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CONTENTS
1. MOLECULES AND THEIR INTERACTION RELAVENT TO BIOLOGY
A. Structure of atoms, molecules and chemical bonds. B. Composition, structure and function of biomolecules (carbohydrates, lipids, proteins, nucleic acids and vitamins). C. Stablizing interactions (Van der Waals, electrostatic, hydrogen bonding, hydrophobic interaction, etc.). D. Principles of biophysical chemistry (pH, buffer, reaction kinetics, thermodynamics, colligative properties). E. Bioenergetics, glycolysis, oxidative phosphorylation, coupled reaction, group transfer, biological energy transducers. F. Principles of catalysis, enzymes and enzyme kinetics, enzyme regulation, mechanism of enzyme catalysis, isozymes. G. Conformation of proteins (Ramachandran plot, secondary, tertiary and quaternary structure; domains; motif and folds). H. Conformation of nucleic acids (A‐, B‐, Z‐,DNA), t‐RNA, micro‐RNA). I. Stability of protein and nucleic acid structures. J. Metabolism of carbohydrates, lipids, amino acids, nucleotides and vitamins.
2. CELLULAR ORGANIZATION
A. Membrane structure and function: Structure of model membrane, lipid bilayer and membrane protein diffusion, osmosis, ion channels, active transport, ion pumps, mechanism of sorting and regulation of intracellular transport, electrical properties of membranes. B. Structural organization and function of intracellular organelles: Cell wall, nucleus, mitochondria, Golgi bodies, lysosomes, endoplasmic reticulum, peroxisomes, plastids, vacuoles, chloroplast, structure & function of cytoskeleton and its role in motility. C. Organization of genes and chromosomes: Operon, interrupted genes, gene families, structure of chromatin and chromosomes, unique and repetitive DNA, heterochromatin, euchromatin, transposons. D. Cell division and cell cycle: Mitosis and meiosis, their regulation, steps in cell cycle, and control of cell cycle. E. Microbial Physiology: Growth, yield and characteristics, strategies of cell division, stress response.
3. FUNDAMENTAL PROCESSES
A. DNA replication, repair and recombination: Unit of replication, enzymes involved, replication origin and replication fork, fidelity of replication, extrachromosomal replicons, DNA damage and repair mechanisms. B. RNA synthesis and processing: Transcription factors and machinery, formation of initiation complex, transcription activators and repressors, RNA polymerases, capping, elongation and termination, RNA processing, RNA editing, splicing, polyadenylation, structure and function of different types of RNA, RNA transport. C. Protein synthesis and processing: Ribosome, formation of initiation complex, initiation factors and their regulation, elongation and elongation factors, termination, genetic code, aminoacylation of tRNA, tRNA‐identity, aminoacyl tRNA synthetase, translational proof‐reading, translational inhibitors, post‐ translational modification of proteins. D. Control of gene expression at transcription and translation level: Regulation of phages, viruses, prokaryotic and eukaryotic gene expression, role of chromatin in regulating gene expression and gene silencing.
4. CELL COMMUNICATION AND CELL SIGNALING
A. Host parasite interaction: Recognition and entry processes of different pathogens like bacteria, viruses into animal and plant host cells, alteration of host cell behavior by pathogens, virus‐induced cell transformation, pathogen‐induced diseases in animals and plants, cell‐cell fusion in both normal and abnormal cells. B. Cell signaling: Hormones and their receptors, cell surface receptor, signaling through G‐protein coupled receptors, signal transduction pathways, second messengers, regulation of signaling pathways, bacterial and plant two‐component signaling systems, bacterial chemotaxis and quorum sensing. C. Cellular communication: Regulation of hematopoiesis, general principles of cell communication, cell adhesion and roles of different adhesion molecules, gap junctions, extracellular matrix, integrins, neurotransmission and its regulation. D. Cancer: Genetic rearrangements in progenitor cells, oncogenes, tumor suppressor genes, cancer and the cell cycle, virus‐ induced cancer, metastasis, interaction of cancer cells with normal cells, apoptosis, therapeutic interventions of uncontrolled cell growth. E. Innate and adaptive immune system: Cells and molecules involved in innate and adaptive immunity, antigens, antigenicity and immunogenicity. B and T cell epitopes, structure and function of antibody molecules, generation of antibody diversity, monoclonal antibodies, antibody engineering, antigen‐antibody interactions, MHC molecules, antigen processing and presentation, activation and differentiation of B and T cells, B and T cell receptors, humoral and cell‐mediated immune responses, primary and secondary immune modulation, the complement system, Toll‐like receptors, cell‐mediated effector functions, inflammation, hypersensitivity and autoimmunity, immune response during bacterial (tuberculosis), parasitic (malaria) and viral (HIV) infections, congenital and acquired immunodeficiencies, vaccines.
5. DEVELOPMENTAL BIOLOGY
A. Basic concepts of development: Potency, commitment, specification, induction, competence, determination and differentiation; morphogenetic gradients; cell fate and cell lineages; stem cells; genomic equivalence and the cytoplasmic determinants; imprinting; mutants and transgenics in analysis of development. B. Gametogenesis, fertilization and early development: Production of gametes, cell surface molecules in sperm‐egg recognition in animals; embryo sac development and double fertilization in plants; zygote formation, cleavage, blastula formation, embryonic fields, gastrulation and formation of germ layers in animals; embryogenesis, establishment of symmetry in plants; seed formation and germination. C. Morphogenesis and organogenesis in animals: Cell aggregation and differentiation in Dictyostelium; axes and pattern formation in Drosophila, amphibia and chick; organogenesis – vulva formation in Caenorhabditis elegans; eye lens induction, limb development and regeneration in vertebrates; differentiation of neurons, post embryonic development‐ larval formation, metamorphosis; environmental regulation of normal development; sex determination. D. Morphogenesis and organogenesis in plants: Organization of shoot and root apical meristem; shoot and root development; leaf development and phyllotaxy; transition to flowering, floral meristems and floral development in Arabidopsis and Antirrhinum. E. Programmed cell death, aging and senescence.
6. SYSTEM PHYSIOLOGY PLANT
A. Photosynthesis: Light harvesting complexes; mechanisms of electron transport; photoprotective mechanisms; CO 2
fixation‐
C 3
, C
4
and CAM pathways. B. Respiration and photorespiration: Citric acid cycle; plant mitochondrial electron transport and ATP synthesis; alternate oxidase; photorespiratory pathway. C. Nitrogen metabolism: Nitrate and ammonium assimilation; amino acid biosynthesis. D. Plant hormones: Biosynthesis, storage, breakdown and transport; physiological effects and mechanisms of action. E. Sensory photobiology: Structure, function and mechanisms of action of phytochromes, cryptochromes and phototropins; stomatal movement; photoperiodism and biological clocks. F. Solute transport and photoassimilate translocation: Uptake, transport and translocation of water, ions, solutes and macromolecules from soil, through cells, across membranes, through xylem and phloem; transpiration; mechanisms of loading and unloading of photoassimilates. G. Secondary metabolites ‐ Biosynthesis of terpenes, phenols and nitrogenous compounds and their roles. H. Stress physiology: Responses of plants to biotic (pathogen and insects) and abiotic (water, temperature and salt) stresses; mechanisms of resistance to biotic stress and tolerance to abiotic stress
7. SYSTEM PHYSIOLOGY ANIMAL
A. Blood and circulation: Blood corpuscles, haemopoiesis and formed elements, plasma function, blood volume, blood volume regulation, blood groups, haemoglobin, immunity, haemostasis. B. Cardiovascular System: Comparative anatomy of heart structure, myogenic heart, specialized tissue, ECG – its principle and significance, cardiac cycle, heart as a pump, blood pressure, neural and chemical regulation of all above. C. Respiratory system: Comparison of respiration in different species, anatomical considerations, transport of gases, exchange of gases, waste elimination, neural and chemical regulation of respiration. D. Nervous system: Neurons, action potential, gross neuroanatomy of the brain and spinal cord, central and peripheral nervous system, neural control of muscle tone and posture. E. Sense organs: Vision, hearing and tactile response. F. Excretory system: Comparative physiology of excretion, kidney, urine formation, urine concentration, waste elimination, micturition, regulation of water balance, blood volume, blood pressure, electrolyte balance, acid‐base balance. G. Thermoregulation: Comfort zone, body temperature – physical, chemical, neural regulation, acclimatization. H. Stress and adaptation I. Digestive system: Digestion, absorption, energy balance, BMR. J. Endocrinology and reproduction: Endocrine glands, basic mechanism of hormone action, hormones and diseases; reproductive processes, neuroendocrine regulation.
