2. Chemistry for Biology Part 1 - Elements and Atoms

3. What is Chemistry? All substances are made of chemicals. Chemistry is the study of those chemicals.

4. Chemistry also studies: Chemical changes - how substances change from one substance to another. What is contained in food. What is contained in our bodies. How to purify chemicals and make new chemicals.

5. Why Study Atoms? All chemicals are made of smaller substances called atoms. Understanding atoms explains why chemicals do what they do. For example: Why do 2 hydrogen atoms join with 1 oxygen atom to form a molecule of water (H 2 O)? Why does Sodium (an explosive white metal), join with Chlorine (a deadly gas), to form harmless table salt (NaCl)?

6. Elements There are about 112 kinds of elements which are listed on the Periodic Table.  Examples: Hydrogen, Gold, Carbon, Oxygen These elements combine to make up all the substances we know of.

7. Most substances contain more than 1 type of element and are called Compounds.  For example: Water, Soap, CO 2, & DNA. The smallest particles of an element are the atoms of that element. So, the atoms are the smallest building blocks of all substances.

8. 3 Parts of an Atom In the middle of an atom is a tiny nucleus which contains 2 types of particles - protons and neutrons The nucleus is surrounded by orbiting electrons.

9. Sample Atom

10. The Atomic Nucleus The nucleus is 100,000 times smaller than the diameter of the atom. E.g. An ant in a football stadium, or a tennis ball and 2 miles on each side. Protons and neutrons are about the same size. Protons have a charge of +1 (a “positive” charge). Neutrons have no charge (they are “neutral”).

11. Electrons Electrons are much smaller than protons and neutrons. In fact, it takes 1800 electrons to equal the mass of just 1 proton. Electrons have a charge of -1 (they are “Negatively” charged) Electrons only orbit in certain energy levels (specific spaces around the nucleus). They orbit so fast, the energy levels are more like an ‘electron cloud’.

12. Atomic Size Aluminum foil is about 50,000 atoms thick. Even a dust particle contains millions of atoms. The mass of a proton is 1.7 x 10 -24 grams..0000000000000000000000017 grams To make it easier, the SI unit of a proton is 1 AMU (Atomic Mass Unit)

13. Atoms compared Atoms vary a lot in mass, but little in size. Plutonium- Atomic Mass = 244.1 Hydrogen - Atomic Mass = 1.0

14. How atoms differ The number of protons in an atom determines which element it is. All atoms of a certain element have the same number of protons.  Example: All gold atoms have 79 protons Note: Atoms of the same element “may” have different numbers of Neutrons.

15. The number of Protons in an atom is called the ‘Atomic Number’, and is the top (left) number in the boxes of the Periodic Table.

16. 2 Simple Atoms Hydrogen atoms always have 1 proton. They also have 1 electron and usually have no neutrons. Helium atoms always have 2 protons. They have 2 electrons and usually have 2 neutrons. P e PP N N e e H He

17. Isotopes Atoms of the same element that have different numbers of neutrons are called Isotopes. Even Hydrogen has different Isotopes. One version has no neutrons, and one version has 1 neutron. Some isotopes are radioactive. P e P e N H-1 H-2

18. Mass Number The Mass Number is the sum of the protons plus neutrons in an atom. Below are two Lithium Isotopes. Each has 3 protons which makes them Lithium. One isotope has 3 neutrons, with a Mass Number of 6 (3P+3N) One isotope has 4 neutrons, with a Mass Number of 7 (3P+4N). Li-6Li-7 Protons Neutrons

19. Question What is the atomic number of this atom? What element is this? What is the mass number of this atom? Proton Neutron

20. Atomic Mass The Atomic Mass of an element is the weighted average of the masses of its isotopes found in nature. For example: 50%Li - 6 = 3.0 20%Li - 7 = 1.4 20%Li - 8 = 1.6 10%Li - 9 =.9 100% 6.9 (Atomic Mass)

21. Atomic Mass The Atomic Mass is the larger number in the Element Boxes on the Periodic Table.

22. Calculating the # of Neutrons Sorry, it’s not in the boxes of the Periodic Table. If you are given the Atomic Number (# of protons) and the Mass Number (# of protons + neutrons), you can easily calculate the number of neutrons.

23. Example: If the Mass Number (#P + #N) =45, and the Atomic Number (#P) =20 that atom must have 25 neutrons (45 - 20 = 25)

24. Calculating the Number of Electrons It’s the Same as the number of Protons! That’s why an atom is Electrically Neutral overall.  E.g. for Carbon, 6 P’s = +6, 6 e - ’s = -6, so +6 and -6 = 0 Total charge. When an atom loses or gains electrons from normal, it is called an Ion. More on Ions when we discuss Chemical Bonding.

25. The Periodic Table The Zig Zag Line - Divides Metals to the Left, from Non-Metals to the Right. Along the Zig Zag Line are the Metalloids. Rows = “Periods” Columns = “Groups” or “Families”  Elements in a group have the same number of electrons in their outermost shell (energy level)  So, members of a group tend to act the same in chemical reactions.

26. Group Similarities Group 1 elements all have 1 electron in their outermost energy level (shell). Group 2 has 2 electrons in their outermost shell. Group 18 has 8 electrons in their outermost shells, (so their outermost shells are full.) Group 17 has 7 electrons in the outermost shells. (Tip-subtract 10 from the group number.)

