Organic and Biological Molecules

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Organic and Biological Organic and Biological MoleculesMolecules

Chapter 22Chapter 22

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Organic Chemistry and Biochemistry

•The study of carbon-containing

compounds and their properties.

•The vast majority of organic

compounds contain chains of rings

of carbon atoms.

•The study of the chemistry of living

matter

3

Hydrocarbons• compounds composed of carbon and

hydrogen.

• Saturated compounds (alkanes) have the maximum number of hydrogen atoms attached to each carbon atom

• Saturated: carbon-carbon bonds are all single - alkanes [CnH2n+2]

H C

H

H

C

H

H

H

4

Unsaturated compounds have fewer hydrogen atoms attached to the carbon chain than alkanes

• Unsaturated: They contain carbon-carbon multiple bonds (double or triple)

H C

H

H

C

H

CH

H

5

22.1 Alkanes: Saturated hydrocarbons

• Saturated hydrocarbons, CnH2n+2

– “Saturated” because they can’t take any more hydrogen atoms

– Straight chains are H3C–(CH2)n–2–CH3

– Waxes, oils, & fuel gases as n decreases.

6

Alkanes: Saturated Hydrocarbons

• Hydrocarbons are molecules composed of carbon & hydrogen– Each carbon atom forms 4 chemical bonds– A saturated hydrocarbon is one where all C - C bonds are

“single” bonds & the molecule contains the maximum number of H-atoms

– Saturated hydrocarbons are called ALKANES

7

Methane is a tetrahedral molecule

8

The Lewis structure of ethane.

9

A ball-and-stick model of ethane.

10

Propane

11

Butane

12

The First 10 “Normal” AlkanesNameName FormulaFormula M.P.M.P. B.P.B.P. # Structural Isomers# Structural Isomers

• Methane CH4 -183 -162 1

• Ethane C2H6 -172 -89 1

• Propane C3H8 -187 -42 1

• Butane C4H10 -138 0 2

• Pentane C5H12 -130 36 3

• Hexane C6H14 -95 68 5

• Heptane C7H16 -91 98 9

• Octane C8H18 -57 126 18

• Nonane C9H20 -54 151 35

• Decane C10H22 -30 174 75

C1 - C4 are Gases C1 - C4 are Gases at Room Temperatureat Room Temperature

C5 - C16 are Liquids C5 - C16 are Liquids at Room Temperatureat Room Temperature

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The C-H Bonds in Methane

14

IUPAC Rules for Naming Branched Alkanes

• Find and name the parent chainFind and name the parent chain in the hydrocarbon - this forms the root of the hydrocarbon name

• Number the carbon atoms in the parent chainNumber the carbon atoms in the parent chain starting at the end closest to the branching

• Name alkane branchesName alkane branches by dropping the “ane” from the names and adding “yl”. A one-carbon branch is called “methyl”, a two-carbon branch is “ethyl”, etc…

• When there are more than one type of branch (ethyl and methyl, for example), they are named alphabeticallyalphabetically

• Finally, use prefixesuse prefixes to indicate multiple branches

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Rules for Naming Alkanes

1. For alkanes beyond butane, add -ane to the Greek root for the number of carbons.

C-C-C-C-C-C : hexane

2. Alkyl substituents: drop the -ane and add -yl

-C2H5 is ethyl

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17

Rules for Naming Alkanes

3.Positions of substituent groups are specified by numbering the longest chain sequentially.

C C-C-C-C-C-C

3-methylhexane

• Start numbering at the end closest to the branching

4.Location and name are followed by root alkane name. Substituents in alphabetical order and use di-, tri-, etc.

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Normal vs Branched Alkanes

• Normal alkanes consist of continuous chains of carbon atoms

• Alkanes that are NOT continuous chains of carbon atoms contain branches

• The longest continuous chain of carbons is called the parent chain

CH3

CH2CH2

CH2CH3

CH3

CH2CH

CH3

CH3

19

Structural Isomerism

• Structural isomers are molecules with the same chemical formulas but different molecular structures - different “connectivity”.

