Methods and Tools in Science - Minor 2 - Introduction to Biochemistry PDF

Methods and Tools in Science Minor 2- Introduction to Biochemistry Knowledge: It is the awareness or understanding of something like facts or skills gained through experience or learning. In the context of science, knowledge refers to information that is verified and validated through e...

Methods and Tools in Science Minor 2- Introduction to Biochemistry Knowledge: It is the awareness or understanding of something like facts or skills gained through experience or learning. In the context of science, knowledge refers to information that is verified and validated through empirical evidence and the scientific method. Knowledge can be Practical, Theoretical and Scientific. Practical Knowledge: It is the knowledge gained through hands on experience or doing task or action. Characteristics of Practical knowledge Hands on : learn by doing tasks and solving real world problems. Context specific: It can be applied to specific situation. It can not be easily generalized. Tacit: This knowledge is difficult to express in words but is understood through doing. Examples of Practical knowledge: Cooking, Fixing an engine, Repairing an AC Minor 2- Introduction to Biochemistry Theoretical knowledge: Understanding concepts, Principles and Ideas gained through Study and Education. Characteristics: Conceptual: It involves theories and ideas that explain how things function. Abstract: Not directly linked to practical use. Analytical: Emphasizes understanding the connections between ideas. Examples: Learning about economic theories. Understanding the principles of physics. Minor 2- Introduction to Biochemistry Scientific Knowledge: Scientific knowledge is a well-organized and systematic understanding built through the scientific method. This involves observation, experimentation and the testing of hypotheses. Characteristics: Empirical: Based on observation and experimentation. Systematic: Follows a structured approach to inquiry, such as the scientific method. Reproducible: Can be tested and verified by others. Objective: Seeks to minimize bias and rely on factual evidence. Examples: Understanding the structure of DNA through molecular biology. Discovering the principles of electricity and magnetism. Minor 2- Introduction to Biochemistry  Science- Definition Science is a systematic and evidence-based knowledge or approach to understanding the natural world. It involves observation, experimentation, and the use of the scientific method. Scientific knowledge is empirical, reproducible, and falsifiable. Eg: All scientific areas - physics, chemistry, biology etc. Non science- Definition Nonscience refers to areas of knowledge that do not based on the scientific method or empirical evidence. These fields include disciplines like art, philosophy, and religion. This is based on subjective interpretation, or personal beliefs rather than objective, testable data. Eg: Art, Philosophy and Religion Pseudoscience- Definition Pseudoscience is a set of beliefs, theories or practices that claim to be scientific but do not have evidence or methodology. Pseudoscience is not empirical, reproducible, and falsifiable. Eg: Astrology, Phrenology Minor 2- Introduction to Biochemistry  Scientific laws: Scientific laws are rules that describe how things work in nature. They are based on repeated observations and experiments. Scientific laws tell what happens under specific conditions, but they don’t explain why it happens. Eg: Newton’s Law of Gravity, Laws of thermodynamics. Basis of Law of Science 1.Repeated Observations: The same pattern is observed consistently. 2.Empirical Evidence: Data from experiments and measurements support it. 3.Consistency: It works the same way every time in similar conditions. 4.Mathematical Formulation: Often expressed with a formula. 5.Predictive Power: It can reliably predict future outcomes. Minor 2- Introduction to Biochemistry  Factual truths: Factual truths are any statements that can be proven true, not just in science but in everyday life. Scientific laws describe specific rules about how something works in nature. Eg: “Water boils at 100°C at sea level” is a factual truth but is not in the form of scientific law. Laws of Science describe how things happen in nature. Factual truths are things that can be proven to be true. Basis of Factual Truths: 1.Objective Evidence: Based on observable and measurable facts. 2.Verification: Can be confirmed by anyone through testing or observation. 3.Reproducibility: The same result can be consistently observed under the same conditions. 4.Direct Observation: Often derived from what can be directly seen or measured. 5.Universality: True everywhere under the same conditions. Minor 2- Introduction to Biochemistry Tools applied to answer Scientific Questions- Mendel's studies of genetic traits in pea plants. Gregor Mendel is known as the father of genetics because of his ground-breaking work on inheritance in pea plant 150 years ago. He applied several scientific tools and methods to answer key questions about inheritance. He started his research with mice, then moved to honeybees and plants, and finally chose garden peas as his main model for experiments. Mendel studied the inheritance of seven different features in peas, including height, flower color, seed color, and seed shape. He cross-pollinated plants with different traits and observed how the traits appeared in the next generation. He counted the offspring and noticed patterns of dominant and recessive traits. Mendel found that traits followed clear patterns, leading to his discovery of the basic rules of inheritance. His experiments revealed how traits are inherited, now known as Mendel's Laws. Minor 2- Introduction to Biochemistry Mendel’s Experiment on Pea plants Minor 2- Introduction to Biochemistry Scientific tools in Mendel’s study to develop law of inheritance: 1. Selection of Model Organism: Tool: Pea plant A model organism is one that helps researchers easily study scientific questions, like how traits are passed down. Mendel chose pea plants because they had clear, easy- to-see traits, such as flower color, seed shape, and pod color. They have a short generation time and produce many offspring (seeds). 