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Parmod P. Mahulikar, Shama M.Chavan, H.P. Gajera
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Parmod P. Mahulikar
Parmod P. Mahulikar: Head, Department of Industrial Chemistry, School of Chemical Sciences, North Maharashtra University, Jalgaon- 425 001, Maharashtra, India

Shama M.Chavan
shama M.Chavan: Research Associate: School of Chemical Sciences, North Maharashtra University, Jalgaon- 425 001, Maharashtra, India

H.P. Gajera
H.P. Gajera (Asso. Prof.) S.V. Patel (Professor), B.A. Golakiya (Prof & head), Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Gunagadh-632 001, Gujarat

After learning a huge text, the theories and practices are abstracted in the form of mind charts or brief summaries in the mind. The purpose of this collection is to quickly recall the understanding of Biochemistry, Genetics, Biotechnology up to post graduate level. This text will help to get command on the above subject for students appearing for JEE, JRF, SRF, NET, SET, ARS etc. and the teachers involved in couching these students.

0 Start Pages

Is the life beyond the molecules? Our knowledge about the chemistry of life is not sufficient enough to answer this question. However, our quest to resolve the secret of life is continual. Today the biochemical wisdom is quite in depth about the building blocks of living beings i.e. Carbohydrates, Fates, Proteins and Nucleic acids. Enough understanding is also generated about the control, rate, extent of biological processes and multiplication of biological replicates. The blue print of life is there in the genomics and the life is throbbing everywhere due to physiological processes. The knowledge should be perpetuated down the generations to carry this lamp ahead on the path of wisdom. This is possible through teaching, learning and skill development. It is also required to test the knowledge gained . The mind accumulates, classify, analyze and synthesized logical facts to produce the analog for further inferences and hypotheses. After learning a huge text, the theories and practices are abstracted in the form of mind charts or brief summaries in the mind. After a long experience in the teaching and learning we have distillated those mind charts into "Biochemistry, Molecular Biology and Biotechnology – Instant Notes". The purpose of this collection is to quickly recall the understanding of Biochemistry, Genetics, Biotechnology up to post graduate level. This text will help to get command on the above subject for students appearing for JEE, JRF, SRF, NET, SET, ARS etc. and the teachers involved in couching these students.

1 Water, pH and Buffer

WATER IS VERY SPECIAL IN BIOLOGY Most abundant chemical of life Special properties:

1 - 10 (10 Pages)
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2 Macromolecules

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:

11 - 54 (44 Pages)
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3 Energy in Biology

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

55 - 60 (6 Pages)
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4 Enzymes and Kinetics

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.

61 - 74 (14 Pages)
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5 Coenzymes and Vitamins

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: Essential ions - metal ions -inorganic 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:

75 - 82 (8 Pages)
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6 Cell Structure and Their Organelles

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

83 - 94 (12 Pages)
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7 Cell Wall - Structure and Functions

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”.

95 - 104 (10 Pages)
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8 Biological Membrane and Function

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.

105 - 118 (14 Pages)
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9 Membrane Transport

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

119 - 128 (10 Pages)
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10 Metabolism of Macromolecules

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.

129 - 192 (64 Pages)
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11 Photosynthesis

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

193 - 204 (12 Pages)
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12 Mitosis : Cell Reproduction, Growth and Repair

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)

205 - 212 (8 Pages)
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13 Meiosis : Sexual Reproduction

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)

213 - 220 (8 Pages)
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14 Mendelian Genetics

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

221 - 228 (8 Pages)
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15 Genetics : Beyond Mendel

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

229 - 234 (6 Pages)
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16 Chromosomes and Inheritance

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

235 - 240 (6 Pages)
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17 DNA and Inheritance

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)

241 - 246 (6 Pages)
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18 DNA Replication, Transcription and Translation

DNA replication. The double helix is unwound and each strand acts as a template. Bases are matched to synthesize the new partner strands. DNA replication, the basis for biological inheritance, is a fundamental process occurring in all living organisms to copy their DNA. This process is “replication” in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand. Therefore, following DNA replication, two identical DNA molecules have been produced from a single double-stranded DNA molecule. Cellular proofreading and error toe-checking mechanisms ensure near perfect fidelity for DNA replication. In a cell, DNA replication begins at specific locations in the genome, called “origins”. Unwinding of DNA at the origin, and synthesis of new strands, forms a replication fork. In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.

