Lecture 1 Tareq - Biotechnology PDF

Chapter I What is meant by biotechnology? Biotechnology is an area of applied bioscience and technology which involves the practical application of biological systems to manufacturing a desired end product and to environmental management.  The biological systems (biocatalysts) utilized as c...

Chapter I What is meant by biotechnology? Biotechnology is an area of applied bioscience and technology which involves the practical application of biological systems to manufacturing a desired end product and to environmental management.  The biological systems (biocatalysts) utilized as constituents of the biotechnology or industrial processes are a- Microorganisms including bacteria, fungi (yeasts and molds) and algae b- Plant / plant cell cultures or animals / mammalian cell cultures and c- Sub-cellular components of organisms (enzymes).  Successful application of biotechnology results only from the integration of a multiplicity of technologies and scientific disciplines, ‫إدماج عديد من التقنيات والتخصصات العلمية‬ including microbiology, biochemistry, genetics, molecular biology, chemistry and processes of engineering.  Biotechnological processes normally involve the production of cells or biomass, and the achievement ‫ إنجاز‬/‫ تحقيق‬of desired products. The later may be further subdivided into: a- Formation of a desired end product (e.g., alcohol, amino acids, vitamins, enzymes, antibiotics, organic acids such as citric and acetic acids, and steroids, …)  b- Engineered products / systems (hormones, insulin, genetically modified plants/ animals, and systems/instruments; biosensors and biodetectors,….. c- Decomposition of a given starting material ,e.g., sewage disposal, ‫التخلص من مياه‬ ‫الصرف الصحي‬ , destruction of industrial wastes / ‫المخلفات‬ ‫النفايات الصناعية‬ and oil spillages ‫ انسكابات النفط‬.  Biotechnology can be classified into: a - old or traditional biotechnology; includes mainly fermentation processes which are ranging from beers, wines , bread, cheese, alcohol, to antibiotics, amino acids, vitamins, traditional vaccines (e.g., measles and mumps vaccines), traditional water and waste treatment, and parts of food technology. and  b- recent biotechnology; an increasing range of novel ‫غير مألوف‬ applications ranging from biomedicals (interferon, insulin, interleukins, clotting factors, …) to metal – recovery from – low – grade ones. This is based on recombinant DNA technology  Historical evolution of biotechnology Contrary to popular belief biotechnology is not a new pursuit ‫ حرفة‬/ ‫نشاط‬, but dates for back into history. In practice, four major developmental phases can be identified in arriving at modern biotechnological systems. 1. First developmental phase: Biotechnological production of foods and beverages. Activities such as baking ‫( الخبيز‬i.e., cook food, by dry heat without direct exposure to a flame, typically in an oven or on a hot surface, or sun, brewing ‫ تخمير‬and wine making are known to date back several millennia ‫ ;آالف السنين‬ex. a- the ancient Sumerians and Babylonians were drinking beer by 6000 B.C.‫ قبل الميالد‬, b- the Egyptians were baking leavened bread ‫ الخبز المخمر‬by 4000 B.C.,. - Fermented dough ‫ العجين‬was discovered by accident when dough was not baked immediately. ;Dough was not directly cooked but left away for time - While wine was known in the Near East ‫ الشرق األدنى‬by the time of the book of Genesis ‫كتاب سفر التكوين‬ - the Egyptians, by 5000 B.C., made wine from grapes.  c- Vinegar has been made and used by people for thousands of years. Traces of it have been found in Egyptian urns‫ جرار‬from around 3000 B.C. ‫ = جرة حفظ‬urn ‫جرة تحفظ رماد الوتى‬ In the Bible, it is mentioned as something not very pleasant, but Boaz allows Ruth " to ‫ ولكن بوعز يسمح راعوث إلى "تراجع لها قطعة من الخبز في الخل‬،‫لطيفا جداجرة تحفظ رماد الوتى‬  The recognition ‫ اعتراف‬that these biotechnological processes, were being affected by living organisms, such as yeasts, was not formulated until the 17th century, by Anton van Leeuwenhoek. Definitive proof ‫ أدلة قاطعة‬of the fermentative abilities of the microorganisms came from the studies of Pasteur between 1857 and 1876. Pasteur can justifiably ‫ له ما يبرره‬be considered as the father of biotechnology.  d- Other microbial based processes - the production of fermented milk products, e.g., cheeses and yogurts, and various oriental foods ‫األطعمة الشرقية‬, e.g., soy sauce ‫ صلصة الصويا‬and tempeh (an Indonesian dish made by deep-frying fermented soybeans) ‫قلي فول الصويا المخمر‬ etc., can equally claim distant ancestry ‫األجداد البعيدة‬. - Of more recent introduction is mushroom cultivation which probably dates back many hundreds of years for the cultivation of mushroom's Japanese, shiitake. and about 300 years for the Agaricus mushroom now widely cultivated throughout the temperate world. 