The Chemistry of Life:

1. The Chemistry of Life: The nature of matter Properties of water Macromolecules

2. Atoms • Basic unit of matter • Subatomic particles • Making up the nucleus • Protons (positive charge) • Neutrons (no charge) • Orbiting nucleus • Electrons (negative charge) http://www.eskom.co.za/nuclear_energy/fuel/atom.jpg

3. Elements • Elements  • a pure substance that consists entirely of one type of atom • Atomic number: Number of protons http://www.astro.virginia.edu/class/oconnell/astr121/im/periodic_table.gif

4. Isotopes • Same element  different number of neutrons (same chemical properties)Atomic mass # = weighted average mass of the isotopes http://www.uwm.edu/Dept/EHSRM/RAD/Figure_1.jpg

5. Ions • Same element but different number of electrons then protons • Example • Sodium Na + missing one electron so the atom has a positive charge.

6. Radioactive Isotopes • Nuclei are unstable and break down at a constant rate • Can be used as a dating tool, treatment for cancer, tracers to follow movement in bodies.

7. Chemical compounds • Compound – • Formed by the chemical combination of 2 or more elements in definite proportions • Example: C6H12O6 (glucose) http://www.biochem.arizona.edu/classes/bioc462/462bh2008/462bhonorsprojects/462bhonors2007/gsantarelli/experimentbackground.html

8. Covalent vs. Ionic chemical bonds • Ionic bonds • Electrons are transferred from one atom to another • Covalent bonds (strongest bond) • Electrons are shared between atoms • Forms molecules

9. Chemistry quiz refer to textbook Chapter 2 section 1 • Subatomic particles • their location • Electric charge • relative mass • Ionic bonds vs covalent bonds • Ions • Isotopes • Compounds • Chemical formulas

10. Van der Waals Forces • Forces between molecules – an attraction between oppositely charged regions of nearby molecules • These are NOT the forces that keep the atoms within a molecule together but weaker forces that attract 2 or more molecules together.

11. The WATER molecule H2O • ¾ of the Earth’s surface is covered by liquid water • 2/3 of your body is composed of water • Tropical rain forests are bursting with life / dry deserts are almost lifeless Vs

12. The WATER molecule H2O • Polarity • Uneven distribution of electrons between the H and O atoms • Hydrogen end  slightly positive • Oxygen end  slightly negative http://academic.brooklyn.cuny.edu/biology/bio4fv/page/polar_c.htm

13. Answers to “A Sticky Molecule” • The elements found in water are hydrogen and oxygen. The ratio of hydrogen to oxygen is 2:1 • The atoms of H and O are covalently bonded. Each of the two hydrogen atoms share one electron with the oxygen atom.

14. 3. A polar molecule has electrons that are not spread out equally. The oxygen has a negative charge the hydrogens have a positive charge 4. They will tend to attract each other. 5. The positive end and negative ends of the water molecules are attracted to one another and cause the molecules to stick together.

15. A polar molecule has electrons that are not spread out equally. The oxygen has a negative charge the hydrogens have a positive charge

16. http://www.tumblr.com/tagged/polar-molecule

17. Hydrogen bonds in WATER • Hydrogen bonds • Negative to positive attractions between molecules • Strongest bond that can form between molecules • Cohesion = attraction between molecules of the same substance (ex. Water on a penny) • Adhesion = attraction between molecules of different substances (ex. meniscus) http://mw2.concord.org/public/student/solution/water.cml

18. Molecular workbench: • http://ri-itest.portal.concord.org/preview/ • Chemistry • Intermolecular attractions • Hydrogen “bonds”

19. Hydrophilic versus Hydrophobichttp://ri-itest.portal.concord.org/preview/lipids an carbohydrates (not long version): introducing Lipids page 1 • Water loving • In order for a substance to dissolve in water, it must also be polar so that it can attract to water molecules as much as they attract to each other. • Soluble, does dissolve • Water hating • Non polar molecules do not attract water and instead the nonpolar molecules will remain in groups when mixed with water instead of moving apart. • Insoluble