8. INHERITANCE BIOLOGY A. Mendelian principles: Dominance, segregation, independent assortment, deviation from Mendelian inheritance. B. Concept of gene: Allele, multiple alleles, pseudoallele, complementation tests. C. Extensions of Mendelian principles: Codominance, incomplete dominance, gene interactions, pleiotropy, genomic imprinting, penetrance and expressivity, phenocopy, linkage and crossing over, sex linkage, sex limited and sex influenced characters. D. Gene mapping methods: Linkage maps, tetrad analysis, mapping with molecular markers, mapping by using somatic cell hybrids, development of mapping population in plants. E. Extra chromosomal inheritance: Inheritance of mitochondrial and chloroplast genes, maternal inheritance. F. Microbial genetics: Methods of genetic transfers – transformation, conjugation, transduction and sex‐duction, mapping genes by interrupted mating, fine structure analysis of genes. G. Human genetics: Pedigree analysis, lod score for linkage testing, karyotypes, genetic disorders. H. Quantitative genetics: Polygenic inheritance, heritability and its measurements, QTL mapping. I. Mutation: Types, causes and detection, mutant types – lethal, conditional, biochemical, loss of function, gain of function, germinal verses somatic mutants, insertional mutagenesis. J. Structural and numerical alterations of chromosomes: Deletion, duplication, inversion, translocation, ploidy and their genetic implications. K. Recombination: Homologous and non‐homologous recombination, including transposition, site‐specific recombination.
13. METHODS IN BIOLOGY
A. Molecular biology and recombinant DNA methods: Isolation and purification of RNA , DNA (genomic and plasmid) and proteins, different separation methods; analysis of RNA, DNA and proteins by one and two dimensional gel electrophoresis, isoelectric focusing gels; molecular cloning of DNA or RNA fragments in bacterial and eukaryotic systems; expression of recombinant proteins using bacterial, animal and plant vectors; isolation of specific nucleic acid sequences; generation of genomic and cDNA libraries in plasmid, phage, cosmid, BAC and YAC vectors; in vitro mutagenesis and deletion techniques, gene knock out in bacterial and eukaryotic organisms; protein sequencing methods, detection of post‐translation modification of proteins; DNA sequencing methods, strategies for genome sequencing; methods for analysis of gene expression at RNA and protein level, large scale expression analysis, such as micro array based techniques; isolation, separation and analysis of carbohydrate and lipid molecules; RFLP, RAPD and AFLP techniques B. Histochemical and immunotechniques: Antibody generation, detection of molecules using ELISA, RIA, western blot, immunoprecipitation, flow cytometry and immunofluorescence microscopy, detection of molecules in living cells, in situ localization by techniques such as FISH and GISH. C. Biophysical methods: Analysis of biomolecules using UV/visible, fluorescence, circular dichroism, NMR and ESR spectroscopy, structure determination using X‐ray diffraction and NMR; analysis using light scattering, different types of mass spectrometry and surface plasma resonance methods. D. Statistical Methods: Measures of central tendency and dispersal; probability distributions (Binomial, Poisson and normal); sampling distribution; difference between parametric and non‐parametric statistics; confidence interval; errors; levels of significance; regression and correlation; t‐test; analysis of variance; X
2 test;; basic introduction to Muetrovariate statistics, etc. E. Radiolabeling techniques: Properties of different types of radioisotopes normally used in biology, their detection and measurement; incorporation of radioisotopes in biological tissues and cells, molecular imaging of radioactive material, safety guidelines. F. Microscopic techniques: Visulization of cells and subcellular components by light microscopy, resolving powers of different microscopes, microscopy of living cells, scanning and transmission microscopes, different fixation and staining techniques for EM, freeze‐etch and freeze‐fracture methods for EM, image processing methods in microscopy. G. Electrophysiological methods: Single neuron recording, patch‐clamp recording, ECG, Brain activity recording, lesion and stimulation of brain, pharmacological testing, PET, MRI, fMRI, CAT. H. Methods in field biology: Methods of estimating population density of animals and plants, ranging patterns through direct, indirect and remote observations, sampling methods in the study of behavior, habitat characterization‐ground and remote sensing methods. I. Computational methods: Nucleic acid and protein sequence databases; data mining methods for sequence analysis, web‐ based tools for sequence searches, motif analysis and presentation.
A1. Structure of Atoms, Molecules
- Elements consist of only one kind of atom and cannot be decomposed into simpler substances. Our planet is made up of some 90 elements. (Tiny amounts — sometimes only a few atoms — of additional elements have been made in nuclear physics laboratories, but they play no role in our story). Of these 90, only 25 or so are used to build living things.
- The table shows the 11 most prevalent elements in the lithosphere (the earth's crust) and in the human body.
- Living matter uses only a fraction of the elements available to it but, as the table shows, the relative proportions of those it does acquire from its surroundings are quite different from the proportions in the environment.
So, the composition of living things is not simply a reflection of the elements available to them
For example, hydrogen, carbon, and nitrogen together
represent less than 1% of the atoms found in the earth's crust but some 74% of the atoms in living matter. One of the properties of life is to take up certain elements that are scarce in the nonliving world and concentrate them within living cells.
Some sea animals accumulate elements like vanadium and iodine within their cells to concentrations a thousand or more times as great as in the surrounding sea water. It has even been proposed that uranium be "mined" from the sea by extracting it from certain algae that can take up uranium from sea water and concentrate it within their cells.
- There is still some uncertainty about the exact number of elements required by living things. Some elements, e.g., selenium and aluminum, are found in tiny amounts within living things, but whether they are playing an essential role (selenium is) or are simply an accidental acquisition (aluminum probably) is sometimes difficult to determine. 5. Atoms: Each element is made up of one kind of atom. We can define an atom as the smallest part of an element that
can enter into combination with other elements. Each atom consists of a small, dense, positively‐charged nucleus surrounded by much lighter, negatively‐charged electrons.
- The nucleus of the simplest atom, the hydrogen atom (H), consists of a single positively‐charged proton. Because of its single proton, the atom of hydrogen is assigned an atomic number of 1 and a single electron.
- The charge of the electron is the same magnitude as that of the proton, so the atom as a whole is electrically neutral. Its proton accounts for almost all the weight of the atom.
- The nucleus of the atom of the element helium (He) has two protons (hence helium has an atomic number of 2) and two neutrons. Neutrons have the same weight as protons but no electrical charge. The helium atom has two electrons so that, once again, the atom as a whole is neutral.
- The structure of each of the other kinds of atoms follows the same plan. From Lithium (At. No. = 3) to uranium (At. No. = 92), the atoms of each element can be listed in order of increasing atomic number. There are no gaps in the list. Each element has a unique atomic number and its atoms have one more proton and one more electron than the atoms of the element that precedes it in the list.
Electrons
- Electrons are confined to relatively discrete regions around the nucleus. The two electrons of helium, for example, are confined to a spherical zone surrounding the nucleus called the K shell or K energy level.
- Lithium (At. No. = 3) has three electrons, two in the K shell and one located farther from the nucleus in the L shell. Being farther away from the opposite (+) charges of the nucleus, this third electron is held less tightly.
- Each of the following elements, in order of increasing atomic number, adds one more electron to the L shell until we reach neon (At. No. = 10) which has eight electrons in the L shell.
