Science vs Engineering

Science is defined as the branch of knowledge or the study that deals with a systematically
arranged body of truths or facts which can be logically and rationally explained. It is knowledge of
the physical and material world that is derived from one’s observation and experimentation.
It is closely related to philosophy, physics, chemistry, geology, and biology. It is divided
into two major groups of empirical sciences wherein knowledge is based on phenomenon that can
be observed and validated through research, namely:
 Natural sciences, which study natural phenomenon such as biology.
 Social sciences, which study human behavior and society.

Two other categories are based on specific fields of discipline like interdisciplinary and applied
sciences such as: Mathematics, which is similar to empirical sciences because it involves the careful
and systematic study of an objective. It is important in the formation of hypotheses, theories and
laws.

Engineering, which is the discipline of gaining and using scientific, mathematical,

economic, social, and practical knowledge to design and build machines, devices, and structures to
improve the lives of the people.
Engineering, therefore, is a science that is broad and has four main branches:
 Chemical engineering, which is the study of chemicals and their principles for the design and
production of materials and fuels essential to man.
 Civil engineering, which involves the planning and construction of infrastructure like roads,
bridges, and buildings.
 Electrical engineering, which includes design and production of electrical and electronic systems
such as electrical and electronic circuits, devices, computer systems, motors, telecommunication,
etc.
 Mechanical engineering, which involves the design of physical and mechanical systems like
aircraft, weapons, transportation, and other mechanical devices.
There are several more branches including naval engineering, architecture, biomedical,
industrial, and nuclear engineering. Engineering applies the sciences of physics and mathematics
and works with nature to design things that are necessary to man.
One important tool that engineers use to help check their designs for flaws and mistakes
is the computer. Computer-aided design (CAD) software is used to create 3D models and drawings
which allow engineers to analyze their designs without having to build prototypes.
Science is very helpful to man. It makes life easier, and it helps us in our search for
knowledge, truth, and the creation of things that are essential to us.

Camera vs Eyes: Similarities

Comparison of various similarities and differences found in the working of the human eye
and a photo camera.
Image focusing: Human and camera lenses both focus an inverted image onto light-sensitive
surface. In the case of a camera, it‘s focused onto film or a sensor chip. In your eyes, the light-
sensitive surface is the retina on the inside of your eyeball.
Light adjustment: Both the eye and a camera can adjust quantity of light entering. On a camera,
it‘s done with the aperture control built into your lens, whilst in your eye, it‘s done by having a
larger or smaller iris.
Eye as a camera
1. Cornea behaves much like the front lens element of a lens. Together with the lens, which
is behind the iris, they are the eye‘s focusing elements. The cornea takes widely diverging rays of
light and bends them through the pupil, the round opening in the central portion of the coloured iris.
2. Iris and pupil act like the aperture of a camera. The iris is a muscle which, when
contracted, covers all but a small central portion of the lens, allows adjustable control of the
quantity of light entering the eye so that the eye can work well in a wide range of viewing
conditions, from dim to very bright light.
3. Finally, Retina is the sensory layer that lines the very back of our eyes. It acts very much
like the imaging sensor chip in a digital camera. The retina has numerous photoreceptor nerve cells
that help change the light rays into electrical impulses and send them through the optic nerve to the
brain where an image (of what we see) is finally received and perceived. Because of this reception
and perception function, retina is, perhaps, the most important component of our eyes. As with the
camera, if the ―film‖ is bad in the eye (i.e. the retina), no matter how good rest of the eye is, we
will not get a good quality image or picture.

Bird flight vs Aircraft

Airplanes eradicated the problem of accessibility and made it faster and more convenient to do
business. Birds fly so effortlessly because of the adaptations that they have. Birds have streamlined
shapes so that when they are in flight the air can flow on their surface smoothly. Engineers used the
shape of the birds as inspiration to model the planes.
Most airplanes have a streamlined shape so that they do not face air resistance when they are in
motion.
Secondly, birds have smooth and sometimes glossy surface. Birds groom their feathers with
their beaks to makes sure that their body is smooth as they fly. Airplanes also have polished
surfaces, and this prevents air resistance. Thirdly, birds use a concept where they fly in a V shape
when they are in a flock. This mode of flying has enabled birds to travel greater distances. The V
formation aids in collaboration, because as each bird flies, it adds more energy to the group, and
they can keep up many miles in flight.
The birds keep changing positions and rotate their place in the stack, and this helps them go
for long distances without tiring. There are some researchers from Stanford University who utilized
this trait and concluded that if jets use the same trait, they can save on fuel. They purported that if
jets fly in a V-shape and alternate their positions, they would manage to save their fuel up to 15%.

Thermodynamics & Brownian motion Brownian motion

Brownian motion is the random movement of particles in a fluid due to their collisions with
other atoms or molecules. Brownian motion is also known as pedesis, which comes from the
Greek word for "leaping." Even though a particle may be large compared to the size of atoms and
molecules in the surrounding medium, it can be moved by the impact with many tiny, fast- moving
masses. Brownian motion may be considered a macroscopic (visible) picture of a particle
influenced by many microscopic random effects.
Brownian motion takes its name from the Scottish botanist Robert Brown, who observed
pollen grains moving randomly in water. He described the motion in 1827 but was unable to
explain it. While pedesis takes its name from Brown, he was not the first person to describe it. The
Roman poet Lucretius describes the motion of dust particles around the year 60 B.C., which he used
as evidence of atoms.
The transport phenomenon remained unexplained until 1905 when Albert Einstein
published a paper that explained the pollen was being moved by the water molecules in the liquid.
As with Lucretius, Einstein's explanation served as indirect evidence of the existence of atoms and
molecules. At the turn of the 20th century, the existence of such tiny units of matter was only a
theory. In 1908, Jean Perrin experimentally verified Einstein's hypothesis, which earned Perrin the
1926 Nobel Prize in Physics "for his work on the discontinuous structure of matter."

