[Lec 2] Mastering Biology: Structure of RNA Flashcards
Write out the steps in the Central Dogma. List where each step occurs in the cell. For each arrow, name the process that the arrow represents and the primary enzyme (complex) responsible for completing that step. (): where it occurs []: what enzyme is used
duplication–>DNA (the nucleus) [DNA polymerase]–transcription(the nucleus) [RNA polymerase]–>RNA–translation (the cytoplasm) [the large subunit of the ribosome]–>protein
Role of mRNA
- the product in transcription 2. the template for protein synthesis 3. contains exons 4. specifies the amino acid sequence for a protein
Role of tRNA
- the adaptors during translation 2. reads the template and brings the appropriate amino acid 3. has amino acids covalently attached 4. contains an anticodon
Role of rRNA
- a structural component of the ribosome 2. the catalytic component for peptide bond formation in translation 3. is the most abundant form of RNA
Identify the type(s) of secondary structure present in this tRNA.
Check all that apply.
a. helix
b. internal loop
c. stem
d. hairpins
b.,c.,d.
Identify any noncanonical base pairing.
Enter your answers as pairs written with colon separated by a comma.
G:U,U:U
Which of the following events does NOT occur after the transcription of poly-A signal sequences into mRNA?
a. formation of peptide bonds during protein synthesis
b. removal of introns during trans-esterification reactions involved in certain mRNA splicing
c. cleavage of precursor RNAs into mature tRNAs
d. formation of phosphodiester bonds during transcription (i.e, synthesis of complementary RNA from DNA
d.
The RNA-DNA hybrid hammerhead ribozyme structure (Pley et al., 1994) and the all-RNA hammerhead ribozyme structure (Scott et al., 1995) have what structural elements in common?
a. Stem I, stem II, stem III, domain 1 with a CUGA sequence, domain 2
b. Stem I, stem II, stem III, domain 1 with a CUGA sequence, domain 2, a conserved Cytosine at position 17 (C17)
c. Stem I, stem II, stem III, a conserved cytosine at position 17 (C17)
d. Domain 1 with a CUGA sequence, domain 2, a conserved cytosine at position 17 (C17)
b.
Where is the conserved cytosine base (C17) located in the all-RNA hammerhead ribozyme structure?
a. Between stems II and III
b. Between stems I and III
c. Between stems I and II
b.
How many Watson-Crick (W-C) base pairs (bp) comprise stem I in the RNA-DNA hybrid hammerhead ribozyme structure? In stem I of the all-RNA hammerhead ribozyme structure?
a. 4 W-C bp in the RNA-DNA structure and 5 W-C bp in the all-RNA structure
b. 5 W-C bp in the RNA-DNA structure and 5 W-C bp in the all-RNA structure
c. 7 W-C bp in the RNA-DNA structure and 7 W-C bp in the all-RNA structure
d. 7 W-C bp in the RNA-DNA structure and 5 W-C bp in the all-RNA structure
d.
Naturally occurring hammerhead ribozymes are autocatalytic; once the single stranded RNA folds into its characteristic tertiary (3D) structure, the cleavage reaction automatically takes place. This presented a challenge to researchers who were attempting to determine the structure of intact ribozyme molecules using X-ray crystallography. To circumvent this problem, a hybrid RNA-DNA hammerhead ribozyme was constructed that cannot be cleaved.
What prevents the cleavage reaction in the RNA-DNA hammerhead ribozyme?
a. The DNA strand does not allow for formation of stem III in the hybrid ribozyme. Therefore cleavage of the ribozyme cannot occur.
b. The 2’ position on the sugar attached to C17 in the DNA strand contains a free hydroxyl group, which prevents the cleavage reaction from taking place.
c. The 2’ position on the ribose sugar of C17 nucleotide in the DNA strand does not contain a free hydroxyl group, which prevents the cleavage reaction from taking place.
c.
What are the two major steps in the hammerhead ribozyme cleavage reaction?
a. Mg++ deprotonates the 3’ hydroxyl on the conserved cytosine (C17), creating a nucleophilic oxygen. Next, the nucleophilic oxygen attacks the phosphorus bonded to the 2’ oxygen on the same sugar, resulting in cleavage of the RNA strand.
b. Mg++ deprotonates the 2’ hydroxyl on conserved cytosine (C17), creating a nucleophilic oxygen. Next, the nucleophilic oxygen attacks the oxygen at the 3’ location on the same sugar, resulting in cleavage of the RNA strand.
c. Mg++ deprotonates 2’ hydroxyl on C17 creating a nucleophilic oxygen. Next, the nucleophilic oxygen attacks the phosphorus bonded to the 3’ oxygen on the same sugar, resulting in cleavage of the RNA strand.
c.