- Sodium places its eleventh electron in a still higher energy level, the M shell.
- From sodium to argon, this shell is gradually filled with electrons until, once again, a maximum of eight is reached. Note that after the K shell with its maximum of two electrons, the maximum number of electrons in any other outermost shell is eight. As we shall see, the chemical properties of each element are strongly influenced by the number of electrons in its outermost energy level (shell).
- This table shows the electronic structure of the atoms of elements 1 – 36 with those that have been demonstrated to be used by living things. Four elements of still higher atomic numbers that have been shown to be used by living things are also included.
- The electronic structure of an atom plays the major role in its chemistry. The pattern of electrons in an atom — especially those in the outermost shell — determines the valence of the atom; that is, the ratios in which it interacts with other atoms, and to a large degree, the electronegativity of the atom; that is, the strength with which it attracts other electrons.
- Elements with the same number of electrons in their outermost shell show similar chemical properties.
Elemental composition of the lithosphere and the human body. Each number represents the percent of the total number of atoms present. For example, 47 of every 100 atoms found in a representative sample of the lithosphere are oxygen while there are only 19 atoms of carbon in every 10,000 atoms of lithosphere. Composition of the Lithosphere
Composition of the Human Body Oxygen 47 Hydrogen 63 Silicon 28 Oxygen 25. Aluminum 7.9 Carbon 9.
Iron 4.5 Nitrogen 1. Calcium 3.5 Calcium 0. Sodium 2.5 Phosphorus 0. Potassium 2.5 Chlorine 0. Magnesium 2.2 Potassium 0. Titanium 0.46 Sulfur 0. Hydrogen 0.22 Sodium 0. Carbon 0.19 Magnesium 0. All others <0.1 All others <0.
- Atomic weights are expressed in terms of a standard atom: the isotope of carbon that has 6 protons and 6 neutrons in its nucleus. This atom is designated carbon‐ or 12C. It is arbitrarily assigned an atomic weight of 12 daltons (named after John Dalton, the pioneer in the study of atomic weights). Thus a dalton is 1/12 the weight of an atom of 12C. Both protons and neutrons have weights very close to 1 dalton each. Carbon‐12 is the commonest isotope of carbon. Carbon‐13 (13C) with 6 protons and 7 neutrons, and carbon‐14 (14C) with 6 protons and 8 neutrons are found in much smaller quantities. 3. Isotopes as "tracers": One can prepare, for example, a carbon compound used by living things that has many of its normal 12 C atoms replaced by 14 C atoms. Carbon‐14 happens
to be radioactive. By tracing the fate of radioactivity within the organism, one can learn the normal pathway of this carbon compound in that organism. Thus 14C serves as an isotopic "label" or "tracer".
- The basis of this technique is that the weight of the nucleus of an atom has little or no effect on the chemical properties of that atom. The chemistry of an element and the atoms of which it is made — whatever their atomic weight — is a function of the atomic number of that element. As long as the atom had 6 protons, it is an atom of carbon irrespective of the number of neutrons. Thus while 6 protons and 8 neutrons produce an isotope of carbon, 14 C, 7 protons and 7 neutrons produce a totally‐different element, nitrogen‐14.
A2. CHEMICAL BONDS
- All interactions between atoms are electrical attractions between charges.
- Ionic and covalent bonds hold atoms together to form molecules
- Weak bonds (hydrogen, van der Waals and other types) hold molecules together 1. Ionic bonds: Compounds with ionic bonds split into ions in water. Ions conduct electricity. Gives specialized cells (nerve, muscle) excitable properties. Suppose Na gives one of its electrons to Cl; the Na now has a (+) charge and the Cl will have a (‐) charge
These charged atoms are referred to as
ions, and since they have opposite charges they attract each other and form a chemical bond (they form NaCl, common table salt)
Positively charged ions = cations (i.e., Na +)
Negatively charged ions = anions (i.e., Cl ‐^ )
2. Covalent bonds: Each atom donates 1 or more electrons to the bond. The bonding electrons spend most of their time between the 2 atoms, attracting both nuclei and pulling them together. If each atom donates 2 electrons to a bond a double bond is formed
double bonds are stronger and more rigid
than single bonds A triple bond is formed when each atom donates 3 electrons to the bond. This type of bond holds together the long chains of macromolecules. These molecules do not split apart in water.
3. Hydrogen bonds: Occur when a hydrogen ion is sandwiched between 2 atoms, usually nitrogen and oxygen. It is much weaker (about 25 times) than covalent or ionic bonds and mainly occur between molecular groups with permanent dipoles.
In Water hydrogen bonds makes water molecules stick together. It is responsible for many of the strange properties of water such as cohesion, high boiling point.
Hydrogen bonds cause protein chains to spiral and bend, giving unique shapes. In DNA they hold together the 2 chains to form the double helix. Allow chains to "unzip" for replication and transcription.
4. Van der Waals & other weak bonds: Weak forces that can bond like atoms together. They are specially important between chains of carbon atoms. They are although weak, numerous bonds between the chains can add up to produce significant cohesion
Such bonds determine physical state of compounds: gas, liquid or solid and occur when one atom induces a temporary dipole in another atom. These are important in holding like molecules together. Often determine the solid, liquid or gas state of a compound. Saturated fats are solid at room temperature because the have more van der Waals attractions than unsaturated fats, which are liquid.
B1. Composition, Structure and function of Carbohydrates
Carbohydrates are mainly compounds of carbon, hydrogen and oxygen. Carbohydrates are so called because in most of them, the proportion of hydrogen and oxygen is the same as in water (H 2 O) i.e., 2:1. Their general formula is C X H 2X O X. These are also knows as saccharides (compounds containing sugar). Carbohydrates are produced by green plants during photosynthesis. These constitute about 80% of the dry weight of plants. Carbohydrates are divided into 3 main classes – monosaccharides , derived monosaccharides and oligosaccharides.
1. Monosaccharides
- These have single saccharide units which cannot be hydrolysed further into still smaller carbohydrates; have general formula C n( H 2 O) n. These are composed of 3‐7 carbon atoms, and are classified according to the number of C atoms as trioses (3C), tetroses (4C), pentoses (5C), hexoses (6C) and heptoses (7C). Of these, pentoses and hexoses are most common. Monosaccharides are important as energy source and as building blocks for the synthesis of large molecules.
- All monosaccharides are either polyhyroxy aldoses or ketoses. The two simplest monosaccharides are trioses e.g., glyceraldehydes and dilhydroxyacetone.
- Tetroses (e.g. erythrose) are quite rare. Erythrose takes part in the synthesis of lignin and anthocyanin pigments.
- Ribose, ribulose, xylulose and arabinoses are pentoses. Xyluloses and arabinoses polymerise to form xylans and arabans which are cell wall materials.
- Glucose, fructose, mannose, galactose are hexoses. These are white, sweet‐tasting, crystalline and extremely, soluble in water.
- Glucose is the universal sugar. It is also known as dextrose or grape sugar or corn sugar.
- Fructose is the most common form of sugar in fruit. It is also known as levulose. It is the sweetest among naturally occurring sugars. - Monosaccharides have ‘free’ aldehyde or ketone group which can reduce Cu ++^ to Cu +. Hence, these are also called reducing sugars. 2. Derived monosaccharides - Deoxy sugar – Loss of oxygen atom from ribose yields deoxyribose, a constituent of DNA. - Amino sugar – Monosaccharides having an amino group e.g., glucosamine, galactosamine. - Sugar acid – e.g., Ascorbic acid, glucuronic acid, galacturonic acid. - Sugar alcohol – e.g. glycerol and mannitol (present in brown algae). 3. Oligosaccharides : The sugars with limited numbers (2‐ 10) of monosaccharides are called oligosaccharides. These include trisaccharides, tetra saccharides, hexasaccharides, heptasaccharides etc. - Disaccharides : These are formed by condensation reactions between two monosaccharides (usually hexoses). The bond formed between two monosaccharides is called a glycosidic bond. It normally forms between C‐atoms 1 and 4 of neighbouring units (1,4 bond). Once linked, the monosaccharide units are called residues. (a) Maltose (glucose + glucose), lactose (glucose + galactose), sucrose (glucose + fructose) are most common disaccharides. Sucrose is most abundant in plants and is known as cane sugar or table sugar. It is the sugar we buy from market. (b) On hydrolysis , disaccharides release their respective constituent monosaccharides (e.g., hydrolysis of sucrose yields one molecule each of glucose and fructose). - Trisaccharides : Sugars composed of 3 monosaccharide units are called trisaccharides (e.g., raffinose). Raffinose is a common saccharide found in plants. Upon hydrolysis, it yields one molecule each of glucose, fructose and galactose. - Larger oligosaccharides are attached to the cell membrane and cell recognition is due to their presence. They also take part in antigen specificity.
