Biol 190A: Introduction to Cell and Molecular Biology Lecture Notes PDF

Biol 190A: Introduction to Cell and Molecular Biology Instructor: Dr. Rafferty Email: [email protected] Office Hours: Tuesdays 10-11am in-person and Zoom Office: WHI 309A Course Information and Organization Loading… Your job as a student is to fill in the gaps in your moti...

Biol 190A: Introduction to Cell and Molecular Biology Instructor: Dr. Rafferty Email: [email protected] Office Hours: Tuesdays 10-11am in-person and Zoom Office: WHI 309A Course Information and Organization Loading… Your job as a student is to fill in the gaps in your motivation bridge. Loading…  Pre-chapter reading- completion by deadline only In-class/Participation assignments- ensures class attendance Post-chapter quizzes- graded for correctness (open book) Engagement 1. 2. Test 1- Feb 12 Test 2- Mar 20 25% 3. Test 3- Apr 22 4. Final- May 8 EXAMS Doing all of this may seem like enough compared to engagement in high school, 75% but success requires more! Pre-chapter Assignments You can access all pre-chapter assignments now Must be completed by the day we cover that chapter in class Plan the time that works best for your schedule Give 1-1.5 hours to complete Can start and stop over multiple days Drop the lowest grade at end of semester This is a deadline picked because it gives me time to review the class data before class time. You can pick a different, earlier deadline for your schedule. Pre-chapter Assignments Post-chapter Assignments Open on Thursdays at 2pm. Closes Sunday night at midnight. Plan the time that works best for your schedule Must complete in ONE sitting Grade is recorded Drop the lowest grade at end of semester How to keep track of it all? Making use of your in-class time Set peer groups in the 3rd or 4th class Lots of problem solving embedded in the lecture slides Section–based learning objectives and questions handed out each class Loading… I don’t post these to Canvas, but you can get them from a group member We often create summary tables or figures to capture the bulk of each chapter Feel free to ask questions in class When we work in groups, Adam and I will walk around to answer questions (good time to ask if you do not like speaking in front of whole class)  Keep info in Syllabus: 1. Email response times 2. Absences Email response time Within 2 business days (Monday-Friday) Absences If you have a religious holiday, UNLV event, or medical/legal emergency with documentation then you can make up the work. Situation Your action Can you make up the work? Woke up with fever on Emailed me that you were sick. Yes, we will reschedule the exam day Within 3 business days, emailed me a make up exam for the last Friday copy of doctor’s note (Quickcare, of the term. UNLV health center, etc). Had doctors appt Emailed me ahead of time that you Yes. But I don’t keep track of scheduled during class would miss class that day. who’s in class, so email to and we had an in-class Check Canvas to see if we had an remind me to send you an assignment and email me to request an alternate assignment. assignment that day alternate in-class work. Jury duty/Appt with Emailed me ahead of time that have a You can make up in-class work lawyer jury summons legal obligation. or exams, but not Pre- and Post- chapter assignments. Military duties Email me ahead of time to discuss. Yes, but each situation is unique so let’s make a plan. I have a family Email me as soon as you can. This really depends. For equity emergency to the class, I need some kind of Absences If you have a religious holiday, UNLV event, or medical/legal emergency with documentation then you can make up the work. Situation Your action Can you make up the work? Student falls behind in Email me to explain Most likely not. I drop the lowest Pre-, classwork. post-, and in-class assignment to accommodate the rare need to miss class. Some personal Please talk with me. Maybe. Let’s talk about what is going situation that is on and what support you need. Your affecting success in all academic needs may be greater than just a make up assignment in Biol 190. classes. Missed pre- or- post-assignments These assignments are open in very large windows, so please plan to complete them at a time that fits your schedule. Given that the completion window is so big, connectivity to wireless issues are not valid reasons for me to offer a make up. Utilize your on-campus time to complete them with good connectivity Please look at what you are clicking on before you click on it. Are you advancing to the next question or submitting the assignment altogether? Please email when the Connect system is down or a question is not displaying correctly. I can edit specific questions or give a deadline extension to everyone if the system is down. Biol 190A Study Time Everything is great until Test 1 scores are released. And then students either love the class or hate this class. Biology is tough to learn because the problems are not discrete like in a math class. Because