DNA Replication Practice Questions

1.   The nucleotide 3TC diagrammed below is an anti-HIV drug that has been particularly useful in combination cocktails for AIDS therapy. It is a nucleotide that has a sulfur atom (S) in the place where normal nucleotides have an OH group. The point of this question is to figure out how this helps AIDS patients.

 

 

a.   Is this a nucleotide appropriate for RNA or DNA? How do you know? Hint: Compare the sugar in 3TC, above, with the sugar in the nucleotides below.

 

b.   Sketched here is a portion of an RNA molecule from HIV that has just infected a cell. In the correct position, sketch the nucleotide that will pair with the U nucleotide as reverse transcriptase copies this strand into a daughter DNA strand. (The reverse transcription starts at the bottom and moves towards the top.)

 

 

c.    Now pretend like you are the reverse transcriptase, so continue synthesizing a new stand, placing the 3TC nucleotide in where it would go in the new strand.

 See part b, above.

d.   Use your diagram to explain how 3TC could work as a therapy for AIDS.

 See part b, above.

 

Transcription and Translation Questions

2.     Here is a hypothetical gene showing the sequence of DNA nucleotides for the coding strand (i.e. coding strand is the strand that is transcribed). This sequence includes the regions that code for start and stop codons in translation.

 

Coding Strand of DNA:   3' A A T G G C A T A C T C G A T A G 5'

                                   

a.   What is the order of the bases in the mRNA that would be transcribed from this gene? Indicate the 5' and 3' ends of your molecule.

 

5' U U A C C G U A U G A G C U A U C 3'

 

b.   Consider what you have learned about the structure of DNA and RNA. List 3 ways that the structure of mRNA differs from the structure of the DNA from which it was transcribed.

i.          mRNA is single-stranded, DNA is double-stranded

 

ii.         Uracil in RNA, Thymine in DNA

 

iii.         Ribose is the sugar in RNA, deoxyribose in DNA

 

c.   Using the start codon to determine the reading frame, what is the amino acid sequence of the protein that this gene codes for? (See below for a table of codons)

                                 Amino Acid Sequence:                                     Met - Ser - Tyr         (i.e. methionine - serine - tyrosine)

 

m RNA:     5' U U A C C G U A U G A G C U A U C 3'

 

d.   What is the order of the bases of the 2^nd codon?   A G C   Name the kind of molecule where the 2^nd codon is found:            mRNA                  

 

e.   What is the order of the bases of the 2^nd anticodon?   UCG       Name the kind of molecule where the 2^nd anticodon is found.           tRNA          

 

This table shows the 64 codons and the amino acid each codon codes for. (from: http://en.wikipedia.org/wiki/Codon)

		2nd base
		U	C	A	G
1st base	U	UUU (Phe/F)Phenylalanine UUC (Phe/F)Phenylalanine UUA (Leu/L)Leucine UUG (Leu/L)Leucine,	UCU (Ser/S)Serine UCC (Ser/S)Serine UCA (Ser/S)Serine UCG (Ser/S)Serine	UAU (Tyr/Y)Tyrosine UAC (Tyr/Y)Tyrosine UAA (Stop) UAG  (Stop)	UGU (Cys/C)Cysteine UGC (Cys/C)Cysteine UGA  (Stop) UGG (Trp/W)Tryptophan
	C	CUU (Leu/L)Leucine CUC (Leu/L)Leucine CUA (Leu/L)Leucine CUG (Leu/L)Leucine,	CCU (Pro/P)Proline CCC (Pro/P)Proline CCA (Pro/P)Proline CCG (Pro/P)Proline	CAU (His/H)Histidine CAC (His/H)Histidine CAA (Gln/Q)Glutamine CAG (Gln/Q)Glutamine	CGU (Arg/R)Arginine CGC (Arg/R)Arginine CGA (Arg/R)Arginine CGG (Arg/R)Arginine
	A	AUU (Ile/I)Isoleucine, AUC (Ile/I)Isoleucine AUA (Ile/I)Isoleucine AUG (Met/M)Methionine, Start1	ACU (Thr/T)Threonine ACC (Thr/T)Threonine ACA (Thr/T)Threonine ACG (Thr/T)Threonine	AAU (Asn/N)Asparagine AAC (Asn/N)Asparagine AAA (Lys/K)Lysine AAG (Lys/K)Lysine	AGU (Ser/S)Serine AGC (Ser/S)Serine AGA (Arg/R)Arginine AGG (Arg/R)Arginine
	G	GUU (Val/V)Valine GUC (Val/V)Valine GUA (Val/V)Valine GUG (Val/V)Valine,	GCU (Ala/A)Alanine GCC (Ala/A)Alanine GCA (Ala/A)Alanine GCG (Ala/A)Alanine	GAU (Asp/D)Aspartic acid GAC (Asp/D)Aspartic acid GAA (Glu/E)Glutamic acid GAG (Glu/E)Glutamic acid	GGU (Gly/G)Glycine GGC (Gly/G)Glycine GGA (Gly/G)Glycine GGG (Gly/G)Glycine

¹The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins.
 

