Structure & Molecular organization of

a Living Cell

The living cell consists of mass of protoplasm surrounded by a

plasma membrane (P.M). The protoplasm is the living material of the
cell and it is considered as the life itself, has two compartments,
cytoplasm and nucleoplasm.

1- The cytoplasm is aqueous gel material limited by the P.M and

consist of many essential organelles, such as mitochondria, Golgi
apparatus, centrioles, lysosomes and others, as well as non-living
inclusions, e.g. pigments and stored food vacuoles.

2- The nucleoplasm of a nucleus is surrounded by a nuclear envelope

and it is mainly consists of a chromatin material, nucleolus,
ribosome and RNA molecules.
 The protoplasm is colloid material made up of chemical molecules

inorganic and organic

1) Inorganic molecules

A - Water:
is the most abundant and important molecule in cells and tissues.
Human are about two thirds water. The functions of water are:-

1- 95% of the cellular water found free, used as

a- a solvent for virtually all cellular compounds and dispersion
medium for the solutes.
 b- Act as a reactant or product in thousands of biochemical reactions
catalyzed by enzymes, including the synthesis and degradation of
protein & nucleic acids (synthesis & hydrolysis of adenosine
triphosphate). An important determinant of biological structure,
as lipid bilayer, folded proteins.

2- 5% of the cellular water found bounded to the organic molecules by

hydrogen bonds. Its also associates with small inorganic ions.

B- Salts and Mineral Components

 Inorganic and mineral constituents of the cell are found in the
form of salts or combined with proteins, carbohydrates and lipids.

 Salts dissociated into anions (e.g., Cl −) and cations (e.g., Na+ and
K+), these are important in maintaining osmotic pressure and
acid-base equilibrium of the cell.

 The concentration of various ions in the intracellular fluid differs

from that in the interstitial fluid. For example, the cell has a high
concentration of K+ and Mg++, while Na+ and Cl+ are mainly
localized in the interstitial fluid. The dominant anion of cells is
phosphate, and some bicarbonate is also present.

 Mineral component such as Calcium ions are found in the

circulating blood and in cells.
2) Organic molecules

A- Proteins and amino acid

 Proteins are organic compounds that contain nitrogen in addition
to carbon, hydrogen and oxygen.
 The subunits of proteins are called amino acids. There are twenty
different kinds of amino acids found in living cells.
 All amino acids have a central carbon atom, which makes four
attachments. Three of the attachments are the same for all kinds
of amino acids. The fourth attachment differs for each of the 20
kinds of amino acids as in this diagram.

Structure of Amino acid

 Proteins are long , unbranched chains of amino acids that fold up

into complex shapes because of attractive and repulsive forces
between the R groups of different kinds of amino acids in the
polypeptide chain.
 Some proteins are composed of more than one polypeptide chain
which fit together to form a complex three-dimensional functional
protein.
 The functions of proteins are the essence of life itself. They are
present in every cell and cell organoid; they constitute the
enzymes and contractile machinery of the cell, and are present in
the blood and other intercellular fluids.
  Some long-chain proteins, such as collagen and elastin, play an
important role in the organization of tissues that form the
extracellular framework.
 There are also conjugated proteins, which attached to a
nonprotein moiety, such as nucleoproteins associated with nucleic
acids,
 the glycoproteins such as chondroitin sulfate, lipoproteins and
chromoproteins that have a pigment as hemoglobulin and
cytochromes.

1- Primary structure of proteins

 The straight polypeptide chain built of globular amino acid of the
protein molecule as in bovine pancreatic ribonuclease.
 In the protein molecule, amino acids are arranged like beads on a
string, and their sequence is of great biologic importance.

2- Secondary structure of proteins

 The linear sequence of the protein begins to fold into regular
repeating patterns.
 The two most common secondary structures of proteins are the
alpha helix and the beta sheet.

3- Tertiary structure of proteins

 The tertiary arrangement is basically a higher level of protein
folding.
 As the secondary structures become spatially further apart
along the polypeptide chain, the polypeptide chains begin to
interact with their respective side chains, creating a more
complex level of folding.
4- Quaternary structure of proteins
 Quaternary structure refers to the spatial arrangement of the
subunits within the protein.
 Subunits are categorized as individual polypeptide sequences
that begin with a positively charged amino group and end with
a negatively charged carboxylic acid terminus.
 These subunits are formed from individual messenger RNA
transcripts and come together to form dimeric (two subunits)
or multimeric (more than two subunits) structure. For
example, the protein hemoglobin is composed of two pairs of
identical subunits that are united by noncovalent interactions.
B- Carbohydrate (CHO)
1- Monosaccharides. Simple sugar may have as few as three carbon
atoms (trioses), but those play the central role in energy storage
have six carbon atoms, as in this formula C6H12O6 as glucose
molecule.

