Soil Factor – Parent Material

Soil Factor – Parent Material

The unconsolidated mass from the soils are formed is the parent material. It constitutes the basic mineral framework of most soils and consists of small fragments of inorganic matter which has been derived from solid rock by mechanical or chemical types of weathering,

Depending on the mode of origin, most parent materials can be classified as: residual parent material and transported parent material.

Residual Parent Material – Rocks

Rocks are residual or in-place parent material. The composition of rocks determines the chemical composition of the soil. The rocks may be:

Igneous Rocks, formed when a hot mixture of elements called magma cools. These may be present above or below the surface of the earth.

Sedimentary Rocks, formed by the material deposited in lakes and oceans. Over time and under the pressure of overlying materials, layers of these accumulated sediments consolidate into rocks. Over geological time, these rocks have been exposed by uplift and wearing away of mountains. The examples are shale and limestone

Metamorphic Rocks, formed when either igneous rocks or sedimentary rocks are heated or subjected to intense pressure at considerable depths within earth. The Original minerals melt and form new minerals. The common examples are slate and marble.

Transported Parent Material

The transported parent materials are derived from mineral particles which have been brought from their place of origin by various agents such as wind, water, glaciers, and gravity. The soils developed from transported material are commonly more fertile than soils derived from in-place parent material because of the diversity of materials.

On the basis of transportation agencies, the transported material Can be subdivided into: colluvial (by gravity), alluvial (by water), glacial (by ice), and eolian (by wind).

Colluvial Transportation by Gravity (Colluvial Soil)

colluvial parent materials are moved by the pull of gravity and are composed of fragments of rocks detached from the heights above and carried down the slopes. The material deposited is known as talus. Colluvial parent materials are restricted to mountainous regions and most hillside deposits (slopes or cliffs) are colluvial.

Colluvial parent material consists of coarse and stony fragments the soils developed from colluvial materials are not of great agricultural Importance because of unfavorable physical and chemical characteristics. The colluvial deposits are without stratification.

Alluvial Transportation by Water (Alluvial Soil)

The parent materiel deposited by running water is termed as alluvial. There are general classes of alluvial deposits: floodplains, delta deposits and alluvial fans.

Floodplain IS the part of the valley inundated during floods. The floodplains provide significant parent materials for other important soil areas. The soils derived from these sediments are generally rich in nutrients and productive.

Delta Deposits are the deposits near the mouth of the river. Where streams enter a river or the sea the suspended material (silt and clay) settle out near the mouth of river forming a delta. A delta is continuation of a floodplain, clayey in nature and soils originating from such parent material are fertile and productive from agricultural point of view.

Alluvial Fans are formed when streams leave a narrow valley in a mountainous area and suddenly descend to a much broader valley below deposit sediment in the shape of a fan. Fan material contains gravel and stone, somewhat porous and well drained, Alluvial fan deposits are found in mountainous and hilly areas.

Eolian Transportation by Wind (Eolian Soil)

The Wind transported parent material is termed eolian. It is classed either as dune or loess (luss). Winter conditions are suitable for transport of material by wind.

Sand Dunes: Sand dunes are found along the shores of seas and lakes, along river valleys and in dry regions. Water currents erode and deposit the sand particles snores, banks or upon floodplains which is moved by wind onto the land upon. In dry regions weathering of sandstone and other rocks may produce sand blown and deposited as dunes. Sahara Desert is famous for its sand dunes. Dune sand is composed of particles of nearly uniform size and chemical composition.

Loess (Pronounced Luss): The windblown materials, comprised primarily of silt with some fine sand and clay are called loess. The material is derived from rock deposited by the melt waters of glaciers then blown onto plans.

Glacial Transportation by Glaciers (Glacial soil)

The materials deposited directly by the ice are called glacial till, and materials of glacial origin whether deposited by the ice or associated waters is called drift. The glacial till comprises of particles of all sizes from clay to boulders that are thoroughly mixed without any kind of sorting. Glacial till is found mostly as irregular deposits caned moraines. An outwash stream is formed by streams that are heavily laden with glacial sediment flowing from the ice. The outwash plain consists of sand and gravel usually and found in valleys and plains where glacial waters are able to flow away freely. When the ice front came to a standstill where there was no escape for the water, ponding began and ultimately very large lakes were forms. Such lakes are called glacial lakes.

Types of Soils on the Basis of Parent Material

The terms designating the parent material are also applied to the soils that occur on these deposits, for example residual soils, colluvial soils, glacial soils, alluvial soils and eolian soils.


Soil Factor

The word soil is derived from Latin solum meaning soil or land,

Soil is the upper and biochemically weathered portion of the regolith.


Soil is a collection of natural bodies of Earth that is composed of mineral organic matter and is capable of supporting plant growth.


Soil is the weathered outer layer of Earth’s crust, which ranges front a thin film to thick layers composed of weathered rock materials and organic matter interspersed with pores filled with air and water, and which support plant life.

The soil is the product of both destructive and synthetic forces. The former includes weathering and decomposition of organic matter by the microbes and the later Involves formation of new minerals, organic compounds and development of characteristics layer patterns called horizons.

Regolith and Parent Material

The unconsolidated geological material present below the soil and above the rocks is called regolith. It may be in form of a thin layer or several meters in thickness, and maybe weathered from the underlying rock or transported elsewhere by the action of wind, water or ice.

The upper part of the regolith is called parent materials It is the basic inorganic framework of the soil into which organic matter. living organisms, water and gases are incororporated. The upper 1 -2 meters of regolith is rich in organic matter because plant concentrate there and is subject to more weathering. The products of this weathering give rise to characteristics layering called horizons.

Pedology and Edaphology

Pedotogy the study of soil as a natural body. It includes the origin of soil, classification and its description. One who studies, examines and classifies soils as they occur their natural environment is known as a pedoloist.

Soil is natural habitat for plants, therefore the study of soil from standpoint of higher plants is Edaphology. one who considers the various properties of soils in relation to plant production is an edaphologist.


A three-dimensional soil body large enough that we can study all Its physical and properties and its horizons is called pedon. Thus, it ranges in area from one to 100 square meters.

Land and Earth

Land is the physical environment consisting of soil, water, climate and vegetation.

Earth is a general name used by engineers for unconsolidated land masses that can be dug, moved or formed by equipment. The scientific study of earth’s crust, rock strata and history of Its development is called geology.

