Each
of the small molecules can be a unit of a large organic molecule often called a
macromolecule. A unit is called monomer and the macromolecule is called polymer
(Greek: polys means 'many' and meros means 'part'). Cells contain only four
classes macromolecules e.g. polysaccharides, lipids, proteins and nucleic
acids. These macromolecules still have great variety and therefore play
different roles in cells.
Water
As
we have already seen that life first originated in water, so no life can exist
on the earth without water. All living things are composed of 70% - 90% of water.
Water provides an environment for the organisms that live in it. Water is an
inorganic substance as carbon is absent in H-O-H.
Polar Molecule
The
oxygen of water contains a negative charge and its hydrogen contains a positive
charge, so water molecules are called polar molecules. As a result, the oxygen
atom tends to attract the single electron of the hydrogen atom.
Biological importance of water
The
water content varies from 65% to 90% percent in different organisms. Human
tissues contain about 20% water in bone cells and 85% in brain cells.
 |
Water Molecule
|
Importance of hydrogen bond in water
A
hydrogen bond is much weaker than a covalent bond with in a water molecule, but
taken together, hydrogen bonds cause water molecules to cling together. Without
hydrogen bonding between molecules, water would boil at 80 degree Celsius and
freeze at 100 degree Celsius, making life impossible. But because of hydrogen
bonding, water is a liquid at temperature suitable for life. It boils at 100
degree C and freezes at 0 degree C.
Solvent properties
Water
is an excellent solvent for solar substances. These include ionic substances
like salts which have charged particles i.e. ions and some non-ionic substance
like sugar having polar group i.e. slightly negative hydroxyl group (-OH). On
contact with water, the ions and the polar groups are surrounded by water
molecules which separate the ions or molecules from each other. This is what
happens when a substance dissolves in water. Once a substance is in solution,
its molecules or ions can move freely, thus making it chemically more reactive
then if it were solid. Thus, in the majority of the cells chemical reactions
take place in aqueous solutions. Non-polar molecules are hydrophobic. Such
hydrophobic interaction is important in the information of membrane and helps
to determine the three dimensional structure of many protein molecules and
nucleic acids etc. water’s solvent properties also mean that it acts as a
transport medium e.g. blood and excretory system etc.
High heat capacity
Water
has high heat capacity i.e. a large increase in heat energy results in a
relatively small rise in temperature. The specific heat capacity of water the
number of calories required to raise the temperature of 1g of water from 15
Centigrade to 16 Centigrade is 1.0. The many hydrogen bonds that link water
molecules help water to absorb heat without a great change in temperature and
when water cools down, heat is released. However water holds heat and its
temperature falls more slowly than other liquids. The property of water is
important not only for aquatic organisms but also for all living things. Water
protects organisms from rapid temperature change and helps them to maintain
their normal internal temperature.
High heat of vaporization
It
is expressed as calories absorbed per gram of water vaporized. The specific
heat of vaporization of water is 574 kcal/kg. Evaporation of 2ml out of one
liter of water lowers the temperature of remaining 998 ml by 1 degree
Centigrade. Hydrogen bonds must be broken to change water to steam. For this, a
large amount of heat is needed for evaporation. This property of water helps to
moderate the temperature of Earth. It also gives animals in hot environment an
efficient way to release heat. When an animal sweats its body heat is used to
vaporize the sweat, thus cooling the animal.
High heat of fusion
Having
high heat capacity, water requires relatively large amount of heat to thaw.
Likewise liquid, water must lose a relatively large amount of heat to freeze.
Contents of cells and their environment are therefore less likely to freeze.
Density and freezing properties
As
water cools down, the molecules come closer together and water expends as it
freezes. The density of water decreases below 4 degree Centigrade and ice
therefore tends to float, as ice is less dense then liquid water. Water always
freezes from the top of down. When a body of water freezes on the surface, the
ice acts as an insulator to prevent the water below it form freezing. This
protects many aquatic organisms so that they can survive in winter.
Water molecules are cohesive and adhesive
Cohesion
is the force whereby individual molecules stick together. The water molecules
cling together because of hydrogen bonding. Because of cohesion water flows
freely. Thus water is an excellent transport agent. They adhere to surface,
particularly polar surfaces, therefore water exhibits adhesion. Cohesion and
adhesion both contribute to the transport of water in plants.
High surface tension
At
the surface of water a force called surface tension exists between the
molecules as a result of cohesive forces between the molecules. These cohesive
forces are due to hydrogen bonds. A water strider can even walk on the surface
of a pond without breaking the surface of water.
