Karp's Cell and Molecular Biology: Concepts and Experiments

Janet Iwasa, Wallace Marshall

Chapter 11

The Central Dogma: DNA to RNA to Protein - all with Video Answers

Educators

Chapter Questions

Problem 1

Look at the codon chart of Figure $11.38 .$ Which codons would you expect to have a unique $\mathrm{tRNA}$, that is, one that is used only for that codon? Why is it that many codons do not have their own unique tRNA?

Sana Riaz

Sana Riaz

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Problem 2

Proflavin is a compound that inserts itself into DNA and causes frameshift mutations (page 447 ). How would the effect on the amino acid sequence of a proflavin-induced mutation differ between an overlapping and a nonoverlapping code?

Sana Riaz

Numerade Educator

Problem 3

You have just isolated a new drug that has only one effect on cell metabolism; it totally inhibits the breakdown of pre-rRNA to ribosomal RNA. After treating a culture of mammalian cells with this drug, you give the cells $\left[^{3} \mathrm{H}\right]$ uridine for 2 minutes, and then grow the cells in the presence of the drug in unlabeled medium for 4 hours before extracting the RNA and centrifuging it through a sucrose gradient. Draw the curves you would obtain by plotting both absorbance at $260 \mathrm{nm}$ and radioactivity against the fraction number of the gradient. Label the abscissa (X-axis) using S values of RNA.

Sana Riaz

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Problem 4

Using the same axes as in the previous question, draw the profile of radioactive RNA that you would obtain after a culture of mammalian cells had been incubated for 48 hours in $\left[^{3} \mathrm{H}\right]$ uridine without any inhibiting drugs present.

Sana Riaz

Numerade Educator

Problem 5

Suppose you were to construct a synthetic RNA from a repeating dinucleotide (e.g., $A G A G A G A G)$ and then use this RNA as a messenger to synthesize a polypeptide in an in vitro protein-synthesizing system, such as that used by Nirenberg and Matthaei to produce polyphenylalanine. What type of polypeptide would you make from this particular polynucleotide? Would you expect to have more than one type of polypeptide produced? Why or why not?

Sana Riaz

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Problem 6

Suppose that you found an enzyme that incorporated nucleotides randomly into a polymer without the requirement for a template. How many different codons would you be able to find in synthetic RNAs made using two different nucleotide precursors (e.g., CTP and ATP)? (An enzyme called polynucleotide phosphorylase catalyzes this type of reaction and was used in studies that identified codons.)

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Problem 7

Draw the parts of a $15 \mathrm{S}$ globin pre-mRNA, labeling the noncoding portions.

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Problem 8

What is the minimum number of GTPs that you would need to synthesize a pentapeptide in a bacterium?

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Problem 9

It was suggested on page 437 that synonymous codon changes do not generally alter an organism's phenotype. Can you think of an occasion where this might not be true? What does this say about the coding requirements of the genetic material?

Sana Riaz

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Problem 10

Would you agree with the following statement? The discovery that sickle cell anemia resulted from a single amino acid change was proof that the genetic code was nonoverlapping. Why or why not?

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Problem 11

Thalassemia is a disease characterized by mutations that convert amino acid codons into stop codons. Suppose you were to compare the polypeptides synthesized in vitro from mRNAs purified from a wide variety of thalassemia patients. How would you expect these polypeptides to compare? Refer to the codon chart of Figure 11.38 ; how many amino acid codons can be converted into stop codons by a single base substitution?

Sana Riaz

Numerade Educator

Problem 12

Do you think it would be theoretically possible to have a genetic code with only two letters, $A$ and $T ?$ If $s 0$, what would be the minimum number of nucleotides required to make a codon?

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Problem 13

On page 430 , experiments are reported that led to the synthesis of ribozymes with unique catalytic properties. In 2001 , an artificial ribozyme was isolated that was capable of incorporating up to 14 ribonucleotides onto the end of an existing RNA using an RNA strand as a template. The ribozyme could use any RNA sequence as a template and would incorporate complementary nucleotides into the newly synthesized RNA strand with an accuracy of 98.5 percent. If you were a proponent of an ancient $\mathrm{RNA}$ world, how would you use this finding to argue your case? Would this prove the existence of an ancient RNA world? If not, what do you think would provide the strongest evidence for such a world?

Sana Riaz

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Problem 14

How is it possible that mRNA synthesis occurs at a greater rate in bacterial cells than any other class, yet very little mRNA is present within the cell? Try to write an equation describing the steady-state concentration of mRNA in terms of the rate of transcription and the rate of mRNA decay. Assume that mRNA is produced at a constant rate and that mRNA decays at a rate proportional to its concentration. (See Quantitative Tutorial Video).

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Problem 15

If a codon for serine is $5^{\prime}-\mathrm{AGC}-3^{\prime},$ the anticodon for this triplet would be 5' - - - 3' (write the nucleotides on the lines). How would the wobble phenomenon affect this codon-anticodon interaction?

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Problem 16

One of the main arguments that proteins evolved before DNA (i.e., that the RNA world evolved into an RNA-protein world rather than an RNA-DNA world) is based on the fact that the translational machinery involves a large variety of RNAs (e.g., tRNAs, rRNAs), whereas the transcriptional machinery shows no evidence of RNA involvement. Can you explain how such an argument about the stages of early evolution might be based on these observations?

Sana Riaz

Numerade Educator

Problem 17

Frameshift mutations and nonsense mutations were described on pages 447 and $448 .$ It was noted that nonsense mutations often lead to the destruction by NMD of an mRNA containing a premature termination codon. Would you expect mRNAs containing frameshift mutations to be subject to NMD?

Sana Riaz

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Problem 18

The arrowheads in Figure 11.14 indicate the direction of transcription of the various tRNA genes. What does this drawing tell you about the template activity of each strand of a DNA molecule within a chromosome?

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Problem 19

Genes are usually discovered by finding an abnormal phenotype resulting from a genetic mutation. Alternatively, they can often be identified by examining the DNA sequence of a genome. Why do you suppose that the genes encoding miRNAs were not discovered until very recently?

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Problem 20

It has recently been discovered that under stress conditions, ribosomes can add amino acids onto the end of growing protein chains independently of mRNA. When translation stalls in eukaryotes, the small ribosomal subunit dissociates, taking the mRNA with it. The large subunit, containing the nascent peptide chain, binds two proteins called Rqc2 and Ltn1 which mediate direct recruitment of alanine and threonine charged tRNA, causing the peptide chain to continue growing by addition of alanine and threonine. Does this ability of the ribosome to add amino acids independently of mRNA argue against the RNA world hypothesis? Does the fact that this elongation is mRNAindependent mean that it is independent of all RNA? What challenges would a "protein world" scenario face compared to an RNA world, in terms of being able to propagate specific sequence information?

Sana Riaz

Numerade Educator