Introduction to Engineering Biology PDF

MODULE - 1 INTRODUCTION TO ENGINEERING BIOLOGY NBA Accredited MBA Programme & L E A R N. G ROW. E X C E L Member Of ACBSP  Module 1 Overview of Biological P...

MODULE - 1 INTRODUCTION TO ENGINEERING BIOLOGY NBA Accredited MBA Programme & L E A R N. G ROW. E X C E L Member Of ACBSP  Module 1 Overview of Biological Principles Biology is the scientific study of life and living organisms, encompassing their structure, function, growth, evolution, distribution, and taxonomy. Branches of biology: Biology Molecular Genetics Ecology Microbiology Evolutionary biology biology L E A R N. G ROW. E X C E L  Cell Theory Cells are the basic unit of life or the fundamental unit of life. All living organisms are composed of one or more cells. Types of Cells: Prokaryotic - cells without nucleus, e.g., bacteria. Eukaryotic - Cells with a nucleus that is enclosed within a well-defined nuclear membrane, e.g., plants, animals. Genetic Information: DNA (Deoxyribonucleic Acid) stores genetic information. RNA (Ribonucleic Acid) plays a role in translating this information into proteins. Genes: Genes are segments of DNA that encode for proteins. Chromosomes: Chromosomes are structures within cells that contain a person's genes. L E A R N. G ROW. E X C E L L E A R N. G ROW. E X C E L  Metabolism: The set of life-sustaining chemical reactions in organisms. Catabolism: Catabolism breaks down molecules to produce energy. Anabolism uses energy to construct components of cells such as proteins and nucleic acids. Enzymes: Biological catalysts that speed up biochemical reactions without being consumed. Homeostasis: The ability of an organism to maintain a stable internal environment despite changes in external conditions. Examples: Regulation of body temperature, pH balance, and glucose levels. L E A R N. G ROW. E X C E L  Evolution: Theory of Evolution: Proposed by Charles Darwin, it explains how species change over time through natural selection. (The process where organisms better adapted to their environment tend to survive and produce more offspring.) Ecology: The study of interactions between organisms and their environment. Ecosystems: Communities of living organisms interacting with their physical environment. Includes biotic (living) and abiotic (non-living) components. Biodiversity: The variety of life in the world or in a particular habitat or ecosystem. Biodiversity is crucial for ecosystem resilience, providing ecosystem services, and maintaining genetic resources. L E A R N. G ROW. E X C E L  Ecosystem Resilience: Biodiversity helps ecosystems recover from disturbances (like natural disasters or human impact).E.g. Coral Reefs: Diverse coral species can better withstand changes in temperature and acidity. When some species are stressed, others may thrive, helping to maintain the reef structure and function. Ecosystem Services: Biodiversity contributes to services that are vital for human well-being, such as clean air and water, pollination of crops, climate regulation, and soil fertility. Genetic Resources: A diverse gene pool allows species to adapt to changing environments and resist diseases. E.g. Crop Diversity: Different varieties of rice or wheat offer genetic traits that can improve resistance to diseases, pests, or climate change. L E A R N. G ROW. E X C E L  BIOLOGICAL CLASSIFICATION Taxonomy: The science of classifying organisms. Uses hierarchical system of classification including Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species. Five Kingdoms Monera e.g. Fungi e.g. Plantae e.g. Protista e.g. Animalia e.g. bacteria, mushroom, flowering plants, protozoa, algae mammals, birds archaea yeast conifers L E A R N. G ROW. E X C E L L E A R N. G ROW. E X C E L  Biochemical Cycles Carbon cycle: Describes how carbon moves through the Earth's ecosystems. L E A R N. G ROW. E X C E L  Nitrogen cycle: Describes the conversion of nitrogen into multiple chemical forms as it circulates among atmosphere, terrestrial, and marine ecosystems. L E A R N. G ROW. E X C E L  Application in Engineering Biotechnology: Use of living systems and organisms to develop or make products. 1. Insulin Production: Using genetically engineered bacteria to produce human insulin, which is essential for managing diabetes. 2. Genetically Modified Crops: Developing crops that are resistant to pests, diseases, or harsh environmental conditions, such as Bt cotton or herbicide-resistant soybeans. 3. Bioplastics: Producing biodegradable plastics from renewable biomass sources using microorganisms. 4. Probiotics: Incorporating beneficial bacteria into food products to promote gut health. L E A R N. G ROW. E X C E L  Genetically engineered human insulin Bt cotton Bioplastics Probiotics L E A R N. G ROW. E X C E L Biomedical Engineering: Application of engineering principles to the medical field to design and develop equipment, devices, computer systems, and software used in healthcare. Environmental Engineering: Use of biological principles to solve environmental problems, such as waste management and pollution control. 