of that, mastering the information takes more study time than other classes. Please plan an extra 9+ hours per week into your schedule to study for Biol 190A. Biol 190A Study Time Do pre-chapter 2 assignment Write down topics that are unclear or questions I do not understand Flip through the posted Lecture slides ahead of time See if any of my tough-topics are addressed Attend class Keeping an ear/eye for explanations of my tough-topics Ask questions at this time or in small group work Find answers the Learning objectives in Chapter 2 handout (next slide) For those tough-topics that are still muddy, STOP and write a post in the Course Discussion board for help. This way you do not spin your wheels and get frustrated Attend SI sessions each week if possible or attend  tutoring in the Leid library. Biol 190A Study Time  Biol 190A Study Time. Do pre-chapter 2 assignment Write down topics that are unclear or questions I do not understand. Flip through the posted Lecture slides ahead of time See if any of my tough-topics are addressed. Attend class Keeping an ear/eye for explanations of my tough-topics Ask questions at this time or in small group work. Find answers the Learning objectives in Chapter 2 handout (next slide) For those tough-topics that are still muddy, STOP and write a post in the Course Discussion board for help. This way you do not spin your wheels and get frustrated Biol 190A Study Time Chapter 1 – An Introduction to Biology Chapter Outline 1. Principles of biology and the levels of biological organization 2. Biological evolution 3. Classification of living things (taxonomy) 4. Biology as a scientific discipline Remember blue font color marks important ideas and bold marks terms to master 1.1 Principles of Biology & Levels of Organization Section 1.1 Learning Outcomes 1. Describe the principles of biology 2. Identify and explain examples of each principle of biology 3. Explain how life can be viewed at different levels of biological complexity 1.1 Principles of Biology & Levels of Organization Biology is the study of life Investigations of living things can lead to discoveries with far- reaching benefits Ex: salicylic acid (aspirin) from the willow tree and blood pressure medicine (ACE inhibitor) from poisonous snakes Group work You just came back from a mission to Mars claiming that you have discovered life there. What types of things must your “lifeform” do or have to justify your claim? (throw out some ideas please!) 1. Interact w/ environment somehow 2. Use energy 3 should have at least I cell. 1.1 Principles of Biology & Levels of Organization The Study of Life Has Revealed a Set of Unifying Principles Biologists have described a set of principles that apply to all fields of biology; principles 1 through 6 define the basic features of life Principle 1: Cells are the simplest units of life S The cell theory is a foundation of biology All organisms are composed of 1 or more cells Cells are the smallest units of life - [ New cells come from pre-existing cells by cell division Principle 2: Living organisms use energy The maintenance of organization requires energy 1.1 Principles of Biology & Levels of Organization The Study of Life Has Revealed a Set of Unifying Principles Principle 3: Living organisms interact with their environment Both living (ex: predator) and non-living components (ex: light) Principle 4: Living organisms maintain homeostasis The amount of variability for a parameter may differ between species (ex: body temperature in mammal versus reptile) 1.1 Principles of Biology & Levels of Organization The Study of Life Has Revealed a Set of Unifying Principles Principle 5: The genetic material (DNA) provides a blueprint that allows organisms to grow, develop, and reproduce Principle 6: Populations of organisms evolve from one generation to the next and are related by an evolutionary history All organisms contain genetic material composed of DNA, [ deoxyribonucleic acid ] The genetic information of a population can change over time Lines of evidence include DNA sequences and fossils 1.1 Principles of Biology & Levels of Organization The Study of Life Has Revealed a Set of Unifying Principles In addition to the preceding 6 characteristics of life, biologists have identified other principles and skills that are important in all fields of biology Principle 7: Structure determines function ~ Principle 8: New properties of life emerge from complex interactions Loading… screenin Principle 9: Biology is an experimental science 1.1 Principles of Biology & Levels of Organization The Study of Life Has Revealed a Set of Unifying Principles Principle 10: Biology is a quantitative science Principle 11: Biologists use models and simulations to test experimental predictions and convey their ideas A model is a conceptual, mathematical, or physical depiction of a real-world phenomenon Principle 12: Biology affects our society 1.1 Principles of Biology & Levels of Organization Organisms Are Studied at Different Levels of Organization The organization of living organisms can be analyzed at different levels of biological complexity, ranging from atoms to the biosphere Atoms Molecules Cells Tissues Organs Organ systems Organism individuals Population multiple · organisms or species. a me of Community different · z or more of Populations species. Ecosystem biotic : abiotic · - factors in system Biosphere Everyecosystem - · on the Ex Earth. planet : Group work At what organizational level would you classify Death Valley National Park? ecosystem be biotic = chiotic What information did we just learn that explains the “UNITY” among all living things? - All have a Common ancestor. 