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Chapter 25: Organic Compounds and

Biochemicals
•  Organic chemistry is the study of the
compounds of carbon not classified as
inorganic
•  Of the several million known compounds of
carbon, only a very few are not organic
•  Carbon atoms are unique because they form
strong covalent bonds with each other while
at the same time binding atoms of other
nonmetals strongly
•  Isomers are compounds with identical
molecular formulas, but whose molecules
have different structures
•  Organic compounds are rich in isomers
Formula Number of Isomers
C8H18 18
C10H22 75
C20H42 366,319
C40H82 6.25x1013 (estimated)
•  Organic families are defined by functional
groups
•  Functional groups are small structural units
within a molecule at which most of the
compound’s reactions occur
•  Condensed structures are usually used to
represent organic molecules
•  C-H bonds are usually understood
•  Lone pairs of electrons are not shown
•  These saves both time and space when writing
formulas
Characteristic
Family Feature Example Some Important Families
Alkanes only single bonds CH 3CH 3
of Organic Compounds
Alkenes C=C CH 2 = CH 2
Alkynes C≡C CH ≡ CH
Alcohols ROH CH 3CH 2 OH
Ethers ROR' CH 3OCH 3
O O
|| ||
Aldehydes RCH CH 3 C H
O O
|| ||
Ketones R C R' CH 3 C CH 3
O O
|| ||
Carboxylic acids R C OH CH 3 C OH
O O
|| ||
Esters R C OR' CH 3 C OCH 3
Amines RNH 2 CH 3 NH 2
More general forms of
O O
both amines and amides
Amides
||
R C NH 2 CH 3 C NH 2
||
exist.
R and R' represent any alkyl (purely alkine - like) group
•  An advantage to collecting molecules into
families is 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 generally
expected to occur
Carbon atoms can be
found in continuous
sequences (called
straight chained
molecules) or with
“branches” off the
main chain (called
branched
compounds).
•  Carbon can also form rings
Rings are often
represented as
polygons where
the corners
represent carbon
atoms. Heterocylic
rings contain
atoms other than
carbon, called
heteroatoms.
•  The functional groups and size, for
example, determine if a molecule is soluble
in water
–  Hydrocarbons are only slightly polar and tend
to be insoluble in water
•  These include alkanes, alkenes, alkynes, and
aromatic compounds
–  Molecules with polar functional groups tend to
be soluble in water
•  These include alcohols, carboxylic acids, amines,
and amides
–  Large molecules, even if they contain polar
functional groups, tend to be insoluble
•  Alkanes are hydrocarbons that contain only
single bonds
•  They are called saturated compounds
•  Hydrocarbons with double or triple bonds
(alkenes, alkynes, and aromatic compounds)
are called unsaturated compounds
•  Many hydrocarbons come from fossil fuels
(coal, petroleum, and natural gas)
•  One operation in petroleum refining is to
boil the crude oil and selectively condense
the vapors between preselected temperature
ranges
•  The liquid collected at each range is called a
fraction and the process is called fractional
distillation
•  Each fraction is made almost entirely of
alkanes
•  For example, gasoline is the fraction collected
between about 40 and 200oC
•  All open-chain alkanes have the general
formula CnH2n+2, where n is the number of
carbon atoms in the chain
•  Their boiling point increases with mass (see
Table 25.2) as their London forces become
greater with molecular size
•  The International Union of Pure and
Applied Chemistry (IUPAC) rules for
organic nomenclature are very systematic
•  IUPAC rules for naming the alkanes
1)  The name ending for all alkanes is –ane.
2)  The parent chain is the longest continuous chain
of carbons in the structure.
3)  A prefix is added to the name ending –ane to
specify the number of carbon atoms in the parent
chain. The prefixes for up to ten carbons are:
meth- 1 C eth- 2C prop- 3 C
but- 4C pent- 5C hex- 6 C
hept- 7 C oct- 8C non- 9 C
dec- 10 C
4) The carbon atoms are number from the end that
gives the lower of the two possible numbers for the
first branch.
5) Each branch attached to the parent is named as an
alkyl group, which is an alkane with one hydrogen
removed to allow attachment to the parent chain.
The names of alkyl groups end in –yl.
methyl − CH 3 −
ethyl − CH 3CH 2 −
propyl − CH 3CH 2 CH 2 −
isoproply − CH 3 C HCH 3
|
6) The name of each alkyl group is attached to the
name of the parent as a prefix, each is named and
located with a number in front, separating the
number from the name by a hyphen.
7) When two or more groups are attached the parent,
each is named and located with a number. The
names of the alkyl substituents are assembled in
alphabetical order. Use hyphens to separate the
numbers from words.
8) When two or more substituents are identical,
multiplier prefixes are used: di (for 2), tri (for 3),
trtra (4), and so forth. The location number of every
group must appear in the final name. Separate a
number from a number with a comma.
9) When identical groups are on the same atom, the
number of this position is repeated in the name.
CH 3
|
Example : CH 3 − C − CH 2CH 3
|
CH 3
2,2 - dimethylbutane