1. Bioremediation: Using microorganisms to clean up contaminated environments, such as oil spills or heavy metal pollution in soil and water. L E A R N. G ROW. E X C E L  Interdisciplinary nature Interdisciplinary Nature: The interdisciplinary nature of engineering biology stems from the convergence of multiple scientific and engineering disciplines. Key areas that contribute to the field; Biology: Understanding the fundamental principles of life, including cellular processes, genetics, and molecular biology. Engineering: Applying engineering principles to design and develop biological systems and devices. This includes mechanical, electrical, chemical, and materials engineering. Examples- Centrifuge, micropipette, spectrophotometer, electrocardiogram, electroencephalogram, pacemaker, biosensors etc., L E A R N. G ROW. E X C E L  Micropipette Centrifuge Spectrophotometer Biosensor – glucose testing strips L E A R N. G ROW. E X C E L  Electroencephalogram Electrocardiogram pacemaker L E A R N. G ROW. E X C E L  Computer Science: Utilizing computational tools for modelling biological systems, bioinformatics, and data analysis. Example: Smart wearable devices Physics: Applying physical principles to understand biological processes and develop technologies like imaging techniques. Example: Thermodynamics- energy transfer in glycolysis, Mechanics-analysing the forces involved in walking, electromagnetism- transmission of electrical signals as neurons, optics- microscopy, etc. Chemistry: Designing and synthesizing molecules for biological applications, such as drugs and bio- based materials. Examples: Hydrogen bonds, ionic bonds, covalent bonds, acid-base-pH and buffer systems, enzyme activity, thermodynamics-ATP hydrolysis, etc. Mathematics: Using mathematical models to simulate biological systems and predict their behavior. Examples: Mathematical equations help to understand how enzyme conc. affect rate of biochemical reactions, Statistics- Mendelian genetics L E A R N. G ROW. E X C E L  Applications of Engineering Biology 1. Drug Development: Engineering microbes to produce pharmaceuticals 2. Tissue Engineering: Creating artificial organs and tissues for transplantation. 3. Genetically Modified Organisms (GMOs): Enhancing crop resistance to pests, diseases, and environmental conditions. 4. Synthetic Fertilizers: Designing microorganisms that can fix nitrogen or produce essential nutrients. L E A R N. G ROW. E X C E L 5. Bioremediation: Using engineered microbes to clean up pollutants and contaminants. 6. Biofuels: Producing renewable energy sources from biomass. 7. Waste Management: Developing biological processes for waste treatment and recycling. 8. Bioinspired Robotics: Designing robots that mimic biological systems, such as the movement of animals or the structure of plants, for applications in search and rescue. L E A R N. G ROW. E X C E L  Role of Biology in next-generation technology development 1. Interdisciplinary Nature: Biology, traditionally seen as a natural science, increasingly intersects with technology, leading to innovations that leverage biological principles for technological advancements. 2. Technological Impact: Biotechnology, synthetic biology, and bioengineering are at the forefront, driving advancements in various sectors including medicine, agriculture, environmental science, and materials science L E A R N. G ROW. E X C E L  Role of Biology in next-generation technology development Biotechnology and Medicine: Genetic engineering uses tools like CRISPRCas9 to make exact changes to DNA. This can help fix genetic problems and could potentially cure diseases caused by faulty genes. Personalized Medicine: Tailoring medical treatment to individual genetic profiles enhances treatment efficacy and minimizes side effects. Agriculture and Food Production: Genetically Modified Organisms (GMOs): Engineering crops to be resistant to pests, diseases, and environmental conditions improves food security. Precision Agriculture: Utilizing data from sensors, drones, and satellites to optimize farming practices increases yield and reduces environmental impact. L E A R N. G ROW. E X C E L  Role of Biology in next-generation technology development Environmental Science and Sustainability: Bioremediation- Using microorganisms to clean up contaminated environments, such as oil spills and heavy metal pollution, restores ecosystems. Biofuels: Developing renewable energy sources from biological materials reduces dependency on fossil fuels and decreases greenhouse gas emissions. Biomaterials: Designing materials inspired by biological systems (e.g., spider silk, nacre) for use in medical devices, construction, and textiles. L E A R N. G ROW. E X C E L  Role of Biology in next-generation technology development Computing and Data Science: Bioinformatics: Managing and analyzing biological data (genomics, proteomics) to discover new biological insights and medical applications. Leveraging biological systems for computational purposes, such as DNA computing, which uses DNA strands for data storage and processing. Future Prospects: Interdisciplinary Collaboration: Continued collaboration between biologists, engineers, and technologists will drive innovation. L E A R N. G ROW. E X C E L  Role of Biology in next-generation technology development 3. Educational Importance: Understanding biological principles is crucial for engineers to contribute to the next generation of technologies. 