The mathematical description of Brownian motion is a relatively simple probability

calculation, of importance not just in physics and chemistry, but also to describe other statistical
phenomena. The first person to propose a mathematical model for Brownian motion was Thorvald
N. Thiele in a paper on the least squares method that was published in 1880. A modern model is the
Wiener process, named in honor of Norbert Wiener, who described the function of a continuous-
time stochastic process. Brownian motion is considered a Gaussian process and a Markov process
with continuous path occurring over continuous time.

Brownian motion is a physical example of a "random walk". A discrete random walk is made of
individual steps of length L whose direction is random. Although the motion of individual
molecules in a liquid is entirely unpredictable, the average property of many random walks obeys a
simple law, as we will demonstrate.

The movement of particles in a fluid can be described in terms of the average behaviour of a large
number of particles in random motion

Thermodynamics
Thermodynamics is the branch of physics that deals with the relationships between heat and other
forms of energy. In particular, it describes how thermal energy is converted to and from other forms
of energy and how it affects matter.
Thermodynamics involves measuring this energy, which can be "exceedingly complicated,"
according to David McKee, a professor of physics at Missouri Southern State University. "The
systems that we study in thermodynamics … consist of very large numbers of atoms or molecules
interacting in complicated ways. But, if these systems meet the right criteria, which we call
equilibrium, they can be described with a very small number of measurements or numbers. Often
this is idealized as the mass of the system, the pressure of the system, and the volume of the system,
or some other equivalent set of numbers. Three numbers describe 10 26 or 1030 nominal independent
variables."

The fundamental principles of thermodynamics were originally expressed in three laws. Later, it
was determined that a more fundamental law had been neglected, apparently because it had seemed
so obvious that it did not need to be stated explicitly. To form a complete set of rules, scientists
decided this most fundamental law needed to be included. The problem, though, was that the first
three laws had already been established and were well known by their assigned numbers. When
faced with the prospect of renumbering the existing laws, which would cause considerable
confusion, or placing the pre-eminent law at the end of the list, which would make no logical
sense, a British physicist, Ralph H. Fowler, came up with an alternative that solved the dilemma:
he called the new law the ―Zeroth Law.‖ In brief, these laws are:

The Zeroth Law states that if two bodies are in thermal equilibrium with some third body, then
they are also in equilibrium with each other. This establishes temperature as a fundamental and
measurable property of matter.

The First Law states that the total increase in the energy of a system is equal to the increase in
thermal energy plus the work done on the system. This states that heat is a form of energy and is
therefore subject to the principle of conservation.

The Second Law states that heat energy cannot be transferred from a body at a lower temperature
to a body at a higher temperature without the addition of energy. This is why it costs money to run
an air conditioner.

The Third Law states that the entropy of a pure crystal at absolute zero is zero. As explained
above, entropy is sometimes called "waste energy," i.e., energy that is unable to do work, and since
there is no heat energy whatsoever at absolute zero, there can be no waste energy. Entropy is also a
measure of the disorder in a system, and while a perfect crystal is by definition perfectly ordered,
any positive value of temperature means there is motion within the crystal, which causes disorder.
For these reasons, there can be no physical system with lower entropy, so entropy always has a
positive value.

The science of thermodynamics has been developed over centuries, and its principles apply to
nearly every device ever invented. Its importance in modern technology cannot be overstated.
Classification of Organisms:
Classification involves the techniques of characterization, identification, nomenclature and
grouping of organisms. Sometimes, the terms such as biological classification, taxonomy and
systematic are used as synonyms.

Need of Classification:

Classification is the arrangement of organisms into groups and sub-groups on the basis of
similarities and dissimilarities and placing them in a hierarchy that brings out their relationships.

The organisms should be classified due to following reasons:

1. Classification makes identification and the study of a wide variety of organisms easy.
2. It reveals inter-relationships among different groups of organisms.

3. It gives information about the organisms and fossils of other localities.

Based on Cellularity

Unicellular Organisms:

They are single celled organisms. Each cell survives on its own and carry out all the basic
metabolic activities. All prokaryotes, few protists, few types of fungi, and protozoa (zooplankton),
algae (phytoplankton) are examples for unicellular organisms. Some live in colonies and some live
as individuals.

Multicellular Organisms:

These organisms consist of more than one cell. A group of cells integrate together to perform a
specific function contrast to unicellular organisms where each is independent. Plants, Animals,
majority of fungi algae are examples of multicellular organisms.

Based on Ultrastructure

Prokaryotes: Pro = before; karyon= nucleus.

A prokaryote is a unicellular organism that lacks a proper membrane bound nucleus or any
membrane bound organelle. They are divided into two domains Bacteria and Archaea. They contain
the genetic material freely floating in proper nucleus called nucleoid. They also lack nucleolus.
Locomotory organs are fimbriae, flagellum, pilus.

Eukaryotes: Eu = true; karyon= nucleus

Eukaryotes are organisms which have a definitive membrane bound nucleus and other membrane
bound organelles.They belong to the domain Eukaryota or Eukarya. Eukaryotes have much larger
size and cell volume when compared to prokaryotes. Plant cells have a cell wall but animal cells do
not.

Based on Nutrition

1. Autotrophs: The term Autotrophic is derived from two Greek words - 'auto' meaning 'self'
and 'trophe' meaning 'nutrition'.

Autotrophs or primary producer is an organism that produces complex organic compounds from
simple substances present in its surroundings, generally using energy from light or inorganic
chemical reactions. They are the producers in a food chain, such as plants on or algae in water.