28. Chemical Bonding Part 2

29. What is a Chemical Bond ??? A force of attraction that holds atoms together due to their electrical charges.

30. 3 Types of Bonds Covalent Ionic Metallic

31. Energy Levels Electrons are located in areas around the nucleus called Energy Levels. Only a certain number of electrons can occupy each Energy Level. The first level can hold 2. The second level can hold 8. The energy levels are often drawn as circles. (It’s actually much more complicated)

32. Electron Configurations One way to show the electrons in an Atom is to draw Electron Dot Diagrams. Here is an electron dot diagram for Nitrogen: N

33. The Essence of Chemical Bonding Atoms are “happiest” and most “content” when their outermost energy levels are Full of Electrons. Atoms can borrow, give away, or share electrons with other atoms to reach a full outermost level. Electrons in the outermost level are called Valence Electrons. Full!

34. Electron Dot Diagram - Nitrogen For Nitrogen, first determine the Atomic Number for Nitrogen - 7 That means it has 7 Protons. Therefore, it must also have 7 Electrons. Start filling energy levels with electrons from the inside out.

35. The first energy level can hold only 2 electrons For Nitrogen, that leaves 5 more electrons for the next level. (7-2 = 5) N

36. The second energy level can hold 8 electrons. So, Nitrogen has room for 3 more electrons in its 2nd energy level. N The last 5 electrons of Nitrogen all fit in the 2nd energy level.

37. Remember, Atoms prefer to have full outer energy levels... So, Nitrogen would be “Happier” if it could find a way to get 3 more electrons to bring it’s outer level up to 8 Electrons. That’s where Bonding comes in. Nitrogen will seek out a willing-partner; an Atom, or Atoms, that want to share, or give away, 3 of their electrons. N

38. Giving Away Electrons Some atoms can reach a full outer level more easily by giving away electrons. For example, a Sodium Atom has 1 electron in its outermost energy level. If it gives one away, it has a Full outer level. Na

39. Covalent Bonds Covalent Bonds occur when atoms ‘Share’ electrons. The resulting substance is called a Molecule. Most organic molecules (molecules of living things) have this type of bond. This is usually the type of bond between non-metals.

40. For a simple Example, lets look at Chlorine... 2 Chlorine Atoms bond together to form a Chlorine Molecule. The Chemical Formula is Cl 2

41. Each Cl Atom has 7 valence electrons Each atom needs 1 more electron to have a full outer shell Cl

42. By sharing electrons, each now has a full outer level Cl

43. DNA MOLECULE

44. ‘Polar’ Covalent Bonds Sometimes, the electron sharing isn’t exactly equal. One atom hogs them.  Example: In a water molecule, the shared electrons spend more time around Oxygen than the two Hydrogen atoms.  This makes one end slightly negative.  And the other end slightly positive. O H H (+) (-)(-)

45. Next, Ionic Bonds One type of atom gives away (donates) electrons, the atom other receives (gains) electrons. They aren’t “sharing”. After the exchange, Both types of atoms are called Ions.

46. Types of Ions Atoms who received electrons are called negative ions.  Their “total” charge becomes “more negative”.  E.g. Cl atom has 17 P’s and 17 e - ’s. If gains 1 e -, now 17 P’s and 18 e - ’s. (+17 - 18 = -1) Total charge now -1.

47. Atoms who donated electrons are called positive ions.  Their “total” charge becomes “more positive”.  E.g. K atom has 19 P’s and 19 e - ’s. If lose 1 e -, now 19 P’s and 18 e - ’s. (+19 - 18 = +1) Total charge now +1.

48. Positive Ions Atoms with few electrons in their outermost level usually like to donate electrons. This includes metals. They are on the left side of the Periodic Table. Na

49. Negative Ions Atoms with almost full outermost levels don’t give them away easily. They prefer to gain electrons. These include non-metals. They are on the right side of The Periodic Table. Cl

50. Ionic Bond Positive and Negative Ions have an electrical attraction for each other. In other words, they form an Ionic Bond. Cl Na Positive IonNegative Ion Cl - Ion Na + Ion

51. Why are Ions attracted? In nature - opposite electrical charges attract. A positive and negative ion have opposite charges, so they are naturally attracted to each other. The resulting substance isn’t a molecule. It’s an ionic compound.

52. Bonding and the Periodic Table Group 18 doesn’t like to bond with any other elements, Why? Group 1 forms Ionic Bonds with Group 17. Why? Group 2 forms Ionic Bonds with which Group? Carbon has 4 electrons in its outermost shell. How many covalent bonds does it usually make?

54. Chemical Reactions Part 3

55. Chemical Reactions Defined The process by which substances change to produce different substances. The new substances have different properties from the original substances.

56. Chemical Reaction Terminology ‘Yield’ C + O 2 CO 2 ‘Reactants’ ‘Products’ In common English: The reactants Carbon and Oxygen combine to yield a product called Carbon Dioxide.

57. How do substances change? Chemical bonds break Atoms rearrange New chemical bonds form

58. Common Chemical Reactions Burning Fuel Converting the energy of Food into ATP A bomb explosion Photosynthesis - plants creating food Rusting iron

59. 2 Types of Reactions 1. Synthesis two or more one 2. Decomposition one two or more

60. Chemical Formulas They are a shorthand notation for chemically combined atoms. They use chemical symbols and numbers - H 2 O CO 2 3C 6 H 12 O 6 The small numbers after the symbols are called Subscripts. Numbers placed in front of a formula are called Coefficients.

61. Coefficients A Coefficient means there are that number of whatever follows. Example: 2H 2 SO 4 means there are 2 H 2 SO 4 ’s How many atoms are in that formula? 14.  Each “H 2 SO 4 ” has 7 atoms, and there are 2 of them.

62. How many atoms are in these Chemical Formulas? CO 2 MgCl 2 2C 3 H 8 C 6 H 12 O 6 3AgNO 3