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Related Concept Videos

Ribozymes02:47

Ribozymes

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The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
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Ribozymes02:47

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Catalytically Perfect Enzymes01:07

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The theory of catalytically perfect enzymes was first proposed by W.J. Albery and J. R. Knowles in 1976. These enzymes catalyze biochemical reactions at high-speed. Their catalytic efficiency values range from 108-109 M-1s-1. These enzymes are also called 'diffusion-controlled' as the only rate-limiting step in the catalysis is that of the substrate diffusion into the active site. Examples include triose phosphate isomerase, fumarase, and superoxide dismutase.
 
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Enzyme Inhibition01:30

Enzyme Inhibition

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Inhibitors are molecules that reduce enzyme activity by binding to the enzyme. In a normally functioning cell, enzymes are regulated by a variety of inhibitors. Drugs and other toxins can also inhibit enzymes. Some inhibitors bind to the enzyme’s active site, while others inhibit enzymatic activity by binding to other sites on the protein structure.
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Heterogeneous Catalysis01:22

Heterogeneous Catalysis

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Heterogeneous catalysis involves a catalyst in a different phase from the reactants. It is a process where the catalyst and the reactants are in distinct phases, typically solid and gas or liquid.Most heterogeneous catalysts are metals, metal oxides, or acids. The list includes transition metals like iron (Fe), cobalt (Co), nickel (Ni), palladium (Pd), platinum (Pt), chromium (Cr), manganese (Mn), tungsten (W), silver (Ag), and copper (Cu). These metals possess partially vacant d orbitals that...
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Enzymes and Activation Energy01:13

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RNA Catalyst as a Reporter for Screening Drugs against RNA Editing in Trypanosomes
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Minimal Hammerhead Ribozymes with Uncompromised Catalytic Activity.

Sara M O'Rourke1, William Estell1, William G Scott1

  • 1Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

Journal of Molecular Biology
|May 19, 2015
PubMed
Summary
This summary is machine-generated.

A single trans-Hoogsteen base-pairing interaction significantly boosts hammerhead ribozyme catalytic activity. This discovery simplifies designing efficient synthetic ribozymes for research and therapeutic applications.

Keywords:
RNA catalysisRNA structureRNA tertiary contactshammerhead ribozymeribozyme kinetics

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • RNA Catalysis

Background:

  • Hammerhead ribozymes are RNA enzymes crucial in various biological processes.
  • Natural hammerhead ribozymes exhibit complex tertiary structures and high catalytic efficiency.
  • Minimal hammerhead ribozymes often show lower catalytic activity compared to their natural counterparts.

Purpose of the Study:

  • To investigate the impact of a single trans-Hoogsteen base-pairing interaction on hammerhead ribozyme activity.
  • To determine if this interaction can enhance the catalytic efficiency of minimal hammerhead ribozymes.
  • To understand the role of tertiary contacts in stabilizing the ribozyme active site.

Main Methods:

  • Utilized minimal hammerhead ribozyme constructs.
  • Introduced a single trans-Hoogsteen base-pairing interaction by modifying the substrate RNA.
  • Assessed catalytic activity through RNA cleavage assays.
  • Maintained the GUGA tetraloop of Stem II in the enzyme strand.

Main Results:

  • A single additional trans-Hoogsteen base-pairing interaction dramatically increased catalytic activity.
  • Enhanced activity in the modified minimal ribozyme mimicked that of full-length natural hammerhead RNAs.
  • This interaction requires a Uracil (U) at a specific position in the substrate RNA.
  • The enzyme strand sequence did not require modification, preserving the GUGA tetraloop.

Conclusions:

  • A single Hoogsteen base-pairing interaction is sufficient to stabilize the hammerhead ribozyme active site.
  • This interaction correctly aligns the nucleophile for the inline cleavage mechanism.
  • Natural tertiary contacts may have evolved to prevent alternative, non-productive pairings.
  • The findings simplify the design of highly active synthetic hammerhead ribozymes for various applications.