2. Heterotrophs: Heterotroph is an organism that cannot produce its own food, relying instead
on the intake of nutrition from other sources of organic carbon, mainly plant or animal matter. In
the food chain, heterotrophs are primary, secondary and tertiary consumers, but not producers.
Heterotrophs include all animals on the Earth, fungi and other prokaryotic animals including some
non- green flowering plants also.
 Heterotrophic Nutrition can be of three types
a. Saprophytic Nutrition
b. Parasitic Nutrition
c. Holozoic Nutrition

a. Saprophytic Nutrition: The worse Saprophytic is derived from two Greek words - 'sapro'
meaning rotten and 'phyto' meaning plants.The Organisms which get their food from supply of dead
and decaying organic matter are known as Saprotrophs. Their mode of Nutrition is Saprophytic. The
Saprophytes produce digestive enzymes that break down the food into soluble form which is then
absorbed. Ex:Bacteria , Fungi , yeast , mushrooms and moulds etc.

b. Parasitic Nutrition : The word Parasitic is derived from Two Greek words - 'para' meaning
'other' and 'site' meaning 'grains'. Parasite is an organism which lives outside or Inside of the body
of an living organism called host and it derives nourishment from the host . Ex: Protozoans such as
plasmodium , round worm , filarial worms. etc, Fungi like Puccinia and parasites on weak plants.

c. Holozoic Nutrition: The word Holozoic is derived from two Greek words - 'holos' meaning
whole and 'zoic' meaning animal. Holozoic mode of Nutrition can be defined as the feeding of
complex organic matter by ingestion, which is digested and then absorbed. Ex: Amoeba ,
Paramecium , frogs and Human Beings , etc.

On the Basis of Food Habits, Holozoic Organisms are further divided into three types
a. Herbivores
b. Carnivores
c. Omnivores

3. Lithotrophs: A lithotroph is an organism that uses an inorganic substrate (usually of

mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation)
or energy conservation via aerobic or anaerobic respiration. Known chemolithotrophs are
exclusively microbes; Macrofauna and lithotrophs can form symbiotic relationships, in which case
the lithotrophs are called ―prokaryotic symbionts‖. Ex. iron-oxidising bacteria, nitrifying
bacteria.etc

Based on Excretion

1. Ammonotelic: Most aquatic animals (pisces) are ammonotelic, that is they excrete waste
nitrogen as molecular ammonia or ammonium ions. This is the least energetically costly method of
nitrogen boundary excretion and is circumneutral waters of low ammonia is thought to occur largely
by passive diffusion of ammonia to water aided by diffusional trapping of ammonia to ammonium
ions through acidification of the surface boundary layer. Ammonia is highly toxic , highly soluble
in water.
2. Ureotelic: Ureotelic organisms excrete the waste nitrogen in their body in the form of urea.
Urea is less toxic and moderately soluble in water than ammonia. Most terrestrial animals are
ureotelic. Ex. Chondrichthyes
3. Uricotelic: Uricotelic animals excrete the waste nitrogen from their bodies in the form of
 uric acid or it‘s salts. In comparison to ammonia and urea, uric acid is least soluble in water and
least toxic. Ex. Birds

Based on Habitat

Aquatic Organisms: Animals that entirely live in water are known as aquatic animals. Fish,

jellyfish, octopus, etc are some of the aquatic animals. Some animals like frog, tortoise, crocodile,

etc can survive in land as well as water. They are known as amphibious animals.

Terrestrial Organisms: Animals that live on land are called as terrestrial animals. Dog, fox, lion,

elephant, etc are terrestrial animals.

Based on Molecular Taxonomy

Molecular taxonomy is the classification of organisms on the based on the distribution and
composition of chemical substances in them. Molecular techniques in the field of biology have
helped to establish genetic relationship between the members of different taxonomic categories.

The Three Domain System, proposed by Woese.

Based on differences in the sequences of nucleotides in the cell's ribosomal RNAs (rRNA),
as well as the cell's membrane lipid structure and its sensitivity to antibiotics. Comparing rRNA
structure is especially useful. Because rRNA molecules throughout nature carry out the same
function, their structure changes very little over time. Therefore similarities and dissimilarities in
rRNA nucleotide sequences are a good indication of how related or unrelated different cells and
organisms are. Because all cells are similar in nature, it is generally thought that all cells came from
a common ancestor cell termed the last universal common ancestor (LUCA). These LUCAs
eventually evolved into three different cell types, each representing a domain.

The three domains are the Archaea, the Bacteria, and the Eukarya.

1. The Archaea (archaebacteria)

Archaea are prokaryotic cells. Unlike the Bacteria and the Eukarya, the Archaea have
membranes composed of branched hydrocarbon chains (many also containing rings within the
hydrocarbon chains) attached to glycerol by ether linkages. The cell walls of Archaea contain no
peptidoglycan. Archaea are not sensitive to some antibiotics that affect the Bacteria, but are
sensitive to some antibiotics that affect the Eukarya. Archaea contain rRNA that is unique to the
Archaea as indicated by the presence molecular regions distinctly different from the rRNA of
Bacteria and Eukarya. Archaea often live in
 extreme environments and include methanogens, extreme halophiles, and hyper- thermophiles.

One reason for this is that the ether-containing linkages in the Archaea membranes is
more stable than the ester-containing linkages in the Bacteria and Eukarya and are better able
to withstand higher temperatures and stronger acid concentrations.

