Ch 22. Organic Compounds, Polymers,and Biochemicals

Ch 22. Organic Compounds, Polymers,and Biochemicals

Brady & Senese, 5th Ed.

2

22.1. Organic chemistry is the study of carbon compounds22.2. Hydrocarbons consist of only C and H atoms22.3. Ethers and alcohols are organic derivatives of water22.4. Amines are organic derivatives of ammonia22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids22.6. Polymers are composed of many repeating molecular

units22.7. Most biochemicals are organic compounds22.8. Nucleic acids carry our genetic information

Index

22.1. Organic chemistry is the study of carbon compounds 3

Organic Compounds Are Diverse

Carbon compounds are greatly variant due to the properties of C: C is able to bond multiply C is able to catenate C is able to bond with a wide variety of elements Isomers are possible when there is a carbon chain Combinations of functional groups give great diversity Carbon can form rings


Carbon Compounds

• Carbon containing compounds exist in large variety, mostly due to the multiple ways in which C can form bonds

• Some groups of atoms with similar bonding are commonly seen, called functional groups.

• Molecules may contain more than one functional group

• Can form chiral compounds


VSEPR Structures

HC

CC

CC

H

H H H

HH

H H H

HH

• Show all atoms• Show attachments between atoms but not how many

pairs of electrons were used• Show the geometric arrangement of the atoms


Condensed Structures

CH3CH2CH2CH2CH3

• show the general arrangement of the atoms and the number of atoms

• no effort is made to indicate geometry, types of bonds, or lone pairs


Alcohols & Ethers Are Polar

• Contain C, H, and O, all with single bonds.• Alcohols end in –OH (R-OH)• Ethers have an O atom in the chain (R-O-R’)


The Carbonyl Group

• When C in a chain has a double bond to an oxygen, the group is termed a carbonyl

• Aldehydes, ketones, carboxylic acids, and amides all contain carbonyl groups

acid carboxylic ketone aldehyde

O ' ||||||

H

O

CRR

O

CRH

O

CR


Aldehydes & Ketones Are Polar

• Each has a carbon chain terminating in a carbonyl.• Aldehydes then have an added H (RCOH)• Ketones have another carbon chain (RCOR’)


Amines & Amides Are Polar

• Amines contain -NH2 on carbon chain (RNHR’)

• Amides contain NH2 on carbon chain with carbonyl (RCONH2)


Carboxylic Acids & Esters Are Polar

• Both have a carbon chain terminating in a carbonyl

• Carboxylic acids then have an –OH group• A combined carbonyl and hydroxyl group form a

carboxyl group (RCOOH)• Esters then have a singly bound O, then another

carbon chain (RCOOR’)


Identify The Functional Groups Present


• Collecting molecules into families means that only a few kinds of reactions must be learned

• The emphasis is on the properties of the functional group, not individual molecules

• Once the center of reactivity is identified, its characteristic reactions are expected to occur

Using Functional Groups


Functional Groups And Their Properties

• Polar functional groups contain O and N • Like dissolves like: polar solvents will dissolve

the polar functional groups• As the carbon chain increases in size, the polarity

decreases


Your Turn!

Which of the following contains an amide group?

A. The top structure

B. The middle structure

C. The bottom structure

D. None of these

22.2. Hydrocarbons consist of only C and H atoms 16

Lewis Structures Of Hydrocarbons

H C C C C C H

H

H

H

H

H

H

H

H

H

H

• Show all atoms, and all electrons• Bond pairs usually shown as a line• Non-bonding (lone) pairs of electrons are shown

as dots


Stick Figures

• Each vertex and terminus is a carbon• Assumes that the termini contain as many H as

needed for saturation of the C (hydrogens attached to hetero-atoms are shown)

• All hetero-atoms are shown explicitly• Double bonds explicitly shown

HC

CC

CC

H

H H H

HH

H H H

HH

CC

CC

C


Learning Check

Fill in the missing atoms and derive the condensed structure

O

O

C5H12 C4H8O2


Your Turn!

Which is the correct formula for the structure shown?

