Welcome AP Biology teachers

1. Welcome AP Biology teachers Chapter 2: Basic Chemistry

2. Chapter 2, Students need to know… • basic chemistry: covalent vs. ionic bonds • Essential elements of life: C, H, O, N, P, S • What a valence shell is, and why it matters • Atoms with open valence shells (e.g. C, and O) are going to be reactive • Basic periodic trends, but focus mainly on the essential elements of life and the “go to” trace elements: K, Na, Ca, Mg, Fe

3. Important THEME Teach the Skill • Compound • Two or more elements bonded together resulting in NEW chemical properties to emerge for the compound. • This is an example of the Emergent Properties theme. (Fig. 2.2) An example: Water (H20) – a stable liquid and can sometimes be used to out a fire. Hydrogen by itself is a flammable gas; Oxygen by itself is also a flammable gas.

4. IMPORTANT BIG PICTURE ITEM • Electrons (These particles carry a negative charge.) (They are located in the “Electron cloud”. The cloud is created because electrons move at the speed of light which creates a blur around the atom.)(The electrons moving, which is called kinetic energy, is why they are associated with energy and batteries. It is potential energy when they are bonded. • The number of electrons can change. (Atoms with different numbers of electrons than the normal amount for that element are called Ions.)

5. IMPORTANT • Energy (represented by the symbol “E”) • Energy comes from the rapid movement of electrons (e-) normally, but it could be neutrons too. • Potential Energy (PE) – Energy of position. (Usually refers to electrons “locked” in a chemical bond.) • Kinetic Energy (KE) – Energy of movement. (Usually refers to electrons that can move freely.) • E levels or e- shells – Where the electrons or E is located within an atom or molecule.(FIG. 2.7) • Adding energy to electrons makes them move farther out; losing energy causes them to move inward.

6. IMPORTANT • Valence Shell- Where the outer most electrons are located on an atom. • Valence e- - Refers to the outer most electrons. (These are the most important for chemical bonds and properties.) • Valence – Refers to the bonding capacity of an atom. (Depends on the number of valence electrons.)

7. Fig: 2.8

8. IMPORTANT and Teach the skill • Covalent Bonds (Fig. 2.11) • This type is the strongest type of chemical bond. • Results from sharing electrons between elements or molecules to fill BOTH outer shells. • They always create a molecule. (The size of the molecule may differ though.) • Two or more atoms together of any kind. • Polar molecules (Fig. 2.12) carry an electrical charge at opposite poles(poles refers to the “ends” of the molecule) and non-polar molecules do not have an electrical charge • Electronegativity • Refers to the element’s or molecule’s DESIRE to acquire or release electrons. • Hydrogen atoms (LEASTelectronegative biological element)(It wants to RELEASE e-) • Oxygen (MOST electronegative biological element)(It wants to ACQUIRE e-)

9. Oxygen is at the end

10. Important • Ionic Bonds • These are Fairly strong bonds while dry – but are weak in water so they dissolve into ions. • These bonds are created by swappingelectrons between elements so that each element can fill it’s outer most shell. (Fig. 2.13) • When dissolved in water Ions are created. (Gatorade is a ion loaded drink.) • Cations – possess a positive charge because it has more protons than electrons. • Anions – possess a negative charge because it has more electrons than protons. • THESE LOVE WATER. (because water is a polar molecule too.)

11. IMPORTANT BIG PICTURE ITEM • Hydrogen Bonds (Fig. 2.15) • Fairly weak bonds. (It is “like” a magnet) (A positive Hydrogen attracted to a negative “Substance”…USUALLY oxygen.) • THESE ARE THE MOSTIMPORTANT BIOLOGICAL BONDS

12. Important andTeach the skill • Van der Waals Interactions • These are temporary bonds. (Usually a fraction of a second.)(Involves enzymes mostly.) • These INTERACTIONS are created when electrons clump on one side of an atom making that side temporarily “negative” and the other side “positive” so that charged particles can attach momentarily and then they unclump, because electrons are moving, and the “interaction” disappears because of loss of the charge

13. AP Biology Chapter 3: Properties of Water

14. Chapter 3, students need to know… • water is a polar molecule • water molecules “stick together” via hydrogen bonds • water has a relatively high specific heat, • Water has a high heat capacity • Why these characteristics of water matter to biological systems • Water can ionize into H+ and OH- and this is the chemical basis of the pH scale • The basics of the pH scale (acids vs. bases) • How to describe adhesion and cohesion, • How to identify hydrophobic &hydrophilic molecules.

