eChapters

Conservation Biology emerged as the scientific study of the nature and status of Earth’s biodiversity with the aim of protecting species, their habitats, and ecosystems from excessive rates of extinction. Biodiversity itself has a wider meaning unifying and taking into account species, within species breeds/ varieties, ecosystem, genetic and molecular diversity.

Need for Conservation

The progenitor of modern-day chicken has been the Red Jungle Fowl and over the years breeds have been developed slowly for commercial purpose as layers and broilers. However we still have lot of indigenous birds which cannot be defined in either category.

Breeding capabilities Vs biodiversity erosion: Presently only about 3-4 poultry breeding companies provide meat stocks for farms around the world. A similar number of companies supply birds for commercial egg production. As a result modern animal industry now uses only a few breeds of any species. Of the many breeds once commonly seen on farms, many have declined sharply in numbers and others have disappeared almost completely.

Productivity Vs Conservation: On one hand, to increase productivity we want certain natural characters to be eliminated and on the other we talk of conserving the indigenous varieties, which sounds contradictory.

Project for Rural People on Chicken

For rural people Desi (indigenous) chicken plays an important role. Family poultry farming is a part and parcel of a typical rural household in India touching social, cultural and economic aspects. People residing in rural areas primarily maintain their indigenous chicken under backyard farming. With the same management system the rural people can rear improved varieties of chicken instead of their traditional counterpart. The improved varieties being Giriraja, Vanaraja, Kuroiler, Gramapriya, Gramalaxmi, Swarnadhara, Krishna J etc. A model project on improved chicken is given herewith:

A unit consisting of 100 number Vanaraja or Giriraja is economical and remunerative to the farmers whose family labour will be utilized for rearing these chickens. Initially, the farmer will buy about 225 straight-run day- old chicks. The males will be sold at 20 weeks of age. The females will be maintained for 1.5 years. In order to have continuous operation, next batch of 225 chicks have to be procured 6 months before disposal of the old batch. Birds will collect their feed through foraging or scavenging in the field. Supplementary feeding will be provided to meet their requirements.

Housing constitutes the second largest component of cost of poultry production. An ideally located and well planned poultry farm is an essential requirement for efficient egg and meat production. Poultry housing normally serves the following major functions:

Provides shelter and protection to the birds

Provides comfort to the birds.

Helps in organization of large flock into a manageable unit.

Types of Brooders

Brooding is a mechanism of providing auxiliary or supplementary heat to chicks through artificial heat using brooders. Brooders are of several types depending upon the size and the nature of fuel used. These are individual, multiple units or central heating systems run by coal, wood, oil, gas or electricity. The essentialities of a good brooder are i) a dependable mechanism, ii) supply of fresh air, iii) dryness, iv) adequate space, v) easy for cleaning and disinfection, vi) protection against enemies, vii) safety from fire and viii) economy.

i) Hover brooders

Such brooders are more widely used in India wherever electricity is available. They maintain uniform temperature, convenient for operation and require very little attention. However, eclectic brooders do not heat house appreciably in very cold weather. Wet litter may be another problem requiring frequent stirring and renewal of litter.

Care and Management of Commercial Growers (09-20 weeks) Under Deep Litter System

Grower management essentially remains the same as that of chick management (brooding management) except for the additional space required for floor, feeders and waterers to keep with the size of birds. The growers may be reared in separate grower-houses or continued to be reared in brooder-cum-grower houses.

Floor space: 1260 cm² (1.4 ft²) per bird.

Feeder space: 6-8 cm per bird. One linear feeder of 120 cm length and 8 cm depth for 40 growers.

Waterer space: 2 cm per bird; a circular waterer of 36 cm and 8 cm depth of 6 lit. capacity for 50 growers. Growers are to be provided with fresh, cool and potable drinking water at least twice a day. Water requirement is increased during hot days. Care must be made not to spill water on litter.

Lighting management: No artificial lighting is given other than natural day light since they require only 9 hours of light per day.

In India, poultry judging refers to selection of birds on the basis of their physical appearances, breed characteristics and production performances; however, in other countries, like USA judging is also used for eggs, carcasses and further processed products. The Directorate of Extension, Ministry of Agriculture, Govt. of India annually conducts livestock and poultry shows in various parts of the country in collaboration of state governments. Besides, state Agricultural/ Veterinary Universities or other institutions also conduct such shows. In these shows judging contests are carried out mostly for the undergraduate students by using a score card to grade birds either for production characters or breed characters. The winners are awarded trophies and cash prizes. The birds meant for judging are kept in individual cages and the participants are requested to score under various sub-headings and to finally rank the bird. Any deviation from “ideal” or “perfection” (as described by the American Standard of Perfection or the British Poultry Standards) but not serious enough to constitute a disqualifications in the show room is considered to be a defect. Serious defects are regarded as disqualifications and will bar a bird from winning any prize. Both layers and broilers can be physically evaluated for their performance rating.