A. C42H12

B. C24H12

C. C36G12

D. None of these


Alkanes & Alkenes Are Non-polar

• Alkanes are hydrocarbons (contain only C and H) have a ratio of atoms CnH2n+2

• Alkenes- hydrocarbons with fewer H than the alkanes (CnH2n) Use the same prefixes, but have the suffix -ene.


Alkanes (CnH2n+2)

• Composed of hydrocarbon chains in which carbons are attached to one another by single bonds

• Are named by the number of C in the chain and where any substitutions are found

• Prefixes and the associated numbers of carbon atomsmeth-1 hex-6

eth-2 hept-7

prop-3 oct-8

but-4 non-9

pent-5 dec-10


Naming Alkanes

1. Find the longest continuous chain of carbons-the root.

2. a. Name the root by adding “-ane” to the appropriate prefix (a 4-carbon chain would be butane)b. Identify any branches, and name each by the

number of carbons (a 1-carbon branch is methyl-)3. a. List side chains in alphabetical order, before the

rootb. Use di, tri, tetra (etc…) if you have more than one of something (these do not count in alphabetizing)


Naming (Cont.)

4. Number root from side closest to the first branch

5. Use numbers to tell where the side chains sprout from the root

6. Put a dash between any number and letter or any letter and number. Use a comma between two numbers

7. Use the prefix “cyclo” for ring systems


Name the following

3-ethyl-2-methylhexane

3-methylheptane

2,3,3,4-tetramethylhexane

3-ethyl-4-methylhexane


Your Turn!

Name the structure shown:

A. 1,2-dimethylpentane

B. 3-methylhexane

C. 2-ethylpentane

D. None of these


Reactions Of Alkanes

• Alkanes are generally stable at room temperature• They burn in air to given carbon dioxide• When heated at high temperature they crack (break into

smaller molecules)

ethene ethane

HCHCHCHCH

2HCCH

222raturehigh tempe

33

2raturehigh tempe

4


• Hydrocarbons with one or more double bonds are members of the alkene family open chain alkenes have the general formula C2H2n

• Hydrocarbons with triple bonds are in the alkyne family open chain alkynes have the general formula, CnH2n−2

Unsaturated Hydrocarbons


Naming Alkenes

• The parent chain must include the double bond• The parent alkene chain must be numbered from

whichever end gives the first carbon of the double bond the lowest number

• This number, followed by a hyphen, precedes the name of the parent chain, unless there is no ambiguity about where the double bond occurs

• The locations of branches are not a factor in numbering the chain

• Alkyl groups are named and located as before


Name The Following

ethylene 2,3-dimethyl-1-pentene


Your Turn!

Which name is not correct?

A.

B.

C.

D. All are correct

3-pentene

2-pentene

2-methyl-1-butene


Geometric Isomers

• Cis and trans isomers exist when there is a plane of a double bond or of a ring structure

• cis –same• trans-opposite


Your TurnWhich isomer is shown:

A. cis-

B. trans-

C. can’t tell


• Alkenes undergo addition reactions that eliminate the pi-bond CH2=CH2 + HCl(g) Cl- CH2-CH3

• Inorganic compounds that undergo addition reactions with alkenes include: H2O, Cl2, Br2, I2, and H2.

• Ozone (O3) reacts with anything that has a carbon-carbon double or triple bond, forming a variety of products

Addition Reactions of Alkenes


Aromatic Compounds

• Contain a benzene(C6H5-) ring with delocalized electrons

• Aromatic compounds undergo substitution reactions instead of addition reactions because of the resonance energy of the ring example: C6H6 + Cl2C6H5Cl + HCl

22.3. Ethers and alcohols are organic derivatives of water 35

Ethers (ROR’)

• Result when both hydrogen atoms in water are replaced with alkyl groups

• Are almost as chemically inert as alkanes: they burn and are split apart when boiled in concentrated acid

• Are named by naming each alkyl group, alphabetically, and end with “ether”

• Learning Check: CH3OCH3 CH3CH2OCH3

CH3CH2OCH2CH3

dimethyl etherethyl methyl etherdiethyl ether


• When an alkyl group replaces a hydrogen in water, an alcohol results

• The name ending for alcohols is –ol • The parent chain must include the carbon containing the