• They arise because of the many ways to create branched hydrocarbons.

CH3

CH2CH2

CH2CH3

CH3

CH2CH

CH3

CH3

n-pentane, C5H12

2-methlbutane, C5H12

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Isomer Naming• Older conventions would have that

as “isooctane,” but a good IUPAC name results from the following:– Name the longest C chain (pentane)– List the side groups in alphabetical

order with Greek prefixes (trimethylpentane)

– Supply (smallest possible) positional indices (2,2,4 trimethylpentane)

21

Example : Show the structural formula of 2,2-dimethylpentane2,2-dimethylpentane

• The parent chain is indicated by the ROOT of the name - “pentanepentane”. This means there are 5 carbons in the parent chain.

CH3

CH2CH2

CH2CH3

• “dimethyldimethyl” tells us that there are TWO methyl branches on the parent chain. A methyl branch is made of a single carbon atom.

• “2,22,2-” tell us that BOTH methyl branches are on the second carbon atom in the parent chain.

CH31

CCH23

CH2

4

CH35

CH3

CH3

1

2

3

4

5

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Example: Structural formula of 3-ethyl-2,4-dimethylheptane?3-ethyl-2,4-dimethylheptane?

• The parent chain is indicated by the ROOT of the name - “heptaneheptane”. This means there are 7 carbons in the parent chain.

CH3

CH2CH2

CH2CH2

CH2CH3

• “2,4-dimethyl2,4-dimethyl” tells us there are TWO methyl branches on the parent chain, at carbons #2 and #4.

• “3-ethyl3-ethyl-” tell us there is an ethyl branch (2-carbon branch) on carbon #3 of the parent chain.

1

2

3

4

5

76

CH3

CHCH

CHCH2

CH2CH3

CH2

CH3

CH3 CH3

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Example: 2,3,3-trimethyl-4-propyloctane2,3,3-trimethyl-4-propyloctane

• The parent chain is indicated by the ROOT of the name - “octaneoctane”. This means there are 8 carbons in the parent chain.

• “2,3,3-trimethyl2,3,3-trimethyl” tells us there are THREE methyl branches - one on carbon #2 and two on carbon #3.

• “4-propyl4-propyl-” tell us there is a propyl branch (3-carbon branch) on carbon #4 of the parent chain.

1

2

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5

7

6

8

1

23

45

7

6

8

CHC

CHCH2

CH2

CH2CH3

CH3

CH3

CH3

CH3CH2

CH2

CH3

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Example : Name the molecules shown

• parent chain has 5 carbons - “pentane”

• two methyl branches - start counting from the right - #2 and #3

• 2,3-dimethylpentane2,3-dimethylpentane

CH3

CH2

CHCH

CH3

CH3

CH3

• parent chain has 8 carbons - “octane”

• two methyl branches - start counting from the left - #3 and #4

• one ethyl branch - #5

• name branches alphabetically

3,4-dimethyl3,4-dimethyl

4433

octaneoctane

55

5-ethyl-5-ethyl-

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Reactions of alkanes

• Combustion reactions

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

• Substitution ReactionsSubstitution Reactions

CHCl Cl CCl HClh3 2 4

CH4 + Cl2 CH3Cl + HCl

CH3Cl + Cl2 CH2Cl2 + HCl

CH2Cl2 + Cl2 CH Cl3 + HCl

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Dehydrogenation ReactionsDehydrogenation Reactions

CH3CH3 CH2 CH2

Ethylene

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Cyclic alkanesCyclic alkanes

• A cycloalkane is made of a hydrocarbon chain that has been joined to make a “ring”.

CH3

CH2

CH3 CH2

CH2

CH2

n-propaneC3H8

cyclopropaneC3H6

60° bond angleunstable!!

109.5° bond angle

•Note that two hydrogen atoms were lost in forming the ring

•What is the general formula for a cycloalkane?

