Deck 3: The Versatility of RNA

Question 1

Hairpin loops, base-paired stems, and bulges make up what part of RNA's structure?

A) primary
B) secondary
C) tertiary
D) quaternary

Answer 1

secondary

Question 2

Base-paired stems in RNA

A) form a B-type double helix
B) form a Z-type double helix
C) form an A-type double helix
D) do not form a double helix

Answer 2

form an A-type double helix

Question 3

A GU wobble is an example of

A) a noncanonical base pair
B) a base triple
C) a Watson-Crick base pair
D) a modified base

Answer 3

a noncanonical base pair

Question 4

Which of the following statements about tRNA is not true?

A) In general, tRNAs contain more than 50 modified bases, such as pseudouridine.
B) tRNA loops each have a separate function.
C) Base-paired stems are often involved in long-range interactions with other stems bycoaxial stacking.
D) The three-dimensional structure of tRNA is referred to as a "cloverleaf."

Question 5

Pseudoknots and tetraloops make up what part of RNA's structure?

A) primary
B) secondary
C) tertiary
D) quaternary

Question 6

Which statement about a pseudoknot motif is not true?

A) Pseudoknot motifs have only been characterized in plant RNA viruses.
B) A highly conserved pseudoknot is required for telomerase activity.
C) Coaxial stacking of base-paired stems forms a quasicontinuous double helix.
D) A single-stranded loop base pairs with a complementary sequence outside this loop.

Question 7

An A-minor motif is characterized by which of the following folding patterns?

A) Hydrogen bonding occurs between the 2 '-OH of a ribose in one helix and the 2-oxygen ofa pyrimidine base of the other helix between their respective minor groove surfaces.
B) Single-stranded adenosines make tertiary contacts with the minor grooves of RNA doublehelices by hydrogen bonding and van der Waals contact.
C) An asymmetric internal loop embedded in RNA double helices has a sharp bend in thephosphodiester backbone of the three-nucleotide bulge associated with this structure.
D) Base-stacking interactions promote and stabilize the stem-loop structure.

Question 8

A particular RNA chain

A) always folds into the same secondary structure.
B) can fold into many different secondary structures and still be functional.
C) can misfold into different secondary structures by incorrect base-pairing, but will stillalways form the same tertiary structure.
D) can misfold and become trapped in a misfolded structure in the absence of RNAchaperones.

Question 9

There is a tremendous versatility of functional RNA products involved in a wide range of
Cellular processes. One of the key contributing factors to this versatility is

A) the ability of RNA to form unique 3D structures that act similarly to proteins
B) the ability of RNA to cleave phosphodiester bonds in other nucleic acids
C) the ability of RNA to be copied into DNA
D) the ability of RNA to serve as a messenger during protein synthesis

Question 10

The term ribozyme describes what property of RNA molecules?

A) they are single-stranded
B) they can be catalytic
C) their shape
D) the formation of hairpin loops

Question 11

You are characterizing the properties of a self-splicing ribozyme and obtain the following
Results: in the presence of Mg²⁺, self-splicing occurs. However, in the absence of Mg²⁺, self-splicing does not occur. Which of the following hypotheses does this observation support?

A) Mg²⁺ is a cofactor for the ribozyme.
B) Mg²⁺ is a substrate for the ribozyme.
C) Mg²⁺ helps maintain the tertiary or quaternary structure of the protein.
D) Mg²⁺ is not required for the activity of the ribozyme

Question 12

Which statement is true?

A) All proteins are enzymes.
B) All proteins are enzymes, and some RNA molecules also are catalytic.
C) All enzymes are proteins.
D) Most enzymes are proteins, but some RNA molecules also are catalytic.

Question 13

Many ribozymes

A) are autocatalytic
B) are metalloenzymes
C) cleave phosphodiester bonds
D) all of the above

Question 14

Which of the following is not an example of a tertiary RNA structure?

