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George Mason UniversityGeneral Chemistry 212

Chapter 15Organic Chemistry

AcknowledgementsCourse Text: Chemistry: the Molecular Nature of Matter and

Change, 7th edition, 2011, McGraw-HillMartin S. Silberberg & Patricia Amateis

The Chemistry 211/212 General Chemistry courses taught at George Mason are intended for those students enrolled in a science /engineering oriented curricula, with particular emphasis on chemistry, biochemistry, and biology The material on these slides is taken primarily from the course text but the instructor has modified, condensed, or otherwise reorganized selected material.Additional material from other sources may also be included. Interpretation of course material to clarify concepts and solutions to problems is the sole responsibility of this instructor.

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Organic Chemistry Life on earth is based on a vast variety of reactions

and compounds based on the chemistry of Carbon – Organic Chemistry

Organic compounds contain Carbon atoms, nearly always bonded to other Carbon atoms, Hydrogen, Nitrogen, Oxygen, Halides and selected others (S, P)

Carbonates, Cyanides, Carbides, and other carbon-containing ionic compounds are NOT organic compounds

Carbon, a group 4A compound, exhibits the unique property of forming bonds with itself (catenation) and selected other elements to form an extremely large number of compounds – about 9 million

Most organic molecules have much more complex structures than most inorganic molecules

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Organic Chemistry Bond Properties, Catenation, Molecular Shape

The diversity of organic compounds is based on the ability of Carbon atoms to bond to each other (catenation) to form straight chains, branched chains, and cyclic structures – aliphatic, aromatic

Carbon is in group 4 of the Periodic Chart and has 4 valence electrons – 2s22p2

This configuration would suggest that compounds of Carbon would have two types of bonding orbitals each with a different energy

If fact, all four Carbon bonds are of equal energy This equalization of energy arises from the

hybridization of the 2s & 2p orbitals resulting in 4 sp3 hybrid orbitals of equal energy

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Organic Chemistry Hybrid orbitals are orbitals used to describe

bonding that is obtained by taking combinations of atomic orbitals of an isolated atom

In the case of Carbon, one “s” orbital and three “p” orbitals, are combined to form 4 sp3 hybrid orbitals

The Carbon atom in a typical sp3 hybrid structure has 4 bonded pairs and zero unshared electrons, therefore, Tetrahedral structure

AXaEb (a + b) 4 + 0 = AX4

The four sp3 hybrid orbitals take the shape of a Tetrahedron

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Organic Chemistry

C atom

(ground state)

En

ergy

1s

2p

2s

sp3

1s

sp3

1sC atom

(hybridized state)

C atom

(in CH4)

C-H bonds

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Organic Chemistry

Shape of sp3 hybrid orbital different than either s or p

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Organic ChemistryThe bonds formed by these 4 sp3

hybridized orbitals are short and strong

The C-C bond is short enough to allow side-to-side overlap of half-filled, unhybridized p orbitals and the formation of “multiple” bonds

Multiple bonds restrict rotation of attached groups

The properties of Organic molecules allow for many possible molecular shapes

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Organic Chemistry Electron Configuration, Electronegativity, and

Covalent Bonding

Carbon ground-state configuration – [He 2s22p2]

Hybridized configuration – 4 sp3

Forming a C4+ or C4- ion is energetically very difficult (impossible?):

● Required energy

Ionization Energy for C4+ - IE1<IE2<IE3<IE4

Electron Affinity for C4- - EA1<EA2<EA3<EA4

Electronegativity is midway between metallic and most nonmetallic elements

Carbon, thus, shares electrons to bond covalently in all its elemental forms

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Organic Chemistry Molecular Stability

Silicon and a few other elements also catenate, but the unique properties of Carbon make chains of carbon very stable

Atomic Size and Bond strength

● Bond strength decreases as atom size and bond length increase, thus, C-C bond strength is the highest in group 4A

Relative Heats of Reaction

Energy difference between a C-C Bond(346 kJ/mol) vs C-O Bond (358 kJ/mol) is small

Si-Si (226 kJ/mo) vs Si-O (368 kJ/mol) difference represents heat lost in bond formation

Thus, Carbon bonds are more stable than Silicon

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Organic ChemistryOrbitals available for Reaction

● Unlike Carbon, Silicon has low-energy “d” orbitals that can be attacked by lone pairs of incoming reactants

● Thus, Ethane (CH3-CH3) with its sp3 hybridized orbitals is very stable, does not react with air unless considerable energy (a spark) is applied

● Whereas, Disilane (SiH3 – SiH3) breaks down in water and ignites spontaneously in air

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Organic Chemistry Chemical Diversity of Organic Molecules

Bonding to Heteroatoms (N, O, X, S, P) Electron Density and Reactivity

● Most reactions start (a new bond forms) when a region of high electron density on one molecule meets a region of low electron density of another C-C bond: “Nonreactive” – The

electronegativities of most C-C bonds in a molecule are equal and the bonds are nonpolar

C-H bond: “Nonreactive” – the bond is nonpolar and the electronegativities of both H(2.1) & C(2.5) are close

C-O bond: “Reactive” – polar bond Bonds to other Heteroatoms: Bonds are long &

weak, and thus, reactive

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Carbon Geometry

sp3 sp2 sp spTetrahedral trigonal planar linear linear AX4 AX3 AX2 AX2

The combination of single, double, and triple bonds in an organic molecule will determine the molecular geometry

Review Chapter 11 – Multiple bonding in carbon compounds

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Hydrocarbons Compounds containing only C and H

Saturated Hydrocarbons: Alkanesonly single () bonds

Unsaturated Hydrocarbons: Alkenes Alkynes

Double (=) Bonds Triple () bonds Aromatic Hydrocarbons (Benzene rings)