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Cyclic alkanes, CnH2n

• If the two end C’s lose 1 H each, they have free valence to close a ring

• Again, properties similar to straight chains.– Can now have conformational

isomers!

– E.g., BOAT cyclohexane versus CHAIR

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Cyclohexane - Boat & Chair Conformations

• Cyclohexane is NOT a planar molecule. To achieve To achieve its 109.5° bond angles and reduce angle strainits 109.5° bond angles and reduce angle strain, it adopts several different conformations.

• The BOATBOAT and CHAIRCHAIR (99%) are two conformations

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Unsaturated hydrocarbomns22.2 Alkenes and Alkynes

Alkenes: hydrocarbons that contain a carbon-carbon double bond. [CnH2n]

C=C Ethene

CC=C propene

Alkynes: hydrocarbons containing a carbon-carbon triple bond. [CnH2n-2]

C C Ethyne

CCCCC 2-pentyne

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Alkenes & AlkynesAlkenes & Alkynes

• Alkenes are hydrocarbons that contain at least one one carbon-carboncarbon-carbon double bonddouble bond

• Alkynes are hydrocarbons that contain at least one one carbon-carboncarbon-carbon triple triple bondbond

• The suffix for the parent alkane chains are changed from “ane” to “ene” and “yne”– e.g. ethene, ethyne

• Where it is ambiguous, the BONDS are numbered like branches so that the the location of the multiple location of the multiple bond may be indicatedbond may be indicated

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Alkenes, CnH2n

• Cycle formation isn’t the only possible result of dehydrogenation.

• Adjacent C’s can double bond, C=C, making an (unsaturated) alkene.

Sp2

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The Bonding in Ethylene

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Nomenclature for Alkenes

1.Root hydrocarbon name ends in -ene

C2H4; CH2=CH2 is ethene

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

C=CCC is 1-butene

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Alkene Isomers

• While an sp3 CX2Y2 has only 1 isomer,• (every X and Y is adjacent to all the others)

• the sp2 alkene C2X2Y2 has cis & trans isomers (where X is or isn’t on the same side of = as X).

– For longer hydrocarbons, cis & trans refer to the side the chain extends:

CXX

YY

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Cis and Trans Isomers

Double bond is fixed Cis/trans Isomers are possible

CH3 CH3 CH3

CH = CH CH = CH

cis trans CH3

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Addition Reactions

• Weaker bonds are broken and new (stronger) bonds are formed to atoms being added.

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Hydrogenation

Adds a hydrogen atom to each carbon atom of a double bond

H H H H

Ni

H–C=C–H + H2 H–C–C–H

H H

ethene ethane

CHCH33-CH-CH33

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Halogenation

Adds a halogen atom to each carbon atom of a double bond

H H H H

Ni

H–C=C–H + Cl2 H–C–C–H

Cl Cl

ethene dichloro ethane

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Halogenation Reactions

CH2 CHCH2CH2CH2 + Br2

CH2Br CHBrCH2CH2CH2

1,2-dibromopentane

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Alkynes, CnH2n–2

Carbon-carbon triple bonds Names end in -yne

HCCH ethyne(acetylene)

HCC-CH3 propyne

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The Bonding in Acetylene

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Naming Alkenes and Alkynes

When the carbon chain has 4 or more C atoms, number the chain to give the lowest number to the double or triple bond.

1 2 3 4

CH2=CHCH2CH3 1-butene

CH3CH=CHCH3 2-butene

CH3CHCHCH3 2-butyne

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Question

Write the IUPAC name for each of the following unsaturated compounds:

A. CH3CH2CCCH3

CH3

B. CH3C=CHCH3

2-pentyne

2-methyl-2-butene

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Question

• Name the following compound

CH3CH2C CCHCH2CH3CH2CH3

CH3CH2C CCHCH2CH3CH2CH3

1 2 3 4 5 6 7

5-ethyl-3-heptyne

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Additions reactions:Hydrogenation and Halogenation

Hydrogens and halogens also add to the triple bond of an alkyne.

