AP Biology Review – Unit 1

1. AP Biology Review – Unit 1 Chapter 1-3

2. 1. Briefly summarize the characteristics of life shared by all living organisms • Common set of chemical components (cells) • Contains genetic info (DNA) • Convert molecules from environment into new molecules • Extract energy from environment to do work • Metabolism • Homeostasis • Replicate genetic info • Share sequence similarities with others • evolve

3. 2. How do scientists define a theory? • Biologists define “theory” as a body of scientific work which is rigorously tested and well-established facts and principles are used to understand, explain, and make predictions about the natural world.

4. 3. Design an experiment… • Testable hypothesis • Independent variable – specific to it’s values and range • Dependent variable – specific on how and when it is being measured. • Large sample size or repeat experiment several times • State your control variables • Statistical analysis of data • State results expected as they relate to hypothesis

5. Actual key answer… • The independent variable is the type of goldfish food. For the sake of this experiment, we will assume that feeding goldfish fish flakes is customary or the “control,” while feeding shrimp pellets is the independent variable. • Hypothesis: Feeding goldfish shrimp pellets instead of fish flakes produce larger fish. • In the experiment, twenty 5-gallon tanks are filled with 5 gallons of water, kept at the same temperature of 68 degree F. Twenty young goldfish of identical age, which have each been measured in length prior to commencement of the experiment, are placed into the tanks, one fish per tank. The water in each tank is filtered and aerated with the same type of aeration system, and the tanks are placed near each other with equal exposure to periods of light and darkness. In the first ten tanks, the goldfish are fed shrimp pellets, according to the directions on the package. In the second group of ten tanks, the control group, the goldfish are fed fish flakes, also in accordance with package directions. • At the end of each week, the goldfish are carefully removed from their respective tanks and individually measured before being returned to the tank. This process is continued for twelve weeks. The food should be weighed and its nutritional content should be matched between the two treatments. • *** Many other examples are possible. ***

6. 4. electrons, protons, neutrons, atomic number Remember protons = atomic number ALWAYS!! Remember protons = electrons in a NEUTRAL atom. Remember mass number on periodic table is rounded then subtract the atomic number to get # of neutrons

7. 5. Strongest  Weakest • Covalent (sharing of electrons) • Ionic (transfer of electrons) • Hydrogen (attraction between partial + and partial – charges – like between water molecules) • Van Der Waals – (weak electric forces)

8. 6. Cation vs. Anion • Cations are positively charged ions • Examples are Mg2+, Na+1, Al+3 • Anions are negatively charged ions • Examples are F-1, O-2, P-3

9. 7. NaCl explanation of ionic bond • A sodium atom has only one electron in its outermost shell, which is an unstable condition. • A chlorine atom has seven electrons in its outermost shell, also unstable. • They achieve stability by transferring an electron from sodium to chlorine, making sodium a cation and making chlorine an anion. • The electrical attraction between the anion and the cation is an ionic bond, which holds these ions together as dry salts, but this weak bond gives way when the ions are dissolved in water.

10. 8. Name that molecule • Water or H20 • The oxygen molecule in water, however, has a higher electronegativity than the hydrogen molecules. When they combine to form water, the electrons involved are unequally shared, tending to be nearer to the oxygen nucleus because of its greater electronegativity, giving the oxygen end of the chemical bond a slightly negative charge (δ- added to picture) and the hydrogen end a slightly positive charge (two δ+ added to picture).

11. 9. Explain A and B/same vs. different number of atoms • This demonstrates the formation of a hydrogenbond between two water molecules B. Thisis an example of how hydrogen bonds can form between different parts of the same large molecule. More atoms are represented in drawing B because it is a protein and not all of the atoms are being shown in the picture.

12. 10. Explain prompts • Choice A is more water-soluble because it contains more polar covalent bonds, causing it to be hydrophilic or more attracted to the hydrogen atoms in water. • Choice B is less water-soluble because it is a nonpolar molecule, containing mostly carbon and hydrogen atoms, which tend to aggregate with one another rather than with the more polar water molecules. This type of molecule is hydrophobic.

13. 11. Number carbons and name

14. 12. Label molecule The hydrophobic tail includes Hydrocarbon chains. The hydrophilic head includes Choline and phosphate.

15. 13. Steroids and other fatty substances pass readily through most cell membranes because: • … they are fat soluble. The lipid molecules line up in a way that the center of the lipid bilayer (the fatty acid tails) are nonpolar, so they do not readily interact with polar molecules such as water. • Their nonpolar nature makes them hydrophobic, so they do not dissolve in water.

16. 14. Draw amino acid and label

17. 15. Explain how the diversity of different proteins is created. • The primary structure of a protein/peptide/polypeptide is determined by its precise linear sequence of amino acids. • Since there are 20 different amino acids, combinations of two amino acids could mathematically generate 400 distinct dipeptides; combinations of three amino acids could generate 8,000 tripeptides. Even a small polypeptide of 100 amino acids has 20100 possible sequences, making the potential diversity of proteins essentially immense.

