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2.1 Chemical Elements Chemistry as it related to biology.

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2 2.1 Chemical Elements Chemistry as it related to biology

3 QOD: (after quiz) Read the article and try to answer the question: 1.Why does the doctor not recommend the use of external cooling (such as ice baths, cold water or even air conditioners) to reduce a fever. 2.Are there any exceptions? 3.What is recommended to treat fever? Why? Your should have thorough answers, including evidence you find in the article.

4 A. Matter What is matter?

5 Biochemistry Ch 2.1 Write a vocabulary list for yourself: try to define the ones you remember: Element Compound Protons Neutrons Electrons Atomic number Atomics Mass Isotope Orbital

6 Matter: “stuff” has mass, takes up space Made up of elements: substance that cannot be broken down into other substances by a chem rxn Compound: consist of 2 or more elements in a fixed ratio

7 Six elements: C, H, N, O, P, S: make up 98% of living things. C, H, O and N make up about 96% “SHNOPS”

8 B. Atomic Structure a. Protons (p + ): positively charged particles; neutrons have no charge; both have about 1 atomic mass unit of weight. Both are found in the nucleus b. Electrons (e - ) are negatively charged particles that orbit the nucleus

9 Atomic number= number of protons - can’t change or it changes the atom Atomic mass: about equal to the sum of its protons and neutrons All atoms of an element have the same number of protons, the atom's atomic number Periodic Table (mass)

10 Interactive Periodic TableInteractive Periodic Table | Cartoon Periodic TableCartoon Periodic Table

11 Isotopes Isotopes are atoms with the same number of protons but differ in number of neutrons; e.g., a carbon atom has six protons but may have more or less than usual six neutrons.

12 Carbon 14 - Break it Down! Carbon- 12 is the most common form of carbon, it has 6 protons, 6 electrons, and 6 neutrons It is called Carbon 12 because that is its weight (6 + 6 ) Carbon 14 has 2 extra neutrons, its weight is 14 (6 + 8 ); it is an isotope of carbon

13 A carbon with eight rather than six neutrons is unstable; it releases rays and subatomic particles and is a radioactive isotope. Sample Question: A 200 g sample of muskopfonian is left in a container, the half life of muskopfonian is 1 hour. How much of the sample will be left after 4 hours? Answer: 200 x.5 = 100 (hour 1) 100 x.5 = 50 (hour 2) 50 x.5 = 25 (hour 3) 25 x.5 = 12.5 (hour 4) or 200 x.5 4 = 12.5

14 Low levels of radiation such as radioactive iodine or glucose allow researchers to trace the location and activity of the atom in living tissues; therefore these isotopes are called tracers which are used in CAT scans

15 High levels of radiation can cause cancerous tissues and destroy cells; careful use of radiation in turn can sterilize products and kill cancer cells.

16 Pick your favorite element from the table. Turn and tell your lab partner how many protons, electrons and neutrons it has, and what it's atomic weight is (if you can see it). Have your table partner then name the element.

17 E. Electrons and Energy 1. Electrons occupy an orbital at some level near or distant from the nucleus of the atom. S orbital: innermost, hold 2 elections P orbital: after s, holds 8 elections Outer elections have more energy and are less stable. So?

18 2. Electrons can be used to store and release energy! 3. When atoms absorb energy during photosynthesis, electrons are boosted to higher energy levels. 4. The innermost shell of an atom is complete with two electrons; all other shells are complete with eight electrons. 5. The outermost shell is the valance shell, and the number of valance e - in the outermost shell determine many of the atoms properties

19 DRAW IT! QUICK!! 1. Draw six protons in the nucleus of the atom. 2. Draw six neutrons in the nucleus of the atom. 3. Draw two electrons in the first energy level and label them with their charge. 4. Draw four electrons in the second energy level and label them with their charge. 5. What element is it!? __________ (the future of the human race depends on it!)

20 What can easily be added to carbon to complete it’s valence shell?

21 2.2 Elements and Compounds A. Compounds: When two or more different elements react or bond together, they form a compound (e.g., H2O). Electrons possess energy and bonds that exist between atoms in molecules contain energy. Glycine

22 B. Ionic Bonding Ionic bonds: when electrons are transferred from one atom to another. -Attraction of oppositely charged ions holds the two atoms together in an ionic bond. -Losing or gaining elections gives ions a filled outer shell, so they are more stable Ex: sodium (Na+) and Chlorine (Cl- ) make NaCl

23 Cation: positively charged ion anion: negatively charged ion

24 Why and how do ionic bonds form?

25 C. Covalent Bonding Hydrogen can give up an electron to become a hydrogen ion (H+) or share an electron with another atom to complete its outer shell of two electrons. Covalent bonds: when two atoms share electrons so each atom has octet of electrons in the outer shell. Strongest type of bond

26 Carbon has amazing bonding properties, as we will learn in the next chapter Structural formulas represent shared atom as a line between two atoms; e.g., single covalent bond (H-H), double covalent bond (O=O)

