Biochemistry

1. Biochemistry AP Biology - Summer 2013 WEEK 1

2. INTRO QUIZ Every week we’ll have a short quiz to review last week’s material and check our understanding. This week, I just want to know a couple things about you for my own information. What grade are you in? Are you taking AP Bio in the next school year? Are you taking the AP Bio exam next May? Have you taken a (high school) biology class before? What is your favorite school subject?

3. Atomic Basics An atom is a tiny piece of matter made of protons, neutrons, and electrons. Two atoms with the same number of protons behave the same—we say they are the same element. Elements are organized in the periodic table, with an abbreviation of 1 or 2 letters. (e.g. Oxygen is O, Carbon is C, Potassium is K, Iron is Fe)

4. Atomic Details The number of protonsdetermines the element—that’s what makes it carbon or radium. The number of electronsdetermines a charge. More electrons than protons means that it is a negative ion. Fewer electrons than protons means that it is a positive ion. The number of neutronsdetermines the isotope. NOTE: In experiments, scientists will use a weird isotope to label certain atoms and track them in a reaction.

5. Bonds Make Molecules Protons and neutrons are stuck in the center, or nucleus of the atom—they don’t change. Electrons are on the outside, so they move around. Atoms make bonds with other atoms when they share or trade electrons. Atoms that are bonded together are called molecules, and we write the abbreviations for the atoms right next to each other, with little subscripts for how many of each atom. carbon dioxide CO2 H2O dihydrogen monoxide

6. Do You Buy Organic? ORGANIC MOLECULES INORGANIC MOLECULES carbon dioxide methane benzene sulfur hexafluoride Organic molecules are associated with life and life processes Organic molecules involve carbon, which is covalently bonded.(A covalent bond is a strong bond.) Some people define organic molecules as having C-H bonds. Examples of organic molecules: Inorganic molecules are not always associated with life, but they may be important for life anyway. Many inorganic molecules have no carbon. Sometimes inorganic molecules do have carbon, but it doesn’t make the characteristic C-H bonds that are present in organics molecules. Examples of inorganic molecules.

7. Unequal charge makes water form weak hydrogen bonds with other water molecules. • These bonds make water “sticky” and give it special properties. • Water is not the only molecule that makes hydrogen bonds! They are important in DNA and other large molecules too. WATER: the magic molecule! The water molecule is very important to life chemistry. The electrons in water are shared unevenly: the oxygen hogs the electrons, while the hydrogens become more positive. This is called being polar.

8. Adhesion: sticks to things • Cohesion: sticks to itself • Surface tension is caused by cohesion and adhesion. This pulls water up the stems of plants by capillary action • Heat capacity: stores heat • Water helps animals stabilize their body temperatures • Solvent: dissolves stuff • Water pulls apart polar molecules like salt and makes them into solutions WATER: the magic molecule! REMEMBER! Water molecules are polar due to unequal electron sharing. They form weak hydrogen bonds with other water molecules.

9. Making Bigger Molecules • Some molecules are tiny, but the molecules we need for life need to be bigger and more complex. • A single unit or piece is called a monomer. “mono-” means “one” • A larger molecule is made up of many repeated monomers bonded together: this is called a polymer. “poly-” means “many” • When we stick monomers together, we are polymerizing them—and water comes out! When we break polymers apart, we put in water to hydrolyze them. • (Remember, one of water’s skills is acting as a solvent and breaking things apart.) Polymer Monomer

10. Chemical Reactions • We “read” a chemical reaction from left to right. • On the left are the reactants, that go in. • On the right are the products, that come out. • There are the same number of C’s, H’s, and O’s on the left and the right: the equation is balanced. • Atoms are only being rearranged, not created or destroyed • The little marker “light” is not necessary, but it shows that in this reaction energy is going in, or being stored.

11. Catalysts Speed Up Chemical Reactions Catalysts are molecules that speed up, or catalyze, chemical reactions. Every reaction has an activation energy: a little “you must be this tall” energy requirement before the reaction can go. Catalysts lower the activation energy, so more reactants can turn into products more quickly.

