Ketone

Secondary alcohol

Preparation

CO

H H

CO

H3C H

Methanal(Formaldehyde)

Ethanal(Acetaldehyde)

CO

H3C CH3 Propanone(Acetone)

Nomenclature for Nomenclature for AldehydesAldehydesand and KetonesKetonesAldehydesAldehydes ((--ee -al)

KetonesKetones ((--ee -one)

CO

H3CHCH2C HCl

1234

3-Chlorobutanal

OH

Benzenecarbaldehyde(Benzaldehyde)

OH

OHOCH3

CO

H

Vanillin

Cinnamaldehyde

CO

H3CH2C CH31234

1 2 3 4

2-Butanone

OH3C

Methyl phenyl ketone(Acetophenone)

(methyl ethyl ketone)

Carboxylic Acids and Their Nomenclature

Oxidation

KMnO4(aq)Primary Alcohol Carboxylic acidCH3CH2OH CH3COOH

R CO

O HCarboxylic acids Carboxyl group

((--ee oic acid)Carboxylic acid

234 1CH3CH2CH2C

O

OHButanoic acid

CH3CHCH2CH2CO

OH

5 234 1

Br4-Bromopentanoic acid

CO

C OHCl

ClCl

Trichloroethanoic acid

O OH

Benzoic acid

R CO

O H

Esters and Their NomenclatureEsters and Their Nomenclature

CH3CO

OH OCH2CH3H+ CH3CO

OCH2CH3 + H2OCarboxylic acid Alcohol Ester

R CO

O R'Carboxylic acids + Alcohol

Nomenclature (-oic acid oate): alcohol + acid

CO

H3C OC8H17CO

H3C OCH2CH2CH2CH2CH3

Pentyl ethanoate (n-amyl acetate) Octyl ethanoate (n-octyl acetate)

Salicylic acid Acetic acid Acetylsalicylic acidAspirin (painkiller)

O H

OO H

CCH3O

H O O

OO H

CCH3O

++ H2O

Secondary(N,N)-Diphenylamine

PrimaryAniline

TertiaryTrimethylamine(CH3)3N

SecondaryDimethylamine(CH3)2NH

PrimaryEthylamineCH3CH2NH2

PrimaryMethylamineCH3NH2

TypeCommon NameFormula

Table Some Common Amines

H2N

NH

Amines

Primary amine (1o) Secondary amine (2o) Tertiary amine (3o)

R NH

HR N

R'

HR N

R'

R''H N

H

HAmmonia

NH2Amino-

CH3CHCH2CH32 3 41

NH2

2-aminobutane

Synthetic Polymers

Monomer

Polymerize

Thermoset Polymer

Thermoplastic Polymer

Material Product

Material Product

mold

mold

heat

Linear PolymersCross-linked Polymers

HomopolymerCopolymer

Diblock PolymerTriblock Polymers

C CH

H H

HH C C

O

H H

HHOH

C CH

H H

HH C C

O

H H

HCH

HCH

HH

C CH

H H

H

H C CO

H H

HCH

HH

HCH

H n

Addition Polymerization

Condensation Polymerization

Free radical

NH

HN

H

H H OC

OC

O

O HCH2 N

H

HC

O

O HCH2CH2 N C

H O+ H2O

NH

* CO

*CH2CH2 N CH O

CH2 6 4 6 4

6 4 n

Condensation

nylon

homopolymer

copolymer

Polyethylene (PE)

Dimer

(initiation, propagation, termination)

Polymers Based on Ethylene(Thermoplastic material)

Low density polyethylene (LDPE): contain many branches

High density polyethylene (HDPE): contain mostly straight-chain

1) Manufactured under conditions of high pressure and high temperature

2) Lower reaction pressures and temperatures have become possible throughthe use of catalysts

Ex: Triethylaluminum, Al(C2H5)3 /titanium(IV) chloride (Ziegler/Natta Catalyst)Chromium(III) oxide (Cr2O3) and aluminosilicate (linear low density PE)

Factors governing the properties of polymers1) Molecular Weight of Polymers2) Chemical Structure of Monomer

CH

CH

H X X = CH3, CN, Cl, Phenyl,…….