2- Disaccharides. Disaccharides are sugars formed by condensation

of two monomers of monosaccharide with the lost of one
molecule of water.

3- Polysaccharides. Polysaccharides result from the condensation of

many molecules of monosaccharides with a corresponding loss
of water molecules. The most important polysaccharide in
animal cell biology is glycogen. It is a polymer composed of
many molecules of glucose, it is found in high proportion in liver
cells and muscle fibers.

 In addition to the polysaccharides made of hexose monomers,

there are many more complex long molecules that contain amino
nitrogen (e.g., glucosamine) or that can in addition be acetylated
(e.g., acetylglucosamine).

 Still more complex are those have a substitution of sulfuric or

phosphoric acid. All these polymers are important in molecular
organization, particularly as intercellular substances. These
polysaccharides may exit either free or combined with proteins.
The most important are:
1) Lipids
 This large group of compounds is characterizes by their relative
insolubility in water and solubility in such organic solvents as
benzene, ether and chloroform.
 This general property of lipids and related compounds is caused
by the predominance of long aliphatic hydrocarbon chains or of
benzene rings.
 Such structures are nonpolar and hydrophilic.
 In many lipids, these chains may be attached at one end to a polar
group, which makes it hydrophilic and capable of binding water by
hydrogen bonds.
Lipids can be classified as
1- Simple Lipids. Simple lipids are alcohol esters of fatty acids and
among these are:

A- Natural Fats (glycerides or triglycerides) are tri-esters of fatty

acids and glycerol. Glycerides are divided into fats and oils.
Fat are solid like human fat and cocoa butter, whereas oils are
liquid like fish oils and castor oil.
B- Waxes have a higher melting point than natural fats, and are
esters of fatty acids with alcohols other than glycerol, such as
beeswax.

2- Steroids
 are an aliphatic ring system that may have one or more
unsaturated double bonds as well as various side-chains.
 The steroids include a series of highly important substances in
the body, such as the sex hormones, adrenocortical hormones,
vitamin D and bile acids.
 Steroids that posses an –OH group are called sterols.
 Cholesterol is a widely distributed sterol found in bile, brain,
the adrenal glands and other organs.
 3- Compound Lipids.
 These lipids contains beside alcohol and acids, together with
sterols they are called lipoids because of the solubility
properties.
 Lipoids serve mainly as structural components of the cell,
particularly in cell membranes like phospholipids, glycolipids
and sphingolipids.

Lipids functions
 The lipids of primary cytologic interest include triglycerides
composed of glycerol and fatty acids.
 In the organism, the role of lipids varies greatly according to their
location and distribution.
1. Glycerides serve as stores of energy.
2. Phospholipids are found principally in nervous tissue as
constituents of myelin.
3. Cholesterol is important in the mechanical functions of
epidermis and hair,
4. and the steroid hormones regulate a number of essential
metabolic and reproductive processes.
5. Lipoproteins (lipids linked to a protein molecule) is common
components of tissues. They also occur in cell membranes
and in cell nuclei, as well as in the blood.

 Lipids
1. form the framework of biological membranes
2. anchor soluble proteins to the surface of membranes
3. store energy
4. and carry information as extracelluar hormones and as
intracellular second messengers.
2) Nucleic Acids
 Nucleic acids are chemical compounds of the most biologic
importance.
 All living organisms contain nucleic acids in the form of
deoxyribonucleic aids (DNA) and ribonucleic acids (RNA).
 DNA is combined with proteins-histones or protamines-
forming nucleoproteins.
 Nucleic acids have a complex chemical structure. They are
formed from a sugar moiety (pentose & deoxypentose),
nitrogenous bases (purines & pyrimidines) and phosphoric
acid.
 Nucleic acids are long polynucleotides, resulting from the
linkage of many units called nucleotides.
 Within the nucleotide, the combination of a pentose with a
base constitutes a nucleoside. For instance, deoxythymidine is
the nucleoside of thymine.

1- Phosphoric acid
 links the nucleotides by joining the pentose of two consecutive
nucleotides with an ester-phosphate bond.
 These bonds link carbon 3' in one nucleoside with carbon 5' in
the next. In this way, phosphoric acid uses two of the three
acid groups. The remaining acid group enables the molecule to
form ionic bonds with basic proteins.

2- Pentoses.
There are two pentoses, one for each type of nucleic acid (ribose in
RNA & deoxyribose in DNA). Both ribose & deoxyribose have a
pentagonal ring with five carbons , two of which (3' and5') are
linked to phosphoric acid and a third one (carbon 1') to the base .
3- base :
 Pyrimidine Bases. Comprise mainly from cytosine, thymine
and uracil. Cytosine is found in both DNA and RNA while
thymine is characteristic of DNA and uracil of RNA.
 Purine Bases. Comprise mainly adenine and quinine, which are
common to both DNA & RNA.