BIOL220 General Biology Lecture 1 - The Chemistry of Life PDF

BIOL220 – General Biology 08/19 - Lecture 1: Intro to the course The Chemistry of Life Dr. Paula Spiniello BIOL220 – GENERAL BIOLOGY 4 CREDITS CLASSES: MONDAYS LABORATORY: (PLEASE REVIEW THE AND THURSDAYS WEDNESDAYS 11:00...

BIOL220 – General Biology 08/19 - Lecture 1: Intro to the course The Chemistry of Life Dr. Paula Spiniello BIOL220 – GENERAL BIOLOGY 4 CREDITS CLASSES: MONDAYS LABORATORY: (PLEASE REVIEW THE AND THURSDAYS WEDNESDAYS 11:00 SYLLABUS POSTED 11:00 TO 12:15 TO 12:45 ON SAKAI- RESOURCES) LECTURER Ms. Atoum Abdullah School of Medicine Department of Biochemistry COURSE DIRECTOR AND LECTURER Dr. Paula Spiniello School of Arts and Science Department of Biology, Ecology and Conservation What is this course about? Life processes at the molecular, cellular, organismal, population, community and ecosystem levels.  Cell organization and communication  Metabolism and harvesting of energy through cellular respiration  The cell cycle – meiosis, mitosis  Genetics, evolution and the origin of species  The biology of virus, bacteria, protists, plants, invertebrates and vertebrates  The emergent properties of populations, communities and ecosystems THE BOOK Campbell BIOLOGY – 12th Edition Find it posted on Resources COURSE GRADING  FOUR (4) Exams = 70% of the final grade Exam 1 = 15% of final grade Exam 2 = 20% of final grade Exam 3 = 15% of final grade Exam 4 = 20% of final grade  ONE (1) Oral Presentation = 5% of final grade  Nine (9) Lab Assignments and quizzes - 25% of the final grade  Lab Assignments and quizzes 1 to 3 and 6 to 9 – 3% of the final grade  Lab Assignments and quizzes 4 and 5 – 2% of the final grade (each) See files posted on Resources (Schedule and Syllabus) THERE IS NO EXTRA POINTS FOR ATTENDANCE  EXAMS Exams will be Multiple Choice Questions (usually 40-50 questions)  ORAL PRESENTATION Form GROUPS OF MAX 3 students/group Each group will select a recent BIOLOGY NEWS ARTICLE from the local, regional or international media and present the main topic of your selected story. Please choose a NEWS ARTICLE from any of the following media: Science, ScienceDaily, Phys.org, Sci.News, The Guardian/Biology, Scientific American, BBC News/Biology, New Scientist/Biology, AP News/Biology The New York Times in Education/Biology, Science News, Reuters/Science Each group will prepare and deliver a 12-15-minute presentation to the class, followed by 5 minutes period of Q&A and discussion. Each group member should present a similar length of material. Please indicate to the lecturer the names of the members of your group by Wednesday 10 am THE LATEST. If you do not have a group by Wednesday 10 am, I will assign you to one. Please send me the title of the NEWS ARTICLE you have selected in order to be approved for presentation. Deadline for this submission is 1 WEEK BEFORE your presentation. Presentation are to be made in Power Point. Please check files on Resources (Oral Presentation Instructions and Oral Presentation Rubric) Presentation date will be assigned by Course Director Lab assignments and quizzes There will be 9 lab sessions Ms. Abdullah and Dr. Spiniello will be your lab instructors IT IS VERY IMPORTANT STUDENTS READ THE LAB SESSION INSTRUCTIONS BEFORE THE CORRESPONDING SESSION. Find Lab session instructions and Assignment files on Resources. Lab quizzes can be found on SAKAI (test and quizzes) Late submission of lab assignments and quizzes are not accepted. Students who do not submit assignments or quizzes before the deadline will receive a zero (0) points on both. If you miss a lab session, your assignment and quiz will not be received, and you grade will be zero (0). Lab sessions are mandatory and cannot be repeated. Attendance This is a 100% face to face course and you are expected to come to all the class and laboratory sessions at the scheduled time. Attendance will be taken regularly. Students unable to sit on exams on the scheduled day must complete an online Medical Excuse form in order to be granted permission to take the exam at another date. Please remember that the 3rd Medical Excuse in A YEAR will result in an automatic LOA (Leave of Absence) Oral Presentations and Lab sessions cannot be rescheduled.  TIPS FOR SUCCESS 1) Attend to all lectures and laboratory sessions. Be attentive and participative during class, lab sessions and oral presentations 2) Take time to review the lecture of the day 3) Do not hesitate to ask questions to your Lecturers during lectures or lab sessions. 4) Make appointments for Lecturers Office hours to clarify lecture or lab material 5) Join a study group 6) Come to the exams well prepared 7) Be attentive of deadlines for assignments and quizzes submission, and oral presentation schedule 8) Practice your presentation THE CHEMISTRY OF LIFE  LEARNING OUTCOMES  Describe the components of an atom.  Differentiate between an element, a molecule and a compound.  