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INTRODUCTION

The Identifying Characteristics of Matter

 They are complicated and highly organized.

 Each component of a living organism appears to have a specific purpose or function
 Living organisms have the capacity to extract and transform energy from their environment
which they use to build and maintain their intricate structures from simple raw materials.
 Living organism have the capacity for precise self – replication, a property that may be
regarded as the very quintessence of the living state.

Biochemistry and the Living State

 The central goal of Biochemistry is to determine how the collections of inanimate molecules
found in living organisms interact with each other to constitute, maintain, and perpetuate the
living state.

 Two parent lines in the genealogy of the Science of Biochemistry

o One line arose from Medicine and Physiology, a by – product of early inquiries into the
chemical composition of blood, urine, and the tissues and their variation in health and
disease.
o The other lineage traces from Organic Chemistry, from early studies on the structure of
naturally occurring organic compounds.

 Two major developments that allowed Biochemistry to emerge as a full – fledged Science.

o The recognition of multienzyme systems as catalytic units in the major metabolic

pathways and the development of a unifying hypothesis for the transfer of energy in
living cells.
o The recognition that heredity, one of the most fundamental aspects of Biology, has a
rational molecular basis.

 The success of Biochemistry in explaining many cellular phenomena has been so great that
many scientists have come to a conclusion that Biology is Chemistry.

 If Biology is Chemistry, it must be a kind of “superchemistry” because the molecules found

in living organisms do not only conform to all the familiar physical and chemical principles
governing behavior of all molecules but, in addition, interact with each other in accordance
with another set of principles, “The Molecular Logic of the Living State.”

 These principles should be regarded as a set of ground rules that govern the nature, function,
and interactions of the specific types of molecules found in living organisms, that endow
them with the capacity for self – organization and self – replication. The principles will be
uncovered in the next topics to be discussed.
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Biomolecules

 The organic compounds present in living matter occur in extraordinary variety and most of
them are extremely complex. Bacteria contain a very large number of different organic
compounds. E. coli is estimated to contain about 5,000 different kinds of proteins and 1,000
kinds of nucleic acids. Most organic matter in living cells consists of macromolecules with
very large molecular weights. The more complex the organism, the greater the number of
proteins and nucleic acids. Each species of organism has its own chemically distinct sets of
proteins and nucleic acids.

 The immense diversity of organic molecules in living organisms is reducible to a surprising

simplicity Cell macromolecules are composed of simple, small building – block molecules
strung together in long chains.

o Starch and cellulose consists of long strings of covalently linked glucose (simple
carbohydrate) molecules.
o Proteins are built from 20 amino acids
o DNA is built from 4 nucleotides and RNA is also built from four nucleotides..

 The few simple building – block molecules from which all macromolecules are constructed
have another striking characteristic. Each serves more than one function: some Are extremely
diverse and play a number of roles.

o The amino acids do not only serve as building blocks of proteins but also as precursors of
hormones, alkaloids, porphyrins, pigments, and many other biomolecules.
o Various nucleotides do not only serve as building – blocks of nucleic acids but also as
coenzymes and energy carrying molecules.

 This leads us to the following axioms in the molecular logic of living organisms:

o 1st = There is an underlying simplicity in the molecular organization of the cell. Because
they are constructed from a few simple building – block molecules.
o 2nd = All living organisms have a common ancestor. Because the building – block
molecules are identical in all known species.
o 3rd = The identity of each species of organism is preserved by its possession of
characteristic sets of nucleic acids and proteins. Because each organism has its own
distinctive sets of nucleic acids and proteins.
o 4th = There is an underlying principle of molecular economy in living organisms. Because
of the functional diversity of the building – block molecules.
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Energy Transformations in Living Cells

 The molecular complexity and the orderliness of structure of living organisms in contrast to
the randomness of inanimate matter have profound implications to the physical scientist. The
2nd Law of Thermodynamics, the branch of Physics dealing with energy and its
transformations, states that all physical and chemical processes always proceed with an
increase in the disorder and randomness in the world, i.e., its entropy. How can living
organisms create and maintain their intricate orderliness in an environment that is relatively
disordered and becoming more so with time?

 Living organisms are not exceptions to the Laws of Thermodynamics. They maintain their
high degree of molecular orderliness because they transform one form of energy into another
because the 1st Law of Thermodynamics states that energy can neither be created nor
destroyed.

 Cells of living organisms absorb a useful form of energy called “free energy” which can do
work at constant temperature and pressure. The less useful type of energy that the cells return
to their environment consists of heat and other forms that quickly become randomized in the
environment and it increases its disorder or entropy.

 This leads us to the 5th axiom in the molecular logic of living organisms: Living organisms
create and maintain their essential orderliness at the expense of the environment, which they
cause to become more disordered and random. Living organisms are open systems because
they can exchange both energy and matter with their environment and in so doing, transform
it. They exist in a steady state not in a state of equilibrium. The steady state is a condition of
an open system in which the rate of transfer of matter and energy from the environment into
the system is exactly balanced by the rate of energy and matter out of the system.

 The energy transforming machinery of the cell is built entirely of relatively fragile and
unstable organic molecules that are unable to withstand high temperatures, strong electric
currents, or extremely acid or basic conditions. It is essentially isothermal: at any given time,
all parts of the cell have essentially the same temperature. There are no significant
differences in pressure between one part of the cell and another. It is for these reasons that
the cells are unable to use heat as a source of energy. Heat can do work at constant pressure
only if it passes from a zone of higher temperature to a zone of lower temperature.