(6-C ring with alternating double and single bonds)

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Hydrocarbons A close relationship exists among Bond Order,

Bond Length, and Bond Energy Two nuclei are more strongly attracted to two

shared electrons pairs than to one: The atoms are drawn closer together and are more difficult to pull part

For a given pair of atoms, a higher bond order results in a shorter bond length and a higher bond energy, i.e.,

A shorter bond is a stronger bond The Relation of Bond Order, Bond Length, and Bond Energy

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Hydrocarbons Alkanes (Aliphatic Hydrocarbons)

Normal-chain: linear series of C atoms

C-C-C-C-C-C- Branched-chain: branching nodes for C atoms

Cycloalkanes: C atoms arranged in rings

Cyclohexane

Methyl Propane

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Hydrocarbons Alkanes: CnH2n+2

Straight Chained Alkanes

Ethane Butane

Methane Propane

C H

H

H

H

C C C C

H

H H

H

H

H

HH

H

H

C C

H

H

H

C

H

H

H

H

H

C C

H

H

H

H

H

H

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Hydrocarbons Branched Chained Alkanes

Cycloalkanes

3-Ethyl-4-MethylHexane

Cyclobutane Methylcyclopropane

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Hydrocarbons Molecular Formulas of n-Alkanes

Methane: C-1: CH4

Ethane: C-2: CH3CH3

Propane: C-3: CH3CH2CH3

Butane: C-4: CH3CH2CH2CH3

Pentane: C-5: CH3CH2CH2CH2CH3

Hexane: C-6: CH3(CH2)4CH3

Heptane: C-7: CH3(CH2)5CH3

Octane: C-8: CH3(CH2)6CH3

Nonane: C-9: CH3(CH2)7CH3

Decane: C-10: CH3(CH2)8CH3

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Hydrocarbons Straight Chain (n) Alkanes

Physical Properties of Straight–Chain Alkanes

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Hydrocarbons Petroleum Fractions

Boiling

PointName

Carbon Atoms

Use

< 20 0CGases C1 to C4 Heating,

Cooking

20-200 0C Gasoline C5 to C12 Fuel

200-300 0C Kerosene C12 to C15 Fuel

300-400 0C Fuel oil C15 to C18 Diesel Fuel

> 400 0Cover C18 Lubricants,

Asphalt, Wax

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Hydrocarbons Cycloalkanes: CnH2n

Cyclopropane Cyclobutane

Cyclohexane

C

C

C

C

C

C

H

H

H

H

HH

H

H

H

H

HH

C C

C

H

H

HH

H

H

C C

CC

H

H

H

HH

H

H

H

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Hydrocarbons Structural Isomers

Structural (or constitutional) isomers are compounds with the same molecular formula, but different structural formulas. Created by branching, etc.

Butane IsobutaneC4H10 C4H10

H3C C C CH3

H

H H

H

C CH3

CH3

H3C

H

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Hydrocarbons Structural Isomers of Pentane

C5H12

Pentane 2-Methylbutane2,2-Dimethylpropane

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Hydrocarbons Chiral Molecules & Optical Isomerism

Another type of isomerism exhibited by some alkanes and many other organic compounds is called Stereoisomerism

Sterioisomers are molecules with the same arrangement of atoms but different orientations of groups in space

Optical Isomerism is a type of stereoisomerism, where two objects are mirror images of each other and cannot be superimposed (also called enantiomers)

Optical isomers are not superimposable because each is asymmetric: there is no plane of symmetry that divides an object into two identical parts

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Hydrocarbons Chiral Molecules & Optical Isomerism

An asymmetric molecule is called “Chiral”

The Carbon atom in an optically active asymmetric (l) organic molecule (the Chiral atom) is bonded to four (4) different groups.

Optical Isomers of3-methylhexane

Mirror images

1C1 & 1C2 of molecule 1 (left) can be moved to the right to sit on top of2C1 & 2C2 of molecule 2, i.e.,

1C & 2C groups can be superimposed

But, the two groups on C3 are opposite

The two forms are optical isomers and cannot be superimposed, i.e., no plane of symmetry to divide molecule into equal parts

C-3 is the “Chiral” Carbon

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Hydrocarbons Optical Isomers

In their physical properties, Optical Isomers differ only in the direction each isomer rotates the plane of polarized light

● One of the isomers – dextrorotary isomer - rotates the plane in a clockwise direction (d or +)

● The other isomer – levorotary isomer - rotates the plane in a counterclockwise direction (l or -)

● An equimolar mixture of the dextrorotary (d or +) and levorotary (l or -) isomers:

recemic mixturedoes not rotate the plane of light because the dextrorotation cancels the levoratation

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Hydrocarbons Optical Isomers

In their chemical properties, optical isomers differ only in a chiral (asymmetric) chemical environment● An optically active isomer is distinguished

by the chiral atom being attached to 4 distinct groups

If the attached groups are not distinct the molecule is NOT optically active

● An isomer of an optically active reactant added to a mixture of optically active isomers of an another compound will produce products of different properties – solubility, melting point, etc.

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Nomenclature of Alkanes Determine the longest continuous chain of

carbon atoms. The base name is that of this straight-chain alkane.