2. The Bacteria (eubacteria)

Bacteria (also known as eubacteria or "true bacteria") are prokaryotic cells that are common in
human daily life, encounter many more times than the archaebacteria. Eubacteria can be found
almost everywhere and kill thousands upon thousands of people each year, but also serve as
antibiotics producers and food digesters in our stomachs. Bacteria are prokaryotic cells.
Like the Eukarya, they have membranes composed of unbranched fatty acid chains attached to
glycerol by ester linkages. The cell walls of Bacteria, unlike the Archaea and the Eukarya,
contain peptidoglycan. Bacteria are sensitive to traditional antibacterial antibiotics but are resistant
to most antibiotics that affect Eukarya. Bacteria contain rRNA that is unique to the Bacteria as
indicated by the presence molecular regions distinctly different from the rRNA of Archaea and
Eukarya. Bacteria include mycoplasmas, cyanobacteria, Gram- positive bacteria, and Gram-
negative bacteria.

3. The Eukarya (also spelled Eucarya)

Eukarya have eukaryotic cells.Like the Bacteria, they have membranes composed of unbranched
fatty acid chains attached to glycerol by ester linkages.Not all Eukarya possess cells with a
cell wall, but for those Eukarya having a cell wall, that wall contains no peptidoglycan.
Eukarya are resistant to traditional antibacterial antibiotics but are sensitive to most antibiotics that
affect eukaryotic cells. Eukarya contain rRNA that is unique to the Eukarya as indicated by the
presence molecular regions distinctly different from the rRNA of Archaea and Bacteria.
 Biomolecules
One of the most mind-boggling facts is that all living things are essentially made up of non-living
atoms and molecules. In chemistry, we strive to learn more about these molecules that are named
biomolecule. Our bodies are made up of various of these complex biomolecules such as proteins,
carbohydrates etc.

Carbohydrates:
Carbohydrates are the principal energy producing substances present in the body next to
lipids. Carbohydrates were initially considered as compounds, which contain carbon, hydrogen and
oxygen where hydrogen and oxygen are present in the ratio of 2:1 as in the case of a water
molecule. They are subjected to catabolism in the body through Glycolysis and krebs cycle to
liberate energy

This statement holds good for compounds like Glucose & Fructose which are carbohydrates and are
found to possess the ratio of 2:1, In certain compounds which are carbohydrates like deoxy ribose
C5H1004 the ratio of hydrogen to oxygen is not 2:1, and in certain organic compounds like acetic and
lactic acid the ratio is 2:1 but we cannot call them as carbohydrates. Thus this definition is a highly
ambiguous definition and cannot be taken into consideration.

Definition:

Emil Fischer proposed the exact definition of a carbohydrate and according to him Carbohydrates
are Poly hydroxyl aldehydes or poly hydroxy ketones or the compounds, which produce them on
hydrolysis. They fill numerous roles in living things, such as the storage and transport of energy
(starch , glycogen ) and structural components (cellulose in plants, chitin in animals).
General Classification:
1. Based on their nature, carbohydrates are of two types namely Sugars and Non Sugars
Sugars Non Sugars
Sweet in taste Tasteless
Soluble in water Insoluble in water
Crystalline in appearence Amorphous in nature
Example: Glucose, Sucrose Example: Starch
2. Based on their Reactivity, carbohydrates are of two types namely reducing ( containing free
functional group) carbohydrates and Non reducing ( no free functional group) carbohydrates.

Reducing Sugars Reducing Non Sugars

Free Functional Groups Functional groups not free
Can participate in chemical Will not participate in chemical
reactions reaction
Eg: Glucose Eg: Sucrose

3. Based on their Composition or more specifically based on the number of individual sugar units
present carbohydrates are of four types namely:

Sugars Non Sugars

Monosaccharides Single Sugar Unit
Disaccharides Two Monosaccharide units
Oligosaccharides Three to Six Monosaccharide units
Polysaccharides More than six Monosaccharide units

Monosaccharide:
They are simplest of all carbohydrates and are often called simple sugars. They have a molecular
formula of (CnH2O)n. These are sugars that cannot be further hydrolyzed. These are divided into two
categories based on the functional group present and based on the number of carbon atoms.

Structures and Biochemical Importance of Monosaccharides:

Trioses: The smallest possible monosaccharides, those with three carbon atoms, are called trioses
e.g. glyceraldehyde is an aldotriose and dihydroxy acetone is a kettriose.

Significance: The phosphate forms of these two sugars are intermediates in Glycolysis pathway
concerned with conversion of glucose to pyruvate.

Tetroses: Those with four are called tetroses such as erythrose (Aldotetrose) and erythrulose
(Ketotetrose)
 The Erythrose in its form of phosphate is intermediate in HMP shunt pathway, associated with
Interconversion of sugars

Pentoses: Those with five carbon atoms are called pentoses viz. Aldopentoses such as xylose and
ribose and ketopentoses such as xylulose and ribulose etc.

1. Ribose is an essential constituent of RNA and Vitamin riboflavin

2. Xylose is an essential constituent of Gums and Glycoproteins
3. Ribulose and Xylulose are intermediate in HMP shunt pathway

Hexoses: Those with six carbon atoms are called hexoses viz glucose is an aldohexose (a six-
carbon aldehyde and fructose is ketohexose. These two systems of classification are often
combined.

Glucose is the most readily metabolizable sugar present in the human body. It is the important sugar
of life also called sugar fuel of life Fructose is the sweetest sugar in the nature, a constituent of
honey and is converted to glucose during metabolic reactions Mannose is an important constituent
of gums and glycoproteins, Galactose is considered as the backbone of lipids.

Disaccharides:

Carbohydrates that are made up of two similar or dissimilar monosaccharides are called
disaccharides. In other words Carbohydrates that on hydrolysis produces two similar or dissimilar
monosaccharides are called disaccharides. Based on their composition the disaccharides are of two
types namely homo disaccharides such as Maltose made up of Glucose and Glucose and hetero
disaccharides such as lactose made up of glucose and galactose and sucrose made up of glucose and
fructose.

