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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
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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.

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.
Energy Transformations in Living Cells
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 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.

Chemical Reactions in Living Cells

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 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 their 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.

 ATP serves as a common intermediate or connecting link between two large

networks of enzyme – catalyzed reactions in the cell.
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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 to carry out the
biosynthesis of cell components from simple precursors with the simultaneous
breaksown 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.
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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 10th 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.
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.

BIOMOLECULES AND CELLS

The Biological Fitness of Organic Compounds

 Only 27 of the 90 naturally occurring chemical elements in the earth’s crust have
been found to be essential components in various living organisms and the chemical
elements in living organisms are not distributed in proportion to their occurrence in
the earth’s crust. The 4 most abundant elements in the earth’s crust are oxygen,
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silicon, aluminum, and iron while the 4 most abundant elements in living organisms
are hydrogen, oxygen, carbon, and nitrogen which make up about 99% of the mass of
most cells. Therefore, the compounds of hydrogen, oxygen, carbon, and nitrogen
possess unique molecular fitness for the processes that collectively constitute the
living state.

 Properties of the four elements that make them biologically fit.

o CHON possess a common property: they readily form covalent bonds by

electron pair sharing. H needs 1, O needs 2, N needs 3, and C needs 4 electrons to
complete their outer electron shells and thus form stable covalent bonds. They
can react with each other to form a large number of different covalent
compounds. Furthermore, CNO can share either one or two electron pairs to
form single or double bonds , a capacity that endows them considerable
versatility of chemical bonding.
o CHON are the lightest elements capable of forming covalent bonds. They
can form very strong covalent bonds because the strength of a covalent bond is
inversely related to the atomic weights of the bonded atoms.
o Carbon atoms another and most significant property: the capacity to bond
with each other. Since a carbon atom may either accept or donate four electrons
to complete an outer octet, it can form covalent bonds with four other carbon
atoms. Covalently linked carbon atoms can form linear or branched or cyclic
backbones for an immense variety of different organic molecules.
o Carbon atoms also form covalent bonds with oxygen, hydrogen, nitrogen,
& sulfur, many different kinds of functional groups may be introduced into the
structure of organic molecules.
o Many different three – dimensional structures can be achieved by carbon
to carbon bonding because of the tetrahedral configuration of electron pairs
around singly bonded carbon.
o No other chemical element can form molecules of such widely different
sizes and shapes or with such a variety of functional groups.

Hierarchy of the Molecular Organization of Cells

 The biomolecules of living organisms are ordered into a hierarchy of increasing

molecular complexity as shown in the table below:

The Cell
Organelles Nucleus
Mitochondria
Chloroplasts
Golgi Bodies
Supramolecular Assemblies (particle weight Ribosomes
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106 – 109) Enzyme Complexes

Contractile Systems
Microtubules
Macromolecules (molecular weight 103 – 109) Nucleic Acids
Proteins
Polysaccharides
Lipids
Building Blocks (molecular weight 100 – 350) Nucleotides
Amino Acids
Monosaccharides
Fatty Acids
Glycerol
Metabolic Intermediates (molecular weight 50 Pyruvate
– 250) Citrate
Malate
Glyceraldehyde – 3 – phosphate
Precursors from the environment (molecular Carbon Dioxide
weight 18 – 44) Water
Ammonia
Nitrogen

The Primordial Biomolecules

 The Amino Acids = Glycine, Alanine, Valine, Leucine, Isoleucine, Serine,

Methionine, Threonine, Phenylalanine, Tyrosine, Tryotophan, Cysteine, Proline,
Aspartic Acid, Asparagine, Glutamic Acid, Glutamine, Histidine, Arginine, and
Lysine.

 The Pyrimidines = Uracil, Thymine, and Cytosine

 The Purines = Adenine and Guanine
 The Sugars = α – D- glucose and α – D – ribose
 A Sugar Alcohol = Glycerol
 A Nitrogenous Alcohol = Choline
 A Fatty Acid = Palmitic Acid

Specialization and Differentiation of Biomolecules

 As living organisms evolved into more highly differentiated and complex forms,
new biomolecules of greater complexity and variety are believed to have evolved
from the primordial biomolecules.

o Over 150 different biologically occurring amino acids are known today
but nearly all of them are derived from the primordial amino acids.
o Dozens of different nucleotides and nucleotide derivatives are known, all
containing descendants of the 5 primordial nitrogenous bases, the purines and the
pyrimidines.
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o Over 70 simple sugars are biologically derived from glucose and from
them a large variety of polysaccharides are formed in different organisms.
o There are many different fatty acids, all descended from one or a few
primordial fatty acids.
o The table below shows specialized derivatives of some of the primordial
biomolecules.

