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chemistry

RNA polymerase II

RNA polymerase II is a chemistry 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 RNA polymerase II rather than just read about it. In short: RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells.

RNA polymerase II — main illustration
RNA polymerase II — illustration

Key takeaways

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

Reference excerpt

RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.

Discovery

Early studies suggested a minimum of two RNAPs: one which synthesized rRNA in the nucleolus, and one which synthesized other RNA in the nucleoplasm, part of the nucleus but outside the nucleolus. In 1969, biochemists Robert G. Roeder and William Rutter discovered there are total three distinct nuclear RNA polymerases, an additional RNAP that was responsible for transcription of some kind of RNA in the nucleoplasm. The finding was obtained by the use of ion-exchange chromatography via DEAE coated Sephadex beads. The technique separated the enzymes by the order of the corresponding elutions, Ι,ΙΙ,ΙΙΙ, by increasing the concentration of ammonium sulfate. The enzymes were named according to the order of the elutions, RNAP I, RNAP II, RNAP IΙI. This discovery demonstrated that there was an additional enzyme present in the nucleoplasm, which allowed for the differentiation between RNAP II and RNAP III. RNA polymerase II (RNAP2) undergoes regulated transcriptional pausing during early elongation. Various studies has shown that disruption of transcription elongation is implicated in cancer, neurodegeneration, HIV latency etc.

Subunits

The eukaryotic core RNA polymerase II was first purified using transcription assays. The purified enzyme has typically 10–12 subunits (12 in humans and yeast) and is incapable of specific promoter recognition. Many subunit-subunit interactions are known.

DNA-directed RNA polymerase II subunit RPB1 – an enzyme that in humans is encoded by the POLR2A gene and in yeast is encoded by RPO21. RPB1 is the largest subunit of RNA polymerase II. It contains a carboxy terminal domain (CTD) composed of up to 52 heptapeptide repeats (YSPTSPS) that are essential for polymerase activity. The CTD was first discovered in the laboratory of C.J. Ingles at the University of Toronto and by JL Corden at Johns Hopkins University. In combination with several other polymerase subunits, the RPB1 subunit forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA. It strongly interacts with RPB8. RPB2 (POLR2B) – the second-largest subunit that in combination with at least two other polymerase subunits forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA. RPB3 (POLR2C) – the third-largest subunit. Exists as a heterodimer with another polymerase subunit, POLR2J forming a core subassembly. RPB3 strongly interacts with RPB1-5, 7, 10–12. RNA polymerase II subunit B4 (RPB4) – encoded by the POLR2D gene is the fourth-largest subunit and may have a stress protective role. RPB5 – In humans is encoded by the POLR2E gene. Two molecules of this subunit are present in each RNA polymerase II. RPB5 strongly interacts with RPB1, RPB3, and RPB6. RPB6 (POLR2F) – forms a structure with at least two other subunits that stabilizes the transcribing polymerase on the DNA template. RPB7 – encoded by POLR2G and may play a role in regulating polymerase function. RPB7 interacts strongly with RPB1 and RPB5. RPB8 (POLR2H) – interacts with subunits RPB1-3, 5, and 7. RPB9 – The groove in which the DNA template is transcribed into RNA is composed of RPB9 (POLR2I) and RPB1. RPB10 – the product of gene POLR2L. It interacts with RPB1-3 and 5, and strongly with RPB3. RPB11 – the RPB11 subunit is itself composed of three subunits in humans: POLR2J (RPB11-a), POLR2J2 (RPB11-b), and POLR2J3 (RPB11-c). RPB12 – Also interacts with RPB3 is RPB12 (POLR2K).

