Preface Conceptual development in any science is a painful path. With the simple experiments on garden peas; Geoger Mandel laid down the foundation of Modern Genetics. Watson & Creek explored the molecular base of genetics; which started the era of biotechnology. Genetics and Biotechnology are the two side of the same coin. In fact we have been working in this science since last three sanctuaries. The factual knowledge has been distilled drop by drop. When it is placed at proper place the whole picture assumed on astonishing shape, color and texture. It becomes a master piece. Several hundreds of scientists have devoted their whole life behind both the branches of biological science. Of course whatever they have found it was with full-proof. If we want to work in this science to move it forward or to put it in use for the better life on this planate we need to install these innovations, ideas, processes and products and principles in our mind. Transgenic integration by plants is a natural phenomenon, so much so that we are still trying to figure out exactly how Mother Nature does it. Plant biotechnology has already made significant and positive contributions in plant breeding and development of resistant genotypes. It has the potential to be a powerful new tool for plant breeders, one that they will surely need in facing the challenges of rapid climate change, flood and drought, global warming, as well as the new pests and diseases that these changes may bring. This text is devised for proper installing of biotechnology and genetics in the minds of those; whose are in the vicinity of these sciences. Past investigations forms the base for further leap forward in the particular direction. Continuous efforts and knowledge-recollection forms groves or passages to move ahead. We need to assimilate the previous know-how and knowledge on the first place before we initiate thought or working in the branches of our concerned. In a way this is a conditioning of the scientific minds. But it is essential because the passages which have been paved are resultant of long tiresome efforts within the frame of cause effect-relations. The subject of Biotechnology and Genetics is expanding its horizons. Most of the branches of biological science are mingling in this particular branch. The recent innovations are touching even to the psyche of mankind. Of course, we should not play God. Because we are still not wise enough to do so. We still want to understand origin, cause, purposes, interdependent, free will (if any?) in the life perpetuating on this planate. But one thing is sure that these two branches of the bioscience have drifted us nearer to God. Hope, this expanded text will illuminate the minds of all who have some interest in the biotechnology and genetics. This text will be of helpful to the students who want to pursue their career in the area of genetics and biotechnology since it contains the short of each topic followed by objective questions.

A Overview Genetics is a branch of biology concerned with heredity and variation. Genes are the unit of inheritance and are composed of DNA. The effects of genes are noticeable at the molecular, cellular, family, and population levels. Genes are DNA sequences that instruct cells to produce particular proteins, which in turn determine traits. Genes can exist in more than one form and the variants of a gene arise by mutation. An allele is a variant of a gene that alters its expression in a detectable way. Alleles can be dominant or recessive. A polymorphism is a particular sequence of DNA that varies in one percent or more of the population. Single nucleotide polymorphisms are single base pair sites that differ among individuals. Chromosomes consist of genes and associated proteins. The human genome consists of 22 pairs of autosomes and one pair of sex chromosomes. A karyotype is the photographic catalog of the human chromosomes. Specialized cells and tissues arise by differentiation from the stem cells of the early embryo. Pedigree diagrams enable recessive and dominant traits to be followed through multiple generations of a family. A gene pool is the collection of alleles in a population. Comparative genomics is leading to a more detailed and subtle understanding of evolutionary relationships among species

Cells are the Working Units of Life With the possible exception of viruses, every form of life on Earth either is a cell or composed of cells. All cells come into existence through the activity of other cells. All Cells are either Prokaryotic or Eukaryotic All cells can be classified as prokaryotic or eukaryotic. All plants, animals, fungi, and protists are either single eukaryotic cells or are composed of eukaryotic cells. Prokaryotic cells are either bacteria or archaea. Eukaryotic cells have most of their DNA contained in a membrane-lined nucleus, whereas prokaryotic cells do not have a nucleus. Eukaryotic cells also have more specialized structures, called organelles, than do prokaryotic cells. All prokaryotes are single-celled, whereas many eukaryotes are multi-celled. The Eukaryotic Cell There are five principal components to the eukaryotic animal cell: the nucleus, other organelles, the cytosol, the cytoskeleton, and the plasma membrane. Organelles are “tiny organs” within the cell that carry out specialized functions, such as energy transfer and material recycling. The cytosol is the fluid in which these organelles are immersed (The cytoplasm is the region of the cell inside the plasma membrane but outside the nucleus.) The cytoskeleton is composed of several groups of proteins that give the cell support and facilitate transportation of cellular elements. The plasma membrane is the chemically active outer boundary of the animal cell. Plant cells have a plasma membrane that has, outside of it, a cell wall.