4. Global Impact: Biotechnological advancements will address global challenges such as health, food security, and environmental sustainability. L E A R N. G ROW. E X C E L  Understanding Cell Structure and Function:  Introduction to Cell Structure Cells are the fundamental units of life, and understanding their components is essential for comprehending biological processes. PROKARYOTES EUKARYOTES Simple, no nucleus, few organelles. Complex, membrane-bound organelles, nucleus Thrive in extreme environments: deep oceans, high present. atmospheres. Presence of cytoplasm which contains cytosol Absence of membrane bound compartments, and organelles All plants and animal cells are eukaryotes, proteins are localized in the cytosol. including fungi (molds & yeasts) and protozoans Bacteria account for about 1-1.5kg of average Dimension – 10-100μm across human’s weight E.g. fibroblast - 15 μm across, amoeba – E.g. E.coli, Salmonella 0.5mm across, ostrich egg largest visible cell. Introduction to Cell Structure Nucleus: The Control Center Nucleus meaning ‘kernel’ Present in every eukaryotic cell. The nucleus contains the chromosomes that houses the genetic material, DNA, which dictates cellular activities. Nucleoli – present within nucleus, rich in nucleic acids, RNA. Nucleolus produces ribosomes for protein synthesis. Nucleus: The Control Center Nucleus – enclosed by a double membrane, consisting of lipid bilayer, i.e., four layers of lipid associated with carbohydrates and proteins.. Nuclear pores, inner and outer nuclear membrane pinched together and scattered over nucleus, allow transport of molecules (e.g., mRNA). The nucleus plays a pivotal role in cell division and gene expression. Endoplasmic Reticulum Functions First observed in 1940s, name suggested in 1953 by Keith Porter of Rockefeller Institute. ER as a system of broad sheets forming channels. ER is continuous with both cell membrane and outer nuclear membrane, that is involved in transportation of materials from cell’s environment to the nucleus. Endoplasmic Reticulum Functions The endoplasmic reticulum (ER) is divided into rough and smooth types. The rough ER is studded with ribosomes and synthesizes proteins, it has sandpaper like appearance. The smooth ER is involved in secreting and storing carbohydrates, steroid hormones, lipids and detoxification. Ribosomes are not bound to the membranes but they float freely in cytoplasm. Present in cells of endocrine glands. Golgi Apparatus: Processing Center Discovered by Camillo Golgi in 1898. Golgi bodies are flattened, bag like membranous sacs (saccules) lying close to the nucleus The Golgi apparatus (derived from ER) functions as the cell's packaging and distribution center. It modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles. In plants golgi bodies are directly involved in cell division and growth, by releasing complex carbohydrates into the developing cell membrane, which are then deposited in the cell wall.  Lysosomes Lysosomes are membrane-bound organelles containing powerful hydrolytic enzymes synthesized and packed by golgi bodies. Viz digestive sacs. If these enzymes float freely in cytoplasm, the cell itself would get digested. Christian de Duve, described Lysosomes as "suicide bags," as they sometimes destroy the cells that contain them. They break down waste materials and cellular debris (autophagy), playing a vital role in cellular recycling and maintaining cellular health. Their function is crucial for preventing the accumulation of harmful substances.  Lysosomes After phagocytosis, the lysosome fuses with vacuole to empty it contents, aid in digestion. Lysosomes play a role in the regular turnover of cell components, destroying various cell organelles at a constant rate to allow for their replacement, keeping the cell youthful and healthy. Genetic disorders – altered or absence of certain lysosomal enzymes. The unreacted substrates of these enzymes accumulate in the cell, leading to storage diseases, which are fatal in the first year of human life, such as Tay-Sachs disease. Mitochondria: Powerhouses of the Cell Mitochondria are known as the powerhouses of the cell, responsible for energy production through the process of cellular respiration. They are oval structures, with the inner membrane folded into structures called cristae, which extend partway across the inner cavity. The number of mitochondria present in a cell varies depending on its metabolic level. Mitochondria specializes in respiration. Mitochondria: Powerhouses of the Cell Cristae increases the inner surface area of the organelle and biochemical reactions acts on the cristae. Cristae is covered by round granule F1 particles, which contain many of the enzymes associated with the mitochondria's energy producing activity. They convert nutrients into adenosine triphosphate (ATP), the energy currency of the cell, essential for various metabolic processes.  