Management of the poultry house environment forms an essential aspect towards maximizing production performance. Generally, proper maintenance of poultry litter is seldom given emphasis. The condition of litter significantly influences bird’s performance and ultimately affects the economy for rearing. The litter is defined as the bedding materials of around 5-6 cm height consisting of locally available materials like rice husk, peanut hull, wood shavings, paper shreds, sawdust or groundnut hulls. These materials can be used alone or in combination to rear the birds on floor under deep litter system of management. The excreta, feathers, spilled feed and water are mixed with bedding material, get further decomposed due to heat and bacterial action resulting in built-up-litter towards the end of rearing.

Any deviation from optimum state could be referred as stress. Every living creature has to pass through one or the other type of stresses in life. Most of the farm animals including poultry suffer from various types of stresses. These include due to:

Adverse environment

Managemental practices

Diseases

Nutritional deficiency

Transportation etc.

Vices of poultry are undesirable behavioural pattern manifested by the bird in the flock and spreads fast among the members resulting in financial losses.

Types of Vices

Pecking

Cannibalism

Egg eating

Water is the most important and abundantly required nutrient for poultry. A continuous supply of clean, fresh and wholesome potable water is essential for poultry. Poultry rearing is becoming more and more intensive with which the chances of the infectious diseases being sustained in the different flocks also increase. Consequently, the need for effective disease control measures to be adopted also gains further importance.

Most often, poultry farmers get alarmed only when the mortality level or death rate in a farm is high. However, even the existence of disease at a sub-clinical level may hinder the performance of the birds, in terms of body weight or egg number; such economic losses, sometimes relatively less and unnoticed, may mean the difference between success or failure in the poultry business. Treatment of a sick flock after the onset of any disease becomes costlier and more frequently impracticable. The recovered birds may not regain their production to original levels and may also continue as source of infection to other healthy birds. Hence, the adage ‘prevention is better than cure’ applies more to poultry industry than any other field.

Biosecurity means protection against infectious biological agents. These agents include bacteria, viruses, protozoa, fungi, parasites, and any other agents capable of introducing infectious diseases into a poultry flock. Biosecurity therefore means maintaining a flock, poultry house or premises in such a way that infectious agents do not have a chance to enter to cause diseases. The biosecurity may be categorized into three: Conceptual biosecurity, Structural biosecurity and operational Biosecurity.

Importance of Biosecurity

In modern poultry production, birds are reared under intensive system where large numbers are concentrated in small area. As a result, when an infectious agent enters a poultry house, there is probability for widespread dissemination if it is not contained. Besides, the broiler and egg industry of today is under increasing consumer and regulatory pressures to guarantee food safety and meet export requirements. As a result, broiler and layer operations around the world require the supply of breeding stock free of salmonellas specific to avian species (such as S. pullorum and S. gallinarum) and those that could cause outbreaks of human food-borne illness. Inadequate biosecurity can contribute to wide epidemics of highly pathogenic or exotic diseases. An infection by a virulent organism within a facility can be devastating, reducing without overt signs of disease. Once contaminated with pathogens, poultry facilities are extremely difficult and expensive to clean, sanitize and disinfect. Prevention of disease is always less expensive than treatment. The cost of implementing biosecurity system is smaller when compared to financial profit that can be made from production. Good biosecurity is therefore vital requirement in the best possible control of disease.

For maximization of productivity in any kind of poultry venture the knowledge on the behaviour of birds and its application play very significant role. Behaviour is the reaction of the whole organism to certain stimuli, or the manner in which it interacts to its environment. Behavioural patterns are not inherited as such, but develop through the process of growth and get differentiated under the influence of genetic and environmental factors. Primary function of behaviour is to enable the bird to adjust itself to some changes in condition, whether external or internal. Most animals have a behavioural pattern which can be tried out in a given situation and in this way they learn to apply one or the other according to that which produces the best adjustment.

Digestive System and Digestion in Chicken

Studies on structure and functions of digestive system of chicken play important role for their nutrition and feeding. Functions of each part are given below (Fig 35):

Mouth: Birds feed through the beak. The horny upper and lower mandibles form the beak. Lips, teeth, cheek and soft palate are absent. The dagger-like tongue helps to force the feed into the esophagus. Chicken has 24 taste buds with high sense of taste. Absence of teeth makes the particle size of the feed important.

Esophagus (Gullet): It is made of loose fibrous tissue and serves as a tube to pass the food from mouth to crop. This is relatively long because of the long neck of the fowl.

Crop: (Ingluvius): It is a pouch like structure of esophagus to store, moisten and soften the food. It gives information about the feeding habits of the fowl.

Proventriculus (Glandular stomach or True stomach): It is an enlarged glandular ovoid structure of the esophagus connected to gizzard. It secretes pepsin and Hydrochloric acid.

