5.1 Organic
Molecules
A. Definitions
1. Most common elements in living things are carbon, hydrogen, nitrogen, and
oxygen.
2. These four elements constitute
about 95% of your body weight.
3. Chemistry of carbon allows the
formation of an enormous variety of organic molecules.
4. Organic molecules
have carbon bonded to other atoms and determine structure and function of
living things.
5. Inorganic molecules
do not contain carbon and hydrogen together; inorganic molecules (e.g., NaCl) can play
important
roles in living things.
B. Carbon Skeletons and Functional Groups
1. Carbon has four electrons in outer shell; bonds with up to four other atoms
(usually H, O, N, or another C).
2. Ability of carbon to bond to
itself makes possible carbon chains and rings; these structures serve as the
backbones
of organic
molecules.
3. Functional groups
are clusters of atoms with characteristic structure and functions.
a. Polar
molecules (with +/- charges) are attracted to water molecules and are hydrophilic.
b. Nonpolar molecules are repelled by water and do not
dissolve in water; these are hydrophobic.
c.
Hydrocarbon is hydrophobic except when it has an attached ionized functional
group such as carboxyl (acid)
(--COOH); then molecule is hydrophilic.
d. Cells are
70-90% water; the degree organic molecules interact with water affects their
function.
4. Isomers are
molecules with identical molecular formulas but differ in arrangement of their
atoms
(e.g., glyceraldehyde and dihydroxyacetone).
C. Building Polymers
1. Four classes of polymers (polysaccharides, triglycerides,
polypeptides, and nucleic acids)
provide
great diversity.
2. Small organic molecules (e.g., monosaccharides, glycerol and fatty acid, amino acids, and
nucleotides)
serve as monomers,
the subunits of polymers.
D. Condensation and Hydrolysis
1. Polymers are the large macromolecules composed of three to
millions of monomer subunits.
2. Polymers build by different
bonding of different monomers; mechanism of joining and breaking
these bonds
is condensation and hydrolysis.
3. Cellular enzymes
carry out condensation and hydrolysis of polymers.
4. During condensation
synthesis, a water is removed (condensation) and a bond is made
(synthesis).
a. When two
monomers join, a hydroxyl (--OH) group is removed from one monomer and a
hydrogen
is removed from the other.
b. This
produces the water given off during a condensation reaction.
5. Hydrolysis reactions
break down polymers in reverse of condensation; a hydroxyl (--OH) group from
water
attaches to
one monomer and hydrogen (--H) attaches to the other.
5.2
Carbohydrates
A. Monosaccharides and Disaccharides
1. Monosaccharides are simple sugars
with a carbon backbone of three to seven carbon atoms.
a. Best
known sugars have six carbons (hexoses).
1) Glucose and fructose isomers have same formula (C6H12O6) but differ in
structure.
2) Glucose is commonly found in blood of animals; is immediate
energy source to cells.
3) Fructose is commonly found in fruit.
4) Shape of molecules is very important in determining how they interact with
one another.
2. Ribose and deoxyribose are five-carbon sugars (pentoses); contribute to the backbones of RNA
and DNA
respectively.
3. Disaccharides
contain two monosaccharides joined by condensation.
a. Lactose
is composed of galactose and glucose and is found in
milk.
b. Maltose
is two glucose molecules; forms in digestive tract of humans during starch
digestion.
c. Sucrose
is composed of glucose and fructose and is transported within plants.
B. Polysaccharides are chains of glucose molecules or modified glucose
molecules (chitin).
1. Starch is straight chain of glucose molecules with few side
branches.
2. Glycogen is highly
branched polymer of glucose with many side branches; called "animal
starch,"
it is
storage carbohydrate of animals.
3. Cellulose is
glucose bonded to form microfibrils; primary
constituent of plant cell walls.
a. Cotton is
nearly pure cellulose.
b. Cellulose
is not easily digested due to the strong linkage between glucose molecules.
c. Grazing
animals can digest cellulose due to special stomachs and bacteria.
4. Chitin is polymer
of glucose with amino acid attached to each; it is primary constituent of crabs
and
related
animals like lobsters and insects.
