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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