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Five topics:

‡ The importance of carbon

‡ The importance of water

‡ The importance of selectively permeable membrances

‡The importance of synthesis by polymerization of small


‡The importance of self-assembly

The Importance of Carbon
‡The domain of organic chemistry is to Fig. 2-1 Electron configuration of some
study carbon-containing compounds biologically important atoms and molecules
‡Biochemistry studies the chemistry of
living systems
‡Carbon atom is the most important
atoms in biological molecules
‡Valence of four, lacking four
electron at its outermost electron
‡Methods of satisfaction of stable
status: electron sharing with other
electron deficient atoms (such as
other carbon atoms) -- formation of
covalent bonds with ´lightµ elements
(such as carbon, oxygen, hydrogen,
and nitrogen) to form stable
compounds as relative to their atom
‡ Single bonds, double bonds and triple
Carbon-Containing Molecules Are Stable
Energies of biologically important
transitions, bonds, and wavelengths of
‡Calorie: amount of energy electromagnetic radiations
needed to raise the temperature
of one gram of water one degree

‡Bond energy: the amount of

energy required to break 1 mole
(about 6 x 1023) of bonds: C-C
(83 kilocalories/mole or
kcal/mol), C-N (70), C-O (84),
and C-H (99). Others, C=C (146),
C C (212), and the diamonds!
The Carbon-carbon bonds are the fittest for the biological
chemistry under solar radiation
The relationship between energy (E) and
‡The relationship of wavelength (*) for electromagnetic
electromagnetic radiation and radiation
the wavelength: E = 28,600/* (E,
kcal/einstein; *, nm; 28,600, the
constant with the units of kcal-
nm/einstein, an einstein is equal
to 1 mole of photons)

‡The ultraviolet light at a

wavelength of 300 nm confers
energy of ~95.3 kcal/einstein,
sufficient to breakdown C-C
bonds of ~83 kcal/mol -- pollution
and ozone layer protection.
The diversity of carbon-containing molecules

‡Hydrocarbons are the major Simple hydrocarbon compounds

component of fuels (gasoline).
However, with limited function in
biological systems -- the
phospholipid tail of membranes;

Common functional groups found in biological molecules

‡Functional groups
‡Ionized or protonated
‡Uncharged at pH7, but
Stereoisomers of carbon-containing molecules
Stereoisomers of biological molecules

‡A tetrahedral structure of carbon

atoms have geometric symmetry - An asymmetric carbon
when four different atoms or groups atom has four different D-glucose has four
of atoms are bonded to the four substituents. Both L- and asymmetric carbon atom
corners of such a tetrahedral D-alanine present in and has 24 or 16 kinds of
structure, two different spatial nature but only L- type is possible stereoisomers.
configurations are possible, but not present in proteins.
The importance of water
‡Water is the single most Hydrogen bonding
abundant component of cells and between water
organisms. 75-85% of a cell is
water (10-20 in spores and dry
‡The polarity of water molecules
are caused by the angles that
hydrogen atom bond to the
oxygen atom (104.50), making the
oxygen atom electronegative (Î-).
This property accounts for the
cohesiveness, the temperature-
stabilizing capacity and the
solvent properties of water.
More properties of water
‡Water molecules are cohesive --
Hydrogen bonds form between the
originated from its polarity
hydrogen atoms and the oxygen atoms of
water molecules and are responsible for
The solubilization of sodium chloride
its high boiling point, high specific heat,
because water molecules form spheres of
and high heat of vaporization.

‡Water has a high temperature-

stabilizing capacity -- Π is
the amount of heat a substance absorb
per gram to increase its temperature 10C.
The specific heat of water is 1.0 calorie
per gram.

‡Water has a high heat of vaporization,

the amount of energy required to convert
one gram of a liquid into vapor.