2. Second developmental phase: Biotechnological processes initially developed under non-sterile conditions Many important industrial compounds such as ethanol, organic acids (as acetic acid), butanol and acetone were being produced by the end of the 19th century by microbial fermentation procedures. By World War I – fermentation of organic solvents for explosives (glycerol)  This in turn were open to the environment the control of nonsterile condition), i.e., control contaminating microorganisms was achieved by careful manipulation (careful handling) of the ecological environment and NOT by complicated engineering practices. Moreover, by controlling the production process (e.g., pH values and butyrate conc.) to avoid mixture product such as butanol and acetone by Clostridium acetobutylicum  - Other outstanding examples of non- sterile biotechnology are 1- waste water treatment and municipal ‫ البلدية‬composting of solid wastes ‫التحويل إلى سماد البلدي للمخلفات الصلبة‬ ; microorganisms have long been exploited for purposes of 2- decomposing and detoxifying human sewage and to a lesser extent ‫ بدرجة أقل‬/ ‫ الى حد ما‬, in 3- the treatment of industrial toxic wastes such as those from the chemicals industry. 3. Third developmental phase: The introduction of sterility to biotechnological processes. - in the 1940s, and by World War II a new direction in biotechnology came with the introduction of complicated engineering techniques to the mass cultivation of microorganisms to ensure that the particular biological process could proceed with the exclusion of contaminating by undesired microorganisms, i.e., construction of reactors  Thus, these techniques provide sterilization of the medium and the reactors (bioreactors or fermenters) exclude incoming contaminants. Only the chosen biocatalyst was present in the reactor. Most of these processes are complicated, expensive and suitable only for high value products.  Examples of such products, which represent an increasing volume of biotechnological activity, include antibiotics, amino acids, organic acids (of pure and higher yields), enzymes, steroids, polysaccharides and traditional vaccines (e.g., cholera, measles and mumps vaccines). These were achieved over about 2 decades till the discovery of the gene manipulating techniques in the early 1970’s and starting the fourth phase of development. In the 1950’s, cholesterol was converted to cortison and sex hormones by reactions; such as microbial hydroxylation (addition of - OH group). … biotransformation / bioconversion By the mid-1950’s, amino acids and other primary metabolites (needed for cell growth) were produced, as well as enzymes and vitamins  By the 1960’s, microbes were being used as sources of protein and other molecules called secondary metabolites (i.e. that are not needed for cell growth) in large scale, such as ………. - Biomass for commercial and animal consumption (single-cell protein) - Pharmaceutical compounds such as antibiotics, amino acids,………….. - Many chemicals, hormones, and pigments. - Enzymes with a large variety of uses  4. Fourth developmental phase : The New dimensions and possibilities for biotechnological industries. Within the last 4-5 decades there have been outstanding development in molecular biology and process control (see table 1), ‫تطور متميز في البيولوجيا الجزيئية والتحكم في العملية‬ which have created new and exiting opportunities ‫ فرص‬not only to create new dimensions but also to improve greatly the efficiency and economics of the established biotechnological industries.  It is largely from these discoveries and developments that there have been such euphoric statements ‫ الحماسية‬/‫التصريحات البهيجة‬ about the future role of biotechnology to the world economy.  Table 1: Techniques stimulating the development of biotechnology. Recombinant DNA manipulation Bioinformatics Tissue culture techniques Protoplast fusion Monoclonal antibody preparation Protein structural modification  Table 1 continue : Techniques stimulating the development of biotechnology. Immobilized enzyme and cell catalysis Sensing with the aid of biological molecules ……… by construction of biodetectors/biodiagnostics based on immobilized biocatalyst and bioinformatics * Computer linkage of reactors and processes by monitoring production processes based on immobilized biocatalyst and bioinformatics New biocatalytic reactor design ….. and downstream processing based on immobilized biocatalyst and bioinformatics  What then are these new innovations? ‫االبتكارات‬ A- Generic engineering. a- Manipulation ‫ معالجة بارعة‬of the genome of industrially important organisms: by sexual recombination as in fungi and/or by artificial or induced mutation has long been part of the innovative repertoire of the industrial geneticist..