BIO 181 General Biology I Fall 2017 Lecture Notes PDF

BIO 181: General Biology I The Chemical Foundation of Life Instructor: Dr. Cayle Lisenbee Office: UCENT 355 Phone: (602) 496-0641 Email: [email protected] Office Hours: Posted on Blackboard...

BIO 181: General Biology I The Chemical Foundation of Life Instructor: Dr. Cayle Lisenbee Office: UCENT 355 Phone: (602) 496-0641 Email: [email protected] Office Hours: Posted on Blackboard Arizona State University Downtown Phoenix Campus College of Integrative Sciences and Arts  Learning Objective Consider the hierarchical nature of biological organization by recognizing that all living organisms are composed of smaller and smaller non-living building blocks. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 2 Composition of Life – Organization  The components of life form an organized hierarchy. All living organisms exhibit this hierarchy in their composition. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 3 Composition of Life – Cells  Our goal is to examine the composition of living organisms. What types of building blocks establish the foundations of life?  Cells are the smallest units of biological organization that retain the characteristics of life. But, can we break cells down further? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 4 Composition of Life – Chemicals  When we break cells down further, we find that they are made of highly-organized assemblies of non-living molecules, each of which contains one or more types of atoms. N Other Other Other H 3% 4% Ca 9% O 1% 10% 3% 21% Fe 5% Al C 8% O 18% * O 49% 65% Si N 26% 78% Human Body Earth’s Crust Atmosphere  Study the charts carefully. How is life unique in its composition? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 5  Learning Objective Describe the structure of an atom, and relate its structure to the composition of living organisms. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 6 Atomic Structure – Periodic Table BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 7 Atomic Structure – Atoms  What is the general structure of an individual atom? nucleus electron proton neutron  Pick an element from the periodic table. Can you identify from the information provided how many protons, neutrons, and electrons may be found in a single atom of your chosen element? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 8 Atomic Structure – Isotopes  Isotopes are versions of atoms of a particular element with alternate numbers of neutrons in their nuclei.  Some isotopes are stable, whereas others are unstable such that they “decay,” or split apart, into smaller atoms and/or subatomic particles. For example, carbon atoms typically contain six protons and six neutrons. Atoms of the stable isotope carbon-13 contain six protons and seven neutrons. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 9 Atomic Structure – Isotopes  Unstable isotopes for a given element tend to “decay” at a relatively constant rate.  Geologists and archeologists use this property to date materials radiometri- cally. Unstable isotopes of carbon and uranium are particularly useful for dating the fossilized remains of once- living organisms.  Physicists and engineers use unstable isotopes for generating large quantities of electricity in nuclear fission reactors, and for studying the origins of the universe. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 10 Atomic Structure – Electron Shells  Niels Bohr developed a model of the atom in 1913 that placed an atom’s electrons into a series of concentric shells surrounding the nucleus.  Shells closer to the nucleus are lower in energy than those that are further away. Electrons fill the shells in order of increasing energy by occupying the lowest energy shells first.  A packet, or photon, of light energy can boost an electron into a higher energy shell. Once there, the “excited-state” electron is unstable and quickly returns to its “ground state” by releasing a photon of light. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 11 Atomic Structure – Electron Shells  The electron configuration of an atom refers to the number of electrons in each of its electron shells.  Atoms with partially-filled outermost, or “valence,” shells are likely to gain or lose electrons to achieve stable electron configurations.  Thus, the electron con- figuration characteristics of an atom dictates its chemical properties and tendencies for interacting with other atoms. We’ll see shortly how this is the basis for chemical bonds. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 12 Atomic Structure – Electron Shells  Researchers attempting to define the exact position of an electron at a given point in time learned that a) it can’t be done due to the complexities of the speed of light, and b) the positions of electrons form subshells that determine the overall shapes of atoms.  The shapes of an atom’s subshells ultimately dictate the shapes of the molecules it may form with other atoms. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 13  Learning Objective Explain how atoms associate with each other in two main ways to form molecules. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 14 Chemical Bonds  Chemical bonds occur when two atoms, interacting through their valence electrons, form an association that is energetically more stable than it is for the atoms to remain apart.  Typically, this occurs when the interatomic association allows each atom to fill its valence shell. The result is a molecule.  Ionic bonds  Covalent bonds  Note: hydrogen bonds, van der Waals forces, and electrostatic interactions are intermolecular processes that do not apply here! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 15 Chemical Bonds – Ionic  Ionic bonds typically occur between metal and nonmetal atoms that effectively transfer an electron from the former to the latter.  The atom that donates an electron becomes a positively charged cation. The atom that receives an electron becomes a negatively charged anion. cation anion BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 16 Chemical Bonds – Covalent  Covalent bonds occur when atoms fill their valence shells by sharing one or more pairs of electrons. Notice that for each pair of shared electrons, one is contributed by the oxygen atom (red) and the other by the hydrogen atom (white). BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 17 Chemical Bonds – Covalent  The attraction of an atom’s nucleus for the shared electrons in a covalent bond is called electronegativity. In general, larger atoms are more electronegative than smaller ones.  Nonpolar bond  Polar bond BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 18 Chemical Bonds – Covalent  The shape and arrangement of polar and nonpolar covalent bonds in a single molecule determines the molecule’s overall polarity.  If water is a polar molecule, which types of molecules do you think water interacts with best? Worst?  Derive a rule that explains the behavior of molecules with respect to their overall polarity/nonpolarity. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 19  Learning Objective Describe how the properties of water relate to solution chemistry and the pH scale, and apply these concepts to the functions of living organisms. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 20 Properties of Water  List at least four properties of water, and describe how each is relevant to the persistence of life on earth.  Solid water (ice) is less dense than liquid water.  Water is an excellent solvent for polar molecules and ions.  Cohesion between molecules gives water its strong surface tension.  Adhesion between water molecules and other materials facilitates capillary action within thin tubes.  Water has a relatively large specific heat value. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 21 Properties of Water – Solutions  What happens when you place a solid chemical in water? Will the chemical dissolve? And what the heck does that mean?  When table salt (NaCl) dissolves in water, the sodium and chloride ions dissociate to produce an aqueous solution. The ions are the solutes and the water is the solvent.  Does table sugar (sucrose, C12H22O11) dissolve in water in the same manner as table salt? Why or why not? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 22 Properties of Water – The pH Scale  The pH scale reflects the concentration of hydrogen ions (H+) in an aqueous solution.  Acids contain high concentrations of H+ ions in solution. They are capable of adding these ions to biological molecules like proteins and lipids. Where are they positioned on the pH scale?  Bases contain low concentrations of H+ ions in solution. They like to steal these ions from biological molecules.  What happens to biological molecules that are altered by strong acids and bases? BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 23  Learning Objective Describe the structure of a carbon atom and how it establishes the structural diversity of organic macromolecules. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 24 Organic Chem. – Carbon Atoms  Carbon is the second most common element in living organisms, yet it is relatively absent from earth’s crust and atmosphere. Why is carbon such an important element for life? 1 4 2 3 A carbon atom needs four electrons to fill its valence Methane, CH4. shell. It can do this by forming four covalent bonds!  Carbon-containing matter, like that found in living organisms, is composed of organic molecules. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 25 Organic Chem. – Functional Groups  Organic molecules often incorporate regular patterns, or functional groups, of atoms bonded to carbon  Recognizing these groups helps you understand a mo- lecule’s function  These are NOT to be memorized! BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 26 Organic Chem. – Macromolecules  Long chains of carbon atoms form organic macromolecules. The four bonding positions afforded by each carbon atom in the chain allow for incredible structural, and thus functional, diversity. BIO 181: General Biology I C. Lisenbee, Ph.D. ASU DPC CISA 27