1.2 Biological Evolution Section 1.2 Learning Outcomes 1. Explain the 2 basic mechanisms by which evolutionary change occurs: vertical descent with mutation and horizontal gene transfer 2. Describe how evolution accounts for unity and diversity in biology 1.2 Biological Evolution - Bacteria-- Archaea - Unity and diversity are terms often used to describe life Unity refers to the common - characteristics displayed by - all forms of life - - Eukcrya- Principles 1 through 6 in previous section Diversity refers to the many different forms of unicellular and multicellular life The underlying factor that explains the unity and diversity of modern species is evolution, the changing - - genetic composition of a population over time 1.2 Biological Evolution Life Is Connected by an Evolutionary History Life began on Earth, as primitive cells, between 3.5 to 4 billion years ago (bya); those primitive cells underwent evolutionary changes to give rise to the species of today Evolutionary history helps us understand the structure and function of an organism Evolutionary change involves modifications of pre-existing characteristics; structures may be modified to serve new purposes Ex: walking limbs were modified into a dolphin’s flipper or a bat’s wing 1.2 Biological Evolution Vertical Descent with Mutation in Animals Vertical descent with mutation involves transfer of genetic information from parents to offspring - DNA = Parents ↓ offspring 1.Offspring inherit mutations from parents 2. Nature determines if those mutations lead to success/death 1.2 Biological Evolution Horizontal Gene Transfer Can Also Promote Evolution Horizontal gene transfer is a distinct process of exchanging genetic information that is common in microbes An organism incorporates genetic material from another - re c e i organism without being the offspring of that organism - Can occur between different species DNA & v DNA 1 ⑪ E Coli , Strep Fig 1.8, Biology, Brooker 1.2 Biological Evolution The Frequency of the Tuskless Elephant Appears to Be Increasing in Elephant Populations Due to Poaching Evolution via natural selection results in adaptations that favor reproductive success * where living organisms adapt Change naturally An adaptation is a characteristic in a species that is the result of natural selection; adaptations affect survival and reproduction Artificial selection is a human driven form of selection (ex: ↑ S human choices of desirable traits led to various breeds of dogs) Tuskless elephants appear to be increasing due to poaching where organisms traits byhumans see are The tuskless condition is an adaptation that may lessen poaching Less than 2% of elephants in well- protected populations are tuskless Approximately 50% of the survivors of a poached population were tuskless Group work 1 What information did we just learn that explains. the “diversity” found across all living things? 2. List the two modes of evolution. 3. What evolutionary method is described here? Genes that confer antibiotic resistance are sometimes transferred between different bacteria species. = norizontal Tuskless elephants are becoming more common. How does this fact support the concept that evolution via natural/artificial selection results in adaptations that favor reproductive success? 1.2 Biological Evolution The Frequency of the Tuskless Elephant Appears to Be Increasing in Elephant Populations Due to Poaching All tuskless elephants are female (females normally have tusks) The tuskless gene is found on the X chromosome; female elephants have two X chromosomes (XX) whereas males have only 1 (XY) Tuskless (T) is a dominant allele Female tuskless elephants have the genotype XTXt Males cannot be tuskless because a single T allele is lethal 1.3 Classification of Living Things Section 1.3 Learning Outcomes 1. Outline how organisms are classified (taxonomy) 2. Describe the 3 domains of life and gives examples of - organisms classified within each domain 1.3 Classification of Living Things The Classification of Living Organisms Allows Biologists to Appreciate the Unity and Diversity of Life Taxonomy is the grouping of species based on common ancestry Classification involves sorting at multiple levels, where species are placed into progressively smaller groups that are more closely related to each other evolutionarily The largest groups are the three domains