Biology for AP Courses · Genes and Proteins
Prokaryotic Transcription
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In 30 seconds
transcription Synthesis of an RNA copy of a DNA gene Full entry → is the synthesis of an RNA copy of a gene — the first step of the central dogma (DNA → RNA → protein). In bacteria, a single RNA polymerase The enzyme that builds RNA from a DNA template Full entry → makes all RNA types (mRNA, rRNA, tRNA) and needs no primer. A sigma (σ) factor guides it to the promoter DNA sequence upstream of a gene where polymerase binds Full entry →, recognizing the −10 element (Pribnow box, TATAAT) and the −35 element (TTGACA). Transcription proceeds in three phases — initiation (closed → open complex → promoter escape), elongation (RNA grows 5′→3′ in a moving transcription bubble Locally unwound DNA at the active site Full entry → of ~12–17 bp, commonly taught), and termination — in two flavors: rho-independent (intrinsic) via a GC-rich hairpin plus a run of U's, and rho-dependent via the rho helicase.
Because bacteria have no nucleus, transcription and translation are coupled — ribosomes translate an mRNA while it is still being made — and one mRNA often carries several genes (polycistronic), the basis of operons like the lac operon. Bacterial mRNAs are short-lived and get no 5′ cap or poly-A tail.
Why this matters
Prokaryotic transcription powers every bacterial gene — virulence factors, antibiotic-resistance enzymes, and the metabolic enzymes of operons that AP Biology loves to test. It is also a proven drug target: rifampicin (rifampin), used against tuberculosis, binds the bacterial RNA polymerase β subunit and blocks RNA synthesis — human polymerases are unaffected, so it kills Mycobacterium tuberculosis inside a person without stopping human cells. Comparing prokaryotic and eukaryotic transcription is a standard exam theme: one polymerase vs. three, sigma vs. general transcription factors, polycistronic vs. monocistronic mRNA. This topic also sets up eukaryotic transcription, RNA processing, and translation.
The college version
Core Concepts
RNA polymerase and sigma
The bacterial core enzyme (commonly written α₂ββ′ω) synthesizes RNA but cannot initiate at the right places alone. The sigma factor Subunit that recognizes promoter sequences Full entry → binds the core to form the holoenzyme and confers promoter specificity. The housekeeping sigma (σ⁷⁰ in E. coli) recognizes most promoters; alternative sigmas reprogram the cell — σ³² for heat shock, sporulation sigmas in Bacillus — switching gene batteries without changing DNA. Unlike DNA polymerase, RNA polymerase needs no primer, uses ribonucleotides (ATP, UTP, GTP, CTP), and has no proofreading exonuclease — faster but less accurate (RNA errors are transient, usually harmless).
Promoters: where the sigma factor docks
A promoter is the DNA sequence upstream of a gene that directs transcription. The two most important elements in E. coli, positioned relative to the transcription start site (+1):
- −10 element (Pribnow box): consensus TATAAT, where strands separate.
- −35 element: consensus TTGACA, recognized first by σ⁷⁰.
- Some strong promoters add an UP element upstream.
Promoters matching the consensus are stronger — so a single base change can silence or overdrive a gene.
Initiation
The holoenzyme binds the promoter as a closed complex (DNA double-stranded), then melts the DNA around −10 into an open complex, exposing the template strand The DNA strand RNA polymerase reads (3′→5′) Full entry →. The polymerase begins at +1 but first makes and releases short (2–9 nt) RNAs in abortive initiation. Once the RNA grows past ~10 nucleotides, the polymerase escapes the promoter and sigma is released (and reused). The template is read 3′→5′; RNA is synthesized 5′→3′, complementary and antiparallel.
Elongation
As the polymerase moves, it unwinds DNA ahead and re-anneals behind, keeping a transcription bubble of ~12–17 bp (commonly taught) with an RNA–DNA hybrid of ~8–9 bp. RNA is added to the 3′ end at a commonly cited ~40–50 nucleotides per second; the transcript matches the coding (non-template) strand except U replaces T. Topoisomerases relieve supercoiling ahead of the polymerase.
Termination
- Rho-independent (intrinsic): the transcript forms a GC-rich hairpin followed by 4–8 uracils; the hairpin disrupts the RNA–DNA hybrid and weak rU–dA pairing lets the transcript peel away — the polymerase falls off.
- Rho-dependent: rho protein binds a rut site on the nascent RNA, translocates 5′→3′, catches the paused polymerase, and unwinds the hybrid, releasing the transcript.
Coupled translation and polycistronic mRNA
With no nuclear envelope, a ribosome attaches to the 5′ end of an mRNA and begins translating while RNA polymerase is still elongating the 3′ end — coupled transcription-translation. One transcript often carries several genes (polycistronic mRNA One mRNA carrying several genes Full entry →), which is how operons work: the lac operon's mRNA carries lacZ, lacY, lacA, so all three enzymes are made from one promoter. Bacterial mRNAs are short-lived (half-lives of a few minutes, commonly cited), allowing rapid responses.
