SEHH2231-21 T09 Biochemical Pathway of Nucleic Acids

1. Examine these two monosaccharides and answer the following questions.

a) Which monosaccharide is found in DNA, and which is found in RNA?

b) Circle the key difference that distinguishes between the two monosaccharides.
c) Use arrows to point to the areas where other groups bond to make them into nucleotides.

2. Study the anatomy of this nucleotide to answer the following.

a) Box the nitrogenous base. Which base is being used in this nucleotide?
b) Circle the monosaccharide. Which monosaccharide is it? Is it found in DNA or RNA?
c) Put a triangle around the phosphate group.
d) Put a star next to carbon 5 in the monosaccharide.
e) Point an arrow at the anomeric carbon.
3. Using the following directions, sketch the nucleotide being described: Uses a
monosaccharide present in RNA, and a nitrogenous base found only in RNA. Point an
arow to the glycosidic bond.

4. The linking of two nucleotides into a dinucleotide involves bonding at which site? What
type of bond is this?

5. Each DNA strand will have a complementary strand. What is the sequence that
complements the strand dGCTAGATC? How many H-bonds allow this structure to
maintain its integrity and shape?

6. List the three types of RNA and their functions.

7. Consider the following in light of the concept of levels of structure (primary, secondary,
tertiary, quaternary) as defined for proteins.

a) What level is shown by double-stranded DNA?

b) What level is shown by tRNA?

c) What level is shown by mRNA?

8. Why does DNA with a high A-T content have a lower transition temperature than DNA
with a high G-C content?

9. Give the DNA sequence for the template strand that gives rise to the following sequence gel,
prepared using the Sanger method with a radioactive label at the 5’ end of the primer.

10. The following DNA fragment was sequenced by the Sanger–Coulson method.

*5 -------------- 3’-OH
3’--------------TATCCAAGCG ---5’

A sample of the DNA was reacted with DNA polymerase and each of the nucleotide mixtures
are listed below.

i) dATP, dTTP, dCTP, dGTP, ddTTP

ii) dATP, dTTP, dCTP, dGTP, ddGTP

How many types of nucleotide will be found in the mixtures?

11. How are DNA microarrays used to screen a patient’s cells for a cancer prognosis?

12. Why is the use of temperature-stable DNA polymerase an important factor in the
polymerase chain reaction?

13. Bacteria do not have the cellular apparatus for splicing introns out of RNA transcripts to
give functional mRNA. Complementary DNA (cDNA) is a DNA copy of a messenger RNA
(mRNA) molecule produced by reverse transcriptase. How can we use cDNA to produce
mammalian protein we need in a large quantity?

14. How would you use bacteria to produce human hormone?

15. Outline a series of steps by which reverse transcriptase produces DNA on an RNA
template.
16. It is possible to increase the amount of a given DNA many times over without cloning that
DNA. The method that makes this amplification possible is the polymerase chain reaction
(PCR). Any chosen DNA can be amplified, and it need not be separated from the rest of the
DNA in a sample before the procedure is applied. PCR copies both complementary strands
of the desired DNA sequence.

The most important part of the science behind PCR is the design of the primers. They have
to be sufficiently long to be specific for the target sequence but not so long that they are too
expensive. Usually, the primers are 18 to 30 bases long. They must also have optimal
binding properties, such as an amount of G and C that is sufficient to allow them to anneal
before the entire DNA renatures. In addition, the two primers should contain similar
amounts of G and C so that they have the same melting temperature. The sequence of the
primer must not lead to secondary structures within a primer or between the two different
primers; otherwise, the primers bind to themselves instead of the DNA being amplified.
For example, if a primer had the sequence AAAAATTTTT, it would form a hairpin loop
with itself and would not be available to bind the DNA.

Using your biochemical knowledge, brief describe the PCR process.