Bio_2000_01.pdf

Bio-2000 An Introduction to Biology Contacts • Dr. Vladimir Poltoratsky • Department of Biology • Room SAH 219 • Email: • Office hours: Tu, Fr 9:30 – 11:00 AM, • or by appointment Course Policies 1. All material covered in class is considered exam material 2. Be courteous to your colleagues: don’t be late, and do not carry on private conversations in class 3. No cell phones usage in the classroom. If you feel you must use your phone during class please leave the room 4. No recording of lectures allowed without previous authorization Course Policies 5. Make-up exams will be allowed at the discretion of the instructor, ONLY IN THE CASES OF ILLNESS, FAMILY EMERGENCY, OR RELIGIOUS HOLIDAYS WITH PROVIDED DOCUMENTATION. Make-up exams will be different from in class exams – short answer/assay questions, no multiple-choice questions. 6. Academic integrity is expected at all times. Cheating will not be tolerated in any shape or form and may result in a failing grade, disciplinary action, or both Course Policies 7. All students MUST BRING THEIR STORM CARD TO EXAMINATIONS. If you fail to do so you will not be permitted to take the examination and will be given a grade of zero for that examination Office Hours • Tuesday, Friday 9:30 PM – 11:00 AM, or by appointment • Tutoring is available through the Biology Department (dates/times not yet available) • Specific help is also available through the University Freshman Center at 718- 990-5858 Blackboard • Syllabus • Course outline • Movies and animations –already available • Lectures –available immediately after each lecture Grading Class participation (Attendance/Answering Qs) 15% • Homework 25% • Mid Term Exams (two exams)* 30% • Final Exam 30% • Total % Cumulative 100% IMPORTANT: YOU ARE TO HAVE CELL PHONE or iPAD or COMPUTER TO PARTICIPATE IN ACTIVE LEARNING ACTIVITIES DURING THE LECTURE. • *The best one of two midterms (one of two exams) will be counted towards the final grade at 30% each. There are no make-up exams. All three exams must be taken. Cell phone is not allowed for personal use in the class: NO CALLING, TEXTING, or EMAILING Point System • CLASS PARTICIPATION, Attendance/Answering Qs via Kahoot, or during class discussion is mandatory, 90% attendance results in 15% of the course cumulative % grade • Home works are assigned after each lecture. A home work is due at 11:55 pm the day before the next lecture. Two the lowest HW grades will be dropped. The HWs contribute 25% to the cumulative % grade. • One on-line and one in-class midterm exams, ACADEMIC INTEGRITY IS STRICTLY ENFORCED. Total contribution of one of two MTEs to the cumulative % grade is 30% • Final exam: 30% contribution to the cumulative % grade. • Extra Credits: Totally you may get 5 extra credit points that will be added to the cumulative %-grade of the course • 1. 90% of correctly answered Kahoot Qs (all kahoots count) will result in 2-extra-credit points. • 2. 90% of total possible score for all LS assignments (one LS assignment for each chapter) will result in 3-extra-credit points. In-class Exams Exam Date Material Midterm 1 October 4-5 Chapters 2-7 30 % Midterm 2 November 5-6 Chapters 8-15 30 % Exam #3 (Final Exam) TBD (December 2018) Chapters 16-21 30 % In-class Exams • Schedule permitting, there will be a review class ahead of each exam • To help you during the review process, practice test will be available on Blackboard Home Assignments • Each home assignment has to be taken directly through Blackboard by clicking on the “Home Assignments” link • You will need a student access code to register with Connect Home Assignments • Each assignment is 3-4 multiple-choice questions • Home works are assigned after each lecture. A home work is due at 11:55 pm the day before the next lecture. Two the lowest HW grades will be dropped. The HWs contribute 25% to the cumulative % grade. Extra Credit • Totally you may get 5 extra credit points that will be added to the cumulative %-grade of the course 1. 90% of correctly answered Kahoot Qs (all kahoots count) will result in 2-extra-credit points. 2. 