Bio 171 - Introduction to Biology I PDF Lecture Notes

8/20/2024 Bio 171 – Introduction to Biology I Dr. Jeremy Rae Chapter 1 – The Science of Biology © McGraw Hill, LLC 1 Lecture Out...

8/20/2024 Bio 171 – Introduction to Biology I Dr. Jeremy Rae Chapter 1 – The Science of Biology © McGraw Hill, LLC 1 Lecture Outline 1.1 The Science of Life 1.2 The Nature of Science 1.4 Core Concepts in Biology Soames Summerhays/Natural Visions © McGraw Hill, LLC 2 Learning Objectives 1.1 The Science of Life 1. Compare biology to other natural sciences. 2. Describe the characteristics of living systems. 3. Characterize Describe the hierarchical organization of living systems. 1.2 The Nature of Science 1. Compare the different types of reasoning used by biologists. 2. Demonstrate how to formulate and test a hypothesis. 1.4 Core Concepts in Biology 1. Discuss the core concepts that underlie the study of biology. © McGraw Hill, LLC 3 1  8/20/2024 The Science of Life Biology unifies much of natural science Living systems are the most complex chemical systems on Earth. Life is constrained by the properties of chemistry and physics. Science is becoming more interdisciplinary A combination of multiple fields. Life defies simple definition E.g. Biochemistry, Molecular Biology, Molecular Genetics © McGraw Hill, LLC 4 Characteristics of all living organisms 1. Cellular organization 2. Ordered complexity 3. Sensitivity to environment 4. Growth, development, and reproduction 5. Energy utilization 6. Homeostasis 7. Evolutionary adaptation © McGraw Hill, LLC 5 Discussion You are part of an interdisciplinary team researching a distant exoplanet. Your team observes an object that has sparked a debate whether it is extraterrestrial life or not. As the biologist, what experiments or tests might you conduct to answer this question? © McGraw Hill, LLC 6 2  8/20/2024 Discussion Viruses are NOT considered life. Why? What characteristics of life do they not possess? 1. Cellular organization 2. Ordered complexity 3. Sensitivity to environment 4. Growth, development, and reproduction 5. Energy utilization 6. Homeostasis 7. Evolutionary adaptation © McGraw Hill, LLC 7 Hierarchical Organization of Living Systems Living systems show hierarchical organization Cellular level Atoms, molecules, organelles, cells Cell is the basic unit of life (that is Cell Theory). Organismal level Tissues, organs, organ systems © McGraw Hill, LLC 8 Cellular Level Hierarchical Organization (Organelle): Keith R. Porter/Science Source; (Cell): SPL/Science Source; (Tissue): Ed Reschke; Access the text alternative for slide images. © McGraw Hill, LLC 9 3  8/20/2024 Organismal Level Hierarchical Organization (Organism): Russell Illig/Getty Images; Access the text alternative for slide images. © McGraw Hill, LLC 10 Hierarchical Organization—Additional Levels Populational level Population, community Ecosystem level Biosphere Earth is an ecosystem we call the biosphere. Each level has emergent properties. Result from interaction of components. Cannot be deduced by looking at parts themselves. “Life” is an emergent property. © McGraw Hill, LLC 11 Populational Level Hierarchical Organization (Population): George Ostertaga/gefotostock/Alamy Stock Photo; (Species): Sander Meertins/iStock/Getty Images; Pictureguy/Shutterstock; (Community): Ryan McGinnis/Alamy Stock Photo; (Ecosystem): Robert and Jean Pollock; (Biosphere): Goddard Space Flight Center/NASA Access the text alternative for slide images. © McGraw Hill, LLC 12 4  8/20/2024 The Nature of Science Science aims to understand the natural world through observation and reasoning. Science begins with observations, therefore, some science is purely descriptive. Classification of all life on Earth Human genome sequencing © McGraw Hill, LLC 13 Science Uses Deductive and Inductive Reasoning Deductive reasoning uses general principles to make specific predictions Estimate of the circumference of the Earth Inductive reasoning uses specific observations to develop general conclusions Access the text alternative for slide images. © McGraw Hill, LLC 14 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 15 5  8/20/2024 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 16 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 17 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 18 6  8/20/2024 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 19 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 20 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 21 7  8/20/2024 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 22 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 23 Science Is Hypothesis-Driven Scientists use a systematic approach to gain understanding of the natural world. Access the text alternative for slide images. © McGraw Hill, LLC 24 8  8/20/2024 Definition of Hypothesis A hypothesis is a possible explanation for an observation A hypothesis 1. MUST BE TESTABLE AND FALSIFIABLE 2. Must be tested to determine its validity. 3. Is often tested in many different ways. 4. Allows for predictions to be made. Iterative Hypotheses can be changed and refined with new data. © McGraw Hill, LLC 25 Hypothesis Examples Testable and falsifiable hypothesis: Mutation “Y” promotes tumor formation. Untestable and unfalsifiable hypothesis: Aliens secretly designed mutation “Y” and bio-hacked their victims to promote tumor progression. © McGraw Hill, LLC 26 Using Experiments to Test Hypotheses Experiment 1. Tests the hypothesis. 