Any chain branching off the longest chain is named as an “alkyl” group,

changing the suffix –ane to –yl For multiple alkyl groups of the same type,

indicate the number with the prefix di, tri, …

Ex. Dimethyl, Tripropyl, Tertbutyl The location of the branch is indicated with the

number of the carbon to which is attached

Note: The numbering of the longest chain begins with the end carbon closest to the carbon with the first substituted chain or functional group

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Nomenclature Example

CH3

H2C

CH3

CH3

CH3

CH3 CH

CH2

CH2

HC

HC

(Con’t)

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Nomenclature Example Determine the longest chain in the molecule

7 Carbons

Substituted Heptane (7 C)

CH3

H2C

CH3

CH3

CH3

CH3 CH

CH2

CH2

HC

HC

(Con’t)

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Nomenclature Example The base chain is 7 carbons – Heptane

Add the name of each chain substituted on the base chain

“methyl” groups at Carbon 3 and Carbon 5

“ethyl” group at Carbon 4

3,5-dimethyl-4-ethylheptane

1234

5 6 7

CH3

H2C

CH3

CH3

CH3

CH3 CH

CH2

CH2

HC

HC

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Nomenclature Example Guidelines for numbering substituted

carbon chainsThe numbering scheme used in

developing the name of a organic compound begins with the end carbon closest to the carbon with the first substituted group or functional group

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Hydrocarbons Reactions of Alkanes

Combustion (reaction with oxygen) – Burning

C5H12(g) + 8 O2(g) 5 CO2(g) + 6 H2O(l)

Substitution (for a Hydrogen)

C5H12(g) + Cl2(g) C5H11Cl(g) + HCl(g)

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Hydrocarbons Alkenes

When a Carbon atom forms a double bond with another Carbon atom, it is now bonded to 2 other atoms instead of 3 as in an Alkane

The Geometry now changes from 4 sp3 orbitals (Tetrahedral AX4E0) to 3 sp2 hybrid orbitals and 1 unhybridized 2p orbital (AX3E0 Trigonal Planar) lying perpendicular to the plane of the trigonal sp2 hybrid orbitals

Review Chapter 10 - Geometry

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Hydrocarbons Alkenes

Two sp2 orbitals of each carbon form C – H sigma () bonds by overlapping the 1 s orbitals of the two H atoms

The 3rd sp2 orbital forms a C-C () bond with the other Carbon

A Pi () bond forms when the two unhybridized 2p orbitals (one from each carbon) overlap side-to-side, one above and one below the C-C sigma bond

A double bond always consists of 1 and 1 bond

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Hydrocarbons Alkenes: CnH2n

Alkenes substitute the single sigma bond () with a double bond – a combination of a sigma bond and a Pi () bond

The double-bonded (-C=C-) atoms are sp2

hybridizedThe carbons in an Alkene structure are

bonded to fewer than the maximum 4 atoms

Alkenes are considered: unsaturated hydrocarbons

Etheneor

EthylenePropene

C CH

H

H

CH3

C CH

H

H

H

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Hydrocarbons Molecular Formulas of Alkenes

Ethene: CH2=CH2

Propene: CH2=CHCH3

Butene: CH2=CHCH2CH3

Pentene: CH2=CHCH2CH2CH3

Decene: CH2=CH(CH2)7CH3

Conjugated MoleculesAlkene (or aromatic) with alternating Sigma bonds and Pi bonds)

Ex. 2,5-Dimethyl-2,4-HexadieneCH3CH3=CH-CH=C(CH3CH3)

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Hydrocarbons Reactions of Alkenes

Addition Reactions

CH3CH=CH2 + HBr CH3CHBrCH(H2)

Why does the Bromine (Br) attach to the middle carbon?

Markownikov’s Rule:

When a double bond is broken, the H atom being added adds to the carbon that already has the most Hydrogens CH2 → CH3

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Hydrocarbons An addition reaction occurs when an unsaturated

reactant (alkene, alkyne) becomes saturated( bonds are eliminated)

● Carbon atoms are bonded to more atoms in the “Product” than in the reactant (Ethene is reduced)

Addition Reaction – Heat of Formation

Reaction is Exothermic

Formation of two strong bonds from a single

bond and a relatively weak bond

o o orxn bondsbroken bondsformedΔH = ΔH + ΔH = 2693 kJ + (-2751 kJ) = - 58 kJ∑ ∑

Reactants (bonds broken Product (bonds formed) 1 C = C = 614 kJ 1 C – C = – 347 kJ 4 C – H = 1652 kJ 5 C – H = – 2065 kJ 1 H – C = 427 kJ 1 C – Cl = – 339 kJ Total = 2693 kJ Total = – 2751 kJ

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Hydrocarbons Elimination Reactions

● The reverse of “addition reaction”:

A saturated molecule becomes “unsaturated”

Typical groups “Eliminated” include: Pairs of Halogens – Cl2, Br2, I2 H atom and Halogen – HCL, HBr H atom and Hydroxyl (OH) –

Driving force – Formation of a small, stable molecule, such as HCl, H2O, which increases Entropy of the system

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Hydrocarbons Substitution Reactions

● A substitution reaction occurs when an atom (or group) from an added reagent substitutes for an atom or group already attached to a carbon

Carbon atom is still bonded to the same number of atoms in the product as in the reactant

Carbon atom may be saturated or unsaturated “X” & “y” may be many different atoms (not C)

Reaction of “Acetyl Chloride” and “isopentylalcohol” to form “banana oil”, an ester

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Hydrocarbons Nomenclature of Alkenes

Alkenes (-C=C-) are named just as alkanes, except that the –ane suffix is changed to –ene

Alkynes (-CC-) are named in the same way, except that the suffix –yne is used

In either case, the position of the double bond is indicated by the number of the carbon

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Hydrocarbons Nomenclature of Alkenes - Example

First, find the longest carbon chain containing the double bond

3-propyl-5-methyl-2-heptene1 2 3 4 5

6 7CH2CH3

CH2CH2CH3

CH2CHCH3H3CHC C

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Hydrocarbons Alkenes – Geometric Isomerism