90% of total possible score for all LS assignments will result in 3-extra-credit points. • You will need a student access code to register with Connect Extra Credit • Each extra credit assignment has to be completed ahead of class, before that chapter is covered in class • Each extra credit assignment is designed to take 30- 40 minutes to complete on average • There is no time limit to complete each extra credit assignment, although it has to be completed ahead of class The Take Home Message • This is a demanding, challenging course that requires hard work • At the same time, the course material is a great foundation for those of you who are planning a career in the biomedical field • Take advantage of all the tools at your disposal (lecture slides, animations, Connect, office hours, tutoring, practice tests, etc…) The Take Home Message • Don’t fall behind! Start studying from the very beginning • If you get an F in the first exam, you will be flagged for early intervention through the Early Alert System • Don’t miss home assignments and extra credit assignments! Those are easy points that can significantly and positively impact your grade Chapter 1 An Introduction to Biology • Principles of Biology • Levels of Biological Organization • Unity and Diversity of Life • Biology as a Scientific Discipline 18 Key Concepts: What is life? A set of unifying principles Very broad 19 Principles of Biology 20 Principles of Biology 21 Enid A. Haupt Conservatory 22 23 24 Lithops Lithos (stone)+ ops (face) What is biology? What characterizes life? How do we classify life? What is Biology • Biology- study of living things and their interaction with the environment – Molecular Biology- study of the structure and function of the macromolecules essential to life. – Cell Biology- study of the cells and their interactions within the organism – Genetics- study of how heritable traits are transmitted from parents to offspring Characteristics of Life; Principles of Biology 1. Cells are the simplest units of life. 2. Living organisms use energy. 3. Living organisms interact with their environment. 4. Living organisms maintain homeostasis. 5. Living organisms grow and develop. 6. The genetic material provides a blueprint for reproduction. Principles of Biology, continued 7. Populations of organisms evolve from one generation to the next. 8. All species (past and present) are related by an evolutionary history. 9. Structure determines function. 10. New properties of life emerge from complex interactions. 11. Biology is an experimental science. 12. Biology affects our society. 1. Cells are the simplest units of life 2. Living organisms use energy Metabolism Metabolism the entire network of chemical reactions carried out by living cells Anabolic reactions reactions that synthesize molecules synthesis of compounds needed for cell maintenance, growth and reproduction amino acids, carbohydrates, coenzymes, nucleotides, and fatty acids larger molecules such as proteins, polysaccharides, nucleic acids, and complex lipids Catabolic reactions reactions that degrade molecules 32 33 anabolism and catabolism Phototrophsobtaining energy from sunlight to synthesize organic compounds for nutrition Heterotrophsderiving its nutritional requirements from complex organic substances. Greek trophos ‘feeder.’ 3. Living organisms interact with their environment. Neutrophil 4. Living organisms maintain homeostasis 5. Living organisms grow and develop. Bacterial growth 6. The genetic material provides a blueprint for reproduction 11. Biology is an experimental science 12. Biology affects our society Biology affects our society Disease Max. number of cases Number of cases in 2003 Percent change Diphtheria 206,939 (1921) 1 -99.99 Measles 894,134 (1941) 42 -99.99 Mumps 152,209 (1968) 194 -99.90 Pertussis 265,269 (1934) 8,483 -96.80 Rubella 57,686 (1969) 8 -99.97 Tetanus 1,560 (1923) 14 -99.10 Haemophilus influenzae type B ∼20,000 (1984) 20 -99.90 Hepatitis B 26,611 (1985) 6,711 -75.03 Adapted from Orenstein WA, AR Hinman, KJ Bart, and SC Hadler. Immunization. In Mandell GL, JE Bennett, and R Dolin (eds). Principles and Practices of Infectious Diseases, 4th ed. Churchill Livingstone, New York, 1995, and Morbidity and Mortality Weekly Report 52:, 2004 40 Levels of organizations 42 1 2 3 4 5 6 7 8 9 Atoms Molecules and macromolecules Cells Tissues Organs Organism Population Community Biospher Ecosystem 10 Genomes and Proteomes • Genome The complete genetic makeup of an organism • Genomics Techniques used to analyze DNA sequences Comparison of genomes of different species • Proteome The complete complement of proteins of an organism • Proteomics Techniques used to analyze the proteins of a species Comparison of proteomes of different species 43 44 Transport proteins: Proteins facilitate the uptake and export of substances. Cell organization: Proteins organize the components within cells. Extracellular proteins: Proteins hold cells together in tissues. Cytoskeleton: Proteins are involved in cell shape and movement. In eukaryotes, most of the genome is contained within chromosomes that are located in the cell nucleus. Cell signaling: Proteins are needed for cell signaling with other cells and with the environment. Enzymes: Proteins function as enzymes to synthesize and break down cellular molecules and macromolecules. (a) The genome Extracellular fluid (b) The proteome Most genes encode mRNAs that contain the information to make proteins. Cytoplasm Chromosome Sets of chromosomes Nucleus