‫مرجع مبتكر لعلم الوراثة الصناعية‬/ ‫ مخزون‬  b- New recombinant DNA, The discovery of the gene manipulating techniques in the early 1970’s with other new ones was starting the fourth phase of biotechnology development. - 1971-1972,scientists manipulated DNA and placed them into bacteria, i.e., scientists joined two DNA molecules from different sources using the, e.g., the endonuclease EcoRI (to cut) and DNA ligase (to reseal /rejoin). This is called (new recombinant DNA / Gene technology Restriction endonucleases  In recombinant DNA; purification and subsequent selective DNA fragmentation by highly specific enzymes: the sorting, analysis, selection and purification of a fragment containing a required gene; chemical bonding to the DNA of a carrier molecule (vector) and the introduction of the hybrid DNA into a selected cell (expression host) for reproduction and cellular synthesis.  B- Biochemical engineering. Construction of bioreactors / fermenters play a central role in biotechnological processes by providing a link between the starting materials or substrates and final products. Why? Biochemical engineering provides major advances in construction of bioreactors by providing a link between starting materials or substrates and final products. These major advances have been made in a- bioreactor designs, in process monitoring techniques and in computer control of fermentation processes, based on bioinformatics b- New-approaches to- the processing of the products – of biotechnology (downstream processing) will improve the economics of all processes. …… i.e., increase quality and yield C- Enzyme technology. Isolated enzymes have long been a part of many biotechnological processes, and their catalytic properties are being further utilized with the 1-development of suitable immobilization techniques allowing reuse of the biocatalyst.  Of particular importance has been the development of high fructose syrups (annual production 3 million tones) using immobilized bacterial glucose isomerase. 2- A further development is the immobilization of whole cells for biocatalytic purposes. The immobilized biocatalysts are served in production of engineered product / systems  D- Engineered products / systems. The ability to produce in quantity biological molecules such as antibodies or enzymes together with the techniques of protein and cell / enzyme immobilization are allowing the development of radically biosensors, in addition to bioreactors  Such systems can be combined with micro-electronic devices and ultimately computers allowing sophisticated control programming in many biotechnological industries and health care services. Examples immobilized biocatalysts-based systems include; A- Biosensors: a- biodiagnostic...Kits for ELISA, blood sugar b- biodetectors…. Monitoring biological reactions in fermenters B- Bioreactors; a- biosynthesis.. e.g., fructose syrup production b- bio-detoxification of waste & water, i.e., bioremediation c- bio conversion.. Converts L- amino acid to D form  NB; Some definitions 1- Genetic engineering: How to deal with genetic elements; cutting , joining it into another DNA, introducing it into new host cells. This involves taking one or more genes from a location in one organism and either transferring them to another organism or putting them back into the original organism in different combinations.  2- Tansgenic organism: an organism which acquired genetic material by genetic engineering are said to be transgenic organism. This organism is also called genetically altered or Genetically modified organisms (GMOs)  The organisms that have been genetically modified include bacteria and yeast, insects, plants, fish, and mammals. Importance of genetically modified organisms are a- the source of genetically modified foods and are also widely used in scientific research and to produce goods other than food. b- drug production; novel ‫غبر مالوف‬/ ‫ جديدة‬drugs c- developed disease resistant animals and plants.  3- Fermentation: a controlled process for high yield production of a desired component ,e.g., alcohol, organic compounds, vitamins, amino acids, antibiotics, ….using certain microorganisms. 