OH group• Learning Check: Name the following

CH3CH2OH

CH3CH2CH2CH2OH

Alcohols (ROH)

ethanolbutanol


If the alcohol carbon atom holds at least one H atom, it can be replaced with bonds to oxygen

OH

O

CCHH

O

CCHOHCHCH

acid carboxylic aldehyde alcohol

OH

O

CRH

O

CROHRCH

||

3oxidationFurther||

3oxidation

23

||oxidationFurther||

oxidation2

Oxidation of Alcohols

22.3.Ethers and alcohols are organic derivatives of water 38

The “reverse” the the addition of water to an alkene, it is an example of an elimination reaction

OHCHCHCHH

OH

CH

H

CCH 2232||

3

Dehydration Of Alcohols:


Substitution Reactions Of Alcohols

Under acidic conditions, the -OH group can be replaced by a halogen atom

nebromopropa-1 propanol-1

OHBrCHCHCHHBr(conc)OHCHCHCH 2223223


Your Turn!

What type of structure is shown

A. Alcohol

B. Ether

C. Peroxide

D. aldehyde

22.4. Amines are organic derivatives of ammonia 41

Amines

• Are derivatives of ammonia where one or more hydrogens have been replaced with alkyl groups NH3 is ammonia

CH3NH2 is methylamine

(CH3)2NH is dimethylamine and (CH3)3N is trimethylamine (bp 3oC).

• Amines are bases, and react with strong proton donors to form ammonium ion-like structures

(aq)NHCHCH(aq)H(aq)NHCHCH

(aq)NH(aq)H(aq)NH

323223

43

22.4. Amines are organic derivatives of ammonia 42

• Are more soluble in water than amines• Protonated amines (like protonated ammonia) are weak

acids that can react with base

OH(aq)NHCHCH(aq)OH(aq)NHCHCH

OH(aq)NH(aq)OH(aq)NH

2223323

234

Protonated Amines

22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids

43

• The IUPAC name ending for an aldehyde is –al• The parent chain is the longest chain that includes

the aldehyde group

Aldehydes


44

Ketones

The IUPAC ending for ketones is –one. The parent chain must include the carbonyl group

propanone 3-pentanone


45

Reactions Of Aldehydes & Ketones

• Aldehydes and ketones can be hydrogenated to give alcohols

• Aldehydes undergo oxidation to form carboxylic acids, while ketones strongly resist oxidation

propanol-2 CHH

OH

CCH HCH

O

CCH

propanol-1OH CH CHCH H H

O

CCHCH

3

|

323

||

3

2232

||

33


46

Carboxylic Acids

The IUPAC name ending for carboxylic acids is –oic acid. the parent chain must include the carbonyl carbon, which is numbered as position 1

The common names are used for these: formic acid and acetic acid


47

Your Turn!

Which of the following contain a carbonyl group?

A. amine

B. amide

C. carboxylic acid

D. All contain a carbonyl


48

Esters

• In esters, the OH of the carboxyl group is replaced by -OR’

• Name the alkyl group attached to the O atom followed by a separate word generated from the name of the parent acid by changing –oic acid to -ate

methyl methanoate ethyl ethanoate


49

Esters can be prepared by heating the parent acid with an alcohol in the presence of an acid catalyst

ethanoate ethyl ethanol acid ethanoic

OHCHOCH

O

CCH CHCHHOCHOH

O

CCH CH

OHOR'

O

CRHOR'OH

O

CR

232

||

23H

32

||

23

2

||H

||

Preparation Of Esters


50

• Carboxylic acids and alcohols can be obtained by heating esters with acid in a large excess of water

• Esters are split apart by the action of base in a reaction called saponification

ethanol ion ethanoate

)()(

ethanoate ethyl

)()(

23

||

23

32

||

23

OHCHCHaqNaaqO

O

CCHCH

aqNaOHaqCHOCH

O

CCHCH heat

Reactions of Esters


51

Amides (RCONH2)

• Carboxylic acids can also be converted into amides, a functional group found in proteins

• Simple amides are those in which the nitrogen bears no alkyl groups, only hydrogen atoms