5.3 Lipids
A. Lipids are varied in structure.
1. Many are insoluble in water because they lack polar groups.
2. Fat provides insulation and
energy storage.
3. Phospholipids from plasma
membranes and steroids are important cell messengers.
B. Fats and Oils
1. A fatty acid is a long hydrocarbon chain with a carboxyl
(acid) group at one end.
a. Because
the carboxyl group is a polar group, fatty acids are soluble in water.
b. Most
fatty acids in cells contain 16 to 18 carbon atoms per molecule.
c. Saturated
fatty acids have no double bonds between their carbon atoms.
d. Unsaturated
fatty acids have double bonds in the carbon chain where there are less
than
two hydrogens per carbon atom.
e. Saturated
animal fats are associated with circulatory disorders; plant oils can be
substituted
for animal fats in the diet.
2. Glycerol is a
water-soluble compound with three hydroxyl groups.
3. Triglycerides are
glycerol joined to three fatty acids by condensation.
4. Fats are
triglycerides containing saturated fatty acids (e.g., butter is solid at room
temperature).
5. Oils are
triglycerides with unsaturated fatty acids (e.g., corn oil is liquid at room
temperature).
6. Animals use fat rather than
glycogen for long-term energy storage; fat stores more energy.
C. Waxes
1. Waxes are a long-chain fatty acid bonded to a long-chain
alcohol.
2. Solid at room temperature, waxes
have a high melting point and are waterproof and resist degradation.
3. Waxes form a protective covering
that retards water loss in plants, and maintains animal skin and fur.
D. Phospholipids
1. Phospholipids are like neutral fats except one fatty acid is
replaced by phosphate group or a
group with
both phosphate and nitrogen.
2. Phosphate group is the polar
head; hydrocarbon chains become nonpolar tails.
3. Phospholipids arrange themselves
in a double layer in water, so the polar heads face outward
toward water
molecules and nonpolar tails face toward each other
away from water molecules.
4. This property enables them to
form an interface or separation between two solution (e.g., the interior
and exterior
of a cell); the plasma membrane is a phospholipid bilayer.
E. Steroids
1. Steroids differ from neutral fats; steroids have a backbone of
four fused carbon rings;
vary
according to attached functional groups.
2. Functions vary due primarily to
different attached functional groups.
3. Cholesterol is a
part of an animal cell’s membrane and a precursor of other steroids, including
aldosterone and sex hormones.
4. Testosterone is the
male sex hormone.
5.4 Proteins
A. Protein Functions
1. Support proteins include keratin, which makes up hair
and nails, and collagenfibers, which support
many organs.
2. Enzymes are
proteins that act as organic catalysts to speed chemical reactions within
cells.
3. Transport functions
include channel and carrier proteins in the plasma membrane and hemoglobin
that carries
oxygen in red blood cells.
4. Defense functions
include antibodies that prevent infection.
5. Hormones include insulin
that regulates glucose content of blood.
6. Motion is provided
by myosin and actin proteins
that make up the bulk of muscle.
B. Amino Acids
1. All amino acids contain an acidic group (---COOH) and an amino group
(--NH2).
2. Amino acids differ in nature of R
group, ranging from single hydrogen to complicated ring compounds.
3. R group of
amino acid cysteine ends with a sulfhydryl
(--SH) that serves to connect one chain of amino
acids to
another by a disulfide bond (--S—S).
4. There are 20 different amino
acids commonly found in cells.
C. Peptides
1. Peptide bond is a covalent bond between amino acids in a
peptide.
2. Atoms of a peptide bond share
electrons unevenly (oxygen is more electronegative than nitrogen).
3. Polarity of the peptide bond
permits hydrogen bonding between parts of a polypeptide.
4. A peptide is two or
more amino acids joined together.
5. Polypeptides are
chains of many amino acids joined by peptide bonds.
a. Protein
may contain more than one polypeptide chain; it can have large numbers of amino
acids.
