Kyle’s Section BIBC100 – Structural [email protected] Summer 2005Problem Set #41. Why does RNA form different structures in solutions than DNA? What are the two main types of structural features that can be seen in complex RNA molecules?Ans: RNA behaves differently because it is single stranded, and thus can base-pair with fellow RNA ribonucleotides on the same strand. Stem structures and Loop structures can be seen.2. Name at least 4 different forms of RNAAns: 1) mRNA (messenger RNA) 2) rRNA (ribosomal RNA)3) tRNA (transfer RNA)4) siRNA (small inhibitory RNA) 3. Draw out the structure of tRNA. Label the major parts and loops (arms). Ans: acceptor stem, D-arm, Anticodon arm, T-Psi-C arm, variable arm. The 5’ terminus is always phosphorylated. The 7 bp acceptor stem may have non-Watson-Crick base pairing (G-U). tRNA looks L-shaped in three dimensions. 4. Which compound is responsible for the catalytic activity of a ribosome?Ans: RNA, not the protein. 5. What does the Psi stand for in the T-Psi-C arm?Ans: Pseudouridine, derived from uracil6. What does the D stand for in the D-arm?Ans: Dihydrouridine, derived from uracil7. Describe, in detail, tRNA processing and maturation. What are the names of the threemain tRNA states? What are the different steps in this process?Ans: 1) Primary Transcript 2) Intermediate 3) Mature tRNASteps in this process include the 5’cleavage (RNase P cut), the 3’ cleavage (RNase D cut), the CCA addition, and base modifications. These all lead to the intermediate state, which is spliced to leave the mature tRNA.8. What is the name of the enzyme responsible for attaching amino acids to tRNAs?Ans: Aminoacyl-tRNA synthetase. This enzyme has two domains: 1) synthetic domain 2) editing domain9. What do scientists mean when they say the genetic code is “degenerate”? How many different codon combinations are possible? How many amino acids are there?Ans: this means that an amino acid may be specified by more than one codon. Thereare 4^3 (64) possible combinations of codons, but yet we only need 20 for the 20 amino acids. 10. What is the “codon”? What is the “anticodon”?Ans: The codon is the grouping of 3 consecutive ribonucleotides on a strand of mRNA which encode for a single amino acid. The anticodon is the grouping of three consecutive ribonucleotides on the tRNA strand which are complimentary to the codon. 11. What is the “wobble hypothesis”?Ans: The wobble hypothesis describes the not-so-precise base pairing at the 5’anticodon position with the 3’ codon position. Anticodon bases like Uracil can bindwith both Adenine and Guanine. A methylated Guanine can bind with both Cytosine and Uracil. An Inosine can bind with U,C, or A. 12. Do RNA ribonucleotides assist in the wobble of base pairing between tRNA and mRNA? How was this proven?Ans: Yes, ribonucleotides A1492 and A1493 assist in forming favorable interactions. This was proven by unstacking these bases, thus producing an unfavorable situation in which near-cognate (wobble) tRNA could not bind. 13. Name three hexoses that are commonly found in living systemsAns: 1) D-glucose 2) D-mannose 3) D-galactose14. Name a commonly found pentoseAns: D-ribose15. Draw out a “pyran” ring. Draw out a “furan” ring. Does glucose form a furan ring ora pyran ring? What about fructose?Ans: glucose forms a glucopyranose ring structure, while fructose forms a fructofuranose ring structure.16. Define the term “anomer”Ans: Anomers are two molecules that have different positioning of the OH group around carbon 1. These are classified as alpha and beta.17. What is a “glycosidic bond”? Describe the glycosidic bond in starch and in cellulose.Ans: A glycosidic bond is formed when two individual glucose units (monosaccharides) bond through a condensation reaction. The glycosidic bond in starch is an alpha(1-4), while the glycosidic bond in cellulose is a beta(1-4).18. What is amylase? What does it do?Ans: Amylase is an enzyme, found in saliva, which breaks down amylose (starch) into maltose products. Maltose is a disaccharide. 19. What are two types of variability that polysaccharides exhibit?Ans: 1) branching 2) different monomer types (heteropolysaccharide)20. Why is cellulose more stable than most other polysaccharides?Ans: Through its beta(1-4) glycosidic linkages, cellulose forms a bonding pattern in which intra-molecular hydrogen bonds exist. 21. Which type of glycosidic bond typically encourages a polysaccharide to form a helical conformation? Ans: alpha glycosidic bonds form helices, while beta glycosidic bonds remain straight
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