 This leads us to the 6th axiom in the molecular logic of living organisms: Living cells function
as isothermal chemical engines. The energy that cells absorb from the environment is
transformed into chemical energy which is then used to carry out chemical work involved in
the biosynthesis of cell components, the osmotic work required to transport materials into the
cell, and the mechanical work of contraction and locomotion; all these transformations take
place at essentially constant temperature.
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Chemical Reactions in Living Cells

 Cells can function as chemical engines because they possess enzymes, catalysts capable of
greatly enhancing the rate of specific chemical reactions. Enzymes are highly specialized
protein structures. Each enzyme can catalyze only one specific type of chemical reaction.

 Enzyme catalyzed reactions proceed with 100% yield; there are no by – products because
enzymes can enhance a single reaction pathway of a given molecule without enhancing its
other possible reactions. This allows the living organisms to carry out, simultaneously, many
different individual reactions without bogging down in a morass of useless by – products.

 This leads us to the 7th axiom in the molecular logic of living organisms: The specificity of
molecular interactions in cells results from the structural complementarity of the interacting
molecules. Enzyme molecules combine with their substrates during the catalytic cycle in
such a way that the active site of the enzyme molecule fits the substrate with a near perfect
lock – and – key complementarity.

 The enzyme – catalyzed reactions do not take place independently of each other but are
linked into sequences of consecutive reactions having common intermediates, so that the
products of the 1st reaction becomes the substrate or reactant of the 2nd and so on. Such linked
or coupled sequences are in turn connected into networks of converging or diverging
pathways.

 This arrangement has important biological implications:

o Such systems of sequential reactions provide for the channeling of chemical reactions
along specific routes to specific end products.
o Sequential reactions makes the transfer of chemical energy possible.

 Living cells can be divided into two major classes according to the type of energy they obtain
from the environment.

o Photosynthetic cells utilize sunlight as their main source of energy; the radiant energy is
absorbed by the pigment chlorophyll and transformed into chemical energy.
o Heterotrophic cells obtain energy from the degradation of highly reduced, energy rich
organic molecules, such as glucose, which they require as nutrients in the environment.

 Both classes transform the energy obtained from the environment in the form of adenosine
triphosphate (ATP). ATP is the major carrier of chemical energy in the cells of all living
species. It transfers energy to other molecules by losing its terminal phosphate group to for
adenosine diphosphate (ADP). Energy is added to ADP in the form of a phosphate group to
form ATP once again.
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 ATP serves as a common intermediate or connecting link between two large networks of
enzyme – catalyzed reactions in the cell.

o One of these networks conserves chemical energy derived from the environment by
causing the phosphorylation of the energy – poor ADP to the energy – rich ATP.
o The other network utilizes the energy of ATP to carry out the biosynthesis of cell
components from simple precursors with the simultaneous breakdown of ATP to ADP.

 This leads us to the 8th axiom in the molecular logic of living organisms: Consecutively
linked sequences of enzyme catalyzed reactions provide the means for transferring chemical
energy from energy yielding to energy requiring processes.

Self – Regulation of Cell Reactions

 A simple bacterial cell like E. coli simultaneously synthesizes all its thousand of different
complex molecular components from just three simple precursors – glucose, ammonia, and
water because of the linking of enzyme catalyzed reactions.

 The linkage of enzyme – catalyzed reactions into consecutive sequences makes the regulation
of metabolism possible and endows it with self – adjusting properties. A simple example is as
follows: The over – accumulation of an end product of metabolism, such as an amino acid,
can inhibit the rate – determining step in the sequence of reactions by which it was formed, a
type of control known as feedback inhibition.

 Living cells also possess the power to regulate the synthesis of their own catalysts. The cell
therefore can “turn off” the synthesis of the enzymes required to make a given product from
its precursors whenever the product is available, ready – made, from the environment.

 This leads us to the 9th axiom in the molecular logic of living organisms: Cells are capable of
regulating their metabolic reactions and the biosynthesis of their enzymes to achieve
maximum efficiency and economy.

Self – Replication of Living Organisms

 The most remarkable of all properties of living cells is their capacity to reproduce themselves
with nearly perfect fidelity for thousands of generations. Three features immediately out.

o First, some living organisms are so immensely complex that the amount of genetic
information transmitted seems out of all proportion to the minute size of cells that must
carry it, namely, the sperm cell and the egg cell. This leads us to the 10 th axiom in the
molecular logic of living organisms: The symbols in which the genetic information is
coded in DNA are sub – molecular in dimension.
o A 2nd remarkable characteristic is the extraordinary stability of genetic information stored
in DNA. The capacity of living cells to preserve their genetic information is the result of
the operation of the principle of structural complementarity. One DNA strand serves as
the template for the enzymatic replication of a structurally complementary DNA strand.
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o The 3rd remarkable characteristic is that genetic information is encoded in the form of
specific sequence of four different nucleotide building blocks in the linear DNA
molecule. This leads us to the 11th and most crucial axiom in the molecular logic of living
organisms: The one – dimensional information of DNA is translated into three –
dimensional macromolecular and supramolecular components of living organisms by
translation of DNA structure into protein structure.

 We may now summarize the different axioms or principles by the following statements: A
living cell is a self – assembling, self – regulating, self – replicating isothermal open
system of organic molecules operating on the principle of maximum economy of parts
and processes; it promotes many consecutive, linked organic reactions for the transfer
of energy and for the synthesis of its own components by means of organic catalysts that
it produces itself.

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