Polymerisation of a large number of small molecules results in the formation of large molecules of high molecular weights, which may be branched or unbranched. These are
- Derived lipids – These are isoprenoid structures e.g., steroids, terpenes, carotenoids. 4. Fatty acids are carboxylic acid with a chain of more than four carbon atoms ending with COOH group. Plants can
synthesize all fatty acids. Animals can not synthesize linoleic, linolenic and arachidonic acid. These are called essential fatty acids. Their deficiency causes sterility, kidney failure and stunted growth.
- Saturated fatty acids have no double bond. Their melting point is high. Palmitic acid, stearic acid are saturated fatty acids. Unsaturated fatty acids are commonly present in vegetable oils, cod/shark oil. Their melting points are low. Oleic acid has one double bond, linoleic acid has two, linolenic acid has three and arachiodonic acid has 4 double bonds. Fatty acids with more than one double bond are called polyunsaturated fatty acid (PUFA). ¾ Drying oils are unsaturated fatty acids which can be converted in hard fats on being exposed. ¾ Edible oils can be converted into hard fats through hydrogenation.
- Waxes are esters of long chain monohydric alcohols like cetyl, ceryl or mericyl. ¾ Lanolin forms a protective, water insoluble coating on animal fur.
¾ Bees wax secreted from abdominal glands of honey bees has palmitic acid and mericyl alcohol. ¾ Paraffin wax is a petroleum product. ¾ Cutin is formed by cross esterification and polymerization of hydroxyl fatty acids and other fatty acids without esterification by alcohols other than glycerol. Cuticle has 50‐90% cutin. ¾ Suberin is condensation product of glycerol and phellonic acid. It makes the cell wall impermeable to water.
7. Phospholipids are triglycerides in which one fatty acid is replaced by phosphoric acid which is often linked to additional nitrogenous groups like choline (in lecithin), ethanolamine (in cepalin), serine or inositol. These are amphipathic i.e. have both polar and non polar groups. These form cell membranes along with proteins. 8. Sphingolipids have amino alcohol sphingosine. Sphingomyelins are present in myelin sheath of nerves. They have additional phosphate attached to choline, are present in nerve membrane. Cerebrosides are present in nerve membrane and have galactose. 9. Gangliosides – have glucose, galactose, sialic acid and acetyl glucosamine , present in grey matter, receptors of viral particles, excess causes Tay Sachs disease. 10. Sterols or steroids contain 4 fused hydrocarbon rings called cyclopentane perhydro phenanthrene and a long side chain e.g. cholesterol, stigmasterol, campesterol, sitosterol, ergasterol. ¾ Cholesterol helps in absorption of fatty acids, sex hormones, vitamin D and bile salts. Potato is rich in cholesterol. Excess of cholesterol causes atheroscherosis. 11. Prostagladins are hormone modulators.
- Terpenes are lipid like carbohydrates formed of isoprene units e.g., menthol, camphor, carotenoids.
- Major function of lipids is to act as energy stores. ¾ Plants usually store oil than fats. Seeds, fruits and choloroplasts are often rich in oils. ¾ Glycolipids are important components of cell membranes, chloroplast membranes. ¾ Fatty substance in the cell wall (Wax, cutin, suberin) helps reduce transpiration and provide mechanical protection from injury and parasites. ¾ Diosgenin is a steroid obtained from the plant called Dioscorea. It is used for manufacturing antifertility pills.
B3. Amino Acids & Proteins
1. Amino acids: Amino acids are building blocks of polypeptides. Polymerization of amino acids forms polypeptides. Amino acids are linked by a peptide bond in a polypeptide. Peptide bond are synthesized during translation of messenger RNA
- Primary structure of a protein is the sequence of amino acids. Both peptides and polypeptides can be functional
- Amino acids may be functional. Various amino acids functions as neurotransmitters glutamate and aspartate (excitory) glycine, taurine, and γ‐aminobutyric acid (GABA) (inhibitory) Structure ‐^ OOC‐CH 2 ‐CH 2 ‐NH 3 +^ GABA Structure +^ H 3 N‐CH 2 ‐CH 2 ‐SO 3 ‐^ TAURINE
- Amino Acids can act as precursors to other molecules metabolic intermediates: citrulline and ornithine in urea cycle can be metabolized to form glucose or acetyl CoA neurotransmitters ‐ serotonin, dopamine, epinephrine, etc.
tyrosine (thyroid hormone) porphyrins creatine (energy storage) histamine (mediator of immune response) nucleotide synthesis ‐ S‐adenosylmethionine
5. Structure of amino acids : All proteins are composed of 20 standard amino acids, which are specified by the genetic code. The standard amino acids are called α‐amino acids because they have a primary amino group and a carboxyl group bound to the same carbon atom (the α carbon). Only proline has a secondary amino group attached to the α carbon, but it is still commonly referred to as an α‐amino acid. The generic structure of an amino acid at pH 7 is shown below.
At pH 7, the amino acid is a zwitterion, or dipolar ion. A unique side chain, or R group, characterizes each amino acid.
There are 20 standard α‐amino acids (although proline is regarded as α‐imino acid). An Amino acid has a alpha‐ carbon, alpha‐amino group, alpha‐carboxyl group and a side chain (R group). These "standard" amino acids are encoded by messenger RNA. Amino acids are abbreviated by a 3‐ letter and 1‐letter code
Abbreviations for the 20 "standard" amino acids
alanine Ala A leucine Leu L
arganine Arg R lysine Lys K
asparagines Asn N methioneine Met M
aspartic acid Asp D phenylalanine Phe F
cysteine Cys C proline Pro P
glycine Gly G serine Ser S
glutamine Gln Q threonine Thr T
glutamic acid Glu E tryptophan Trp W
histidine His H tyrosine Tyr Y
isoleucine Ile I valine Val V
Chemical Properties of Amino Acids
- Charge : Amino acids are dipolar ions (zwitterions) at neutral pH. Zwitterion is a dipolar molecule with positive and negative charges spatially separated. Ionic states of amino acids depend on pH. Amino acids have two or three dissociable protons. pKa of the dissociable proton and the pH determine its degree of dissociation.
- Amino acids are polymerized by condensation reactions to form a chain called a polypeptide. Each polypeptide is polarized: One end has a free amino group and the other end has a free carboxyl group, referred to as the N‐terminus and the C‐terminus, respectively.
- The R groups of the standard 20 amino acids are classified into three categories based on their polarities and charge at pH 7: the nonpolar amino acids, the polar uncharged amino acids, and the charged amino acids.
- Among the nonpolar amino acids, glycine (shorthand Gly or G) has a hydrogen atom as its R group. Alanine (Ala; A), valine (Val; V), leucine (Leu; L), isoleucine (Ile; I), and methionine (Met; M) have aliphatic chains as R groups (Met has a sulfur rather than a methylene group). Tryptophan (Trp; W) and phenylalanine (Phe; F) contain bulky indole
and phenyl groups, respectively. These tend to orient inside of a protein.