In Alkanes, the C-C bond allows rotation of bonded groups; the groups continually change relative positions

In Alkenes with the C=C bond, the double bond restricts rotation around the bond

Geometric isomers are compounds joined together in the same way, but have different geometries

The similar groups attached to the two carbon atoms of the C=C bond are on the same side of the double bond in one isomer and on the opposite side for the other isomer

cis-2-butene trans-2-butene

C C

HH

CH3H3C

C C

H

H CH3

H3C

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Hydrocarbons Alkynes

General Formula - CnH2n-2

The Carbon-Carbon (-C-C-) bond is replaced by a triple bond

Each Carbon of an Alkyne structure (-CC-) can only bond to one other Carbon in a linear structure

Each C is sp hybridized (sp – linear geometry)

Alkyne compound names are appended by thesuffix “yne”

The electrons in both alkenes (-C=C-) and alkynes (-CC-) are “electron rich” and act as functional groups

Alkenes and alkynes are much more “reactive” than alkanes

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Hydrocarbons Alkynes

PropyneA Terminal Acetylene

C C HH

C C CH3H3C CH2 CH2

3-Hexyne

Ethyneor

Acetylene

C C CH3H

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Aromatic Hydrocarbons Aromatic Hydrocarbons are “Planar” molecules

consisting of one or more 6-carbon rings Although often drawn depicting alternating and

bonds, the 6 aromatic ring bonds are identical with values of length and strength between those of –C-C– & –C=C – bonds

The actual structure consists of 6 bonds and 3 pairs of electrons “delocalized” over all 6 carbon atoms

The bond between any two carbons “resonates” between a single bond and a double bond

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The orbital picture shows the two “lobes” of the delocalized cloud above and below the hexagonal plane of the -bonded carbon atoms

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Aromatic Hydrocarbons Molecular Orbitals of Benzene

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Aromatic Hydrocarbons

Benzene Benzene

Condensed Resonance Form of Benzene

CC

CC

C

C

H

H

H

H

H

H CC

CC

C

C

H

H

H

H

H

H

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Aromatic Hydrocarbons Substituted Benzenes

Methylbenzene(Toluene)

3,4-Dimethyl-ethylbenzenem,p-Dimethyl-ethylbenzene

CH3 CH3

CH3

C2CH3

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Aromatic Compounds Substituted Benzenes

Methoxybenzoate Nitrobenzene

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CH3

CH3

2 (o)

3 (m)

4 (p)

1

5 (m)

6 (o)

Aromatic Compounds Benzene ring naming conventions - ring site

locations

Starting at the carbon containing the first substituted group, number the carbons 1 thru 6 moving clockwise

Alternate names: 2 (ortho); 3 (meta); 4 (para)

ortho-toluene1,2-dimethylbenzene

meta-toluene1,3-dimethylbenzene

para-toluene1,4-dimethylbenzene

CH3

CH3

3 (m)

2 (o)

4 (p)

1

5 (m)

6 (o)

CH3

CH3

3 (m)

2 (o)

4 (p)

1

5 (m)

6 (o)

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Reactions of Aromatic Compounds The stability of the Benzene ring favors

“substitution” reactions

The “delocalization” of the pi bonds makes it very difficult to break a –C=C- bond for an “addition” reaction

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Reactivity – Alkenes vs Aromatics The double bond (-C=C-) is electron–rich Electrons are readily attracted to the partially

positive H atoms of hydronium atoms (H3O+) and

hydrohalic acids (HX), to yield alcohols and alkyl Halides, respectively

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Reactivity – Alkenes vs Aromatics The pi electrons in an alkene double bond represent

a localized overlap of unhybridized 2p orbitals, where two regions of electron density are located above and below the bond

The localized nature of alkene double bonds is very different from the “delocalized” unsaturation of aromatic structures

Although aromatic rings are commonly depicted as having alternating sigma () and () bonds, the () bonds are actually delocalized over all 6 –C– () bonds

The reactivity of benzene is much less than a typical alkene because the electrons are “delocalized” requiring much more energy to break up the ring structure to accommodate an “addition” reaction

“Substitution” is much more likely from an energy perspective because the delocalization is retained

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Redox Processes in Organic Reactions “Oxidation Number” is not applicable for carbon atoms Oxidation-Reduction in organic reactions is based on

movement of “electron density” around Carbon atom The number of bonds joining a carbon atom and a

“more” electronegative atom (group) vs. the number of bonds joining a carbon atom to a “Less” electronegative atom (group)

The more electronegative atoms will attract electron density away from the carbon atom

Less electronegative atoms will donate electron density to the carbon atom

When a C atom forms more bonds to Oxygen or fewer bonds to Hydrogen, the compound is oxidized

When a C atom forms fewer bonds to Oxygen or more bonds to Hydrogen, the compound is reduced

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Redox Processes in Organic Reactions Combustion Reactions (burning in Oxygen)

Ethane is converted to Carbon Dioxide (CO2) and water (H2O)

Each Carbon in CO2 has more bonds to Oxygen than in ethane (none) and few bonds to Hydrogen

Reaction is “Oxidation” Oxidation of Propanol

● C-2 has one fewer bonds to H and one more bond to O in 2-propanone - Oxidation

3 3 2 2 22CH - CH + 7O 4CO + 6H O

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Redox Processes in Organic Reactions Hydrogenation of Ethene

Each carbon has more bonds to H in Ethane than in Ethene

Ethene is reduced, H2 is oxidized (loses e-)

Pd2 2 2 3 3CH = CH + H CH - CH

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Organic Reactions Functional groups

A functional group is a reactive portion of a molecule that undergoes predictable reactions