Polysaccharides

Carbohydrates that are made up of more than ten monosaccharide‘s are called polysaccharides. In
other words Carbohydrates that on final hydrolysis produces a single monosaccharide are called
polysaccharides.

Classification

Based on their composition if a polysaccharide is made up of a single sugar or a single sugar

throughout its structure such polysaccharides are called Homo polysaccharides.
If a polysaccharide is made up of a sugar and sugar derivatives throughout its structure such
polysaccharides are called Hetero polysaccharides or Muco polysaccharides or heteroglycans or
glycosyl amino glycans. E.g. Heparin, Chondroitin sulphate.

Homopolysaccharides Starch:

Starch is wide spread in nature and is the reserve carbohydrate in plants. It is also an important
constituent of most of the tuberous plants like potato, sweet potato etc. To a limited extent, starch is
also found in grains & seeds.

When a raw sample of starch or many of these sources are observed under a microscope, the
granules may appear as concentric layers of material. Starch is basically made up of two units
namely the amylose & amylopectins.

The amylose units are considered as soluble fraction of starch. The basic color reactions of starch
i.e., blue colour solution with Iodine is due to these amylose units
present in starch. The unbranched amylose units in starch are joined through α 1, 4 glycosidic
linkages.

Amylopectin units are present to the extent of 80% of the entire starch molecule. These are the
branched and insoluble units of starch. The amylopectin units in starch are joined together by α 1,6
linkage. When treated with Iodine they give pale purple colored solution.

Structure of starch : amylose with unbranched units and Amylopectin with Branched units.

Cellulose:

It is the chief constituent of fibrous part of the plant and is the major component of plant cell wall. It
is considered as most abundant carbohydrate present in nature. It is made up of repeated units of
glucose that are joined by β-1,4 linkages.

Cellulose cannot be utilized or digested by human beings, because of the absence of enzyme
cellulase in the gastrointestinal tract. It is nitrated to form nitro-cellulose that is used in the
manufacture of explosive substances. It can be acylated to form cellulose acetate, which is used in
manufacture of photographic plates.
 Fig: Structure of Cellulose; unbranched glucose in β-1,4 linkage.

AMINO ACIDS and PROTEINS

Proteins are regarded as biomolecules concerend with maintaining the integrity of life. The
word protein is derived from Greek word proteos meaning substances holding primitive place.
Amino acids are regarded as the building blocks of proteins. The constitution of a protein shows the
presence of 20 standard amino acids that are mixed in various permutations and combinations
structurally they are defined as those compounds that contain at least one amino and one carboxylic
group in their structure. Even though in the nature a large number of amino acids are present only
20 of them are involved in the formation of a protein, these 20 amino acids are called as standard
amino acids and often referred as Magic-20. Amino acids play central roles both as building blocks
of proteins and as intermediates in metabolism. The 20 amino acids that are found within proteins
convey a vast array of chemical versatility. The precise amino acid content, and the sequence of
those amino acids, of a specific protein, is determined by the sequence of the bases in the gene that
encodes that protein.
Structures of Amino Acids:
The general structure of a standard amino acid could be given as

In the above structure the R‘ group is called the variable group or substituent group and to draw the
structures of the standard amino acids only the R group is replaced by some other group and the
remaining skeleton structure is same for all amino acids except Proline which does not satisfy the
general structure of the amino acid.
 Lipids
Introduction

When the individual is on a low carbohydrate diet, or unable to utilize or metabolize the
dietary carbohydrates, then lipids serve as alternate energy producing substances in the organism.
When a lipid is subjected to catabolism as much as 129 ATP‘s of energy is liberated, but, because
lipids are completely insoluble in water and their digestion begins only in the small intestine, they
are considered as energy suppliers but only next to carbohydrates.

Definition

A lipid is defined as a water-insoluble biomolecule which has a high solubility in nonpolar organic
solvents such as chloroform. The simplest lipids are the fats, which are tri esters made up of one
glycerol and three fatty acids. The term fats is also used as a general Synonym for lipids, so the
more precise terms tri acyl glycerol‘s or triglycerides are preferable for the simplest lipids.

Triacylglycerols are used primarily for energy storage in animals. More complex lipids, the
phospholipids, glycolipids, and cholesterol, are the major constituents of biological cell membranes.

Classification of lipids.

Lipids are a heterogeneous group of compounds that are directly or potentially related to fatty acids.
They are the alternate suppliers of energy in the body next to carbohydrates.Bloor classified the
lipids into three major categories and after his name the classification is called as Bloor’s
classification. The major three classes are

1. Simple lipids
2. Compound lipids
3. Derived lipids
1. Simple lipids:

Lipids that are made up of fatty acids and glycerol or any high molecular weight monohydric
alcohol are called simple lipids. Based on the nature of the alcohol present they are classified as
Fats or oils and waxes.

Fats or oils: Simple lipids that are made up of fatty acids and glycerol are called Triglycerides or
fats or oils or tri acyl glycerols. A triglyceride is the most potential form of lipid that constitutes
98% of our dietery lipid.

These are further defined as Esters of fatty acid and glycerol. When one molecule of glycerol
combines with three molecules of a fatty acid the resulting structure is called a triglyceride. If all
 the fatty acids present in the triglyceride are similar then it is called as a simple triglyceride, and if
all fatty acids are different or at least two of the three fatty acids are different then such triglycerides
are called mixed triglycerides.

Waxes: When the fatty acid is in combination with any other alcohol other than glycerol then those
compound lipids are called waxes..