- The polar uncharged amino acids include asparagine (Asn; N), glutamine (Gln; Q), serine (Ser; S), threonine (Thr; T), tyrosine (Tyr; Y), and cysteine (Cys; C). Amide functional groups occur in Gln and Asn. Alcoholic functional groups occur in Ser and Thr. Tyrosine and cysteine are characterized by a phenolic group and a thiol group, respectively.
- Hydropathicity for an amino acid is a index of solubility characteristics in H 2 O. It combines hydrophobic and hydrophilic tendencies, It can be used to predict protein structure
- Among the charged amino acids, aspartate (Asp; D) and glutamate (Glu; E) contain carboxylic groups in their R groups. Lysine (Lys; K), arginine (Arg; R), and histidine (His; H) contain a butylammonium group, a guanidino group, and an imidazole group, respectively. Both polar uncharged and charged aminacids tend to orient to the outside of proteins
- The p K values of ionizable groups depend on the electrostatic influences of nearby groups. Inside of proteins, the p K values of ionizable R groups may shift by several pH units from their values in the free amino acids.
- Aromatic amino acids (Trp, Tyr, Phe) absorb UV light between 260‐280 nm with maxima at 280 nm.
- Cysteine can form disulfide bonds. Disulfide bridges formed between cysteines are important in protein structure. Cysteine is the reduced form (sulfhydryl) whereas cystine is the oxidized form (disulfide).
B 4 Protein Structure and Protein Folding
1. Peptide bond – Chemically it is an amide bond between alpha‐amino and alpha‐carboxyl groups of 2 amino acids. Peptide bond is polar and planar electron resonance structure has partial (40%) double bond character amide group is planar, usually trans. Synthesis of peptide bond involves condensation and water is produced. Energy is required for this process which is obtained by ATP hydrolysis. 2. Peptide bond is hydrolysable: Acid hydrolysis with 6N Hydrochloric acid heated at 110 0 C for 24 hr in a vacuum generates free amino acids breaking all peptide bonds. Base hydrolysis with 4N Sodium hydroxide heated at 100 0 C for 4 hr also generates free amino acids. Cyanogen bromide cleaves at the COOH‐terminal side of Met. Enzymatic hydrolysis of peptide bonds by proteases like trypsin cleave after –COOH terminus Lys or Arg; Chymotrypsin after carboxy terminus of aromatic amino acids yield peptides of various length 3. Polypeptides are polyampholytes: Ampholyte has both acidic and basic pKa values. Isoelectric point is the pH at which the net charge is zero For example: H 3 N+‐Ala‐Lys‐Ala‐Ala‐COO ‐ pKa of the Alpha‐carboxyl group = 3.
pKa of the Alpha‐amino group = 8. pKa of the delta‐amino of the Lysine = 10. at pH = 1 the net charge is + at pH = 6 the net charge is + at pH = 14 the net charge is ‐ The isoelectric point pI = (pKa2 + pKa3)/2 = (8 +10.6)/ = 9.
- Nomenclature of Peptides on basis of size dipeptide(2 amino acids & 1 peptide bond), tripeptide(3 amino acids & 2 peptide bonds) oligopeptide ‐ several amino acids (up to 20) polypeptides (more than 20 amino acids). All proteins are polypeptides 5. Physical Forces Governing Protein Conformation: Physical forces govern 3‐D structure of proteins (Pauling and Corey) bond lengths and angles should be distorted as little as possible structures must follow Van der Waal's rules for atomic radii peptide bond is planar and trans noncovalent bonding stabilizes structure conformation can change without breaking bonds (flexibility)
- Types of non covalent forces important to protein conformation Hydrophobic forces: Hydrophobic residues orient to inside while hydrophilic residues orient out Van der Waal's potential: includes electron shell repulsion, dispersion forces, and electrostatic interactions Salt bridges, electrostatic forces and Hydrogen bonds 7. Angles of rotation of the polypeptide chain determine structure angles of rotation around alpha‐carbon are (ψ psi and ϕ phi). ψ (psi) is the angle of the alpha‐ carbon bond to the carbonyl‐carbon. ϕ (phi) is the angle of the alpha‐carbon bond to the amide‐ nitrogen. primary sequence and angles of rotation for each alpha‐carbon completely define protein conformation only a small number of psi and phí angles are allowed. Statistical analysis of all proteins yields groups of prefered angles. Areas of repeating (psi) and (phi) angles are secondary structures 8. Primary Structure of protein is amino acid sequence of a polypeptide. Primary structure determines 3‐dimensional structure. Primary structure is always represented NH 2 ‐ terminus to COOH‐terminus 9. Secondary structure is formed by regular local conformation of linear segments of the polypeptide chain. Secondary structure are stabilized by hydrogen bonds between amide and carbonyl groups. Several types of secondary structure alpha helix: It is right handed helix with 3. amino acids per turn, rise per helix 5.4 A o, rise per amino acid 1.5 A o^. Here carbonyl oxygen hydrogen of one amino acid is bonded to 4 th^ amide hydrogen (nÆn+4). Amino acids R‐groups orient out. Mostly proline breaks the helix. beta pleated sheet: Here polypeptide chains side by side. Polypeptide chains can be parallel or anti‐ parallel. Carbonyl oxygen hydrogen bonded to amide hydrogen. Beta‐strand is a single pass of the polypeptide reverse turn, beta bend allows a sharp turn in polypeptide chain. Here carbonyl oxygen hydrogen bonded to 3 rd^ amide hydrogen (nÆn+3). Glycine is required.
- Fibrous proteins demonstrate secondary structure. Fibroin: silk is fibroin which has anti parallel‐ beta‐pleated sheet α Keratin and tropomyosin: alpha‐keratins occurs in wool and hair and epidermal layer. Tropomyosin is a thin filament in muscle. Both have α‐helix. Alpha‐helix allows elasticity. α‐ keratin converts to β‐pleated sheet with heat or stretching. Disulfides are important to maintenance of keratin secondary structure. α‐ alpha‐keratins are β‐pleated sheets in feathers and claws of birds. Collagen: It is structural protein found in skin, bones. It has triple helix (not α‐helix). It has repeating sequence (Gly‐X‐Pro) X or (Gly‐X‐ HyPro)X. Glycine required for triple helix to form, contains many modified amino acids. Hydroxyproline stabilizes the structure, vitamin C required for hydroxylation thus in Vitamin C deficiency cause scurvy. 11. Tertiary structures are overall folded conformation of the polypeptide. Physical forces affect tertiary structure. The main driving force is hydrophobic force , as a result,
hydrophobic residues orient to inside and hydrophilic orient out. To some extent salt bridges, electrostatic forces, Van der Waals radii, Hydrogen bonds and Disulfide bridges also play important role in maintaining tertiary structure. Myoglobin has a tertiary structure.
12. Quaternary structure are formed by aggregation of 2 or more subunits. These may be hetero‐ or homo‐ polymers. Same forces drive tertiary and quaternary structure. Haemoglobin has quaternary structure.
- Protein folding: Folding is driven by hydrophobic forces. Folding occurs step‐wise with several intermediates. UnfoldedÆsecondary structureÆdomainsÆmolten globuleÆnative tertiary structure A collapsed structure (molten globule) occurs very quickly. Steps between molten globule and native tertiary structure usually occur slowly. The intermediates are isolatable and there may be multiple pathways for folding.
- Proteins can self assemble but in vivo folding is facilitated by proteins. Chaperones are binding proteins
which assist folding. Chaperones cause misfolded protein to unfold rather than aggregate. Many chaperones require ATP hydrolysis for activity. More than one chaperone may act simultaneously and sequentially in the folding of a single protein. Chaperones are specific for specific protein synthesis pathways (cytosolic vs. mito. vs. endoplasmic reticulum)
- Enzymes catalyze kinetically slow steps in folding cis trans prolyl isomerase: Both cis and trans peptide bonds to proline naturally occur. The isomerization of peptidyl‐proline bonds may be slow so this enzyme catalyzes reaction at enhanced rate. protein disulfide isomeras e: catalyzes disulfide bond formation and isomerization
16. Denaturation is unfolding: It requires some input to overcome hydrophobic forces. The heat or other denaturant (urea or guanidinium) can unfold the proteins. For reducing disulfide bridges to sulfhydryls certain reductant (Meracaptoethanol) are required.
