Today’s Plan: 1/5/09

1. Today’s Plan: 1/5/09 • Find a seat any place that has paperwork and • Put your preferred 1st and last name on the card. If you need to sit up front, put FRONT on the card as well • On the back of the card: • Write your parent/guardian’s name(s) • Write your phone number(s), esp. parent numbers • Email contact info for you and your parents (if you have it with you) • Go over syllabus/expectations/HW (20 mins) • H2Olympics Lab (40 mins) • Chemistry pre-assessment (10 mins)

2. Today’s Plan: 1/6/10 • Finish Water Lab (20 mins) • Homework Circle (20 mins) • Compare concept maps with your group and create a group concept map (5 mins) • Map sharing (5 mins) • Go over atomic structure (10 mins) • Chemical Bonding Activity (20 mins) • If you finish-work on the periodic properties activity • Biochemistry notes (20 mins)

3. Today’s Plan: 1/7/09 • Bellwork: Finish Discussing/modeling bonding (20 mins) • Water and pH Thinkables with Chemical Model Kits (20 mins) • Biochemical Modeling (20 mins) • Continue notes (20 mins)

4. Today’s Plan: 1/8/10 • Bellwork: Set up bags for lab Monday (15 mins)-SKIP this today, we’ll do it Monday • Biochemical Modeling Activity (40 mins) • Continue notes (20 mins)

5. Today’s Plan: 1/11/10 • Bellwork: Set-up bags for lab #2 (20 mins) • Do AP Lab #2 (40 mins) • Continue notes (20 mins)

6. Today’s Plan: 1/12/10 • Bellwork: Finish Notes (20 mins) • Discussion on Lab 2 and demo (40 mins) • Finish Lab 2 (the rest of class)

7. Today’s Plan: 8/4/09 • Bellwork: Controls on enzyme function demo (20 mins) • Finish Enzyme Notes (30 mins) • Focus on Biology Themes (10 mins) • Study guide/finish Lab #2 (the rest of class)

8. Today’s Plan: 1/13/10 • Bellwork: Test Q&A (10 mins) • Biochemistry Test (as needed) • If you finish early, finish the enzyme lab and Continue with homework assignments (the rest of class)

9. The Chemistry of Living Things • Matter-2 things: Mass and space • Elements vs. Compounds-The difference? Examples? • Only about 25 elements are used in living things, the most important 6 being CHNOPS • Atoms are the smallest units of elements, composed of p+,e-,no • Atomic number=? • Atomic mass=?

10. Atomic Composition • Nucleus-only part necessary for mass determination (e- mass is negligible) • Why are neutrons necessary? • Electron cloud-Consists of shells or energy levels • Only outermost shell involved in bonding • Only outermost shell determines valence=valence shell • Shells composed of orbitals • Isotopes=?

11. Atomic Interactions • Bonding, to get the octet=? • The interactions that make bonds are called chemical reactions and have reactants (left side of the arrow) and products (right side of the arrow) • Ionic bonds=? • Molecule=? • Chemical formula: ex: CH4 • Covalent bonds=? • Involve only 1 type of atom b/c have the same electron affinity • Polar-covalent bonds=? • Involve different types of atoms b/c have different electronegativites-nuclear size matters!!

12. Weak Atomic Interactions • Necessary for most chemical signaling between cells, but only occur when atoms/molecules are in close proximity • Ionic Bond (see previous definition) • Hydrogen bond=Occurs when H is covalently bonded to N or O (usually) and is attracted to the electronegative part of another molecule • Van der Waals interactions=as electrons move, even in non-polar molecules, attraction points occur because of temporary polarity (transient dipole or induced dipole)

13. Consequences of Weak Atomic interactions-Water Properties • Water’s “bent” geometry allows for hydrogen bonding-Note: this is NOT a covalent bond! It’s a special case of a dipole-dipole interaction in which the partial + H is attracted to the electrons orbiting the O on the other water molecule (just as Na+ is attracted to Cl-) • This tends to make water “sticky,” giving it unique properties

14. Water’s properties • Cohesion and Adhesion-Water is attracted to itself (cohesion) and to other polar substances (adhesion) • Water is the universal biologic solvent-molecules surround substances and separate them • Water expands when it freezes because of the tetrahedral arrangement of its molecules when it freezes • Ice is fully hydrogen-bonded while liquid water only contains temporary hydrogen bonds

15. Water and Heat • Heat=kinetic energy of the molecules in a substance (temperature is a measure of this energy) • Like all energy, the flow of heat goes from high to low (Ice absorbs the heat from water to cool your drink-it does NOT release “cold”) • “Cold” does not exist in a thermodynamic sense! It’s simply the removal (absorption) of heat (kinetic energy)

16. Water and Heat continued • Water has a high specific heat (amount of energy it takes to raise the temperature of 1g 1 degree C)-water is good at resisting temperature change • How is this useful to organisms? • Water also has a high heat of vaporization (amount of energy a substance must absorb to convert 1g from liquid to gas) • Evaporative cooling-”hottest” molecules leave as a gas • How is this useful to organisms?

