1. 1 Biology Sylvia S. Mader Michael Windelspecht Chapter 2 Basic Chemistry Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1

2. Mills Biology 2001 Mader Chapter 2 ~ Basic Chemistry This chapter should be a review. We will go over this material very quickly. Read second ½ of Ch 2 for tomorrow. You should also read appropriate pages of CliffsAP Take the Sample test on page 27, grade it and turn in by Sept 2. Topics 2.1 Chemical Elements 2.2 Compounds and Molecules 2.3 Chemistry of Water 2.4 Acids and Bases

3. 3 2.1 Chemical Elements Matter is defined as anything that has mass and occupies space. Matter exists in three states: solid, liquid, and gas. All matter (both living and non-living) is composed of elements. 3

4. 4 Elements An element is a substance that cannot be broken down into substances with different properties; composed of one type of atom. Six elements make up 95% of the body weight of organisms: (acronym CHNOPS)  Carbon  Hydrogen  Nitrogen  Oxygen  Phosphorus  Sulfur 4

5. 5 60 40 20 0 FeCaKSPSiAlMgNaONCH Earth’s crust organisms Element Percent by Weight Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. © Gunter Ziesler/Peter Arnold, Inc. Composition of Earth’s Crust and Its Organisms

6. 6 Atoms An atom is the smallest part of an element that displays the property of the element. An element and its atom share the same name.  Composed of subatomic particles: protons, neutrons, electrons  Central nucleus Protons- positively charged Neutrons- no charge  Orbiting clouds around nucleus (electron shells) Electrons- negatively charged, very low mass- negligible in calculations 6

7. 7 c. Subatomic Particles = proton = neutron = electron b. a. Particle Proton Neutron Electron Nucleus Electron shell +1 0 –1 1 1 0 Atomic Mass Unit (AMU) Location Electric Charge Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

8. 8 Atomic Number and Mass Number Each element is represented by one or two letters to give it a unique atomic symbol.  H = hydrogen, Na = sodium, C = carbon The atomic number is equal to the number of protons in each atom of an element. The mass number of an atom is equal to the sum of the number of protons and neutrons in atom’s nucleus.  The atomic mass is approximately equal to the mass number. 8

9. 9 mass number atomic number atomic symbol Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Atomic number? Atomic mass?

10. 10 Periodic Table 10 Atoms of an element are arranged horizontally by increasing atomic number in rows called periods. Atoms of an element arranged in vertical columns are called groups.  Atoms within the same group share the same binding characteristics. Atoms shown in the periodic table are electrically neutral.  Therefore, the atomic number tells you the number of electrons as well as the number of protons.

11. 11 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Periods 1 2 3 4 atomic number atomic symbol atomic mass VIII Groups 20.1819.0016.0014.0112.0110.819.0126.941 22.9924.3139.9535.4532.0730.9728.0926.98 83.6079.9078.9674.9272.5969.7240.0839.10 KrBrSeAsGeGaCaK 3619203132333435 1112131415161718 NaMgAlSiPSClAr NeFONCBBeLi 109876543 4.003 He 2 VIIVIVIVIIIII 1.008 I 1 H A Portion of the Periodic Table

12. Mills Biology 2001 2.1 Chemical Elements Know highlighted elements

13. 13 Isotopes Isotopes are atoms of the same element that differ in the number of neutrons (and therefore different atomic masses). SSome isotopes spontaneously decay Radioactive isotopes give off energy in the form of rays and subatomic particles Can be helpful or harmful 12 6 Carbon 12 C 13 6 Carbon 13 C 14 6 Carbon 14 C 13

14. 14 b. a. larynx thyroid gland trachea a: © Biomed Commun./Custom Medical Stock Photo; b (left) : Courtesy National Institutes of Health; b: (right) © Mazzlota et al./Photo Researchers, Inc Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Uses of Low Levels of Radiation Low levels of radioactive Iodine are used to “see” the thyroid gland. In a PET scan an isotope of glucose is used to detect active tissues.

15. 15 Uses of High Levels of Radiation Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a: (Peaches): © Tony Freeman/PhotoEdit; b: © Geoff Tompkinson/SPL/Photo Researchers, Inc. a.b.

16. 16 Electrons and Energy Electrons are attracted to the positively charged nucleus, thus it takes energy to hold electrons in place. It takes energy to push them away and keep them in their own shell.  The more distant the shell, the more energy it takes to hold in place. Electrons have energy due to their relative position (potential energy). Electrons determine chemical behavior of atoms.