CH3C CCH2CH3 + Br2 CH3C CCH2CH3

Br Br

Br Br

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22.3 Aromatic hydrocarbonsUnsaturated Cyclic hydrocarbons

• Alternating single/double bond

cycles occur in many organic molecules– This class is called “aromatic” (by

virtue of their aroma).– The structure is often preserved in

their chemical reactions; they don’t add, they substitute instead.

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Lewis structures for the benzene ring.

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Benzene C6H6

sp2

sp2sp2

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Shorthand notation for benzene rings

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The bonding in the benzene ring is a combination of different Lewis structures.

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Aromatic Hydrocarbons

Substitution reaction

+ Cl2

FeCl3

Cl

+ HCl+H2O+HCl

benzene

Chlorobenzene

HNO3

HNO3

CH3Cl

-NO2

-CH3

Nitroobenzene

Toluene

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Nomenclature of benzene derivatives

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More Complex Aromatic Systems

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22.4 Hydrocarbon Derivatives(Functional Groups)

Molecules that are fundamentally hydrocarbons but have additional atoms or group of atoms called functional groups

Part of an organic molecule where chemical reactions take place

Replace an H in the corresponding alkane Provide a way to classify organic

compounds

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The Common Functional Groups

Class General Formula

Halohydrocarbons RX Alcohols ROH

Ethers ROR

AldehydesR C

O

H

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Class General Formula

Ketones

Carboxylic Acids

Esters

Amines

R C

OR'

R C

OOH

R C

OOR'

R NH2

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Some Types of Functional Groups

Haloalkane -F, -Cl, -Br CH3Cl

Alcohol -OH CH3OH

Ether -O- CH3-O-CH3

Aldehyde

Ketone

C H

OCH3CH

O

C

O

CH3CCH3

O

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More Functional Groups

Carboxylic acid -COOH CH3COOH

Ester -COO- CH3COOCH3

Amine -NH2 CH3NH2

Amide -CONH2 CH3CONH2

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Haloahydrocarbons

An alkane in which one or more H atoms is replaced with a halogen (F, Cl, Br, or I)

CH3Br bromomethane

Br (methyl bromide)

CH3CH2CHCH3 2-bromobutane

Cl

chlorocyclobutane

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Nomenclature

Name the following:

bromocyclopentane

1,3-dichlorocyclohexane

Br

Cl

Cl

1 2 3

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Substituents

List other attached atoms or groups in alphabetical orderBr = bromo, Cl = chloro

Cl Br

CH3CHCH2CHCH2CH2CH3

4-bromo-2-chloroheptane

1 2 3 4 5

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Nomenclature

The name of this compound is:

Cl CH3

CH3CH2CHCH2CHCH3

1) 2,4-dimethylhexane

2) 4-chloro-5-methylhexane

3) 4-chloro-2-methylhexane

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Solution

The name of this compound is:

Cl CH3

CH3CH2CHCH2CHCH3

3. 4-chloro-2-methylhexane

123456

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Alcohols: R–OH • The –OH makes alcohol polar enough

to hydrogen bondhydrogen bond.

• Thus, they are water solublewater soluble

• Ethanol is a fermentation product acid.

yeastC6H12O6

Glucose2CH3CH2OHEthanol + 2 CO2

CO + 2H2O CH3OH Methanol

• Methanol is produced industrially by hydrogenation of carbon monoxide

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Uses of alcohols

• Methanol is used to synthesize adhesives, fibers, plastics and recently as motor fuel

• It is toxic to human and can lead to blindness and death

• Ethanol can be added to gasoline to form gasohol and used in industry as solvent

• Commercial production of ethanol:

CH2=CH2 + H2O CH3CH2OH

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Classes of alcohols

R CH2OH Primary alchol

CHOHR'R

Secondary alcohol

CR'R

R"OH Tertiary alcohol

Alcohols can be classified according to the number number of hydrocarbon fragments bonded to the carbonof hydrocarbon fragments bonded to the carbon where the –OH group is attached

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Naming Alcohols

In IUPAC name, the -e in alkane name is replaced with -ol.