17. Aqueous Solutions and pH • Water Dissociation: H2OH+ and OH- • H+=Hydronium Ion=? • OH-=Hydroxide Ion=? • Therefore, because water has equal amounts of these Ions, it is ? • pH 0-6.9999=acid (H+conc>OH- conc) • pH 7 is neutral • pH 7.1-14=base (H+ conc<OH- conc) • Buffers=maintain the pH of a solution by accepting H+ when in excess and releasing H+ when there are too few (extremely important to biologists!!)

18. Carbon’s versatility • Valence=? • Capable of single bonds (-ane), double bonds (-ene), and triple bonds (-yne) • Readily forms hydrocarbons, which are the backbones of biochemicals • Carbon molecules often form isomers (same formula, different architecture) • Isomers can be Structural (chains vs. rings), geometric (variation around a double bond), or enantiomers (chiral compounds which vary aroun an asymmetric central carbon)

19. Distinguishing between hydrocarbons • Since many molecules are composed of C, H, and O, functional groups are used to distinguish them, since these groups cause the molecules to behave differently: • Hydroxyl group (OH-)=alcohols • Carbonyl group (C=O)=if at the end, is an aldehyde, if in the middle, is a ketone • Carboxyl group (COOH)=organic acid • Amino group (NH2 )=amine (organic base) • Sulfhydryl group (SH)=Thiols • Phosphate group (PO4)=energy transfer group (ATP)

20. Polymers and Monomers • Monomer=1 subunit (link in a chain) • Polymer=a chain of small subunits • Polymers are put together by condensation reactions (also called dehydration synthesis reactions) • Polymers are taken apart by hydrolysis (hydro=water, lysis=splitting) • All Biochemicals are polymers

21. Condensation reaction: monomer in, water out Figure 3-6a (Water)

22. Hydrolysis: water in, monomer out Figure 3-6b (Water)

23. Carbohydrates • Sugars are mono- or disaccharides • Disaccharides (like starches) joined by glycosidic linkage • Used for energy • Starches are polysaccharides (fiber is also a polysaccharide) • Used for energy (checking account) or storage • Animals use glycogen for energy and chitin for structure • Plants use cellulose for structure and amylose or amylopectin for energy • Difference is in the types of glycosidic linkage between the monomers and the degree of branching within the molecules

24. Figure 5-1 An aldose A ketose Carbonylgroup atend of carbonchain Carbonylgroup inmiddle of carbonchain

25. Glucose Galactose Figure 5-2 Differentconfiguration of hydroxyl groups

26. Figure 5-3 Linear form of glucose Ring forms of glucose Oxygen from the5-carbon bonds to the1-carbon, resulting in a ring structure -Glucose -Glucose

27. Monosaccharides polymerize when hydroxyl groups react to form glycosidic linkages… Maltose (a disaccharide) -Glucose -Glucose Figure 5-4 The hydroxyl groups from the1-carbon and 4-carbon reactto produce an -1,4-glycosidiclinkage and water …between various carbons and with various geometries. Lactose (a disaccharide) -Galactose -Glucose In this case, the hydroxyl groups fromthe 1-carbon and 4-carbon react toproduct a -1,4-glycosidic linkage and water

28. Figure 5-5-Table 5-1

29. Lipids • Fats, oils, waxes (sterols) • Energy storage-savings acount (chemically stable, takes a lot to break them apart) • Triglyceride is typical structure consisting of a glycerol and 3 fatty acid chains • Main component of phospholipids, which form micells in water and are responsible for? • Saturated fats contain all single bonds on the main hydrocarbon chain, while unsaturated fats contain double or triple bonds. • What’s a trans-fat?

30. Isoprene Fatty acid Carboxyl group Figure 6-2 Hydrocarbon chain

31. Figure 6-3 Fats form via dehydration reactions. Fats consist of glycerol linked by ester linkages to three fatty acids. Glycerol Ester linkages Dehydration reaction Fatty acid

32. Carbon dioxide Figure 5-9 A carbohydrate A fatty acid

33. Proteins • Held together by peptide bonds, and are therefore sometimes called polypeptides (special case of condensation where N is bonded to C) • Workhorses of cells, doing a variety of tasks such as communication, structure, movement, storage, transport, defense and enzymes • Monomer is the amino acid (20 amino acids exist in living things, distinguished by their R groups)

34. Non-ionized form of amino acid Figure 3-2 Amino group Carboxyl group Side chain Non-ionized Non-ionized Ionized form of amino acid Amino group Carboxyl group Side chain Ionized Ionized

35. Nonpolar side chains Figure 3-3 Glycine (G) Gly Alanine (A) Ala Valine (V) Val Leucine (L) Leu Isoleucine (I) Ile No charged or electronegative atoms to form hydrogen bonds; not soluble in water Methionine (M) Met Phenylalanine (F) Phe Tryptophan (W) Trp Proline (P) Pro Polar side chains Partial charges can form hydrogen bonds; soluble in water Serine (S) Ser Threonine (T) Thr Cysteine (C) Cys Tyrosine (Y) Tyr Asparagine (N) Asn Glutamine (Q) Gln Acidic Basic Electrically charged side chains Charged side chains form hydrogen bonds; highly soluble in water Aspartate (D) Asp Glutamate (E) Glu Lysine (K) Lys Arginine (R) Arg Histidine (H) His