•  Alkanes are generally stable at room


temperature
•  They burn in air to given carbon dioxide
•  When heated at high temperature they
“crack”, meaning they break up into smaller
molecules
CH 4 ⎯high
⎯ ⎯temperature
⎯⎯→ C + 2H 2
high temperature
CH 3CH 3 ⎯⎯ ⎯ ⎯⎯→ H 2 C = CH 2 + H 2
ethane ethene
•  Hydrocarbons with one or more double
bonds are members of the alkene family
–  Open chain alkenes have the general formula
C2H2n
•  Hydrocarbons with one or more triple bonds
are members of the alkyne family
–  Open chain alkynes have the general formula
CnH2n-2
•  Like all hydrocarbons, alkenes and alkynes
are insoluble in water and flammable
•  IUPAC rules for alkenes are adaptations of
those for alkanes
•  The parent must include the double bond
•  The parent chain is number from the end that gives
the first carbon of the double bond the lower of two
possible numbers
•  Some alkenes have two double bonds and
are called dienes, some have three double
bonds and are called trienes, and so forth
•  Each double bond has to be located by a
number
•  Example: CH2=CHCH=CHCH3 is 1,3-pentadiene
•  There is no free rotation about the carbon-
carbon double bond
•  Thus, many alkenes exhibit geometric
isomerism
CH 3 CH 3 CH 3 H
| | | |
C = C C = C
| | | |
H H H CH 3
cis − 2 - butene trans − 2 - butene
o o
bp 3.72 C bp 0.88 C

