Week # 11 - DNA-RNA
Lectures - 29, and 30
http://www.elmhurst.edu/~chm/vchembook/580DNA.html
Concepts:
Parts lists for DNA and RNA - sugars, phosphate, bases
Structure of DNA and RNA - hydrogen bonding - base pairing
DNA replication and transcripition to RNA
Types of RNA - mRNA, tRNA, rRNA
Genetic Code and use in protein synthesis
Recombinant DNA, PCR, DNA Fingerprinting
Ques. 1. List by name the heterocyclic amines in DNA and RNA.
Ques. 2. What are the three major chemical compounds in a DNA nucleotide?
Ques. 3. a. List and explain the major primary structural features in an DNA
polynucleotide. What are the "backbone" and the "side chains"?
b. What are the differences in a similar description for RNA?
Ques. 4: Use the above structures to answer the questions below:
a. Which structure is a phosphate?
b. Which structure is a pentose sugar or ribose?
c. Which structure is a heterocyclic amine or a base?
d. Which structure is a nucleotide?
e. Which structure is a phosphate ester bond?
Ques. 5: Use the structures above to answer the following questions:
a. In base pairing if the name is given for cytosine, then the other base with letter A must be
_______?
b. In base pairing if the name is given for adenine, then the other base with letter B in RNA must
be ___________?
c. The dotted green balls represent what kind of bond? ___________
Ques. 6: a. The structure represented by A is _________? By B is ________?
b. The structure represented by C is __________? c. The backbone of
alternating structures of A and B is held together by what kind of bond _______?
d. The heterocyclic amine "side chains" structures represented by C are held
together by what kind of bond__________?
Ques. 7. Describe all types of bonding in a double helix DNA. Include the
"backbone" as well as the "interchain interactions".
Ques. 8. Using the short segment of DNA below, replicate the DNA in
preparation for all division. Clearly label the "original" and "new" DNA strands.
original DNA #1
A T A G C T A
T A T C G A T
DNA #2
Ques. 9. Using the DNA strand above, describe fully the DNA replication
process. Include template, hydrogen bonding, base pairing, complementary
strand.
Ques. 10. Starting with the given strand of DNA #1, make a replication of the
strand into another strand of DNA # 2.
DNA #1
C T T G G G T C C G C A G T T
DNA # 2
Ques. 11. Make a transcription of the second strand of DNA #2 (made in QUES.
10) to messenger RNA.
DNA #2
mRNA
Read and translate the codons on m-RNA into the appropriate amino
acids.
Ques. 12. Make a transcription of the strand of DNA #1 to messenger RNA.
DNA # 1
A G A T G A
mRNA
Read and translate the codons on m-RNA into the appropriate amino
acids.
Ques. 13. Read and translate the codons on m-RNA into the appropriate amino
acids.
m-RNA =
C A G A A U G U C U G G
Write out the complete structure of the protein to be made.
Ques. 14. List, contrast, and explain the function of the three types of RNA
molecules.
Describe r-RNA =
m-RNA =
Describe t-RNA =
Ques 15. What is the anticodon? What is the difference between an anticodon
and a codon?
Ques. 16. Explain the complete process for protein synthesis as exemplified in
the above questions starting with DNA and finishing with making of the protein.
Use all of the types of DNA and RNA and the processes involved.
http://www.elmhurst.edu/~chm/vchembook/584proteinsyn.html
See graphic on next page.
Ques. 17. Make a transcription of the strand of DNA #1 to messenger RNA.
DNA # 1
A G A T G AG T G
a. mRNA
b. Read and translate the codons on m-RNA into the appropriate amino
acids.
c. If a mutation of the first G-guanine is mutated into C-cytosine, how does this
change the amino acid sequence? Be specific by redoing the problem with this
one mutation.
d. In a frame shift mutation, one base is either added or deleted. If a C-cytosine
is added after the first A, how does this mutation change the sequence of amino
acids produced?
e. Explain how this frame shift mutation is probably responsible for many of the
enzyme genetic defect diseases?
Ques. 18. In Hb-S, the abnormal hemoglobin found in individuals with sickle cell
anemia, glutamic acid at position #6 in the beta chain is replaced by valine.
a. List the two codons for glu and the four codons for val that might be read from
the mRNA.
b. Show how a single change in the codon of one base (heterocyclic amine) on
the mRNA results in val substitution for glu.
c. Continue going backwards, what base is the mutation on the DNA that would
give a wrong base on mRNA and hence give the wrong code for glu instead of
val in the hemoglobin.
d. Explain why the change of one amino acid - the substitution of valine in place
of the correct glutamic acid cause such a drastic change in properties.
Ques. 19: Explain how recombinant DNA is able to cause E. coli bacteria to
make human insulin.
Ques. 20: Explain the basic principle of DNA finger printing for identification or
for genetic screening.
Ques. 21: Explain the basic principles of PCR or gene cloning. What is the
purpose? And how can it be combined with DNA fingerprinting.
Ques. 22: Explain the basic principles of how a virus works and how a vaccine
can prevent a viral infection.
Ques. 23: What are the principles involved with various treatments to control HIV
and AIDS?
Anticancer Drug Actions:
http://www.elmhurst.edu/~chm/vchembook/655cancer2.html
Catagories of Chemotherapy Drugs:
In general, chemotherapy agents can be divided into three main categories based on their
mechanism of action.
Stop the synthesis of pre DNA molecule building blocks:
These agents work in a number of different ways. DNA building blocks are folic acid, heterocyclic
bases, and nucleotides, which are made naturally within cells. All of these agents work to block
some step in the formation of nucleotides or deoxyribonucleotides necessary for making DNA).
When these steps are blocked, the nucleotides, which are the building blocks of DNA and RNA,
can not be synthesized. Thus the cells can not replicate because they cannot make DNA without
the nucleotides. Examples of drugs in this class include (1) methotrexate (Abitrexate®), (2)
fluorouracil (Adrucil®), (3) hydroxyurea (Hydrea®), and (4) mercaptopurine (Purinethol®).
Directly damage the DNA in the nucleus of the cell:
Agents chemically damage DNA and RNA. They disrupt replication of the DNA and either totally
halt replication or cause synthesis of nonsense DNA or RNA (i.e. the new DNA or RNA does not
code for anything useful). Examples of drugs in this class (7) include cisplatin (Platinol®)
antibiotics - daunorubicin (Cerubidine®), doxorubicin Adriamycin®), and etoposide (VePesid®).
Effect the synthesis or breakdown of the mitotic spindles:
Mitotic spindles serve as molecular railroads with "North and South Poles" in the cell when a cell
starts to divide itself into two new cells. These spindles are very important because they help to
split the newly copied DNA such that a copy goes to each of the two new cells during cell division.
These drugs disrupt the formation of these spindles and therefore interrupt cell division.
Examples of drugs in this class (8) of miotic disrupters include: Vinblastine (Velban®), Vincristine
(Oncovin®) and Pacitaxel (Taxol®).