CH4 methane

CH3OH methanol (methyl alcohol)

CH3CH3 ethane

CH3CH2OH ethanol (ethyl alcohol)

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OH

Phenol(Aromatic alcohol)

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More Names of Alcohols

IUPAC names for longer chains number the chain from the end nearest the -OH groupend nearest the -OH group.

CH3CH2CH2OH 1-propanol

OH CH3CHCH3 2-propanol

CH3 OH CH3CHCH2CH2CHCH3 5-methyl-2-hexanol

5 2

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Some Typical Alcohols

OH

“Rubbing alcohol” CH3CHCH3

2-propanol (isopropyl alcohol)

Antifreeze HO-CH2-CH2-OH

1,2-ethanediol1,2-ethanediol (ethylene glycol)

OH

glycerol HO-CH2-CH-CH2OH

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Name the following alcohols:A. OH

CH3CHCHCH2CH3

CH3

OHB.

Example

3-methyl-2-pentanol

Cyclobutanol

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Reactions of Alcohols

Combustion

CH3OH + 2O2 CO2 + 2H2O + Heat

Dehydration

H OH heat

H-C-C-H H-C=C-H + H2O

H H H H

alcohol alkene

76

Ethers

• Contain an -O--O- between two carbon groups• Simple ethers named from -yl names-yl names of the

attached groups and adding adding etherether.

CH3-O-CH3 dimethyl ether

CH3-O-CH2CH3 ethyl methyl ether

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Aldehydes and Ketones

In an aldehyde, an H atomH atom is attached to a carbonyl group

O carbonyl group CH3-C-H

In a ketone, two carbon groupstwo carbon groups are attached to a carbonyl group

O carbonyl group CH3-C-CH3

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Naming Aldehydes

IUPAC Replace the -e in the alkane name -alCommon Add aldehyde to the prefixes form

(1C), acet (2C), propion(3), and butry(4C)

O O O

H-C-H CH3-C-H CH3CH2C-H

methanal ethanal propanal(formaldehyde) (acetaldehyde) (propionaldehyde)

methaneethane propane

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Aldehydes as Flavorings

CH

O

CH

O

HO

OCH3

CH=CH CH

O

Benzaldehyde Vanillin Cinnamaldehyde(almonds) (vanilla beans) (cinnamon)

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Naming Ketones

In the IUPAC name, the -e in the alkane name is replaced with -one

In the common name, add the word ketone

after naming the alkyl groups attached to the

carbonyl group

O O

CH3 -C-CH3 CH3-C-CH2-CH3

Propanone 2-Butanone

(Dimethyl ketone) (Ethyl methyl ketone)

O

Cyclohexanone

Acetone

propane butane

cyclohexane

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Preparation of aldehydes and Ketones

They are produced by oxidation of alcohols:

CH3CH2OHOxidation

CH3CHCH3

OH

Oxidation CH3CCH3O

CH3CO

Hacetaldehyde

acetone

Primary alcohol

Secondary alcohol

ethanal

propanone

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Question

Classify each as an aldehyde (1), ketone (2) or neither(3).

O

A. CH3CH2CCH3 B. CH3-O-CH3

CH3 O

C. CH3-C-CH2CH D.

CH3

O

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Solution

Classify each as an aldehyde (1), ketone (2) or neither(3).