Gizzard (Muscular stomach): Disc shaped muscular organ with two pairs of strong thick muscles and lined internally with a thick horny epithelial covering called the Koilin layer. Coarse materials are ground well by its powerful contractions with the support of the grit that birds consume.

Common Poultry Diseases

Infectious diseases

Bacteria

Commonly known as “germs”, bacteria are very small living microorganisms. Only a few bacteria cause diseases. In birds these include Salmonella, Clostridia, Pasteurella, Vibrio, Staphylococci, Streptococci, Mycoplasma, Hemophilus, and Mycobacterium etc.

Chicken’s eggs have been used as a food item by human beings since antiquity. The egg is composed largely of the proteins out of the three most important dietary essentials (proteins, fats and carbohydrates). The egg proteins are highly digestible and remarkably complete, containing the most important essential amino acids. The amino acid profile of egg is similar to the ideal balance of amino acids needed by humans. It also supplies various minerals, some in significant amounts, and contains a range of vitamins. The nutritive excellence of the egg enhances the value of any food in which it is incorporated. Meeting consumer demands is a constant challenge for the poultry industry. Present day consumers desire somewhat distinct products with respect to safety, healthfulness, freshness, taste, color, etc. To remain competent, various companies have developed several designer and specialty eggs which have appeared in supermarkets.

Breeder management includes pure line management, parent stock management, and grandparent stock management depending on the context. Except for small variations in management among these stocks basics are common within layer breeder stocks and broiler breeder stocks. The main objective of the breeder management is to produce more fertile eggs per pullet and increasing the hatchability by hygienic handling of these fertile eggs.

Location of the breeder farm

Location of the breeder farm should be away from commercial poultry farms in order to prevent the spread of diseases between the flocks. However, they must be in close vicinity of the city/town to have a good transport facility and other amenities such as water, electricity and availability of labour.

Artificial insemination (AI) is the deposition of the semen or male germ cells (spermatozoa) in the female genital tract by artificial means (instruments). Artificial insemination includes collection of semen from the male, preservation, handling and deposition into the female reproductive tract hygienically replacing natural mating by a male. In India this technique is gaining momentum in chickens due to improved animal husbandry practices and economic considerations, initiated by IVRI, Izatnagar and JNKVV, Jabalpur. In many parts of the world, turkey, ducks, goose and guinea fowl are bred solely by AI. Chicken species are endowed with the behaviour and capacity of each male to mate several females and also 25 to 40 times a day. Further, the process of ovulation in birds is almost daily and stimulated by intensity and duration of light.

In modern poultry managemental practices of using cages, environmentally controlled houses and breeding and hybridization techniques employed for developing highly economical chickens, selection for faster growth and heavy body weight in broilers, which has led to loss of fertility and hatchability and use of dwarf female parents in broiler industry have demanded the use of AI in poultry.

Principles of Incubation

Incubation is a process by which the embryo within egg develops into a fully formed chick capable of breaking free from the shell. Basically, when a hen incubates an egg, it means she is on the egg in order to keep it warm for a certain period of time, 21 days for chicken, until the chick embryo has fully formed and is ready to hatch. The incubation period in other species is given in Table 41. The following factors affect the incubation on egg

1. Temperature

Incubator temperature should be maintained between 99 and 100 oF. The acceptable range is 97 to 102 ^oF. Overheating is more critical than under heating. An incubator should be operated in a location free from drafts and direct sunlight. Temperature is probably the most important single factor influencing the development of the embryo. A higher temperature will advance the hatch and a lower temperature will delay hatch. Younger embryos are especially susceptible to high temperatures because the upper lethal limit is very close to the optimum incubating temperature. High temperature will cause the embryonic membranes to dry out too soon. Chicks that hatch may have an unsteady gait.

1.1. INTRODUCTION

The word research derives from the French “recherche”, which means to search closely. Research is a process of investigation. It is an examination of a subject from different points of view. It’s not just a trip to the library to pick up a stack of materials, or picking the first five hits from a computer search. Research is a hunt for the truth. It is getting to know a subject by reading up on it, playing with the ideas, choosing the areas that interest you and following up on them. Research is the way you educate yourself.

Research can be defined as the search for knowledge or any systematic investigation to establish facts. The primary purpose for research is discovering, interpreting, and the development of methods and systems for the advancement of human knowledge on a wide variety of scientific matters of our world and the universe. Research can use the scientific method, but always not necessary.

Scientific research relies on the application of the scientific method, a harnessing of curiosity. This research provides scientific information and theories for the explanation of the nature and the properties of the world around us. It makes practical applications possible. Scientific research can be subdivided into different classifications according to their academic and application disciplines.

2.1. INTRODUCTION

The purpose of collecting data is to collect evidence for reaching a sound and clear solution to a problem. In this chapter we will study the sources of data, mode of data collection and its techniques.