Water as a reagent
Water
is biologically significant as an essential metabolite, that is, it
participates in chemical reactions of metabolisms e.g. as a source of hydrogen
in photosynthesis, and is used in hydrolysis reaction.
Water ionizes
When
water ionizes, it releases an equal number of hydrogen ions (H+) and hydroxide
ion (OH-)
H-O-H after reaction H+ + OH-
This
reaction is reversible but equilibrium is maintained at 25 degree Centigrade.
The H+ and OH- ion effect and takes part in many of the reactions that occur in
cells, e.g. it helps to maintain or charge the pH of the medium.
Condensation and Hydrolysis
During
condensation, when two monomers join, a hydroxyl (-OH) group is removed from
one monomer and a hydrogen (-H) is removed from other. Water is given off during
a condensation reaction. Condensation involves dehydration because water is
removed (dehydration) and bond is made (synthesis). Condensation does not take
place unless the proper enzyme is present and the monomers are in an activated
energy-rich from. Polymers are broken down by hydrolysis, which is essentially
the reverse of condensation. Water is added during hydration, an OH group from
water attaches to the other monomer. Hydration involves a hydrolysis reaction
because water is used to break a bond. Again, the proper enzyme is required.
 |
| Condensation |
 |
| Hydrolysis of polymers |
(a)
In cells, synthesis often occurs when monomers are joined by condensation
(removal of H2O).
(b)
Hydrolysis occurs when the monomers in a polymer separate after the addition of
H2O.
Carbon
Carbon
is an element that is found in all organic molecules. The term organic means
‘living’. Carbon has the atomic number 6 and each atom of carbon has two
electron in the first shell and four electrons in its second shell. Thus each
atom has four electrons which can be shared allowing four covalent bonds to be
formed, with other atoms. The other atoms include hydrogen, oxygen and nitrogen
atoms and additional carbon atoms. The valency of carbon is four. Here carbon
has formed four simple bonds of hydrogen.
Multiple bonds
Carbon
can form double bonds with itself, C = C in fact carbon, oxygen and nitrogen
can all form strong multiple bonds.
Double
bonds: C = C, C = O, C =
N
Triple
bonds: C ≡ C, C
≡ N
 |
| structures formed by c-c bonds |
In a
saturated carbon compounds all carbon – carbon bonds are single (C-C).
Compounds containing double or triple carbon (C=C, C triple bond C) carbon
bonds are called unsaturated. Carbon forms chain of various lengths and shapes
or the size of the organic molecules is determined by the number of carbon
atoms present. The chemistry of organic molecule is determined by the elements
and the chemical groups attached to the carbon atoms and how much saturated the
carbon skeleton is. Shape of the organic molecules is determined by the
geometry of the bonds of carbon. The C – H bonds is a potential source of
energy. Energy may be released when hydrogen atom are removed in an oxidation
reduction process. Some of the molecules formed by carbon in combination of
other atoms are so unstable that they last for only the briefest time and then
break down, releasing energy, e.g. ATP. In other cases the molecules built with
carbon skeletons may be so stable that they hardly react at all, and are so big
that they cannot dissolve in water. Such compounds make up the wood of trees.
Because of these special properties and reactions of carbon atom, we can almost
guess the answer of the question “Could there be life without carbon?”
PROTEINS
Proteins
are the main structural components of the cell. All proteins contain C, H, and
O and N. some contain P, S and few have Fe, I and Mg incorporated into the
molecule.
Amino acids
Amino
acids are the building blocks of proteins. Some other types of molecules may be
attached to proteins e.g. nucleic acids, lipids and carbohydrates. There are
many amino acids known to occur, but only 20 are commonly found in proteins.
Plants are able to make all amino acids from simpler substances. The amino
acids are built on a common plan. Each contain of carbon atom. It is called
alpha carbon, to this a hydrogen atom, an amino group – NH2, a carboxyl group
–COOH and a variable group known as – R group are attached. The R group has a
different structure in each of the 20 biologically important amino acids and
determines their individual chemical properties.
 |
| General structure of an amino acid |
Chains of Amino Acids
Peptide
bond: How amino acids fit together? The bond formed to unite two amino acids is
called peptide bond. It is between two group of one amino acid and carboxyl
group of another amino acid. Thus the bond is between C-N. The linkage of C=O
and NH is called amide or peptide linkage. Water is removed in this process.
The chain of amino acids joined by peptide bonds is called a polypeptide chain.