About Mendel Born in what is now the Czeck Republic. Grew up in an agricultural environment. Became a priest-teacher at a local monastery. Took courses in botany, physics, and mathematics at the University of Vienna. Gregor Mendel was the first person to comprehend some of the most basic principles of genetics. He reached these understandings in the mid-nineteenth century; working in what is now the Czech Republic and using as his experimental subjects a species of garden pea, Pisum sativum.. Carried out “hybridization” experiments with the common garden pea. Mendel’s hypotheses became the laws of inheritance in modern genetics. Mendel’s work re-discovered by Correns, DeVries, and Tschermak in 1900. Period of modern “Mendelian” genetics begin.

When Gene Expression Appears to Alter Mendelian Ratios Lethal Allele Combinations Us recessive lethal alleles eliminaters a progeny class. Multiple Alleles A gene can have more than two alleles, but a diploid individual only has one or two of them. Different allele combinations can produce different phenotypes and different severities of symptoms. Different Dominance Relationships Incomplete dominance of an allele produces a phenotype in the heterozygote that is intermediate between that of either homozygote. Codominant alleles are both expressed in a heterozygote. Epistasis-When One Gene Affects Expression of Another In epistasis, one gene masks the effect of another. An example of epistasis in humans is the Bombay phenotype. The Bombay phenotype results in O type blood for individuals homozygous recessive for the recessive “h” allele.

Genetic Transfer and Mapping in Bacteria Bacteria can transfer genetic material during conjugation Hfr strains contain an f factor integrated into the bacterial chromosome Conjugation experiments can be used to map genes along the E. coli chromosome A detailed genetic map of the E. coli chromosome has been obtained from many conjugation studies Bacteriophages can also transfer genetic material from one bacterial cell to another in the process of transduction Cotransduction can be used to map genes that are within 2 minutes of each other Bacteria can also transfer genetic material by transformation Horizontal gene transfer is the transfer of genes among different species

Linkage and Crossing Over Crossing over may produce recombinant phenotypes. Bateson and Punnett discovered two traits that did not assort independently. Morgan provided evidence for the linkage of several X-linked genes and proposed that crossing over between X chromosomes can occur. A chi square analysis can be used to distinguish between linkage and independent assortment. Creighton and McClintock correlated crossing over that produced new combinations of alleles with the exchange of homologous chromosomes. Crossing over occasionally occurs during mitosis. Genetic Mapping in Plants and Animals The frequency of recombination between two genes can be correlated with their map distance along a chromosome Alfred Sturtevant used the frequency of crossing over in dihybrid crosses to produce the first genetic map. Trihybrid crosses can be used to determine the order and distance between linked genes. Interference can influence the number of double crossovers that occur in a short region.

Genetic Transfer and Mapping in Bacteria a Bacteria can transfer genetic material during conjugation Hfr strains contain an F factor integrated into the bacterial chromosome Hfr strains can transfer a portion of the bacterial chromosome to recipient cells Conjugation experiments can map genes along the E. coli chromosome A genetic map of the E. coli chromosome has been obtained from many conjugation studies Bacteria may contain different types of plasmids Bacteriophages transfer genetic material from one bacterial cell to another via transduction Cotransduction can be used to map genes that are within 2 minutes of each other Bacteria can also transfer genetic material by transformation Bacteria may acquire new genes by horizontal gene transfer

Sex Chromosomes Sex can be considered at chromosomal, gonadal, phenotypic, and gender identity levels. Human females are homogametic (XX) and males are heterogametic (XY). The Y chromosome contains few identified genes, while the larger X chromosome contains several thousand genes. Pseudoautosomal regions at both tips of the Y chromosome contain genes that have counterparts on the X chromosome. The male determining gene, SRY, has been found on the Y chromosome.

Portrait of a Chromosome Cytogenetics is the study of chromosome abnormalities and associated effects on health or other traits. Excess or deficient genetic material can cause syndromes or end prenatal development. Chromosomes consist of highly coiled DNA, RNA, histones, and nonhistone proteins. Telomeres and Centromeres are Essential Telomeres consist of repeat sequences and protect chromosome tips. A centromere is a constricted site where spindle fibers attach during cell division. Centromeres are regions of repeated DNA bound to centromere-associated proteins.