Vacuoles Membrane-bound body with little or no inner structure. Plant cells typically have more and larger vacuoles than animal cells. In plant cells the vacuoles generally dominates central parts of a cell. Vacuoles are filled with cell sap, which contains water and other substances (atmospheric gases, sugars, pigments etc.) either in solution or suspension. In plants metabolic wastes and other poisons are sequestered in the central vacuoles, often forming crystals. Some plants store large amounts of waste poisons in their vacuoles, potentially serving as a protective mechanism against herbivores. Centrioles Centrioles are found in the cells of animals, most protists, fungi, and lower plants, though higher plants appear to have lost their centrioles during evolution. In organisms with centrioles, this tiny organelle plays an important but not well-understood role in cell division. Under a light microscope, the centriole appears as a tiny dot very close to the nucleus, made more prominent by an array of short rays projecting in all directions from it. During cell division, these rays become more prominent and form the two asters and the spindle of the mitotic apparatus. Cilia and Flagella Cilia and flagella are structurally almost identical, differing only in their number and mode of operation. Cilia are usually present in large numbers and beat in a regular, wavelike manner, like oars, propelling organisms like Paramecium through their environments. Flagella, on the other hand, are usually long, few in number, and whip-like, moving in waves from base to tip, propelling an organism like Chlamydomonas through its environment. common structure of 9 + 2 microtubules Basal Body Cilia and flagella arise from basal bodies, which are identical in structure to centrioles. Basal bodies are believed to be the ancestors of centrioles. Both centrioles and basal bodies consist of a group of nine clusters of three fused microtubules arranged in a cylindrical array. From this cylinder, the 9 + 2 microtubular structure of cilia and flagella arises. Microtubules Constituent – protein – tubulin All microtubules are small, hollow tubes. Single microtubules are invisible under a light microscope, but they are visible when they are tightly aligned, as in the asters and the mitotic spindle.  Peroxisomes Peroxisomes are membrane-bound bodies that often lie near mitochondria or chloroplasts. Present in variety of organisms, including plants, animals, and protists. In animals, they are most common in liver and kidney cells. Peroxisomes appear as very dense bodies with a unique crystalline core of tiny tubes, making the organelle stand out unmistakably when it appears in electron micrographs. Peroxisomes contain enzymes and may be a special class of lysosomes. The principal enzyme of liver and kidney peroxisomes is catalase, which helps break down hydrogen peroxide into water and oxygen. Plastids Plastids are intracellular, membrane-bound inclusions in plant cells. no plastids in animal cells. Chloroplast – important plastid, which was reported as early as 1720, although it wasn't named until 1883. Other kinds of plastids - leucoplasts and chromoplasts. All proper plastids are related and that each type can develop from a single primitive type known as a proplastid.  Plastids Plastids have double membrane and contain their own packet of DNA. Leucoplasts – white plastids – present in onion, leaf epidermal cells, apple storage cells etc. Role – storage of starch after it is formed from glucose. Chromoplasts contain pigment – impart colour to flowers In ripening fruit and dying leaves in autumn, chloroplast lose bright green color and reds and yellow of chromoplasts predominate. Coloured pigments include – orange carotenes, yellow xanthophylls Exploration of Common Biological Signals Introduction Biological signals are electrical or chemical changes in the body. Measured to gain insights into physiological processes. Non-invasive monitoring of organs like the heart and brain. Types of Biological Signals Electrical Signals: Generated by cells, especially in the nervous system, heart, and muscles. Chemical Signals: Reflect changes in chemical concentrations, hormones, or metabolites. Mechanical Signals: Related to