Molecular Modeling of Biological
Molecules
Goals
• Review chemical bonding (ionic and covalent),
periodic table
• Describe the properties of carbon that make it
important to living things
• Become familiar with the major functional
groups found in biological molecules
• Assemble subunits of 3 biological molecules–
carbohydrates, proteins, and lipids
Basic atomic structure- protons,
neutrons, and electrons
The periodic table logically arranges
and describes all matter
Valence electrons determine bonding
Atoms seek complete valence electron
shells (the octet rule)
In Ionic bonding, atoms strip valence
electrons from partners, forming ions
In covalent bonding, electron pairs are
shared, and molecules are formed
In neutral molecules, carbon always
forms 4 bonds
Structural
formula
Ball-and-stick
model
Space-filling
model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.
LE 3-1b
Ethane
Propane
Carbon skeletons vary in length.
LE 3-1c
Butane
Isobutane
Skeletons may be unbranched or branched.
LE 3-1d
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
LE 3-1e
Cyclohexane
Benzene
Skeletons may be arranged in rings.
Organic Chemistry
• The chemistry of carbon
• Hydrocarbons are the
most basic example
– Combustible
– Can form rings
The variety of carbon compounds is
limitless
The physical/chemical properties of carbon
skeletons can be modified by functional groups
figure 02-20b.jpg
2.20 –
Part 2
Figure 2.20 – Part 2
LE 4-9
Estradiol
Female lion
Testosterone
Male lion
• The six functional groups that are most important in
the chemistry of life:
– Hydroxyl group
– Carbonyl group
– Carboxyl group
– Amino group
– Sulfhydryl group
– Phosphate group
– Methyl group
LE 4-10aa
STRUCTURE
(may be written HO—)
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
NAME OF COMPOUNDS
Propanal, an aldehyde
Ketones if the carbonyl group is
within a carbon skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Acetic acid
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
LE 4-10ba
STRUCTURE
EXAMPLE
Glycine
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
NAME OF COMPOUNDS
Amine
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
(ionized)
Ionized, with a charge of 1+,
under cellular conditions
LE 4-10bb
STRUCTURE
EXAMPLE
(may be written HS—)
Ethanethiol
NAME OF COMPOUNDS
Thiols
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
structure (see Figure 5.20).
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
Organic phosphates
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
Organic molecules are good energy sources
Energy is required to form covalent bonds;
energy is released when bonds are broken
Most molecules in living things fall into
four categories
•
•
•
•
Carbohydrates
Lipids
Proteins
Nucleic acids
These all exhibit modular construction
Modular housing
Made of interchangeable parts
Freight trains have modular assembly
Most biopolymers of life are formed by
dehydration synthesis
Hydrolysis is
the reverse
reaction
(Catabolic)
Carbohydrates
• “Carbon” + “Hydro”
• Formula (CH2O)n
• Different from
hydrocarbons
• Soluble in water
• Includes: table
sugar, honey, starch,
glycogen, cellulose,
high fructose corn
syrup
• Glucose is the
monomer
Glucose can cyclize to form a ring
structure
Atoms in bonds are free to rotate around the bonds
Glucose + Glucose = Maltose
Sugar dimer)
(A
Chain can be extended to thousands
Proteins are polymers made of 20
different kinds of amino acid monomers
table 03-02bc.jpg
Table 3.2 – Part 2
Table 3.2 – Part 2
table 03-02d.jpg
Table 3.2 – Part 3
Table 3.2 – Part 3
Proteins: Polymers of Amino Acids
• Amino acids are covalently bonded
together by peptide linkages. Review
Figure 3.4
figure 03-04.jpg
3.4
Figure 3.4
Lipids
•
•
•
•
•
•
Non-polar
High-energy molecules
For energy storage
Forms cell membranes
Hormones
Members of family
include oils, fats, waxes,
and cholesterol
(steroids)
Triglycerides are a primary lipid structure
Dehydration synthesis links fatty acids to
glycerol
Fatty acids can be saturated and
unsaturated (cis and “trans”)
Review
•
•
•
•
•
•
•
Atomic structure- protons, neutrons electrons
Valence electrons
Carbon
Functional groups
Carbohydrate structure
Protein structure
Lipid structure
An –NH2 group represents which of the
following?
A.
B.
C.
D.
E.
Alcohol
Hydroxyl
Carboxyl
Amine
Phosphoryl
Things left unsaid
• Isotopes of all elements exist (some of these are
radioactive)
• Electronegativity determines polarity of covalent
bonds, and thus solubility
• Water has important physical properties essential
to life on earth
• Isomers have the same molecular formula but
not the same shape in space
• Nucleic acids are comprised of nucleotide
monomers