Variation in Chromosome Structure Natural variation exists in chromosome structure Changes in chromosome structure include deletions, duplications, inversions, and translocations The loss of genetic material in a deletion tends to be detrimental to an organism Duplications tend to be less harmful than deletions Duplications provide additional material for gene evolution, sometimes leading to the formation of gene families Copy number variation is relatively common among members of the same species Comparative genomic hybridization is used to detect chromosome deletions and duplications Inversions often occur without phenotypic consequences Inversion heterozygotes may produce abnormal chromosomes due to crossing over Translocations involve exchanges between different chromosomes Individuals with reciprocal translocations may produce abnormal gametes due to the segregation of chromosomes

Identification of DNA as the Genetic Material Experiments with pneumococcus suggested that DNA is the genetic material Hershey and Chase provided evidence that the genetic material injected into the bacterial cytoplasm is T2 phage DNA RNA functions as the genetic material in some viruses Work Before Watson and Crick Nucleotides are the building blocks of nucleic acids Nucleotides are linked together to form a strand In 1869, Miescher first isolated DNA and named it “nuclein.” In 1902, Archibald Garrod linked heredity to enzyme (protein) defects. In 1909 he published a book entitled “Inborn Errors of Metabolism.” In 1928, Griffith identified a “transforming factor” that transmitted infectiousness in bacteria. In 1944, Avery, MacLeod and McCarty showed that the transforming factor was DNA) In 1950, Hershey and Chase, using their famous “blender” experiment, confirmed that DNA, not protein, is the genetic material. The work of chemist Phoebus Levene showed that DNA includes deoxyribose, nitrogenous bases, and phosphates, in equal proportions. Chargaff s data showed that the number of purines equals the number of pyrimidines. Using Rosalind Franklin’s X-ray diffraction patterns, Watson and Crick deduced that DNA is a double helix

Overview of Transcription Gene expression requires base sequences that perform different functional roles The three stages of transcription are initiation, elongation, and termination RNA transcripts have different functions Transcription in Bacteria A promoter is a short sequence of DNA that is necessary to initiate transcription Bacterial transcription is initiated when RNA polymerase holoenzyme binds at a promoter sequence The RNA transcript is synthesized during the elongation stage Transcription is terminated by either an RNA-binding protein or an intrinsic terminator

The Genetic Basis for Protein Synthesis Archibald Garrod proposed that some genes code for the production of a single enzyme Beadle and Tatum’s experiments with Neurospora led them to propose the one gene-one enzyme hypothesis During translation, the genetic code within mRNA is used to make a polypeptide with a specific amino acid sequence Exceptions to the genetic code are known to occur, which include the incorporation of selenocysteine and pyrrolysine into polypeptides Synthetic RNA helped to decipher the genetic code The use of RNA copolymers and the triplet binding assay also helped to crack the genetic code A polypeptide chain has directionality from its amino terminal to its carboxyl terminal end The amino acid sequences of polypeptides determine the structure and function of proteins Cellular proteins are primarily responsible for the characteristics of living cells and an organism’s traits

The Structure of Proteins Proteins are composed of building blocks called amino acids. A string of amino acids is called a polypeptide chain. Once such a chain has folded into its working three-dimensional shape, it is a protein. Though there are tens of thousands of different proteins, all of them are put together from a starting set of 20 amino acids. It is the order in which the amino acids are linked in a polypeptide chain that determines which protein will be produced.

General Effect of Mutation Gene mutations are molecular changes in the DNA sequence of a gene Gene mutations can alter the coding sequence within a gene Gene mutations are also given names that describe how they affect the wild-type genotype and phenotype Gene mutations can occur outside of the coding sequence and still influence gene expression DNA sequences known as trinucleotide repeats may cause mutation Changes in chromosome structure can affect the expression of a gene Mutations can occur in germ line or somatic cells

Sister Chromatid Exchange and Homologous Recombination The staining of harlequin chromosomes can reveal recombination between sister chromatids The holliday model describes a molecular mechanism for the recombination process More recent models have refined the molecular steps of homologous recombination Various proteins are necessary to facilitate homologous recombination Gene conversion may result from DNA gap repair synthesis or DNA mismatch repair

Recombinant DNA Technology A transgenic organism contains foreign DNA. Biotechnology is the industry dedicated to using altered cells or molecules for various applications. Recombinant DNA technology (i.e. gene cloning) was the first of the modern biotechnologies. Gene targeting uses precision techniques to “knockout” a gene or substitute a gene for one on a chromosome. Bioethics questions, gene patenting, and potential uses and risks of biotechnology pose treat questions for society.

