Chapter 25: Organic Compounds and Biochemicals

1
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

2

• Isomers are compounds with identical molecular
  formulas, but whose molecules have different
  structures
• Organic compounds are rich in isomers

3

• Organic families are defined by functional groups
  
• Functional groups are small structural units
  within a molecule at which most of the compounds
  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

4
Some Important Families of Organic Compounds

More general forms of both amines and amides
exist.
5

• 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

6

Carbon atoms can be found in continuous sequences
(called straight chained molecules) or with
branches off the main chain (called branched
compounds).
7

• 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.
8

• 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

9

• 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)

10

• 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

11

• All open-chain alkanes have the general formula
  CnH2n2, 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

12

• IUPAC rules for naming the alkanes
• The name ending for all alkanes is ane.
• The parent chain is the longest continuous chain
  of carbons in the structure.
• 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

13

• 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.

14

• 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.

15

• 9) When identical groups are on the same atom,
  the number of this position is repeated in the
  name.
• Alkanes are generally stable at room temperature
• They burn in air to given carbon dioxide

16

• When heated at high temperature they crack,
  meaning they break up into smaller molecules
• Hydrocarbons with one or more double bonds are
  members of the alkene family
• Open chain alkenes have the general formula C2H2n

17

• 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

18

• 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 CH2CHCHCHCH3 is 1,3-pentadiene
• There is no free rotation about the carbon-carbon
  double bond
• Thus, many alkenes exhibit geometric isomerism

19

• Alkenes undergo addition reactions, reactions
  which eliminate the pi-bond

20

• CH2CH2 HCl(g) ? 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 C6H6Cl2?C6H5ClHCl

21

• 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

22

• 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

23

• Dehydration of alcohols this is the reverse
  the the addition of water to an alkene. It is an
  example of an elimination reaction
• Substitution reactions of alcohols under acidic
  conditions, the OH group can be replaced by a
  halogen atom

24

• 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

25

• Protonated amines (like protonated ammonia) are
  weak acids that can react with base
• The carbonyl group, CO, occurs in several
  organic families
• What is attached to the CO determines the
  specific family

26

• Aldehydes and ketones
• The IUPAC name ending for an aldehyde is al. The
  parent chain is the longest chain that includes
  the aldehyde group.

27

• The IUPAC ending for ketones is one. The parent
  chain must include the carbonyl group
• Aldehydes and ketones can be hydrogenated to give
  alcohols

28

• 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

29

• 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

30

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

31

• 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

32

• 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

33

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

34

• 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

35

• 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

36

• 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.

37

• 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

38

• 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

39

• 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

40

• 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

41

• 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

42

• The lipids involved in animal cell membrane are
  called glycerophospholipids

The lipid molecules of animal cell membranes are
organized as a bilayer.
43

• 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

44

• 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.
45

• 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

46
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.

47

• 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

48

• 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

49

• 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

50

• 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.

51

• 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

52

• 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

53

• 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

54

• 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

55

• 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