Sources and Types of Data

Statistical data can be obtained from two sources:

Primary and

Secondary

3.1. CENSUS AND SAMPLE SURVEYS

Census or Complete Enumeration

A survey, which includes every element of the population, is known as Census or the Method of Complete Enumeration. If certain agencies are interested in studying the total population of a country, they have to obtain information from all the households in rural and urban area.

The essential feature of this method is that this covers every individual unit in the entire population. We cannot select some and leave out others. We may be familiar with the Census of a country, which is carried out after a particular period like every ten years. A housetohouse enquiry is carried out, covering all households. Human demographic data on birth and death rates, literacy, workforce, life expectancy, size and composition of population, etc. are collected and published by a government agency.

4.1. INTRODUCTION

The number of individuals to be included in a research study (the sample size of the study), is an important consideration in the design of many studies. This chapter will provide information on basic factors that determine an appropriate sample size and provides methods for its calculation in some simple, yet common, cases. Sample size is closely tied to statistical power, which is the ability of a study to enable detection of a statistically significant difference. A trade-off exists between a feasible sample size and adequate statistical power. Strategies for reducing the necessary sample size while maintaining a reasonable power is also important.

How many individuals will I need to study? This question is commonly asked by the clinical, ecological and behavioural investigator and exposes one of many issues that are best settled before actually carrying out a study. Consultation with a statistician is worthwhile in addressing many issues of study design, but a statistician is not always readily available.

The amount of information that can be gained from a sample depends upon its absolute size and not upon its size as a proportion of the population size, Just as to decide if the wine is good we need only a sip, irrespective of the bottle size, similarly we do not need to know the exact size of the parent population, provided complete homogeneity exists, But in reality, and more so in biological sciences, such homogeneity is rarely seen. Therefore, appropriate sample size becomes pertinent for drawing valid conclusions and is among the most difficult decisions to be taken for a study.

The size of the sample would depend upon (i) the permissible error in assessment of inference i.e. accuracy and (ii) sampling error. Sampling error measures the amount of variability between sample results; the lesser it is the better. The main determinant of the sample size, therefore, is how accurate results do we used. This in turn, depends on the purpose and type of study.

5.1. INTRODUCTION

The word ‘probability’ means “reasonable likelihood of happening of an event”. In biology it is difficult to predict an outcome with absolute certainty. Probability helps us to estimate the occurrence of relative frequency of any (biological) event and is an accepted measure of uncertainty.

Mathematically, the probability ‘P’ that an event ‘E’ will occur, is expressed as:

6.1. INTRODUCTION

The word hypothesis is made up of two words Hypo + thesis = Hypothesis. ‘Hypo’ means tentative or subject to the verification and ‘Thesis’ means statement about solution of a problem.

The world meaning of the term hypothesis is a tentative statement about the solution of the problem. Hypothesis offers a solution of the problem that is to be verified empirically and based on some rationale. Hypothesis is the composition of some variables which have some specific position or role of the variables i.e. to be verified empirically. It is a proposition about the factual and conceptual elements. Hypothesis is called a leap into the dark. It is a brilliant guess about the solution of a problem. A tentative generalization or theory formulated about the character of phenomena under observation are called hypothesis. It is a statement temporarily accepted as true in the light of what is known at the time about the phenomena. It is the basis for planning and action in the research for new truth.

1.1. INTRODUCTION

Researchers interested in taking up research have initial difficultes in picking up a problem worth for investigation. At time they waste considérable amount of time in just thinking about the pros and cons of problems suggested by some ones or identified by himself/herself. It is basically due to misunderstanding about "what is research". Usual notion about research is that it must resuit in something spectacular or it must come up with a new discovery or theory. It must be pointed out that a study which brings forward new facts, or which demolishes or establishes a hypothesis or a theory or principal already in vogue, or which puts a variety of information in to order or system, or which prepares ground for further research is as valid as one which ends with a new discovery. The best research problem for researcher is one which arises from the researcher's own curiosity. The only thing is that researcher must know the tools which can handle the problems he proposed to take up. Before choosing for a problem for research one should as question to himself: is this problem really of interest to me?; Is it significant in the sense that it extends the frontiers of knowledge or fills an important gap in knowledge?; Can I handle this problem within the constraints of resources of money, time etc?; has this problem not been investigated by someone else? A good research proposai describes situation of problem, problem area, justification, methodology adopted for data collection, analysis, expected results and institution/ organisation that may use the outcome.

