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RNA polymerase

RNA polymerase 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 rather than just read about it. In short: In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template strand. Along with the enzyme helicase, RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process cal…

RNA polymerase — main illustration
RNA polymerase — illustration

Key takeaways

  • RNA polymerase 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 to a quantity you can measure, compute or draw — that is where exam questions come from.
  • Reproduce the core statement of RNA polymerase from memory before moving on to harder problems.

Reference excerpt

In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template strand. Along with the enzyme helicase, RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only initiates RNA transcription, it also guides the nucleotides into position, facilitates attachment and elongation, has intrinsic proofreading and replacement capabilities, and termination recognition capability. RNAP can produce different types of RNA, including: Messenger RNA (mRNA)

An RNA copy of the coding strand of a gene which is translated into a polypeptide chain at a ribosome; Transfer RNA (tRNA) Transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthesis during translation; Ribosomal RNA (rRNA) Incorporates into ribosomes; Micro RNA (miRNA) Regulates gene activity; and, RNA silencing Catalytic RNA (ribozyme) Functions as an enzymatically active RNA molecule. RNA polymerase is essential to life, and is found in all living organisms and many viruses. Depending on the organism, a RNA polymerase can be a protein complex (multi-subunit RNAP) or only consist of one subunit (single-subunit RNAP, ssRNAP), each representing an independent lineage. The former is found in bacteria, archaea, and eukaryotes alike, sharing a similar core structure and mechanism. The latter is found in phages as well as eukaryotic chloroplasts and mitochondria, and is related to modern DNA polymerases. Eukaryotic and archaeal RNAPs have more subunits than bacterial ones do, and are controlled differently. Bacteria and archaea only have one RNA polymerase. Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA:

Structure

In most prokaryotes (archaea, bacteria), a single RNA polymerase species transcribes all types of RNA. RNA polymerase "core" from the bacteria E. coli consists of five subunits: two alpha (α) subunits of 36 kDa, a beta (β) subunit of 150 kDa, a beta prime subunit (β′) of 155 kDa, and a small omega (ω) subunit. A sigma (σ) factor binds to the core, forming the holoenzyme. After transcription starts, the σ factor can unbind and let the core enzyme perform transcription. The core RNA polymerase complex forms a "crab claw" or "clamp-jaw" structure with an internal channel running along the full length. Eukaryotic and archaeal RNA polymerases have a similar core structure and work in a similar manner, although they have many extra subunits. The 2006 Nobel Prize in Chemistry was awarded to Roger D. Kornberg for creating detailed molecular images of RNA polymerase during various stages of the transcription process. All RNAPs contain metal cofactors, in particular zinc and magnesium cations which aid in the transcription process.

Function

Control of the process of gene transcription affects patterns of gene expression and, thereby, allows a cell to adapt to a changing environment, perform specialized roles within a multicellular organism, and maintain basic metabolic processes necessary for survival. The activity of RNAP is complex and highly regulated. In Escherichia coli bacteria, more than 100 transcription factors have been identified, which modify the activity of RNAP. RNAP can initiate transcription at specific DNA sequences known as promoters. It then produces an RNA chain, which is complementary to the template DNA strand. The process of adding nucleotides to the RNA strand is known as elongation; in eukaryotes, RNAP can build chains as long as 2.4 million nucleotides (the full length of the dystrophin gene). RNAP will preferentially release its RNA transcript at specific DNA sequences encoded at the end of genes, which are known as terminators. Products of RNAP include:

Messenger RNA (mRNA)—template for the synthesis of proteins by ribosomes. Non-coding RNA or "RNA genes"—a broad class of genes that encode RNA that is not translated into protein. The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role than previously thought. Transfer RNA (tRNA)—transfers specific amino acids to growing polypeptide chains at the ribosomal site of protein synthesis during translation Ribosomal RNA (rRNA)—a component of ribosomes Micro RNA—regulates gene activity Catalytic RNA (Ribozyme)—enzymatically active RNA molecules RNAP accomplishes de novo synthesis. It is able to do this because specific interactions with the initiating nucleotide hold RNAP rigidly in place, facilitating chemical attack on the incoming nucleotide. Such specific interactions explain why RNAP prefers to start transcripts with ATP (followed by GTP, UTP, and then CTP). In contrast to DNA polymerase, RNAP includes helicase activity, therefore no separate enzyme is needed to unwind DNA.

Action

… excerpt ends here. Continue reading the full article.

Illustrations

RNA polymerase illustration
RNA polymerase: RNA polymerase (purple) unwinding the DNA double helix. It uses one strand (darker orange) as a template to create the single-stranded messenger RNA (green).
RNA polymerase (purple) unwinding the DNA double helix. It uses one strand (darker orange) as a template to create the single-stranded messenger RNA (green).
RNA polymerase illustration
RNA polymerase illustration
RNA polymerase: An electron-micrograph of DNA strands decorated by hundreds of RNAP molecules too small to be resolved. Each RNAP is transcribing an RNA strand, which can be seen branching off from the DNA. "Begin" indicates the 3′ end of the DNA, where RNAP initiates transcription; "End" indicates the 5′ end, where the longer RNA molecules are completely transcribed.
An electron-micrograph of DNA strands decorated by hundreds of RNAP molecules too small to be resolved. Each RNAP is transcribing an RNA strand, which can be seen branching off from the DNA. "Begin" indicates the 3′ end of the DNA, where RNAP initiates transcription; "End" indicates the 5′ end, where the longer RNA molecules are completely transcribed.

Worked examples

Example 1 — a first encounter with RNA polymerase

Start with the simplest possible case. Write down what RNA polymerase 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 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 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

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

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

Frequently asked questions

What is RNA polymerase in simple terms?

In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template strand. Along with the enzyme helicase, RNAP locally opens the double-stra…

Why does RNA polymerase 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?

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.

Tags

  • EC 2.7.7
  • Enzymes
  • Gene expression
  • RNA

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