Some Common Synthetic Polymer

Synthetic rubberStyrene-butadie-ne rubber (SBR)

Butadiene& styrene

Tire tread, coating resin

Polybutadiene(PBD)

Butadiene

Containers, thermal insulations, toys

Polystyrene(PS)

Styrene

Cooking utensils, electrical insulation, bearings

TeflonTetrafluor-oethylene

Carpets, fabricsPolyacryloni-trile (PAN)

Acrylonitrile

Piping, siding, floor tile, clothing, toys

Polyvinyl chlo-ride (PVC)

Vinylchloride

Film for packaging, carpets, lab wares, toys

Polypropylene(PP)

Propylene

Plastic piping, bottles, electrical insulation, toys

Polyethylene(PE)

Ethylene

UsesPolymerMonomerH2C CH2

H2C CCH3

H

H2C CCl

H

H2C CCN

H

F2C CF2

C CH

CH2

HH2C

(See above)

CH

CH2

CH2* *nCH2

CH2* *nCHCH3

CH2* *nCHCl

CH2* *nCHCN

CF2* *nCF2

CH2* *nCH

CH2CH CHCH2 *n*

CH2CH CHCH2 *nCH2* CH

CH

CH

H CN CCH H

HH

C CHH

C CH

H

H

Acrylonitrile-Butadiene-Styrene (ABS) coploymer

+ +Acrylonitrile Butadiene Styrene

CH2 CHCN

CH2 CH CH2 CHCHH2C

n

Polypropylene (PP)

CH

CHH CH3Propylene

CH2 CHCH3

CH2 CHCH3n

Isotactic Chain

Syndiotactic Chain

Atactic Chain

H

H H H H H H H

CH3

H

CH3 CH3

H H

CH3

H

CH3

H

CH3

H

CH3

H

H H H H H H

H

H H H H H H H

CH3

H

H CH3

H H

H

H

CH3

H

H

H

CH3

H

H3C H H3C H H3C H

Nylon can be carried outat the interface

dissolved in H2OHexamethylenediamine

C C4

CH2

OCl

OCl

dissolved in CCl4Adipic chloride

H2N NH26CH2

Preparation of Nylon

Dacron (polyester)

CCOO

OOCH2CH2 n

-H2OCCOO

HO OHHOCH2CH2O H

Ethylene glycol p-terephthalic acid

Natural Polymers

I. Proteins (Fibrous/Globular)

N CH

RC

O

OHH

H

α-carbonamino group carboxyl group

α-amino acids

(starch, hair, silicate chain in soil and rock, silk and cotton fiber, and the cellulose in woody plants)

N CH

RC

O

OHH

HN C

H

R'C

O

OHH

HN C

H

RC

H

H ONH

CH

R'C

O

OH+ H2O

CO

NH dipeptide

Peptide linkage

N CH

RCO

NH

CH

R'CO

NH

CH

CH

R''

O

Side Chain: Hydrophilic v.s. Hydrophobic

polypeptide(protein)

* Chiral carbon atoms

CC

OH

C OH H

OH HH

CC

O H

CO HH

O HHH

D-form L-formGlyceraldehyde

a a

a a

C C

C C

d d

dd

b

b

b

bcc

c

c

Mirror

NonpolarR group

Polar Rgroup

H2N CHCH

OHO

H2N CHCCH3

OHO

HN

C OHO

H2N CHCCH2

OHO

H2N CHCCH

OHO

CH3CH2CH3

H2N CHCCH2

OHO

HN

H2N CHCCH2

OHO

CH2SCH3

H2N CHCCH2

OHO

CHCH3CH3

H2N CHCCH

OHO

CH3CH3

H2N CHCCH2

OHO

OH

H2N CHCCH2

OHO

CH2CNH2

O

H2N CHCCH2

OHO

OH

H2N CHCCH2

OHO

NNHH2N CHC

CH2

OHO

CNH2

O H2N CHCCH

OHO

OHCH3

H2N CHCCH2

OHO

COH

O

H2N CHCCH2

OHO

SH

H2N CHCCH2

OHO

CH2COH

O

H2N CHCCH2

OHO

CH2CH2CH2NH2

H2N CHCCH2

OHO

CH2CH2NHCNH2

NH

Glycine(Gly)

Alanine(Ala) Proline

(Pro) Phenylalanine(Phe)

Isoleucine(Ile)

Tryptophen(Trp)

Methionine(Met)

Leucine(Leu)

Valine(Val)

Serine(Ser)

Glutamine(Gln) Tyrosine

(Try)

Histidine(His)

Asparagine(Asn)

Threonine(Thr)

Aspartic acid(Asp)

Cysteine(Cys)

