AP Biology Summer Assignment

John Moon

1. Distinguish between the terms hydrophilic and hydrophobic. Which term better describes a polar molecule? Hydrophilic parts are those that are water-loving and thus are soluble in water. Hydrophobic, on the other hand, are water-fearing and are not soluble in water. Hydrophilic describes it better, as they are dissolvable in polar solutions. 2. Explain how the polarity of water molecule makes it a versatile solvent. Since polar solvents only dissolve polar solutes, and the stronger the polar bond, the stronger the solute. Water is an extremely polar substance, thus making it a versatile and powerful solvent. 3. List 4 characteristics of water that are emergent properties resulting from hydrogen bonding. Four include cohesion (attraction of like molecules), adhesion (attraction of dissimilar molecules), surface tension (waters clinging tendencies), and being the universal solvent. 4. Write the equation of the dissociation and reformation of water. How does this relate to pH? The equation is as follows: H20<-->H+ + OH-. pH is the concentration of the H+/OHions in water, for either basic/acidic solutions. 5. What is a buffer? Why is important that chemical reactions in biological systems are buffered? A buffer is a solution that minimizes pH changes in either direction. Since living organisms are highly specific about the pH that its reactions occur in, it is essential that the pH stays in the right zone. 6. Describe the causes of acid precipitation and explain two specific ways it harms the environment. Any consumption of fossil fuels, such as cars and factories, cause acid precipitation to form. One way it harms the environment is by altering the soils pH, distorting the natural pH and thus harming the living things that live in the soil. Another are in bodies of water, and as the pH shifts in the water, some fishes and mammals cannot tolerate a certain level of pH, and thus causes harm. 7. Explain how carbons electron configuration makes carbon an essential building block for macromolecules.

With 4 valence electrons, it can make single, double, and triple bonds with essential life elements such as hydrogen, oxygen, nitrogen, and of course, itself. With this versatility in molecule creation, it is an essential building block for the creation of macromolecules. 8. Explain how the terms monomers, polymers, condensation reaction, dehydration synthesis (hydrolysis) are related to one another. Polymers are created by many monomers undergoing a condensation reaction, which is where two molecules combine to create a new one at the loss of a small molecule. In the case that the particular small molecule is water, you are essentially dehydrating it, which is known as dehydration synthesis. 9. What are the four macromolecules essential for life? What is the monomer for each? Give an example of each. Carbohydrates, Amino Acids, Nucleic Acids, and Lipids are the four macromolecules for life. For carbohydrates, the monomer is the monosaccharide. For Amino Acids, the monomer is itself; it creates proteins out of combined amino acids. For Nucleic Acids, the monomer is a nucleotide. Lipids have no monomers. Cellulose, Thymine, DNA, and wax are all examples of these groups. 10. Label the four major components of an amino acid. Between which two does a peptide bond form? An amino (NH2) end and a carboxyl (COOH) end, a hydrogen (H) group, and the side chain that differs between each amino acid. The peptide bond forms between the amino and carboxyl ends. 11. Distinguish between a saturated and unsaturated fat and list some unique emergent properties that are a consequence of these structural differences. Saturated fats are those that have an evenly distributed hydrogen atom count, while remaining solid at room temperature. Unsaturated fats include double bonds within the structure, and are liquid at room temperature. While saturated fat clogs your arteries and increases the level of bad cholesterol due to its packed nature, unsaturated fats increase the amount of the good cholesterol in your body. 12. Distinguish between monosaccharides and disaccharides. Give an example of each. Disaccharides are simply composed of two monosaccharides. Monosaccharides include glucose, and disaccharides include sucrose. 13. How is enzyme structure related to enzyme function? What happens when an enzyme changes shape? What is this called?

Enzymes are highly specific, and their shape determines which substrate they deal with. When an enzyme changes shape, it barely functions, sometimes not even working at all. This process is called denaturation. 14. Explain how the following affect the rate of an enzyme-controlled reaction.: substrate concentration, enzyme concentration, temperature, pH. Increasing the substrate concentration allows the enzyme to work quickly with more molecules to work with. With more enzymes, the rate will grow proportionally to how many there are. Depending on the comfort zone of the enzyme with respect to temperature, enzymes can work faster, or slow down. At certain pHs, certain enzymes will not function. 15. What is the difference between an oxidation and a reduction? An oxidation reaction loses electrons while a reduction reaction gains electrons. 16. What is the importance of ATP in a cell? List the three components of ATP. How is this structure related to ATPs function? ATP is the cells method of storing and utilizing energy. It is composed of an adenine ring, a ribose sugar, and a phosphate group. With this structure, energy is stored and released in a most efficient way. 17. Give an example in nature or a biological system for the following: endergonic reaction, exergonic reaction, oxidation, reduction, catabolic pathway. Cellular respiration is an endergonic reaction, photosynthesis is an exergonic reaction, rusting metal in air is an oxidation, hydrogen peroxide turning into hydroxide is a reduction, ATP synthesis is an example of a catabolic pathway. 18. How did Griffith and Averys experiments show the transforming principle of DNA? By injecting dead virulent strains combined with live unvirulent strains, the subject would still die regardless, as the DNA would just transform to become virulent. 19. Why did Hershey and Chase use sulfur and phosphorus to label macromolecules? What was the result of this study? Since sulfur exists in protein and not in DNA, and phosphorous exists in DNA and not protein, they could easily distinguish their results. The result was the confirmation that DNA was indeed the genetic material. 20. Distinguish between a pyrmidine and a purine. Why must a pyrimidine always bind to a purine in the structure of DNA?