•  Alkenes undergo addition reactions,


reactions which eliminate the pi-bond
CH2=CH2 + HCl(g) à Cl- CH2-CH3
•  Other inorganic compounds that undergo addition
reactions with alkenes include: water, chlorine,
bromine, iodine, and hydrogen
–  Ozone reacts with anything that has a carbon-
carbon double or triple bond, forming a variety
of products
•  This high reactivity makes it dangerous because
may important compounds in living systems contain
double bonds
–  Aromatic compounds undergo substitution
reactions instead of addition reactions because
of the resonance energy of the ring
–  Example: C6H6+Cl2àC6H5Cl+HCl
•  When an alkyl group replaces a hydrogen in
water, an alcohol results
–  IUPAC names for alcohols: The name ending
for alcohols is –ol. The parent chain must
include the carbon containing the OH group
•  Examples: CH3OH is methanol and CH3CH2CH2OH
is 1-propanol
•  Ethers result when both hydrogens in water
are replaced with alkyl groups
•  Some common names: CH3OCH3 is dimethyl ether,
CH3CH2OCH3 is ethyl methyl ether, and
CH3CH2OCH2CH3 is diethyl ether
•  Ethers are almost as chemically inert as
alkanes: they burn and are split apart when
boiled in concentrated acid
•  Alcohols undergo a number of reactions
–  Oxidation of alcohols: if the alcohol carbon
atom holds at least one H atom, it can be
replaced with bonds to oxygen
O O
|| Further ||
oxidation oxidation
RCH 2OH ⎯⎯ ⎯
⎯→ R C H ⎯⎯ ⎯
⎯→ R C OH
alcohol aldehyde carboxylic acid
O O
|| Further ||
oxidation oxidation
CH 3CH 2OH ⎯⎯ ⎯
⎯→ CH 3 C H ⎯⎯ ⎯
⎯→ CH 3 C OH
–  Dehydration of alcohols: this is the “reverse”
the the addition of water to an alkene. It is an
example of an elimination reaction
CH 3 C H C H 2 → CH 3CH = CH 2 + H 2O
| |
H OH
–  Substitution reactions of alcohols: under acidic
conditions, the OH group can be replaced by a
halogen atom
CH 3CH 2CH 2OH + HBr (conc) → CH 3CH 2CH 2 Br + H 2O
1 - propanol 1 - bromopropane
•  Amines are derivatives of ammonia where
one or more hydrogens have been replaced
with alkyl groups
•  Some common names and boiling points (bp): NH3
is ammonia (bp –33.4oC), CH3NH2 is methylamine
(bp –8oC), (CH3)2NH is dimethylamine (bp 8oC),
and (CH3)3N is trimethylamine (bp 3oC).
•  Amines are bases, and react with strong
proton donors to form ammonium ion-like
structures
•  This can greatly increase their solubility in
water
NH 3 (aq ) + H + (aq ) → NH 4+ (aq )
CH 3CH 2 NH 2 (aq ) + H + (aq ) → CH 3CH 2 NH 3+ (aq )
•  Protonated amines (like protonated
ammonia) are weak acids that can react with
base
NH 4+ (aq ) + OH − (aq ) → NH 3 (aq ) + H 2O
CH 3CH 2 NH 3+ (aq ) + OH − (aq ) → CH 3CH 2 NH 2 (aq ) + H 2O
•  The carbonyl group, C=O, occurs in several
organic families
•  What is attached to the C=O determines the
specific family
O O O
|| || ||
RC H R C R' R C OH
aldehyde ketone carboxylic acid
•  Aldehydes and ketones
–  The IUPAC name ending for an aldehyde is –al.
The parent chain is the longest chain that
includes the aldehyde group.
O O O
|| || ||
HCH CH 3 C H CH 3CH 2 C H
methanal ethanal propanal
(bp − 21o C) (bp 21o C) (bp 49o C)
–  The IUPAC ending for ketones is –one. The
parent chain must include the carbonyl group
O O
|| ||
CH 3 C CH 3 CH 3CH 2 C CH 2CH 3
propanone 3 - pentanone
(bp 56.5o C) (bp 101.5o C)
–  Aldehydes and ketones can be hydrogenated to
give alcohols
O
||
CH 3CH 3 C H + H 2 → CH 3CH 2 CH 2OH 1 - propanol
O OH
|| |
CH 3 C CH 3 + H 2 → CH 3 C H CH 3 2 - propanol
–  Aldehydes undergo oxidation to form
carboxylic acids, while ketones strongly resist
oxidation
•  The IUPAC name ending for carboxylic
acids is –oic acid. The parent chain must
include the carbonyl carbon, which is
numbered as position 1
O O
|| ||
H C OH CH 3CH 2 C OH
methanoic acid ethanoic acid
(bp 101o C) (bp 118 o C)
•  Carboxylic acids are used to synthesize two
important derivatives of the acids, esters
and amides
•  In esters, the OH of the carboxyl group is
replaced by OR
•  The IUPAC names for esters begins with
the name of 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
O O
|| ||
H C OCH 3 CH 3 C OCH 2CH 3
methyl methanoate ethyl ethanoate
(bp 31.5o C) (bp 77 o C)
•  Esters can be prepared by heating the parent
acid with an alcohol in the presence of an
acid catalyst
O O
|| ||
H+
R C OH + HOR' ⎯⎯→ R C OR'+ H 2O
O O
|| ||
H+
CH 3 CH 2 C OH + HOCH 2CH 3 ⎯⎯→ CH 3 CH 2 C OCH 2CH 3 + H 2O
ethanoic acid ethanol ethyl ethanoate
•  The reaction is reversible
•  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
O
||
CH 3 CH 2 C OCH 2CH 3 (aq ) + NaOH (aq ) ⎯heat
⎯→
⎯
ethyl ethanoate
O
||
CH 3 CH 2 C O − (aq ) + Na + (aq ) + CH 3CH 2OH
ethanoate ion ethanol
•  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
hydrogens
•  The IUPAC names of simple amides are
generated by replacing the –oic acid of the
parent carboxylic acid with -amide
CH 3
|
CH 3CH 2CONH 2 CH 3CH 2 − CH − CONH 2
propanamide 2 - methylbutanamide
•  One way to prepare simple amides is by
heating a carboxylic acid in excess
ammonia
O O
|| ||
heat
R C OH + NH 3 ⎯⎯→
⎯ R C NH 2 + H 2O
O O
|| ||
heat
CH 3CH 2 C OH + NH 3 ⎯⎯→
⎯ CH 3CH 2 C NH 2 + H 2O
propanoic acid propanamide
•  Amides, like esters, can be hydrolyzed
O O
|| ||
heat
R C NH 2 + H 2O ⎯⎯→
⎯ R C OH + NH 3
O O
|| ||
heat
CH 3CH 2 C NH 2 + H 2O ⎯⎯→
⎯ CH 3CH 2 C OH + NH 3
propanamide propanoic acid
•  Amides are not bases
•  The O on the carbonyl draws electron
density to itself and “tightens” the unshared
electrons on N, “preventing” their donation
•  Biochemistry is the systematic study of the
chemicals of living things
•  Living things are composed mostly of
organic compounds
•  Living systems require materials, energy,
and information or “blueprints”
•  This brief survey of biochemistry
concentrates mostly on the structures of
selected biochemical materials
•  A variety of compounds are required for
cells to work:
–  Lipids include fats and oils. They are a major
component of the membranes that surround the
cells and a source of chemical energy.
–  Carbohydrates include starch, table sugar, and
cotton. They are a major source of chemical
energy.
–  Proteins are found, for example, in meat and
eggs. Enzymes (chemical catalysts) and many
hormones are proteins.
–  Nucleic acids, as genetic code, store the
information required to operate a living system.
Defects in the code are responsible for diseases like
cystic fibrosis and sickle-cell anemia
•  Carbohydrates are naturally occurring
polyhydroxyaldehydes or polyhydroxyketones,
or else compounds that react with water to give
these
•  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
•  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
•  Polysaccharides are naturally occurring
polymers whose molecules involve
thousands of monosaccharide units linked to
each other by oxygen bridges
–  They include starch, glycogen, and cellulose all
of which give only glucose upon hydrolysis
•  Plants store energy as starch
–  The hydrolysis of amylose (the simplest starch)
can be represented as:
Glu − (O − Glu) n − OH + nH 2O → n glucose
amylose (n is large)
•  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
•  Lipids are natural products that are
nonpolar, so they do not dissolve in water
•  The lipid family is very large
–  Triacylglycerols are esters between glycerol
and include edible fats and oils like olive oil,
butterfat, and lard
•  They are called vegetable oils when derived from
plants and animal fats when derived from animals,
and are made from fatty acids
•  The vegetable oils tend to have more alkene double
bonds per molecule than animal fats and are said to
be polyunsaturated
•  The lipids involved in animal cell
membrane are called glycerophospholipids