mechanical changes like pressure and movement. Electrical Signals: Examples ECG (Electrocardiogram): Measures electrical activity of the heart. EEG (Electroencephalogram): Measures brain electrical activity. EMG (Electromyogram): Records electrical activity of muscles. EOG (Electrooculogram): Measures eye muscle activity. Electrocardiogram Electrocardiogram (ECG) records the electrical changes during heart contractions. The curve reflects the heart's ability to eject blood, rhythm, and speed. Diagnoses cardiac arrhythmias: Abnormalities in sinus node, atrial node, or myocardium. Diagnoses atrial and ventricular hypertrophy by monitoring myocardium depolarization and repolarization. Detects conduction disorders and myocardial infarction.  Electrocardiogram Diagnosis of ischemic heart disease: The ischemic (lack of blood supply) heart muscle shows abnormal waveforms. Electrolyte disorders: Changes in sodium, potassium, and calcium levels affect ECG results. Monitors pacemakers and detects drug toxicity, e.g., digoxin and antidepressants.  Electroencephalogram EEG records bioelectrical activity of the brain using electrodes placed on the scalp. The electrical activity forms brain waves that are recorded on the electroencephalogram. EEG helps diagnose abnormal brain waves and related brain diseases. Detects epilepsy, headaches, sleep problems, seizures, traumatic brain injuries. Used for diagnosing brain tumors and diseases of the central nervous system. Chemical Signals: Examples Blood Glucose Levels: Measures glucose concentration in blood. Hormone Levels: Measures hormones like insulin and cortisol. Mechanical Signals: Examples Blood Pressure: Measures the force of blood on vessel walls. Respiratory Signals: Tracks breathing mechanics.  Acquisition of Biological Signals Sensors and Electrodes: Detect and measure biological signals. Amplification: Weak signals need amplification for proper recording. Filtering: Removes noise to ensure accuracy. ADC: Converts analog signals to digital for processing.  Signal Processing Signal Filtering: Removes unwanted noise from the signal. Feature Extraction: Identifies key characteristics or patterns. Time-Frequency Analysis: Techniques like Fourier and Wavelet Transform. Pattern Recognition: Detects specific patterns in normal or pathological conditions. Machine Learning & AI Machine Learning and AI improve diagnosis accuracy. Used in large datasets of biological signals. Applications: Medical Diagnostics Cardiology: ECG diagnoses arrhythmias, heart attacks. Neurology: EEG diagnoses epilepsy, brain injuries. Respiratory Medicine: Signals diagnose sleep apnea, COPD. Continuous Monitoring: Wearable devices monitor vital signs. Telemedicine: Remote monitoring enables timely intervention.  Applications: Research Cognitive Neuroscience: EEG, MEG study brain function. Human Performance: EMG, ECG used in sports science. Biofeedback: Train control of heart rate or muscle tension. Neurofeedback: EEG trains the brain for conditions like ADHD. Challenges in Biological Signal Processing Noise and Artifacts: Contamination from muscle movement or interference. Individual Variability: Affects signal consistency. Technical Limitations: Issues with sensitivity, resolution. Future Directions in Signal Analysis Advanced Signal Processing: New algorithms for real-time analysis. AI and Big Data: Improve diagnostics and personalized treatments. Wearable Devices: Compact devices for continuous monitoring.  Future Directions in Signal Analysis Multimodal Signal Integration: Combining multiple biological signals (e.g., ECG, EEG, EMG) for a more comprehensive understanding of physiological states and conditions. Telemedicine and Remote Health Monitoring: Expanding the use of biological signals in telehealth to provide care to remote or underserved populations.  SODIUM POTTASIUM PUMP Active transport Found especially in nerve and muscle cells Hydrolysis of one molecule of ATP to ADP & Pi exports 3 Na ions & imports 2 K ions  WHAT? Process of using natural catalysts like enzymes or whole cells, to BIOCATALYSIS perform chemical transformations ✓ Integral to green chemistry ✓ Offering more sustainable & environmentally friendly methods ✓ Operates under mild conditions - reduced energy requirements ✓ Minimized production of hazardous by-products MECHANISM  TYPES OF BIOCATALYSTS ENZYMES Hydrolases Oxidoreductases Transferases Lyases Isomerases Ligases Whole cells  INDUSTRIAL APPLICATIONS OF BIOCATALYSTS Pharmaceuticals Food Industry Biofuels Fine Chemicals Chiral synthesis Enzymatic processing Cellulose to ethanol Biocatalytic synthesis Antibiotics Flavor & aroma Biodiesel Polymerization Vitamins & hormones Beverages ADVANTAGES & CHALLENGES ADVANTAGES CHALLENGES ✓ Environment friendliness ✓ Enzyme stability ✓ High selectivity & specificity ✓ Cost of production ✓ Perform complex reactions ✓ Substrate range ✓ Catalyst renewability ✓ Product inhibition