Ch 1: The Chemistry of Life

1. Ch 1: The Chemistry of Life We are made up of and surrounded by chemicals… 1 2

2. Why? • It holds heat well • It is a good solvent • High boiling point • Ice floats • High surface tension All based on its chemical properties! Life on Earth = 70-90% water Life on Earth must have Water • 3 States • Solid • Liquid • Gas 4 6 3 5

3. Molecule: two or more atoms bonded together Water is H2O Oxygen is O2 Compound: molecule which contains more than one element Eg. H2O, CH4 Element: Substances that cannot be broken down by chemical reactions. Eg. Oxygen, hydrogen, carbon Atom: smallest unit of an element that still has all the same properties. Eg. O, H, C What happens if we take smaller and smaller and smaller drops of water? 7 What’s matter? The “stuff” that everything is made of! It has mass and takes up space.

4. Sodium (Na)30 Chlorine (Cl)31 Sodium Chloride (NaCl)32 Compounds: More than 1 element + What do the formulae tell you? Na + Cl NaCl • Reactants are what you start with. • Products are what you end up with. • Chemical equations show what exists before and after a chemical reaction occurs (reactants and products). • Equations must have the same number of each atom on each side of the equation. (Law of Conservation of Matter)

5. What’s wrong with these equations? H2+1/2 O2 2H2O Not balanced Na + Cl  NCl Not using same atoms on both sides What are the product(s) of the first equation? Water (H2O) The reactant(s)? Hydrogen and oxygen Quick Quiz

6. Nucleus (a) (b) Cloud of negative charge (2 electrons) 8 2 Protons Neutrons 2 Electrons 2 So what exactly IS an Atom? Atom (Greek):“A” = not“tomo” = cut/divide Figure 2.5 It is all based on John Dalton’s atomic theory

7. Elements in Order • Each atom has name and a 1 or 2 letter symbol • Which atom is it? Number of protons or p = the atomic number on the periodic table of elements (P.799).

8. 8 Atomic numbers, electrons, and orbitals… • p = atomic number = identity of atom • e determines charge • p + n = atomic mass • Only valenceelectrons (outer shell, highest energy) can interact with other atoms’ electrons Inner shell/orbital has a maximum of 2 electrons Outer shells/orbitals have a maximum of 8 valence electrons If the atom on the left has one proton in its nucleus and the atom on the right has 8 protons… What are they? Hydrogen, oxygen

9. 11 1 By electron dot configuration 11 H O By structural drawing H By space fill model Many ways to draw chemicals… H2O By formula By structural formula Think about what kinds of information you get from each representation.

10. Neutrons and Isotopes Isotope: Atoms of the same element (same p) but different # of neutrons and therefore different mass. Unstable, or radioactive, isotopes give off radiation and are used in nuclear energy, medicine, and research. 10

11. So what can we do with atoms?10 Chemically reactive atoms tend to interact with other atoms, so they’re the ones that are biologically interesting.

12. Chemical Reactions • Changes in the chemical composition of matter are called chemical reactions Hydrogen gas Oxygen gas Water Products Reactants Unnumbered Figure 2.1

13. H + H H2 2 H2 + C  CH4 Covalent Bonding10 Covalent bonds involve shared outer shell electrons

14. 8 Numbers of Bonds • Number of bonds = number of additional e- the atom needs to fill its valence shell • 1 bond = 2 e- How many bonds can each atom form? H O 1, 2

15. Endergonic (Endothermic) Products > Reactants Energy absorbed Eg. Making sugar Exergonic (Exothermic) Products < Reactants Energy given off Eg. Fire A Different Look at Reactions Activation Energy = Energy needed to get the reaction started

16. Polar Covalent One atom attracts electrons more Internal charge (poles) created in the molecule Covalent All atoms attract electrons equally NO internal charge on the molecule Types of Covalent Bonds 10

17. () () () () Polar Molecules & Hydrogen Bonds Remember that Oxygen is greedy… and turns water into a polar molecule (Chemists call this high electronegativity.) Partial charge Hydrogen bonds are weaker, and not “real” bonds. So, they don’t get a chemical equation/reaction. 33 H-Bonding ~ Opposites attract!

18. Life on Earth must have Water Why? • It holds heat well • It is a good solvent • High boiling point • Ice floats • High surface tension • 3 States • Solid • Liquid • Gas 4 6 3 All based on its HYDROGEN BONDS! Life on Earth = 70-90% water 5

19. Why does ice float? Hydrogen bond Ice Liquid water Stable hydrogen bonds Hydrogen bonds constantly break and re-form Figure 2.15

20. 12 Ionic Bonding Ions are made from neutral atoms that gain or lose electrons to produce charged atoms. Ionic bonds involve transfer of outer shell electrons Na + Cl  NaCl 13

21. Cats have paws (Cations have positive charge) Anion is negative Cations and Anions Sodium atom (Na) Chlorine atom (Cl) Complete outer shells Na + Cl NaCl Sodium ion (Na) Chloride ion (Cl) Sodium chloride (NaCl) Figure 2.8

22. Ions and Living Cells10 Ioniccompoundsdissociate in water to produce ions Ionization/DissociationIonic compound  Ions

23. Like dissolves like Polar Covalent Bonds Polar molecules dissolve in water or other polar solvents Covalent Bonds Non-polar molecules dissolve in non-polar solvents Ionic Bonds Charged atoms/molecules dissolve in water or other polar solvents

24. H+ Ions and pH33 pH = power of Hydrogen Logarithmic scale Living things must maintain a specific internal pH to survive

25. Organic Chemistry The chemistry of living things. Compounds based on carbon (C) Carbon atoms can bond with 4 others at a time (look at the # of outer shell electrons) CO2, CO, H2CO3 don’t count as organic! Elements in the human body CHONPS make up 97% of the mass of living organisms.