‡Water is an excellent solvent. A solvent

is a fluid in which another substance,
called the solute, can be dissolved.
‡Hydrophobic: ´water fearingµ
‡Hydrophilic: ´water lovingµ
The importance of selectively permeable membranes
‡Membranes are physical barriers of
cells and subcellular compartments
controlling material exchange
between the internal environment
and the extracellular environment

‡A ››   is essentially a
hydrophobic permeability barrier
consisting of phospholipids,
glycolipids, and membrane proteins
Polar head
‡Membranes contain amphipathic Nonpolar tail
molecules such as phosphatidyl
ethanolamine, an example of
phosphoglycerides, the major class
of membrane phospholipids in most
The properties of membranes
A membrane is a lipid bilayer with
proteins embedded in it. Each layer
is about 3-4 nm thick, with the
hydrophobic tails facing each other
in the middle.

‡Functions of the associated proteins:

transport proteins; enzymes, receptors,
electron transport intermediates
(mitochondria), or chlorophyll-binding
proteins (chloroplast)

‡Membranes are selectively permeable.

‡Freely diffusing molecules: H2O, CO2 or MW <
100 Dalton
‡However, ions like Na + and K+ are effectively
excluded (10 8 times less efficient). They need
either hydrophilic channels or carriers for their
crossing of the membrane
The importance of synthesis by polymerization
‡Macromolecules: proteins, ribonucleic
acids (DNA or RNA), and
polysaccharides (starch, glycogen, and
cellulose), and lipid (?, with different
synthesizing method)

‡Macromolecules are responsible for

most of the form and function in living
systems. They are, however, generated
by polymerization of small organic
molecules, a fundamental principle of
cellular chemistry

‡The monomers: glucose, amino acids,


‡Informational macromolecules: DNA

and proteins

‡Storage macromolecules & structural

Macromolecules are synthesized by stepwise polymerization of monomers
Biological polymers
Proteins Nucleic acids Polysaccharides
Macromolecules Informational Informational Storage Structual
E.g. Enzymes, hormone, DNA, RNA Starch, glycogen Cellulose
and antibodies
Repeating Amino acid Nucleotide Monosaccharides Monosaccharides
Number of 20 4 in DNA and 4 in One or a few One or a few
Repeating units RNA

The basic principles for the

synthesis of macromolecules:

1. Macromolecules are synthesized by

stepwise polymerization of similar or
identical monomers
2. The addition of each monomeric units
occurs with the removal of a H2O
molecule -- condensation reaction
3. Momomeric units are activated
4. Activation usually involves coupling
of monomers to carrier molecule
5. ATP (adenosine phosphate provides
energy )
6. Directionality of macromolecules
The importance of self-assembly
The principle of self-assembly: the information required to specify the folding of
macromolecules and their interactions to form more complicated structures with specific biological
functions is inherent in the polymers themselves
‡Many proteins self-assemble
‡Polypeptide VS. protein
‡Denaturation VS. renaturation Heat Cool

‡Molecular chaperones assist

the assembly of some proteins
‡Strictly self-assembly
‡Assisted self-assembly (by
preventing the formation of
incorrect confirmation)

‡Noncovalent interactions are

important in the folding of
‡Covalent bonds: atoms share
‡Noncovalent interactions:
hydrogen bonds, ionic bonds,
van der Waals interactions, and
hydrophobic interactions
Self-assembly of cellular structures

‡Self-assembly of cellular structures:

ribosome, membranes, and primary cell

‡The tobacco mosaic virus (TMV), a

case study in self-assembly
‡Structure: A RNA helical core
surrounded by a cylinder of protein
subunits (´coat proteinsµ)
‡17 subunits disc ring - conformational
change to a helical shape and each
binds 102 nt RNA, repeat...
The limits of self-assembly and advantages of hierarchical assembly

‡Some kinds of assembly

requires preexisted structures
such as addition of extra
components to cell walls,
membranes and chromosomes

‡Hierarchical assembly is the

basic cellular strategy. The
´alphabet of biochemistryµ
contains 20 amino acids, 5
aromatic bases, 2 sugars, and 3
lipid molecules

‡Chemical simplicity
‡Efficiency of assembly --
the story of ´Tempus Fugit
and the fine art of watch-