12. (the ONLY Chemical Reaction Biologists Care About) • Photosynthesisgoes this way  • Plants take carbon dioxide from the atmosphere • They mix it with water from the ground, using the energy of sunlight to power the reaction. • Out comes glucose (a sugar) and waste oxygen • Cellular respiration goes this way  • Living things (animals and plants) take oxygen from the air • They break down glucose and other foods into water (which is useful) and carbon dioxide (which is waste)

13. Which of the following best characterizes the reaction represented below? A + B + energy → AB (A) Hydrolysis (B) Catabolism (C) Oxidation-reduction (D) Exergonic reaction (E) Polymerization

14. Which of the following best characterizes the reaction represented below? A + B + energy → AB (A) Hydrolysis (B) Catabolism (C) Oxidation-reduction (D) Exergonic reaction (E) Polymerization

15. The 4 Macromolecules of Life 1. CARBOHYDRATES 2. LIPIDS

16. The 4 Macromolecules of Life 1. CARBOHYDRATES 2. LIPIDS Monomer: simple sugars like the glucose molecule Polymer: starches like cellulose and glycogen Starches are used to store energy in plants (cellulose) and animals (glygocen) Monomer: carboxyl (C and H) Polymer: fatty acid chains Lipids are non-polar; they share electrons equally and don’t dissolve in water.

17. The 4 Macromolecules of Life 3. PROTEINS 4. NUCLEIC ACIDS

18. The 4 Macromolecules of Life 3. PROTEINS 4. NUCLEIC ACIDS Monomer: amino acid There are 20 amino acids. Polymer: peptide bonds link amino acids into proteins Note that proteins have nitrogen, unlike carbohydrates and lipids. Monomer: nucleotide Each nucleotide is made of a phosphate, sugar, and base. Polymer: DNA or RNA DNA has a double helix structure caused by hydrogen bonds between the bases.

19. Protein Structure Proteins are complex molecules with 4 levels of structure (1) Primary structurethe order of amino acids in the polymer (2) Secondary structure weak hydrogen bonds bend the chain into a helix or pleated sheet (3) Tertiary structure the 3D shape of the protein (polypeptide) chain (4) Quaternary structurea collection of separate polypeptide chains linked together.

20. Enzymes are Protein Catalysts Enzymes are proteins that serve as catalysts. When something catalyzes a reaction, it speeds the reaction up. Enzymes have a complicated protein structure with an active site. The reactants in a reaction bind here—they are called the substrate. • Enzymes work best in an environment with a specific temperature and pH (acidity). High temperatures or very acidic environments can denature a protein—destroying its structure and making it useless.

21. Which of the following can be used to determine the rate of enzyme-catalyzed reactions? (A) rate of disappearance of the enzyme (B) rate of disappearance of the substrate (C) rate of disappearance of the product (D) change in volume of the solution (E) increase in activation energy

22. Which of the following can be used to determine the rate of enzyme-catalyzed reactions? (A) rate of disappearance of the enzyme (B) rate of disappearance of the substrate (C) rate of disappearance of the product (D) change in volume of the solution (E) increase in activation energy

23. CNOPS Keep in mind which elements were in those molecules! They are very important for living things. Lots of CARBON{C}in all of the macromolecules. Plenty of OXYGEN {O} in there too! NITROGEN{N} in proteins and nucleic acids. PHOSPHORUS {P} in nucleic acids especially! Many amino acids also contain SULFUR {S} Living organisms have to get these atoms from somewhere—eating, pulling them from the air, or from the soil. Cycles of these atoms are important in nature.

24. How Life Began…? As we saw, the macromolecules of life are large, complicated polymers composed of many monomers linked together with bonds. It is difficult to make these large molecules without the complicated machinery of a living cell to coordinate their creation. But where did the first cells get their molecules from? • The primordial soup hypothesis suggests that atoms and molecules were exposed to energy (from sunlight, lightning, etc) and catalysts (minerals on rocks, etc). • This formed the basic organic monomers: amino acids, nucleotides, and monosaccharides. • Eventually, chemical reactions polymerized the monomers and made polymer chains.

27. 2) A feature of amino acids not found in carbohydrates is the presence of Phosphorus Nitrogen Hydrogen Oxygen Carbon

28. 2) A feature of amino acids not found in carbohydrates is the presence of Phosphorus Nitrogen Hydrogen Oxygen Carbon

29. For questions 3-6, match a letter to each description. A single letter may be used once, twice, or not at all. • Glycogen • Cellulose • Triglyceride • Polypeptide • Nucleic Acid • 3) A name for a polymer of amino acids. • 4) The stored form of sugar in humans • 5) A lipid that consists of three fatty acids covalently bonded to glycerol. • 6) A substance which humans cannot digest.