26. First electron shell (can hold 2 electrons) Outermost electron shell (can hold 8 electrons) Electron Hydrogen (H) Atomic number = 1 Carbon (C) Atomic number = 6 Nitrogen (N) Atomic number = 7 Oxygen (O) Atomic number = 8 Figure 2.7 Atoms of the four elements most common in life

27. Carbon can use its bonds to Carbon skeletons vary in length • Attach to other carbons • Form an endless diversity of carbon skeletons Carbon skeletons may be unbranched or branched Carbon skeletons may have double bonds, which can vary in location Carbon skeletons may be arranged in rings Figure 3.2

28. Contain only C and H atoms • Simplest = methane, CH4 The simplest organic compounds are hydrocarbons Structural formula Ball-and-stick model Space-filling model Figure 3.3

29. Larger hydrocarbons • Gasoline • Fats for energy Figure 3.4

30. Form Follows Function • The molecules of your body recognize one another based on their shapes • Eg. Cellular messages Receptor molecule Transmitting cell Receiving cell Signal molecule Figure 3.5

31. Hydroxyl group Carbonyl group Amino group Carboxyl group Found in amino acids and urea in urine (from protein breakdown) Found in amino acids, fatty acids, and some vitamins Found in alcohols and sugars Found in sugars Some common functional groups • The unique properties of an organic compound depend not only on its carbon skeleton but also on the atoms attached to the skeleton – Functional Groups

32. Macromolecules Large, complex molecules, generally made of smaller monomers Held together primarily by covalent bonds • Carbohydrates • Lipids • Proteins • Nucleic Acids Cholesterol 10 Glucose 15 16 DNA 17 Hexokinase – an enzyme

33. Dehydration Synthesis Synthesis: small molecules chemically joined to make bigger, more complex ones Monomer = smallest subunit Polymer = chain of many monomers H H HO HO H HO Building a Polymer Chain H2O

34. H H HO HO H HO Breaking A Polymer Chain • Hydrolysis • “Cutting with water” • Decomposition: large molecules broken down into simpler ones by chemical reactions H2O

35. P 18 = PO32- Carbohydrates: Sugars and Starches Monosaccharide: 3-7 Carbon sugarOften named “-ose” May have Phosphate Glucose– Primary E source for most organisms 10 CHOP (CnH2nOn) Function: Energy storage, cell stucture Monomer: Monosaccharide Hydrophilic, Polar

36. In aqueous solutions, monosaccharides form rings • Monosaccharides are the main fuel that cells use for cellular work (b) Abbreviated ring structure (a) Linear and ring structures Figure 3.10

37. Disaccharides 2 monosaccharides joined by dehydration synthesis Glucose Glucose Remember to look for the formation of a covalent bond which produces water Maltose Figure 3.11

38. Glucose and fructose are isomers • Same chemical formula • Different atom arrangement Glucose Fructose Figure 3.9

39. Polysaccharides Glucose monomer Starch granules in potato tuber cells (a) Starch Glycogen Granules In muscle tissue (b) Glycogen Cellulose fibril in a plant cell wall Cellulose molecules 19 Cellulose fibers in paper (c) Cellulose Figure 3.13

41. Chitin forms the exoskeleton of arthropods such as insects and also the cell walls of fungi

42. Most animals cannot get nutrition from fiber • How do grazing animals survive on a diet of cellulose? • They have bacteria in their digestive tracts that can break down cellulose Figure 3.14

44. Why is it called an acid? Carboxyl Functional Group Saturated vs. Unsaturated Fatty Acids 10 20 Lipids: Fats and Oils First we start with some fatty acids… CHOP Function: Energy and carbon storage, cell membrane structure Monomer: Fatty Acids + Glycerol (+ Phosphate) Hydrophobic, Non-Polar

45. Triglycerides ~ Ordinary Fats Look~ Dehydration synthesis again! (Also called condensation) Triglycerides = 3 Fatty Acids + Glycerol (a) Dehydration synthesis linking a fatty acid to glycerol Doctors often measure triglyceride levels in blood as a health indicator. (b) A fat molecule

46. p50 Unsaturated fatty acids are liquid at room temperature Hydrogenating them makes them saturated Saturated fatty acids are solid at room temp

49. Trans-double bonds straighten the fatty acid chain and make them act like saturated fats

50. The Skinny On Trans Fat It's found almost everywhere, but even a small amount of trans fat can drive up cholesterol levels, says a nutrition expert at Tufts University. Boston [08.15.02] -- Found in over 42,000 food products and considered more potent than saturated fat, trans fat is difficult to avoid. While the average American consumes close to 5 grams of the substance a day, researchers say even one gram--which can drive up LDL cholesterol levels--is too much in a healthy diet. To help better educate consumers, nutrition experts including Tufts' Alice Lichtenstein are working on new ways to inform the public about the dangers of trans fat and ways to avoid it. "Anything above zero will increase the LDL cholesterol levels," Lichtenstein, a nutritional biochemist at Tufts University and a member of the National Academy of Sciences, told the San Jose Mercury News. "If you double the trans intake, you [nearly] double the rise in LDL cholesterol. So the recommendation is to minimize it."