Chemistry of Life

1. "Organic chemistry is the study of carbon compounds. Biochemistry is the study of carbon compounds that crawl." ~Mike Adams Chemistry of Life Biochemistry is the study of the chemical substances and vital processes occurring in living organisms.

2. Unit 2: Key learnings • Atoms interact with one another using ionic, covalent and hydrogen bonds. • Biologically important matter is categorized into 4 types of macromolecules. • Several properties of water make it very biologically important.

3. Unit 2: Essential question How are the properties of biologically important molecules explained by their specific chemical structures?

4. Launch activity: Phenylthalein magic! Demo with Phenylthalein

5. Unit 2: Concepts • Atomic structure and bonding(I) • Properties of water (I) • Macromolecules (E) • Enzymatic reactions(E)

6. Essential question 1.1: How are the numbers of subatomic particles in a given atom determined using the periodic table?

7. Biochemistryis the study of biologically important interactions between compounds. • Biology is, at its simplest form, the study of chemistry. • Even large-scale events in biology are controlled by some molecular scale chemical action.

8. Everything in the universe is composed of matter. • Matter consists of atoms. • Atoms are the smallest unit that cannot be broken down by chemical means. • A group of like atoms is called an element (purist form).

9. Atomic structure is shown as a Bohr model. • Thenucleusis composed of protons(+charge)and neutrons(no charge). • Electronssurround the nucleus (held by their - charge). • An atom has one electron (-) for every one proton (+). This makes it neutral (a balance of positive and negative charges). • Chemistry occurs when electrons move from atom to atom and cause changes in reactivity.

10. A Bohr Model shows the protons and neutrons surrounded by electrons in their proper energy levels. Watch energy levels video clip

11. Atoms of the same element sometimes differ in the number of neutrons they have in the nucleus. • The number of protons is written as the atomic number on the Periodic table. • The number of neutronsis usually equal to the number of protons. • The number of neutrons can be determined by subtracting the atomic number from the atomic mass. • An atom is an isotopewhen it has a different number of neutrons than the periodic table predicts.

12. The Periodic Table

14. Isotopes of carbon Watch isotopes video clip

15. Organization of electrons 2, 8, 8

16. Going Further: Electrons are organized in a 2,8,8 format. • Electrons exist in energy levels that can hold limited numbers of electrons. • The first level (up to 2 electrons ) must be filled before electrons are placed into the next. The second level (up to 8 electrons)needs to be filled before electrons are placed into the 3rd (up to 8 electrons). • Each level beyond that has it’s own limit, but we will only concern ourselves with the first 3 during this course. • Question: If an atom has 7 electrons, how many shells are there? How many electrons in each? • 2 shells with 2 and 5 • Question: If an atom has 12 electrons, how many shells are there? How many electrons in each? • 3 shells, with 2, 8 and 2

17. Assign Bohr model project • Design a Bohr atom for the element assigned to you by your teacher. • Create a key that indicates each major component with its own color. • Be sure to label your atom and draw easy to identify neutrons, protons, electrons and energy shells.

18. Essential questions 1.2-1.3: How does the valence number of an atom determine its reactivity? Why do the relative strengths of ionic, covalent and hydrogen bonds differ?

19. Compoundsare groups of 2 or more different type of atoms that are joined together. • Atoms can be joined together using three different types of bonds. • Covalent Bonds • Ionic Bonds • Hydrogen Bonds

20. Covalent Bonds Covalent bonds occur when two or more atoms share electrons.

21. Examples of covalent bonds

22. Question: How many electrons does carbon need to gain in order to produce a full outer shell? 4 This means that it has the ability to bond to four other atoms that can produce complex macromolecules.

23. Hydrogen bonds occur in water when oxygen shares the electrons unequally. • This causes the water to be more negative on the oxygen side and more positive on the hydrogen sides. • The presence of charges within a molecule causes it to be polar. Polarmolecules which will attract other polar molecules and ions(charged particles).

24. Hydrogen Bonding

25. Ions are atoms that have a strange number of electrons (+ or -) and attractions to one another, as well as polar molecules. • Electrons are gained or lost to achieve stability. • Sodium (Na) has one electron in its outer shell while Chlorine (Cl) has 7. Sodium loses its extra and Chlorine picks it up. • Sodium is now positive and is attracted to the negative Chlorine. This is called anIonic Bond.