Topsoil & Subsoil

The upper 12-18 cm surface layer of the soil is topsoil. It can be ploughed and cultivated. It is also called furrow slice. Topsoil is the major zone of root development for crop plants. It contains many nutrients available to plants and supply much of the water needed for their growth.

The soil layers underneath the topsoil are subsoil. It is not affected by tillage; however, it affects crop production. The roots of the plants penetrate the subsoil and it provides moisture and nutrients to the plants.

Major Phases of Soil

The soil consists of three major phases:

Solid Phase: The solid phase is major reservoir of plant nutrients. It is composed primary and secondary minerals, amorphous substances and fragments of parent rocks; and organic components including soil fauna (animals) and flora (plants), plant residues and humus.

Liquid Phase: The liquid phase of the soil consists of water held among spaces and minerals dissolved in it. It is also called water solution. The liquid phase is responsible for nutrient transport in the soil and is immediate source of most nutrients and water absorbed by the plant roots.

Gaseous Phase: Soil gases occupying the soil pores make gaseous phase of the soil. The gases phase provides oxygen to plant roots and soil micro-organisms for respiration. The carbon dioxide concentration in soil atmosphere is higher than in air due to root respiration and decomposition of soil organic matter

Soil Profile

Any vertical cut through a body of soil or pedon is the soil profile.


The individual layers are called horizons. The horizons develop largely through the action of rainwater which leaches materials from surface and deposits most or all of them at a slightly greater depth. Each horizon has a characteristic set of features. particularly color, that distinguishes it from other horizons. Each horizon has its own thickness, texture, structure, consistency, porosity, chemistry and composition. The horizons differ in their Characteristics from Soil to soil; therefore, the soils can be differentiated on the basis of characteristics of their horizons.

In general soil has five major horizons. These are designated using the capital O, A, E, B and C. 0 is an organic layer and A, E, B and C are the mineral layers. Below the four may the R (regolith) or non-soil horizon. Subordinate layers are found in horizons These are designated by lowercase letters, for example Oi, Oe and Oa. Horizons A constitute true soil or solum.

O Horizon (Organic): The O horizon is the surface layer composed of fresh or partially decomposed organic matter that has not been mixed into mineral soil. It usually found in forest regions and absent in grasslands and cultivated soils. The O horizon is further subdivided into:

Oi, the litter layer composed of plant and animal residues. This layer fluctuates with seasons. In temperate regions, it is thickest in fall, when new litter is added, and thinnest in the summer after the decomposition has taken place,

Oe, the humus layer in which organic matter is partially decayed,

Oa, the humus layer in which organic matter is highly decomposed.

A horizon: It is the upper layer of mineral soil with a high content of organic matter. it is darker in color and consists of humus derived from O horizon.

E Horizon (Eluviations): E horizon is the zone of maximum leaching or eluviations. Suspended and dissolved materials such as clay, iron, aluminum oxides, etc., move out of it through weathering and leaching. It is lighter in color, composed of resistant minerals as quartz and silt particles, and poor in organic matter.

B Horizon (Illuviation): It is the zone of illuviation. The leached materials from horizons above accumulate in this layer. It accumulates silicates, clay, iron, aluminum and humus from E horizon.

C Horizon: It consists of unconsolidated material either like or unlike the material from, which the soil has developed. This layer is without biological activity and weathering process

Soil Genesis or Soil Formation

Soil formation is the creation of soil from a non-soil parent material. The process involves breakdown of parent material into smaller particles (weathering), rearranging and changing their mineral structure, adding organic matter (humification), producing clays, and creating horizons.

Ecology – Level of Organizations

Ecology – Level of Organizations

Ecology can be considered on a wide scale, moving from an individual the entire global ecosystem. However, four identifiable sub-divisions of scale are of interest. These are: organisms (individuals), populations, communities and ecosystems. At each level the subject of interest to ecologist’s changes.

  1. Organism

Organism refers to any living individual, either unicellular or multicellular. An organism possesses certain characteristics and exhibits individuality, i.e., it is different from other members of the same species in certain respects. At organism level ecologist’s the response of individuals to their environment, -both biotic and abiotic.

The branch of ecology that is concerned with how organisms interact environments by adaptations in their morphology, physiology and behavior is called or species ecology. It involves study of distribution of organisms in relation to environment.

  1. Population

A population is a group of living organisms of same species that occur together one place and at one time. A population is reproductively isolated from other such groups.

It is higher level of organization than an organism. All populations have characteristic features, such as size, density, dispersion (the way the individuals of a population arranged), and demography (statistical study of population). This level has its own attributions such as gene frequency, gene flow, age distribution, population density, population pressure, etc. The branch of ecology concerned with population growth, regulation, intraspecific and interspecific competition is called population ecology. Population ecology concentrates mainly on factors that affect population size and composition.

  • Community

Populations of different species that live together in the same area (habitat) is a community.

Ecologists are interested in the processes determining their composition structure Interactions within a community include predator-prey Interactions and symbiosis (commensalism, mutualism, parasitism). The ecological study at Community level is known as community ecology.

  1. Ecosystem

A community in certain area, together with the non-living factors with which it interacts, is called an ecosystem.

An ecosystem regulates the flow of energy derived from the sun and the cycling of essential elements on which the lives of its constituent plants, animals and other organisms depend. Individual organisms live in a small part of ecosystem known as their habitat. How an organism lives as well as where it lives is its niche.

The study of ecosystem is termed ecosystem ecology.

  1. Biosphere and Biome


The part of the earth containing living organisms is called the biosphere. It is the sum of communities and ecosystems found on the planet Earth. It includes the both Living and non-living components. The biosphere extends from the bottom of the oceans to atmosphere, and amounts to a relatively narrow belt around the Earth.


A major life zone characterized by the dominant plant life, and climatic and soil conditions is called a biome. It is the largest ecological unit. The examples include rain forests, coniferous forests, grasslands, etc. Study of biomes from ecological view is called biome ecology.

Major Biomes of the World

A brief introduction to world’s major terrestrial and aquatic biomes is as follows:

  1. Grasslands

Grasslands occur where rainfall ranges between 250 and 1200 mm (10-60 inches) There are two major types of grassland depending on the temperature: tropical grassland (savannah) and temperate grassland (steppe, prairie and pampas). Grassland soils receive a large amount of organic matter and are very rich. Grassland communities are dominated by grass species but include trees also such as Acacia. In temperate grasslands, the broadleaved flowering perennials are found. The grasslands support large populations of grazing and browsing animals and large mammalian carnivores. Intensive grazing can lead to the destruction of grassland communities, soil erosion and desertification. Grasslands occupy vast areas in North America, northern Europe and Africa.