Chromosome DNA Sets of chromosomes Nucleus Gene Egg Larva Adult Pupa Lyfe Cycle of the Gypsy Moth • Science is the observation, identification, experimental investigation, and theoretical explanation of natural phenomena • The Scientific Method is used to test theories • Some scientists also gather information “Fact-finding mission” 46 Biology as a Scientific Discipline The scientific method • Observations • Testable hypothesis • Experiments • Data analysis • Interpretation of results 47 Hypothesis or Theory? • Hypothesis A proposed explanation for a natural phenomenon Based on previous observations or experiments Hypotheses must make predictions that can be shown to be correct or incorrect (must be testable) Additional observations or experiments can support or reject a hypothesis, but a hypothesis is never really proven • Example: “Maple trees drop their leaves in autumn because of shortened hours of sunlight” 48 • Theory Broad explanation of some aspect of the natural world that is substantiated by a large body of evidence Allows us to make many predictions Also can never be proved true, but due to overwhelming evidence, may be very likely to be true • Two key attributes of a theory: 1. Consistent with a vast amount of known data 2. Able to make many correct predictions • Example “DNA is the genetic material” Overwhelming body of evidence supports this theory 49 Understanding biology • Two general approaches 1. Discovery-based science 2. Hypothesis-driven 50 Common features • Data are often collected in parallel Control and experimental groups Differ by only a single variable • Data analysis Apply statistical analysis to determine if the control and experimental groups are different because of the single variable that is different Are differences statistically significant? If the two sets are found not to be significantly different, we must reject our hypothesis. If the two sets of data are significantly different, we accept our hypothesis (though it is not proven) 51 example: Blood Circulation • Galen (129 - c216) • thought that “blood is created in the liver from ingested food and flows to the right side of the heart. Some of it flows to the lungs where it gives off ‘sooty vapors’ and some flows through invisible pores into the left side of the heart, where it gains ‘vital spirits’ when mixed with pneuma brought in by the trachea.” 52 • Galen’s ideas were first challenged by an Arab physician, Ibn-al-Nafiz in the thirteenth century, but despite this Galen’s theory remained accepted by society until William Harvey () published “De Motu Cordis” in 1628. Even then it took many years for his theory of systemic circulation (similar to modern accepted theory) to succeed Galen’s. 53 You can repeat Harvey’s experiment with guidance from The Naked Scientists: • ins/ Example 2: Cystic Fibrosis • Affects about 1 in every 3,500 Americans • Persons with CF produce abnormally thick and sticky mucus that obstructs the lungs and pancreas • Average lifespan for people with CF is currently in their mid- to late 30s 54 example: Cystic Fibrosis • In 1945, Dorothy Anderson determined that cystic fibrosis is a genetic disorder • In 1989, research groups headed by Lap-Chi Tsui, Francis Collins, and John Riordan identified the CF gene • Discovery-based science, not hypothesistesting, found the CF gene 55 Hypothesis for function of CF gene • Hypothesis: The CF gene encodes a protein that transports chloride ions (Cl- ) across the membrane of cells • Led to experiments to test normal cells and cells from CF patients for ability to transport Cl- CF cells were found defective in chloride transport Transferring a normal CF gene into cells in the lab corrects this defect • Chloride transport hypothesis is accepted 56 57 Lung cell with faulty CF gene Cl– Cl– Defective transporter Cl– export is defective, affecting water balance and causing sticky mucus. Lung cell with normal CF gene Cl– Cl– Transporter encoded by normal CF gene Proper Cl– export occurs, and water balance is normal. • Results supported the hypothesis that the CF gene encodes a protein that transports Cl- across the plasma membrane • A mutation in this gene causes it to encode a defective transporter protein, leading to a salt imbalance • This imbalance affects water levels outside the cell, which explains the thick and sticky mucus in CF patients • In this example, hypothesis testing has provided a way to accept or reject an idea regarding how a disease is caused by a genetic change 58 Science is social • Within a lab, students, postdocs, technicians, and the PI work together • Different labs often collaborate • At meetings, scientists discuss new data – and debate! • You can discuss science without having “all the answers” • Science is a never-ending series of questions 59 Time to Play