247 - 264 (18 Pages)
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19 Genetics of Viruses

Viruses are much simpler than cells Protein capsid Genetic information stored on DNA or RNA: Types of genome: Double strand DNA: sometimes circular Single strand DNA: sometimes circular Double strand RNA Single strand RNA Some can be crystallized

265 - 268 (4 Pages)
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20 Genetics of Bacteria

BACTERIA HAVE SMALL, COMPACT GENOMES We now know the complete DNA sequences for about a dozen bacteria Bacteria seem to need about 500 to 5000 genes to conduct their lives Because they are small, bacterial genomes are highly organized Most of the time there are only a few bases between the end of one gene and the beginning of the next Few introns are found in bacteria Bacteria contain accessory “chromosomes” called plasmids; each has only a few genes

269 - 276 (8 Pages)
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21 Recombinant DNA Technology

Restriction enzymes cut only at specific sequences of 4 to 8 bases A long restriction site is rare. Cutting rare sites will produce a few large pieces of DNA. Restriction enzymes with long sites → small number of large fragments Restriction enzymes with short sites → large number of small fragments

277 - 282 (6 Pages)
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22 Genetic Engineering: PCR, RFLP Analysis and Gene Therapy

The polymerase chain reaction (PCR) is a rapid way of amplifying (duplicating) specific DNA sequences Method was devised by Kary Mullis of Cetus Corporation, Emeryville He recieved a $20,000 bonus and later a Nobel Prize DNA heated to high temperature is not destroyed; separates into single strands, but reforms helix when cooled PCR Method: DNA to be amplified is put into solution containing:

283 - 292 (10 Pages)
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23 Introduction to Plant Physiology

WHAT IS PLANT? A. Definition - by most definitions, a plant: is multi-cellular; is non-motile has eukaryotic cells has cell walls comprised of cellulose is autotrophic; and exhibits alternation of generations - has a distinctive diploid (sporophyte) and haploid (gametophyte) phase.

293 - 302 (10 Pages)
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24 Water, Diffusion and Osmosis

Water, of its very nature, as it occurs automatically in the process of cosmic evolution, is fit, with a fitness no less marvelous and varied than that fitness of the organism which has been won by the process of adaptation in the course of organic evolution. WATER IS ABSOLUTELY ESSENTIAL FOR ALL LIVING ORGANISMS The evidence: Most organisms are comprised of at least 70% or more water. Some plants, like a head of lettuce, are made up of nearly 95% water; When organisms go dormant, they loose most of their water. For example, seeds and buds are typically less than 10% water, as are desiccated rotifers, nematodes and yeast cells; Earth is the water planet (that’s why astronomers get so excited about finding water in space). Water is the limiting resource for crop productivity in most agricultural systems.

303 - 322 (20 Pages)
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25 Transpiration / Gas Exchange

I. Definitions Transpiration - evaporation of water from a plant surface Evapotranspiration - evaporation of water from a plant surface and the soil (and abiotic surroundings. Take-home-lesson: Plants loose a lot of water by transpiration. See text for some specific examples.

323 - 334 (12 Pages)
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26 Solute Transport: Phloem Structure and Function

I. Definition Solute transport in plants, translocation, primarily occurs in the phloem, but it can occur in the xylem. II. Solute Transport in the Xylem Some solutes are transported in the xylem Water and dissolved ions are the main substances in vessels/tracheids These materials are transported via transpiration stream Xylem sap may also contain organic materials, usually in relatively low concentration (with a notable exception being maple sap in the spring which is comprised of 2% or more sucrose). Substances move at different rates depending on matrix effects, metabolic needs, etc.

335 - 342 (8 Pages)
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27 Mineral Nutrition in Plants

PLANT NUTRITION Plants use inorganic minerals for nutrition, whether grown in the field or in a container. Complex interactions involving weathering of rock minerals, decaying organic matter, animals, and microbes take place to form inorganic minerals in soil. Roots absorb mineral nutrients as ions in soil water. Many factors influence nutrient uptake for plants. Ions can be readily available to roots or could be “tied up” by other elements or the soil itself. Soil too high in pH (alkaline) or too low (acid) makes minerals unavailable to plants.

343 - 350 (8 Pages)
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28 Phytohormones

Plant hormones - They are defined as: Small Organic compounds; Synthesized by the plant; Active in low concentration (<10-6); Promote or inhibit growth and developmental responses; Often show a separation of the site of production and the site of action (although this isn’t as clear a distinction as in animals). Based on these criteria, would the following substances be considered hormones? Ca2+, sucrose, 2 4 - D, glycine, or K+?

351 - 372 (22 Pages)
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