  1. Tundra

The arctic tundra forms a circumpolar band between Arctic Ocean and polar ice caps to the north and the coniferous forests to the south but ecologically similar regions found above the tree line on high mountains are called alpine tundra. The temperature is freezing, precipitation is low and occurs mainly as snow, and below a certain depth the ground remains permanently frozen forming permafrost. Tundra has low productivity but is rich in species contents, Animals of tundra include reindeers and other migrants, Tundra vegetation and soils are very slow to recover from disturbance.

  1. Forests

Forest type is dependent on rainfall and temperature. It can be divided into:

Boreal Forests: These forests develop in cold climate and high elevation, are characterized by long winters with high precipitation in the winter and more rain in summer. The soils are Podolsk. These are dominated by coniferous tree species. These forest support herbivorous mammals and predatory species.

Temperate Forests: Temperate forests occur at lower latitudes where there is sufficient rainfall. The soils in these forests are well developed and rich. They consist of broad-leaves, deciduous species and their vegetation exhibit layered structure. Birds and small mammals are common animals of these forests.

Tropical Forests: Tropical forests are present near the equator and characterized by heavy rainfall and warm climate. The soils are leached, acidified and poor in nutrients. These forests contain a great diversity of tall trees, canopy forming species, shade-tolerant plants, epiphytes and lianas. They support a great amount of animal diversity as well. The clearing of rains forests result in biodiversity loss, depletes the soil and may lead to erosion.

  1. Deserts, Semi-deserts and Shrub Lands: Hot deserts are found around latitudes 30 °N and 30 ‘S. The main, desert regions are in northern and south-western Africa (the Sahara and Namib deserts), parts of the Middle East and Asia (Gobi), Australia, the Great Basin and southwestern United States, and northern Mexico. In less arid regions semi-deserts occur while temperate shrub land is found around the shores of Mediterranean Sea, where it is known as marquis and southern California, where it is called chaparral.

Deserts have less than 50 mm of annual rainfall, hot days and cold nights. Soils are poor in nutrients, thin and freely drained. Hot desert vegetation includes thorny shrubs ephemeral annuals, and succulents. Cool deserts have dense shrub Vegetation. Chaparral contains species with small, thick, drought-resistant leaves and the community is maintained and regulated by fire. The most common desert animals are reptiles and insects, however some mammals including rodents and camels are also found.

  1. Saltwater Biomes

The primary saltwater biomes are:

Open Oceans: Open oceans cover of the world’s surface. Although these are most extensive biome but are poor in nutrients and unproductive. The surface photic zone where light can penetrate contains phytoplankton and Zooplankton. Below it carnivorous and detritivorous animals occur, feeding on material from the communities above. Light levels and productivity decreases with depth. Bottom or benthic fauna sparse

Continental Shelves: These occur around coasts to a depth of about 200 m and include coral reefs. The continental shelves support some of the most productive marine ecosystems such as kelp forests and fisheries. Coral reef communities occur in warm and very shallow water. Corals are colonial which structurally complex calcareous skeletons on which algae, invertebrates and herbivorous and carnivorous fishes live.

The intertidal Zone: The intertidal zone occurs at land margins and includes sandy beaches and rocky shores. Intertidal rocky shores are dominated by algae. Zonation of algal and animal communities with exposure and distance from the sea occurs. Sandy beaches provide an unstable, abrasive and nutrient-poor substrate colonized by filter-feeding burrowing animals which are themselves food for wading birds.

Salt Marsh, Mudflats and Mangroves: Salt marsh, mudflats and mangroves develop where there is less tidal influence. Salt marsh occurs in sheltered areas protected from wave action and is dominated by salt-tolerant higher plants. Mudflats and estuarine silts are fine substrates rich in organic matter and low in oxygen. Their higher invertebrate’s density supports fish and bird populations. Mangrove forests replace salt marshes in tropical regions and support a rich fauna.

  1. Freshwater Biomes

Fresh water biomes include lakes, rivers, bogs, marshes and swamps. These systems are fed by water and nutrient leaching from the surrounding catchment areas.

Streams and Rivers: The physical characteristics of streams and rivers alter along their length. They change from being small near their source to wider and slower at their mouth. Plant and animal diversity and production tends to highest in middle regions where flow rates and substrate allow the growth of macrophytes.

Lakes and Ponds: Lakes have very little or no current, allowing the water body to acquire vertical stratification with illuminated, warm water at the surface and dark, cold water below. Lakes can be nutrient rich (eutrophic) or nutrient poor (oligotrophic).



Ecology is the scientific study of the interactions between organisms and their environment.

The environment includes both abiotic factors: such as temperature, light, water, wind, soil and nutrients; and biotic factors: the other living organisms. The interactions may be competition, predation, parasitism and cooperation.

The work ecology was first used by a German Ernst Haeckel in 1869. It comes from two Greek words oikos meaning home, place to live; and logos meaning understanding. Therefore, generally speaking ecology is “the study of reciprocal relationship between living things and their environment.

Divisions of Ecology

Ecology is divided into autecology and synecology.


Autecology is the study of an individual organism or an individual species. Autecological studies are concerned with the relationship between the population and its sizes and its stability may be studied.


Synecology is the study of a group of different populations associated together as a community. Synecology involves analysis of the abiotic and biotic aspects of a community in the environment they occur.

Ecological Fields

Following are different fields of ecology

Behavioral Ecology:

It is concerned with the ways the animals interact with their living and non-living environment as influenced by natural selection.


It deals with the physiological responses of individual organisms to temperature, moisture, light, nutrients, etc.

Evolutionary Ecology

It is related to interactions of population dynamics, genetics, natural selection and evolution.

Chemical Ecology

The study of chemical reactions of organisms to their environment is termed chemical ecology. it involves use of chemicals by plants and animals as attractants, repellents and defensive mechanisms, their evolution and chemical structure.

Applied Ecology

The impact of human activities on environmental that provides a base for ecosystem and natural resource management, preservation and restoration is applied ecology.

Scope of Ecology

Ecology attempts to tell us:

Why particular kinds of organisms can be found living in one place and not another.