2.Experimental Design Tool: Cross pollination technique He manually cross-pollinated plants to determine which traits were inherited by the next generation. 3. Observation Tool: Visual Examination Mendel observed and recorded the traits of the parent plants and their offspring. 4. Data Collection Step: Counting Offspring He counted the number of offspring displaying each trait to identify patterns in inheritance. Minor 2- Introduction to Biochemistry 5. Generational Tracking Step: Tracking Multiple Generation He followed traits through parental (P), first filial (F1), and second filial (F2) generations to analyze how traits were inherited. 6. Hypothesis Formation Hypothesis: Traits are Inherited as Discrete Units Mendel hypothesized that each trait is controlled by two alleles, one from each parent, which segregate during reproduction. 7. Ratio Analysis Step: Analyzing Ratios He calculated the ratios of traits in the offspring, leading to conclusions about dominant and recessive traits (e.g., a 3:1 ratio in F2). 8. Repetition Step: Repeating Experiments Mendel repeated his experiments with different traits to verify the consistency of his results. 9. Conclusion Tool: Data Interpretation Mendel concluded that traits are inherited according to specific patterns, leading to his formulation of the laws of inheritance. Minor 2- Introduction to Biochemistry  Revolutions in Science with Focus on Biochemistry Scientific revolutions are major discoveries that change how we understand life. In biochemistry, several breakthroughs have helped explain processes at the molecular level. 1. Discovery of DNA Structure (1953) James Watson and Francis Crick discovered that DNA has a double helix shape, like a twisted ladder. This showed how genetic information is stored and passed from one generation to the next, which became the basis for genetics and biotechnology. 2. Central Dogma of Molecular Biology (1958) Francis Crick proposed the central dogma, explaining how information flows in cells: from DNA to RNA to proteins. This describes how genes control the production of proteins, which carry out many essential functions in the body. 3. Enzymes and How They Work The Michaelis-Menten model explained how enzymes act as catalysts, speeding up chemical reactions in the body. This understanding helped in studying metabolism and designing drugs that target enzymes in diseases. Minor 2- Introduction to Biochemistry  4. The Krebs Cycle (1937) Sir Hans Krebs identified a series of chemical reactions that take place in cells to produce energy. This cycle explains how cells break down food to generate energy, crucial for understanding metabolism. 5. Recombinant DNA Technology (1970s) Scientists developed techniques to cut and recombine DNA, allowing genes to be modified or transferred between organisms. This led to the creation of genetically modified organisms (GMOs) and advancements in medicine, including gene therapy. These discoveries in biochemistry have led to major advances in medicine, agriculture, and our understanding of life itself. Minor 2- Introduction to Biochemistry Theory: A theory is a well-supported explanation of how something works in nature, based on lots of evidence. A theory explains why and how something happens based on evidence. Example: The Theory of Evolution explains how species change over time. Law: A law is a statement that tells what always happens in nature under certain conditions but doesn’t explain why. It is often expressed mathematically. A law describes what happens consistently in nature, without explaining why. Example: Newton’s Law of Gravitation describes how objects attract each other due to gravity. Minor 2- Introduction to Biochemistry  Observation Observations are facts or details noticed through the senses or tools. They are the first step in scientific investigation. observations can be qualitative (descriptive) or quantitative (measurable). Eg: Observing that the smartphone battery drains faster when use certain apps are used. Evidence Evidence is the data collected from observations and experiments that support or challenge a hypothesis or theory. Eg: You track the battery percentage while using different apps and find that gaming apps decrease battery life by 50% more than social media apps over the same time period. Proof Proof is strong support for an idea based on consistent evidence, but it can change if new information is found. Studies show that high-performance apps, like games, consistently drain battery life more quickly than other types of apps, providing strong proof of the relationship between app type and battery usage. Minor 2- Introduction to Biochemistry  Other examples: Observation The grass in your yard grows taller in spring than in winter. Evidence You measure the height of the grass weekly during both seasons and find that the average height in spring is 20 cm, while in winter, it is only 5 cm. Proof Studies across different regions show