8.1. INTRODUCTION

The existence of Science could be in danger, if scientists did not record experiment performed, data collected and resuit obtained. Scientific writing doesn't mean to only keep records of progress and information, but to actually publish the results of studies in scientific journals. While keeping records is quite easy to do, publishing scientific papers can be really difficult, and especially for young researchers who are just starting to discover the world of scientific publications. A scientific writing is a method of communication, an attempt to tell others about some specific data that you have gathered and what you think those data mean in the context of your research. The rules of writing a scientific paper are rigid and are différent Uorr\ those that apply when we write an English theme. Scientific paper must be written clearly and concisely so that readers with backgrounds similar to yours can understand easily what you have done and how you have done it. The ultimate aim of most scientists is to publish their research findings in professional scientific reports. This includes peer-reviewed journal articles, which report original findings and contribute to the global pool of scientific knowledge. Scientists spend their time writing proposais, planning research, undertaking experiments, analysing data, tracing research, and reading related articles. Published reports and journal articles provide evidence of this dedication. Therefore, a scientific report is not simply some extra work that is done at the end of a project; it is an important historical document that provides evidence of work to the wider scientific community.

9.1. INTRODUCTION

A data are generally voluminous, so they need to be put in a compact and presentable form. This chapter deals with presentation of data precisely so that the voluminous data collected could be made usable readily and are easily comprehended. There are generally three forms of presentation of data:

Textual or Descriptive presentation

Tabular presentation

Diagrammatic presentation

Plant physiology is a sub-discipline of botany concerned with the functioning, or physiology of plants. Closely related fields include plant morphology (structure of plants), plant ecology (interactions with the environment), phytochemistry (biochemistry of plants), cell biology, genetic, biophysics and molecular biology. Fundamental processes such as photosynthesis, respiration, plant nutrition, plant hormone functions, tropism, nastic movements, photoperiodism, photo-morphogenesis, circadian rhythms, environmental stress physiology, seed germination, dormancy, stomata function and transpiration, both parts of plant water relations, are studied by plant physiologists. The field of plant physiology includes the study of all the internal activities of plants those chemical and physical processes associated with life as they occur in plants. This includes study at many levels of scale of size and time. At the smallest scale are molecular interactions of photosynthesis and internal diffusion of water, minerals, and nutrients. Major sub disciplines of plant physiology include phytochemistry (the study of the biochemistry of plants) and phytopathology (the study of disease in plants). The scope of plant physiology as a discipline may be divided into several major areas of research.

Tissue or cell samples from a living organism, different cell cultures grown in a laboratory incubator under controlled conditions, homogenates or extracts of cells and tissues, solutions of isolated and purified components (e.g. proteins, nucleic acids) can all be referred to as biological samples. As the medium of life is water, the majority of biological samples can be defined as aqueous solutions with one or more components, colloidal systems, or water-based suspensions (e.g. bacterial cells dispersed in a liquid medium). Consequently, most biochemical experiments also take place in aqueous environments. Different solids (e.g. chemical substances obtained from different companies, synthetic oligonucleotides or peptides) are also often necessary for biochemical research. In most cases, solids are dissolved in water (or sometimes in other solvents) prior to the experiments. Therefore, the methods of preparing solutions and measuring accurately the weight of the required solids will also be discussed below. Sometimes we use gases in the laboratory. These can be stored in gas cylinders (e.g. O₂), in Dewar flasks in liquid state (e.g. liquid nitrogen), or dissolved in water (e.g. HCl or NH₃). By working with gases it is very important to follow all safety instructions to avoid fire, explosions, frostbite or (in case of inhalation) asphyxia or poisoning.

Units/measures are used to specify quantities. Every unit has a well-defined standard basic value, which is used as a reference in measurements. The units used in scientific practice constitute a scientifically established system, SI (Système International). Although only SI units are official , numerous non-SI units are still widely used (calorie, Ångström, Celsius etc.). We distinguish two types of quantities with two corresponding types of SI units. The base quantities cannot be derived from other quantities. Many of these are used in biochemistry (names of units and their symbols are given in brackets) to quantify the mass (gram, g), the length (meter, m), the time (second, s), the temperature (kelvin, K) and the charge (coulomb, C). Much larger is the group of derived quantities. Of these, the various units of concentration (to characterise the abundance of materials in solutions and other mixtures), volume and energy are the ones most frequently used in biochemistry. It is important to note that the terms mass and weight are often used interchangeably as alternatives. Technically, however, they have different meanings. The mass is the total quantity of matter in an object, which comes from the mass of all of its protons and neutrons, although not simply additively. Weight is a measure of the gravitational force exerted on an object. As the mass of protons and neutrons is the unit mass, their total mass in an object (e.g. the mass of a molecule, the molar mass) is a unitless number (e.g. the molar mass of water is 18). In other words, the molar mass is a relative number that would reflect the number of protons and neutrons in an atom or molecule, if the masses of protons and neutrons were additive. We make mass measurable by expressing it in grams because this way we can handle it as weight and measure it with a balance, the device developed for this purpose. 