The factors that control the number of particular kind of organisms and maintain them at certain levels; and

The principals that may allow us to predict the future behavior of groups or organisms.

Practical Applications of Ecology

Human Impact on the Environment

Man lives in nature and depends on the resources of nature. Food, shelter and clothing are the primary requirements of man. In order to obtain this man has natural resources to the maximum that has resulted in undesirable changes in the habitats. Consequently, some natural stocks of plants (forests) and animals (wildlife) disappeared. About 1000 animal species and well over 20,000 plant species have either become extinct or declared endangered. Deforestation has caused soil erosion and other damage. Similarly, mineral resources are facing exhaustion due to consumption (mismanagement). Also, overpopulation, urbanization, industrialization and mechanized agriculture have resulted in rapid increase in air, water and soil pollution.

All the above mentioned human activities have lessened -Earth’s ability to support a diversity of life, including humans.

Applied Ecology

Ecological theories and models help us understand the human environment. They provide a basis for ecosystem and natural resource preservation and restoration. All these activities make up applied ecology.

Applied of ecology is concerned with application of ecological to environmental and resource management problems. Traditionally, applied ecology forest, range, and wildlife and fishery management. Recently applied ecology has the new fields of conservation biology, restoration ecology, and landscape.

Application of ecological principles to resource management has helped improve various fields such as:


Forests are natural ecosystems dominated by trees. these cover about one-third world’s land surface and provide habitat for Wildlife, fuel wood, fodder, fibre, fruit, timber and raw materials used in wood-based industries. They also regulate climatic conditions such rainfall, humidity and temperature of area and protect soil wind and water erosion. Forests transform solar energy into plant biomass which is consumed by animals and humans. Continued deforestation has resulted in desertification which led to soil erosion, destruction of wildlife habitat and increase in the rate of extinction, change in the climate in terms of decrease in rainfall and increase in temperature and humidity, and shortage of timber, firewood and pulpwood. Therefore, afforestation, i.e., cultivation of forests at new sites, is necessary.

One of the practical applications of ecology is forestry, it is treated as industry now-a-days, it is not simply raising of trees for harvest, but emphasizes biomass accumulation, nutrient cycling, the effects of timber harvesting on nutrient budgets, and the role of fire in forest ecosystems.

There are two schools of thought regarding the management of forests,

  1. According to one the forests should be managed as tree crop or monoculture (single species harvest) in the same way as we managed the food crops. This would help in increase in yield, faster growth and artificial selection of high yield varieties, However, raising tree farms require use of, fertilizer and pesticides that would increase pollution and danger of disease outbreak.
  2. The other school of thought maintains that forests may be managed as multiple-use forest and not as a crop which may provide wildlife habitat, air and water sheds, recreation and harvest as well.

However, it has been recognized that tree farms and naturally developed multiple use forests are entirely different ecosystems in terms of cost of maintenance and their impact on environment, therefore:

  1. It would be desirable to adapt naturally adapted forest as it provides best and safest cover for mountains and soils where tree farms cannot be maintained.
  2. The tree farms may be restricted to fertile lands and to soil types suitable for good agriculture such as along canal banks and farm boundaries,
  3. Wildlife Management

Wildlife refers to all non-cultivated plants and non-domesticated animals in an ecosystem. It includes game and fur-bearing vertebrates, and plants and animals which interact directly with game species. Wild animals are an important source of food and skin (leather), Also these are used in research as experimental animals, for recreational purposes and economic benefits (animal hunting). Similarly, wild flora is facing extinction because of habitat destruction and natural calamities. As a result, many species of wildlife have become extinct or on their way to extinction.

Wildlife is a renewable resource; therefore, its management is necessary because:

  1. Intensive study of Individual game species has contributed a great deal to population ecology.
  2. Genetic variations and interbreeding lead to evolution. The process of evolution would be affected if wildlife is destroyed.
  3. It is important economically and source of recreation.

Wildlife management is a high-ranking field of applied ecology. Thus, consideration the principles of ecology, would help in wildlife management.

  1. The habitats for wildlife may be conserved.
  2. The rare species may be protected from being hunted.
  3. Exotic species may be introduced.
  4. Predators may be Introduced in the ecosystem so that primary population remain within limits.
  5. Legislation may be introduced to prevent hunting.
  6. Sanctuaries and National Parks may be developed to protect endangered and threatened plants and animals. This would help in establishing gene banks.

Range Management

Range is grassland meant for grazing animals. Range management are interested in the functioning of grassland ecosystems, the effects of grazing intensities on grasslands on above ground and below ground production by plants, and the structure of grassland communities.

Grasslands are important from man’s viewpoint; however, these are the abused natural biomes by man. The grasslands provide natural pastures for grazing but domesticated grazing animals have destroyed or disturbed most of the grassland Similarly, the principal agricultural food plants have evolved from grasses; therefore, man has converted most of the grasslands into agricultural croplands.

The effect of grazing on seed output, reproduction capacity, establishment, vegetative growth and flowering in relation to climate, soil and biotic pressure of grazing are some of the more important ecological aspects. Therefore, principles may be taken into consideration and applied for proper range management. For instance,

  1. The rate of removal of resource (grasses) should be regulated to a level up to which the system can rebuild itself. For example, enough net Productivity maybe left in the range so that the range may remain stable in case of adverse climatic condition, i.e., drought, etc. For this purpose, number of grazing animals (stock level) may be regulated properly.
  2. The effect of grazing is an important factor to be considered in range management. The intensity and frequency of grazing have to be regulated. For this purpose, the forage production may be maintained at higher rate. The range maybe divided into compartments and grazing may be allowed alternately, i.e. a grazing year must alternate with non-grazing year.
  3. Geographical races of palatable grasses with high nutrient value may be introduced into the ranges.
  4. Fire, herbicides and pesticides may be used to destroy unwanted species so that palatable species may grow better.

Fishery Management (Fish Farming)

Since the demand of animal protein is increasing, steps are being taken for proper management of protein sources. One such common practice is aquaculture, i.e., cultivation of aquatic life such as fish, crabs, lobsters, oysters, prawns, etc. For food. Aquaculture is based on principles of applied ecology and is an effective means for increasing protein food for mankind.