2. Compound Lipids:

Lipids that are usually made up of a fatty acid, an alcohol and a non-lipid group are called
compound lipids. Based on the non-lipid group or prosthetic group present these lipids are
classified as ;

1. Phospholipids
2. Glycolipids
3. Lipoproteins
4. Sulpholipids

Phospholipids:

These are compound lipids that contain a phosphoric acid group in their structure. Based on the
nature of alcohol present in the phospholipid they are classified as

Phosphoglycerides containing glycerol, phosphosphingosides containing an unsaturated amino

alcohol called sphingosine and phosphoinositides containing a hexa hydric alcohol called inositol.

Glycolipids

Glycolipids: In these lipids the non-lipid group is a carbohydrate These are compound lipids that do
not contain glycerol but instead contain sphingosine. The basic composition of a glycolipid is sugar,
fatty acid and sphingosine.

Based on the variation in the nature of the fatty acid the glycolipids are further classified as
cerebrosides, and, based on the number of individual sugar units present the glycolipids are called
as gangliosides.

Sulpholipids

Sulpholipids: In these lipids the non lipid group is a sulphur containing group. They are found in a
few bacterial species
 Lipoproteins

Lipoproteins: In these lipids the non-lipid group is a protein. Based on the relative concentration of
lipid and protein present the lipoproteins are classified as very low density, low density and high-
density lipoproteins.

3. Derived Lipids:

Lipids that are obtained on the hydrolysis of a simple or a compound lipid are called derived lipids.
The major derived lipids are monoglycerides, diglycerides, glycerol and fatty acids. However
certain compounds that are obtained from fatty acids (that themselves are derived lipids) such as
cholesterol and prostaglandins are also derived lipids.

Derived Lipids Fatty acids

Fatty acids are long chain or short chain organic acids that contain a primary carboxylic acid group
and a terminal methyl group. These are further divide into may categories selecting a specific
criterion.

Based on the number of carbon atoms the fatty acids could be short chain, medium chain and long
chain fatty acids. Based on the presence or absence of double bonds the fatty acids could be
Saturated, monounsaturated and poly unsaturated fatty acids.

The saturated fatty acids are called ionic fatty acids and the unsaturated fatty acids are called enoic
fatty acids. The unsaturated fatty acids or saturated fatty acids are numbered from left to right with
COOH group given number one and the CH3 group the last number.

On the other hand in the Greek system the COOH group has no designation and the carbon adjacent
to the COOH group is designated as α next β the next γ and so on and terminal group the omega
carbon atom.

In unsaturated fatty acids the position of the double bond is designated by a triangle symbol writing
the number as superscript. In unsaturated fatty acids the number of carbon atoms, the number of
double bonds and the position of double bond are indicated by three digits. For example in the
number 18:1:9 the number of carbon atoms is 18, the number of bonds is 1 and the position is
between 9 and 10.

The unsaturated fatty acids are of two types namely monoenoic and polyenoic fatty acids for
monounsaturated fatty acids the general formula is CnH2n-1 COOH.
Poly-unsaturated fatty acids

These are also referred as essential fatty acids as they cannot be synthesized in the body and need
to be supplied only through the diet. These are poly-enoic acids containing more than one double
bonds in their structure. Some of the important polyunsaturated fatty acids have been tabulated
below. These are considered as very good for the heart when taken through the diet, and are
associated with formation of edible fats, especially vanaspathi.

Simple Lipids

Simple lipids: lipids that are made up of fatty acids and glycerol or any high molecular weight
monohydric alcohol are called simple lipids. Based on the nature of the alcohol present they are
classified as Fats or oils and waxes.

Fats or oils: Simple lipids that are made up of fatty acids and glycerol are called Triglycerides or
fats or oils or tri acyl glycerols. A triglyceride is the most potential form of lipid that constitutes
98% of our dietery lipid. These are further defined as Esters of fatty acid and glycerol. When one
molecule of glycerol combines with three molecules of a fatty acid the resulting structure is called a
triglyceride. If all the fatty acids present in the triglyceride are similar then it is called as a simple
triglyceride, and if all fatty acids are different or at least two of the three fatty acids are different
then such triglycerides are called mixed triglycerides.
 NUCLEIC ACIDS

Introduction:

The term "nucleic acid" is the generic name for a family of biopolymers named for their role in the
cell nucleus. They are responsible for carrying genetic information and are also responsible for
forming structures within cells. They are biopolymers that are composed of a chain of number of
monomeric nucloetides .These were first discovered by Friedrich Miescher .Nucleic acids are found
in all living organisms and viruses and hence are of universal importance.

Types of Nucleic acids:

Based on their biological functions and their ability to carry out various biological functions,
Nucleic acids are mainly of two types;

1. DNA Deoxy ribonucleic acid 2.RNA Ribonucleic acid

Chemical Composition:

The various components seen in the structure of nucleic acids are sugars Nitrogen bases and
Phosphate, the combination of Nitrogen base and sugar is called nucleoside and the combination of
sugar, nitrogen base and phosphate is called a nucloetide. Many such nucloetides unite together
forming a biopolymer called nucleic acid.