A) tetraloop
B) kink-turn
C) base-paired stem
D) ribose zipper

Question 15

Which of the following is not a critical cellular role for non-coding RNAs?

A) mRNA splicing
B) Ribosome function
C) DNA replication
D) Regulation of gene expression

Question 16

A retrovirus, such as HIV-1,

A) uses non-coding RNAs to package its genome into a capsid
B) stores its genome as an RNA sequence
C) uses host cell ribozymes to process its genome
D) converts its DNA genome to an RNA once inside the host cell

Question 17

Subviral RNA particles such as viroids and satellite RNAs differ from viruses in that

A) subviral RNA particles usually do not encode proteins
B) subviral RNA particles can only infect plant cells
C) subviral RNA particles usually do not cause disease
D) the infectious form of subviral RNA particles are usually encased by proteins

Question 18

Which of the following is a similarity between the catalytic mechanisms of self-splicing introns and DNA polymerase?

A) both use two metal ions in their active sites
B) both bind to their substrates by base-pairing
C) both use enzyme-RNA covalent intermediates
D) both cleave phosphodiester bonds

Question 19

Draw the general structure of a nucleoside monophosphate. Show the sugar structure in detail and indicate the positions of attachment of the base and the phosphate. Also indicate the location of the 2′-OH group.

Question 20

Summarize the major types of secondary structure found in RNA. Include a labeled diagram.

Question 21

Give an example of a common noncanonical base pair in RNA and discuss the functional significance of this type of base pair.

Question 22

Give an example of a common base modification in RNA and discuss the functional significance of base modifications.

Question 23

The study of tRNA structure has provided many important insights into RNA structural motifs. Discuss this statement.

Question 24

Discuss why Francis Crick stated that "tRNA looks like Nature's attempt to make RNA do the job of a protein."

Question 25

Give examples of the structural and functional importance of the 2′-OH group on the ribose sugar of RNA.

Question 26

You are characterizing a novel ribozyme. Describe an experiment to analyze the folding kinetics of the ribozyme.

Question 27

For many years the pathway of gene expression from DNA to functional product via an RNA intermediate emphasized proteins as the ultimate goal. Discuss how this view has changed.

Question 28

You are investigating a ribosomal RNA (rRNA) gene with one large intron and two short exons. Show the results of R looping experiments performed with:
a. final rRNA product and single-stranded DNA
b. final rRNA and double-stranded DNA
c. rRNA precursor and single-stranded DNA
d. rRNA precursor and double-stranded DNA

Question 29

Show where the 2′-OH group is located on the NTP below. What role does the 2′-OH play in a hammerhead ribozyme?
‪

Question 30

You have discovered an RNA that you think is a self-splicing ribozyme. You also have evidence that it requires a pseudoknot for catalytic activity. Briefly outline an experiment you could perform to test these two hypotheses.

Question 31

Compare and contrast the mode of action of "ribozymes" and "enzymes."

Question 32

Make up an RNA sequence that will form a hairpin with a 9 bp stem and a 7 bp loop. Draw both the primary structure and the secondary structure.

Question 33

What addition(s) would you need to make to the primary sequence in question 36 to allow pseudoknot formation?

Question 34

You suspect that a tetraloop is critical for folding of a ribozyme into its active form. Describe an experiment to demonstrate whether the RNA folds into a similar tertiary structure when the tetraloop is deleted.

Question 35

You have discovered a small RNA involved in removal of a novel class of introns. Design an experiment to determine whether the small RNA functions as a catalytic RNA or RNP. Show sample positive results.

Question 36

Explain how the discovery of ribozymes spawned the RNA World hypothesis.

Question 37

Compare and contrast small ribozymes and large ribozymes.

Question 38

The most effective therapies known for the treatment of HIV infection are inhibitors of RNA-dependent DNA polymerases (also known as reverse transcriptases). Explain how this class of inhibitors would affect the virus's activities.

Question 39

How do eukaryotic RNA viruses differ from retroviruses?