15. IMPORTANT BIG PICTURE ITEM • Water is a Polar Molecule • Water’s polarity allows for it to make HYDROGEN bonds easily which helps with nutrient transport. • This polarity makes it possible to conduct electricity very well. (Remember, electricity is flowing electrons.) • The polarity allows for a single water molecule to bind to 4 other water molecules at a time. ( Fig. 3.2)

16. Important and Teach the skill • Cohesion • This term refers to water molecules binding to other water molecules. • This property is made possible because of HYDROGEN bonds. • This is important in the Cohesion-Tension Principle that describes how water moves upward in plants xylem tissues by making water “chains”. (Fig.3.3) • Adhesion • This term refers to water molecules binding to something other than water molecules. (Fig. 3.2) • This property is made possible because of HYDROGEN bonds.

17. Cohesion Visual

18. Important and Teach the Skill • Surface Tension • This is the linking together of water molecules on the surface of a body of water. (Fig. 3.4) • This property is made possible because of HYDROGEN bonds.

19. Surface Tension Visual

20. IMPORTANT BIG PICTURE ITEM • Water helps with Temperature Regulation in organisms and on the earth. • Water can act as a huge heat “piggy” bank. (Such as when the sunlight hits the oceans and other water bodies and the water heats up SLOWLY as it absorbs the light energy.) • Thisproperty is made possible because of HYDROGEN bonds. • It takes tremendous amounts of E to break ALL four hydrogen bonds at once and turn liquid water to a gas. • This is a important worldly effect as it helps to keep the temperature of earth stable (the water absorbs the energy of sunlight, so we don’t fry, and then releases that same energy at night, so we don’t freeze… remember that one side of earth is always in the sun and the other side is dark so temperature is stable.) • Kinetic E terms associated with water. • Heat – This measurement is the total amount of kinetic E in a substance. • Temperature – This measurement is the intensity of all the heat in a substance as the molecules move. (The faster they move… the hot it gets and the slower they move… the colder it gets.)

21. IMPORTANT • Specific Heat • This measurement is the amount of heat required to raise or lower 1g ofa substance 1⁰ Celsius. • The specific heat of water = 1 Calorie = 4.2 Joules. • Water requires a huge amount of E to raise 1 gram of it 1⁰Celcius. (1 gram = 1 cm³) • The HYDROGEN bonds prevent kinetic E from increasing. (Need to break 4 at a single time!) • Water vs. Steel (Steel has a very low specific heat and that is why it gets hot QUICKLY.) • Think of it as the ability to RESIST a change in temperature. • The fact that humans and other organism are mostly water, this keeps us from burning up in the sunlight literally.

22. IMPORTANT BIG PICTURE ITEM • Evaporative Cooling • Putting heat E into water, causing the water to evaporate and carry the heat E away from the body thus providing a cooling of the organism to occur as the E leaves. • Wind increases the effect of cooling by carrying the water vapor away from the body. Humidity, water vapor in the air, decreases the effect because water can’t evaporate into the air as it is already full of water vapor.

23. Evaporative Cooling Demo

24. Important Terms • Water is the Universal Solvent • Solvent – Liquid that is doing the dissolving of another substance. • Solute – Substance being dissolved in the solute. • Solution – Substance possessing equal distribution of material. (Kool-aid is a good example.)

25. Important Terms • Hydrophobic “hydro” means water; “phobic” means fear of • Water cannot attach to the substance because the substance is non-polar. • The substance “hates” water’s polarity. • Hydrophilic “philic” means love of • Water can attach to the substance because the substance is polar. • The substance “loves” water’s polarity.