As homogeneity is a basic criterion, it is important to know the solubility of solutes, which is a temperature dependent property. Besides temperature, solubility is influenced by the acidity (pH) of the solvent due to the acid-base character of the solute. Bases tend to dissolve better in acidic solutions, whereas acids do in basic solutions. Therefore, one often needs to change the pH of solutions accordingly. As the most widely used concentration units (molarity, w/v% and v/v%) refer the amount of solute in a given volume of the solution, it is the volume of the complete solution that must be set to the desired (calculated) value thus, one must consider not only the solvent but the solute(s) as well. Another reason why one must add the solute(s) to an amount of solvent which is less than the final volume might be that one will need to set the pH subsequently in order to enhance solubility and/or to reach a desired pH value. The volume of acid or base solutions used for pH setting is usually not known in advance and is not negligible. If the solute was initially dissolved in the final desired volume, one would exceed this volume during pH setting (even if the volume of the solute is negligible) and, thus, the solution would not have the desired (calculated) concentration but a smaller (and mostly unknown) one. Thus, according to the correct procedure, one must take into consideration the fact that the final volume will contain the volume of the buffering component. value particularly in the case of dissolving proteins, which have a tendency to stick to the bottom of the dish, thereby making dissolution substantially slower.

A buffer is an aqueous solution consisting of a mixture of a weak acid and its conjugate base or a weak base and its conjugate acid. Its pH changes very little when a small amount of strong acid or base is added to it and thus it is used to prevent changes in the pH of a solution. Buffer solutions are used as a means of keeping pH at a nearly constant value in a wide variety of chemical applications. Many life forms thrive only in a relatively small pH range so they utilize a buffer solution to maintain a constant pH. One example of a buffer solution found in nature is blood.

Carbon assimilation or carbon fixation is the conversion of inorganic carbon (carbon dioxide) to organic compounds by living organisms. The most prominent example is photosynthesis, although chemosynthesis is another form of carbon fixation that can take place in the absence of sunlight. Organisms that grow by fixing carbon are called autotrophs. Autotrophs include photoautotrophs, which synthesize organic compounds using the energy of sunlight, and lithoautotrophs, which synthesize organic compounds using the energy of inorganic oxidation. Heterotrophs are organisms that grow using the carbon fixed by autotrophs. The organic compounds are used by heterotrophs to produce energy and to build body structures. “Fixed carbon”, “reduced carbon”, and “organic carbon” are equivalent terms for various organic compounds.

A carbohydrate is a large biological molecules, or macromolecules, consisting of carbon (C), hydrogen (H), and oxygen (O) atoms, usually with a hydrogen : oxygen atom ratio of 2:1 (as in water); in other words, with the empirical formula C_m(H₂O)_n (where m could be different from n). Some exceptions exist; for example, deoxyribose, a sugar component of DNA, has the empirical formula C₅H₁₀O₄. Carbohydrates are technically hydrates of carbon; structurally it is more accurate to view them as polyhydroxy aldehydes and ketones.

The term is most common in biochemistry, where it is a synonym of saccharide. The carbohydrates (saccharides) are divided into four chemical groups: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. In general, the monosaccharides and disaccharides, which are smaller (lower molecular weight) carbohydrates, are commonly referred to as sugars. While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose. For example, grape sugar is the monosaccharide glucose, cane sugar is the disaccharide sucrose, and milk sugar is the disaccharide lactose.

Nitrogen assimilation is the formation of organic nitrogen compounds like amino acids from inorganic nitrogen compounds present in the environment. Organisms like plants, fungi and certain bacteria that cannot fix nitrogen gas (N₂) depend on the ability to assimilate nitrate or ammonia for their needs. Other organisms, like animals, depend entirely on organic nitrogen from their food.

Plants absorb nitrogen from the soil in the form of nitrate (NO₃ ^-) and ammonia (NH₄). In aerobic soils where nitrification can occur, nitrate is usually the predominant form of available nitrogen that is absorbed. However this need not always be the case as ammonia can predominate in grasslands and in flooded, anaerobic soils like rice paddies. Plant roots themselves can affect the abundance of various forms of nitrogen by changing the pH and secreting organic compounds or oxygen. This influences microbial activities like the interconversion of various nitrogen species, the release of ammonia from organic matter in the soil and the fixation of nitrogen by non-nodule-forming bacteria.

Proteins are large biological molecules, or macromolecules, consisting of one or more chains of amino acid residues. Proteins perform a vast array of functions within living organisms, including catalysing metabolic reactions, replicating DNA, responding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in folding of the protein into a specific three-dimensional structure that determines its activity. A polypeptide is a single linear polymer chain derived from the condensation of amino acids. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in certain organisms the genetic code can include selenocysteine and, in certain archaea-pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.

Like other biological macromolecules such as pollysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signalling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals’ diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism.