that grass consistently grows taller in spring due to warmer temperatures and increased sunlight, providing strong proof of the seasonal influence on grass growth. Minor 2- Introduction to Biochemistry  Posing a Question Scientific inquiry starts with asking a question based on an observation. This question must be specific and testable. Example: Why do plants grow taller in sunlight than in the shade? Formulation of Hypothesis A hypothesis is a testable, educated guess about the answer to the question. It must be measurable and falsifiable (capable of being proven wrong). Example: If plants are exposed to more sunlight, then they will grow taller because sunlight promotes photosynthesis. Minor 2- Introduction to Biochemistry  The hypothetico-deductive model and the inductive model are two scientific approaches used to investigate phenomena, test ideas, and develop theories. The hypothetico-deductive model is a scientific approach that starts with a hypothesis (a testable statement). Then make predictions from it, and do experiments to see if those predictions are correct or not. Inductive Model The inductive model involves gathering data from specific observations and using that data to form a general conclusion or theory. Minor 2- Introduction to Biochemistry  Comparison: Hypothetico-Deductive Model: Starts with a hypothesis and makes predictions that are then tested through experiments. Inductive Model: Begins with observations, finds patterns, and forms general conclusions or theories based on those patterns. The key difference is that the hypothetico-deductive model moves from a specific idea to test (hypothesis) and checks its validity through experimentation, while the inductive model looks at specific observations and builds broader theories from them. Minor 2- Introduction to Biochemistry  Example: Studying Sleep and Alertness Hypothetico-Deductive Model: Hypothesis: Getting 8 hours of sleep improves alertness during the day. Prediction: People who sleep 8 hours will perform better on attention tests than those who sleep less. Experiment: Two groups are tested—one sleeps 8 hours, the other sleeps less. Their attention is measured in a test. Result: If the group with 8 hours of sleep performs better, the hypothesis is supported. Inductive Model: Observation: A teacher notices that students who report getting 8 hours of sleep seem more focused in class. Pattern: The teacher sees this pattern in many students over the school year. Conclusion: The teacher concludes that more sleep leads to better focus, based on observing this repeated pattern. Minor 2- Introduction to Biochemistry MODULE II Minor 2- Introduction to Biochemistry  Experimentation in Science: Experimentation is a core method in science used to test hypotheses, verify theories, and gain deeper understanding of phenomena. 1. Design of an Experiment: It is the process of planning how to test a hypothesis or answer a scientific question. 1.Key Steps:Choose a question you want to answer. 2.Make a hypothesis: This is your best guess about what might happen. Independent variable: The one thing you change in the experiment. 3.Identify variables Dependent variable: What you measure to see if the change made a difference. Control variables: Things you keep the same to make the test fair. Minor 2- Introduction to Biochemistry  Have a control group: This group does not get the change (independent variable), so you can compare. Plan the steps of your experiment. 2. Experimentation: Doing the experiment based on your plan. 3. Observation: The act of noticing and recording events or phenomena during the experiment. Qualitative observation: Describes characteristics without numbers (e.g., color changes, texture). Quantitative observation: Involves numerical measurements (e.g., temperature, weight). Minor 2- Introduction to Biochemistry  4. Data Collection: Collecting evidence from the experiment, often in the form of numbers, descriptions, or images or Writing down what you observe during the experiment. 5. Interpretation and Deduction: The process of analyzing the collected data to identify patterns, trends, or relationships. 6. Necessity of Units and Dimensions: Units: Standard measurements are important to keep data consistent and easy to compare in experiments. Examples include meters for length, seconds for time, and grams for mass. A dimension refers to the category of a physical quantity. It describes what type of measurement it represents (such as length, time, or mass). Minor 2- Introduction to Biochemistry 7. Repeatability and Replication: Repeatability: The ability to achieve the same results when an experiment is performed under identical conditions. It ensures the reliability of the results. Example: If two different people measure the same sample’s mass with the same balance, they should get the same result. Replication: Conducting the same experiment multiple times (or by different researchers) to confirm the consistency of the findings. Example: Repeating a plant growth experiment with the same conditions several times to ensure consistent results. Minor 2- Introduction to Biochemistry  Scientific Instruments Scientific instruments are tools used to measure, observe, and analyze various physical properties and phenomena. They play a crucial role in experiments and research, enabling scientists to obtain accurate and reliable data. 1. Choice and Selection of Instruments: Choosing the right instrument depends on the type of measurement required and the level of precision needed. 