Transcription Steps

Why This Matters

Transcription is the bridge between your genetic code and the proteins that make life possible—it's the first half of the Central Dogma and a guaranteed topic on the AP Biology exam. You'll see transcription concepts woven into questions about gene regulation, mutations, biotechnology, and even evolution, so understanding this process gives you a foundation for multiple units.

Here's the key: the exam won't just ask you to list the steps in order. You're being tested on why each step matters, how the molecular machinery ensures accuracy, and what would happen if something went wrong. Don't just memorize the sequence—know what principle each step demonstrates, whether that's enzyme specificity, complementary base pairing, or the directionality of nucleic acid synthesis.

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Initiation: Setting the Stage

Before RNA can be made, the cell must identify exactly where to start. Initiation involves recognition, binding, and preparing the DNA template for reading—errors here mean the wrong genes get expressed (or the right genes don't).

RNA Polymerase Binds to the Promoter

• Promoter sequences are specific DNA regions upstream of genes that act as "start here" signals—in prokaryotes, look for the TATA box around -10 and -35 positions
• Transcription factors (in eukaryotes) must bind first, recruiting RNA polymerase to form the transcription initiation complex
• This step determines which genes are expressed—a key concept for understanding gene regulation and cell differentiation

DNA Double Helix Unwinds

• RNA polymerase itself unwinds approximately 10-20 base pairs, creating the transcription bubble where synthesis occurs
• Only the template strand (also called the antisense strand) is read; the coding strand has the same sequence as the RNA product (except T→U)
• Helicase is NOT required for transcription—RNA polymerase handles unwinding, unlike DNA replication

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Elongation: Building the RNA

Once initiation is complete, the real synthesis begins. Elongation is all about directionality and complementary base pairing—two concepts the AP exam tests repeatedly.

Template Strand Is Read 3' to 5'

• RNA polymerase reads the template strand in the 3' to 5' direction, which means the RNA is synthesized 5' to 3'—this directionality is universal for nucleic acid synthesis
• Antiparallel orientation between template and product ensures proper base pairing geometry
• If asked "which direction does RNA polymerase move?"—it moves along the template toward the 3' end of that strand

Complementary RNA Nucleotides Are Added

• Base pairing follows specific rules: A pairs with U (not T!), and C pairs with G—this is how genetic information transfers accurately
• RNA polymerase uses ribonucleoside triphosphates (NTPs) as substrates, releasing pyrophosphate with each addition
• The 2' hydroxyl group on ribose distinguishes RNA nucleotides from DNA's deoxyribose—this makes RNA less stable but more versatile

RNA Strand Elongates

• Phosphodiester bonds form between the 3' hydroxyl of the growing strand and the 5' phosphate of the incoming nucleotide
• Elongation proceeds at roughly 40-80 nucleotides per second in prokaryotes—much slower in eukaryotes due to chromatin
• No proofreading occurs during transcription (unlike DNA replication), resulting in a higher error rate—but this is tolerable because many RNA copies are made

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Termination: Knowing When to Stop

The cell needs precise signals to end transcription at the right place. Termination mechanisms differ between prokaryotes and eukaryotes—a common source of AP exam questions.

Termination Sequence Is Reached

• In prokaryotes, rho-independent termination uses a GC-rich hairpin loop followed by a poly-U sequence that destabilizes the RNA-DNA hybrid
• Rho-dependent termination involves the rho protein chasing RNA polymerase and pulling the transcript away
• In eukaryotes, termination is coupled to RNA processing signals like the polyadenylation sequence (AAUAAA)

RNA Polymerase Detaches

• The transcription bubble collapses as RNA polymerase releases, allowing DNA to re-form its double helix
• RNA polymerase can immediately reinitiate at another promoter—one enzyme can transcribe many genes sequentially
• Multiple RNA polymerases can transcribe the same gene simultaneously, appearing as "Christmas tree" structures in electron micrographs

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Post-Transcription: Preparing the Message

In eukaryotes, the initial transcript (pre-mRNA) isn't ready for translation yet. RNA processing protects the transcript and removes non-coding sequences—this is where eukaryotic gene expression gets complex.

Newly Synthesized RNA Is Released and Processed

• 5' cap (modified guanine) is added co-transcriptionally, protecting against degradation and aiding ribosome binding
• 3' poly-A tail (50-250 adenines) is added after cleavage, increasing stability and helping export from the nucleus
• Splicing removes introns and joins exons—this allows alternative splicing, where one gene can code for multiple proteins

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Quick Reference Table

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Self-Check Questions

1. Directionality check: If the template strand reads 3'-TACGGA-5', what is the sequence of the resulting mRNA, and in what direction is it written?

2. Compare and contrast: What are three key differences between RNA polymerase and DNA polymerase in terms of primers, proofreading, and nucleotide substrates?

3. Process identification: A mutation destroys the TATA box in a gene's promoter. Which step of transcription is affected, and what would be the consequence for gene expression?

4. Mechanism matching: Which termination mechanism (rho-dependent or rho-independent) would be affected by a mutation that prevents RNA from forming secondary structures? Explain your reasoning.

5. FRQ practice: Explain how alternative splicing allows one eukaryotic gene to produce multiple different proteins, and describe why this process is impossible in prokaryotes.