of life: Bacteria (unicellular prokaryote), Archaea (unicellular - prokaryote), and Eukarya (unicellular and multicellular - ~ eukaryotes) [Prokaryote = Eukaryote] The smallest group is the species; each species has a unique scientific name Genus name is capitalized; species descriptor (specific epithet) is not capitalized Both names are italicized (ex: Amphiprion ocellaris, commonly known as the Ocellaris clownfish) 1.3 Classification of Living Things The Classification of Living Organisms Allows Biologists to Appreciate the Unity and Diversity of Life = prokaryote = eukaryote ↓ · animals plants · fungi · · Protists ↑ can be uni multi-cellular Group work Apply an easy to remember acronym to the taxa. List these taxa in order of least to most diverse. ① Species, class, phylum, family, order King Philip Came Over From/For Great/Good Spain/Spaghetti 1.4 Biology as a Scientific Discipline Section 1.4 Learning Outcomes 1. Explain how researchers study biology at different levels, ranging from molecules to ecosystems 2. Distinguish between discovery-based science and hypothesis testing 3. Describe the steps of a scientific method, also called hypothesis testing 4. Explain the usefulness of models in biology 1.4 Biology as a Scientific Discipline Science is the observation, identification, experimental investigation, and theoretical explanation of natural phenomena Many scientists utilize model organisms in their research and use a ~ scientific method to test hypotheses - Different branches of biology study life at different levels using a variety of tools Ex: ecology, anatomy, physiology, cell biology, molecular biology, and systems biology As new tools become available, they allow scientists to ask new questions 1.4 Biology as a Scientific Discipline Biologists Investigate Life at Different Levels of Organization 1.4 Biology as a Scientific Discipline A Hypothesis Is a Proposed Idea, Whereas a Theory Is a Broad Explanation Backed by Extensive Evidence A hypothesis is a proposed explanation for a natural phenomenon Based on previous observations or experiments Must yield predictions that can be shown to be correct or - incorrect (must be testable and falsifiable) * NOT provable - - - Additional observations or experiments can support or reject a hypothesis, but a hypothesis is never really proven Observation: maple trees lose their leaves during autumn Hypothesis: Maple trees drop their leaves in autumn because of shortened hours of sunlight - Alternative hypothesis: Maple trees drop their leaves in autumn because of colder temperatures - 1.4 Biology as a Scientific Discipline A Hypothesis Is a Proposed Idea, Whereas a Theory Is a Broad Explanation Backed by Extensive Evidence A theory is a broad explanation of some aspect of the natural world that is substantiated by a large body of evidence Allows us to make many predictions Biological theories incorporate observations, hypothesis testing, and the laws of other disciplines (physics and chemistry) Theories are viewed as knowledge Two key attributes of a theory: Consistent with a vast amount of known data Able to make many correct predictions Ex: DNA is the genetic material Overwhelming body of evidence supports this theory 1.4 Biology as a Scientific Discipline Discovery-Based Science and Hypothesis Testing Are Scientific Approaches That Help Us Understand Biology Biologists do not follow a rigid path to discovery, rather they ask questions make observations conduct experiments ask modified questions learn from failure (lots of “trouble-shooting”) repeat experiments try new experimental approaches communicate their findings, and more… Researchers typically utilize 2 general approaches: discovery-based science and hypothesis testing 1.4 Biology as a Scientific Discipline Discovery-Based Science and Hypothesis Testing Are Scientific Approaches That Help Us Understand Biology Discovery-based science involves the collection and analysis of data -- without having a preconceived hypothesis - - Goal is to gather information Ex: investigating a newly discovered gene without already knowing the function [ Ex: testing drugs to look for action against disease& Discovery-based science often leads to hypothesis testing  1.4 Biology as a Scientific Discipline Discovery-Based Science and Hypothesis Testing Are Scientific Approaches That Help Us Understand Biology The scientific method of hypothesis testing is designed to be an objective way to gather knowledge - The steps involved:. Observations are made regarding natural phenomena. These observations lead to a testable hypothesis that tries to explain the phenomena. Experiments are conducted to determine if the predictions are correct. The data are analyzed (involves use of statistical analysis). The hypothesis is supported or rejected based on the data Data are often collected in parallel control and experimental groups - - Groups differ by a single factor  1.4 Biology as a Scientific Discipline Discovery-Based Science and Hypothesis Testing Are