Arginine Ornithine
Citrulline
Proline 3 – Hydroxyproline
4 – Hydroxyproline
4 – Hydroxymethylproline
4 – Methyleneproline
4 – Ketoproline
Leucine β – Hydroxyleucine
δ – Hydroxyleucine
γ, δ – Dihydroxyleucine
γ – Hydroxyleucine
Ν – Methylleucine
Guanine 1 – Methylguanine
2 – Methylguanine
1,2 – Dimethyguanine
2 – O – Methylguanine
7 – Methylguanine
D – Glucose D – Mannose
D – Fructose
D – Galactose
N – Acetylglucosamine
D – Glucuronic acid
D – Glucose – 6 – phosphate
Ascorbic acid
Inositol
Sucrose
D – Glucose (continuation) Maltose
Lactose
Palmitic acid Oleic acid
Stearic acid
Lauric acid
Palmitoleic acid
Palmitaldehyde
Stearaldehyde

 Many specialized biomolecules are extremely complex that they seem to have no
semblance to the primordial biomolecules until research proved that they arose from
them. Among these are various pigments, odor – bearing essential oils, hormones,
antibiotics, alkaloids, and various structural molecules, such as lignin of wood.

 Terpenes, which is a large class of biomolecules that includes some of the

vitamins, many essential oils, plant pigments, and such complex natural products as
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rubber, are all ultimately built from acetic acid, the major breakdown product of
glucose and of fatty acids.

Origin of Biomolecules

 In the 1920’s, A. I. Oparin, a biochemist in the Soviet Union, suggested that

natural chemical and physical processes could have led to the spontaneous formation
of simple organic compounds, such as amino acids and sugars, from methane,
ammonia, and water vapor, which he postulated to be components of the primitive
atmosphere. According to his theory, these gases were activated by radiant energy of
sunlight or by lightning discharges to react with each other. The simple organic
products so formed condensed and dissolved in the primitive ocean, which gradually
became enriched in a large variety of organic compounds. Oparin postulated that the
first living cell arose spontaneously from this warm, concentrated solution of organic
compounds, a view independently put forward by J. B. S. Haldane in England.
Theseviews were attended by much controversy and remained an untested
speculation for over 20 years.

 Among the early experiments that supported this view was carried out by Stanley
Miller in 1953. He subjected mixtures of the gases methane, ammonia, water, and
hydrogen, then believed to be predominant in the primitive atmosphere, in a closed
flask at 80oC to electric sparking across a pair of electrodes, to simulate lightning, for
periods of a week or more. Then he collected and analyzed the contents of the
system. The gas phase contained CO, CO2, and N2 which were evidently formed from
the gases initially introduced. In the chilled and dark colored condensate he found
significant amounts of water – soluble organic substances, which he separated by
chromatographic methods. Among the compounds Miller identified were a number of
∞ - amino acids, including some known to be present in proteins, i. e., glycine,
alanine, aspartic acid, and glutamic acid. He also found several of the simple organic
acids known to occur in living organisms, such as formic, acetic, propionic, lactic,
and succinic acids.

Fitness of Biomolecules

 Much evidence supports the concept that the biomolecules we know today were
selected from a much larger number of available organic compounds.

 Ample evolutionary time was available for living organisms to have acquired the
ability to use the selected primordial biomolecules.

The Dimensions and Shapes of Biomolecules

‘
 Molecular dimensions were formerly given in units of angstroms, cell dimensions
in microns, and wavelengths in millimicrons, where 1 micron = 10-3 mm. However,
by international agreement, the metric units nanometers, micrometers, and
millimeters are now recommended.
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 There are two classes of molecular models:

o Crystallographic models show the covalent skeleton with the correct bond
angles and lengths, but such models do not indicate the actual space occupied by
the molecule.
o Space – filling models show few details of bond angles and distances in
the backbone but they do show the van der Waals contour, or surface, of the
molecule.

 Three – dimensional shape and surface topography are especially important for
macromolecules. Protein molecules usually have only one characteristic three –
dimensional conformation under normal intracellular conditions, called the native
conformation, which is indispensable for their biological activity.