Amino acids are biologically important organic compounds composed of amine (-NH₂) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known and can be classified in many ways. They can be classified according to the core structural functional groups’ locations as alpha- (?-), beta- (β), gamma- (?), or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acrylic, aromatic, containing hydroxyl or sulphur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis. Amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance in biochemistry. They are known as 2-, alpha-, or ?-amino acids (generic formula H₂NCHRCOOH in most cases where R is an organic substituent known as a “side-chain”); often the term “amino acid” is used to refer specifically to these. They include the 22 proteinogenic (“protein-building”) amino acids, which combine into peptide chains (“polypeptides”) to form the building-blocks of a vast array of proteins. These are all L-stereoisomers (“left-handed” isomers), although a few D-amino acids (“right-handed”) occur in bacterial envelopes and some antibiotics. Twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as “standard” amino acids. The other two (“non-standard” or “non-canonical”) are pyrrolysine (found in methanogenic organisms and other eukaryotes) and selenocysteine (present in many noneukaryotes as well as most eukaryotes). For example, 25 human proteins include selenocysteine (Sec) in their primary structure, and the structurally characterized enzymes (selenoenzymes) employ Sec as the catalytic moiety in their active sites. Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element. Codon–tRNA combinations not found in nature can also be used to “expand” the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids.

Lipids are a group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, phospholipids, and others. The main biological functions of lipids include storing energy, signalling, and acting as structural components of cell membrane. Lipids have applications in the cosmetic and food industries as well as in nanotechnology.

Lipids may be broadly defined as hydrophobic or amphiphilic small molecules; the amphiphilic nature of some lipids allows them to form structures such as vesicles, liposomes, or membranes in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of biochemical subunits or “building-blocks”: ketoacyl and isoperen groups. Using this approach, lipids may be divided into eight categories:fatty acids, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).

Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids called triglycerides. Lipids also encompass molecules such as fatty acids and their derivatives (including tri-, di-, monoglycerides and phospholipids), as well as other sterol containing metabolites such as chloestrol. Although humans and other mammals use various biosynthetic pathways to both break down and synthesize lipids, some essential lipids cannot be made this way and must be obtained from the diet.

Plant nutrition is the study of the chemical elements and compounds that are necessary for plant growth, and also of their external supply and internal metabolism. The criteria for an element to be essential for plant growth:

In its absence the plant is unable to complete a normal life cycle; or

That the element is part of some essential plant constituent or metabolite.

Biological pigments, also known simply as pigments or biochromes are substances produced by living organisms that have a colour resulting from selective colour absorption. Biological pigments include plant pigments and flower pigments. Many biological structures, such as skin, eyes, fur and hair contain pigments such as melanin in specialized cells called chromatophores.

Pigment colour differs from structural colour in that it is the same for all viewing angles, whereas structural colour is the result of selective reflection or iridescence, usually because of multilayer structures. For example, butterfly wings typically contain structural colour, although many butterflies have cells that contain pigment as well.

In organic chemistry, phenols, sometimes called phenolics, are a class of chemical compounds consisting of a hydroxyl group (—OH) bonded directly to an aromatic hydrocarbon group. The simplest of the class is phenol, which is also called carbolic acid C₆H₅OH. Phenolic compounds are classified as simple phenols or polyphenols based on the number of phenol units in the molecule.

Plant secondary metabolism produces products that aid in the growth and development of plants but are not required for the plant to survive. Secondary metabolism facilitates the primary metabolism in plants. This primary metabolism consists of chemical reactions that allow the plant to live. In order for the plants to stay healthy, secondary metabolism plays a pinnacle role in keeping all the of plants’systems working properly. A common role of secondary metabolites in plants is defense mechanisms. They are used to fight off herbivores, pests, and pathogens. Although researchers know that this trait is common in many plants it is still difficult to determine the precise role each secondary metabolite. Secondary metabolites are used in anti-feeding activity, toxicity or acting as precursors to physical defense systems.

Plant hormones (also known as phytohormones) are chemicals that regulate plant growth, which are termed ‘plant growth substances’.

Plant hormones are signal molecules produced within the plant, and occur in extremely low concentrations. Hormones regulate cellular processes in targeted cells locally and, when moved to other locations, in other locations of the plant. Hormones also determine the formation of flower, stems, leaves, the shedding of leaves, and the development and ripening of fruit. Plants, unlike animals, lack glands that produce and secrete hormones. Instead, each cell is capable of producing hormones. Plant hormones shape the plant, affecting seed growth, time of flowering, the sex of flowers, senescence of leaves, and fruits. They affect which tissues grow upward and which grow downward, leaf formation and stem growth, fruit development and ripening, plant longevity, and even plant death. Hormones are vital to plant growth, and, lacking them, plants would be mostly a mass of undifferentiated cells. So they are also known as growth factors or growth hormones..

Phytohormones are found not only in higher plants, but in algae too, showing similar functions, and in microorganisms, like fungi and bacteria, but, in this case, they play no hormonal or other immediate physiological role in the producing organism and can, thus, be regarded as secondary metabolites.