17. 17 The Distribution of Electrons The Bohr model is a useful way to visualize electron location.  Electrons revolve around the nucleus in energy shells (energy levels).  For atoms with atomic numbers of 20 or less, the following rules apply: the first energy shell can hold up to 2 electrons each additional shell can hold up to 8 electrons each lower shell is filled first before electrons are placed in the next shell  These rules cover most of the biologically significant elements.

18. 18 Valence Electrons The outermost energy shell is called the valence shell. The valence shell is important because it determines many of an atom’s chemical properties. The octet rule states that the outermost shell is most stable when it has eight electrons.  Exception: If an atom has only one shell, the outermost valence shell is complete when it has two electrons. The number of electrons in an atom’s valence shell determines whether the atom gives up, accepts, or shares electrons to acquire eight electrons in the outer shell. –Atoms that have their valence shells filled with electrons tend to be chemically stable. –Atoms that do not have their valence shells filled with electrons are chemically reactive.

19. 19 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H PS C O N electronvalence shell nitrogencarbonhydrogen sulfurphosphorus 32 16 15 31 8 16 14 76 12 1 1 HN C S P O oxygen electron shell nucleus Bohr Models of Atoms

20. 20 2.2 Compounds and Molecules A molecule is two or more elements bonded together. A compound is a molecule containing at least two different elements bonded together.  CO 2, H 2 O, C 6 H 12 O 6, etc. In Biology – usually used interchangeably (molecule and compound) A formula tells you the number of each kind of atom in a molecule. one molecule indicates 6 atoms of carbon indicates 6 atoms of oxygen indicates 12 atoms of hydrogen

21. 21 Chemical Bonding Bonds that exist between atoms in molecules contain energy. Bonds between atoms are caused by the interactions between electrons in outermost energy shells. The process of bond formation is called a chemical reaction.

22. 22 Types of Bonds Covalent bonds Ionic bonds Hydrogen bonds An ion is an atom that has lost or gained an electron. An ionic bond forms when electrons are transferred from one atom to another atom and the oppositely charged ions are attracted to one.  Example: formation of sodium chloride Salts are solid substances that usually separate and exist as individual ions in water.

23. 23 NaCl sodium atom (Na)chlorine atom (Cl) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Formation of Sodium Chloride

24. 24 Na Cl sodium atom (Na)chlorine atom (Cl) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

25. 25 + – NaCl Na Cl sodium ion (Na + ) chloride ion (Cl – ) sodium chloride (NaCl) sodium atom (Na)chlorine atom (Cl) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

26. 26 + – Na sodium atom (Na)chlorine atom (Cl) sodium ion (Na + ) sodium chloride (NaCl) a.b. chloride ion (Cl – ) NaCl Cl – Na + Cl Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. b (middle): © Evelyn Jo Johnson; b (right): © Evelyn Jo Johnson

27. 27 Types of Bonds: Covalent Bonds Covalent bonds result when two atoms share electrons so each atom has an octet of electrons in the outer shell.  Note: In the case of hydrogen, the outer energy shell is complete when it contains 2 electrons. In a nonpolar covalent bond electrons are shared equally between atoms.  Examples: hydrogen gas, oxygen gas, methane

28. 28 a. Hydrogen gas b. Oxygen gas c. Methane Structural Formula Electron Model HCH HH H H OO C OO H H HH HH CH 4 O2O2 H2H2 Molecular Formula Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Covalently Bonded Molecules

29. 29 Types of Bonds: Covalent Bonds In a polar covalent bond electrons are shared unequally.  Example: water Electronegativity is the ability of an atom to attract electrons towards itself in a chemical bond.  In water, the oxygen atom is more electronegative than the hydrogen atoms and the bonds are polar. O HH Oxygen is partially negative Hydrogens are partially positive

30. 30

31. 31 2.3 Chemistry of Water Water is a polar molecule.  The shape of a water molecule and its polarity make hydrogen bonding possible. A hydrogen bond is a weak attraction between a slightly positive hydrogen atom and a slightly negative atom.  Can occur between atoms of different molecules or within the same molecule  A single hydrogen bond is easily broken while multiple hydrogen bonds are collectively quite strong.  Help to maintain the proper structure and function of complex molecules such as proteins and DNA

32. 32 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Fig. 2.9 H HH H H H HH O O O O Electron Model Ball-and-stick Model Space-filling Model Oxygen attracts the shared electrons and is partially negative. b. Hydrogen bonding between water molecules hydrogen bond Hydrogens are partially positive. a. Water (H 2 O) 104.5˚ ++ ++ -- ++ ++ -- 2.3 Chemistry of Water

33. Mills Biology 2012 2.3 Chemistry of Water Properties of water  Makes up 60-80% of most living cells  Most abundant compound in living tissue  Makes up about 66% of weight of an adult human About 75% of your brain is water! Why do we need it?  Cohesion, adhesion, surface tension, heat transfer, solvent, transport, properties of freezing.