 Complex physical methods, particularly x – ray diffraction analysis, are required

to establish the precise conformation of biological macromolecules. Indeed, charting
the three – dimensional structure of macromolecules by x – ray analysis and
correlating their structure with their biological activity are major objectives of
biochemistry and molecular biology.

Biomolecules, Supramolecular Structures, and Cell Organelles

 The size and shape of biomolecules are of crucial importance in another way. The
dimensions, shape, and properties of the simple building – block biomolecules must
determine the dimensions and properties of macromolecules, whose shape and
surface topography must in turn determine how they fit together to form
supramolecular structures, which in turn determine the structure of the organelles
and ultimately the cell itself.

 An example of the effect of the size, shape, and properties of a small building
block biomolecule can influence the size, shape, and biological behavior of an entire
cell is the human genetic disease, sickle cell anemia. The hemoglobin of patients
differ slightly in composition to normal hemoglobin as the result of a genetic
mutation: two molecules of glutamic acid in normal hemoglobin are replaced by two
molecules of valine in the sickle cell hemoglobin. This slight change alters the
structure of sickle cell hemoglobin molecule so that it “stacks” improperly with
neighboring molecules. This defect in turn causes a profound change in the shape of
the RBC which assumes the shape of a sickle, or a crescent, whereas normal RBCs
are flat disks. As a consequence, sickled RBCs tend to aggregate in small blood
vessels, blocking the circulation, and causing other serious disturbances.

The Structural Organization of Cells

 Structural Organization of Prokaryotic Cells

Cell Component Molecular Composition Properties and Functions

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Cell Wall and The cell wall contains a rigid The cell wall protects bacteria
Cell Membrane framework of polysaccharide against swelling in hypotonic
chains cross – linked with short media. It is porous and allows
peptide chains. Its outer surface is most small molecules to pass.
coated with lipopolysaccharide. Some of the pili are hollow and
The pili, not found in all bacteria, serve to transfer DNA during
are extensions of the cell wall. sexual conjugation.

The cell membrane contains The cell membrane is a

about 45% lipid and 55% protein; selectively permeable boundary
the lipids form a continuous non which allows water, certain
– polar phase. Infoldings of the nutrients, and metal ions to pass
cell membrane are called freely. Enzymes responsible for
mesosomes. conversion of nutrient energy into
ATP are located in the membrane.

Nuclear Zone The genetic material is a single DNA is the carrier of genetic
chromosome of double – helical information. During division,
DNA 2 nm in diameter and about each strand is replicated to yield
1.2 mm long, which is tightly two daughter double – helical
coiled. molecules. From one strand of
DNA the genetic message is
transcribed to form messenger
RNA.

Ribosomes Each E. coli cell contains about Ribosomes are sites of protein
15,000 ribosomes. Each ribosome synthesis. Messenger RNA binds
has a large and small subunit. in the groove between the
Each subunit contains about 65% subunits and specifies the
RNA and 35% protein. sequence of amino acids in the
growing polypeptide chains.
Storage E. coli and many other bacteria When needed as fuel, these
granules contain storage granules that are polymers are enzymatically
polymers of sugars. Some degraded to yield free glucose or
bacteria contain granules of poly free β – hydroxybutyric acid.
– β – hydroxybutyric acid.
Cytosol The soluble portion of the Most of the proteins in the cytosol
cytoplasm is highly viscous; the are enzymes required in
protein concentration is very metabolism. The cytosol also
high, exceeding 20% contains metabolic intermediates
and inorganic salts.

 Structural Organization of Eukaryotic Cells

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Cell Component Molecular Composition Properties and Functions

Cell Membrane The cell coat of hepatocytes is Ghe adhesive properties of cell
flexible and sticky. It is composed coats are specific and play an
of acid mucopolysaccharides, important role in cell – cell
glycolipids, and glycoproteins. recognition and thus tissue
organization.

The plasma membrane is about 9 The plasma membrane is

nm tick and contains about equal selectively permeable. It contains
amounts of lipids and proteins; active – transport systems for Na+
the lipids are arranged in a and K+, glucose, amino acids, and
bilayer. It contains a greater other nutrients, as well as a
variety of lipids than bacterial number of important enzymes.
membranes

.
Nucleus The nucleus, about 4 – 6 µm in During mitosis, chromosomes
diameter, is surrounded by a undergo replication of their DNA
perinuclear envelope. The DNA and separation into daughter
within is combined with histones chromosomes.
and organized into chromosomes.
The nucleolus is rich in RNA.

