Stages of Protein Synthesis

Why This Matters

Protein synthesis is the central process connecting genotype to phenotype—it's how your cells read genetic instructions and build the molecular machines that do everything from catalyzing reactions to providing structural support. You're being tested on your understanding of information flow, molecular recognition, and energy-coupled processes. Every stage involves specific enzymes, nucleic acid interactions, and quality control mechanisms that examiners love to probe.

Don't just memorize the sequence of events. Know why each stage exists, what molecular players are involved, and how errors at each step would affect the final protein product. When you understand the logic behind transcription, RNA processing, and translation, you can reason through any question—even ones featuring unfamiliar scenarios.

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Information Transfer: DNA to RNA

The first major phase converts the stable DNA archive into a portable RNA message. This is where genetic information leaves the nucleus and becomes accessible for protein production.

Transcription

• RNA polymerase binds to the promoter region and synthesizes mRNA in the 5' to 3' direction—the enzyme reads the template strand 3' to 5'
• Template vs. coding strand—the mRNA sequence matches the coding strand (except U replaces T), which is why we call it the "sense" strand
• Occurs in the nucleus for eukaryotes, producing a primary transcript (pre-mRNA) that requires processing before translation

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RNA Processing: Preparing the Message

Before mRNA can leave the nucleus, it must be modified for stability, export, and accurate reading. These modifications distinguish eukaryotic gene expression from prokaryotic.

Post-Transcriptional Modifications

• 5' cap (7-methylguanosine) protects mRNA from degradation and signals ribosome binding—added co-transcriptionally
• Poly-A tail (100-250 adenine nucleotides) enhances stability and aids nuclear export—longer tails generally mean longer mRNA lifespan
• Splicing removes introns and joins exons via the spliceosome—alternative splicing allows one gene to encode multiple protein variants

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Translation: Building the Polypeptide

Translation occurs at the ribosome and involves three distinct phases. Each phase requires specific factors, energy input, and precise molecular recognition between codons and anticodons.

Translation Initiation

• Start codon (AUG) signals where translation begins and codes for methionine—every eukaryotic protein initially starts with Met
• Small ribosomal subunit binds first, scanning for AUG; the large subunit joins after initiator tRNA is positioned
• GTP hydrolysis powers the assembly process—initiation factors (eIFs in eukaryotes) coordinate the complex formation

Translation Elongation

• Aminoacyl-tRNA enters the A site, matching its anticodon to the mRNA codon—this codon-anticodon pairing ensures fidelity
• Peptidyl transferase (a ribozyme within the large subunit) catalyzes peptide bond formation between amino acids
• Translocation moves the ribosome one codon forward, shifting tRNAs from A→P→E sites—requires EF-G and GTP hydrolysis

Translation Termination

• Stop codons (UAA, UAG, UGA) have no corresponding tRNAs—they're recognized by release factors instead
• Release factors trigger hydrolysis of the bond between the polypeptide and the final tRNA, freeing the completed chain
• Ribosome dissociation separates the subunits, releasing mRNA for potential reuse or degradation by cellular machinery

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Protein Maturation: Functional Finishing

A polypeptide chain isn't necessarily a functional protein. Post-translational modifications fine-tune activity, direct localization, and enable regulation.

Post-Translational Modifications

• Phosphorylation (adding $PO_4^{3-}$ groups) is reversible and commonly regulates enzyme activity—kinases add, phosphatases remove
• Glycosylation attaches carbohydrate chains, crucial for membrane proteins and secreted proteins—affects folding, stability, and cell recognition
• Ubiquitination tags proteins for degradation by the proteasome—this is how cells control protein lifespan and remove misfolded proteins

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Quick Reference Table

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Self-Check Questions

1. Which two stages of protein synthesis require GTP hydrolysis, and what specific processes does the energy power in each case?

2. Compare and contrast the functions of the 5' cap and poly-A tail—how do both contribute to successful gene expression?

3. If a mutation prevented spliceosome function, what would happen to the mRNA and the resulting protein?

4. A ribosome reaches a UAG codon. Explain why no tRNA binds and describe the molecular events that follow.

5. How do phosphorylation and ubiquitination differ in their typical effects on protein function? Give a scenario where each would be biologically important.