Pyrmidines are 1-ring structures while purines are 2-ring structures. These two must bond together to keep even structure, as a pyrmidine-pyrmidine is not the same size as a purine-purine. 21. Explain the base-pairing rule and describe its significance in the structure of DNA. This is the rule that Adenine must always be paired with Thymine, and Cytosine with Guanine. With this rule, there are opportunities to form hydrogen bonds between each other. Thus this defines the structure and the nature of bonds in DNA. 22. Explain the roles of DNA ligase, primer, helicase, Okazaki fragments, and DNA polymerase in DNA replication. DNA ligase is there to patch up, to sew the Okazaki fragments together, which are produced by coding the lagging strand. Helicase unzips the actual DNA strand. Primer allows the deduction of the starting location, and DNA polymerase helps bring the nucleotides into the actual strand. 23. Why is there a difference between the leading and lagging strand? How is the lagging strand synthesized? The leading strand is processed continuously while the lagging strand is processed into fragments. These fragments are known as Okazaki fragments, named after the scientist who discovered them. Afterwards, ligase patches them up into a complete strand. 24. Which enzymes involved in transcription are also involved in DNA replication? The only one that is involved in both is helicase, to unzip the DNA. 25. What are the three types of RNA? How are each involved in protein synthesis? mRNA, or messenger RNA, carries the code into the cytoplasm. rRNA, or ribosomal RNA, combines with protein to create a ribosome. This serves as the site and carries the enzymes necessary for protein synthesis. tRNA, or transfer RNA, is the one that reads the code, and is basically the transport for the amino acid. 26. What is a codon? Where do you find an anticodon? A codon is a set of 3 nucleotides that codes for a certain amino acid. The anticodon can be found on the edge of the clover shaped tRNA. 27. Using the following DNA strand find the corresponding amino acid strand that will be produced. Here is a link to a codon chart. http://waynesword.palomar.edu/images/codon1.gif GAA TAG AAA CTT ACT TAG AGC ATT CTT CGA TGC ATC Glu-Stop-Lys-Leu-Thr-Stop-Ser-Ile-Pro-Arg-Ser-Ile

28. What would a mutation in the stop codon result in? Without the correct stop codon, the strand would be continuously processed without halt, since there is no signal to stop. 29. What type of mutation is sickle-cell anemia? Describe what happens to a person with this disease. It is a point mutation in a specific chain. With this disease, normal, healthy blood cells become oddly skinny and pointy shaped, and a whole host of problems begin to occur, including but not limited to strokes, ulcers, infections, etc. 30. Define differentiation and describe at what level gene expression is generally controlled. Differentiation is the process at which a less specialized cell becomes more specialized to a task. Gene expression is most commonly controlled at transcription. 31. Distinguish between proto-oncogenes and oncogenes. Describe the genetic changes that can convert proto-oncogenes to oncogenes. An oncogene is a gene that has been modified, or a set of nucleotides that code for a protein. Oncogenes cause cancer whereas proto-oncogenes do not. A proto-onocogene is a normal gene that can become an oncogene after mutation or increased expression. 32. Explain how the creation of sticky ends by restriction enzymes is useful in producing a recombinant DNA molecule. When sticky ends are created, if you can find a matching sticky end from another molecule that you wish to combine with to create the recombinant DNA molecule, then it is simple to splice it into the DNA. 33. Outline the procedures for cloning a eukaryotic gene in a bacterial plasmid. First, with the usage of a restriction enzyme, you must cut the gene you wish to put in, and with the same enzyme, cut the plasmid. Then after completing this, the bacteria with the plasmid will divide, thus cloning the gene. 34. Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure. This is a technique that allows one to enhance/amplify DNA pieces, allowing you to generate millions of copies of a DNA sequence. Limitations include the lack of enough substrates and/or reagents. 35. Explain how gel electrophoresis is used to identify someones unique DNA. By separating DNA fragments based on the size of the individual fragments and comparing them to those of several individuals, you can identify which is whose.

36. Describe how gene manipulation has practical applications for environmental and agricultural work. By manipulating the genes in crops/seeds, you can make them immune to pesticides, stronger against weather, and yielding more than they could naturally. You can engineer genetically modified foods that are more nutritious, healthier, and reduce adverse side effects. 37. Describe the two important properties of stem cells. Explain their significance to medicine They have the ability to turn into specialized cells later, and are very versatile. They can provide an otherwise impossible cure for diseases that have no answer. 38. Describe how homeotic genes serve to identify parts of the developing organism Since they are the master regulatory genes, they encode for transcription factors that influence the genes responsible for specific structures. This way they can identify parts of the developing organism.