 

 

3.  You are investigating the cause of a disease that you suspect is inherited. You have isolated the gene that you think is responsible for the symptoms of the disease from both normal people; and people with the disease. In your lab you have the equipment needed to figure out the nucleotide sequence of the gene and any other equipment you might need.

·        Describe the steps you would do to determine if the gene you found is causing the disease. Assume the person you are explaining this to is intelligent, but has not had a biology course.

 

Step 1:  Use PCR to make many copies of the gene in question from healthy people and from people with the disease.

Step 2:  Determine the base sequence of the gene from healthy people and from people with the disease.

Step 3: Compare the base sequences. If they are the same, then the gene would not be the cause of the disease. If different, then see how they differ and determine if they would code for a protein that would have a different amino acid sequence that might cause the protein to have a nonfunctional shape.

 

 

 

 

4.  For the DNA strand 5'-TACGATCATAT-3' the correct complementary DNA strand is:

A	3'-TACGATCATAT-5'
B	3'-ATGCTAGTATA-5'
C	3'-AUGCUAGUAUA-5'
D	3'-GCATATACGCG-5'
E	3'-TATACTAGCAT-5'

 

5.   Three types of RNA involved in comprising the structural and functional core for protein synthesis, serving as a template for translation, and transporting amino acid, respectively, are:

A mRNA, tRNA, rRNA

B rRNA, tRNA, mRNA

C tRNA, mRNA, rRNA

D tRNA, rRNA, mRNA

E rRNA, mRNA ,tRNA

 

6.   A messenger acid is 336 nucleotides long, including the initiator and termination codons. The number of amino acids in the protein translated from this mRNA is:

A 999

B 630

C 330

D 111

E 110

 

7.     A synthetic mRNA of repeating sequence 5'-CACACACACACACACAC... is used for a cell-free protein synthesizing system like the one used by Niremberg. If we assume that protein synthesis can begin without the need for an initiator codon, what product or products would you expect to occur after protein synthesis.

A.	one protein, consisting of a single amino acid
B.	three proteins, each consisting of a different, single amino acid
C.	two proteins, each with an alternating sequence of two different amino acids
D.	one protein, with an alternating sequence of three different amino acids
E.	one protein, with an alternating sequence of two different amino acids

 

8.   Under conditions where methionine must be the first amino acid, what protein would be coded for by the following mRNA?

5'-CCUCAUAUGCGCCAUUAUAAGUGACACACA-3'

 

A.	pro his met arg his tyr lys cys his thr
B.	met arg his tyr lys cys his thr
C.	met arg his tyr lys
D.	met pro his met arg his tyr lys cys his thr
E.	arg his ser glu tyr tyr arg leu tyr ser

 

9.   Which mRNA codes for the following polypeptide?

Met-arg-ser-leu-glu

 

A.	3'-AUGCGUAGCUUGGAGUGA-5'
B.	3'-AGUGAGGUUCGAUGCGUA-5'
C.	5'-AUGCGUAGCUUGGAGUGG-3'
D.	1'-AUGCGUAGCUUGGAGUGA-3'
E.	3'-AUGCGUAGCUUGGAGUGA-1'

 

10. With what mRNA codon would the tRNA in the diagram be able to form a codon-anticodon base pairing interaction?

A. 3'-AUG-5' B. 3'-GUA-5' C. 3'-CAU-5' D. 3'-UAC-5' E. 3'-UAG-5'

 

 

11. Which of the following tools of recombinant DNA technology is INCORRECTLY paired with its use?

A.	restriction endonuclease - production of DNA fragments for gene cloning.
B.	DNA ligase - enzyme that cuts DNA, creating sticky ends.
C.	DNA polymerase - copies DNA sequences in the polymerase chain reaction.
D.	reverse transcriptase - production of cDNA from mRNA.
E.	electrophoresis - RLFP analysis.

 

12. Match the following terms to the appropriate part of the central dogma by placing an "X" in the corresponding box. There is only one answer for each term.
 

 

Biotechnology Practice Problems

13. What are restriction enzymes?  Why are there so many different kinds?  Why do bacteria make them?

 

14. Explain how the following processes work and what they are used for:

·        Gel electrophoresis

·        Polymerase chain reaction (PCR)

 

15. What is gene therapy?  How is carried out? What is the difference between somatic and germ-line gene therapy? What are the major challenges faced by gene therapy in going from an experimental science to a common medical practice?