Nucleic acids are polymeric macromolecules, or large biological molecules, essential for all known forms of life. Nucleic acids, which include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), are made from monomers known as nucleotides. Each nucleotide has three components: a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is deoxiribose, the polymer is DNA. If the sugar is ribose, the polymer is RNA. Together with proteins, nucleic acids are the most important biological macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information—in other words, information is conveyed through the nucleic acid sequence, or the order of nucleotides within a DNA or RNA molecule. Strings of nucleotides strung together in a specific sequence are the mechanism for storing and transmitting hereditary, or genetic, information via protein synthesis.

The term nucleic acid is the overall name for DNA and RNA, members of a family of biopolymers, and is synonymous with polynucleotide. Nucleic acids were named for their initial discovery within the nucleus, and for the presence of phosphate groups (related to phosphoric acid). Although first discovered within the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life forms as well as some nonliving entities, including within bacteria, archaea, mitochondria, chloroplasts, viruses and viroids. All living cells contain both DNA and RNA (except some cells such as mature red blood cells), while viruses contain either DNA or RNA, but usually not both. The basic component of biological nucleic acids is the nucleotide, each of which contains a pentose sugar (ribose or deoxyribose), a phosphate group, and a nucleobase. Nucleic acids are also generated within the laboratory, through the use of enzymes (DNA and RNA polymerases) and by solid-phase chemical synthesis. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, for example peptide nucleic acids.

A vitamin is an organic compound required by an organism as a vital nutrient in limited amounts. An organic chemical compound (or related set of compounds) is called a vitamin when it cannot be synthesised in sufficient quantities by an organism, and must be obtained from the diet. Thus, the term is conditional both on the circumstances and on the particular organism. For example, ascorbic acid (vitamin C) is a vitamin for humans, but not for most other animals. Supplementation is important for the treatment of certain health problems but there is little evidence of benefit when used by those who are otherwise healthy.

By convention, the term vitamin includes neither other essential nutrients, such as dietary minerals, essential fatty acids, or essential amino acids (which are needed in larger amounts than vitamins) nor the large number of other nutrients that promote health but are otherwise required less often. Thirteen vitamins are universally recognized at present. Vitamins are classified by their biological and chemical activity, not their structure. Thus, each “vitamin” refers to a number of vitamer compounds that all show the biological activity associated with a particular vitamin. Such a set of chemicals is grouped under an alphabetized vitamin “generic descriptor” title, such as “vitamin A”, which includes the compounds retinal, retinol, and four known carotenoids. Vitamers by definition are convertible to the active form of the vitamin in the body, and are sometimes inter-convertible to one another, as well.

Vitamins have diverse biochemical functions. Some, such as vitamin D, have hormone-like functions as regulators of mineral metabolism, or regulators of cell and tissue growth and differentiation (such as some forms of vitamin A). Others function as antioxidants (e.g., vitamin E and sometimes vitamin C).

WATER IS VERY SPECIAL IN BIOLOGY

Most abundant chemical of life

Special properties:

Cells Contain 4 Major Types of Giant Molecules (Macromolecules, Polymers)

Carbohydrates

Lipids

Proteins

Nucleic Acids

BIOLOGICAL POLYMERS ARE MADE FROM ABOUT 60 SMALL BUILDING BLOCKS

Cells contain thousands of types of giant molecules (macromolecules, polymers)

Polymers are macromolecules made from a single building block molecule Most of the macromolecules are made from about 60 types of small building block molecules

Most macromolecules are linear: building blocks linked head to tail- a few have branches (some polysaccharides)

This is what you would get if you heated cells in hydrochloric acid overnight at 110 degrees C:

ALL MATTER IS IN MOTION

Everything moves:

In the atom electrons rotate around the nucleus

In gases, liquids and even solids molecules move away from other molecules

An accumulation of matter (i.e., a baseball) can move as a unit

The average velocity of movement is the distance travelled divided by the time

Bodies in motion have energy; the faster the velocity the more energy

ENZYMES

Enzymes are the heart of Biochemistry

Protein based catalysts.

Enormously effective catalysts: typically enhance rates by 10⁶ to 10¹² fold.

Operate under mild conditions: 0 - 100 °C (or perhaps even 300+ °C for some bacteria in deep ocean), 20 - 40 °C for most organisms; and low pressures (atmospheric).

Very specific: Generally catalyze reaction for a very restricted group of molecules, sometimes for a single naturally occurring molecule of a single chirality.

There are other groups that contribute to the reactivity of enzymes beside amino acid residues.

These groups are called cofactors - chemicals required by apoenzymes (inactive) to become holoenzymes (active).

There are two types of cofactors:

1. Essential ions - metal ions -inorganic
2. Coenzymes - organic molecules that act as group-transfer reagents (accept or donate groups)- can also be H⁺ and/or e^-

Both provide reactive groups not found on amino acids side chains.

Coenzymes can be either cosubstrates (loosely bound to enzyme; is altered, then regenerated) or prosthetic groups (tightly bound to enzyme).

Coenzymes can be classified by their source: