eChapters

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:

ALL LIVING ORGANISMS ARE MADE UP OF UNITS CALLED CELLS

All living creatures are made from 1 or more cells

All cells are produced from previously existing cells (no spontaneous generation)

All cells appear to be descended from the first cell which existed about 4 billion years ago

For a species to exist its reproductive cells must be potentially immortal (no aging)

Our bodies start from a single cell and contain about 100,000,000,000,000 (10^14) cells at maturity

I. WALL COMPONENTS – CHEMISTRY

The main ingredient in cell walls are polysaccharides (or complex carbohydrates or complex sugars) which are built from monosaccharides (or simple sugars). Eleven sugars are common in these polysaccharides including like glucose and galactose. Carbohydrates are good building blocks because they can produce a nearly infinite variety of structures. There are a variety of other components in the wall including protein, and lignin. Let’s look at these wall components in more detail:

A. Cellulose: β1,4-glucan (structure provided in class). Made of as many as 25,000 individual glucose molecules. Every other molecule (called residues) is “upside down”. Cellobiose (glucose-glucose disaccharide) is the basic building block. Cellulose readily forms hydrogen bonds with itself (intra-molecular H-bonds) and with other cellulose chains (inter-molecular H-bonds). A cellulose chain will form hydrogen bonds with about 36 other chains to yield a microfibril. This is somewhat analogous to the formation of a thick rope from thin fibers. Microfibrils are 5-12 nm wide and give the wall strength - they have a tensile strength equivalent to steel. Some regions of the microfibrils are highly crystalline while others are more “amorphous”.

COMMON FEATURES OF BIOLOGICAL MEMBRANES

Membranes are sheetlike, just a few molecules thick and form closed boundaries between cell compartments.

Membranes contain lipids and proteins, with small amounts of carbohydrayes linked to the lipids and proteins.

Lipids in membranes are small with hydrophobic and hydrophilic portions. Lipid bilayers provide a barrier to the diffusion of polar molecules.

Characteristic functions of membranes are mediated by specific proteins, serving as pumps, channels, receptors, energy transducers and enzymes.

Membrane components associate through noncovalent interactions.

Membranes are asymmetrical, with two sides of the membrane differing from each other.

Lipid and protein molecules often diffuse rapidly in the plane of the membrane.

Central transport of ions and molecules into and out of the cell.

Generate proton gradients for ATP production by oxidative phosphorylation.

Receptors bind extracellular signals and transduce the signal to cell interior.

ALL MOLECULES MOVE CONTINUOUSLY BY SIMPLE DIFFUSION

Heat energy causes molecules to move randomly (sometimes called Brownian motion)

If the concentration of molecules is different in 2 regions (this produces a concentration gradient), diffusion will cause molecules to move from a region of high concentration to one of low concentration

The higher the concentration gradient the more rapid the net diffusion

Diffusion evens out the concentrations so they are equal everywhere (maximum entropy)

If 2 different substances have the same concentration gradient, usually one will move faster than the other

Differences in speed between molecules with the same concentration gradient are given in terms of diffusion constants

A substance with a high diffusion constant moves faster than one with a low diffusion constant

In general, large molecules move slower than small molecules

Diffusion across a membrane is called permeability, and membrane diffusion constants are called permeability constants

Metabolism - sum total of all chemical reactions in living cells

Catabolic reactions - degrade macromolecules and other molecules to release energy

Anabolic reactions - used to synthesize macromolecules for cell growth, repair, and reproduction

Can divide metabolism into 4 groups: carbohydrates, lipids, amino acids, nucleotides.

MOST OF THE ENERGY FOR LIFE COMES FROM SUNLIGHT

Total rate of energy delivery from sun to earth (at the top of the atmosphere) = 175,000 terrawatts

Terrawatt = 10^12 watts

Rate of energy capture by plants from the sun = net primary productivity (NPP) = 100 terrawatts

Only ~ 0.06% of sunlight is captured

Captured in chemical bonds, especially in sugar

Small amounts of energy are available to specialized microorganisms from chemical reactions not linked to sunlight

It is estimated that 99% of the energy used by living cells comes from the sun

Incorporation of sunlight into chemical bonds occurs through the process of photosynthesis

“Invented” by cyanobacteria about 2 billion years ago

NEW CELLS ARE PRODUCED BY DIVISION OF PREVIOUSLY EXISTING CELLS

All cells come from previously existing cells

To make a new cell identical to itself a cell must perform 4 tasks:

It must grow and make additional copies of all its organelles, enzymes, etc..

It must duplicate its DNA

It must accurately separate the DNA into 2 units, so that each cell gets a full set

It must divide into 2 cells (cytokinesis)

SEX IS VERY COSTLY

Large amounts of energy required to find a mate and do the mating: specialized structures and behavior required

Intimate contact provides route for infection by parasites (AIDS, syphillis, etc.)

Genetic costs: in sex you pass on only half your genes to your children

Males are an expensive luxury- in most species they contribute little to rearing offspring

But There are Some Advantages

More genetic diversity: more potential for survival of species when environmental conditions change

Shuffling of genes in meiosis (random separation of homologous chromosomes)

Crossing-over in meiosis (see below)

Fertilization (genes from 2 individuals brought together)

A fair number of practical breeding experiments were done in ancient times

People knew there was a connection between sex and reproduction

The idea had developed that “like begets like”

By selecting certain plants and animals and breeding them many domestic varieties of plants and animals had been developed

Example: corn was developed from a wild grass in Mexico and Central America, probably about 5000 years ago

149 of the top 150 plant crops were domesticated by primitive man

MENDEL’S RULES OF GENETICS DO NOT ALWAYS WORK

Mendel’s rules:

Segregation of alleles

Independent assortment of genes for different characters

Hold for characters:

Which have dominant & recessive traits

Determined by single genes

Genes are on separate chromosomes

Different types of chromosomes, or

Different homologues of same type of chromosome

These conditions are not always met, so there are many complications

Chromosomes are giant molecules of DNA

Found in nucleus: never leave except in cell division

Carry hereditary units, genes

Two homologous copies in diplod cells

Unwind when replicating or making RNA

Wind up (condense) in cell division

Attach to spindle and separate in meiosis & mitosis

Crossing over in prophase of 1st meiotic division

Chromosomes are equally distributed in mitosis, meiosis

Gametes have half the number of chromosomes as body cells

Sister chromatids are observed to split apart longitudinally in anaphase

UNTIL THE 1940S BIOLOGISTS ARGUED ABOUT WHETHER DNA OR PROTEIN WAS THE MOLECULE OF HEREDITY

Nuclei observed to divide when cells reproduced themselves

Large amounts of both DNA & protein in the nucleus

Many though protein was most likely molecule of heredity

Proteins made of 20 different amino acids- could have more variety than DNA (made of only 4 different bases)