O

A. CH3CH2CCH3 2 B. CH3-O-CH3 3

CH3 O

C. CH3-C-CH2CH 1 D. 2

CH3

O

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Question

Name the following

O

A. CH3CH2CCH3 B.

CH3 O

C. CH3-C-CH2CH

CH3

O

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Solution

O

A. CH3CH2CCH3 B.

2-butanone (ethyl methyl ketone)

CH3 O

C. CH3-C-CH2CH cyclohexanone CH3

2,2-dimethylbutanal

O

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Question

Draw the structural formulas for each:

A. 3-Methylpentanal

B. 2,3-Dichloropropanal

C. 3-Methyl-2-butanone

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Solution

Draw the structural formulas for each: CH3 O

A. 3-Methylpentanal CH3CH2CHCH2CH

Br O

B. 2,3-Dibromopropanal Br-CH2CHCH

O

C. 3-Methyl-2-butanone CH3CHCCH3

CH3

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Carboxylic Acids and Esters Carboxyl Group

Carboxylic acids contain the carboxyl group as carbon 1.

O

R CH3 — C—OH : CH3—COOH

carboxyl group

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Naming Carboxylic Acids

Formula IUPAC Common alkan -oic acid prefix – ic acid

HCOOH methanoic acid formic acid

CH3COOH ethanoic acid acetic acid

CH3CH2COOH propanoic acid propionic acid

CH3CH2CH2COOH butanoic acid butyric acid

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Naming Rule for Carboxylic acids

• Identify longest chain

• (IUPAC) Number carboxyl carbon as 1carboxyl carbon as 1

CH3

|

CH3 — CH—CH2 —COOH

IUPAC 3-methylbutanoic acid

1234

91

Question

Give IUPAC name:

A. CH3COOH

CH3

|

B. CH3CHCOOH

2

92

Solution

A. CH3COOH

ethanoic acid; acetic acid

CH3

|

B. CH3CHCOOH

2-methylpropanoic acid;

93

Preparation of carboxylic acids

• Oxidation of primary alcohols

CH3CH2OH CH3COOHKMnO4

94

Reaction of carboxylic acid with alcohol

CH3CO

OH + H OCH2CH3

CH3CO

OCH2CH3 + H2O

Ester

Carboxylic acid Alcohol

Esterification

95

Esters

In a ester, the H in the carboxyl group is replaced with an alkyl group

O

CH3 — C—O —CH3 : CH3—COO —CH3

ester group

•Esters give fruity odors

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Naming Esters

• The parent alcohol is named first with a –yl ending

• Change the –oic ending of the parent acid to –ate

acid alcohol O methyl

CH3 — C—O —CH3

Ethanoate methyl ethanoate (IUPAC)(acetate) methyl acetate (common)

97

Some esters and their names

Flavor/Odor

Raspberries

HCOOCH2CH3 ethylmethanoate

(IUPAC)

ethylformate (common)

Pineapples

CH3CH2CH2 COOCH2CH3

ethylbutanoate (IUPAC)

ethylbutyrate (common)

98

Question

Give the IUPAC and common names of the following compound, which is responsible for the flavor and odor of pears.

O

CH3 — C— O —CH2CH2CH3

99

Solution

O propyl

CH3 — C—O —CH2CH2CH3

propylethanoate (IUPAC)

propyl acetate (common)

100

Question

Draw the structure of the following compounds:

A. 3-bromobutanoic acid

B. Ethyl propionoate

101

Solution

A. 3-bromobutanoic acid

Br

|

CH3CHCH2COOH

B. Ethyl propionoate O

CH3 CH2 COCH2CH3 CH3CH2COOCH2CH3

102

Hydrolysis of esters

• Esters react with water and acid catalyst• Split into carboxylic acid and alcohol

O H+

H — C—O—CH2CH3 + H2O

O

H — C—OH + HO—CH2CH3

-OHH

103

Amines

• Organic compounds of nitrogen N; derivatives of ammonia

• Classified as primary, secondary, tertiary

CH3 CH3

CH3—NH2 CH3—NH CH3—N — CH3

Primary Secondary Tertiary

one N-C two N-C three N-Cbond bonds bonds

104

Naming Amines

IUPAC aminoalkane Common alkylamine

CH3CH2NH2 CH3—NH —CH3

aminoethane N-methylaminomethane(ethylamine) (dimethylamine)

NH2

|

CH3CHCH3

2-aminopropane Aniline N-methylaniline(isopropylamine)