Proteins
have levels of structures: An analysis of protein shape shows that proteins can
have up to four levels of structures (1) primary structure (2) Secondary
structure (3) Tertiary structure (4) Quaternary structure.
Primary structure
The
primary structure of protein is the sequence of amino acids joined by
polypeptide bonds. In 1953 Fredric Sanger determined the amino acid sequence of
hormone insulin. It was a laborious ten years task. Insulin is a small protein.
The protein is constructed by two polypeptide chains of 21 and 30 amino acids..
There is also a disulphide bridge between two cysteine of the smaller chain.
.gif) |
| Primary structure of protein (insulin) |
Secondary structure
The
secondary structure of protein comes about when the polypeptide takes a
particular orientation in space. The two possible patterns of amino acids
within a polypeptide are a (alpha) helix structures, B pleated sheet.
 |
| secondary structure of protein |
α (alpha) helix
The
polypeptide chain is loosely coiled in a regular spiral shape called an a-
helix.
The twisting of the chain
There
is a slightly negative charge on the oxygen and nitrogen and slightly positive
charge on the hydrogen associated with a peptide bond. These charges make it
possible for hydrogen bonding to occur between C = O of one amino acid and the
N –H of another amino acid in a polypeptide. Hydrogen bonding between every
fourth amino acid holds the spiral shapes of an helix. Thus amino acid at 1
would be bonded at amino acid 5, number 2 to number 6, and so on. The secondary
structure is usually studied by technique of X-ray crystallography. In this
process X-ray is passed through a purified crystal of protein, when this is
done X-ray are scattered by the crystal and form a characteristic pattern which
can be recorded on photographic state. Using mathematical technique, the
structure of the protein can be inferred from the pattern it produces. X-ray
diffraction data indicate that the helix makes a complete turn for every 3.6
amino acids. Example of helix protein are: keratin (found in hair, nails) wool,
collagen (found in skin).
β-Pleated sheet
In
the B- pleated structure of proteins, the polypeptide chains are more extended
and lie parallel with hydrogen bonding between chains. It is the main protein
component of the silk.
+pleated+sheet.gif) |
| B (Beta) pleated sheet |
Tertiary structure
Usually
the polypeptide chain bends and folds extensively forming a precise compact
globular shaped called the tertiary structure of proteins. The structure is
maintained by the interaction of ionic bonds, hydrogen and disulphide bonds as
well as hydrophobic interaction e.g. myoglobin.
 |
| Tertiary structure |
Quaternary structure
Many
highly complex proteins consist of more than one polypeptide chains. The
separate chains are held together by hydrophobic interaction of hydrogen and
ionic bonds. This is known as Quaternary structure. It can be more
understandable by seeing the structure of hemoglobin. It is the oxygen carrying
red pigment found in the red blood cells of vertebrates. It consists of four
separate polypeptide chains of two types, namely two a and two B chains. Each a
contains 141 amino acids and each B chain contains 146 amino acids.
 |
| Quaternary structure |
Significance of Sequence of amino acids
A
protein molecule may have 51 to 3000 amino acids. All the amino acids must be
in proper position in the polypeptide chain. If the proper site of even a
single amino acid is changed, the normal structure and function of the protein
is changed e.g. sickle cell anemia. Hemoglobin consists of two alpha and two
beta chains. The fault occurs in the sixth amino acid in the B chain. The glutamic
acid of the normal hemoglobin is replaced by valine in the hemoglobin of a
sickle cell.
 |
| Normal and sickle shaped RBC |
Shapes of protein molecules
The
shapes of protein molecules are in accordance with their function. Thus shape
of protein molecules has a significant role. The shapes may be fibrous,
globular and intermediate.
Fibrous
These
proteins have long parallel polypeptide chains cross-linked at intervals
forming long fibers or sheets. These have secondary structures physically tough
and insoluble in water. These perform structural function e.g. collagen
(tendons, bones and connective tissue), myosin (in muscles), silk (spider’s
web) and keratin (hair, horn, nail, feathers).
Globular
Polypeptide
chains are tightly folded to form spherical shape, having tertiary structure.
These are the most important ones and are easily soluble. These form enzymes,
antibodies and some hormones e.g. insulin.
Intermediate
These
proteins are intermediate in shape between globular and fibrous protein and are
soluble e.g. fibrinogen which forms insoluble fibrin when blood clots.
Functions of proteins
Proteins
play important functions in the living organisms. A brief account of functions
of proteins is given as follows.