Mitochondrion There about 800 mitochondria in The mitochondria are the power
each hepatocyte. They are plants of the cell, where
globular and a little over 1 µm in carbohydrates. Lipids, and amino
diameter, occupying about 20% acids are oxidized to CO2 and
of the cytoplasmic volume. Their H2O by molecular oxygen, and
outer and inner membranes differ the energy set free is converted
in lipid composition and in into the energy of ATP. The
enzymatic activity. The matrix is enzymes of electron transport and
rich in enzymes. energy conversion are located in
the inner membrane.
Golgi complex The Golgi complex consists of The Golgiapparatus functions in
flattened, single membrane the secretion of cell products such
vesicles, which are often stacked. as proteins, to the exterior. It also
Small vesicles arise peripherally helps to form the plasma
by a pinching off process. Some membrane and the membranes of
become vacuoles in which the lysosomes.
secretory products are
concentrated.
Microbody Microbodies are single membrane Microbodies participate in the
(Peroxisome) vesicles about 0.5 µm in oxidation of certain nutrients.
diameter. They contain catalase, Hydrogen peroxide, the reduction
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D – amino acid oxidase, urate product of oxygen in these

oxidase, and other oxidative organelles, is decomposed to form
enzymes often present in water and oxygen.
crystalline arrays.
Lysosome Lysosomes are single membrane Lysosomes function n the
vesicles, 0.25 – 0.5 µm in digestion of materials brought
diameter, containing hydrolytic into the cell by phagocytosis or
enzymes, such as ribonuclease pinocytosis. They also serve to
and phosphatase. digest cell components after cell
death.
Endoplasmic The endoplasmic reticulum Proteins synthesized by the
Reticulum consists of flattened, single adhering ribosomes cross the
membrane vesicles whose inner membrane of the endoplasmic
compartments, the cisternae, reticulum and appear in the
interconnect to form channels intracisternal space, which forms
throughout the cytoplasm. The a highly ramified channel for
rough – surface portion is studded intracellular transport to the
with ribosomes, which are larger periphery of the cell. Protein
than those of prokaryotes. synthesis by unattached
ribosomes also occurs, as in
prokaryotes.

WATER

 Water not only makes up 70 – 90% of the weight of most forms of life, it also
represents the continuous phase of living organisms.

 It is often regarded as a bland, inert liquid, a mere space filler in living

organisms.

 However, it is a highly reactive substance with unusual properties that distinguish

it strikingly from most other common liquids.

Physical Properties and Hydrogen Bonding of Water

 Water has a higher melting point, boiling point, heat of vaporization, heat of
fusion, and surface tension than most common liquids. All these properties indicate
that the forces of attraction between the molecules in liquid water and thus its internal
cohesion, are relatively high.

 The strong intermolecular forces of liquid water are caused by the specific
distribution of electrons in the water molecule. Although the water molecule has no
net charge, it is an electric dipole. The hydrogen atom is partially positive while the
oxygen atom is partially negative.
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 When two water molecules approach each other closely, electrostatic attraction
occurs between the partially positive hydrogen of one water molecule and the
partially negative oxygen atom of another water molecule. This is accompanied by a
redistribution of the electronic charges in both molecules that greatly enhances their
interaction. A complex union of this kind is known as a hydrogen bond. Because of
the nearly tetrahedral arrangement of electrons about the oxygen atom, each water
molecule is capable of hydrogen bonding with four neighboring water molecules. It is
the property that is responsible for the great internal cohesion of liquid water.

 Hydrogen bonds are relatively weak compared to covalent bonds.

 Another important property of hydrogen bonds is that they are strongest when the
two interacting groups are oriented to yield maximum electrostatic attraction.

 Hydrogen bonds also have a characteristic bond length, which differs from one
type of hydrogen bond to another, according to the structural geometry and the
electron distribution in the bonded molecules. The length of each hydrogen bond in
ice is 0.177 nm.

The Structure of Liquid Water

 H – bonding between water molecules occurs in all its states:

o In the most common crystalline form of ice called ice I, each water
molecule is hydrogen – bonded with exactly four nearest neighbors in a regular
lattice having an average O – O distance of 0.276 nm.
o In liquid water at 0oC, each water molecule is hydrogen – bonded at any
given time with an average of about 3.6 other water molecules; the average O – O
distance is only slightly greater than ice, about 0.29 nm at 15 oC and 0.305 at
83oC. It is still hydrogen – bonded at 100oC as indicated by its high heat of
vaporization and dielectric constant.

 Many models have been proposed for the structure of liquid water.

o The simplest models suggest that liquid water consists of icelike clusters
of water molecules in labile equilibrium with free water molecules.
o Other models propose that liquid water contains three or more types of
hydrogen – bonded components.
o The continuum model suggests that although the great majority of the
hydrogen bonds between water molecules in ice at 0oC remain unbroken when ice
is melted, they become distorted, i. e., bent at different angles from the most
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stable linear configuration. The higher the temperature of liquid water, the greater
the amount of distortion and the greater the instability.

Other Properties of Hydrogen Bonds

 H – bonds are not unique to water because they tend to form between a small ,
highly electronegative atom, like, oxygen, nitrogen, or fluorine, and a hydrogen
atom covalently bonded to another electronegative atom.

 H – bonds may form between two molecules or between two parts of the same
molecule. The following are some biologically important H – bonds:

o Between a hydroxyl group and H2O

o Between a carbonyl group and H2O
o Between two peptide chains
o Between complementary base pairs in DNA

 As the number of H – bonds increases between molecules, enhancement of the

strength of attraction between two molecules is done by cooperation of many weak
bonds. This is known as cooperativity.

 Cooperative H – bonding is a characteristic of both proteins and nucleic acids

which may contain dozens, hundreds, or even thousands of cooperative H – bonds. It
depends on the relative positions of the functional groups capable of forming H –
bonds.

 H – bonds form and break in aqueous systems faster than most covalent bonds.
This fact, together with their geometrical specificity and directionality, endows H –
bonds with great biological advantage over covalent bonds in biomolecular
phenomena that must occur at very high rates, such as folding of proteins into their
native conformation.

Solvent Properties of Water

 Water is a much better solvent than most common liquids. Many crystalline salts
and other ionic compounds readily dissolve in water but are nearly insoluble in non –
polar liquids like chloroform or benzene.

 Water also tends to oppose the electrostatic attraction between positive and
negative ions. This tendency is given by the dielectric constant D, defined by the
relationship

F = e1e2
Dr2
Where F is the attractive force between two ions of opposite charge, e1 and e2 are the
charges on the ions, and r is the distance between them.
 17

 A 2nd class of substances readily dissolved by water includes the non – ionic but
polar compounds – sugars, simple alcohols, aldehydes, and ketones. Their solubility
is due to the propensity of polar functional groups, such as the hydroxyl group of
sugars and alcohols, the carbonyl oxygen of aldehydes and ketones, to form H –
bonds with water.

Hydrophobic Interactions

 Water also disperses or solubilizes in the form of micelles many compounds

which contain both strongly non – polar and strongly polar groups. These compounds
are called amphipathic. The polar groups love water while the non – polar groups
hate water. Therefore, polar groups are in contact with water while the non – polar
groups are away from water.

 Micelles have additional attractive forces between adjacent hydrocarbon

structures called van der Waals interactions.

 We use the term hydrophobic interaction to refer to the clustering or aggreagation

of hydrophobic portions of amphipathic molecules out of contact with water.

Effect of Solutes on Water Properties

 The presence of dissolved solutes causes the structure and properties of liquid
water to change. Dissolve salts tend to break the structure of water.

 The effect of solute on the solvent is manifest in another set of properties,

namely, the colligative properties of solutions, which depends on the number of
solute particles per unit volume of solvent. Solutes produce such characteristic
changes as depression of freezing point, elevation of boiling point, and depression of
vapor pressure. They also endow a solution with the property of osmotic pressure.

Ionization of Water

 Because the mass of he H atom is so small and because the atom’s single electron
is tightly held by the O atom, there is a tendency for the H atom to dissociate from
the O atom to which it is covalently bonded and “jump” to the O atom of the adjacent
H2O molecule to which it is H – bonded, provided that the internal energy of each
molecule is favorable. In this reaction two ions are produced, the hydronium ion
(H3O+) and hydroxide ion (OH-).

 This tendency of the proton to “jump” may occur in a series of H2O molecules
without little movement of the H2O molecules themselves. Conduction of protons
through H – bonded H2O molecules, called tunneling, may be an important
phenomenon in biological systems.