The reaction of an organic compound takes place at the functional group

A functional group is a combination of bonded atoms that reacts as a group in a characteristic way

Each functional group has its own pattern of reactivity

The distribution of electron density in a functional group affects its reactivity

Vary from carbon-carbon bonds (single, double, triple) to several combinations of carbon-heteroatom bonds

A particular bond may be a functional group itself or part of one or more functional groups

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Organic Reactions Functional Groups (Con’t)

Electron density can be low at one end of a bond and higher at the other end, as in a dipole, an intermolecular force

The Intermolecular Forces that affect physical properties and solubility also affect reactivity

Alkene (-C=C-) and Alkyne (-CC-) bonds have high electron density, thus are functional groups with high reactivity

Classification of Functional Groups● Functional groups with only single bonds undergo

“substitution” reactions● Functional groups with “double” or “triple” bonds

undergo “addition” reactions● Functional groups with both single and double

bonds undergo substitution reactions

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Functional Groups Oxygen containing functional groups:

alcohols, ethers, aldehydes, ketones, esters, carboxylic acids, anhydrides, acid halides

Nitrogen containing functional groups:amines, amides, nitriles, nitro

Compounds containing Carbonyl Group (C=O)acids, esters, ketones, aldehydes,anhydrides, amides, acid halides

Compounds containing Halidesalkyl halides, aryl halides, acid halides

Compounds containing double & triple bondsalkenes, alkynes, aryl structures (benzene rings)

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Functional Groups

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Functional Groups

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Alcohols Functional Groups with “only” single bonds

An alcohol, general formula – R-OH, is a compound obtained by substituting an -OH group for an –H atom in a hydrocarbon

● primary alcohol: one carbon attached to the carbon with the –OH group

● secondary alcohol: two carbons attached to the carbon with the –OH group

● tertiary alcohol: three carbons attached to the carbon with the –OH group

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Alcohols

4,6-dimethyl-3-octanol (a secondary alcohol)

CH3

CH2CH2CH2CH3

CH3CH2CH2CH2CH3

OH

Alcohol NomenclatureDrop final “e” from hydrocarbon and add suffix “ol”

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Alcohols Alcohol Reactions

Alcohol structure similar to water

(R-OH vs H-OH)

Alcohols react with very active metals to release H2

Alcohols form strongly basic “Alkoxide (R-O-) Ions

High melting points and boiling points of alcohols result from Hydrogen Bonding

Alcohols dissolve “Polar” molecules

Alcohols dissolve “some” salts

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Alcohols Alcohol Reactions

Elimination Reactions

● Elimination of a H atom and a hydroxide ion (OH) from a cyclic compound in the presence of acid results in the formation of an “alkene”

● Removal of 2 H atoms from a secondary alcohol in the presence of an oxidizing agent, such as K2CrO7 results in the formation of a “Ketone”

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Alcohols Alcohols Reactions

Oxidation

● For Alcohols with the OH group at the end of a chain (primary alcohol) oxidation to an organic acid can occur in air

Substitution Reactions

● Substitution results in products with other single bonded functional groups, such as the formation of Haloalkanes

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Haloalkanes A Haloalkane (Alkyl Halide) is a Halogen

(X = F, Cl, Br, I) bonded to a carbon atom

Elimination Reactions● Elimination of HX in the presence of a

strong base will produce an Alkene

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Haloalkanes Haloalkanes

Substitution Reactions● Halides of Carbon and most other non-metals,

such as Boron (B), Silicon (Si), Phosphorus (P), all undergo substitution reactions

● The process involves an attack on the slightly positive central atom, such as C, etc. by an OH- group

● -CN, -SH, -OR, and –NH2 groups also substitute for the halide

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Ethers H-O-H water

R-O-H alcohol (OH group – Hydroxyl group)

R-O-R ether (R-O group – Alkoxy group)

where R = any group

Ether Nomenclature:

If R-C-O-CH3 group is part of structure,add “Methoxy” to name

If R-C-O-CH2-CH3 group is part of structure, add “Ethoxy” to name

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Ether Nomenclature

4,6-dimethyl-3-ethoxyoctane

OCH2CH3

CH3CH2CH2CH2CH3

CH2CH2CH2CH3

CH3

4 3 2 1

5 6 7 8

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Amines An Amine is a compound derived by substituting one or

more Hydrocarbon groups for Hydrogens in Ammonia, NH3

Naming convention● Drop the final “e” from the alkane name and add

“amine” (ethanamine) or append “amine” to alkyl name (Methylamine)

Types● primary amine: one carbon attached to the Nitrogen● secondary amine: two carbons attached to the

Nitrogen.● tertiary amine: three carbons attached to the

Nitrogen

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Amine Examples

Methylamine(Primary Amine)

Trimethylamine(Tertiary Amine)

Dimethylamine(Secondary Amine)

NH

H

CH3:

NH

CH3

CH3

: NCH3

CH3

CH3

:

The pair of “unbonded” electrons common to all amines is the key to all amine reactivityAmines act as bases by donating the pair of unshared electrons

Trigonal pyramidalShape – AX3E

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Amines Reactions

Primary and secondary Amines can form H–bonds

● Higher melting points and boiling points than Hydrocarbons or Alkyl Halides of similar mass

● Trimethyl Amines cannot form Hydrogen Bonds and have generally lower melting points

● Amines of low molecular mass are water soluble and weakly basic (donate electrons)

Reaction with water proceeds slowly and produces OH- ions

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Amines Amine Reactions

Substitution Reactions

● The pair of unbonded electrons on the Nitrogen attacks the partially positive Carbon in Alkyl Halides to displace the Halogen (X-) and form a “larger” amine