Scientific Approaches That Help Us Understand Biology Independent variable # z dependent * Prediction: exposure of trees to shorter amounts of daylight will cause leaves to fall 1.4 Biology as a Scientific Discipline Science Is a Social Discipline In addition to being a scientific discipline, biology is also a social discipline; biologists engage in a variety of interpersonal interactions and communication practices Within a lab, undergraduate & graduate students, postdocs, technicians, and the Principal Investigator (PI) all work together Different labs collaborate on projects Research papers are peer-reviewed At meetings, scientists discuss new data – and debate! You can discuss science without having “all the answers”  1. Cells are the 2 Living 1 1 notes organisms. review : 3. Simplest unit ↑ use energy.. Living organisms of life. interact T w/ their A environment Ibiotic VOCAB : : abiotic Principles > - 4 of Living organisms Biology. : Study of life maintain homeostasis. Bio : I. 5 DNA provides blueprint Simplest unit of Cells : life ↑. 6 that allows organisms to grow develop, , reproduce. Populations of evolve from I organisms Cell theory : LEVELS gen to the - 1. All organisms haveo = or more cells next related.. 2 Cells are the smallest unit of life. 3 New cells from of come pre-existing Cells (via Cell division) ORGANIZATION : : D NA : Genetic material Atoms · Ideoxyribonucleic acid) molecules · Population : Multiple individuals/organims of a Cells Single Species. - · Tissues community : & or more populations of a Organs · - different species · organ systems · - Ecosystem : Botic : abiotic factors in system. · Organism · Population Biosphere : Every ecoytem - on the planet. Community (EX Earth) · : - Atoms : Basic particle of chemical elements. · Ecosystem molecules : Group of atoms bonded together. · Biosphere  1 2 notes review : adaptation. Evolutionary ~ u) helps ture is characteristic = in torystrism species VOCAB : - Mirand after natural org- selection unders F O -. Common characteristics tion ↑ ↑ Unity : Shown furt by a forms of life Notes : Refers to manyd rent forms Diversity : of life (multi/uni-cellular) - X Tuskless Evolution : Changing of genetic composition - Condition is of population over time adaptation that -. an - may nothing (hunting) - les - Vertical descent Transfer of genetic info - w/ mutation from parents to spring :. noriz Only. = inherits genetic Organism horizontal microbial geneaster - - - material from another organism gene transfer: - Without being offering of that [ Horizontal A mmm organism. : DNA natural Selection & DNA : linorganisms capt Change - v 1 ⑪ artifical naturally - I = organisms traitsareseea FF,, - Selection : E Coli , Strep -  1 3 notes review : = Eukaryote prokaryotes. = · animals bacteria · VOCAB : · plants · archea fungi Taxonomy : Groupingofspeciesbe · a · protists ProkaryoteN : · AILWAYS unicellular I · Bacteria/archaea EXA Largest group · nucleoid region : ↓ Eukaryote : · Can be multi or uni-cellular · protists, fungi , plants, animals, Distract - > eukarya , etc. · nucleus Sometime- > 1. bacteria kindles - - 3 DOMAINS :. archaea 2 peoples - >. eukarya 3 Cuz - > Often SPECIES > - - : Ex : Amphiprion ocellaris fail - > ↳ smallest M ↑ group descriptor Genus Geniuses-> = name A both Italicized A Super-  Without 1 4 notes. review : Collection t having an analysis of data initial hypothesis ↑ VOCAB : Observation identification, Discovery-based Science - > Goal-gather Science : , experimental, investigation , i leads L info to theoretical explanation ↓ of natural hypothesis Ex testing drugs : to look Phenomena testing. model for action against disease non-human species used for organisms : instigating experiments 4) hypothesis is supported rejected - -T or scientific (problem-solving) method that Dataisaned Scientific - method : involves observation experimenting ,. 3 method For hypotheses - i testing > Objective Of Chypothesis. - - ↑ - way to · hypothes is : proposed explanation for testing ( a - natural phenomenon gather > - must yield predictions ments ↓ knowledge 2 experi that can be are. correct or proven. not 1. > - Observations Ex : conducted are made maple trees lose their if leaves be less sunlight. Ho see - predictions correct) · theory : broad explanation that is are * Data can be collected supported by lots of evidence. Paecontrol via viewed as - knowledge ups EX DNA : is genetic material 1. describe principles of biology - 1 1.. Explain life at different 2 complexity 1. I ways of Evolution ? S in 2. How evolution accounts for unity? diversity - 1 2 ? S biology. - Progeny of parents inherit mutations , work in the environment If DNA/traits : reproduces NATURAL SELECTION! then animal - survives. - Via horizontal gene transfer = vertical evolution. Unity= All species have common ancestor. & vertical A Diversity= DNA can change * Natural Selection 1. Outline how organisms are classified (taxonomy) - 1 3. Htaxonomic groups) : Domain Bacteria- ( : > S Archaea - Prokarya Eukarya > -