Enzyme Classification

Nomenclature and Classification of Enzymes

Naming the Enzymes

Enzymes are generally named according to the substrate they complex with or the type of reaction they catalyze. The usual practice is to add suffix -ase to the name of the substrate involved. Thus, the enzyme cellulase, arginase and tyrosinase are named because their substrate cellulose, arginase and tyrosinase. But as the research progressed and more enzymes were discovered, they need for a standardized system of nomenclature arise. Therefore, in 1961, a systematic nomenclature for enzyme was recommended by a commission of International Union of Biochemistry. The enzymes were placed into six group according to the general type of reaction which they catalyze. Each enzyme was given a systematic name, accurately describing the reaction it catalyzes.

Classification of Enzymes

Classification of Enzymes

The common names of enzymes consist of:

The name of the substrate acted upon the enzyme.

The type of reaction catalyzes, and

Suffix -ase. For example.

Classes of Enzymes

The older system of classification is based on type of chemical reaction is catalyzed. However, numbering system of classification of enzymes have been introduced by commission on enzymes of the International Union of Biochemistry. It recognizes enzymes by numbers. Its understanding requires most professional biochemical and research publications and abstracts. The old system of classification is more convenient and introductory.

Major classes of enzymes based on the types of reactions they catalyze are as following:

Oxidoreductase (Oxidation Reduction Enzymes)

The enzymes that transfer H or O atoms, or electrons from one molecule to another, i.e. catalyze oxidation and reductase processes. The oxidoreductase is of two types:

Dehydrogenase, that involves transfer of hydrogen.


AH2 + B ———————————————– A + BH2 – transfer of H2

CH3CHO + NADH2 ———————————————– CH3CH2OH + NAD

Reductases, which transfers electrons or electron to oxygen.


AH2 + O ———————————————– A + H2O

For example:

Reduced cytochrome + ½ O2 ———————————————– cytochrome + H2O


These are enzymes that catalyze transfer of a specific group from a donor molecule to an acceptor molecule. The group may be methyl-, acyl-, amino-, or phosphate. This group enzymes are very large and includes enzymes such as trans-glycosidases, trans-peptidases, transaminases, etc.

AB + C ———————————————– A + BC

The Transferases may be:

Transaminases, which transfer amino groups.

Phosphorylases, which add inorganic phosphates, for example


Glycogen + Pi ———————————————– glucose 1 -phosphate


The enzymes catalyze the addition of water across a specific bond of the substrate to form the products.

AB + H2O ———————————————– AOH + BH

The Hydrolases include:

Proteinase, that hydrolyze protein by breaking peptide bonds.

Ribonucleases, which hydrolyze RNA.

Deoxy-ribonucleases, responsible for hydrolysis of DNA.

Lipases, which hydrolyzes fats (esters).


These enzymes bring about non-hydrolytic addition or removal of groups from substrates. During the reactions, C-C, C-N, C-O or C-S bonds may be split. These include:

Decarboxylases, that removes CO2.


CH3COCOOH ——————– CH3CHO + CO2

Carboxylases, that add CO2.

RuBP carboxylase

RUBP + H2O + CO2 ———————————————– 2GP


Theses enzymes are responsible for intermolecular rearrangement, i.e., one isomer is converted to another. For example, during respiration glucose 1-phosphate is converted into glucose 1-phosphate by phosphoglucomutase.


These enzymes join two molecules by synthesis of new C-C, C-N, C-O or C-S bonds using energy from MP.

X + Y + ATP ———————————————– XY + ADP + Pi

These include:

Synthetases, that catalyze synthesis of tRNA.

Polymerases, which are responsible for linking monomers (sub-units) into a polymer such as DNA or RNA.


Enzyme Inhibition

Enzyme inhibition types

Competitive inhibitors bind reversible to the enzyme, preventing the binding of substrate. On the other hand, binding of the substrate prevent the binding of the inhibitor. Substrate and inhibitor compete for the enzyme.

Enzyme Inhibition

Enzyme Inhibition

Competitive Inhibition

In competitive inhibition, the inhibitor and the substrate compete for the enzyme (i.e., they cannot not bind at the same time). Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, methotrexate is competitive inhibitor of the enzyme dihydrofolate reductase, which catalyzes the reduction of dihydrofolate to tetrahydrofolate. There is a similarity between the structures of folic acid and this drug. In some cases, the inhibitor can bind to a site other than the binding site of the usual substrate and exert an allosteric effect to change the shape of the usual binding site. For example, strychnine acts as an allosteric inhibitor of the glycine receptor in the mammalian spinal cord and brain stem. Glycine is the major post-synaptic inhibitor neurotransmitter with a specific receptor for glycine, resulting in convulsions due to lessened inhibition by the glycine. In competitive inhibition, the maximum rate of the reaction in not changed, but higher substrate concentrations are required to reach a given maximum rate, increasing the apparent Km.

Uncompetitive Inhibition

In uncompetitive Inhibition, the inhibitor cannot bind to the free enzyme, only to the ES-complex. The ES-complex thus formed is enzymatically inactive. This type of inhibition is rare, but may occur in multimeric enzymes.

Non-Competitive Inhibitors

Non-competitive Inhibitors can bind to the enzyme at the binding site at the same time as the substrate, but not to the active site. Both the EI and EIS complexes are enzymatically inactive. Because the inhibitor cannot be driven from the enzyme by higher substrate concentration (in contrast to competitive Inhibition), the apparent Vmax changes. But because the substrate can still bind to the enzymes, the Kmax stays the same.

Mixed Inhibition

This type of inhibition resembles the non-competitive Inhibition, except that the ES-complex has residual enzymatic activity. This type of inhibitor does not follow Michaelis-Menten equation.

In many organisms, inhibitors may act as part of feedback mechanism. If an enzyme produces too much of one substrate in the organism, that substance may act as an inhibitor for the enzyme at the beginning of the pathway that produces it, causing production of the substance to slow down or stop when there is sufficient amount. This a form of negative feedback. Enzymes that subject to this form of regulation are often multimeric and have allosteric binding sites for regulatory substances. Their substrate/velocity plots are not hyperbolar, but sigmoidal (S-shaped).

The coenzyme folic acid and anti-cancer drug methotrexate are very similar in structure. As a result, methotrexate is a competitive inhibitor of many enzymes that uses folates.

Irreversible inhibitor reacts with the enzyme and form a covalent adduct with the protein. The inactivation is irreversible. These compounds include eflornithine a drug used to treat the parasitic disease sleeping sickness. Penicillin and Aspirin also act in this manner. With these drugs, the compound is bound in the active site and the enzyme then converts the inhibitor into an activated form that reacts irreversibly with one or more amino acid residues.