• The IUPAC names of simple amides are generated by replacing the –oic acid of the parent carboxylic acid with -amide

O

NH2

propanamide

O

H2N

2-methyl-butanamide


52

One way to prepare simple amides is by heating a carboxylic acid in excess ammonia

epropanamid acid propanoic22

||

233

||

23

22

||

3

||

OHNH

O

CCHCHNHOH

O

CCHCH

OHNH

O

CRNHOH

O

CR

heat

heat

Preparation of Amides


53

• Amides, like esters, can be hydrolyzed

• Amides are not bases; the O on the carbonyl draws electron density to itself and “tightens” the unshared electrons on N, “preventing” their donation

acid propanoic epropanamid 3

||

2322

||

23

3

||

22

||

NHOH

O

CCHCHOHNH

O

CCHCH

NHOH

O

CROHNH

O

CR

heat

heat

Reactions of Amides


54

Your Turn!

Which of these can be hydrolyzed (react with water)

A. amides

B. alkanes

C. alcohols

D. None of these

22.6. Polymers are composed of many repeating molecular units 55

Polymers

Are large molecules with repeating units called monomers


Formation Of Addition Polymers

• Initiators attack a monomer and make it receptive for the new bond

• Addition polymers are assembled from molecular units that combine to form one larger molecule


Addition Polymer: Polystyrene

• Styrene is treated with an initiator to form a free radical

• Radical end is free to form a new connection to another styrene molecule


Formation Of Condensation Polymers

Condensation polymers are formed when monomers add and lose a small molecule

• adipic acid and hexamethylene diamine combine and eliminate water to form Nylon 6,6

• The ends are free to continue the process


Crosslinking

• Branches on polymers make them susceptible to interaction with other polymers

• Increased crosslinking leads to increased strength

• The concept behind vulcanized rubber


Learning Check: Teflon

Is formed from the monomer F2C═CF2 . Based on the structure of polytetrafluoroethylene (PFTE), is this an addition or a condensation polymer?

addition


The Polyethylenes: LDPE, HDPE and UHMWPE • Have widely disparate

properties due to the degree of order low density (LD) PE with an

unordered crystal, is used for grocery sacks

high density (HD) PE with highly structured crystal is very strong and used in TYVEK

ultra-high molecular weight (UHMW) PE has very long HDPE fibers and is used in bulletproof vests and sails


Your Turn!

One form of “Gak” can be made by combining dissolved white glue and dissolved borax powder. What characteristics would you expect if the amount of cross-linker (the borax) is increased in the blend?

A. It becomes more viscous

B. It becomes more solid

C. It tears rather than stretches

D. All of the above


• The systematic study of the chemicals of living things• A variety of compounds are required for cells to work:

lipids carbohydrates proteins nucleic acids

Biochemistry

22.7. Most biochemicals are organic compounds 64

• Are naturally occurring polyhydroxyaldehydes or polyhydroxyketones, or else compounds that react with water to give these

• Types: monosaccharides disaccharides polysaccharides

Carbohydrates


Monosaccharides

• Are carbohydrates that do not react with water• The most common monosaccharide is glucose

(pentahydroxyaldehyde) glucose is the chief carbohydrate in blood, and provides

a building units for polysaccharides like cellulose and starch

OHOH

OH

OH

O

OH

CHCH

CH

CH CH

CH2

O

CHCHC

HCHC

HCH2

OH

OH

OH

OH

OH

glucose (open chain polyhydroxyaldehyde) α-glucose


Disaccharides

Are carbohydrates that split into two monosaccharide molecules by reacting with water example: sucrose (table sugar, cane sugar, or beet

sugar) which gives glucose and fructose upon hydrolysis


• Are naturally occurring polymers whose molecules involve thousands of monosaccharide units linked to each other by oxygen bridges include starch, glycogen, and cellulose -all give only

glucose upon hydrolysis plants store energy as starch the hydrolysis of amylose (the simplest starch) can be

represented as:

large) is(n amylose

glucose )( 2 nOnHOHGluOGlu n

Polysaccharides


• Animals store glucose for energy as glycogen excess glucose is converted to glycogen by liver and