36. Figure 3-7 Electrons shared between carbonyl group and peptide bond offer some characteristics of double bonds Peptide bond Amino group Carboxyl group

37. Figure 3-8 Amino acids joined by peptide bonds Polypeptide chain C-terminus N-terminus Peptide-bonded backbone Carboxyl group Amino group Side chains Numbering system C-terminus N-terminus

38. Levels of protein structure • Shape determines how the molecule works and is extremely important • Primary structure=sequence of amino acids (read from amino terminus to carboxyl terminus) • Secondary structure=coiling or folding of the molecule b/c of hydrogen bonds between backbone molecules (therefore, these are regular ex: alpha helices and pleated sheets) • Tertiary structure=contortion of the molecule due to attractions (van der Waals and H bonding) between R groups. Because each protein has a unique AA sequence, these are irregular patterns that are unique to each protein (ex=disulfide bridges between sulfhdryl groups, hydrophobic clustering) • Quaternary structure=overall protein structure resulting from multiple polypeptides (ex=hemoglobin has 4 polypeptide chains held together with heme groups consisting of Fe) • High temperature, extreme salinity and pH changes can cause denaturating of proteins=protein becomes misshapen because the forces controlling the levels of structure above have been interfered with

39. Secondary structures of proteins result. Figure 3-12b -pleated sheet -helix

40. Interactions that determine the tertiary structure of proteins Figure 3-13 Hydrogen bond between side chain and carboxyl oxygen Ionic bond Hydrophobic interactions (van der Waals interactions) Hydrogen bond between two side chains Disulfide bond Tertiary structures are diverse. A tertiary structure composed mostly of -helices A tertiary structure composed mostly of -pleated sheets A tertiary structure rich in disulfide bonds

41. Nucleic Acids • Information storage molecules=DNA and RNA • Monomers are nucleotides • Phosphate group (held in phosphodiester linkage with the sugar to form the backbone) • Sugar (deoxyribose in DNA, ribose in RNA) • Nitrogenous base (purines=A and G pyrimidines=T, C, and U) that bond purine to pyrimidine based on the number of H-bonds each wants to make • Sequential changes in different species are used as an evolutionary clock (more on this in the Evolution unit)

42. Hybrid Biochemicals • Some important biochemicals are actually combinations of 2 different families of biochemicals • Glycoproteins-Protein/carbohydrate complexes important in cell structure • Lipoproteins-LDL, HDLCholesterol packaged in protein by the liver

43. Figure 5-7 Glycoprotein Outside of cell Inside of cell

44. Metabolism • Metabolism is the sum total of all Anabolic (putting together) and Catabolic (taking apart) chemical reactions in the body • Basic Cellular energy molecule fueling metabolism is ATP (adenosine triphosphate) • Releasing the last phosphate group releases 7.6 kcal of energy

45. Figure 9-1 ATP consists of three phosphate groups, ribose, and adenine. Adenine Phosphate groups Ribose Energy is released when ATP is hydrolyzed. ATP Water Inorganic phosphate Energy ADP

46. Enzymes as catalysts • Catalyst=changes the rate of the reaction but is not consumed (used up) by the reaction • Enzymes lower the activation energy of the reaction (activation energy or free energy of activation is usually in the form of heat and is required to make the molecules interact or break) • Enzymes are specific to their substrate because the shape of the active site conforms to the shape of the substrate (induced fit)

47. Figure 3-20 When the substrate binds to the enzyme’s active site, the enzyme changes shape slightly. This “induced fit” results in tighter binding of the substrate to the active site. Substrate (glucose) Enzyme (hexokinase)

48. Enzyme controls • Denaturation due to pH or temperature changes • Cofactors or coenzymes=non-protein attachments to the enzyme’s active site that help it maintain it’s shape • Inhibition • Competitive=mimics the substrate and blocks the active site • Non-competitive inhibition=binds to another site on the enzyme, causing the shape of the active site to change • Allosteric regulation=similar to noncompetitive inhibition but not permanent and either causes activation by stabilizing the protein shape, or can cause inhibition by destabilizing the protein shape (usually at the junction of the polypeptide chains of the enzyme) • Cooperativity=remember that since many enzymes are made of multiple polypeptides, each can have an active site. This means that induced fit at one active site may cause stabilization of other active sites on the enzyme

49. Competitive inhibition directly blocks the active site. Figure 3-23 Competitive inhibitor When the regulatory molecule binds to the enzyme’s active site, the substrate cannot bind Substrate Enzyme Allosteric regulation occurs when a regulatory molecule binds somewhere other than the active site. Substrate or When the regulatory molecule binds to a different site on the enzyme, it induces a shape change that makes the active site either available to the substrate (left) or unavailable (right) Enzyme Regulatory molecule Activating the enzyme Inactivating the enzyme

50. Metabolic pathways and enzymes • Series of chemical reactions in which the products of each step are reactants for the next step • Feedback inhibition of enzymes occurs when the end product of a pathway acts as an enzyme inhibitor