Glutamic acid(Glu)

Lysine(Lys) Arginine

(Arg)

(N C)

Primary Structure

Secondary Structure

H2N CHCCH2

O

CH2CH2CH2NH2

NH CHCCH3

ONH CHC

CH2

OHO

CHCH3CH3

Lysine Alanine Leucine

lys-ala-leu

C O H Nδ- δ+

(sequence of amino acids in the protein chain)

(a) cys-tyr-ile-gln-asn-cys-pro-leu-gly

(b) cys-tyr-phe-gln-asn-cys-pro-arg-gly

Carbon

Nitrogen

α-helixIntrachainH-Bonding

Collagen Pleated-sheet

Secondary Structure

(found in silk fibers)

InterchainH-Bonding

Tertiary Structure

myoglobin

N HHH

CO

O

Ionic Interaction

O

CO

H

Hydrogen bonding

S

S

Covalent bonding

C

C

H

HHH

HH

London dispersion

C

C

HH

O H

HH

OH

Dipole-dipole interaction

(Disulfide linkage)

Denaturation of Proteins

S SS S

S SSS

SH SHSH SH

SH SHSH SH

SH SHSH SH

SH SHSH SH

S SS

S SSS S

Reduction

Chain Shift

Oxidation

Thermal or H+ or OH-

Carbohydrates:

9876543

Number of Carbon Atoms

NonoseOctoseHeptoseHexosePentoseTetroseTriose

General Name of Sugar

CnH2nOncarbon hydrate

Monosaccharides; Disaccharides;Oligosaccharides; Polysaccharides

Polyhydroxy Ketose (Ketose)/Polyhydroxy Aldehyde (Aldose)

CHOOHHHHOOHHOHH

CH2OH

CHOHHOHHOOHHOHH

CH2OH

CHOOHHHHOHHOOHH

CH2OH

D-Glucose D-Mannose D-Galactose

CHOC O

HHOOHHOHH

CH2OH

D-Fructose

Hexoses

PentosesCHO

OHHOHHOHH

CH2OH

D-Ribose

CHOHHOOHHOHH

CH2OH

D-Arabinose

CHOC O

OHHOHH

CH2OH

D-Ribulose

***

***

**

****

***

****

****

* Chiral carbon atoms

Cyclization of glucose

OH

HO

HHO

H

OHOHH

H

OHO

H

HO

HHO

H

HOHH

OH

OH

C

OC

C

C C

OH

HOH H

H

OH

OHH

HO

HC

OC

C

C C

OH

HOH H

OH

H

OHH

HO

H

C

OC

C

C C

OH

HOH H

OHH

HO

H O

H

H

α

β

β

α

123

4

56

AnomericCarbon

CO

C

C COH H

CH2OH

OH

OHH

H

HOH2CC

O

C

C COH H

OH

CH2OH

OHH

H

HOH2C

C

O

C

C COH H

OHH

H

HOH2CO

CH2OH

H

12

345

6

1

2

345

612

345

6

Cyclization of D-Fructose

OH

HO

HHO

H

OHOHH

H

OH

H

HOHO H

H OHOHO

OH

α -D-glucose Fructose

+H2O-H2O

OH

HO

HHO

H

OOHHH

OH

H

HO H

H OHOHO

OHGlycosidelinkage Sucrose

Disaccharide - Sucrose

glucose-α,β(1 2)fructose

D-

Polysaccharides

OH

HO

HHO

H

OHOHH

H

OH

123

4 56

α -D-glucose

OH

HO

HHO

H

HOHH

OH

OH

123

4 56

β -D-glucose

OH

HO

HHO

H

OHH

H

HOOH

O

HHO

H

OHH

H

HOOH

O

HHO

H

OHH

H

HOOH

O

HHO

H

OHH

H

HO

OH

12

3

4 56

12

34

56

Reducing End

Amylose (a major component of starch)(α(1 4))

Glycogen, the main carbohydrate reservoir in animals

OH

HO

HHO

H

HOHH

O

OH

OH

H

HO

H

HHOH

OH

OH

O

HHO

H

HOHH

O

OH

OH

H

HO

H

HHOH OH

OH

123

4 56 123

4 56

Reducing end

Cellulose (β(1 4))

Replication

Transcription

Translation

DNA DNA

The Flow of Biological Informations

RNA

Proteins

Cell Structures and Functions

Nucleic Acids (DNA + RNA)