Uses of Inhibitors

Since inhibitors modulate the function of enzymes they often are used as drugs. A common example of an inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2 enzymes that produce the inflammation messenger prostaglandin, thus suppressing pain and inflammation. However, other enzyme inhibitors are poisons. For example, the poison cyanide is an irreversible enzyme inhibitor that combines with the copper and iron in the active site of the enzyme cytochrome c oxidase and blocks cellular respiration.

Mechanism of Enzyme Action

Mechanism of Enzyme Action

The molecules upon which an enzyme acts are called its substrate. For example, cellulose is broken down by enzyme cellulase, therefore cellulase is the substrate.

Mechanism of Enzyme Action

Mechanism of Enzyme Action

Active Sites

The active site of enzymes is a complex three dimensional-cavity into which the substrate molecule fits. At the active sites the enzymes work by lowering the energy of activation.

The enzymes are far larger molecules then the substrates they act on. Only a very small portion of enzymes, between 3-12 amino acids, comes in direct contact with the substrate in the enzyme substrate complex. This is active site of enzyme. The active sites of enzyme have shape and charge complementary to its substrate. The active site is formed by interactions of R-groups of amino acids in a polypi: de chain. For example, in lysozyme five amino acids at positions 35, 52, 62, 63 and 101 out of linear sequence of 129 amino acids provide their R groups to form its active site.

Enzyme Substrate Complex

Enzymes work by reacting with their substrates to form a short-lived enzyme substrate complex before yielding the products. Studies on kinetics of enzymes confirm the formation of enzyme substrate complex. The complex is formed at active site of the enzyme. The complex breakdown to form the product (s), leaving an unchanged enzyme molecule which is then available to catalyze another substrate molecule. The formation of enzyme substrate complex was first hypothesized by Emil Fischer in 1884 and offers a good explanation of the enzyme specificity.

E + S ——————————— ES ——————————— E + P

Kinetics of Enzyme Action

  1. Michaelis and M. L. Menton (1913) while working with enzyme invertase which catalyzes the hydrolysis of glucose and fructose postulated the existence of enzyme substrate complex. They proposed that enzyme catalyzed reactions involve the following phases:
  2. The formation of a complex (ES) between the enzyme (E) and substrate (S).
  3. Modification of the substrate to form the product (P) or products, which briefly remain associated with the enzyme (EP)
  4. The release of the product or products from the enzyme, i.e.,

                                                              k1                                          k3

E + S ——————————— ES ——————————— E + P


in this equation, it is assumed that combination of enzyme and substrate is reversible and

k1 = constant for formation of -ES;

k2= rate constant for the dissociation of ES

k3 = rate constant for conversion of S to P.

Michaelis and Menton are also credited with the first mathematical study of the relationship between substrate concentration and reaction rates. They introduced two particularly useful mathematical expressions that for any enzyme relate IS] to V (velocity) and permit quick comparisons of various enzymes catalyzed reactions. These two expressions are called Michaelis-Menton constant and Michaelis-Menton equation.

Models of Enzymes Action

Two models were proposed two explain how Enzymes work and how active site of an enzyme selects its substrate out of thousands of molecules present in a cell.

Lock And Key Model

Enzymes are highly specific in the reaction the catalyzed. Some enzymes catalyze the transformation of one particular type of substrate molecule or, at most a very restricted group of substrate molecules; some catalyzes only one type of chemical change. This degree of specificity distinguishes enzymes from other types of catalysts. The specificity 4 enzymes are due to the configuration of the active site. This idea was originally developed as the lock and key model hypothesis. The substrate is the key that fits exactly the enzyme lock.

Lock And Key Model

Lock And Key Model

The lock and key model of enzyme action was proposed by Emil Fischer. According to this model the substrate has polar (positive and negative) and non-polar (hydrophobic) regions, therefore, it is attracted to and associates with active site which is complementary in both shape and charge distribution. The active site of enzymes can be compared to key and substrate to a lock. A specific key can open a particular lock, similarly a substrate having complementary shape and charge to the active site can fit into the active site, and is catalyzed by the enzyme. The lock and key model for enzyme action accounts for enzyme specificity, because that lack the appropriate shape or are too large or too small cannot be bound to the active site.

Induced Fit Model

Evidence from protein chemistry suggests that a small rearrangement of chemical groups occurs in both the enzyme and the substrate molecules when the enzyme substrate complex is formed. It is suggested that strains of these changes may play a part in the catalytic process; it may help induce a chemical change. This suggestion, which is called induced fit model hypothesis, seems to offer a better model to explain enzyme action.

According to lock and key model of enzyme action the active sites are rigid and specific for a given substrate. Thus, reversibility of reaction cannot occur because the structure of the products is different from that of a reaction and these will not fit into the active site. But it was found that in number of cases compounds other than true substrates bind to enzyme, though they fail to form the end products.

Induced Fit Model

Induced Fit Model

In 1973 Daniel E. Koshland proposed that the active sites of enzymes do not initially exist in shape that is complementary to substrate but are induced to assume the complementary shape as the substrate becomes bound. This idea is widely known as induced fit model hypothesis. According to Koshland the enzyme active site is flexible. The active site and the substrate initially have different shapes but becomes complementary on substrate binding. The shape change brings the catalytic residues in positive to alter the bonds in the substrate, following which the product is released and the active sites return to its initial state. However, that molecules that are large or smaller than the true substrates or that have different chemical properties do not bound to the active sites and do not induce it to change its conformation.

What Are Enzymes


Enzyme are partly or entirely a protein that can tremendously increase the efficiency of a biochemical reaction and is generally specific for that reaction.

The term enzyme (Gr. en = in + zyme = living) was first discovered by W. Kuhne in 1878 while working on fermentation.