Proteins
play an important role in membranes where they function as enzymes, receptors
and transport sites.
Proteins
form the structural part in the organisms, such as collagen is the component of
connective tissue of bones, tendons and cartilage. Keratin forms feathers,
nails, and horn. Elastin forms elastic connective tissues in ligament. Viral coat proteins warm up the nucleic acid
of virus.
Enzymes
are proteins e.g. trypsin catalysis hydrolysis of proteins. Some hormones like
insulin, glucagons and ACTH
(Adrenocorticotropic
hormone secreted by anterior Lobe of pituitary Gland) are proteins which help
to regulate glucose metabolism.
Respiratory
pigment hemoglobin transports oxygen in vertebrates Blood in myoglobin stores oxygen
in muscles.
Some
proteins are antibodies; fibrinogen and thrombin have protective functions.
Antibodies form complexes with foreign particles. Fibrinogen form fibrin in
blood clotting. Thrombin takes part in blood clotting mechanism.
Protein
fibers like actin and myosin take part in muscle contraction.
Ova
albumen is egg white protein and casein is milk protein. Their function is
storage.
Snake
venom is enzymes and diphtheria toxin is made by diphtheria causing bacteria.
CARBOHYDRATES
The
word carbohydrate means hydrated carbon. They are composed of C, H, O in the
ratio of 1: 2: 1. Their general formula is Cx(H2O)y. where x is the whole
number from three to many thousand. Chemically carbohydrates are defined as
polyhydroxy aldehydes or ketones or complex substances which on hydrolysis
yield polyhydroxy aldehydes or ketone subunits. The sources of carbohydrates
are green plants. These are the primary products of photosynthesis and other
compounds of plants are produced from carbohydrates by various chemical change.
Carbohydrates
are combined with other molecules to form complex conjugated molecules.
Carbohydrates
+ lipids = glycolipids
Carbohydrates
+ proteins = glycoproteins
Classification
Carbohydrates
are classified into three major classes
(1) Monosaccharides (2) Oligosaccharides (3)
Polysaccharides.
Monosaccharides
(Greek:
Mono, single, saccharide, sweet). These are simple sugars. They cannot be
hydrolyzed into further simple units. They are sweet in taste and are easily
soluble in water. Chemically they are either polyhydroxy aldehydes or ketones.
All carbon atoms in a monosaccharide except one have a hydroxyl group. The
remaining carbon atom is either a part of an aldehydes group or a keto group.
The sugar with aldehydes group is called aldo-sugar and with the keto group as
keto-sugar e.g. the aldehyde form is glyceraldehydes whereas ketonic form is
dihydroxyacetone. The two trioses are intermediate in respiration and
photosynthesis.
They
have general formula Cn(H2O)n. they are classified depending upon
the number of carbon. In nature Monosaccharides with 3 – 7 carbon atoms are
found.
Note: Although glucose and
fructose both have the same molecular formula C6H12O6
they have different molecular structures or arrangement of atoms.
 |
| Some important Monosaccharides |
Ring structure
In
solution, most of the monosaccharides form ring structure. e.g. 5 carbon ring
of ribose and 6 carbon ring of glucose.
Oligosaccharides
The
sugars that yield 2 to 10 monosaccharides on hydrolysis are called
oligosaccharides. Oligosaccharides are less sweet in taste and less soluble in
water.
 |
| Ribose and Glucose Form Ring Shaped Structures |
Disaccharides
Two
monosaccharides combine to form disaccharides.
Glucose +
Glucose = Maltose
Glucose + Galactose = Lactose
Glucose +
Fructose = Sucrose
Trisaccharides
Three
monosaccharides combine to form Trisaccharides.
Glucoside Linkage
The
bond formed between two monosaccharides is called glucoside linkage. Water is
removed during formation of this linkage.
Maltose
= 1, 4 glucoside linkage.
 |
| Disaccharide |
Polysaccharides
These
consist of many glucose polymers linked by glycoside bonds. They are usually
branched. They are tasteless and are sparingly soluble in water. Examples:
starch, glycogen.
Starch
Glucose
is a monomer. Starch is a polymer of glucose. It consists of linear and
branched chain. Starch is insoluble in water. Thus it can be stored in the
plant cell. Plant cells convert glucose to starch. There are two types of
starch, amylase and amylopectin. Amylase starches have unbranched chains of glucose
and are soluble in hot water. Amylopectin are branched and are soluble in hot
and cold water. Starches give blue color with iodine.