Nucleoside: Sugar and Bnitrogen Base

Nucleotide: Sugar, Nitrogen base and Phosphate

Sugars:

The sugar that is present in RNA is ribose which is an aldopentose and that in DNA is deoxy ribose.
Deoxy ribose differs from ribose in the fact that oxygen is absent at second carbon in the
structure of deoxy ribose as compared to ribose.
 Nitrogen Bases:

The nitrogen bases usually present in nucleic acids are

1. Purines : Purine is a nine membered ring and pyrimidine is a six membered ring. The two purines
found in both the nucleic acids DNA and RNA are Adenine (6 amino Purine) and Guanine (2 amino
6 oxy Purine)

2. Pyrimidines.. The three pyrimidines usually found in nucleic acids are Cytosine (2 oxy 6 amino
Pyrimidine), Thymine 2, 4 di oxy 5 methyl Pyrimidine) and Uracil ( 2, 4 di oxy Pyrimidine).
Cytosine and Thymine are present in DNA, whereas Cytosine and Uracil are present in RNA.
3. Thymine is absent in RNA and Uracil is absent in DNA. Structures of Purines:
 Structure of DNA:

1. Watson, Crick, and Wilkins proposed in the early 1950s a model of a double- stranded DNA
molecule.
2. The two strands of this double-stranded helix are held by hydrogen bonds between the purine and
pyrimidine bases of the respective linear molecules.
3. The pairing between purine and pyrimidine nucleotides on the opposite strands are very specific
and are dependent upon hydrogen bonding of A with T and G with C.
4. This common form of DNA is said to be right handed. A to pair only with T by two hydrogen bonds
and G only with C by three hydrogen bonds .
5. Thus, the G–C bonds are much more resistant to denaturation, or ―melting,‖ than
A–T rich regions.
6. In a double-stranded DNA molecule the content of A equals that of T and the content of G equals
that of C.
7. The two strands of the double-helical molecule, each of which possesses a polarity, are antiparallel;
i.e, one strand runs in the 5′ to 3′ direction and the other in the 3′ to 5′ direction.
8. This is analogous to two parallel streets, each running one way but carrying traffic in opposite
directions.
9. A single turn of Double-stranded DNA about the axis of the molecule contains ten base pairs.
10. The distance spanned by one turn of B-DNA is 3.4 nm. The width (helical diameter) of the double
helix in B-DNA is 2 nm.
11. In the double stranded DNA molecules, the genetic information resides in the sequence of
nucleotides on one strand, the template strand.
 Fig: Watson and Crick Structure of DNA

RNA: Ribonucleic Acid

1. Ribonucleic acid (RNA) is a polymer of purine and pyrimidine ribonucleotides linked together by
3′,5′- phosphodiester bridges analogous to those in DNA.
2. In RNA, the sugar moiety to which the phosphates and purine and pyrimidine bases are attached is
ribose. RNA contains the ribonucleotides of adenine, guanine, and cytosine, it does not possess
thymine except in the rare case.
3. Instead of thymine, RNA contains the ribonucleotide of uracil. RNA exists as a single strand. The
single strand of RNA is capable of folding back on itself like a hairpin and thus acquiring double
stranded characteristics.
4. Since the RNA molecule is a single strand complementary to only one of the two strands of a gene,
its guanine content does not necessarily equal its cytosine content, nor does its adenine content
necessarily equal its uracil content. (A+T not equal to (G+C)

Types of RNA:
Based on their role in protein synthesis, RNA‘s are of three types
a. Messenger RNA (mRNA):
b. Transfer RNA (tRNA)
c. Ribosomal RNA ( r RNA)
 This class is the most heterogeneous in size and stability. All members of the class function as
messengers conveying the information in a gene to the protein synthesizing machinery,.

 Eukaryotes mRNAs have some unique chemical characteristics. The 5′ terminal of mRNA is
―capped by a 7-methylguanosine triphosphate that is linked to an adjacent 2′-O-methyl
ribonucleoside at its 5′-hydroxyl through the three phosphates. The cap is involved in the
recognition of mRNA by the translating machinery, and it probably helps stabilize the mRNA by
preventing the attack of 5′-exonucleases.

 The protein-synthesizing machinery begins translating the mRNA into proteins beginning
downstream of the 5′ or capped terminal. The other end of most mRNA molecules, the 3′-hydroxyl
terminal, has an attached polymer of adenylate residues 20–250 nucleotides in length. It helps
specific mRNA by preventing the attack of 3′-exonucleases.

Structure of mRNA

Transfer RNA (tRNA):

 tRNA molecules vary in length from 74 to 95 nucleotides.

 The tRNA molecules serve as adapters for the translation of the information in the sequence of
nucleotides of the mRNA into specific amino acids.

 There are at least 20 species of tRNA molecules in every cell, at least one (and often several)
corresponding to each of the 20 amino acids required for protein synthesis.
 Although each specific tRNA differs from the others in its sequence of nucleotides, the tRNA
molecules as a class have many features in common.
 Secondary structure of tRNA appears like a Cloverleaf. In clover leaf model tRNA molecules
contain four main arms. The acceptor arm . The D arm , TΨC arm , and extra arms help define a
specific tRNA.
Ribosomal RNAs (rRNA):

A ribosome is a cytoplasmic nucleoprotein structure that acts as the machinery for the synthesis of
proteins from the mRNA templates. On the ribosomes, the mRNA and tRNA molecules interact to
translate into specific protein molecule information transcribed from the gene.
The mammalian ribosome contains two major nucleoprotein subunits—a larger one with a
molecular weight of 2.8 × 106 (60S) and a smaller subunit with a molecular weight of 1.4 × 10 6
(40S).
The 60S subunit contains a 5S ribosomal RNA (rRNA), a 5.8S rRNA, and a 28S rRNA; there are
also probably more than 50 specific polypeptides.
The 40S subunit is smaller and contains a single 18S rRNA and approximately 30 distinct
polypeptide chains.
 Enzymes
Introduction

Enzymes are biocatalysts that accelerate the chemical reactions. They are generally the globular
proteins; A small number of RNA-based biological catalysts,(ribosome) are referred to as RNA-
enzymes, or ribozymes. Almost all processes in a biological cell need enzymes. Enzymes are known
to catalyze about 4,000 biochemical reactions. They have high biotechnological applications.
Several enzymes are used commercially,

– in the synthesis of antibiotics and other drugs,

– in biological washing powders,

– in bakeries meat tenderizers

– in gene cloning technology.