Assembly RPB3 is involved in RNA polymerase II assembly. A subcomplex of RPB2 and RPB3 appears soon after subunit synthesis. This complex subsequently interacts with RPB1. RPB3, RPB5, and RPB7 interact with themselves to form homodimers, and RPB3 and RPB5 together are able to contact all of the other RPB subunits, except RPB9. Only RPB1 strongly binds to RPB5. The RPB1 subunit also contacts RPB7, RPB10, and more weakly but most efficiently with RPB8. Once RPB1 enters the complex, other subunits such as RPB5 and RPB7 can enter, where RPB5 binds to RPB6 and RPB8 and RPB3 brings in RPB10, RPB 11, and RPB12. RPB4 and RPB9 may enter once most of the complex is assembled. RPB4 forms a complex with RPB7.

Kinetics Enzymes can catalyze up to several million reactions per second. Enzyme rates depend on solution conditions and substrate concentration. Like other enzymes POLR2 has a saturation curve and a maximum velocity (Vmax). It has a Km (substrate concentration required for one-half Vmax) and a kcat (the number of substrate molecules handled by one active site per second). The specificity constant is given by kcat/Km. The theoretical maximum for the specificity constant is the diffusion limit of about 108 to 109 (M−1s−1), where every collision of the enzyme with its substrate results in catalysis. In yeast, mutation in the Trigger-Loop domain of the largest subunit can change the kinetics of the enzyme. Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between inactivated and activated states by translocating back and forth along the DNA. Concentrations of [NTP]eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP, produce a mean elongation rate, turnover number, of ~1 bp (NTP)−1 for bacterial RNAP, a relative of RNA polymerase II.

RNA polymerase II undergoes extensive co-transcriptional pausing during transcription elongation. This pausing is especially pronounced at nucleosomes, and arises in part through the polymerase entering a transcriptionally incompetent backtracked state. The duration of these pauses ranges from seconds to minutes or longer, and exit from long-lived pauses can be promoted by elongation factors such as TFIIS. In turn, the transcription rate influences whether the histones of transcribed nucleosomes are evicted from chromatin, or reinserted behind the transcribing polymerase.

Alpha-Amanitin

… excerpt ends here. Continue reading the full article.

Illustrations

RNA polymerase II: Function of RNA polymerase II (transcription). Green: newly synthesized RNA strand by enzyme
Function of RNA polymerase II (transcription). Green: newly synthesized RNA strand by enzyme
RNA polymerase II: RNA polymerase II of Saccharomyces cerevisiae consisting of all 12 subunits.[4]
RNA polymerase II of Saccharomyces cerevisiae consisting of all 12 subunits.[4]
RNA polymerase II: Eukaryotic RNA-polymerase II from Saccharomyces cerevisiae, PDB ID.[9] Subunits colored: RPB3 – orange , RPB11 – yellow , RPB2 – wheat, RPB1 – red, RPB6 – pink, the rest 7 subunits are colored gray.
Eukaryotic RNA-polymerase II from Saccharomyces cerevisiae, PDB ID.[9] Subunits colored: RPB3 – orange , RPB11 – yellow , RPB2 – wheat, RPB1 – red, RPB6 – pink, the rest 7 subunits are colored gray.
RNA polymerase II: RNA Polymerase II gray. Alpha-amanitin interaction (red).
RNA Polymerase II gray. Alpha-amanitin interaction (red).

Worked examples

Example 1 — a first encounter with RNA polymerase II

Start with the simplest possible case. Write down what RNA polymerase II claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In chemistry, 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 RNA polymerase II 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 RNA polymerase II 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 RNA polymerase II

In research
RNA polymerase II appears in chemistry 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 RNA polymerase II 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
RNA polymerase II is common in secondary-school and first-year university syllabi. It links to neighbouring topics EC 2.7.7, Gene expression, Proteins, so understanding it makes those chapters shorter.
In everyday life
Look for RNA polymerase II 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 RNA polymerase II in 20 minutes

  1. Read the reference excerpt below once, without taking notes.
  2. Close the page and write down what RNA polymerase II 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 RNA polymerase II out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is RNA polymerase II in simple terms?

RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells.

Why does RNA polymerase II matter?

Because it connects several chemistry 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 RNA polymerase II?

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 RNA polymerase II.

Tags

  • EC 2.7.7
  • Gene expression
  • Proteins

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