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


•  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”
–  If a pin were stuck into the lipid bilayer and
withdrawn, it would automatically close up
•  Proteins are a huge family of substances
that make up about half of a humans dry
weight
•  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
Some proteins consist
exclusively of polypeptide
molecules, but most also
have nonpolypeptide units
such as small organic
molecules, metal ions, or
both.
•  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
•  Some of the most deadly poisons work by
deactivating enzymes
Deoxyribonucleic acid,
or DNA, is a nucleic
acid and carries genetic
information. It is found
as a double helix in
cells. (a) A schematic
drawing in which the
hydrogen bonds
between the two strands
are indicated by dotted
lines. (a) A model of a
short section of DNA.
The “backbones” are in
blue.
•  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
•  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
•  Each polypeptide in a cell is made under the
direction of its own gene
•  The production of a polypeptide can be
represented as:
DNA ⎯transcript
⎯⎯⎯ ion
→ RNA ⎯translatio
⎯⎯⎯n → polypeptide
–  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
•  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. Ribosomes are
manufacturing stations for polypeptides.
–  Messenger RNA or mRNA brings the
blueprints for particular polypeptide to the
manufacturing station (ribosome)
–  Heterogeneous nuclear RNA or hnRNA has
responsibility for picking up the
“prefabricated” parts (amino acids) and getting
them to the ribosome.
•  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
•  Viruses are packages of chemicals usually
consisting of nucleic acid and protein
•  Their nucleic acid is capable of taking 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
•  In genetic engineering, the genetic
machinery of a microorganism is taken over
–  The idea is to get it to make a useful molecule,
such as human insulin which is needed by
diabetics
•  Certain strains of bacteria can be modified to
introduce genes that the bacteria normally do
not have
•  Bacteria carry DNA in large, circular,
supercoiled DNA molecules called plasmids
•  Each plasmid carries just a few genes
•  Plasmids can be removed, modified, and re-
inserted into the bacteria
•  The changed plasmid DNA is called
recombinant DNA
•  When these bacteria reproduce, they
produce more of the altered plasmids
•  The bacteria then manufacture the proteins
specified by the recombinant DNA
•  Genetic engineering has considerable
promise
•  In the future it may be possible to correct
genetic defects by introducing altered
viruses that contribute the “information”
needed to correct the defect

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