30. For questions 3-6, match a letter to each description. A single letter may be used once, twice, or not at all. • Glycogen • Cellulose • Triglyceride • Polypeptide • Nucleic Acid • 3) A name for a polymer of amino acids. D • 4) The stored form of sugar in humans. A • 5) A lipid that consists of three fatty acids covalently bonded to glycerol. C • 6) A substance which humans cannot digest. B

33. Questions 114 - 115 refer to an experiment in polypeptide hydrolysis. • Polypeptides are placed into warm watery solutions in separate beakers, each containing a different substance that has been isolated from pancreatic juice or intestinal tissue. After two hours, the contents of the individual beakers are analyzed. The results are below. •  8. It appears that the only substance that has no enzymatic activity is: • A. mucus. • B. trypsin. • C. chymotrypsin. • D. carboxypeptidase. • E. aminopeptidase.

34. Questions 114 - 115 refer to an experiment in polypeptide hydrolysis. • Polypeptides are placed into warm watery solutions in separate beakers, each containing a different substance that has been isolated from pancreatic juice or intestinal tissue. After two hours, the contents of the individual beakers are analyzed. The results are below. •  8. It appears that the only substance that has no enzymatic activity is: • A. mucus. • B. trypsin. • C. chymotrypsin. • D. carboxypeptidase. • E. aminopeptidase.

35. Questions 114 - 115 refer to an experiment in polypeptide hydrolysis. • Polypeptides are placed into warm watery solutions in separate beakers, each containing a different substance that has been isolated from pancreatic juice or intestinal tissue. After two hours, the contents of the individual beakers are analyzed. The results are below. • 9. The only substances that act on the terminal residues of the polypeptide are • A. carboxypeptidase and chymotrypsin. • B. mucus and trypsin. • C. trypsin and chymotrypsin. • D. carboxypeptidase and aminopeptidase. • E. polypeptides and aminopeptidase.

36. Questions 114 - 115 refer to an experiment in polypeptide hydrolysis. • Polypeptides are placed into warm watery solutions in separate beakers, each containing a different substance that has been isolated from pancreatic juice or intestinal tissue. After two hours, the contents of the individual beakers are analyzed. The results are below. • 9. The only substances that act on the terminal residues of the polypeptide are • A. carboxypeptidase and chymotrypsin. • B. mucus and trypsin. • C. trypsin and chymotrypsin. • D. carboxypeptidase and aminopeptidase. • E. polypeptides and aminopeptidase.

37. Don’t leave any questions blank. The AP exams have removed the guessing penalty completely. • Try to eliminate answers that you know are wrong before guessing . • Look for word roots like “glyco-”, “mono-”, “poly-”, “-ose” to give you hints for unknown vocabulary. Break words down into pieces • Don’t be disheartened by how tricky these questions are! Luckily, you only have to get about 65% to score a 5 on the AP Bio exam Grade yourself(on the AP curve) 6 out of 9 = grade of 5 5 out of 9 = grade of 4 4 out of 9 = grade of 3 3 out of 9 = grade of 2 2 out of 9 = grade of 1

38. The new AP Biology exam has two types of free response questions—long free response, and short free response. A long free response question might ask you to draw drafts or diagrams, and answer many different sub-questions labelled (a)-(e) Think of these more like short response questions than essays: it is ok to write a short paragraph for each letter. The Free Response Section

39. Always label the question parts (a), (b), (c)… Be clear and direct: you don’t have to be literary. However, you do have to write in sentences. Bullet points or outlines are ignored. Graders will be looking for key words: you can make a vocabulary list before you start writing Don’t do extra work—if a question asks for 3 examples, and you give 4, they will ignore the 4th one. They won’t pick out the correct ones for you. You may draw diagrams to illustrate your answer, but the diagram must be labelled and you must write a few sentence explaining it/referring to it. Free Response Tips

40. (1996) The unique properties (characteristics) of water make life possible on Earth. Select three properties of water and: for each property, identify and define the property and explain it in terms of the physical/chemical nature of water. for each property, describe one example of how the property affects the functioning of living organisms. HW: Free Response Question