Lecture 2: Review of chemistry and structure of nucleic acids
1. Briefly summarize the flow of information from a gene to a final gene product, including the form that the information takes at each step along the way and the names of the major processes that are involved in achieving the flow of information.
2. Distinguish between prokaryotic and eukaryotic in a manner that makes it clear that you know what each is and how they differ.
3. Summarize two different lines of evidence that have demonstrated that DNA is the primary carrier of genetic information.
4. Identify the four nitrogenous bases that are used for the coding of genetic information in DNA. How are they related to the bases used for coding genetic informaiton in RNA?
5. What are the chemical differences between DNA and RNA? You should be to identify two that are always true and a third that is usually true.
6. What is a phosphodiester link and how does it give polarity to nucleic acids?
7. Identify the base pairs in DNA. Which pairs are more stable and why?
8. What is meant by the term "antiparallel" as it applies to double helical DNA?
9. Distinguish between sense and antisense strands in a manner that makes it clear you know what each is and how they differ.
10. What factors determine how rapidly DNA renatures after being denatured?
11. Distinguish between transcription and translation in a manner that makes it clear that you know what each is and how they differ.
12. Explain how electrophoresis can be used to separate nucleic acid molecules by size. What role does the gel play in the process?
13. The nucleotide sequence of the sense strand of a double helical DNA molecule is ATGCGTAACTAACCG.
a. What nucleotide is at the 5'-end?
b. What nucleotide is at the 3'-end?
c. How would you distinguish the 5'-end from the 3'-end if the bases were the same at both ends?
d. What is the nucleotide sequence of the complementary strand? (You always start at the 5'-end when describing a nucleotide sequence).
e. What will be the nucleotide sequence of the mRNA that is transcribed from this DNA?
14. Ribose and deoxyribose are both 5-carbon sugars.
a. What is the difference between ribose and deoxyribose?15. The genome of E. coli is a closed circle of double helical DNA that contains 4,639,221 base pairs (based on sequence analysis - see page 208 of the textbook). Based on your knowledge of the DNA double helix, answer the following.
b. What is attached to carbon #1 of these sugars when they are in nucleic acids?
c. What is attached to carbon #3 of these sugars when they are in nucleic acids?
d. What is attached to carbon #5 of these sugars when they are in nucleic acids?
e. Ribothymidine is an unusual nucleoside that can be recovered from certain types of transfer RNA (transfer RNAs contain a variety of modified bases). What is unusual about finding ribothymidine in a nucleic acid?
a. What is the thickness on one base pair in double helical DNA?
b. How many complete turns of the double helix are contained in the E. coli genome?
c. What is the circumference of the circular genome when it is laid out as a perfect circle?
d. What is the diameter of the genome when it is laid out as a perfect circle.
e. An E. coli cell is relatively short cylinder only about 2 micrometers in diameter. How can that much DNA fit into it. (Hint, look at figures 7.6 and 7.7).
a. ATP
b. dGTP
c. UMP
d. RNA
e. cAMP
f. mRNA
g. TDP
18. Explain why AC and GT base pairs do not normally form. (You will have to go to Example 2.3 on page 31 of the textbook to answer this one -- I expect you to read the textbook in addition to the lecture notes!)
19. Distinguish between nucleoside and nucleotide in a manner that makes it clear that you know what each is and how they differ.
20. One very promising technique for inhibiting unwanted gene expression is the use of antisense RNA, which has a sequence identical to that of the antisense strand of DNA (except for replacement of T with U). Speculate on how antisense RNA might inhibit functional gene expression, based on what has been presented in the course thus far. (We will examine what actually happens later in the semester).
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