The Ion Product of Water: The pH Scale

 18

 The dissociation of water is an equilibrium process:

2H2O ↔ H3O+ + OH-

For which we can write the equilibrium constant

Keq = [H3O+][OH-]
[H2O]2

Where the brackets indicate concentration in moles/liter. The magnitude of the

equilibrium constant at any given temperature can be calculated from conductivity
measurements on pure distilled water. Since the concentration of pure water is very
high (it is equal to the number of grams of water in a liter divided by the gram –
molecular weight of water, or 1,000/18 = 55.5 M) and since the concentrations of
H3O+ and OH- are very low in comparison (1 x 10-7 M at 25oC), the molar
concentration of is not significantly changed by its very slight ionization. The
equilibrium constant expression may thus be simplified to:

[55.5]2 Keq = [H3O+][OH-]

and the term [55.5]2 Keq can then be replaced by a lumped constant Kw, called the ion
product oh water.

Kw = [H3O+][OH-]

The value of Kw at 25oC is 1.0 x 10-14. In an acid solution, H3O+ concentration is

relatively higher and the OH- is correspondingly low; in a basic solution, the situation
is reversed.

 Kw, the ion product of water, is the basis for the pH scale, a means of designating
actual concentration of H3O+ ions in an aqueous solution in the acidity range between
1.0 M H3O+ and 1.0 M OH-. The pH scale is shown below
:
[H+], M pH [OH-], M
-14
1.0 0 10
0.1 1 10-13
0.01 2 10-12
0.001 3 10-11
0.0001 4 10-10
0.00001 5 10-9
0.000001 6 10-8
10-7 7 10-7
10-8 8 0.000001
10-9 9 0.00001
10-10 10 0.0001
10-11 11 0.001
 19

10-12 12 0.01
10-13 13 0.1
10-14 14 1.0
\
 The pH scale was devised by a Danish biochemist, S. P. L. Sorensen. He defined
the term pH as:

pH = log10 1 _ = – log10 [H3O+]

[H3O+]

In a precisely neutral solution at 25oC

[H3O+] = [OH-] = 1.0 X 10-7 M

The pH of such a solution is

pH = log10 1 __ = 7.0
1 x 10-7

The following are pH of some fluids:

Fluid pH
Seawater (varies) 7.5
Blood Plasma 7.4
Interstitial Fluid 7.4
Intracellular Fluids
Muscle 6.1
Liver 6.9
Gastric Juice 1.2 – 3.0
Pancreatic Juice 7.8 – 8.0
Saliva 6.35 – 6.85
Cow’s Milk 6.6
Urine 5–8
Tomato Juice 4.3
Grapefruit Juice 3.2
Soft Drink (cola) 2.8
Lemon Juice 2.3

Measurement of pH

 Measurement of pH is one of the most common and useful analytical procedures

in biochemistry since the pH determines many important aspects of the structure and
activity of biological macromolecules and thus the behavior of cells and organisms.
 20

 The primary standard for measurement of pH is the hydrogen electrode, a

specially treated platinum electrode immersed in the solution whose pH is to be
measured.

 The hydrogen proved too cumbersome for general use and has been replaced by
the glass electrode, which responds directly to H+ concentration in the absence of
hydrogen gas.

 Another way of measuring pH is to use acid – base indicators.

Acids and Bases

 The most general and comprehensive definitions of acids and bases, applicable to
both non – aqueous and aqueous systems are those of G. N. Lewis. A Lewis acid is a
potential electron – pair acceptor and a Lewis base a potential electron – pair donor.

 However, the formalism introduced by J. N. Brönsted and T. M. Lowry is more

widely used in describing acid – base reactions in dilute aqueous systems. According
to Brönsted – Lowry concepts, an acid is a proton donor and a base is a proton
acceptor.

 An acid – base reaction always involves a conjugate acid – base pair, made up of
a proton donor and the corresponding proton acceptor. For example, acetic acid
(CH3COOH) is a proton donor and the acetate anion (CH 3COO-) is the corresponding
proton acceptor; together they constitute a conjugate acid – base pair.

 The equation for the dissociation or ionization of an acid (HA) in dilute aqueous
solution involves the transfer of a proton from the acid to water, which itself can act
as a proton acceptor to yield H3O+:

HA + H2O ↔ H3O+ + A-

Each conjugate base has a characteristic affinity for a proton relative to the proton
affinity of OH-. Acids that have only a slight tendency to give up protons to water are
weak acids; acids that readily give up their protons are strong acids.

