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Twister sister ribozyme

Twister sister ribozyme is a science topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Twister sister ribozyme rather than just read about it. In short: The twister sister ribozyme (TS) is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme.

Twister sister ribozyme — main illustration
Twister sister ribozyme — illustration

Key takeaways

  • Twister sister ribozyme belongs to science; place it in that map before memorising details.
  • Learn the definition first, then one example that makes the definition concrete.
  • Connect Twister sister ribozyme to a quantity you can measure, compute or draw — that is where exam questions come from.
  • Reproduce the core statement of Twister sister ribozyme from memory before moving on to harder problems.

Reference excerpt

The twister sister ribozyme (TS) is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme. The twister sister ribozyme was discovered by a bioinformatics strategy as an RNA Associated with Genes Associated with Twister and Hammerhead ribozymes, or RAGATH. The twister sister ribozyme has a possible structural similarity to twister ribozymes. Some striking similarities were noted, but also surprising differences, such as the absence of the two pseudoknot interactions in the twister ribozyme. The exact nature of the structural relationship between twister and twister sister ribozymes, if any, has not be determined.

Discovery

The twister sister ribozyme was discovered through a bioinformatic search. This study conducted a search for conserved RNA structures near known twister and hammerhead ribozymes as well as certain protein-coding genes based on the fact that many ribozymes are located near to each other and near those genetic fragments. Later they tested the self-cleaving activity of 15 conserved RNA motifs that were found in these regions. 3 out of the 15 RNA motifs showed self-cleaving activity, which were the twister sister ribozyme, the pistol ribozyme and the hatchet ribozyme.

Structure

The crystal structures of the pre-catalytic state of the twister sister ribozymes were solved by two research groups independently. The structure of a three-way junctional twister sister ribozyme is composed of two co-axial stacked helical sections connected with a three-way junction and two tertiary contacts. The active site, a scissile phosphate, is located in a loop with quasihelical character in one coaxial base-stacked helix. Five divalent metal ions are coordinate to RNA ligands, one of which is directly bound to C54 O2’ near the scissile phosphate and exchange inner sphere water molecules with the RNA ligands. The crystal structure of a four-way junctional twister sister ribozyme is different from the three-way junctional one in terms of long-range interaction and active site structure. The active site of a four-way junctional twister sister is splayed-apart with an interaction between guanine and scissile phosphate. Besides, there are seven divalent metal ions in this ribozyme. So far, we only know the pre-catalytic conformation of twister sister ribozymes. Understanding the transition state is needed to explain the relationship between twister ribozyme and twister sister ribozyme as well as the structure differences of the active site between the three-way and four-way junctional twister sister ribozymes.

Catalytic mechanism Generally, nucleolytic ribozymes cleave a specific phosphodiester linkage by SN2 mechanism. The O2' acts as a nucleophile to attack the adjacent P, with O5’ as a leaving group. The catalytic products are a cyclic 2’,3’ phosphate and a 5’-hydroxyl. The catalytic activity of twister sister increases with pH and depends on divalent metal ion. The cleavage speed increases 10 fold with each increase in pH unit and reach a plateau near pH 7, which indicates that the 2-hydroxyl group of cytidine near the active site is fully deprotonated at pH 7 in the ribozyme. However, the structural basis for the catalytic activity is still under investigation. The three-way junctional twister sister is a metalloenzyme. The inner sphere water of a divalent metal ion bound to C54 O2’ acts as a general base to deprotonate the 2-hydroxyl group, making it a stronger nucleophile, but the general acid which can stabilize the oxyanion leaving group remains unknown. This mechanism is supported by the exponential correlation between catalytic activity and the pKa of hydrated metal ion. For the four-way junctional twister sister, Ren and coworkers find that guanine with an amino group is likely to play a role in the catalysis because G5 mutations result in very low catalytic activity. However, it remains unclear whether guanine directly participates in the catalysis as it is not absolutely conserved. The formation of a pseudoknot for four-way junctional TS was found to be highly Mg2+ dependent by conducting SHAPE (Selective-2′ -Hydroxyl Acylation analyzed by Primer Extension) experiments.

References

Illustrations

Twister sister ribozyme illustration
Twister sister ribozyme: Schematic and tertiary structure of the twister-sister ribozyme. a Schematic of the secondary fold of the dC62-containing four-way junctional twister-sister ribozyme. b Schematic of the tertiary fold based on the crystal structure of the dC62-containing four-way junctional twister-sister ribozyme. c A ribbon view of the 2 Å structure of the four-way junctional twister-sister ribozyme color-coded as shown in a and b. The divalent metal ions identified in the tertiary structure are shown as green balls. d Highly conserved residues (shown in red) are brought into close proximity by the interaction between partially zippered-up L1 and SL4 loops in the tertiary fold of the twister-sister ribozyme
Schematic and tertiary structure of the twister-sister ribozyme. a Schematic of the secondary fold of the dC62-containing four-way junctional twister-sister ribozyme. b Schematic of the tertiary fold based on the crystal structure of the dC62-containing four-way junctional twister-sister ribozyme. c A ribbon view of the 2 Å structure of the four-way junctional twister-sister ribozyme color-coded as shown in a and b. The divalent metal ions identified in the tertiary structure are shown as green balls. d Highly conserved residues (shown in red) are brought into close proximity by the interaction between partially zippered-up L1 and SL4 loops in the tertiary fold of the twister-sister ribozyme

Worked examples

Example 1 — a first encounter with Twister sister ribozyme

Start with the simplest possible case. Write down what Twister sister ribozyme claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Twister sister ribozyme before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Twister sister ribozyme ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Twister sister ribozyme

In research
Twister sister ribozyme appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry
Engineering practice reuses Twister sister ribozyme in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom
Twister sister ribozyme is common in secondary-school and first-year university syllabi. It links to neighbouring topics RNA, Ribozymes, so understanding it makes those chapters shorter.
In everyday life
Look for Twister sister ribozyme outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.
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How to study Twister sister ribozyme in 20 minutes

  1. Read the reference excerpt below once, without taking notes.
  2. Close the page and write down what Twister sister ribozyme means in your own words.
  3. Compare your version with the excerpt and mark what you missed.
  4. Work through the three examples above with pen and paper.
  5. Explain Twister sister ribozyme out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Twister sister ribozyme in simple terms?

The twister sister ribozyme (TS) is an RNA structure that catalyzes its own cleavage at a specific site. In other words, it is a self-cleaving ribozyme.

Why does Twister sister ribozyme matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Twister sister ribozyme?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Twister sister ribozyme.

Tags

  • RNA
  • Ribozymes

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