List the elements of life  Define an isotope.  Differentiate between covalent bond and non-covalent bonds.  Differentiate between polar and non- polar covalent bonds.  Describe Ionic, hydrogen and van-der Waals forces. DEFINITIONS Matter ? Element ? Compound ?  MATTER Anything that takes up space and has mass Matter exists in many forms. Examples of matter: Rocks, metals, oils, gases, living organisms Interesting Fact: 70-80% of living matter is composed of water.  Elements Vs Compounds An element is a substance that cannot be broken down by chemical reactions. A compound is a substance consisting of two or more elements combined in a fixed ratio. A Compound has characteristics different from those of its elements Sodium (Na) = Solid rock Chloride (Cl) = Poisonous gas Sodium Chloride = Solid Salt Today chemists recognize there are 92 elements occurring in nature  The ESSENTIAL Elements ESSENTIAL ELEMENTS: Elements that organisms need to live and reproduce. Of the 92 natural elements, about 20–25% are essential elements The essential elements are similar among organisms, but there is some variation—for example, humans need 25 elements, but plants need only 17 WHICH ARE THOSE ESSENTIAL ELEMENTS?  The ESSENTIAL Elements Carbon, Hydrogen, Oxygen, and Nitrogen are essential elements that make up 96% of living matter. Most of the remaining 4% consists of Potassium, Calcium, Phosphorus, and Sulfur Trace elements are those required by an organism in minute quantities (Less than 0.01%) such as Boron, Chromium, Cobalt, Copper, Iron, Iodine and Zinc, among others Given the makeup of the human body, what compound do you think accounts for the high percentage of oxygen?  CONCEPTS CHECK IS A TRACE ELEMENT AN ESSENTIAL ELEMENT ? WHY ?  In humans, iron is a trace element required for the proper functioning of hemoglobin, the molecule that carries oxygen in red blood cells. What might be the effects of an iron deficiency?  ATOMS Each element consists of a unique atom. An element’s properties depend on the structure of its atom. An atom is the smallest unit of matter that still retains the properties of an element. An atom consists of positive nucleus surrounded by negative electrons.  Subatomic Particles The Atom: is composed of subatomic particles: Neutrons (no electrical charge) Protons (positive charge) Electrons (negative charge) The Atomic Nucleus: Contains Neutrons and Protons Electrons form a cloud around the nucleus Attraction between opposite charges is what keeps the electrons in the Figure 2.5 Simplified models of a helium (He) atom.  Atomic Number and Atomic Mass Atoms of the various elements differ in number of subatomic particles Atomic number -the number of protons in its nucleus. An atom is neutral in electrical charge, # of protons = # of electrons. The atomic number tells us the number of protons and also the number of electrons. Atomic Mass is the total number of protons and neutrons in the nucleus of an atom. The contribution of electrons to mass is negligible, almost all of an atom’s mass is concentrated in its nucleus. Practice Atomic number? Atomic Mass? Isotopes Isotopes are atoms of the same element with the same number of protons and only differ in the number of the neutrons and, therefore in the mass number and not the atomic number. Although the isotopes of an element have slightly different masses, they behave identically in chemical reactions. Atomic number = 1 Atomic number = 1 Atomic number = 1 Isotopes Hydrogen-1 1 0 Atomic number Mass number =1 proton neutrons =1 Hydrogen-2 1 1 neutron Atomic number Mass number =2 proton =1 Hydrogen-3 Oxygen-16 1 8 proton 2 8 neutrons Atomicnumber Atomic number Mass number Mass number =3 =16 proton neutrons =1 =8 Oxygen -17 8 proton 9 neutron Atomic number Mass number =17 =8 Oxygen-18 8 proton 10 Atomic number Mass number =18 Carbon-12 6 proton 6 neutrons neutrons Atomic =8 number Mass number =12 =6 Carbon-13 6 proton 7 neutron Atomic number Mass number =13 =6 Carbon-14 6 proton 8 neutrons Atomic number Mass number =14 =6 Nitrogen-14 7 proton 7 neutrons Atomic number Mass number =14 =7 Nitrogen-15 7 proton 8 neutron Atomic number Mass number =15 =7 Nitrogen-16 7 proton 9 neutrons Atomic number Mass number =16 =7 Sodium-23 11 12 Atomic number Mass number =23 proton neutrons =11 Sodium-24 11 13 neutron Atomic number Mass number =24  Which of the following is an isotope of Atom 1? Atom 1 = 6 electrons, 6 protons, 6 neutrons a. Atom 2 = 8 electrons, 8 protons, 8 neutrons b. Atom 3 = 6 electrons, 6 protons, 8 neutrons c. Atom 4 = 6 electrons, 8 protons, 6 neutrons d. Atom 5 = 6 electrons, 8 protons, 8 neutrons e. Atom 6 = 8 electrons, 6 protons, 6 neutrons session id: biol220ps  Several isotopes are unstable, their nuclei decay spontaneously, loosing subatomic particles and emitting energy. These are called radioactive isotopes Radioactive isotopes emits energy in the form of radiation Radioactive