NH2 NH CH3

105

Question

Give the common name and classify:

A. CH3NHCH2CH3

CH3

|

B. CH3CH2NCH3

106

Solution

A. CH3NHCH2CH3

ethylmethylamine, (Secondary)

CH3

|B. CH3CH2NCH3

ethyldimethylamine, (Tertiary)

107

Question

Write a structural formula for

A. 2-aminopentane

B. 1,3-diaminocyclohexane

108

Solution

A. 1-aminopentane

CH3CH2CH2CH2CH2-NH2

B. 1,3-diaminocyclohexane

NH2

NH2

109

PolymersPoly= many; mers=parts

• Polymers are large, usually chainlike molecules that are built from small molecules called monomers joined by covalent bonds

Monomer PolymerEthylene PolyethyleneVinyl chloride Polyvinyl

chlorideTetrafluoroethylene Teflon

110

111

Some common synthetic polymers, their monomers and applications

112

Types of Polymerization

Addition Polymerization:Addition Polymerization: monomers “add together” to form the polymer, with no other products. (Teflon)

Condensation Polymerization:Condensation Polymerization: A small molecule, such as water, is formed for each extension of the polymer chain. (Nylon)

113

Addition Polymerization

OH

C CH

H

H

HCOH

H CH

H

H

C CH

H

H

H

COH

H CH

H

H

COH

H CH

H

HC CH H

H H

The polymerization processIs initiated by a free radical

A species with an unpaired electron such as hydroxyl free radical

Free radical attacks and breakThe bond of ethylene moleculeTo form a new free radical

• Repetition of the process thousands of times creates a long chain polymer• The process is terminated when two radicals react to form a bond; thus there will be no free radical is available for further repetitions.

114

• Depending upon conditions of polymerization, the product may be branched branched or linearlinear polyethylene

(Polythene)

another

115

116

117

118

119

120

121

Condensation PolymerizationFormation of Nylon

NH

H(CH2)6 N

H

H CO

O(CH2)4H

CO

O H

Hexamethylendiamine Adipic acid

NH

H(CH2)6 N

HC (CH2)4 C

O

O H

O+ H2O

• Small molecule such as H2O is formed from each extension of the polymer chain• both ends are free to react

Dimer

Diamine Dicarboxylic acid

122

NH

(CH2)6 NH

( C (CH2)4 COO

)n

Nylon

123

124

Proteins

• Natural polymers made up of -amino

acids (molecular weight from 6000 to

>1,000,000 g/mol).

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

125

Proteins

2. 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

126

-Amino Acids

NH2 always attached to the -carbon (the carbon attached to COOH)

•C = -carbon

H2N C

H

COOH

R

127

Bonding in -Amino Acids

• + H2O

•

A peptide linkage (amide group)

•There are 20 amino acids commonly found in proteins.• Additional condensation reaction produces polypeptide eventually yielding a protein

CNH

H

H

R

C

O

N

H

C

H

R'

CO

OHDipeptide

• The protein polymer is built by condensation reaction between amino acids

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The 20 Alpha-amino Acids found in most proteins

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Levels of Structure•Primary: Sequence of amino acids in the protein chain. (lycine-alanine-leucne: (lys-ala-leu).

– So many arrangements can be predicted.

Tripeptide containing Glycine, Cysteine, and Alanine

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Levels of Structure

•Secondary: The arrangement of the protein chain in the long molecule (hydrogen bonding determines this).

• Hydrogen bonding between lone pairs on an oxygen atom in the carbonyl group of an amino acid and a hydrogen atom attached to a nitrogen of another amino acid

C O NH

This type of interaction can occur with the chain coils to form a spiral structure called - helix- helix

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Hydrogen bonding within a protein chain causes it to form a stable helical structure called the alpha-Helix

This is found infibrous protein likewool and hair givingit the elasticity

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•Tertiary: The overall shape of the protein (determined by hydrogen-bonding, dipole-dipole interactions, ionic bonds, covalent bonds and London forces).