4- Bioinformatics is an interdisciplinary field ‫مجال متعدد التخصصات‬ that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines biology, computer science, mathematics and statistics to analyze and interpret biological data.  Bioinformatics applications: They are used in all aspects of life, analyzing phenotypic and genotypic characters of any organism and studying how normal cellular activities (DNA, protein and other biological activities) are altered and thus the bioinformatics applications involve:  a- In medicine; helps in diagnosis of diseases, identification of causative agents, and understanding of disease, as cancer, development and pharmaco-genomics and personalized medicine.  b- In biotechnology; the production of biopharmaceuticals including (novel drugs) and DNA vaccines, and diagnostic kits. Also stem cell, gene and genetic therapies, and improve the microbial quality and select suitable conditions for maximum production and recovery of desired products and environment management ……. atc …  c- to study of homology and similarity among organisms and to define the origin and descent of species ‫أصل األنواع‬, as well as their change over time 1- Chemical Industry: a-Production of bulk chemicals and solvents such as ethanol, citric acid, acetone and butanol and in pure form. b-Synthesis of fine specialty chemicals such as enzymes, amino acids, alkaloids and antibiotics 2- Environment: a- Biological recovery of heavy metals from mine tailings ‫ مخلفات المناجم‬and other industrial sources b- Bioremediation/ biodegradation of soil and water polluted with toxic chemicals c-Sewage and other organic waste treatment 3- Medicine: a- Development of novel therapeutic molecules for medical treatments b- Diagnostics kits c- Drug delivery systems d- Tissue engineering of replacement organs e- Gene and genetic therapies, and stem cell therapy Their roles in future of medicine a-smart drugs for cancer and autoimmune diseases (arthritis, psoriasis‫الصدفية‬, diabetes) NB; Psoriasis is a long-lasting autoimmune disease characterized by patches of abnormal skin. These skin patches are typically red, dry, itchy, and scaly. On people with darker skin the patches may be purple in colour. Psoriasis varies in severity from small, localized patches to complete body coverage b-gene-based diagnostics and therapies c- stem cells and regenerative medicine ‫الخاليا الجذعية والطب التجديدي‬  d-pharmaco-genomics and personalized medicine Over the past 2 decades, or so, in biomedical research, with the help of the bioinformatics, have unfolded a series of new, predictive sciences ‫ العلوم التنبؤية‬that share the appendage - omics (genomics, proteomics, metabolomics, cytomics ‫)هو علم دراسة نظام الخلية‬. These are opening the possibility of a new approach to drug development as well as the potential of significantly unleashing ‫إطالق العنان‬ more effective diagnosis, therapeutics, and patient care.  The use of genetic information has played a major role in certain aspects of personalized medicine (e.g. pharmacogenomics), and the term was first coined in the context of genetics, though it has since broadened to encompass ‫ يشمل‬all sorts of personalization measures  Pharmacogenomics is the study of genetic variations that influence individual response to drugs. Knowing whether a patient carries any of these genetic variations can help prescribers individualize drug therapy (‫)تخصيص العالج الدوائي‬, decrease the chance for adverse drug events, and increase the effectiveness of drugs.  Personalized medicine / measure is the use of detailed information about a patient's genotype or level of gene expression and a patient's clinical data to select a medication; therapy or preventative measure (drugs) that is particularly suited to‫ مناسبة ل‬that patient at the time of administration. The benefits of this approach are accuracy of selection of drug, and efficacy, safety and speed of effect..  Biotechnology or Biotechnological process involves a three - component central core: A- Biological system (e.g. organisms) - improvement of quality (isolation and selection, mutation, recombinant DNA). B- Construction of bioreactors, technique operation, controls the condition for the production. C- Downstream processing: isolation and purification of the product.  Organism selection Applied genetics Mutation, recombination, gene manipulation Air Energy ± Raw materials Bioreactor Selection, Microbial, animal or Downstream Product preparation Sterilization plant cells or Processing isolated ± Pretreatment enzymes Product separation Heat Formulation processing Process control