D. Levels of Protein Structure
1. Shape of a protein determines function of the protein in the organism.
2. Primary structure
is sequence of amino acids joined by peptide bonds.
a. Frederick
Sanger determined first protein sequence, with hormone insulin,
in 1953.
b. First
broke insulin into fragments and determined amino acid sequence of fragments.
c. Then
determined sequence of the fragments themselves.
d. Required
ten years research; modern automated sequencers analyze sequences in hours.
e. Since
amino acids differ by R group, proteins differ by a particular sequence of the
R groups.
3. Secondary structure
results when a polypeptide takes a particular shape.
a. The alpha
helix was the first pattern discovered by Linus
Pauling and Robert Corey.
1) In peptide bonds oxygen is partially negative, hydrogen is partially
positive.
2) This allows hydrogen bonding between the C=O of one amino acid and the N—H
of another.
3) Hydrogen bonding between every fourth amino acid holds spiral shape of an
alpha helix.
4) Alpha helices covalently bonded by disulfide (--S—S--) linkages between two cysteine amino acids.
b. The beta
sheet was the second pattern discovered.
1) Pleated beta sheet polypeptides turn back upon themselves; hydrogen bonding
occurs between
extended lengths.
2) Beta-keratin includes keratin of feathers, hooves, claws, beaks, scales, and
horns; silk also is protein
with beta sheet secondary structure.
4. Tertiary structure
results when proteins of secondary structure are folded, due to various
interactions
between the R
groups of their constituent amino acids.
5. Quaternary structure results
when two or more polypeptides combine.
a.
Hemoglobin is globular protein with a quaternary structure of four
polypeptides.
b. Most enzymes
have a quaternary structure.
E. Denaturation of Proteins
1. Both temperature and pH can change polypeptide shape.
a. Examples:
heating egg white causes albumin to congeal; adding acid to milk causes
curdling.
b. When such
proteins lose their normal configuration, the protein is denatured.
c. Once a
protein loses its normal shape, it cannot perform its usual function.
2. The sequence of amino acids
therefore causes the protein’s final shape.
5.5 Nucleic
Acids
A. Nucleic Acid Functions
1. Nucleic acids are huge polymers of nucleotides with very
specific functions in cells.
2. DNA (deoxyribonucleic
acid) is the nucleic acid whose nucleotide sequence stores the genetic
code for its
own replication and for the sequence of amino acids in proteins.
3. RNA (ribonucleic
acid) is a single-stranded nucleic acid that translates the genetic
code of DNA
into the
amino acid sequence of proteins
4. Nucleotides have metabolic
functions in cells.
a. Coenzymes
are molecules which facilitate enzymatic reactions.
b. ATP
(adenosine triphosphate) is a
nucleotide used to supply energy.
c.
Nucleotides also serve as nucleic acid monomers.
B. Structure of DNA and RNA
1. Nucleotides are a molecular complex of three types of molecules: a
phosphate (phosphoric acid),
a pentose
sugar, and a nitrogen-containing base.
2. DNA and RNA differ in the
following ways:
a.
Nucleotides of DNA contain deoxyribose
sugar; nucleotides of RNA contain ribose.
b. In RNA,
the base uracil occurs instead of the base thymine,
as in DNA.
c. DNA is
double-stranded with complementary base pairing; RNA is single-stranded.
1) Complementary base pairing occurs where two strands of DNA are
held together by hydrogen
bonds between purine and pyrimidine
bases.
2) The number of purine bases always equals the
number of pyrimidine bases.
d.Two strands of DNA twist to form a double helix;
RNA generally does not form helices.
C. ATP (Adenosine Triphosphate)
1. ATP is a nucleotide of adenosine composed of ribose and
adenine.
2. Derives its name from three
phosphates attached to the five-carbon portion of the molecule.
3. ATP is a high-energy molecule
because the last two unstable phosphate bonds are easily broken.
4. Usually in cells, a terminal
phosphate bond is hydrolyzed, leaving ADP (adenosine diphosphate).
5. ATP is used in
cells to supply energy for energy-requiring processes (e.g., synthetic
reactions);
whenever a cell
carries out an activity or builds molecules it "spends" ATP.