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Carbonyl Group Functional Groups with Double Bonds

The Carbonyl group is a Carbon doubly bonded to an Oxygen (C=O)

Very versatile group appearing in several types of compounds

Aldehydes

Ketones

Carboxylic acids

Esters

Anydrides

Acid Halides

Amides

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Aldehydes and Ketones An Aldehyde is distinguished from a

Ketone by the Hydrogen atom attached to the Carbonyl Carbon

If two Hydrogens are attached to the Carbonyl atom, the compound is specific – Formaldehyde (CH2O)

Aldehyde(- al)

Ketone(-one)

R

RC O

R

H

C O C OH

HFormaldehyde

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Aldehydes and Ketones Aldehydes

In Aldehydes the Carbonyl group always appears at the end of a “chain

Aldehyde names drop the final “e” from the alkane names and “-al” – Propanal, Isobutanal, etc.

Alternate naming conventions:

● Benzaldehyde, Propionaldehyde

Butanal(Butyraldehyde)

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Aldehydes and Ketones Ketones

The Carbonyl Carbon always occurs within a chain as it is bonded to two other Alkyl groups (R, R’)

Ketones are named by numbering the carbonyl C, dropping the final “e” from the alkane name, and adding “-one”, 4-Heptanone

Alternate naming conventions:● Use the Alkyl root and add “ketone”

4-Heptanone(Dipropylketone)

Methylisopropylketone(3-methyl-2-butanone)

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Aldehydes and Ketones Like the –C=C= bond, the Carbonyl (–C=O) bond is

electron-rich Unlike the –C=C= bond, the –C=O bond is highly polar

A - The and bonds that make up the C═O bond of the carbonyl group

B - The charged resonance form shows that the C═O bond is polar (ΔEN = 1.0)

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Aldehydes and Ketones Aldehydes and Ketones are formed by oxidation

of Alcohols

The C=O is an unsaturated structure, thus, carbonyl compounds can undergo “addition” reactions and be reduced (forms more bonds to H) to form alcohols

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Aldehydes and Ketones Organometallic compounds

The Carbonyl group exhibits polarity with the Carbon atom bearing a slight positive charge and the Oxygen bearing a negative charge

An addition reaction to the Carbonyl group would involve an electron-rich group bonding to the positive carbon and an electron-poor group bonding to the negative Oxygen

Organometallic compounds have a metal atom (Li or Mg) attached to an “R” group through a polar covalent bond

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Aldehydes and Ketones Organometallic compounds

The two-step addition of an organometallic compound to a Carbonyl group produces an Alcohol with a different Carbon skeleton

Aldehyde & Lithium Organometallic

Acetone (ketone) & Ethyllithium

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Carboxylic Acids Carboxylic Acids are formed by adding an

“Hydroxyl” group to the Carbonyl Carbon Different R groups lead to many different

carboxylic acids Carboxylic Acids have the “- oic” suffix

with “acid” Example: Ethanoic acid (Acetic acid) –

C2H4O2

Acidic Hydrogen(Hydroxyl Group)

CH3

HO

C O

Carboxyl GroupCarbonyl Group

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Carboxylic Acids Carboxylic Acids are named by dropping the “-e”

from the alkane name and adding “-oic acid” Common names are often used Carboxylic Acids are “Weak Acids” in solution

Typically >99% of an organic acid is “undissociated”

Carboxylic acid molecules react completely with strong base to form salt & water

Carboxylate anion

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Carboxylic Acids Carboxylic acids with long hydrocarbon

chains are referred to as “fatty acids”

Fatty acid skeletons have an “even” number of Carbon atoms (16-18 most common)

Animal fatty acids have “saturated” hydrocarbon chains

Vegetable sources are generally “unsaturated”, with the -C=C- in the “cis” configuration

Fatty acid salts are the “soaps”, with the “cation” usually from Group 1A of 2A

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Examples Straight chain saturated (Aliphatic)

carboxylic acids

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Name Formula

Methanoic (Formic) Acid HCOOH

Ethanoic (Acetic) Acid CH3COOH

Propionic Acid CH3CH2COOH

Butanoic (Butyric) Acid CH3CH2CH2COOH

Pentanoic Acid CH3CH2CH2CH2COOH

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Esters Esterification is a dehydration-condensation reaction

between a Carboxylic acid and an alcohol to form an Ester

The Hydroxyl group (OH) from the Alcohol reacts with the Carboxyl group to form the Ester and Water

R1COOH + R2OH R1COOR2 + H2O

Ester group occurs commonly in “Lipids,” a large group of fatty biological substances, such as “triglycerides

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Esters Hydrolysis is the opposite of Dehydration-

Condensation (Esterification) in which the Oxygen atom from water is attracted to the partially positive Carbon of the ester carbonyl group, cleaving (lysing) the molecule into two parts

One part gets the –OH and one part gets the H

In Saponification, the process used in the manufacture of soap, the ester bonds in animal or vegetable fats are “Hydrolyzed” with a strong base

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Amides Amides are derived from the reaction of an Amine

with a Carboxylic acid or an Ester

Amides are named by denoting the “amine” portion from the amine and the replacing the “-oic acid” from the Carboxylic acid with “-amide”

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Amides The partially negative N (2 unbonded e-) of the

amine is attracted to the partially positive carbonyl carbon of the ester In the Amine & Acid reaction water is lost

In the Amine & Ester reaction an alcohol (ROH) is lost

Amides can be “Hydrolyzed” in hot water to reform the acid and the amine

R1COOH + R2NH2 R1CONHR2 + H2O

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Functional Groups with Triple Bonds Principal Groups with triple bonds