Nature of Enzymes – Physical Properties

The enzymes are proteins wholly or partly. They increase efficiency of a biochemical reaction by increasing their speed, therefore these are also called biological catalysts. The enzymes are vital because in their absence reactions in the cell would be too slow to sustain life. They exhibit many of the physical properties of proteins and inorganic catalysts and thus can be characterized in the followings:



  1. Enzymes are molecules of higher molecular weight. Peroxidase, one of the smallest enzyme, has molecular weight of 40;000, whereas the catalase, one of the largest enzyme has higher molecular weight of 290,000 approx.
  2. Enzymes are colloidal substances. The enzymes being proteins are colloidal in nature, therefore form colloidal suspension in the cytosol. They form micelle and provide large surface area of catalytic actions.
  3. Enzymes are active in small amounts, i.e., only a small amount of enzyme is necessary to convert a large amount of substrate to product in a biochemical reaction. The number of moles of substrate converted per minute by 1 mole of enzyme is called turnover number of the enzyme. This number may vary from 100 to over 3,000,000.
  4. Enzymes are unchanged at the end of a reaction.
  5. Enzymes speed up the rate at which equilibrium position is reached. A catalyst speeds up the rates of both the forward and backward reactions, and the rate at which equilibrium position is attained. A catalyst does not alter the position of equilibrium. Similarly, an enzyme hastens the completion of a reaction, it will not affect the equilibrium of that reaction.
  6. Enzymes lower the reading molecules.
  7. Enzymes are extremely specific. Most enzymes are specific to one particular type of substrate molecule, and usually one isomer of that substance. Other enzymes are specific to a group of similar substances, or to a particular type of chemical linkage.
  8. Enzymes can be denatured. Like most proteins, the enzymes can be denatured by heat and lose their enzymatic activity. Other factors such as metal ions such as those of lead, mercury and silver; concentrated acids and bases; and ultra violet light also being denaturation. Many organic solvents also denature the enzymes.

Chemical Nature of Enzymes – Chemical Properties

Every known enzyme is protein wholly or has a protein as major parts of its structure. The non-protein part of enzyme is called cofactor. The enzyme cofactor complex is called holoenzymes. Whereas enzyme portion without cofactor is known as apoenzyme.

Apoenzyme – Protein Part of Enzymes

Protein of enzymes consists of one or more polypeptide chains of tens to hundreds of amino acids. The composition and size of each protein depends upon the kind and number of its amino acid sub-units.

The total number of amino acid sub-units varies greatly in different proteins and so protein molecular weight also varies from 11,500 (ferredoxin) to 500,000 (ribnlose bisphosphate carboxylase) grams mole-1. The chains of complex enzymes are held together by non-covalent bonds. Often ionic or hydrogen bonds and can be separated in vitro.


Many enzymes that do not have prosthetic group require another organic compound for their activity. These compounds are called coenzymes. These are usually not tightly held to the enzymes. The common examples of coenzymes are NAD (nicotinamide adenine dinucleotide), NADP (nicotinamide adenine dinucleotide phosphate). Coenzyme A, and ATP. Vitamins produced by the plants are source of coenzymes, e.g., NAD is derived from vitamin nicotinic acid.

Enzyme Activator

Enzyme require inorganic ions for their efficient enzymatic activity. These are thought to mold either the enzyme or the substrate into a shape such that an enzyme substrate complex can be formed, hence in the presence of calcium ions. The other activators are metal ions such as Zn, Mg, Ca, Co, Fe etc.


Biochemistry of Biological Nitrogen Fixation

Biochemistry of Biological Nitrogen Fixation 

Nitrogen fixing bacteria that occur in association with higher plants, especially with those of family Leguminaceae (fabaceae), are termed as symbionts.

The symbiotic association of nitrogen-fixing bacteria with plants roots generally occurs in multicellular structures called nodules. The best characterized symbiotic association involving nodules is one occurring on roots of leguminous plants. About 200 legume species are capable of nitrogen fixation. Nitrogen fixing root nodules can fix 100 to 200 times more nitrogen than free-living micro-organisms.

Plants other than legumes can also develop symbiotic relationship with nitrogen-fixing bacteria, for example Alnus (alder) involves nodule formation by an actinomycete Frankia. Similarly, grasses can also develop symbiotic relationships with nitrogen fixing organisms, but these associations do not involve the production of root nodules. These bacteria remained anchored to the root surface.

Biochemistry of Biological Nitrogen Fixation

Biochemistry of Biological Nitrogen Fixation

Azolla, an aquatic water fern, contains colonies of blue-green algae that fixes nitrogen. This association is especially important in rice fields. The fixed nitrogen leaks out from the fern plant and supplies the nitrogen needs of the rice plant.

Certain lichens growing on the surface of trunks and branches of forest trees are able to fix nitrogen. Nitrogen fixed by lichens may be leached down to the forest floor by rain. Aging of bark causes lichens to fall on the forest floor, where these are decomposed and releases fixed nitrogen in trees.

Development of Nodule

The nodules in legume are produced by the host plant root upon affected by nitrogen fixing gram-negative bacteria of the genus Rhizobium.

The following steps are involved in development of a nodule:

  1. Th root excrete substances that attract bacteria and stimulate them to produce a cell-division.
  2. Cells in the root cortex divide o form the primary root nodules meristem.
  3. Bacteria attracts themselves to root hairs.
  4. The cells in the pericycle near xylem are stimulated to divide and form infected threads.
  5. The cells of primary nodule meristem and pericycle continue to divide and two masses of dividing cells fuse into a single clump. The infection threads continue to grow.
  6. The nodule elongates, its vascular tissue differentiates and make a connection with the root stele.
  7. The bacteria enter the nodule cells. Bacterial cells inside infected host cells multiply rapidly and are transformed into nitrogen fixing organelle called bacteriods. These contain enzymes necessary for nitrogen fixation.

Biochemistry of Biological Nitrogen Fixation

The end product of biological fixation is ammonia. It is incorporated into organic compounds such as glutamine or glutamate and is utilized by the micro-organisms or by the host plant in case of symbiotic association. The overall reaction of fixation of molecular nitrogen into ammonia is:

N2 + 8e + 16 ATP ———————————- 2NH3 + H2 + 16 ATP + 16 Pi

The entire reaction is catalyzed by an enzyme complex, nitrogenase.

Conversion of Ammonia to Nitrate

Some plants directly utilize ammonia under certain conditions, but the principal source of nitrogen that is available to higher plants under normal field conditions is nitrate. In most temperate soils, ammonia is rapidly converted to nitrate through nitrification by bacteria that are absorbed by plants through their roots.

Reduction of nitrate to Ammonium

Inside the body of a plant nitrate is assimilated to organic compounds. Prior to assimilation nitrate is reduced to ammonia in the cytosol.

