Chapter 1 Study Guide 1.

Explain what is meant by the term genome and be sure to indicate the different types of genomes that are found in an animal cell. 2. Explain what is meant by the term transcriptome. 3. Explain what is meant by the term proteome. 4. Explain the connection between genome and proteome. 5. Describe the structure of a deoxyribonucleotide. 6. Which bases can be a part of a deoxyribonucleotide. 7. How are 2 nucleotides connected together to form a chain? 8. If one examines nucleotides within a DNA molecule, why is it that the number of adenines equals the number of thymines and the number of guanines equals the number of cytosines? 9. When a double-stranded DNA molecule forms, what is the relative arrangements of the sugar phosphate backbones? 10. Describe the structure of a ribonucleotide. 11. Which bases are normally a part of a ribonucleotide? 12. If a template DNA strand contains 30% guanines, what would be the percentage of uracils in the RNA transcript of that DNA molecule (assumed the entire DNA molecule is transcribed to RNA)? 13. Compare your answer to question 2 above (probably based on figure 1.2 of the text) to figure 1.12 in the text. If necessary, modify your answer to question 2 above to define the term transcriptome in an eukaryotic organism. 14. Describe the general structure of an amino acid. 15. Describe how 2 amino acids are linked into amino acid chain and describe the structure of a peptide bond. 16. Without getting into details of the actual chemical structures, described the properties of the R groups that differentiate the various amino acids from one another. 17. Explain how an amino acid sequence causes a protein to fold into a threedimensional structure. 18. What is a codon, and what is meant by the statement that the genetic code is redundant? 19. Explain the importance of the initiation codon and the termination codon to the structure of the gene as well as the structure of a protein coding RNA molecule? Chapter 2 Study Guide 1. Explain the direction of DNA synthesis relative to the 5 prime and 3 prime orientation of the template DNA. 2. Explaine the necessity of a primer for the synthesis of DNA by DNA polymerase. 3. Explain the concept of a functional protein domain. 4. What are the 3 functional domains of a DNA polymerase? 5. Compare and contrast the functions of endonucleases and exonucleases.

6. What is the purpose of the 5 prime to 3 prime exonuclease activity during a normal cells DNA replication process? 7. What is the purpose of the 3 prime to 5 prime exonuclease activity during a normal cells DNA replication process? 8. How does a Klenow polymerase differ from an unmodified DNA polymerase I? 9. What is a reverse transcriptase? 10. What are the necessary components of a reaction mix to synthesize cDNA molecules? 11. What is a restriction endonuclease and differentiate between the major 2 types of restriction endonucleases (type I and type II). 12. In table 2.3 examined the action of enzyme AluI and Sau3AI. Fully describe the similarities and differences of the action of these two enzymes. 13. In table 2.3 examine enzymes AluI and BsrBI. Fully describe the similarities and differences of the action of these two enzymes. 14. In table 2.3 examine the enzymes BamH1 and EcoRI. Fully describe the similarities and differences of the action of these two enzymes. 15. In table 2.3 examined the enzymes EcoRI and PstI. Fully describe the similarities and differences of the action of these two enzymes. 16. Explain the concept of hybridization. 17. Describe the process of southern blotting. 18. Explain how southern blotting could be used to determine which restriction enzyme will cut genomic DNA so that a specific gene is cut out as a single fragment. Assume you have a cDNA sequence of the entire gene to use as a probe. 19. What enzyme would be used to attach linkers to a blunt ended DNA molecule? 20. If you wish to clone DNA fragments into a plasmid, why would you want to cut both the genomic DNA and the plasmid DNA with the same restriction enzyme? 21. In context of question 21, which of the various types of restriction enzymes (table 2.3) would you use and why? 22. If you had to cut your genomic DNA with the blunt end restriction enzyme, how would you insert the fragment into a plasmid that was cut with EcoRI? 23. Describe the entire process of making a genomic DNA library in plasmids starting with preparations of genomic DNA and plasmid DNA. 24. Explain the importance of the ampicillin resistance gene on the plasmid to this cloning process. 25. Explain the importance of the lacZ gene on the plasmid to this cloning process. Be sure to include the importance of the X-gal molecule in your answer. 26. List other type of vectors, and explain why these other types of vectors were engineered. 27. List all the components necessary for a PCR amplification reaction. 28. Describe the process of a PCR reaction that results in the doubling of the desired DNA sequence.