The two striking properties of enzymes are catalytic power and extraordinary specificity. Enzymes
act by attaching to the reaction molecules, which are called the substrates. Enzymes are highly
specific, meaning that each catalyzes only a single reaction or a very limited class of reactions. The
specific three-dimensional shape of an enzyme is such that only the substrates it acts upon can ―fit‖
into its binding site where a group of amino acids (active site) of the enzyme can catalyze the
reaction. After catalyzing the reaction, the enzyme releases the products of the reaction.

The basic enzyme reaction: E+S = ES= E+P

 The enzyme remains intact in the process and can immediately bind fresh substrate. Thus, an
enzyme molecule can be used over and over again. Enzymes regulate nearly all metabolic activities
and are responsible for the building of complex molecules (anabolism) as well as the breakdown of
large molecules into smaller ones (catabolism).

Brief history of Enzymes

By late 1700s and early 1800s, the digestion of meat, conversion of starch to sugars by plant
extracts and saliva was realized to be a catalytic process.

The "spoilage" (fermentation) of fruit juices, for example, resulted in the formation of primitive
forms of wine.

Louis Pasteur (1822 –1895) was first to recognize that alcoholic fermentation is an act correlated
with the life and organization of the yeast cells.

In 1878, the German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme, which
comes from Greek ‘En’ standing for in and ‘Zyme’ standing for yeast, to describe the process of
fermentation..

The word enzyme was used later to refer to nonliving substances like pepsin, and the word ferment
was used to refer to chemical activity of living organisms. 1897 Eduard Buchner used the term
Zymase – ―cell-free fermentation". (1907 Nobel Prize in Chemistry).

2.1 Classification and Nomenclature

The chemical reaction catalyzed is the specific property which distinguishes one enzyme from the
other. In 1961 IUB (International Union of Biochemists) used this as the basis for the classification
and naming of enzymes.The salient features of IUB system of classification are, the enzymes and
the reactions they catalyze are divided into to 6 major groups which in turn are further divided
into4-8 sub groups. The enzymes according to their serial number in the IUB system are:
 Enzyme major classes

1. Oxido – reductases 2. Transferases

3. Hydrolases 4. Lyases

5. Isomerases 6. Ligases

Enzyme classification number ( E.C. No):

The first Enzyme Commission, in its report in 1961, devised a system for classification of enzymes
that also serves as a basis for assigning code numbers to them. These code numbers, prefixed by
EC, which are now widely in use, contain four elements separated by points, with the following
meaning:

1.The first number shows to which of the six main divisions (classes) the enzyme belongs,
2. The second figure indicates the subclass,
3.The third figure gives the sub-subclass,
4.The fourth figure is the serial number of the enzyme in its sub-subclass.

The 6 major classes of enzymes with some important examples are:

1. Oxido Reductases:

This class comprises the enzymes which were earlier called dehydrogenases, oxidases, peroxidases,
hydroxylases, Oxygenases etc. These group infact includes those enzymes which bring about
oxidation reaction between two substrates.

A (oxd) + B (Red) ---------- B (oxd) + A (Red)

2. Transferases:

Enzymes which catalyses the transfer of a group G (other than hydrogen) between a pair of
substrates S & S1 are called transferases.

A- B + G ----------- B-G + A
3. Hydrolases: These enzymes catalyses the hydrolysis of their substances by adding constituents
of water across the bond they split. The substrate include ester, glycosyl, ether, peptide, acid
anhydrides, C-C halide and P- N bonds

AB + H2O --- > A H + B OH

4. Lyases: (Desmolases); These are enzymes which catalyze the removal of groups from
substrates by mechanisms other than hydrolysis.

AX + BY ------> A = B + XY
 5. Isomerases: These enzymes catalyses inter conversions of optical, geometric (or) positional
isomers by intramolecular rearrangement of atoms (or) groups.

6. Ligases :(Ligase = to bind These are the enzymes catalyzing the linking together of two
compounds utilizing the energy made available due to simultaneous breaking of a pyrophosphate
bond in ATP (or) a similar compound. This category includes enzyme catalyzing reactions forming
C = O, C-S & C = C bonds.

A + B ------- > AB
To date over 2000 different enzymes are known of which the oxide reductase and transferases
predominate.

Mechanism of enzyme Action Lock and Key mechanism

The interaction of substrate and enzyme was visualized in terms of a lock and key. This model was
proposed by Emil Fischer in 1889. According to this model the union between the enzyme and the
substrate takes place only at the active site more or less in a manner in which the key fit into a lock
of its own kind and results in the formation of an enzyme substrate complex.

The enzyme-substrate union depends on the concept of reciprocal fit between the molecular
structure of enzyme and substrate. As the two molecules, that is the enzyme and substrate bearing
more or less the similar conformations fit into each other without bringing any change in the active
site. Such a concept is called concept of inter molecular fit. This enzyme substrate complex
immediately decomposes to form free enzyme and products.
Induced Fit Mechanism

Not all experimental evidence can be adequately explained by using the so-called rigid enzyme
model assumed by the lock and key theory. For this reason, a modification called the induced-fit
theory has been proposed.The induced-fit theory, proposed by Koshland group assumes that the
substrate plays a role in inducing the structural change in the enzyme to accommodate the incoming
substrate to facilitate the reaction. The enzyme is partially flexible. This explains why certain
compounds can bind to the enzyme but do not react because the enzyme has been distorted too
much. Other molecules may be too small to induce the proper alignment and therefore cannot react.
Only the proper substrate is capable of inducing the proper alignment of the active site.