26. Important Terms • WET” Chemistry Terminology • Mole (mol) • Refers to a measurement of molecules that is relative to its molecular weight. • Avogadro’s Number 6.02 x 10²³ • # of molecules of that particular substance present in a 1 mole. • Find the molecular weight of a molecule using the Periodic Table and then weigh out that many grams of the substance and that amount is equal to 1 mole. (Sucrose = 342 so I need 342 grams) • Molarity • Term for telling how many moles of a substance are dissolved in a solution. (usually water)

27. AP Biology Chapter 4: Properties of Carbon

28. Chapter 4, students need to know… • Carbon is tetravalent, and thus lends itself to a variety of functional molecules. • Most biologically important molecules are macromolecules • Macromolecules are polymers comprised of monomers • Polymers are formed by dehydration synthesis • Polymers are broken down by hydrolysis • How to recognize the “Big 6” Functional groups. • The first three have O, and H in some form • The other three are stand alones with S, N, or P in the functional group. • The Essential elements of life are C, H, O, N, P, S…this is not rocket science.

29. IMPORTANT BIG PICTURE ITEM • Carbon’s e- configuration (Figs. 4.3 and 4.4) • Carbon has versatility in four directions because of its Tetravalence. (Tetra means “four”) • The tetravalence allows carbon to act like an intersection in the building of an organic molecules. • Covalent Bonding Capabilities of Carbon • Single Bond between Carbon atoms.(shown as: C-C) • Double Bond between Carbon atoms. (shown as: C=C) • Triple Bond between Carbon atoms. (shown as: C=C)

30. Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model LE 4-3 Methane Ethane Ethene (ethylene)

31. IMPORTANT BIG PICTURE ITEM • Hydrocarbons • Molecules containing mostly Carbon and Hydrogen. • Most hydrocarbons are Energy Sources. (Some examples are: Fossil fuels, Oils, And Fats) • Hydrocarbons are important parts of cell membranes. (The tails of phospholipids)(Fig. 5.13 on page 76) • All hydrocarbons are extremely hydrophobic because the nonpolar molecules. (Hates water’s polarity.)

32. Carbohydrates

33. Hydrocarbon tails

34. Important and Teach the Skill • Isomers • These are molecules with the same molecular formula but different molecular structures. • Three types of isomers exist (Fig.4.7) • Structural Isomers – Same composition but have “different shapes”. • Geometric Isomers – Change is centered “around a central double bond”. • Enantiomers– These are “mirror images of each other”, like your hands. • To types exist: Right orientation (D) and left orientation (L). • They will have verydifferent properties (such as Fig.4.8) and Thalidomide. • Example of Emergent Properties and Structure = Function themes.

35. Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane. LE 4-7 cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon. L isomer D isomer Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

36. Ryan’s Objectives •  Discuss the importance of carbon, the “big 6” functional groups, monomers vs. polymers and dehydration synthesis vs. hydrolysis (notice the importance of water here)

37. IMPORTANT BIG PICTURE ITEM • Functional Groups Associated with Organic Molecules (Fig.4.9 and 4.10) • These are the sites of most organic molecules chemical reactions or properties. (They have a function to do.) • Example of Structure = Function theme. • Hydroxyl s (-OH) • This group allows molecules to act as an alcohol or polar molecule. • Name usually ends with “ol”. • Carbonyls (Only has one double bonded oxygen.) (It takes ONE stroke to make a lower case “n”.) • Aldehydes (A is at one end of the alphabet.)(Carbonyl is located on the end of the molecule.) • Ketones (K is in the middle of the alphabet.)(Carbonyl is located in the middle of the molecule.) • Carboxyl (Has two oxygens…one double bonded and one singled.)(It takes TWO strokes to make an “x”) • These molecules can act as an acid by losing a Hydrogen atom and can also possibly polar too. • Amine (Contains Nitrogen) • Can act as bases by picking up free H+. • Sulfhydrls(Contains Sulfur) • Sulfur can make Di-Sulfide bridges for “pockets” in protein formation .(Fig. 5.20 on Pg. 83) • Phosphate ( Contains Phosphorus) • These molecules are usually involved in E Transfers. (ATP) Also acts like an Anion.(negative)