B5. Nucleic Acid
- Nucleic acids (DNA/RNA) are polymer of nucleotides. As a class, the nucleotides may be considered one of the most important metabolites of the cell. Nucleotides are found primarily as the monomeric units comprising the major nucleic acids of the cell, RNA and DNA. However, they also are required for numerous other important functions within the cell. These functions include: a. serving as energy stores for future use in phosphate transfer reactions. These reactions are predominantly carried out by ATP. b. forming a portion of several important coenzymes such as NAD+, NADP+, FAD and coenzyme A. c. serving as mediators of numerous important cellular processes such as second messengers in signal transduction events. The predominant second messenger is cyclic‐AMP (cAMP), a cyclic derivative of AMP formed from ATP. d. controlling numerous enzymatic reactions through allosteric effects on enzyme activity. e. serving as activated intermediates in numerous biosynthetic reactions. These activated intermediates include S‐adenosylmethionine (SAM) involved in methyl transfer reactions as well as the many sugar coupled nucleotides involved in glycogen and glycoprotein synthesis. 2. The nucleotides found in cells are derivatives of the heterocyclic highly basic, compounds, purine and pyrimidine.
It is the chemical basicity of the nucleotides that has given them the common term " bases " as they are associated with nucleotides present in DNA and RNA. There are five major bases found in cells. The derivatives of purine are called adenine and guanine, and the derivatives of pyrimidine are called thymine, cytosine and uracil. The common abbreviations used for these five bases are, A, G, T, C and U.
- The purine and pyrimidine bases in cells are linked to carbohydrate and in this form are termed, nucleosides. The nucleosides are coupled to D‐ribose or 2'‐deoxy‐D‐ribose through a b‐N‐glycosidic bond between the anomeric carbon of the ribose and the N9 of a purine or N1 of a pyrimidine.
- Nucleosides are found in the cell primarily in their phosphorylated form. These are termed nucleotides. The most common site of phosphorylation of nucleotides found in cells is the hydroxyl group attached to the 5'‐carbon of the ribose The carbon atoms of the ribose present in nucleotides are designated with a prime (') mark to distinguish them from the backbone numbering in the bases. Nucleotides can exist in the mono‐, di‐, or tri‐phosphorylated forms.
- Nucleotides are given distinct abbreviations to allow easy identification of their structure and state of phosphorylation. The monophosphorylated form of adenosine (adenosine‐5'‐ monophosphate) is written as, AMP. The di‐ and tri‐ phosphorylated forms are written as, ADP and ATP, respectively. The use of these abbreviations assumes that the nucleotide is in the 5'‐phosphorylated form. The di‐ and tri‐phosphates of nucleotides are linked by acid anhydride
DNA molecule exists as single strands. This point is the melting temperature (Tm), and is characteristic of the base composition of that DNA molecule. The TM depends upon several factors in addition to the base composition. These include the chemical nature of the solvent and the identities and concentrations of ions in the solution.
14 DNA: The Genetic Material The physical carrier of inheritance
- Friedrich Meischer in 1869 isolated DNA from fish sperm and the pus of open wounds. Since it came from nuclei, Meischer named this new chemical, nuclein. Subsequently the name was changed to nucleic acid and lastly to deoxyribonucleic acid (DNA). Robert Feulgen, in 1914, discovered that fuchsin dye stained DNA. DNA was then found in the nucleus of all eukaryotic cells.
- During the 1920s, biochemist P.A. Levene analyzed the components of the DNA molecule. He found it contained four nitrogenous bases: cytosine, thymine, adenine, and guanine; deoxyribose sugar; and a phosphate group. He concluded that the basic unit (nucleotide) was composed of a base attached to a sugar and that the phosphate also attached to the sugar. He (unfortunately) also erroneously concluded that the proportions of bases were equal and that there was a tetranucleotide that was the repeating structure of the molecule. The nucleotide, however, remains as the fundemantal unit (monomer) of the nucleic acid polymer. There are four nucleotides: those with cytosine (C), those with guanine (G), those with adenine (A), and those with thymine (T).
- During the early 1900s, the study of genetics began in earnest: the link between Mendel's work and that of cell biologists resulted in the chromosomal theory of inheritance; Garrod proposed the link between genes and "inborn errors of metabolism"; and the question was formed: what is a gene? The answer came from the study of a deadly infectious disease: pneumonia.
- During the 1920s Frederick Griffith studied the difference between a disease‐causing strain of the pneumonia causing bacteria (Streptococcus peumoniae) and a strain that did not cause pneumonia. The pneumonia‐causing strain (the S strain) was surrounded by a capsule. The other strain (the R strain) did not have a capsule and also did not cause pneumonia. Frederick Griffith (1928) was able to induce a nonpathogenic strain of the bacterium Streptococcus pneumoniae to become pathogenic. Griffith referred to a transforming factor that caused the non‐pathogenic bacteria to become pathogenic. Griffith injected the different strains of bacteria into mice. The S strain killed the mice; the R strain did not. He further noted that if heat killed S strain was injected into a mouse, it did not cause pneumonia. When he combined heat‐killed S with Live R and injected the mixture into a mouse (remember neither alone will kill the mouse) that the mouse developed pneumonia and died. Bacteria recovered from the mouse had a capsule and killed other mice when injected into them.
- Hypotheses:
- The dead S strain had been reanimated/resurrected.
- The Live R had been transformed into Live S by some "transforming factor". Further experiments led Griffith to conclude that number 2 was correct.
- In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty revisited Griffith's experiment and concluded the transforming factor was DNA. Their evidence was strong but not totally conclusive. The then‐current favorite for the hereditary material was protein; DNA
was not considered by many scientists to be a strong candidate.
- The breakthrough in the quest to determine the hereditary material came from the work of Max Delbruck and Salvador Luria in the 1940s. Bacteriophage are a type of virus that attacks bacteria, the viruses that Delbruck and Luria worked with were those attacking Escherichia coli, a bacterium found in human intestines. Bacteriophages consist of protein coats covering DNA. Bacteriophages infect a cell by injecting DNA into the host cell. This viral DNA then "disappears" while taking over the bacterial machinery and beginning to make new virus instead of new bacteria. After 25 minutes the host cell bursts, releasing hundreds of new bacteriophage. Phages have DNA and protein, making them ideal to resolve the nature of the hereditary material.
- In 1952, Alfred D. Hershey and Martha Chase conducted a series of experiments to determine whether protein or DNA was the hereditary material. By labeling the DNA and protein with different (and mutually exclusive) radioisotopes, they would be able to determine which chemical (DNA or protein) was getting into the bacteria. Such material must be the hereditary material (Griffith's transforming agent). Since DNA contains Phosphorous (P) but no Sulfur (S), they tagged the DNA with radioactive Phosphorous‐32. Conversely, protein lacks P but does have S, thus it could be tagged with radioactive Sulfur‐35. Hershey and Chase found that the radioactive S remained outside the cell while the radioactive P was found inside the cell, indicating that DNA was the physical carrier of heredity. 15. Polymorphism in DNA: A form – having 11 base pairs (instead of 10 base pairs per turn), the base pairs are not perpendicular to the axis, but are tilted. C form – like B form, but having 9 base pairs per turn. D form – like B form, but have 8 base pairs per turn. Z DNA ‐DNA with left handed coiling is called Z DNA. 16. DNA supercoiling: A supercoil is when the double‐helix twists around itself. Supercoils can be positive or negative but natural DNAs exist in the negative supercoiled form. DNA can be supercoiled if it is circular or if is linear and has fixed ends. Supercoiled DNA is more compact than relaxed DNA. Negatively supercoiled DNA molecules are easier to unwind than relaxed molecules. DNA unwinding is required for replication and transcription. Topoisomerases are enzymes that catalyze changes in DNA supercoiling. a. Type I topoisomerases function by breaking a phosphodiester bond of one strand, passing the other strand through the break and resealing the break. They can only remove supercoil and increase linking number by 1. b. Type II topoisomerases function by breaking both strands and passing a double strand region through the break before resealing the break, for this process they require ATP. They dectrease linking number by 2.