Glycogen
Animals
convert glucose into glycogen. It is stored in animal cells. It consists of
long branched chain of amylose. It is insoluble in water and gives red color
with iodine.
Cellulose
It
is polymer of glucose. The rings of glucose are arranged in flip flap manner.
Cellulose is the building and supporting material of the cell wall. It is
highly insoluble in water. Cellulose gives no color with iodine.
Examples:
Wood, paper and cotton fibers.
+starch.gif) |
| (a) starch |
+Glycogen.gif) |
| (b) Glycogen |
Polysaccharides
Polysaccharides
chiefly act as food and energy stores e.g. starch glycogen and as structural
material e.g. cellulose. Commercially cellulose is used to make cotton goods,
and is a constituent paper.
LIPIDS
The
term is simply a convenient name for organic compounds that are hydrophobic
(water-hating) and insoluble in water but soluble in organic solvents such as
acetones, alcohol, chloroform, benzene and ether. Lipids have a greasy or oily
consistency. Lipids are composed of C, H and O. However, they have relatively
less oxygen in proportion to C and H then do carbohydrates. Oxygen atoms are
characteristic of hydrophilic (water-loving) functional group so lipids with
little oxygen are much less soluble in water then most carbohydrates. They
serve as concentrated storage materials, as structural components of cell
membrane and cell organelles. Lipids have been classified as:
Acylglycerol
Phospholipids
Terpenoids
Waxes
Acylglycerol
The
most abundant lipids in living things are the natural fats or acylglycerol.
Chemically, acylglycerol can be defined as esters of fatty acids and alcohol.
An ester is a compound produced as the result of a chemical reaction of an
alcohol with acid and water molecules is released.
C2H5OH
+ HOOCCH3 AFTER REACTION
C2O5OOCCH3 + H2O
Alcohol
+ acetic acid à an
ester.
A
neutral fat consists of glycerol joined to one, two or three fatty acids.
Glycerol is three carbon alcohols that contain three OH groups. A fatty acid is
ling, straight chain of carbon atoms, with a carboxyl group (COOH) at one end.
When a glycerol molecule combines chemically with one fatty acid, a
monoglycerol (or monoglyceride) is formed. When two fatty acids combine with a
glycerol a diglycerol (or diglyceride) is formed and when three fatty acids
combine with one glycerol molecule a triglycerol (or triglyceride) is formed. About
30 different fatty acids are found. Fatty acids vary in length. They have an
even number of carbon atoms. For example butyric acid has four carbon atoms and
oleic has 18 carbon atoms. Fatty acids are either saturated or unsaturated.
Saturated Fatty Acids
Fatty
acids in which all of the internal carbon atoms possess hydrogen side groups
are said to be saturated because they contain the maximum number of hydrogen
atoms that are possible e.g. butyric acid. Saturated fatty acids tend to be
solid at room temperature.
Importance of saturated fatty acids
Fats
are efficient energy-storage molecules because of their high concentration of
CH bonds. Animal’s fats contain more calories than vegetable fats. Large amount
of saturated fats in the human diet may lead to heart diseases. Animal fat
contains over twice as more energy as glycogen.
Saturated Fatty Acids
Fatty
acids in which all of the internal carbon atoms possess hydrogen side groups
are said to be saturated because they contain the maximum number of hydrogen
atoms that are possible e.g. butyric acid. Saturated fatty acids tend to be
solid at room temperature.
Importance of saturated fatty acids
Fats
are efficient energy-storage molecules because of their high concentration of
CH bonds. Animal’s fats contain more calories than vegetable fats. Large amount
of saturated fats in the human diet may lead to heart diseases. Animal fat
contains over twice as more energy as glycogen.
Unsaturated fatty acids
Fatty
acids having double bonds between one or more pairs of successive carbon atoms
are called unsaturated fatty acids. Most of the unsaturated fatty acids are
liquid at room temperature. Liquid fat is called oil. e.g. oleic acid.
Importance of unsaturated Fatty Acids
Triglycerides
containing unsaturated hydrocarbon chains melt at a lower temperature. This is
useful for living things. For example, the feet of reindeer and penguins
contain unsaturated triglycerides, and this helps to protect these exposed pars
from freezing.
Phospholipids (GK: phos light, lipos
fat)
As
implied by the name, contains a phosphate group. Phospholipids are
phosphorylated derivatives of phosphatidic acid. A phospholipids molecule
consists of two fatty acids linked to a glycerol molecule and a phosphate group
linked to the glycerol’s third carbon. The phosphate is linked to an organic
compound such as chlorine, (HO-CH2- CH2-N = (CH3)3,
ethanolamine (HO-CH2-NH2) and serine (CH2
–CHNH2 COOH) etc. The organic compound usually contains
nitrogen. Phosphorus and nitrogen are absent in the neutral fats. Any C-C bonds in the glycerol molecule can be
twisted, so that in the molecule of phospholipids, the strongly polar phosphate
group projects in the opposite direction from the two fatty acids side chains.
One end of the molecule, containing the phosphate group is hydrophilic, in
other words, it is polar and readily soluble in water. The other end,
containing fatty acid side chains, is hydrophobic, that is non polar and
insoluble in water.
Phospholipids
form bilayer sheet: In water, every phospholipids molecule orients so that its
polar head faces water and its non-polar tails face away. By forming two layers
with the tails facing each other, no tails are ever in contact with water. The
structure resulted is called lipid bilayer, which are forming spontaneously.
Lipid bilayer sheet of the sort is the foundation of all biological membranes.
The lipid bilayer forms a barrier to the passage of water-soluble molecules
which is the key biological property of the lipid bilayer.
The lipid bilayer is a fluid
Water
forms hydrogen bonds with individual phospholipid molecule. As a result,
individual lipid molecules are free to move about within the membrane, so the
lipid bilayer is like the “shell” of a soap bubble. The bilayer itself is a
fluid and viscous. Hydrogen bonding of water holds the membrane together. The
tails of phospholipid molecules are attached to one another when they line up
close together. These cause the membrane to stiffen. Some phospholipids have
tails that do not align well because they contain one or more double C=C bonds,
which introduce kinks in the tails, as a result membrane becomes more fluid
than those that lack them.
Terpenoids
Terpenoids
are made from repeating unit of isoprene unit. This unit condenses in different
ways to form many compounds e.g. steroids, carotenoid, terpenes.
Steroids
Steroids
are lipids that do not contain fatty acids. These are complex molecules with
four interlocking carbon rings, three are six sided rings and the fourth one is
a five sided ring. Each particular steroid has its own side group combination
of carbon and hydrogen.
Importance of steroids
Steroids
are important to our bodies in many ways. The male and female sex hormones and
the adrenal gland hormones are steroids. Vitamin D, which helps to regulate
calcium metabolism is a steroid. Cholesterol which is important in membrane and
in brain and nervous tissue is a steroid, and bile acids. Which aid digestion
and the absorption of fats are also steroids.
Carotenoids
Vitamin
A is formed from carotenoid pigments of plants. The major sources of vitamin
are egg yolk, green and yellow vegetables, fruits, liver and butter. The
function of vitamin A is formation of visual pigments, maintenance of normal
epithelia’s structure. Deficiency of vitamin A causes night blindness and skin
lesions.
Terpenes
Terpenes
(from turpentine) include essential oils such as citral, camphor, menthane, the
resin acids and rubber. These commercial products are used by human beings.
Waxes
Waxes
are lipids having odd number of carbon atoms varying from C25 to C35.
Waxes are a mixture of long chain alkanes (Cn H2n+2) with alcohols
(R-OH), ketones (R-O-R), esters(R-CO-R) and long chain fatty acids. Waxes have
protective functions in plants and animals. Forms protective coating on fruits
and leaves. Protects plants from water loss and abrasive damage. Provides water
barrier for insects, birds, sheep etc.
NUCLEIC ACIDS
Nucleic
acid is essential for life. The term ‘nucleic acid’ comes from the fact that
they are found mainly in nucleus. Nucleic acid was first isolated in 1870 by F. Miescher from the nuclei of pus
cells. The two major types of nucleic acid found in the living things are
deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA). Nucleic acid is a
linear unbranched polymer. The monomer is the nucleic acid is called
nucleotide.
Structure of a Typical Nucleotide
Each
nucleotide consists of pentose sugar, a phosphate and nitrogen containing ring
structure called basis. The ring structures are called basis because of
unshared pair of electrons on nitrogen atoms, which can thus acquire a proton.
Phosphoric acid (H3PO4) which gives nucleic acid their acid characteristics
forms the ester linkage with OH groups of a pentose sugar. In a typical
structure the nitrogen base is attached to position 1 of pentose sugar. One
phosphoric acid is attached with two pentose sugars with one ribose at position
3 and at position 5 of another ribose. The combination of a sugar with a base
and addition of phosphoric acid are condensation reaction.
Nucleoside:
Base – Sugar
Nucleotide:
Sugar – Phosphate – Sugar
Phosphate diester linkage
Phosphate
forms linkage with two pentose sugars, the linkage is called phosphodiester
linkage. Bases may be grouped as: purine and pyrimidine.
Purine
Includes
Adenine and Guanine which are double ring structures.
Pyrimidine
It
includes Thymine, Cytosine and Uracil, which are single ring structures.
The
nucleotides are named after the name of base attached to it e.g. Adenine
nucleotide = Adenine-deoxyribose-
phosphate. Bases are represented
by their initial letter i.e. A, G, T, C, and U.
Nucleotides
are not only used as building blocks for nucleic acids, but they form several
coenzymes, including adenosine triphosphate (ATP), nicotinamide dinucleotides
(NAD).
Polynucleotide
Two
nucleotides join to form a dinucleotide by condensation between the phosphate
of one with the sugar of the other. The process is repeated up to several
million times to make a polynucleotide. An unbranched sugar-phosphate backbone
is thus formed.
Mononucleotide
Adenosine
monophosphate is a nucleotide. It is made up of the ribose sugar and the base
is adenine. When a phosphate is added to AMP it becomes ADP or Adenosine
diphosphate. By adding one more phosphate to ADP the ATP or Adenosine
triphosphate is formed. ATP is the most important high energy compound. It is
found in all cells. The two covalent bonds linking these three phosphates
together are usually indicated by a squiggle (~) and are called high-energy
bonds. Addition of inorganic phosphate to an organic phosphate to an organic
molecule is called phosphorylation e.g.
ADP
+ P = ATP
ATP-a
rich energy compound
ATP can be converted to ADP
and inorganic phosphate (Pi) by hydrolysis. This reaction releases energy.
The third phosphate group
splits from the ATP, and this phosphate remains in the cell in inorganic form.
ADP and phosphate can be converted back to ATP, by condensation the two
reactions can be put together:
ATP + H2O
Hydrolysis\condensation ADP + Pi + energy (30.6 KJ per mole of ATP)
ATP is known as the energy
currency of cells. ATP can be used to make muscles contract, make nerve
function, drive active transport and synthesis of proteins etc. ATP is made
from the oxidation of organic molecules during respiration. Since the energy to
add the phosphate to ADP comes from oxidation, the process is known as
oxidative phosphorylation. In photosynthesis ATP is made by using light and the
process is called photophosphorylation. Most of the ATP in the cell is made in
mitochondria. The actual amount of ATP in the cell at any time is small.
Dinucleotide-NAD
Often
enzymes use additional chemical components called cofactors as a tool to aid
the catalysis. When the cofactor is an organic compound other then proteins it
is called a coenzyme e.g. nicotinamide-adenine dinucleotide (NAD) and many
vitamins.
Structure
It
consists of two nucleotides. One nucleotide consists of base-nicotinamide,
sugar and phosphate. Other nucleotide consists of base-adenine-sugar and
phosphate. The two bases are joined by their phosphate group forming a
dinucleotide. It is derived from the vitamin nicotinic acid (niacin) and can
exist in both reduced and oxidized form.
NAD-as coenzyme
In
many enzyme-catalyzed oxidation-reduction reactions, the electrons are passed
in pairs from the active site of enzyme to a coenzyme that serves as the
electron acceptor. When NAD acquires an electron and hydrogen atom (actually
two electrons and a proton) from the active site of an enzyme, it becomes
reduced as NADH. The two energetic electrons and the proton are now carried by
NADH molecule. The oxidation of food stuff takes place by tacking electrons and
donating them to NAD forming NADH. Only a small amount of NADH+ molecule is
present in a cell, because each NAD molecule is used over again and again, FAD
(Flavin adenine dinucleotide) is another coenzyme for oxidation reduction,
which is sometimes used instead of NADH+. FAD accepts two electrons and two
hydrogen ions (H+) to become FADH2.
Deoxyribonucleic Acid (DNA)
It
is generally present in the chromosome. It is also found in mitochondria and
chloroplast. It consists of:
Pentose
sugar: Deoxyribose
Purine:
Adenine, Guanine
Pyrimidine:
Thymine, Cytosine
Phosphate
Structure of DNA
Maurice
Wilkins and Rosalind Franklin used the technique of x-ray diffraction to
determine the structure of DNA. At the same time James D. Watson and Francis
Crick built the scale model of DNA. All the data thus obtained strongly
suggested that DNA is a soluble helix structure. There are two polynucleotide
strands running in opposite directions and winding about each other in a form
of double helix. The double helix looks like a ladder. The sugar phosphate part
of the nucleic acid makes the upright part of the ladder. The nitrogen bases of
the nucleotide make up the rungs of the ladder. Each rung consists of purine
and a pyrimidine. Adenine pairs with thymine and guanine pairs with cytosine.
The base pairs are held together by the hydrogen bond. There are two hydrogen
bonds between A and T and three hydrogen bonds between C and G. the helix is 20
A0 (2nm) in diameter and makes a full spiral turn every 34 A0 (3.4nm) i.e.
after every ten base pairs. The distance between two base pairs is 0.34nm.
There
are four different nucleotides in DNA; each contains phosphate, the pentose
sugar deoxyribose, and a nitrogen-containing organic base. Two bases are
purines; adenine (A) and guanine (G): two bases are pyrimidines: thymine (T)
and cytosine (C). b. DNA has a ladder structure: the sugar-phosphate molecules
make up the sides and the hydrogen-bonded bases make up the rungs. C. Actually,
DNA is a double helix in which the two strands twist about each other.
The
amount of DNA is fixed for particular species. It depends upon the number of
chromosomes. All the somatic (body) cells of an organism have the same amount
of DNA, while the sperms or ova have almost half the amount of DNA.
Ribonucleic Acid (RNA): The carrier of
information
RNA
is concentrated in the cytoplasm. It consists of sugar ribose and bases
Adenine, Uracil, Cytosine and Guanine. RNA is hereditary material in some
viruses. RNA is a single polynucleotide chain. There are three types of RNA
molecules:- (1) tRNA = transfer RNA.
(2) rRNA = ribosomal RNA. (3) mRNA =
messenger RNA.
The
three RNA are synthesized from different parts of DNA in a process called
transcription. The synthesis takes place in the nucleus. Then the RNA is
transported to cytoplasm.
Messenger RNA (mRNA): It
takes the genetic message from the nucleus to the ribosomes in the cytoplasm to
form particular proteins. Base sequence in mRNA is according to the base
sequence of DNA. It becomes attached to ribosome. Where amino acids are
attached to form polypeptide chain as per base sequence of mRNA. A mRNA
consists of a single strand of variable length. Its length depends upon the
size of the gene as well as the protein for which it is tacking the message.
For example, for a protein molecule 1,000 amino acids, mRNA will have the
length of 3,000 nucleotides. mRNA is about 3 to 4 % of the total RNA in the
cell.
Transfer RNA (tRNA): These
are small molecules. Each chain consists of 75 to 90 nucleotides. Specific tRNA
will pick specific amino acid. It will bring the amino acid to the ribosome as
per nucleotide sequence of mRNA. So the cell will have at least 20 kinds of
tRNA molecules. tRNA comprises about 10 to 20% of the cellular RNA.
Ribosomal RNA (rRNA): It
consists of rRNA and protein. mRNA has the genetic information according to
DNA. In ribosome the amino acids are arranged and linked as per sequence of
nucleotides on the mRNA. Thus specific protein molecules are synthesized. It is
the major protein of RNA in the cell, and may be up to 80% of the total RNA. It
is strongly associated with the ribosomal protein where 40 to 50% of it is
present.
CONJUGATED MOLECULES
Molecules
when joined by other kinds of molecules are called conjugated molecules.
Glycolipids:
Glycolipids are association of lipids with carbohydrates. The carbohydrates
form a popular head to the molecule. Glycolipids are found in membrane and
nervous tissue.
Glycoproteins:
Glycoprotein is formed when proteins are covalently bound to carbohydrates.
Glycoproteins are very widely distributed in the cells and perform verity of
functions. These include their role as enzymes, hormones, transport proteins,
structural proteins and receptor. In Antarctica, at 20 C temperature the blood
would freeze. The fish contains antifreeze glycoproteins which lower the
freezing point of water. The blood group antigens contain glycoprotein, which
also play a determinant role in blood grouping.
Lipoproteins: The
lipoproteins are formed by the combination of protein with a lipid.
Phospholipid protein complexes are widely distributed in plant and animal
material. They occur in milk, blood, cell nucleus, egg yolk, cell membrane and
chloroplast of plants. They are also found in bacterial antigens and viruses.
Nucleoprotein: The
nucleoprotein consists of simple basic protein and nucleic acid. They are most
abundant in tissues, both plants and animals having a large proportion of
nuclear material, such as yeast, asparagus, (A plant of genus Liliaceae),
thymus and sperms.
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