Chapter 2 Lecture Notes Essential Chemistry for Biology Biol 100 K. Marr 2009 Topics Discussed in these notes Matter, Elements and Compounds Periodic Table of the Elements: Metals vs. Nonmetals Atomic Structure Chemical Bonding: Ionic vs. Covalent Bonding Chemical Reactions and Chemical Equations The Structure of Water Water as a Solvent The Importance of Water to Living Things Acids, Bases and ph Self-test/Review Questions BASIC CHEMISTRY Organisms and all other things in the universe consist of matter Matter: Elements and Compounds Matter is Matter is composed of Elements are There are 92 naturally occurring elements on Earth Periodic table of the elements Location of... Metals? Nonmetals? 25 Elements are essential to life C, H, O, N: 96% of the weight of the human body Elements Elements Compounds Atom: Each element consists of one kind of atom (a) Hydrogen atom (b) Carbon atom (c) Oxygen atom Examples of Compounds: 1. 2. 3. Proton Neutron Electron Atomic nucleus First shell Second shell 1
Atomic Structure The subatomic particles of an atom Elements Proton Positive charge Determines element Neutron No charge Determines isotope Electron Negative charge Participates in chemical reactions Outer-shell electrons determine chemical behavior Nucleus Consists of neutrons and protons Atomic Number: number Determines Mass number sum of the number Chemical Properties of Atoms Electrons orbit the nucleus of an atom in specific electron shells The number of electrons in the outermost shell determines Atoms of the four elements most abundant in life Electron First electron shell: can hold 2 electrons Outermost electron shell: can hold 8 electrons Hydrogen (H) Atomic number = 1 Carbon (C) Atomic number = 6 Nitrogen (N) Atomic number = 7 Oxygen (O) Atomic number = 8 1 st Shell 2 nd Shell 3 rd Shell Orbital Diagrams of the First 18 Elements 2 8 8 Chemical Bonding and Molecules Chemical reactions: Atoms give up or acquire in order to complete their outer shells Result in atoms staying close together to form molecules Chemical bonds hold molecules together Ionic Bonds Covalent bonds 2
Ionic Bonds: form between metals and nonmetals When an atom loses or gains electrons, it becomes electrically charged Charged atoms are called Ionic bonds are formed between oppositely charged ions Sodium atom (Na) Complete outer shells Chlorine atom (Cl) Sodium ion (Na ) Chloride ion (Cl ) Atoms: electrically neutral (a) Hydrogen atom (H) (c) Sodium atom (Na) 1 electron 1 proton No net electrical charge 11 electrons 11 protons No net electrical charge Ions: Electrically charged (b) Hydrogen ion (H + ) (d) Sodium ion (Na + ) No electron 1 proton 10 electrons 11 protons Sodium chloride (NaCl) Fig. 2.03 Covalent Bonds: form between nonmetallic atoms A covalent bond forms when two atoms one or more pairs of outer-shell electrons Covalent bonding in water Oxygen atom with unfilled shell Water molecule (H 2 O) Full shell with 8 electrons Slightly negative Covalent bond (shared pair of electron) + +Slightly positive Full shells with 2 electrons each Hydrogen atoms with unfilled shells Fig. 2.04a Chemical Reactions Cells constantly rearrange molecules by breaking existing chemical bonds and forming new ones Such changes in the chemical composition of matter are called Hydrogen gas Oxygen gas Water Chemical Equations Chemical Equations: symbolize chemical reactions Reactants: on the side of the equation the starting materials Products: on the side of the equation the ending materials the stuff produced Law of Chemical reactions do not create or destroy matter they only rearrange it Chemical Equations must be balanced = Reactants Products 3
WATER AND LIFE Life on Earth began in water and evolved there for 3 billion years The abundance of water is a major reason Earth is habitable The Structure of Water The water molecule: two hydrogen atoms joined to one oxygen atom by single covalent bonds Modern life still remains tied to water Your cells are composed of 70% 95% water H H O Water: a polar molecule The electrons of the covalent bonds are between oxygen and hydrogen. water a polar molecule makes Water: a polar molecule The electrons of the covalent bonds are shared between oxygen and hydrogen makes water a polar molecule hydrogen atoms: partially positive oxygen atom: partially negative (d -) hydrogen atoms: partially positive oxygen atom: partially negative (d -) The Structure of Water Water s Life-Supporting Properties The polarity of water results in weak electrical attractions between neighboring water molecules These interactions are called Hydrogen bond The polarity of water molecules and the hydrogen bonding that results explain most of water s lifesupporting properties 1. Versatility of water as a solvent 2. Water s cohesive nature 3. Water s ability to moderate temperature (b) 4. Floating ice 4