muscle cells and stored for later use

• Cellulose, a chief component of plant cell walls, is a polymer of glucose that requires a special enzyme to hydrolyze humans lack this enzyme and so are unable to use

cellulose for food cellulose is the “fiber” found in foods like lettuce

Storage of glucose


• Are fats and oils that are non-polar, so they do not dissolve in water

• Are amphipathic: the purely hydrocarbon-like portions (the long R groups

contributed by the fatty acids) avoid water and are called hydrophobic or “water fearing”

the polar heads are hydrophilic or “water loving

Lipids


Triacylglycerols

• Are esters between glycerol and include edible fats and oils like olive oil, butterfat, and lard

• Are called vegetable oils when derived from plants and animal fats when derived from animals, and are made from fatty acids

• Are said to be polyunsaturated; vegetable oils tend to have more alkene double bonds per molecule than animal fats


The lipids involved in animal cell membrane are called glycerophospholipids

The lipid molecules of animal cell membranes are organized as a bilayer.

Glycerophospholipids


Your Turn!

Which are forms of fats?

A. Lipids

B. Glycerols

C. Polysaccharides

D. All of these


Proteins

• The dominant structural units of proteins are macromolecules called polypeptides polypeptides are made from a set of about 20

monomers called amino acids polypeptides are copolymers of the amino acids


• The final shape of a protein, called its native form, is critical to its ability to function

• Physical agents such as heat, poisons, and certain solvents can alter a proteins native form when this happened the protein is said to have been

denatured

• Enzymes are the catalysts in living cells• Virtually all enzymes are proteins

Reactions of Proteins

22.8. Nucleic acids carry our genetic information 75

• Carry the genetic code

• Are made of amino acids

Nucleic Acids


• The best hydrogen bonds are formed when the base pairs that makeup the backbone “match” Adenine (A) pairs with thymine (T), cytosine (C) pairs with

guanine (G), etc

• DNA replicates itself by splitting the “parent” DNA double helix and assembling the matching base pairs on each strand The result is two “daughter” DNA double helixes

Reactions of DNA


Replication of DNA


• A single human gene has between 1000 and 3000 bases the bases do not occur continuously on a DNA

molecule the separated segments of a DNA chain that make up

a gene are called exons because that unit helps to express a message

the sections of DNA between the exons are called introns because they are units that interrupt the gene

DNA Characteristics


• Each polypeptide in a cell is made under the direction of its own gene

• The production of a polypeptide can be represented as:

Transcription: the genetic message is read off in the cell nucleus and transferred to ribonucleic acid (RNA)

Translation: the genetic message, now on RNA outside the nucleus, is used to direct the synthesis of a polypeptide

epolypeptidRNADNA ntranslatioiontranscript

Preparation of Polypeptides


• Four types of RNA are involved in the connection of the gene to the polypeptide ribosomal RNA or rRNA is packed together with

enzymes in ribosomes, the manufacturing stations for polypeptides.

messenger RNA or mRNA brings the blueprints for particular polypeptide to the manufacturing station (ribosome)

heterogeneous nuclear RNA or hnRNA carries the “prefabricated” parts (amino acids) to the ribosome

transfer RNA or t-RNA carries amino acids to the ribosomes

RNA


• About 2000 diseases are attributed to various kinds of defects in the genetic machinery of cells if a single base is wrong in a gene, it could result in

a completely different polypeptide being produced, possibly with fatal consequences

• Atomic radiation and chemical agents can also cause defects, possibly causing cancer

Genetic Defects


• Viruses are packages of chemicals usually consisting of nucleic acid and protein

• Their nucleic acid takes over the genetic machinery in certain cells of the host tissues causing them to manufacture more virus particles

• The host cell bursts, releasing the newly manufactured viruses, which can infect more cells

Viruses


Your Turn!

How many types of RNA are there in a living organism?

A. 1

B. 2

C. 3

D. 4


Your Turn!

How many types of DNA are there in a living organism?

A. 1

B. 2

C. 3

D. 4

Ch 22. Organic Compounds, Polymers,and Biochemicals

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