26. Question: What will happen when NaCl is put into a polar compound like water? The charges on the water will begin to pull the NaCl apart.

27. Question: What’s the difference between an ionic and a covalent bond? Covalent bonds are formed when atoms share electrons. Ionic bonds are formed due to the positive-negative attraction between ions.

28. The strengths of the 3 different types of bonds give the molecules that use them different properties. Watch video from beginning to 4:50 • Covalent bonds are very strong and require much energy to break them (strongest). • Ionic bonds are easily broken by the presence of other local charges • Hydrogen bonds are broken when heat causes the molecules to become more active and break apart. (weakest).

29. Unit 2: Concepts • Atomic structure and bonding (I) • Properties of water (I) • Macromolecules (E) • Enzymatic reactions (E)

30. Essential question 2.1: How are the properties of water biologically important?

31. Drops on a Penny • How many drops of water will stay on top of the penny?

32. Essential question activation: • How does the temperature of pool water compare to the air temperature during the day? • …during the night? • Why is there a difference?

33. Why are 2/3 of the molecules in the human body comprised of H2O? • Water stores heat very efficiently. • The evaporation of water enables organisms to release heat and maintain homeostasis.

34. The hydrogen bonding of water causes ice to freeze in a crystal lattice (extending the distance between molecules). This causes ice to expand, become less dense and float on top of the more dense water once it freezes.

35. An additional property of water that makes it biologically important is its ability to bond to itself and other substances. Surface Tension • Cohesionis the attraction between water molecules due to hydrogen bonding. (surface tension of water- drops and films) • Adhesionis the attraction of water to other polar substances. • Cohesion and adhesion allow water to crawl up the roots and stems of a plant.

36. Transpiration and the flow of water through a plant.

37. A solution is a mixture where one or more substances (solutes) are evenly distributed in another substance (solvent). • Ionic and polar compounds dissolve well in water. • Ions are attracted to the charges on H2O. • Atoms become evenly distributed in the water if their concentration is low enough. • Polar molecules stick together and shove non-polar substances, like oil, together. • Biochemical reactions occur best within a liquid environment which allows molecules to interact with one another.

38. Question: Why do oil slicks form on the surface of water? Oil and water Demo Oil is non-polar, so it gets clumped together. Oil is less dense than water, so it floats on top.

39. Properties of water summary: With your partner, write out: • 3 important properties of water • 2 reasons why life would suffer without these properties • 1 reason why water is a good solvent for dissolving other substances

40. Essential question 2.2: How does the concentration of protons differ between acids and bases?

41. I. Water frequently separates into ions: Hydrogen ions (H+) and Hydroxide ions (OH-). • This reaction works in both directions. • In pure water, the concentration of H+ and OH- are always the same.

42. The pH scale is a measure of the concentrations of H+ and OH-. • Acidshave a higher concentration of H+ than pure water. • Bases have a higher concentration of OH- than pure water. • Pure water has a pH of 7. • Acids are lower than 7. • Bases are greater than 7.

43. The pH scale

44. Ion concentrations along the pH scale

45. Unit 2: Concepts • Atomic structure and bonding (I) • Properties of water (I) • Macromolecules (E) • Enzymatic reactions (E)

46. Essential question 3.1: How are the structures of macromolecules related to their functions in living cells?

47. Macromoleculesare large molecules built around a frame of carbon and are referred to as being organic. These carbon-containing molecules have specific properties which make them biologically important . • Macromolecules are covalently bonded giving them strength. • The four major macromolecules constitute the primary biological building blocks. • Macromolecules are composed of the 6 most biologically important atoms: Sulfur, Phosphorus, Oxygen, Nitrogen, CarbonandHydrogen “SPONCH”

48. Concentrations of biologically important elements.

49. Question: Is this molecule organic? Yes…it contains carbon!

50. Carbohydrates are a key source of cellular energy. Ratio = 1:2:1 1 Carbon: 2 Hydrogen: 1 Oxygen (There may be multiple of each) Example… glucose -> C6H12O6