2. Sensitivity of Instruments: Sensitivity refers to how small a change an instrument can detect. Example: A sensitive thermometer can detect a temperature change of 0.01°C, while a less sensitive one might only detect changes of 1°C. Minor 2- Introduction to Biochemistry  3. Accuracy, Precision, and Errors: Accuracy: How close a measurement is to the true value. Example: If the actual temperature is 25°C, and your thermometer reads 25°C, it is accurate. Precision: How consistently an instrument gives the same reading, even if it’s not necessarily accurate. Example: If a thermometer always reads 24.8°C when the actual temperature is 25°C, it is precise but not accurate. Errors: Differences between measured values and the true value. Errors can arise due to limitations of instruments or human error. Systematic Errors: Consistent, repeatable errors (e.g., a scale that always reads 1 gram too high). Random Errors: Unpredictable variations in measurements (e.g., fluctuations in readings due to environmental factors). Minor 2- Introduction to Biochemistry  Types of Instrumentation: Analog Instruments: Provide continuous readings using dials or meters (e.g., mercury thermometer, analog voltmeter). Digital Instruments: Display readings in numerical format (e.g., digital thermometer, digital balance). These are often more precise and easier to read than analog instruments. Specialized Instruments: Instruments designed for specific purposes (e.g., spectrophotometers for measuring light absorption, microscopes for magnifying small objects). Minor 2- Introduction to Biochemistry  Historical Development and Evolution of Scientific Instruments: Early Instruments: Early scientific instruments were simple, such as the astrolabe for navigation or Galileo’s telescope for observing the stars. 19th Century: The development of instruments like the microscope and thermometers advanced scientific discoveries in biology and physics. Modern Era: The rise of digital technology in the 20th and 21st centuries led to highly precise instruments like atomic force microscopes, digital oscilloscopes, and mass spectrometers. These tools allow scientists to observe and measure at the atomic and molecular levels. Minor 2- Introduction to Biochemistry  Scientific Tools Used in Griffith's Experiment 1.Bacterial Strains: 1. Griffith used two strains of Streptococcus pneumoniae bacteria: the virulent S strain and the non-virulent R strain to observe changes in bacterial properties. 2.Animal Models (Mice): 1. Mice were used as living organisms to study the effect of bacterial infection and observe how virulence was transferred between strains. 3.Heat Treatment: 1. Heat was applied to kill the virulent S strain bacteria, leaving behind their components (including the "transforming principle") without causing disease. 4.Injections: 1. Precise injections were used to introduce live and heat-killed bacterial strains into the mice to observe the effects of transformation. 5.Observation and Analysis: 1. By observing the survival or death of the mice, Griffith could analyze the effects of bacterial transformation, eventually leading to the discovery of genetic material transfer. Minor 2- Introduction to Biochemistry Minor 2- Introduction to Biochemistry  Scientific Tools Used in Thomas Hunt Morgan's Fruit Fly Experiments 1.Model Organism (Drosophila melanogaster): 1. Morgan used fruit flies for their fast reproduction rate, distinct traits (like eye color), and ease of observation. 2.Controlled Breeding (Cross-breeding): 1. Morgan conducted controlled mating experiments to track how traits, such as eye color, were passed down through generations. 3.Microscopes: 1. Used to observe chromosomes in fruit flies and study genetic material at the cellular level. 4.Genetic Mapping: 1. By using recombination frequencies (how often traits are inherited together), Morgan created genetic maps showing the relative positions of genes on chromosomes. 5.Mutation Analysis: 1. Spontaneous mutations, such as a white-eyed fly, were key in studying how genetic changes affect inheritance patterns. 6.Recombination and Linkage Studies: 1. Studied how certain traits are linked to the X chromosome and how genes that are close together on a chromosome tend to be inherited together (genetic linkage). These tools helped Morgan confirm that genes are carried on chromosomes, strongly supporting the chromosome theory of inheritance. Minor 2- Introduction to Biochemistry Minor 2- Introduction to Biochemistry Minor 2- Introduction to Biochemistry  To demonstrate the mechanism of DNA replication and confirm that it follows a semi-conservative model. Tools Used: 1.Isotopes (Nitrogen-15 and Nitrogen-14): 1. Heavy nitrogen (15N) and light nitrogen (14N) isotopes were used to label the DNA. 15N was incorporated into the DNA of bacteria initially, and after replication in 14N media, the distribution of these isotopes was tracked. 2.Bacterial Cultures (E. coli): 1. Escherichia coli bacteria were used as the model organism to study DNA replication. 3.Centrifugation (Density Gradient): 1. The DNA was separated using a cesium chloride (CsCl) density gradient centrifugation. This method allowed the separation of DNA strands based on their density, with DNA containing 15N (heavier) and 14N (lighter) forming distinct bands. 4.Ultraviolet Light Detection: 1. UV light was used to visualize the DNA bands in the density gradient after centrifugation, showing the distribution of 15N and 14N labeled DNA. 5.Time-course Experimentation: 1. DNA samples were taken at different time intervals (generations) to observe how the DNA replicated over successive bacterial divisions. Minor 2- Introduction to Biochemistry