27 Bonds can be represented using structural formation, where a line represent the sharing of 2 elections

28 D. Nonpolar and Polar Covalent Bonds 1. In nonpolar covalent bonds, sharing of electrons is equal = no charge 2. With polar covalent bonds, the sharing of electrons is unequal. = charge Ex: water molecule (H2O), sharing of electrons by oxygen and hydrogen is not equal; the oxygen atom with more protons dominates the H2O association. *The oxygen then assumes a small negative charge *

29 Hydrogen Bond: weak attractive force between slightly positive hydrogen atom of one molecule and slightly negative atom in another or the same molecule. Weakest bond mainly between O, N, F and an atom of hydrogen Many hydrogen bonds taken together are relatively strong. Hydrogen bonds between complex molecules of cells help maintain structure and function. Hydrogen bonds create surface tension.

30 Notice the e - spend more time around the oxygen molecule: it’s has more protons to attract the elections *the shape allows for one side to be more + and the other more -

31 Van der Waals Interactions When you have a molecule which is electrically dipolar (equal but opposite in charge) you have attraction between the negative pole of one molecule and positive pole of the other molecule. They are usually weaker than hydrogen bounds but exist in all matter

32 Biological molecules recognize and interact with each other with specificity based on their shape

33 List the 4 main types of bonds from weakest to strongest: van der waal hydrogen ionic covalent

34 Draw these example and Name the type of bond. What elements are in each bond? 1 2


36 Name the type of bond. What elements are in each bond? 3434

37 Title: Properties of water In your notebook, create a chart listing the properties of water, and why each property is important. Include example whenever possible use pages 29-31

38 PropertyExplanationImportanceExample 1. High Specific Heat 2. High heat of vaporization 3. Universal solvent 4. Cohesive and Adhesive 5. Ice Floats Examples of charts water Property 1 Property 2 Property 3 Property 4 Property 5 Explanation example Pg 29-31

39 2.3. Chemistry of Water A. Facts 1. All living things are 70.90% water. 2. Because water is a polar molecule, water molecules are hydrogen bonded to each other. 3. With hydrogen bonding, water is liquid between 0 C and 100 C which is critical for life.

40 B. Properties of Water 1. High Specific Heat: The temperature of liquid water rises and falls more slowly than that of most other liquids. - Most water stays a liquid Because water holds more heat, its temperature falls more slowly than other liquids; this protects organisms from rapid temperature changes, living things don't freeze or boil easily Calorie is amount of heat energy required to raise temperature of one gram of water 1o C. nmental/458-how-water-works-video.htm

41 2. Water has a high heat of vaporization. a. Hydrogen bonds between water molecules require a large amount of heat to break. b. This property moderates earth's surface temperature; permits living systems to exist here. c. When animals sweat, evaporation of the sweat takes away body heat, thus cooling the animal.

42 Heat of vaporization Evaporative cooling Organisms rely on heat of vaporization to remove body heat

43 3. Water is universal solvent, and facilitates chemical reactions both outside of and within living systems.. a. Water is a universal solvent because it dissolves a great number of solutes. b. Ionized or polar molecules attracted to water are hydrophilic. c. Nonionized and nonpolar molecules that cannot attract water are hydrophobic. Solvents dissolve other substances (solutes) and do not lose their own properties. If we use a simple and easy example, we can get a handle on the idea. Take a glass of warm water, put a teaspoon of table salt in it, and stir it. The salt will dissolve in the water and "disappear" from view. The water is the solvent here, the salt is the solute in this example, and the resulting salt water is a solution that we created. It's that simple.

44 Hydrophobic vs Hydrophilic

45 4. Liquid water is cohesive & adhesive Cohesion = H bonds between water molecules; H2O molecules tend to stick together. Adhesive= ability of water to cling to other polar molecules importance= Higher surface tension Transport H2O against gravity in plants = capillary action


47 And this has made all the difference! Ice! I could use more ice! 5. Ice floats  Most (all?) substances are more dense when they are solid, but not water… Ice floats!  H bonds form a crystal  allowing life to survive the winter

48 Create a Venn Diagram Comparing Acids and Bases  Substances with hydrogen ions (H + )  Substances with hydroxide ions (OH – )  Taste sour  Taste bitter  Feel slippery  pH greater that 7  pH lower that 7 Stomach acid Citrus fruit: orange Soap Cleaning products Baking soda vinegar Neutral = pH of 7

49 Acid molecules dissociate in water, releasing hydrogen ions (H+) ions: HCl ¨ H+ + Cl-. Bases are molecules that take up hydrogen ions or release hydroxide ions. NaOH ¨ Na+ + OH-. See also: Acid & Base ColoringAcid & Base Coloring

50 Acids and Bases Covalently bonded water molecules ionize; the atoms dissociate into ions. When water ionizes or dissociates, it releases a small (107 moles/liter) but equal number of H+ and OH ions; thus, its pH is neutral. Water dissociates into hydrogen and hydroxide ions:

51 -Acid is a substance with pH less than 7; base is a substance with pH greater than 7. -As logarithmic scale, each lower unit has 10 times the amount of hydrogen ions as next higher pH unit; * Buffers keep pH steady and within normal limits in living organisms.. The pH scale indicates acidity and basicity (alkalinity) of a solution.

