Presentation on theme: "RNA and Nucleic Acid Reactions C483 Spring 2013. 1. Which is not a difference between RNA and DNA? A) RNA is more prone to basic aqueous hydrolysis. B)"— Presentation transcript:
1. Which is not a difference between RNA and DNA? A) RNA is more prone to basic aqueous hydrolysis. B) RNA contains uracil; DNA usually does not. C) RNA cannot form helices. D) RNA is usually single-stranded; DNA is double-stranded. 2. ________ catalyze the hydrolysis of phosphodiester linkages to release nucleotide residues from the middle of a polynucleotide chain. A) Topoisomerases B) Endonucleases C) Exonucleases D) Restriction enzymes 3. Which are the products of the RNase A-catalyzed hydrolysis of pGpApUpApApCpG? A) pG + pA + pUpA + pA + pCpG B) pGpApU + pApApC + pG C) pG + pApUpApApCpG D) pGpApUp + ApApCp + G E) two pG + three pA + pU + pC
4. Which does not occur during the hydrolysis of RNA by RNase A? A) Covalent catalysis involving a bond between a pyrimidine and a lysine of RNase A. B) Acid-base catalysis to cleave the phosphodiester bond. C) Abstraction of a proton from the 2'-hydroxyl group by histidine. D) Transition-state stabilization of a pentavalent phosphorous atom. 5. Which enzyme would be least useful for recombination experiments that introduce new fragments of DNA into an existing DNA molecule? A) EcoRI G↓AATTC. B) SmaI CCC↓GGG. C) XhoI C↓TCGAG. D) All are equally useful.
RNA Single stranded with secondary structure, including helices Stem-loop Ribosomal RNA (rRNA) – 80% Transfer RNA (tRNA) – 15% Messenger RNA (mRNA) – 3% Small RNA – 2%
RNA Structure and Stability Structural difference of 2’ hydroxyl – H-bonding in RNA structure – Reactions of catalytic RNA (rare) – Hydrolysis Structure dictates role difference in DNA/RNA
Catalytic Hydrolysis Enzymes can catalyze hydrolysis Very important reactions! Nucleases – RNase vs DNase Single/double strand – Exonuclease vs Endonuclease – Orientation of hydrolysis
RNase A Key protein in study of protein folding Endonuclease Selective for pyrimidines Cleaves ester to give free 5’ hydroxyl (like alkaline hydrolysis)
Products of RNase A Hydrolysis of pGpGpUpApCpUpG gives: Biochemistry 1998, 37, 12121-12132
Mechanism of RNase A Mechanisms of catalysis – Proximity – Acid/base – TS stabilization also includes Lys41 Pentavalent phosphorus Biochemistry 2001, 40, 4949-4956.