20. Soaphttp://www.exploratorium.edu/ronh/bubbles/soap.html • Have you ever tried to blow a bubble with pure water? It won't work. There is a common misconception that water does not have the necessary surface tension to maintain a bubble and that soap increases it, but in fact soap decreases the pull of surface tension - typically to about a third that of plain water. The surface tension in plain water is just too strong for bubbles to last for any length of time. One other problem with pure water bubbles is evaporation: the surface quickly becomes thin, causing them to pop. • Soap molecules are composed of long chains of carbon and hydrogen atoms. At one end of the chain is a configuration of atoms which likes to be in water (hydrophilic). The other end shuns water (hydrophobic) but attaches easily to grease. In washing, the "greasy" end of the soap molecule attaches itself to the grease on your dirty plate, letting water seep in underneath. The particle of grease is pried loose and surrounded by soap molecules, to be carried off by a flood of water. • In a soap-and-water solution the hydrophobic (greasy) ends of the soap molecule do not want to be in the liquid at all. Those that find their way to the surface squeeze their way between the surface water molecules, pushing their hydrophobic ends out of the water. This separates the water molecules from each other. Since the surface tension forces become smaller as the distance between water molecules increases, the intervening soap molecules decrease the surface tension. If that over-filled cup of water mentioned earlier were lightly touched with a slightly soapy finger, the pile of water would immediately spill over the edge of the cup; the surface tension "skin" is no longer able to support the weight of the water because the soap molecules separated the water molecules, decreasing the attractive force between them. • Because the greasy end of the soap molecule sticks out from the surface of the bubble, the soap film is somewhat protected from evaporation (grease doesn't evaporate) which prolongs the life of the bubble substantially. A closed container saturated with water vapor (as in the Exploratorium "Soap Film" exhibit) also slows evaporation and allows soap films to last even longer. I've blown soap bubbles on a watchglass glued to the bottom of a jar with a large mouth. Once I've sealed the jar the environment will support the bubble for quite a long time. My longest lasting bubble survived for three months! Eiffel Plasterer, a dear departed friend, farmer, educator, and bubble fanatic who lived in Huntington, Indiana blew a bubble that lasted for 341 days!

21. Soap decreases Hydrogen bonding in water. In a soap-and-water solution the hydrophobic (greasy) ends of the soap molecule do not want to be in the liquid at all. Those that find their way to the surface squeeze their way between the surface water molecules, pushing their hydrophobic ends out of the water. This separates the water molecules from each other. Since the surface tension forces become smaller as the distance between water molecules increases, the intervening soap molecules decrease the surface tension.

22. Chemistry of Life • “Organic chemistry” = compounds that involve carbon • “It’s all about Carbon” http://www.npr.org/2007/05/01/9943298/episode-1-its-all-about-carbon • Chemical Reactions and Enzymes

23. The chemistry of carbon • Organic chemistry: The study of all compounds that contain carbon • Can form single, double, or triple covalent bonds with other carbon molecules • Macromolecules: molecules in living cells are considered “big” from a chemical point of view. 4 groups = carbohydrates, lipids, nucleic acids, and proteins

24. Molecular workbench • Intro to macromolecules • Nucleic acids and Proteins • Lipids and Carbohydrates

25. Macromolecules are BIG

26. Carbohydrates • Main energy source for living things • Can also be used for structural purposes (ex. cell wall in plants) • Made up of Carbon, Hydrogen, and Oxygen  ratio of 1:2:1 http://whatscookingamerica.net/Cookie/CookiePhotos/PowderedSugar2.jpg http://www.rapunzel.com/images/cornstarch.jpg

27. Types of Carbohydrates Monosaccharide: A simple sugar Example: glucose Disaccharide: Two simple sugars bond together to form a chain of two simple sugars Example:sucrose (glucose + fructose); • Polysaccharide: They are long chains of simple sugar molecules bonded together. • Example: Starch, storage form of sugar in plants.

28. Lipids (fats) • Used to store energy, found in membranes, waterproof coverings, and used as chemical messengers • Typically = glycerol molecule combined with fatty acid molecules • lipid types include fats, phospholipids (made cell membranes) and steroids. • Generally not soluble in water http://onlinestore.smucker.com/images/catalog/prodimages/OliveOil6pack285%20copy.jpg

29. Molecular workbenchIntro to lipids and carbohydrates

30. Cell membranes are made of lipids

31. Saturated vs unsaturated FATS • Saturated – maximum # of hydrogen bonds (no double bonds) in a fatty acid • Unsaturated – at least one carbon-carbon double bond in a fatty acid

