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Exam 4: Nucleic Acids and the Rna World

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Question 1

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Why is it that RNA can catalyze reactions but DNA cannot?

A) The sugar of RNA is much more reactive than the sugar of DNA.
B) The bases of RNA are much more reactive than the bases of DNA.
C) The phosphate groups of RNA are much more reactive than the phosphate groups of DNA.
D) The primary structure of RNA is fundamentally different than the primary structure of DNA.

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Question 2

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Franklin and Wilkins analyzed DNA by bombarding DNA crystals with X-rays.Their analysis yielded two numbers that sparked interest,3.4 nm and 0.34 nm.What is the significance of these numbers?

A) It turned out to be just a coincidence.
B) DNA molecules are 3.4 nm long and 0.34 nm wide.
C) The width of a DNA molecule is 3.4 nm,whereas the width of a nucleotide monomer is 0.34 m.
D) These numbers tell us there are 10 rungs,or steps,on the DNA "ladder" for every turn of the helix.
E) The 10-to-1 ratio signifies that DNA molecules are 10 times longer than they are wide.

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Question 3

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Use the following information when answering the corresponding question(s) . Shu-ichi Nakano reported in Science in February 2000 that "The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a ...[chemical] ...bond." This reaction is inherently slow due to the formation of an unfavorable negative charge on the ribozyme.The author goes on to show that this self-cleavage is made faster by joining it with an acid-base reaction that neutralizes the negative charge.Nakano's model describes a positively charged cytosine base on the ribozyme acting as the acid,and magnesium hydroxide acting as the base.Specifically,the cytosine donates its proton (H⁺) to neutralize the unstable negative charge that would have formed on the ribozyme. -Is Nakano's quote from Science consistent with the textbook's claim that RNA is a good candidate for the first life-form?

You isolate what you think is DNA from a tissue sample.Which of the following will verify that you do,indeed,have DNA (rather than some other type of molecule) ?

Which of the following best describes DNA's secondary structure?

Nucleic acids are polymers made up of which of the following monomers?

What is gel electrophoresis used for?

Nucleic acids have a definite polarity,or directionality.Stated another way,one end of the molecule is different from the other end.How are these ends described?

Why do researchers think the first self-replicating molecule was RNA?

Use the following information when answering the corresponding question(s) . Shu-ichi Nakano reported in Science in February 2000 that "The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a ...[chemical] ...bond." This reaction is inherently slow due to the formation of an unfavorable negative charge on the ribozyme.The author goes on to show that this self-cleavage is made faster by joining it with an acid-base reaction that neutralizes the negative charge.Nakano's model describes a positively charged cytosine base on the ribozyme acting as the acid,and magnesium hydroxide acting as the base.Specifically,the cytosine donates its proton (H⁺) to neutralize the unstable negative charge that would have formed on the ribozyme. -Refer to Nakano's quote.What can be inferred about the free-energy profile for the self-cleavage reaction from the information provided in the paragraph?

In the context of chemical evolution,DNA's structure is interesting because it suggests a possible copying mechanism.What about DNA's structure facilitates copying?

What is/are the variable structure(s) of a nucleotide?

Which one of the following is not a way that RNA is seen as intermediate between DNA and proteins?

Bartel's research group showed that an RNA replicase ribozyme could be created by _____.

DNA double helices are soluble in water but insoluble in alcohol.How do these physical properties reflect the chemical structure of the molecule?

Which of the following is a difference between RNA and DNA?

When nucleotides polymerize to form a nucleic acid _____.

Use the following information when answering the corresponding question(s) . Shu-ichi Nakano reported in Science in February 2000 that "The RNA enzyme (ribozyme) from hepatitis delta virus catalyzes self-cleavage of a ...[chemical] ...bond." This reaction is inherently slow due to the formation of an unfavorable negative charge on the ribozyme.The author goes on to show that this self-cleavage is made faster by joining it with an acid-base reaction that neutralizes the negative charge.Nakano's model describes a positively charged cytosine base on the ribozyme acting as the acid,and magnesium hydroxide acting as the base.Specifically,the cytosine donates its proton (H⁺) to neutralize the unstable negative charge that would have formed on the ribozyme. -In the acid-base reaction described in the preceding paragraph about Nakano's research on RNAs,a proton (H⁺) is being transferred.What is acting as the proton acceptor?

Recall the Bartel lab group experiment to create a ribozyme from scratch.If they had created exact copies of each ribozyme (rather than creating copies with a few differences) ,what would have been the most likely result?

RNA and proteins combine in cells to form structures called ribosomes.Ribosomes contain the active site for peptide bond formation.Based on their chemical structures,do you think protein or RNA molecules actually form the active site within the ribosome?