Alkynes (Acetylenes) -CC-● Addition reactions with H2O, H2, HX, X2,

others

Nitriles -CN● Produced by substituting a cyanide ion (-C

N-) for a Halide ion (X-) in a reaction with an alkyl halide

● Nitriles can be reduced to form amines or hydrolyzed to carboxylic acids

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Polymers Polymers are extremely large molecules

consisting of “monomeric” repeating units

Naming polymers

Add prefix “poly-” to the monomer name

Polyethylene Polystyrene Polyvinyl chloride

Polymer Types

Addition

● Monomers undergo addition with each other (chain reactions)

● Monomers of most addition polymers have the group

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Addition Polymers

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Addition Polymers Free-radical polymerization of Ethene,

CH2=CH2 ,to polyethylene

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Condensation Polymers Condensation polymers have “two” functional groups

A – R – B Monomers link when group A on one undergoes a

“dehydration-condensation” reaction with a B group on another monomer

Many condensation polymers are “Copolymer”, consisting of two or more different repeating units

Condensation of Carboxylic acid & Amine monomers forms “polyamides” (nylons)

Carboxylic Acid and Alcohol monomers form polyesters

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Biological Macromolecules Natural Polymers

Polysaccharides Proteins Nucleic acids Intermolecular forces stabilize the very

large molecules in the aqueous medium of living cells

Structures that make wood strong; hair curly, fingernails hard

Speed up many natural reaction inside cells Defend living organisms against infection Possess genetic information organisms

need to synthesis other biomolecules

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Sugars & Polysaccharides Carbohydrates – substances that provide energy

through oxidation

Monosaccharides Glucose & simple sugars Consist of carbon chains with attached hydroxyl and

carbonyl groups Serve as monomer units of polysaccharides

Polysaccharides

Consist mainly of Glucose units with differences in aromatic ring position of the links, orientation of certain bonds and the extent of cross-linking

Cellulose Starch Glycogen

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Sugars & Polysaccharides Cellulose

Most abundant organic chemical on earth

50% of carbon in plants occurs in stems & leaves

Cotton is 90% celluloseWood strength comes from Hydrogen

bonds between cellulose chainsHumans lack enzyme to links to the C1 &

C4 bonds between units making it impossible to digest

Other animals – cows, sheep, termites, however, have microorganisms in their digestive tracts that can digest cellulose

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Sugars & Polysaccharides Starch

A mixture of polysaccharides of glucose Energy store in plants

● Starch is broken down by hydrolysis of the bonds between units, releasing glucose, which is oxidized in a multistep process

Glycogen Energy storage molecule in animals Occurs in molecules made from 1000 to

500,000 glucose units The cross-linking between the C1 & C4

bonds is similar to starch, but is more highly cross-linked between the C1 & C6 bonds

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Amino Acids & Proteins Amino Acids

An amino acid has a carboxyl group (COOH) and an amine group (NH2) attached to an “-carbon”, the 2nd C atom in a Carbon-Carbon (C-C) chain

In the aqueous cell fluid, the NH2 (amino) and COOH (carboxyl) groups of amino acids are charged because the carboxyl group transfers an H+ ion to H2O to form H3O+ (acid), which transfers the H+ to the amine group

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Amino Acids & Proteins Proteins

Proteins are unbranched polyamide polymers made up of amino acids linked together by “Peptide” bonds”

A “Peptide” (amide) bond is formed by a dehydration-condensation reaction in which the Carboxyl group of one monomer reacts with the Amine group of the next monomer releasing water

“dipeptide”

A “Polypeptide chain” is a polymer formed by the linking of many amino acids by peptide bonds

A “Protein” is a polypeptide with a “biological” function

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Amino Acids & Proteins Peptide Bonds

:N-H

C=O

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Amino Acids & Proteins About 20 different amino acids occur in proteins

See Examples on Next Slide The R groups are screened gray The -carbons (boldface), with carboxyl and

amino groups, are screened yellow The amino acids are shown with the charges they

have under physiological conditions They are grouped by polarity, acid-base

character, and presence of an aromatic ring The R groups, which dangle from the -carbons

on alternate sides of the chain, play a major role in the shape and function of proteins

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Amino Acids & Proteins

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Amino Acids & Proteins Hierarchy of Protein Structure

Each type of protein has its own amino acid composition – a specific number and proportion of various amino acids

The role of a protein in a cell, however, is not determined by its composition

The “sequence” of amino acids determines the protein’s shape and function in the cell

Proteins range from 50 to several thousand amino acids

The number of possible sequences of the 20 types of amino acid, even in the smaller proteins, is extremely large (20n where ‘n’ is the number of amino acids)

Only a small fraction of the possible combinations occur in actual proteins – 105 for a human being

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Amino Acids & Proteins Protein Native Shapes

Proteins have unique shapes that unfold during synthesis in a cell

Simple Complex

Long rods Baskets

Undulating sheets Y-Shapes Spheroid Blobs

Globular Forms

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Amino Acids & Proteins Hierarchy of Protein Structure

● Primary (1o) – Basic Level (sequence of covalently bonded amino acids in polypeptide chain)

● Secondary (2o) – Shapes called -helices and -pleated sheets formed as a result of H bonding between nearby peptide groupings

● Tertiary (3o) – 3-dimensional folding of whole polypeptide chain

● Quarternary (4o) – Most complex, proteins made up of several polypeptide chains

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Amino Acids & Proteins

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Structural Hierarchy of Proteins

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Amino Acids & Proteins Protein Structure and Function

Two broad classes of proteins differ in the complexity of their amino acid composition and sequence, thus, their structure and function