32. Nucleic Acids • Contains H, O, N, C, and P • Stores, transmits hereditary/genetic information • 2 kinds = RNA and DNA • Nucleic acids are composed of nucleotides Nucleotides have three parts:1. Nitrogenous Base2. Five-Carbon Sugar3. Phosphate Group http://z.about.com/d/chemistry/1/7/V/e/DNA.jpg

33. Molecular Workbench: nucleic acids

34. Protein • Contain Nitrogen, Carbon, Hydrogen, Oxygen • Proteins are made of a chain of amino acids • Some proteins: • control the rate of reactions (enzymes), • regulate cell processes, • form bone and muscle, • cell transport, • and fight disease

35. Molecular workbench proteins

36. Chemical Reactions • A process that changes one set of chemicals into another • Always involves the breaking and formation of bonds • Reactants • Enter into a reaction • Bonds are broken • Products • Result from a reaction • New bonds are formed Example Photosynthesis: 6H2O + 6 CO2 C6H12O6 + 6O2

37. Protein: Enzymes • Enzymes in cells speed up the rate of chemical reactions • Enzymes are specific to help one certain chemical reaction take place. • Enzymes are a type of Catalyst = substance that speeds up a chemical reaction • Lowers activation energy • Enzyme simulation McGraw Hill: http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

38. Molecular Workbench about proteins and enzymes: http://ri-itest.portal.concord.org/preview/ Follow links: Biology Protein Partnering and Function Page 2 “A good Fit” addresses the effect of temperature change Biology Four Levels of Protein Structure Page 7 near the bottom “Can proteins take the heat”

39. Molecular workbench: Protein partnering and function

40. http://www.youtube.com/watch?v=NdMVRL4oaUo enzyme song, kind of off key but pretty informative. • NPR program about "Fixing 'misfolded' proteins for new drug treatment" 6:50 minutes. http://sciencefriday.com/playlist/#play/segment/9293

41. Energy in Reactions • Energy changes • Release energy  spontaneous • Absorb energy  needs energy to proceed • Where does this energy come from in plants? Animals? • Activation energy • Energy needed to get a reaction started

42. Activation energy: Energy-Absorbing Reaction Energy-Releasing Reaction products Activation energy Reactants Activation energy products Reactants Example: Photosynthesis high activation energy Products store more energy then the reactants Example: cellular respiration low activation energy Products have less energy then the reactants

43. Video about reaction rateHow to speed up chemical reactions (and get a date) http://www.youtube.com/watch?v=OttRV5ykP7A • Lower volume (molecules more tightly packed • Increase concentration (more molecules) • Raise temperature (speed velocity of molecular movement • Increase surface area • Introduce a catalyst (enzyme)

44. Solutions and Suspensions • Mixture = 2 or more elements or compounds physically mixed (not chemically) • 2 types = solutions and suspensions • Solutions • Components are evenly distributed • Solvent (dissolves the solute) ex. water • Solute (substance that is dissolved) ex. salt • Suspensions • Mixtures of water and nondissolved material • Movement keeps material suspended • Example: Blood  solution and suspension! • Made of mostly water with many dissolved components (solution) • Also contains nondissolved material like blood cells (suspension)

45. Acids and Bases • Water molecules split to form positive hydrogen ions (H+) and negative hydroxide ions (OH-) • NEUTRAL • In pure water the number of (H+) = (OH-) • ACIDIC • More (H+) • BASIC • More (OH-)

46. ACIDS have more +H Acids Vs. Bases BASES have more OH-

47. pH Scale 1…2…3…4…5…6…7…8…9…10…11...12…13…14 Acids neutral Bases water

48. Acids, Bases, and pH

49. Acids, Bases, and pH • pH scale = factor of 10 btw steps • Acids (strong acid = 0/weak acid = 6) • Forms H+ ions in solution • The higher the concentration of H+ more acidic • Bases (strong base = 14/weak base = 8) • Forms OH- ions in solution and low concentrations of H+ • The lower the concentration of H+ more basic • Buffers • Weak acids or bases that can react with strong acids and bases to prevent sharp changes in pH • Helps to maintain homeostasis in the body (pH of the body = 6.5 – 7.5) • http://www.youtube.com/watch?v=V4S1KlJdMbE&feature=youtu.be

50. Purple cabbage indicator in action