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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
22.1. Organic chemistry is the study of carbon compounds 4
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
22.1. Organic chemistry is the study of carbon compounds 5
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
22.1. Organic chemistry is the study of carbon compounds 6
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
22.1. Organic chemistry is the study of carbon compounds 7
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’)
22.1. Organic chemistry is the study of carbon compounds 8
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
22.1. Organic chemistry is the study of carbon compounds 9
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’)
22.1. Organic chemistry is the study of carbon compounds 10
Amines & Amides Are Polar
• Amines contain -NH2 on carbon chain (RNHR’)
• Amides contain NH2 on carbon chain with carbonyl (RCONH2)
22.1. Organic chemistry is the study of carbon compounds 11
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’)
22.1. Organic chemistry is the study of carbon compounds 12
Identify The Functional Groups Present
22.1. Organic chemistry is the study of carbon compounds 13
• 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
22.1. Organic chemistry is the study of carbon compounds 14
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
22.1. Organic chemistry is the study of carbon compounds 15
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
22.2. Hydrocarbons consist of only C and H atoms 17
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
22.2. Hydrocarbons consist of only C and H atoms 18
Learning Check
Fill in the missing atoms and derive the condensed structure
O
O
C5H12 C4H8O2
22.2. Hydrocarbons consist of only C and H atoms 19
Your Turn!
Which is the correct formula for the structure shown?
A. C42H12
B. C24H12
C. C36G12
D. None of these
22.2. Hydrocarbons consist of only C and H atoms 20
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.
22.2. Hydrocarbons consist of only C and H atoms 21
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
22.2. Hydrocarbons consist of only C and H atoms 22
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)
22.2. Hydrocarbons consist of only C and H atoms 23
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
22.2. Hydrocarbons consist of only C and H atoms 24
Name the following
3-ethyl-2-methylhexane
3-methylheptane
2,3,3,4-tetramethylhexane
3-ethyl-4-methylhexane
22.2. Hydrocarbons consist of only C and H atoms 25
Your Turn!
Name the structure shown:
A. 1,2-dimethylpentane
B. 3-methylhexane
C. 2-ethylpentane
D. None of these
22.2. Hydrocarbons consist of only C and H atoms 26
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
22.2. Hydrocarbons consist of only C and H atoms 27
• 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
22.2. Hydrocarbons consist of only C and H atoms 28
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
22.2. Hydrocarbons consist of only C and H atoms 29
Name The Following
ethylene 2,3-dimethyl-1-pentene
22.2. Hydrocarbons consist of only C and H atoms 30
Your Turn!
Which name is not correct?
A.
B.
C.
D. All are correct
3-pentene
2-pentene
2-methyl-1-butene
22.2. Hydrocarbons consist of only C and H atoms 31
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
22.2. Hydrocarbons consist of only C and H atoms 32
Your TurnWhich isomer is shown:
A. cis-
B. trans-
C. can’t tell
22.2. Hydrocarbons consist of only C and H atoms 33
• 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
22.2. Hydrocarbons consist of only C and H atoms 34
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
22.3. Ethers and alcohols are organic derivatives of water 36
• 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
22.3. Ethers and alcohols are organic derivatives of water 37
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:
22.3. Ethers and alcohols are organic derivatives of water 39
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
22.3. Ethers and alcohols are organic derivatives of water 40
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
44
Ketones
The IUPAC ending for ketones is –one. The parent chain must include the carbonyl group
propanone 3-pentanone
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
47
Your Turn!
Which of the following contain a carbonyl group?
A. amine
B. amide
C. carboxylic acid
D. All contain a carbonyl
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.5. Organic compounds with carbonyl groups include aldehydes, ketones, and carboxylic acids
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
22.6. Polymers are composed of many repeating molecular units 56
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
22.6. Polymers are composed of many repeating molecular units 57
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
22.6. Polymers are composed of many repeating molecular units 58
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
22.6. Polymers are composed of many repeating molecular units 59
Crosslinking
• Branches on polymers make them susceptible to interaction with other polymers
• Increased crosslinking leads to increased strength
• The concept behind vulcanized rubber
22.6. Polymers are composed of many repeating molecular units 60
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
22.6. Polymers are composed of many repeating molecular units 61
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
22.6. Polymers are composed of many repeating molecular units 62
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
22.6. Polymers are composed of many repeating molecular units 63
• 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
22.7. Most biochemicals are organic compounds 65
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
22.7. Most biochemicals are organic compounds 66
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
22.7. Most biochemicals are organic compounds 67
• 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
22.7. Most biochemicals are organic compounds 68
• 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
22.7. Most biochemicals are organic compounds 69
• 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
22.7. Most biochemicals are organic compounds 70
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
22.7. Most biochemicals are organic compounds 71
The lipids involved in animal cell membrane are called glycerophospholipids
The lipid molecules of animal cell membranes are organized as a bilayer.
Glycerophospholipids
22.7. Most biochemicals are organic compounds 72
Your Turn!
Which are forms of fats?
A. Lipids
B. Glycerols
C. Polysaccharides
D. All of these
22.7. Most biochemicals are organic compounds 73
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
22.7. Most biochemicals are organic compounds 74
• 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
22.8. Nucleic acids carry our genetic information 76
• 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
22.8. Nucleic acids carry our genetic information 77
Replication of DNA
22.8. Nucleic acids carry our genetic information 78
• 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
22.8. Nucleic acids carry our genetic information 79
• 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
22.8. Nucleic acids carry our genetic information 80
• 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
22.8. Nucleic acids carry our genetic information 81
• 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
22.8. Nucleic acids carry our genetic information 82
• 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
22.8. Nucleic acids carry our genetic information 83
Your Turn!
How many types of RNA are there in a living organism?
A. 1
B. 2
C. 3
D. 4
22.8. Nucleic acids carry our genetic information 84
Your Turn!
How many types of DNA are there in a living organism?
A. 1
B. 2
C. 3
D. 4