Topoisomerases are targets of numerous chemotherapeutic drugs: adriamycin , VP16 ( tenoposide ), VM26 ( etoposide ), camptothecin.
- Hyperchromic effect: On denaturation of dsDNA into SS DNA UV absorption at 260 nm increases. 18. Packaging of DNA in eukaryotes: DNA is packaged in the nucleus as a nucleoprotein complex called chromatin. Levels of chromatin packaging: a. Nucleosomes: Nucleosome core particles consist of ~140 bp of DNA wrapped around a protein octamer consisting of 2 subunits each of histones H2A, H2B, H3,
and H4. Linker DNA (~60 bp) is the DNA between two core particles, histone H1 binds to the linker DNA and the core particle. b. 30 nm fiber(Solenoid): nucleosomes are wound into a solenoid‐like structure. It requires histone H binding to every linker DNA c. chromatin is the template for replication and transcription and the substrate for DNA repair and recombination
B6. NUTRITION AND VITAMINS:
Nutrition is the process of acquiring energy and materials for cell metabolism including the Maintenance and repair of cells, and growth.
HETEROTROPHIC NUTRITION:
- Hetrotrophic organisms or hetrotrophs are organisms that feed on an organic source of carbon. The survival of hetrotrophs is depend either directly or indirectly on the activities of autotrophs. A few bacteria are able to use light energy to synthesise their organic requirements from other raw materials. These are called photoautotrophs.
- The way in which hetrotrophs obtain their food varies considerably. However the way in which it is processed into a usable form within the body is very similar in most of them. It involves following processes: Digestion: This is the process which reduce large complex food molecules into simpler soluble ones. Absorption: In this process the soluble molecules are taken away from the region of digestion into the tissues of the organisms. Assimilation: It use the absorbed nutrients for a particular purpose.
- Forms of Hetrotrophic Nutrition Holozoic Nutrition Saprotrophic Nutrition
- Holozoic Nutrition: The term holozoic is applied mainly to free living animals which have a specialised digestive tract, the alimentary canal. Most animals are holozoic. The characteristic processes involved in holozoic nutrition are as follows: Ingestion is the taking in of food. Digestion is the breakdown of large organic molecules into smaller, simpler soluble molecules. Often two types of digestion occur. Mechanical digestion involves mechanical breakdown of the food, for example by teeth. Chemical digestion involves the activity of enzymes. The type of chemical process these enzyme catalyse during digestion is hydrolysis. Digestion may be extracellular or intracellular. Absorption: It is the uptake of the soluble molecules from the digestive region, across a membrane and into the body tissue proper. The food may pass directly into cells or first pass into the blood stream to be transported to other regions of the body. Assimilation is using the absorbed molecules to provide either energy or materials to be incorporated into the body. Egestion is the elimination from the body of undigested waste food materials. Animals which feed on plants are called as herbivores, those that feed on animals are called as carnivores, and those that eat a mixed diet of animal and vegetable matter are termed omnivores. Some animals take food in the form of relatively small
particles, for ex earthworms and filter feeders like mussels. Some ingest food into liquid form ex., aphids, butterflies and mosquitoes
5. Saprotrophic Nutrition (sapros = Rotten, Trophos = Decay): Organisms which feed on dead or decaying organic matter are called saprotrophs other terms which mean the same thing is saprophytes and saprobiant. Many fungi and bacteria are saprotrophs eg. mucor , rhizophus , yeasts. Saprotrophs secrete enzymes onto their food where it is digested .The soluble end products of this extracellular digestion are than absorbed and assimilated by the saprotrophs. Saprotrophs feed on the dead organic remains of plants and animals and contribute to the removal of such remains by decomposing it. Many of simple substances are not used by the saprotrophs by themselves but are absorbed by plants. In this way the saprotroph provide important links in nutrient cycles by making possible the return of vital chemical elements from the dead bodies organisms to living ones. 6. Saprotophic nutrition of Mucor and Rhizophus: Mucor and Rhizophus are common fungi known as pin moulds. They are often found growing on bread, although they can also live in soil. Their hyphae penetrate the food on which they grow and secrete hydrolyzing enzyme from their tips. Enzymes carbohydrase and protease carry out the extracellular digestion of starch to glucose and protein to amino acids respectively. The thin much branched nature of the mycelium of mucor and rhizophus ensures that there is a large surface area for absorption. Glucose is used during respiration to provide energy for the organisms metabolic activities whilst glucose and amino acids are used for the growth and repair. Excess glucose is converted to glycogen and fat and excess amino acid to protein granules for storage in cytoplasm. 7. Symbiosis: The term symbosis means literally living together. It was introduced by a german scientist de Bary in 1879,who described it as living together of dissimilarly named organisms in other words it is in association between two or more organisms of different species The symbiosis has been restricted by many biologists to meaning a close relationship between two or more organisms of different spp. In which all partners benefit. Since 1970 symbiosis is more important as a topic in biology. For example we now know that the great majority of plants obtain minerals with assistance of fungi and that much nitrogen fixation is carried out by symbiotic bacteria. Symbiosis is the living together in close association of two or more organisms of different species many associations involve three or more partners. Nutrition is commonly involved. 8. Three Common Types of Symbiotic Relationships are Mutualism In which both Partners Benefit Parasitism In which one partner benefits and causes harm to other Commensalism ‐In which one partner benefits but the other recives no harm or benefit.
Glycogen is the body’s auxiliary energy source, tapped and converted back into glucose when we need more energy. Although stored fat can also serve as a backup source of energy, it is never converted into glucose. Fructose and galactose, other sugar products resulting from the breakdown of carbohydrates, go straight to the liver, where they are converted into glucose.
Starches and sugars are the major carbohydrates. Common starch foods include whole‐grain breads and cereals, pasta, corn, beans, peas, and potatoes. Naturally occurring sugars are found in fruits and many vegetables; milk products; and honey, maple sugar, and sugar cane. Foods that contain starches and naturally occurring sugars are referred to as complex carbohydrates, because their molecular complexity requires our bodies to break them down into a simpler form to obtain the much‐needed fuel, glucose. Our bodies digest and absorb complex carbohydrates at a rate that helps maintain the healthful levels of glucose already in the blood.
In contrast, simple sugars, refined from naturally occurring sugars and added to processed foods, require little digestion and are quickly absorbed by the body, triggering an unhealthy chain of events. The body’s rapid absorption of simple sugars elevates the levels of glucose in the blood, which triggers the release of the hormone insulin. Insulin reins in the body’s rising glucose levels, but at a price: Glucose levels may fall so low within one to two hours after eating foods high in simple sugars, such as candy, that the body responds by releasing chemicals known as anti‐ insulin hormones. This surge in chemicals, the aftermath of eating a candy bar, can leave a person feeling irritable and nervous.
Many processed foods not only contain high levels of added simple sugars, they also tend to be high in fat and lacking in the vitamins and minerals found naturally in complex carbohydrates. Nutritionists often refer to such processed foods as junk foods and say that they provide only empty calories, meaning they are loaded with calories from sugars and fats but lack the essential nutrients our bodies need.
In addition to starches and sugars, complex carbohydrates contain indigestible dietary fibers. Although such fibers provide no energy or building materials, they play a vital role in our health. Found only in plants, dietary fiber is classified as soluble or insoluble. Soluble fiber, found in such foods as oats, barley, beans, peas, apples, strawberries, and citrus fruits, mixes with food in the stomach and prevents or reduces the absorption by the small intestine of potentially dangerous substances from food. Soluble fiber also binds dietary cholesterol and carries it out of the body, thus preventing it from entering the bloodstream where it can accumulate in the inner walls of arteries and set the stage for high blood pressure, heart disease, and strokes.