52 Chemistry in Biology  Substances that dissociates into hydrogen ions (H + )  Taste sour  pH lower than 7 Acids Examples Stomach acid Citrus fruit: orange vinegar  Substances that dissociated into hydroxide ions (OH – )  Taste bitter  Feel slippery  pH greater than 7 Base Examples Soap Baking soda Cleaning products

53 pH Scale 10 –1 H + Ion Concentration Examples of Solutions Stomach acid, Lemon juice 1 pH 10 0 Hydrochloric acid0 10 –2 2 10 –3 Vinegar, cola, beer 3 10 –4 Tomatoes 4 10 –5 Black coffee, Rainwater 5 10 –6 Urine, Saliva 6 10 –7 Pure water, Blood 7 10 –8 Seawater 8 10 –9 Baking soda 9 10 –10 Great Salt Lake 10 10 –11 Household ammonia 11 10 –12 Household bleach 12 10 –13 Oven cleaner 13 10 –14 Sodium hydroxide14 tenfold change in H+ ions pH1  pH2 10 -1  10 -2 10 times less H + pH8  pH7 10 -8  10 -7 10 times more H + pH10  pH8 10 -10  10 -8 100 times more H +

54 AP Biology  pH of cells must be kept ~7 to maintain homeostasis! Buffers: solutions used to stabilize the pH of a solution  Control pH by using buffers  reservoir of H +  donate H+ when [H + ] falls  absorb H+ when [H + ] rises 10 0 1 2 3 4 5 6 7 8 9 3 Amount of base added Buffering range 452 pH Buffers & cellular regulation

55 AP Biology B ICARBONATE B UFFER S YSTEM : H 2 O + CO 2  H 2 CO 3  HCO 3 - + H + HCO 3 - = Bicarbonate (weak base) H 2 CO 3 = Carbonic acid (weak acid) Major buffer system in blood Maintains blood pH between 7.38 and 7.42

56 2009-2010 He’s gonna earn a Darwin Award! Any Questions?


58 1. The only atom that has a nucleus with no neutrons is _________. A)argon B)carbon C)oxygen D)hydrogen 2. Which of the following elements is NOT one of the six that make up 98% of most organisms' body weight? A)hydrogen B)nitrogen C)carbon D)iron

59 Which of the following statements is true? A)All isotopes give off subatomic particles. B)All isotopes are radioactive. C)All isotopes have the same number of protons. D)All isotopes have the same number of neutrons. What type of bond is formed when atoms share electrons? A)ionic B)covalent C)hydrogen

60 If an atom has an atomic number of 17 and an atomic mass of 35, the number of neutrons in its nucleus equals _____. A)17 B)18 C)52 Which bond is most easily broken? A)a hydrogen bond B)a triple covalent bond C)a single covalent bond

61 Hydrophobic molecules tend to be _________. A)nonpolar B)inorganic minerals C)ionic D)water soluble The calcium ion (Ca2+) _____. A)has accepted two protons B)has given away two electrons C)will form a covalent bond with the chlorine ion (Cl-) D)All of these

62 The three isotopes of carbon 12C, 13C and 14C have different numbers of _______? A)electrons B)protons C)neutrons The combined number of ___________ will determine the number of electrons in orbital(s) around a neutral atom. A)orbitals B)neutrons C)bonds D)protons

63 Which of the following statements is true? A)There are two polar covalent bonds in water. B)There are two ionic bonds in water. C)There is one ionic and one covalent bond in water. D)Electrons are less attracted to oxygen than hydrogen. The two parallel strands of DNA are held together by _______ bonds. A)nonpolar B)hydrogen C)ionic D)covalent

64 The calcium ion (Ca2+) _____. A)has accepted two protons B)has given away two electrons C)will form a covalent bond with the chlorine ion (Cl-) D)All of these Hydrogen bonds form when ___________. A)atoms share electrons B)a slightly negative atom is attracted to a slightly positive atom C)atoms gain electrons D)atoms lose protons

65 Which of the following has a basic pH? A)lemon juice B)milk of magnesia C)tomatoes D)hydrochloric acid Aquatic living things are able to survive the winter thanks to which property of water? A)It is less dense as a solid than as a liquid. B)It is cohesive and adhesive. C)It is the universal solvent. D)It resists changes of state (from liquid to ice or liquid to steam).

66 QOD: In a group of 4, each pick one paragraph of the article to read. (note: paragraph 2 is the hardest one, the back page will be more helpful) When you are done reading, discuss as a group and try to answer the question: 1.Why does the doctor not recommend the use of external cooling (such as ice baths, cold water or even air conditioners) to reduce a fever. 2.Why do movie theaters put so much salt on popcorn?

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