Water as the Solvent of Life A solution is a liquid consisting of two or more substances evenly mixed The dissolving agent is called the The dissolved substance is called the Ion in solution Salt crystal Dissolving of Sodium Chloride, NaCl, in Water Salt Water Water molecules (H 2 O) Electrical attraction Water molecules dissolve NaCl, breaking ionic bond Hydrogen bonds Edge of one salt crystal Ionic bond Fig. 2.05a The Cohesion of Water Water molecules stick together as a result of hydrogen bonding This is called cohesion Cohesion is vital for water transport in plants Microscopic tubes Surface tension is the measure of how difficult it is to stretch or break the surface of a liquid Hydrogen bonds give water an unusually high surface tension Figure 2.13 Water Moderates Temperature The density of ice is lower than liquid water Because of hydrogen bonding, water has a strong resistance to temperature change Water can absorb and store large amounts of heat while only changing a few degrees in temperature This is why ice floats Hydrogen bond Earth s Oceans cause temperatures to stay within limits that permit life Ice Stable hydrogen bonds Liquid water Hydrogen bonds constantly break and re-form 5
The Biological Significance of Ice Floating When water molecules get cold, they move apart, forming ice A chunk of ice has fewer molecules than an equal volume of liquid water Since ice floats, ponds, lakes, and even the oceans do not freeze solid Marine life could not survive if bodies of water froze solid Acids, Bases, and ph Acid A chemical compound that to solutions Base A compound that and removes them from solution ph scale used to describe the acidity of a solution ph Scale Oven cleaner Household bleach Household ammonia Self-test/Review Questions Use these questions as a self test and then discuss your responses with your study group/classmates your responses will not be collected. : ph < 7 H + > OH - : ph > 7 H + < OH - : ph = 7 H + = OH - Basic solution Neutral solution Acidic solution Milk of magnesia Seawater Human blood Pure water Urine Tomato juice Grapefruit juice Lemon juice; gastric juice 1. Why is carbon dioxide gas, CO 2, classified as a compound but nitrogen gas, N 2, is not? 2. Which of the following are compounds? Elements?: C 6 H 12 O 6, CH 4, O 2, Cl 2, HCl, MgCl 2, Fe, Ca, Ne, NaI, I 3. What is the difference between an atom and an ion? Give examples of each to support your response. 4. Which subatomic particle determines the identity of an atom? 5. Which subatomic particle determines the chemical properties of an atom? Self-test/Review Questions 6. A carbon atom has 6 protons, and the most common isotope of carbon has 6 neutrons. A radioactive isotope of carbon has 8 neutrons. What are the atomic numbers and the mass numbers of the of the stable and radioactive forms of carbon? 7. Explain the difference between an ionic and covalent bond in terms of what happens to the electrons in the outer shell of the participating atoms. 8. Sodium fluoride, NaF, is often added to toothpaste to both kill bacteria that cause cavities. It also helps to harden the enamel of teeth thus helping it resist cavities. Is sodium fluoride an ionic or covalent compound? How do you know? Explain your reasoning. 9. Is carbon dioxide an ionic or covalent compound? How do you know? Explain your reasoning. Self-test/Review Questions (cont.) 10. Why are the following incorrect structures for the substances below? Rewrite their structures with the correct number of chemical bonds. a. Carbon dioxide gas: O C O b. Oxygen gas: O O c. Nitrogen gas: N N 11. Explain how water s versatility as a solvent results from the fact that water is polar molecule. 12. A bottle of Pepsi consists mostly of sugar dissolved in water, with some carbon dioxide gas that makes fizzy and makes the ph less than 7. Describe Pepsi using the following terms: solute, solvent, acidic, aqueous solution 6
Self-test/Review Questions (cont.) 13. Which of the following are chemical changes? Physical changes? If possible, write the balanced chemical equation for those that are a chemical change. a. The alcoholic fermentation in Yeast in which yeast produce ethanol, C 2 H 5 OH, and carbon dioxide, CO 2, from the sugar glucose, C 6 H 12 O 6 b. Water boils to form steam c. The healing of a cut finger d. Cutting a piece of wood with a saw e. Potassium metal, K, and chlorine gas (Cl 2 ) combine to form potassium chloride. f. The rusting of iron, Fe, to produce rust, iron (III) oxide (Fe 2 O 3 ) Self-test/Review Questions (cont.) 14. Which of these is not a subatomic particle? a) proton; b) ion; c) neutron; d) electron 15. The outermost electron shell of every Noble Gas element (except Helium) has electrons. a) 1; b) 2; c) 4; d) 6; e) 8 16. An organic molecule is likely to contain all of these elements except. a) C; b) H; c) O; d) Ne; e) N 17. The chemical bond between water molecules is a bond. a) ionic; b) polar covalent; c) nonpolar covalent; d) hydrogen 18. A solution with a ph of 7 has times more H ions than a solution of ph 9. a) 2; b) 100; c) 1000; d) 9; e) 90 19. The type of chemical bond formed when electrons are shared between atoms is a bond. a) ionic; b) covalent; c) hydrogen Self-test/Review Questions (cont.) 20. The type of chemical bond formed when oppositely charged particles are attached to each other is a bond. a) ionic; b) covalent; c) hydrogen 21. Carbon has an atomic number of 6. This means it has. a) six protons; b) six neutrons; c) six protons plus six neutrons; d) six neutrons and six electrons 22. Each of the isotopes of hydrogen has proton(s). a) 3; b) 1; c) 2; d) 92; e) 1/2 23. A molecule is. a) a mixture of various components that can vary; b) a combination of many atoms that will have different ratios; c) a combination of one or more atoms that will have a fixed ratio of its components; d) more important in a chemistry class than in a biology class 7