18. 16. Explain levels of proteins • Primary The primary structure of a protein is established by covalent bonds between adjacent amino acids. This type of structure is found where amino acid monomers are joined, forming polypeptide chains. The primary structure determines the protien’s secondary, tertiary, and quaternary structures. • Secondary The secondary structure of a protein consists of regular, repeated spatial configurations in different regions of a polypeptide chain. The two basic types are the “alpha helix,” a right-handed coil similar to a wood screw, and “beta pleated sheet,” formed from two or more polypeptide chains that are extended and aligned. Many proteins contain both types of secondary structure. • Tertiary Tertiary structure is formed when the polypeptide chain is bent at specific sites and then folded back and forth. This provides the molecule’s specific three-dimensional shape, including a buried interior as well as an exposed outer surface. These folds are stabilized by hydrogen bonds and disulfide bridges. • Quaternary Quaternary structure refers to the distinct manner in which two or more polypeptide chains or subunits bind together and interact, forming even larger protein molecules.

19. 17. Draw amino acids

20. 17C. Draw dipeptide

21. 18. Leucine substituted for Cysteine • Leucine is nonpolar and hydrophobic, often found clustering with other similar hydrophobic side chains in the interior of the protein. Cysteine, a special type of amino acid which is not hydrophobic , has a terminal SH group that can react with another cysteine side chain to form a covalent bond, called a disulfide bridge, which determines how a polypeptide chain folds. • If leucine were to be substituted for cysteine, the spatial orientation of the molecule would be affected because of the loss of hydrophobic properties, and the folding of the polypeptide chain would be altered. Altered shape usually results in altered functions of proteins.

22. 18. Arginine substituted for Phenylalanine • Arginine is positively charged, hydrophilic, and attracts negatively charged ions of all sorts. Phenylalanine is nonpolar and hydrophobic. • This substitution would likely cause the molecule to alter its orientation toward, instead of away from, water, possibly reducing the protein’s solubility in water. The changed protein would also tend to more readily interact with anions.

23. 18. Alanine substituted for Aspartic Acid • Alanine has nonpolar, hydrophobic side chains, whereas aspartic acid is negatively charged and hydrophilic. • Substitution of alanine for aspartic acid would likely cause the molecule to alter its orientation away from water. It would also reduce its tendency to interact with positively charged ions.

24. 29. Quaternary? Why? • “B” shows a quaternary structure, because the diagram depicts four polypeptides (observe that “B” has 8 terminal amino acids) associated with each other, forming a larger protein molecule. This example is a tetramer, made up of four polypeptide subunits.

25. 30. Explain with terms • Strongacid is an environmental factor that can result in the breakdown of a functional protein’s secondary and tertiary structures, a process also known as denaturation. • The introduction of acid alters the concentration of protons (H+ ) which results in the ionization of exposed carboxyl and amino groups, thus altering polarity. • Since the tertiary structure of a protein determines its three-dimensional shape, the protein loses its original structure and likely, its original function.

26. 31. How does an enzyme speed up a reaction between 2 substrate molecules? • An enzyme speeds the reaction time between two substrate molecules by lowering the activation energy required for a reaction to occur. • Substrate molecules bind themselves to a particular site on the enzyme, called the active site, where catalysis takes place.

27. 32. Label diagram

28. 33. Cofactors vs. Coenzymes? • Cofactors are inorganic ions such as copper, zinc, and iron that bind to certain enzymes. • A coenzyme differs from a cofactor because it is an organic molecule that adds or removes chemical groups from the substrate, although it does not permanently bind to the active site.

29. 34. Allosteric Regulation? Why? • “B” is an example of allosteric regulation. Allosteric regulation occurs when a non-substrate molecule controls enzymatic activity by binding to or modifying a site other than the active site. • This molecule does not attempt to replace the substrate on the active site, but instead binds to a site away from the active site, changing the enzyme’s shape so that the substrate no longer fits.

30. Identifying Molecules • Carbohydrate Monosaccharide C6H12O6 • Carbohydrate Monosaccharide C6H12O6 • Carbohydrate Disaccharide • Carbohydrate Monosaccharide, alpha glucose • Carbohydrate Monosaccharide, beta glucose • Carbohydrate polysaccharide, cellulose • Carbohydrate polysaccharide, glycogen or starch

31. Continued… • Lipid, Steroid • Amino Acid • Carbohydrate, monosaccharide, pentose – deoxyribose • Carbohydrate, monosaccharide, pentose – ribose • Carbohydrate, polysaccharide • Lipid, Triglyceride, saturated

32. Last page! • Lipid, triglyceride, unsaturated • Lipid, phospholipid • Lipid, steroid • Protein, primary • Protein, tertiary • Protein, quaternary • Protein, secondary, alpha helix Study Vocabulary too!