● Fibrous Proteins

Relatively simple amino acid compositions and correspondingly simple structures

Includes “Colagen”, the most common animal protein (30% glycine; 20% proline)

● Globular Proteins

More complex, containing up to all 20 amino acids in varying proportions

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Amino Acids & Proteins Nucleotides and Nucleic Acids

Nucleic Acids – Unbranched polymers that consist of linked monomer units called mononucleotides● Mononucleotides consist of:

Nitrogen-containing base Sugar Phosphate group

Nucleic Acid Types● Ribonucleic Acid (RNA)● Deoxyribonucleic Acid (DNA)● RNA & DNA differ in sugar portions of

mononucleotides RNA contains Ribose, a 5-Carbon sugar DNA contains deoxyribose (H substitutes for

OH on the 2’ position of Ribose

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Amino Acids & Proteins Nucleic Acid Precursors

Nucleoside Triphosphates – Cellular precursors that form a nucleic acid

Dehydration-condensation reactions between cellular precursors:● Releases inorganic diphosphate (H2P2O7

2-)

● Creates Phosphodiester bonds to form a “polynucleotide”

● Sets up the repeating pattern of the nucleic acid backbone

– sugar – phosphate – sugar – phosphate –

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Amino Acids & Proteins DNA

Phosphate group 2’-deoxyribose (a Sugar) Base: Attached to each sugar is one of four N-

containing bases, eithera Pyrimidine (six-membered ring) Pyrimidines – Thymine (T) & Cytosine (C)

ora Purine (six- and five- membered rings

sharing a side) Purines – Guanine (G) & Adenine (A)

RNA● Sugar in RNA is Ribose● Uracil (U) substitutes for Thymine (T)

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Amino Acids & Proteins Nucleic Acid Precursors In a cell, nucleic acids are

constructed from nucleoside triphosphates, precursors of the mononucleic units

Each mononucleic unit consists of:

an N-containing base a sugar a triphosphate group

Nitrogen Containing Bases:Pyrimidines

● Thymine (DNA) Uracil (RNA)

● CytosinePurines

● Guanine● Adenine

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Amino Acids & Proteins Base Pairing

In the nucleus of a cell, DNA exists as two chains wrapped around each other in a “double Helix”

Each base in one chain “Pairs” with a base in the other through Hydrogen Bonding

A double-helical DNA molecule may contain many millions of H-Bonded bases

Base Pair Features● A Pyrimidine (Pyr) is always paired with a Purine

(Pur)● Each base is always paired with the same

partner Thymine (T) (Pyr) with Adenine (A) (Pur) Cytosine (C) (Pyr) with Guanine (G) (Pur)

● Thus, base sequence on one chain is the complement of the sequence on the other chainEx. A-C-T on one chain paired with T-G-A on another

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Practice ProblemWrite the sequence of the complimentary DNA strand that pairs with each of the following:

a. GGTTAC

Ans: CCAATG

b. CCCGAA

Ans: GGGCTT

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Practice ProblemWrite the base sequence of the DNA template from which the RNA sequence below was derived

GUA UCA AUG AAC UUG (RNA)

Ans: CAT AGT TAC TTG AAC (DNA)

(note: Uracil (U) substitutes for Thymine (T) in RNA)

How many amino acids are coded for in this sequence?

Ans: five (CAT) (AGT) (TAC) (TTG) (AAC)

Each 3-base sequence is a word, each word codes for a specific amino acid

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Nucleic Acids (N-Containing Bases)

UracilThymine Cytosine

Pyrimidines

Guanine Adenine

Purines

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Nucleic acid precursors and their linkage

.

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The Double Helix of DNA

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Amino Acids & Proteins Protein Synthesis

A protein consists of a sequence of Amino Acids The Protein’s Amino Acid sequence determines its

structure, which in turn determines its functionSEQUENCE STRUCTURE FUNCTION

The DNA base sequence contains an information template that is carried by the RNA base sequence (messenger and transfer) to create the protein amino acid sequence

In other words, the DNA sequence determines the RNA sequence, which determines the protein amino acid sequence● In Genetic Code, each base acts as a “Letter”● Each three-base sequence is a “Word”● Each word codes for a specific Amino Acid

Ex. C-A-C codes for Histidine A-A-G codes for Lysine

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Amino Acids & Proteins One Amino Acid at a time is positioned and linked to

the next in the process of protein synthesis Outline of Synthesis

● DNA occurs in cell nucleus● Genetic message is decoded outside of cell● RNA serves as messenger to synthesis site● Portion of DNA is unwound and one chain

segment acts as a template for the formation of a complementary chain of messenger RNA (mRNA)

● mRNA made by individual mononucleoside triphosphates linking together

● The DNA code words are transcribed into RNA code words through base pairing

● mRNA leaves the nucleus and binds, again through base-pairing, to an RNA rich-rich particle called a “Ribosome”

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Amino Acids & Proteins Synthesis Outline (con’t)

● The words (3-base sequences) in the RNA are then decoded by molecules of transfer RNA (tRNA)

● The smaller nucleic acid “shuttles” have two key portions on opposite ends of their structures

A three-base sequence (word) which is a complement of a word on the nRNA

A binding site for the amino acid coded by that word

● The Ribosome moves along the bound mRNA, one word at a time, while tRNAs bind to the mRNA

● The Amino acids are positioned near one another in preparation of peptide bond formation and synthesis of the protein

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Amino Acids & Proteins Synthesis Outline (con’t)

● Net resultProtein Synthesis involves the DNA message of

three-base words being transcribed into the RNA message of three-base words, which is then translated into a sequence of amino acids that are linked to make a proteinDNA Base Sequence RNA Base Sequence

Protein Amino Acid Sequence