Summary of the Various Types of Interactions that Stabilize the Tertiary Structure of a Protein: (a) Ionic, (b) Hydrogen Bonding, (c) Covalent, (d) London Dispersion, and (e) Dipole-Dipole

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Summary of the Various Types of Interactions that Stabilize the Tertiary Structure of a Protein: (a) Ionic, (b) Hydrogen Bonding, (c) Covalent, (d) London Dispersion, and(e) Dipole-Dipole

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CarbohydratesCarbohydrates

Food source for most organisms and structural material for plants.Empirical formula = (CH2O)n

Most carbohydrates such as starch and cellulose are polymers of monosacharides or polymers of monosacharides or simple sugar monomerssimple sugar monomersMonosaccharides (simple sugars) are polyhydroxy ketones and aldehydes

Pentoses (5-carbon atoms) - ribose, arabinoseHexoses (6-carbon atoms) - fructose, glucose

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Some Important Monosaccharides

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Chiral carbon atoms in fructose

• Molecules with nonsuperimposable mirror images exhibit optical isomerism

• A carbon atom with different groups bonded to it in a tetrahedral arrangement always has a nonsuperimposable mirror images which gives rise to a pair of optical isomers

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Tetrahedral Carbon atom with four different substituents cannot have its mirror image superimposed

138

The Mirror Image Optical Isomers of Glyceraldehyde

*Chiral carbonatom

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Fructose

D-Fructose

H2OHC

C

CHO H

C

O

H OH

C

CH2OH

OHH

*

*

*

There are 3 chiralCarbon atomsThere are 23 isomersThat differ in the abilityTo rotate light

140

Complex carbohydrates

Disaccharides (formed from 2 monosaccharides joined by a glycoside linkage)

sucrose (glucose + fructose)

Polysaccharides (many monosaccharide units)

starch, cellulose

141

Sucrose is a disaccharideformed from alpha-D-glucose and fructose

142

)a (The Polymer Amylose is a Major Component of Starch and is Made Up of Alpha-D-Glucose Monomers (b) The Polymer Cellulose, which Consists of Beta-D-Glucose Monomers

143

Nucleic Acids

• Life is possible because each cell when it divides can transmit the vital information about how it works to the next generation

• The substance that stores and transmits information is a polymer called deoxyribonucleic acid (DNA)

• DNA together with other similar nucleic acids called ribonucleic acids is responsible for the synthesis of various proteins needed by the cell to carry out its life functions

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Nucleic Acids

• DNA (deoxyribonucleic acids): 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)

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Monomers of nucleic acidNucleotides

1. Five-carbon sugar, deoxyribose in DNA and ribose in RNA.

2. Nitrogen containing organic base

3. Phosphoric acid molecule, H3PO4

• The base and the sugar combine to form a unit that in turn reacts with phosphoric acid to create a nucleotide• The nucleotides become connected through condensation reaction that eliminate water to give a polymer that contain a billion units.

146

The Organic Bases Found in DNA and RNA

147

The base and sugar combine to form a unit that in turn reacts with phosphoric acid to create the nucleotide, which is an ester

148

A Portion of a typical nucleic acid chain

149

Double helix formation

• According to Watson and Crick (Nobel prize winners), CAN is composed of two strands (threads) running in opposite directions that are bridged by hydrogen bonds between specific pyrimidine groups on one strand and purine group on the other

• The two strands are twisted into a double -helix structure

• The strongest hydrogen bonds form between adonine and thymine and between guanine and cystosine. Thus; A-T or G-C bonding interactions will take place

• The sequence of nucleotides on one strand of the double helix determines the sequence of the other

• The sequence of the bases determines what information is stored.

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)a (The DNA double helix contains two sugar-phosphate backbones, with the bases from the two strands hydrogen bonded to each other; the complementarity of the (b) thymine-adenine and (c) cytosine-guanine pairs

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Genetic Code and Protein Synthesis follows!!!!!!!!!!!