The first step is reduction of nitrate to nitrite. This reaction carried out by enzyme nitrate reductase. NADH is the electron donor. The overall reaction is:

NO3 + NADH + H+ + 2e ———————————- NO2 + NAD+ + H2O

Nitrite produced is rapidly transported to into chloroplasts when, it is reduced to ammonia by the activity of nitrite reductase. Ferredoxin is the electron donor. The overall reaction is:

NO2 + 6Fdred + 8H+ + 6e ———————————- NH4+ + 6Fdox + 2H2O

Incorporation of Ammonia into Organic Compounds

Ammonia and ammonium, ions do not accumulate in plant cells but are instead rapidly incorporated into organic compounds. The conversion of ammonia into carbon compounds takes place through two possible ways. Both of these possible ways result in same product, glutamate

The first pathway involves the reductive amination of alpha-ketoglutarate to produce glutamate. The reaction is catalyzed by glutamate dehydrogenase.

Alpha-ketoglutarate + NADH + NH3 ———————————- Glutamate + NAD+ + H2O

The second pathway involves a reaction with glutamate to form its amides, glutamine. This reaction is catalyzed by glutamate dehydrogenase.

Glutamate + NH3 + ATP ———————————- Glutamine + ADP + P

Glutamine can be converted to glutamate by glutamate synthetase by the following reaction:

Glutamine + alpha-ketoglutarate ———————————- 2 Glutamate

Transamination Reactions

Once assimilated into glutamate, the nitrogen can be further incorporated into other amino acids through transamination reaction by enzymes aminotransferases.

Glutamate + Oxaloacetate ———————————- Aspartate + alpha-ketoglutarate

The two amides glutamate and aspartate are metabolic reservoirs for the temporary storage of excess ammonia.

Nitrogen Cycle

Nitrogen Metabolism

Nutrient Assimilation

Higher plants are autotrophic organisms that can synthesize all of their molecular components from inorganic nutrients from the local environment. The mineral nutrients taken up by plants are converted into carbohydrates, lipids and amino acids. It is called nutrient assimilation.

Nitrogen Cycle

Nitrogen Cycle

Nitrogen Assimilation

Nitrogen is a key element in many of the compounds present in the plants. It is found in nucleotides and amino acids that form the building blocks of nucleic acids and proteins.

Biological Nitrogen Cycle

The atmosphere contains 79% nitrogen by volume, however this not available to plants directly because plants are unable to break stable triple covalent bond between two nitrogen atoms. The plants are able to assimilate nitrogen present in the form of nitrate or ammonia. This results in further movement of nitrogen in the food chain. The nitrogen is returned to the soil through the death and decomposition of plants and animals by the action of bacteria and certain fungi that convert organic nitrogen to gaseous nitrogen.

Biological Nitrogen Cycle

Biological Nitrogen Cycle

The cycle of fixation of gaseous nitrogen, assimilation of fixed nitrogen by plants and then animals, and return of gaseous nitrogen to the atmosphere by denitrifying bacteria is called the biological nitrogen cycle.

Nitrogen Fixation

The conversion of molecular nitrogen into other forms such as ammonia or nitrate is known as nitrogen fixation. It can occur as a result of both natural and industrial processes.

Under the conditions of elevated temperature (200 °C)’ and high pressure (about 200 atmosphere), molecular nitrogen will combine with hydrogen to form ammonia (Haber process). About 12% nitrogen is removed each year from atmosphere by industrial methods.

About 5% of natural fixation occurs as a result of lightening during thunderstorm. It causes water vapours, oxygen and nitrogen in the atmosphere to combine to form nitric acid which is brought down by rain to the surface of the earth. The remaining 95% of natural nitrogen fixation occurs through certain micro-organisms, mainly bacteria and cyanobacteria (blue-green algae).

Several steps are involved in nitrogen fixation by micro-organisms:

  1. The ammonia produced during biological nitrogen fixation is assimilation by green plants into amino acids, proteins and other nitrogenous products. Some plants may be consumed by animals. The animals waste and dead plants and animals and micro-organisms undergo decay during which complex organic nitrogenous compounds are decomposed into simpler compounds such as amino acids.
  2. Ammonification: A group of soil bacteria together with certain fungi converts amino acids into ammonia. This is called ammonification. The ammonia produced reacts with other chemicals present in the soil to form ammonium salts such as ammonium carbonate.
  3. Nitrification: Two groups of soil bacteria oxidize ammonia of ammonium salts to nitrite (Nitrosomonas) and nitrite to nitrate (Nitrobacter). The process is called nitrification.

    Nitrogen Fixation

    Nitrogen Fixation

  4. Denitrification: Finally, the nitrates into the soil are reduced by certain soil bacteria to nitrogen and volatile nitrogen oxides, which escape into the atmosphere. This process is called denitrification. Denitrifying bacteria are especially active under anaerobic conditions in wet soils with high organic matter content.

Biological Nitrogen Fixation

The nitrogen fixed through the action of micro-organisms is termed as biological nitrogen fixation.

Biological nitrogen fixation is carried out by free-living bacteria and cyanobacteria, and by bacteria that are in symbiotic association with plants. These organisms contain enzyme systems that can catalyze chemical reactions involving molecular nitrogen.

The nitrogen fixing micro-organisms are known as free fixers.

Free Fixers

Nitrogen-fixing bacteria can be aerobic, facultative or anaerobic.

Aerobic Nitrogen-Fixing Bacteria: These bacteria flourish in aerobic conditions. These include Azotobacter that fix nitrogen during night.

Facultative Nitrogen-Fixing Bacteria: This type of bacteria is able to grow under both aerobic and anaerobic conditions. However, they generally fix nitrogen only under anaerobic condition.

Anaerobic Nitrogen-Fixing Bacteria: They do not require oxygen. These may either by photosynthetic. For example; Rhodospirillum; or non-photosynthetic, such as Clostridium.

Although free-living nitrogen fixing bacteria are found in many soils. However, they contribute to the nitrogen content of the soil only under very special soil conditions such as presence of sufficient decayed plant material and high water contents.

The cyanobacteria that fix nitrogen consists of chains of cells in long filaments contain specialized larger colorless cells with thick walls called heterocysts. These cells are able to fix nitrogen. About forty species of cyanobacteria are capable of fixing nitrogen. These are more active in wet tropical soil, e.g., rice fields. Cyanobacteria uses sunlight energy for nitrogen fixation.