34. 34 Properties of Water Water molecules cling together because of hydrogen bonding.  This association gives water many of its unique chemical properties. Water has a high heat capacity.  The presence of many hydrogen bonds allow water to absorb a large amount of thermal heat without a great change in temperature.  The temperature of water rises and falls slowly. Allows organisms to maintain internal temperatures

35. 35 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Calories of Heat Energy / g 0 800 600 400 200 Solid evaporation occurs Liquid 540 calories Gas 80 calories a. Calories lost when 1 g of liquid water freezes and calories required when 1 g of liquid water evaporates. b. Bodies of organisms cool when their heat is used to evaporate water. freezing occurs b: © Grant Taylor/Stone/Getty Images Temperature (°C) 120100800204060 Temperature and Water

36. 36 Properties of Water Water has a high heat of vaporization.  Hydrogen bonds must be broken to evaporate water.  Bodies of organisms cool when their heat is used to evaporate water. Water is a good solvent.  Water is a good solvent because of its polarity.  Polar substances dissolve readily in water.  Hydrophilic molecules dissolve in water.  Hydrophobic molecules do not dissolve in water.

37. 37 H H HH HHH H HH H An ionic salt dissolves in water. HH Cl – Na + O O OO OO Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Water as a Solvent

38. Cohesion and Adhesion Cohesion  Sticks to itself  Polarity Caused by H bonds Without these bonds water would boil at -80C (instead of +100) and freeze at –100C (instead of 0C) this would not be compatible with life Adhesion  Sticks to other substances  polarity  “add” hesion  Capillary action High surface tension due to hydrogen bonding of water.

39. 39 Water as a Transport Medium Water evaporates, pulling the water column from the roots to the leaves. Water molecules cling together and adhere to sides of vessels in stems. Water enters a plant at root cells. H2OH2O H2OH2O Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

40. 40 Properties of Water Ice is less dense than liquid water.  At temperatures below 4°C, hydrogen bonds between water molecules become more rigid but also more open.  Water expands as it reaches 0°C and freezes.  Ice floats on liquid water. Acts as an insulator on top of a frozen body of water Ice floats, I’m glad!

41. 41 Density of Water at Various Temperatures 04100 1.0 0.9 Density (g/cm 3 ) Temperature (ºC) liquid water ice lattice Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

42. 42 A Pond in Winter Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. ice layer Protists provide food for fish. River otters visit ice-covered ponds. Aquatic insects survive in air pockets. Freshwater fish take oxygen from water. Common frogs and pond turtles hibernate.

43. 43 2.4 Acids and Bases pH is a measure of hydrogen ion concentration in a solution. When water ionizes or dissociates, it releases an equal number of hydrogen (H + ) ions and hydroxide (OH - ) ions. Acids are substances that dissociate in water, releasing hydrogen ions. Bases are substances that either take up hydrogen ions (H+) or release hydroxide ions (OH−).

44. Mills Biology 2012 Soren Sorenson 1909 Beer Brewer Developed pH scale

45. 45 The pH Scale The pH scale is used to indicate the acidity or basicity (alkalinity) of a solution.  Values range from 0-14 0 to <7 = Acidic 7 = Neutral >7 to 14 = Basic (or alkaline) Actually a measure of H ion concentration (negative log of the H ion concentration) (log is the power to which 10 must be raised to get a certain number)  measures grams of ion/liter of solution  pH is a shorthand measurement scale  wide range  10 fold change for each change in pH concentration of 0.1gm H ion/L = pH 1  move decimal to left for each increase of 1 pH pH of 1 = 10 -1 pH of 6 = 10 -6

46. 46 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 0 2 3 4 5 6 7 8 9 13 10 11 12 14 hydrochloric acid (HCl) stomach acid lemon juice soda beer, vinegar tomatoes bread, black coffee normal rainwater root beer, urine milk pure water, tears human blood egg whites, sea water baking soda, stomach antacids Great Salt Lake household ammonia bicarbonate of soda oven cleaner sodium hydroxide (NaOH) Acidic Basic OH – NeutralpH H+H+

47. 47 Buffers and pH A buffer is a chemical or a combination of chemicals that keeps pH within normal limits. Health of organisms requires maintaining the pH of body fluids within narrow limits.  Human blood is normally pH 7.4 (slightly basic) If blood pH drops below 7.0, acidosis results If blood pH rises above 7.8, alkalosis results Both are life-threatening situations.  Body has built-in mechanisms to prevent pH changes. Read Connecting the Concepts with the Big Ideas pg 34

48. Mills Biology 2012 THE END