2. Must be carefully designed to test only one variable at a time. 3. Consists of a test experiment and a control experiment. © McGraw Hill, LLC 27 9  8/20/2024 Example – Restriction Enzymes © McGraw Hill, LLC 28 Using Experiments to Test Hypotheses – Restriction Enzyme Test (+) Control (-) Control Ladder Test 1 Test 2 Test 3 © McGraw Hill, LLC Using Predictions Hypotheses should make predictions. Predictions provide a way to test the validity of hypotheses. Hypothesis must be rejected if the experiment produces results inconsistent with the predictions. The more experimentally supported predictions a hypothesis makes, the more valid the hypothesis. © McGraw Hill, LLC 30 10  8/20/2024 A Hypothesis-Driven Experiment SCIENTIFIC THINKING Question: What is the source of contamination that occurs in a flask of nutrient broth left exposed to the air? Germ Hypothesis: Preexisting microorganisms present in the air contaminate nutrient broth. Prediction: Sterilized broth will remain sterile if microorganisms are prevented from entering flask. Spontaneous Generation Hypothesis: Living organisms will spontaneously generate from nonliving organic molecules in broth. Prediction: Organisms will spontaneously generate from organic molecules in broth after sterilization. Test: Use swan-necked flasks to prevent entry of microorganisms. To ensure that broth can still support life, break swan- neck after sterilization. Result: No growth occurs in sterile swan-necked flasks. When the neck is broken off, and the broth is exposed to air, growth occurs. Conclusion: Growth in broth is of preexisting microorganisms. Figure 1.4 Access the text alternative for slide images. © McGraw Hill, LLC 31 Discussion – Hypothesis Practice 1. Gene X promotes cancer development. What is the INDEPENDENT variable? An independent variable is the cause (Gene X) while a dependent variable is the effect in a causal research study. © McGraw Hill, LLC 32 Discussion – Hypothesis Practice 1. Write your own hypothesis! 2. Share with a neighbor or two 3. Can you identify your neighbor’s independent and dependent variables? 4. How could you test their hypothesis? 5. What data would FALSIFY their hypothesis? © McGraw Hill, LLC 33 11  8/20/2024 Philosophical Approaches to Science Reductionism. To break a complex process down to its simpler parts. Systems biology. Focus on emergent properties that can’t be understood by looking at simpler parts. In vitro vs in vivo experimentation: in vitro is simpler (reductionism); reduce confounding variables in vivo is more complex/harder to study, but more representative of the whole © McGraw Hill, LLC 34 Reductionism vs Systems Discussion You study a transcription factor and are interested in the protein-protein interactions it participates in. You could: Study it in vitro purify the transcription factor and other proteins of interest; mix in test tube and see if there is an interaction Study it in vivo Test for interactions inside complete cells/animal tissues Pros and cons of each? © McGraw Hill, LLC 35 Reductionism vs Systems Discussion In vitro: PRO: Remove the “noise” and confusion of everything else going on in the cell CON: More artificial construct (your purified proteins are not at [physiological] and could “force” interactions In vivo: PRO: You may catch indirect interactions that aren’t possible in a simplified in vitro scenario CON: Your antibody used to detect for protein interactions may recognize multiple similar proteins, making your data less reliable/interpretable © McGraw Hill, LLC 36 12  8/20/2024 Scientific Theory A body of interconnected concepts Supported by much experimental evidence and scientific reasoning Expresses ideas of which we are most certain Compare to general meaning of theory: Implies a lack of knowledge or an educated guess. © McGraw Hill, LLC 37 Basic Versus Applied Research Basic Research is intended to extend the boundaries of what we know. Does not mean it’s easy! Begins with a question/observation and SHOULD follow where the data leads Applied Research Foundation provided by basic research. APPLIES knowledge gained from basic research to a specific problem or goal Generally more focused on pre-determined outcome (designing a new prosthetic) May involve the manufacture of goods such as food additives or drugs. © McGraw Hill, LLC 38 Basic vs Applied Research Basic (Knowledge Oriented) Applied (Goal/Problem Oriented) New Outcome Initial Initial Goal Goal/Hypothesis © McGraw Hill, LLC 39 13  8/20/2024 Core Concepts in Biology Life is subject to chemical and physical laws Biological systems follow known chemical properties, such as molecular bonding. Properties of physics, such as thermodynamics, are also key determining factors of biological systems. © McGraw Hill, LLC 40 Structure Determines Function Study structure to learn function Know a function – look for that structure in other organisms Example Receptor on human cell for insulin known. Find similar molecule in a worm. Might conclude this molecule functions the same in the worm. © McGraw Hill, LLC 41 Living Systems Transform Energy and Matter All life constantly requires energy Energy enters environments in one form, typically as solar energy, and is constantly transformed by organisms Photosynthetic organisms transform solar energy into chemical energy as matter (carbohydrates). Other organisms, humans included, transform chemical energy into other forms of energy (for example kinetic) and matter (for example proteins). © McGraw Hill, LLC 42 14  8/20/2024 Living Systems Depend on Information Transactions Deoxyribonucleic acid (DNA) Sequence of 4 nucleotides encode cell’s information Gene – discrete unit of information Genome – entire set of DNA instructions Continuity of life depends on faithful copying of DNA into daughter cells LAGUNA DESIGN/Science Photo Library/Alamy Stock Photo © McGraw Hill, LLC 43 Information Transactions Information in DNA used to direct synthesis of cellular components Control of gene expression leads to different cells/ tissue types. Cells process environmental information Glucose levels, presence of hormones. Cells in multicellular organisms must coordinate with each other. © McGraw Hill, LLC 44 15