Uses of Microorganisms in Biotechnology Somatostatin was the first human peptide hormone produced by recombinant bacteria Many important medicines are produced by recombinant microorganisms Bacterial species can be used as biological control agents The release of recombinant microorganisms into the environment is sometimes controversial Microorganisms can reduce environmental pollutants

Functional Genomics Expressed genes can be identified in a cDNA library A microarray can identify genes that are transcribed The coordinate regulation of many genes is revealed by a DNA microarray analysis Proteomics The proteome is much larger than the genome 2D gel electrophoresis is used to separate a mixture of cellular proteins Mass spectrometry is used to identify proteins Protein microarrays can be used to study protein expression and function

Genome Sequencing: A Continuation of Genetics The human genome project involves the assembly of a DNA sequence map for the 3 billion base pairs present in all 23 human chromosomes. Two groups, the International Consortium and Celera Genomics, used two opposite strategies to obtain a draft sequence of the human genome. The use of bacterial artificial chromosomes (BACs), shotgun clones, and positional cloning has yielded a detailed look at the human genome and is facilitating the identification of disease causing genes. The Sanger Method of DNA Sequencing The Sanger method of DNA sequencing involves an enzymatic extension reaction to generate complementary copies of an unknown DNA sequence. Incorporation of “dideoxy” base causes chain termination and separation of extension products on polyacrylamide gels reveals the sequence bases in the unknown DNA. DNA sequencing occurs on a vast scale today through the use of automated DNA sequencing machines.

Genetic Analysis of Diseases A genetic basis for a human diseases may be suggested from a variety of observations Inheritance patterns of human diseases may be determined via pedigree analysis Many genetic disorders are heterogeneous Genetic testing can identify many inherited human diseases Prions are infectious particles that alter protein function posttranslationally

Invertebrate Development The early stages of embryonic development determine the pattern of structures in the adult organism The study of Drosophila mutants with disrupted development patterns has identified genes that control development The generation of a body pattern depends on the positional information that each cell receives during development The gene products of maternal effect genes are deposited asymmetrically into the oocyte and establish the anteroposterior and dorsoventral axes at a very early stage of development Gap, pair-rule, and segment-polarity genes act sequentially to divide the Drosophila embryo into segments The expression of homeotic genes controls the phenotypic characteristics of segments The developmental fate of each cell in the nematode Caenorhabditis elegans is known Heterochronic mutations disrupt the timing of developmental changes in C. elegans

Quantitative Traits Quantitative traits exhibit a continuum of phenotypic variation that may follow a normal distribution Statistical methods are used to evaluate a frequency distribution quantitatively Some statistical methods compare two variables with each other Polygenic Inheritance Polygenic inheritance and environmental factors create overlaps between genotypes and phenotypes Polygenic inheritance explains DDT-resistance in Drosophila Quantitative trait loci (QTLs) are now mapped by linkage to molecular markers

Genes in Populations A population is a group of interbreeding individuals who share a gene pool Some genes are monomorphic, and others are polymorphic Population genetics is concerned with allele and genotype frequencies The Hardy-Weinberg Equilibrium The Hardy-Weinberg equation can be used to calculate genotype frequencies based on allele frequencies Nonrandom mating may occur in natural and human populations

Origin of Species A biological species is a group of reproductively isolated individuals Speciation usually occurs via a branching process called cladogenesis Divergent evolution can be allopatric, parapatric, or sympatric Müntzing was able to re-create an allotetraploid species Evolution can proceed gradually or be punctuated by periods of rapid change

When Allele Frequencies Stay Constant The Importance of Knowing Allele Frequencies Population genetics concerns the study of allele frequencies in a population. Genes in a population comprise the gene pool. Gene flow is movement of alleles between populations. Microevolution reflects changes in gene frequencies in populations, which can be traced using the Hardy-Weinberg equation. Allele frequencies are affected by mutation, migration, genetic drift, selection, and non-random mating.

Glossary A : Adenine residue, in either DNA or RNA. A priori : Deduced from first principles; without prior knowledge. A site : The binding site for the aminoacyl-tRNA on the ribosome. Ab : See antibody. Abaxial : Directed away from the stem of a plant; pertaining to the lower surface of a leaf (see adaxial). Abiotic : Pertaining to the absence of life, as diseases not caused by living organisms. Abiotic stress : The effect of non-living factors which can harm living organisms. These non-living factors include drought, extreme temperatures, pollutants, etc. Ablation experiment : An experiment designed to produce an animal deficient in one or a few cell types, in order to study cell lineage or cell function. The idea is to make a transgenic mouse with a toxin gene (often diphtheria toxin) under control of a specialized promoter which activates only in the target cell type. When embryo development progresses to the point where it starts to form the target tissue, the toxin gene is activated, and that specific tissue dies. Other tissues are unaffected. Abortive transduction : An event where the fragment of DNA introduced by transduction fails to be recombined into the recipient chromosome and because the DNA fragment lacks an origin of replication it is only inherited by one of the daughter cells at each cell division.