38. Acetone, the simplest ketone EXAMPLE STRUCTURE LE 4-10ab Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

39. EXAMPLE STRUCTURE LE 4-10ac Acetic acid, which gives vinegar its sour taste FUNCTIONAL PROPERTIES NAME OF COMPOUNDS Has acidic properties because it is a source of hydrogen ions. Carboxylic acids, or organic acids The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

40. AP Biology Chapter 5: Macromolecules

41. IMPORTANT and Teach the Skill • Macromolecules – “Macro” means “large” • Polymers “poly” means many; “mer” means unit. • These are formed from individual units called monomers “Building Blocks”. • Monomers are linked together by covalent bonds. Organisms need these to stay intact so the strongest type of bond is used. • These are another example of the theme: Structure = Function. • Macromolecules are formed by Dehydration or Condensation Reactions. (Fig. 5.2) • Hydroxyl and Hydrogen must be aligned properly to produce water. • This orientation of molecules and making of a bond requires E. • Enzymes help speed up the rate of the reaction. • Macromolecules are broken apart into individual monomers by Hydrolysis reaction. “lysis” means to split. • This process Releases E in the bond breakage. • The process needs water (hydroxyl and hydrogen) to fill the open bonds on the monomers. • Enzymes speed up the rate of the reaction here too.

42. Chapter 5, students need to know… • This is a monster chapter. I divide it up into the energy molecules and the structural molecules. • Part 1: Carbohydrates: • CH2O are primarily energy and structure molecules • Glucose is the “king of the monosacchrides” • Recognize the structure and know the function of the polysaccharides… • Amylose, Glycogen, Cellulose, and Chitin • How the strucutre of these molecules relates to their function

43. Carbohydrates:IMPORTANT • The chemical composition is: Carbon = Oxygen; 2x as many hydrogen also present. • The names usually end with “ose”. Such as Fructose, Glucose, Sucrose. • These are primary E sources for cells.

44. CarbohydratesSee the Carbonyls and Hydroxides?

45. Chapter 5, students need to know… • Part 2: Lipids • Lipids are a diverse set of molecules, all of which are hydrophobic • The difference between saturated and unsaturated fats • How to recognize a steroid • That chloresterol is similar to a steroid • Phospholipids are ambiphatic molecules, and they are the primary component of cell membranes

46. Lipids: IMPORTANT • These macromolecules are fats, oils, waxes, and steroids. • Most lipids are hydrophobic molecules. “Hydro” means “water”; “phobic” means “fear of”. • Lipids are mainly composed of Hydrocarbons (All the Hydrogen means lipids have 2x The E of Carbs.) • Two Main parts (Fig.5.11) • Fatty Acid (Hydrocarbon)(Number of Carbons will be a multiple of 2 if it is made by living cells) • 3 Carbon Glycerol molecule (alcohol) to hold the whole molecule together. • Lipids use a covalent bond called an Ester Linkage to hold the fatty acid and glycerol together. • An Ester linkage is a Carboxyl of the Fatty Acid paired with a hydroxyl of the glycerol molecule

47. Ester linkage LE 5-11b Fat molecule (triacylglycerol)

48. IMPORTANT • Steroids, Hormones, and Cholesterol • A steroid has 4 carbon rings with the top ring looking like a house. • What makes them different are the attached functional groups. These functional groups help determine the function of the steroid.

49. Steroid Structure

50. Chapter 5, students need to know… • Part 4a: Proteins: • Proteins may be the most important of the macromolecules • Proteins are usually pictured as purple images in text books • Proteins have a variety of structural and biochemical roles in cells. • Perhaps the most important roles of proteins include enzymes, channel proteins and proton pumps, communication devices across the cell membrane and structural components of cells.