O

OHOH

HH

HH

HO OH

Ribose

O

HOH

HH

HH

HO OH

Deoxyribose ++Adenine (A)DNA/RNA

N

NNH

NNH2

Guanine (G)DNA/RNA

NH

NNH

NO

NH2

Cytosine (C)DNA/RNA

N

NH

NH2

O

Thymine (T)DNA

NH

NH

O

O

Uracil (U)RNA

NH

NH

O

O

BaseBase

DNARNA

Sugar Purine

Pyrimidine

(Deoxyribonucleic acid)(Ribonucleic acid)

++PO

HO OHOH

PhosphoricAcid

DNA RNA

BaseO

HOH

HHHH

HO

OHO

HOH

HHHH

HO HOO

OHOH

HHHH

HO

BaseO

OHOH

HHHH

HO

BaseO

H

HHHH

OH

OP-OO

O-

BaseO

OH

HHHH

OH

OP-OO

O-

β-D-Riboseβ-D-2-Deoxyribose

Pyrimidine deoxynucleoside Pyrimidine nucleosidePurinePurine

Aldopentose

Nucleoside

Nucleotide

Nucleic Acid(polynucleotides)

Components of DNA and RNA

N

N

NH2

N

N

O

OHOH

H H

CH2

H

O

H

PO

O-OP

O

O-OP

O

O-

-O

1'

2'3'

4'

5'αβγ

Adenosine 5'-monophosphate (AMP)Adenosine 5'-diphosphate (ADP)Adenosine 5'-triphosphate (ATP)

9

Chemical Structures of AMP; ADP; ATP

OHOH2CH

OHH

HO

H1

2

N

N

NH2

N

N

H

9

N

N

NH2

OH

1

OHOH2CH

OHH H

12

5

N

N

NH2

O 12

β configuration

OHOH2CH

HOH H

12

N

N

NH2

N

N9

5

β configuration

cytosine

adenine

2-deoxy-ribose

Formation of Nucleosides

Formation of Nucleic Acids

Backbone:Hydrophilic Region

5’

3’

B a s eO

HO H

HHHH

H OP-OO-

O-

O

B a s eO

HO H

HHHH

OPO-

O

-O

B a s eO

HO H

HHHH

OPO-

O

-O

+

+

B a s eO

HO

HHHH

OPO-

O

B a s eO

H

HHHH

OPO

O

B a s eO

HO H

HHHH

OPO

OO

(nucleotide)Phosphoric acid

DNA (or RNA)

- H2O1'

5'

3'

5'

3'

3'

3'

- H2OO

Double-Helical Structure of DNA

NN

N

N N

NN

O

OH

H

H

NN

N

N O

N

NN

N

O

H

HH

HH

A T

G C

Deoxyribose

Deoxyribose

Deoxyribose

Deoxyribose

Adenine

Thymine

GuanineCytosine

Major Groove

MinorGroove

－G≣C－

A＝T

G≣C

A＝T

T＝A

T＝A

C≣G

C≣GG≣C

A＝T

T＝AT＝A

DNA ReplicationKey Components

DNA polymerase I, II, and IIIThe four deoxyribonucleoside triphosphates DNA templateRNA Primer (4-10 nucleotides); providing 3’-hydroxy groupMg2+ Motion of

Replicationfork

3’

5’

5’

5’

5’

3’

3’

3’

Leading strand

Lagging strand (Okazaki fragments)Parental strands

Transcription

Translation

The Flow of Biological Informations

RNA (messenger/codon)

Proteins

Cell Structures and Functions

ReplicationDNA DNA

(Genes)

tRNA (anticodon)

Transcription

Key Components:RNA polymeraseFour ribonucleoside triphosphatesDNA template (3’ 5’)Mg2+

mRNA (codon) tRNA (anticodon) rRNA

(DNA RNA)Genes

5’

3’

3’

5’

5’

Template strand

Coding strand

RNA polymerase

RNA transcript

downstreamupstream

+1 +2 +3 +4-3 -2 -1

Key Components:Ribosomes (two subunits)mRNAtRNA (translators)Activated amino acids

RNA Proteins4 letters 20 letters

Translation

Translation

Protein Synthesis

NucleusDNA

RNAmRNA

Moves along mRNA

Ribosome

tRNA

Messenger RNA

transfer RNAAmino acid+

tRNA tRNA tRNARibosome

Completedprotein

tRNA

Peptide bond

mRNA