isotopes have many useful applications e.g. fossil dating and as radioactive tracers  Isotopes as tracers of evolution  Use of radioactive decay in fossils to date their lifetime. Fossils provide a large body of evidence for evolution. Using radiometric dating, scientists calculate how long a pool of an original radioactive isotope on a fossil have been decaying, and date the fossil  Applications of Radioactive isotopes in Medicine Radioactive isotope of iodine (I-131) is used in both the diagnosis and treatment of thyroid https://www.sciencedirect.com/topics/medicine-and-dentistry/thyroid- scintiscanning cancer. Cancerous The thyroid will normally throat tissue absorb some iodine to produce iodine- containing thyroid hormones. https://www.healthline.com/health/thyroid-scan An overactive thyroid Electron Shells = Orbitals Electrons are found in different electron shells, each with a characteristic average distance from the nucleus and different energy level. In diagrams, shells can be represented by concentric circles. The first shell is closest to the nucleus, and electrons in this shell have the lowest potential energy. Electrons in the second shell have more energy, and electrons in the third shell even more energy. Electron Shells = Orbitals An electron can move from one shell to another, but only by absorbing or losing an amount of energy equal to the difference in energy between its position in the old shell and that in the new shell. When an electron absorbs energy, it moves to a shell farther out from the nucleus (That’s how plants harness the E of sunlight for photosynthesis) When an electron loses energy, it “falls back” to a shell closer to the nucleus, and the lost energy is usually released to the environment as visible light or ultraviolet radiation  Electron Shells and Valence Shells The farther a shell is from the nucleus, the larger it is, the more electrons it can hold, and the higher the energies of those electrons. The first shell (closest to the nucleus) can hold 2 electrons. The second shell can hold 8 electrons. The third shell can hold 18 electrons. The fourth shell can hold 32 electrons If two or more elements are in the same row, what do they have in common? VALENCE ELECTRONES The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell. We call those outer electrons valence electrons and the outermost electron shell the valence shell. CHEMICAL BONDS Atoms with incomplete valence shells can transfer or share valence electrons with certain other atoms. These interactions result in atoms staying close together, held by attractions called chemical bonds The formation and function of molecules depend on the chemical bonding between atoms Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell. Covalent bonds are the strongest chemical bonds Covalent bonds can form between atoms of the same element or atoms of different elements. Non-Polar Covalent Bonds The force of attraction of atoms by the electrons on a covalent bond is called its electronegativity. The more electronegative an atom is, the more strongly it pulls shared electrons toward itself. In a covalent bond between two atoms of the same element, the electrons are shared equally because the 2 atoms have the same electronegativity. This is called a NON-POLAR COVALENT BOND POLAR When an atom is bonded to a more electronegative atom, the electrons of COVALENT the bond are not shared equally. This type of bond is called a polar covalent BONDS bond  POLAR COVALENT BOND OF THE WATER MOLECULE Oxygen has more electronegativity than Hydrogen, attracting shared electrons much more strongly than hydrogen does. Electrons have a negative charge. The oxygen atom has partial negative charge and the hydrogen atoms have partial positive charges. IONIC BOND When two atoms are very unequal in their attraction, the more electronegative atom strips an electron completely away from its partner. The two resulting oppositely charged atoms (or molecules) are called ions. A positively charged ion is called a cation, while a negatively charged ion is called an anion Because of their opposite charges, cations and anions attract each other; this attraction is called an IONIC BOND HYDROGEN BONDS A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom. This bond creates a weak electrostatic attraction between the slightly positive H of one molecule and the slightly negative charge of another electronegative atom (e.g. oxygen, nitrogen)  Van der Waals Interactions Electrons are not always evenly distributed; they may accumulate by chance in one part of a molecule or another. The movement of electrons in atoms and molecules can result in “hot spots” of positive or negative charge. This result in temporary or induced dipoles. Van der Waals interactions are attractions between molecules that arise due to temporary or induced dipoles. Matching game https://www.purposegame s.com /game/biology-matc hing-game