Insoluble fiber, found in vegetables, whole‐grain products, and bran, provides roughage that speeds the elimination of feces, which decreases the time that the body is exposed to harmful substances, possibly reducing the risk of colon cancer. Studies of populations with fiber‐rich diets, such as Africans and Asians, show that these
populations have less risk of colon cancer compared to those who eat low‐fiber diets, such as Americans. In the United States, colon cancer is the third most common cancer for both men and women, but experts believe that, with a proper diet, it is one of the most preventable types of cancer.
Nutritionists caution that most Americans need to eat more complex carbohydrates. In the typical American diet, only 40 to 50 percent of total calories come from carbohydrates—a lower percentage than found in most of the world. To make matters worse, half of the carbohydrate calories consumed by the typical American come from processed foods filled with simple sugars.
Experts recommend that these foods make up no more that 10 percent of our diet, because these foods offer no nutritional value. Foods rich in complex carbohydrates, which provide vitamins, minerals, some protein, and dietary fiber and are an abundant energy source, should make up roughly 50 percent of our daily calories.
Dietary proteins are powerful compounds that build and repair body tissues, from hair and fingernails to muscles. In addition to maintaining the body’s structure, proteins speed up chemical reactions in the body, serve as chemical messengers, fight infection, and transport oxygen from the lungs to the body’s tissues. Although protein provides 4 calories of energy per gram, the body uses protein for energy only if carbohydrate and fat intake is insufficient. When tapped as an energy source, protein is diverted from the many critical functions it performs for our bodies.
17. Proteins: Proteins are made of smaller units called amino acids. Of the more than 20 amino acids our bodies require, eight (nine in some older adults and young children) cannot be made by the body in sufficient quantities to maintain health. These amino acids are considered essential and must be obtained from food. When we eat food high in proteins, the digestive tract breaks this dietary protein into amino acids. Absorbed into the bloodstream and sent to the cells that need them, amino acids then recombine into the functional proteins our bodies need.
The amino acids which cannot be formed by humans from other amino acids are called essential amino acids. They are eight in number ‐ methionine, threonine, tryptophan, valine, leucine, isoleucine, lysine and phenylalanine. Two amino acids are slow to be formed. They are known as semi‐indispensable, e.g., arginine, histidine.
Animal proteins, found in such food as eggs, milk, meat, fish, and poultry, are considered complete proteins because they contain all of the essential amino acids our bodies need.
Plant proteins, found in vegetables, grains, and beans, lack one or more of the essential amino acids. However, plant proteins can be combined in the diet to provide all of the essential amino acids. A good example is rice lack lysine and beans lack methionine. Each of these foods lacks one or more essential amino acids, but the amino acids missing in rice are found in the beans, and vice versa. So when eaten together, these foods provide a complete source of protein.
Experts recommend that protein intake make up only 10 percent of our daily calorie intake. Some people, especially in the United States and other developed countries, consume more protein than the body needs. Because extra amino acids cannot be stored for later use, the body destroys these amino acids and excretes their by‐products.
Alternatively, deficiencies in protein consumption, seen in the diets of people in some developing nations, may result in health problems. Marasmus and kwashiorkor, both life‐ threatening conditions, are the two most common forms of protein malnutrition. Some health conditions, such as illness, stress, and pregnancy and breast‐feeding in women, place an enormous demand on the body as it builds tissue or fights infection, and these conditions require an increase in protein consumption. For example, a healthy woman normally needs 45 grams of protein each day.
Experts recommend that a pregnant woman consume 55 grams of protein per day, and that a breast‐feeding mother consume 65 grams to maintain health. A man of average size should eat 57 grams of protein daily. To support their rapid development, infants and young children require relatively more protein than do adults. A three‐ monthold infant requires about 13 grams of protein daily, and a four‐year‐old child requires about 22 grams. Once in adolescence, sex hormone differences cause boys to develop more muscle and bone than girls; as a result, the protein needs of adolescent boys are higher than those of girls.
18. Fats: Fats, which provide 9 calories of energy per gram , are the most concentrated of the energy‐producing nutrients, so our bodies need only very small amounts. Fats play an important role in building the membranes that surround our cells and in helping blood to clot. Once digested and absorbed, fats help the body absorb certain vitamins. Fat stored in the body cushions vital organs and protects us from extreme cold and heat. Fat consists of fatty acids attached to a substance called glycerol.
Dietary fats are classified as saturated, monounsaturated, and polyunsaturated according to the structure of their fatty acids. Animal fats‐ from eggs, dairy products, and meats‐are high in saturated fats and cholesterol, a chemical substance found in all animal fat. Vegetable fats‐found, for example, in avocados, olives, some nuts, and certain vegetable oils‐are rich in monounsaturated and polyunsaturated fat. As we will see, high intake of saturated fats can be unhealthy.
To understand the problem with eating too much saturated fat, we must examine its relationship to cholesterol. High levels of cholesterol in the blood have been linked to the development of heart disease, strokes, and other health problems.
Despite its bad reputation, our bodies need cholesterol, which is used to build cell membranes, to protect nerve fibers, and to produce vitamin D and some hormones, chemical messengers that help coordinate the body’s functions. We just do not need cholesterol in our diet. The liver, and to a lesser extent the small intestine, manufacture all the cholesterol we
require. When we eat cholesterol from foods that contain saturated fatty acids, we increase the level of a cholesterol‐carrying substance in our blood that harms our health.
Human diet should have more unsaturated fat because some unsaturated fatty acids cannot be synthesised from others. They are called essential fatty^ acids ,^ e.g.,^ linoleic^ acid,^ linolenic acid, arachidonic acid. Excess of lipids causes obesity, blood pressure and a number of cardiac problems. Daily requirement of adult is 50 gm.
VITAMINS
19. Both vitamins and minerals are needed by the body in very small amounts to trigger the thousands of chemical reactions necessary to maintain good health. Many of these chemical reactions are linked, with one triggering another. If there is a missing or deficient vitamin or mineral‐or link anywhere in this chain, this process may break down, with potentially devastating health effects. Although similar in supporting critical functions in the human body, vitamins and minerals have key differences. Among their many functions, vitamins enhance the body’s use of carbohydrates, proteins, and fats. They are critical in the formation of blood cells, hormones, nervous system chemicals known as neurotransmitters, and the genetic material deoxyribonucleic acid (DNA).
Vitamins are classified into two groups: fat soluble and water soluble.
Fat‐soluble vitamins, which include vitamins A, D, E, and K, are usually absorbed with the help of foods that contain fat. Fat containing these vitamins is broken down by bile, a liquid released by the liver, and the body then absorbs the breakdown products and and unsaturated fats has also been associated with greater risk of developing cancers of the colon, prostate, breast, and uterus. Choosing a diet that is low in fat and cholesterol is critical to maintaining health and reducing the risk of life‐threatening disease. Excess amounts of fat‐soluble vitamins are stored in the body’s fat, liver, and kidneys. Because these vitamins can be stored in the body, they do not need to be consumed every day to meet the body’s needs.
Water‐soluble vitamins, which include vitamins C (also known as ascorbic acid), B1 (thiamine), B2 (riboflavin), B3 (niacin), B6, B12, and folic acid, cannot be stored and rapidly leave the body in urine if taken in greater quantities than the body can use. Foods that contain water‐soluble vitamins need to be eaten daily to replenish the body’s needs.
In addition to the roles noted in the vitamin and mineral chart accompanying this article, vitamins A (in the form of betacarotene), C, and E function as antioxidants, which are vital in countering the potential harm of chemicals known as free radicals. If these chemicals remain unchecked they can make cells more vulnerable to cancer‐causing substances. Free radicals can also transform chemicals in the body into cancer‐ causing