 The tendency of any given acid to dissociate is given by its dissociation constant
at a given temperature

K = [H3O+][A-]
[HA][H2O]

where the brackets indicate concentrations in moles/liter. To simplify the equation:

K = [H+][A-]
[HA]
 21

 It is also convention in Biochemistry to employ dissociation constants based on

the analytically measured concentrations of reactants and products under a given set
of experimental conditions, i.e., at a given total concentration and ionic strength and
with other solutes specified. Such a constant is called an apparent or concentration
dissociation constant, is designated K’.

 pK’ is the logarithmic transformation of K’, just as pH is the logarithmic

transformation of [H+].

pK’ = log 1 = – log K’

K’

Strong acids have low pK’ values while strong bases bases have high pK’ values.

Acid – Base Indicators

 The pH of a solution can be determined by using indicator dyes, most of which

are weak acids (designated Hind) such an indicator dissociates according to the
equilibrium

Hind ↔ H+ + Ind-

Buffers

 Intracellular and extracellular fluids of living organisms contain conjugate acid –

base pairs which acts as buffers at normal pH of these fluids. A buffer is a system
which tends to resist change in pH when a given increment of H+ or OH- is added.

o The major intracellular buffer is the conjugate acid – base pair H2PO4- -
HPO42- (pK’ = 7.2).
o Organic phosphates such as glucose 6 – phosphate and ATP also
contribute buffering power in the cell.
o The major extracellular buffer in the blood and interstitial fluid of
vertebrates is the bicarbonate buffer system (H2CO3 – HCO3-).

 The bicarbonate buffer system (H2CO3 – HCO3-) has some distinctive features. Its
pK’ is 3.8 which is far lower than the normal range of blood pH. In the system, the
proton – donor, carbonic acid, is in reversible equilibrium with dissolved CO2.

H2CO3 ↔ CO2(aq) + H2O

If such an aqueous system comes in contact with a gas phase, the dissolved CO2 will
equilibrate between the gaseous and aqueous phases.

CO2(aq) ↔ CO2(g)

Since by Henry’s Law the solubility of a gas in water is proportional to its partial
pressure, the pH of the bicarbonate buffer system is a function of the partial pressure
 22

of CO2 in the gas phase over the buffer solution. If CO2 pressure is increased, all
other variables remaining constant, the pH of the bicarbonate buffer declines, and
vice versa.

 The bicarbonate buffer system can buffer blood plasma effectively near pH 7.0 at
which the proton – acceptor/proton – donor ration is very high, because a small
amount of proton – donor H2CO3 is in labile equilibrium with a relatively large
reserve capacity of gaseous CO2 in the lungs. Under any conditions in which the
blood must absorb excess OH-, the H2CO3 which is used up and converted to HCO3-
is quickly replaced from the large pool of gaseous CO2 in the lungs.
 There is another distinctive feature of the bicarbonate buffer system. CO2 is a
major end product of the aerobic combustion of fuel molecules and in mammals is
ultimately eliminated via the lungs. The steady – state ratio of [HCO3-]/[H2CO3] in
the blood is a reflection of the rate of CO2 production during tissue oxidation and tha
rate of loss of CO2 by expiration.

 The catalytic activity of enzymes is especially sensitive to changes in pH. They

have maximal activity at a characteristic Ph, called the optimum pH and that their
activity declines sharply on either side of the optimum p. Thus biological control of
the pH of cells and body fluids is of central importance in all aspects of intermediary
metabolism and cellular function.

The Fitness of the Aqueous Environment for Living Organisms

 Living organisms have effectively adapted to their aqueous environment and have
even evolved means of exploiting unusual properties of water.

 The high specific heat of water is useful. To large terrestrial animals because
body water acts as a heat buffer allowing the temperature of the organism to remain
relatively constant as the air temperature fluctuates.

 The high heat of vaporization of water is exploited by vertebrates as an effective

means of losing heat by evaporation of sweat.

 The high degree of internal cohesion of liquid water due to H – bonding is

exploited by higher plants to transport dissolved nutrients from the roots up to the
leaves by transpiration.

 Even the fact that ice has a lower density than liquid water and therefore floats
has important biological consequences in the ecology of aquatic animals.

 But most fundamental to all living organisms is that man important biological
properties of cell macromolecules, particularly proteins and nucleic acids, derive their
interactions with water molecules of the surrounding medium.