Common Confusions
| Do Not Confuse | With | The Difference |
|---|---|---|
| Template strand | Coding strand | Template is read 3′→5′ and dictates the RNA; coding strand matches the RNA (with U for T) |
| Sigma factor | RNA polymerase | Sigma only finds promoters; the core enzyme does the synthesizing. Sigma is released at promoter escape |
| Transcription | Translation | Transcription makes RNA from DNA; translation makes protein from RNA (on ribosomes) |
| rho-dependent | rho-independent termination | rho-independent uses a hairpin + poly-U run (no extra protein); rho-dependent uses the rho helicase riding the RNA |
| Pribnow box (−10) | TATA box | Both AT-rich promoter elements, but Pribnow is bacterial; TATA is a eukaryotic Pol II element (~−30) |
| RNA polymerase | DNA polymerase | RNA polymerase starts RNA de novo (no primer) and has no proofreading; DNA polymerase needs a primer |
| Bacterial mRNA | Eukaryotic mRNA | Bacterial: polycistronic, unprocessed, translated while being made; eukaryotic: monocistronic, processed (cap, splice, poly-A), translated after export |
Eli explains
The same idea, in plain words
Explain it like I’m 10
Making RNA from DNA is like a photocopier that copies one recipe page from a cookbook into a loose sheet for the cooks. The sigma factor is the guide that tells the copier which page to copy. The copier unzips the page, reads the letters, and writes a matching sheet (with U instead of T). At the end, a hairpin-shaped knot in the new sheet makes the copier let go — or a helper protein pushes it off. Because bacteria have no kitchen walls, the cooks start cooking from the sheet while it's still coming out of the copier.
Worked example
Picture E. coli suddenly finding lactose in its environment. σ⁷⁰-containing holoenzymes scan the chromosome; near the lac operon, an activator (CAP, active when glucose is scarce) bends the DNA to help RNA polymerase bind the lac promoter. The polymerase forms a closed complex, melts −10 into an open complex, and begins abortive initiation — spitting out short RNAs before escaping the promoter and committing to elongation. As it moves down the template, a bubble of ~17 bp of unwound DNA travels with it, and the growing transcript — matching the coding strand with U for T — exits the enzyme. Ribosomes attach to the 5′ end almost immediately (coupled transcription-translation) and make β-galactosidase while the rest of the message is still being synthesized. At the end of the operon, the transcript forms a GC-rich hairpin followed by U's; the weak rU–dA pairing lets the mRNA peel away, the polymerase dissociates, and one polycistronic mRNA carrying lacZ, lacY, and lacA is complete. Now the antibiotic lens: if this cell were inside a person treated with rifampicin, the drug would jam the β subunit of RNA polymerase, transcription would stall early, and no new proteins — including the enzymes the bacterium needs to survive — would be made. Human cells are unaffected because their polymerases differ enough that rifampicin doesn't bind them.
Key takeaways
- One RNA polymerase in bacteria (core α₂ββ′ω + sigma = holoenzyme); no primer; RNA grows 5′→3′.
- Sigma = promoter specificity: σ⁷⁰ recognizes −10 (TATAAT) and −35 (TTGACA); alternative sigmas switch programs.
- Initiation: closed → open complex (strand melting) → abortive initiation → promoter escape (sigma released).
- Elongation: transcription bubble (~12–17 bp); transcript matches the coding strand (U for T); topoisomerases relieve supercoiling.
- Termination: rho-independent = hairpin + poly-U run; rho-dependent = rho protein rides the RNA and unwinds the hybrid.
- Polycistronic mRNA (operons like lac); coupled transcription-translation; mRNA short-lived, unprocessed (no cap, no poly-A tail).
- Medical hook: rifampicin inhibits the bacterial RNA polymerase β subunit — kills bacteria, spares human polymerases.
- mRNA = coding-strand sequence with U for T; promoter mutations change transcription levels, not the protein.
Check yourself
6 review questions from the chapter. Try each one, then open the answer.
What are the two consensus promoter elements recognized by σ⁷⁰, and where are they located?
Show answer
The −10 element (Pribnow box, TATAAT) and the −35 element (TTGACA), counted in base pairs upstream of the start site (+1). Both are bound by sigma; close matches to consensus make strong promoters.
Why does RNA polymerase not need a primer, and how does that differ from DNA polymerase?
Show answer
RNA polymerase builds RNA directly from ribonucleotide triphosphates with no primer, whereas DNA polymerase can only add to an existing 3′ OH (hence its RNA primer requirement).
Describe the steps of initiation from closed complex to promoter escape.
Show answer
(1) Holoenzyme binds the promoter as a closed complex; (2) the DNA melts around −10 into an open complex; (3) the polymerase makes and releases short abortive RNAs; (4) once RNA exceeds ~10 nt, the polymerase escapes and sigma is released.
Explain how rho-independent termination Hairpin + poly-U run releases the transcript Full entry → works at the molecular level.
Show answer
The transcript forms a GC-rich hairpin that disrupts the RNA–DNA hybrid; the run of U's forms only weak rU–dA pairs, so the transcript dissociates and the polymerase falls off.
What does it mean that bacterial transcription and translation are "coupled," and what cellular feature makes this possible?
Show answer
Coupled means ribosomes begin translating the 5′ end of an mRNA while RNA polymerase is still transcribing the 3′ end — possible only because bacteria have no nucleus.
Why does rifampicin kill bacteria but not human cells?
Show answer
Rifampicin binds the β subunit of bacterial RNA polymerase and blocks RNA synthesis; eukaryotic polymerases differ in structure and aren't bound, so human transcription continues.
Study tools & related lessonsKey vocabulary · Related
Key vocabulary
- transcription
- Synthesis of an RNA copy of a DNA gene
- RNA polymerase
- The enzyme that builds RNA from a DNA template
- sigma factor
- Subunit that recognizes promoter sequences
- promoter
- DNA sequence upstream of a gene where polymerase binds
- Pribnow box (−10)
- Consensus TATAAT, where strands melt
- template strand
- The DNA strand RNA polymerase reads (3′→5′)
- transcription bubble
- Locally unwound DNA at the active site
- rho-independent termination
- Hairpin + poly-U run releases the transcript
- rho-dependent termination
- Rho unwinds the RNA–DNA hybrid to release RNA
- polycistronic mRNA
- One mRNA carrying several genes
Sources & references
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