Protein Synthesis Process

Why This Matters

Protein synthesis represents the central dogma of molecular biology—the flow of genetic information from DNA to RNA to protein. This process is foundational to virtually everything else you'll study in cell biology, from enzyme function to cell signaling to genetic disorders. When exam questions ask about gene expression, mutations, or how cells respond to their environment, they're really asking whether you understand how information encoded in DNA ultimately becomes functional proteins.

You're being tested on your ability to trace this pathway and identify where regulation, errors, or modifications can occur. The key concepts here include transcription mechanics, RNA processing, ribosome function, and post-translational control. Don't just memorize the steps in order—know what molecular machinery is involved at each stage, what could go wrong, and how cells regulate output. That's what separates a 3 from a 5.

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Information Transfer: From DNA to RNA

The first phase of protein synthesis occurs in the nucleus, where genetic information is copied from DNA into a portable RNA message. This transcription process uses complementary base pairing to create an RNA copy of a gene's coding sequence.

DNA Transcription

• RNA polymerase binds to the promoter region, unwinding DNA and synthesizing a single-stranded mRNA in the 5' to 3' direction
• Transcription factors—proteins that regulate gene expression—must assemble at the promoter before RNA polymerase can begin
• Uracil replaces thymine in the mRNA transcript, a key distinction between RNA and DNA that frequently appears on exams

mRNA Processing

• 5' cap (modified guanine) and 3' poly-A tail are added to protect mRNA from degradation and facilitate export
• Splicing removes introns (non-coding sequences) and joins exons (coding sequences) to create mature mRNA
• Alternative splicing allows one gene to produce multiple protein variants—a major source of protein diversity in eukaryotes

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Quality Control: Ensuring Accurate Export

Before mRNA can be translated, cells verify that processing is complete. This checkpoint prevents defective transcripts from wasting cellular resources or producing harmful proteins.

mRNA Export from Nucleus

• Nuclear pore complexes selectively transport only properly processed mRNA with intact 5' caps and poly-A tails
• Export proteins recognize these modifications as "passports" confirming the mRNA is ready for translation
• Regulation at export provides another control point for gene expression—blocking export effectively silences a gene

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Translation: Building the Polypeptide

Translation occurs in the cytoplasm (or on the rough ER) where ribosomes read mRNA codons and assemble amino acids into proteins. The ribosome serves as the molecular machine that coordinates mRNA reading with tRNA delivery.

Translation Initiation

• Small ribosomal subunit binds mRNA and scans for the start codon (AUG), which always codes for methionine
• Initiator tRNA carrying methionine base-pairs with AUG, establishing the reading frame for the entire protein
• Large ribosomal subunit joins to form the complete ribosome with three tRNA binding sites: A, P, and E

Elongation

• tRNA anticodons base-pair with mRNA codons, delivering specific amino acids according to the genetic code
• Peptide bonds form between amino acids via a dehydration reaction catalyzed by ribosomal RNA (ribozyme activity)
• Translocation shifts the ribosome one codon along mRNA, moving tRNAs from A→P→E sites before ejection

Termination

• Stop codons (UAA, UAG, UGA) do not code for amino acids—no tRNA can recognize them
• Release factors bind the A site when a stop codon is reached, triggering polypeptide release and ribosome disassembly
• Polyribosomes—multiple ribosomes on one mRNA—allow rapid production of many protein copies simultaneously

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Protein Maturation: Folding and Modification

A newly synthesized polypeptide isn't immediately functional. Proteins must fold into precise three-dimensional shapes and often require chemical modifications to become active.

Protein Folding

• Primary structure (amino acid sequence) determines how the protein folds into secondary, tertiary, and quaternary structures
• Chaperone proteins (like Hsp70) prevent misfolding and aggregation by shielding hydrophobic regions during folding
• Misfolded proteins can cause disease—prions in Creutzfeldt-Jakob disease, amyloid plaques in Alzheimer's—making this step clinically significant

Post-Translational Modifications

• Phosphorylation (adding $PO_4$) by kinases is the most common modification, typically activating or deactivating enzyme function
• Glycosylation (adding carbohydrates) occurs in the ER and Golgi, important for membrane proteins and secreted proteins
• Proteolytic cleavage removes signal sequences or activates inactive precursors—insulin is cleaved from proinsulin

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Protein Trafficking: Getting to the Right Place

Proteins must reach specific cellular destinations to function properly. Signal sequences act as molecular "zip codes" directing proteins to organelles, membranes, or secretion pathways.

Protein Targeting and Localization

• Signal sequences—short amino acid stretches, often at the N-terminus—direct proteins to the ER, mitochondria, nucleus, or other locations
• Signal recognition particle (SRP) binds ER signal sequences and pauses translation until the ribosome docks at the ER membrane
• Vesicular transport moves proteins through the endomembrane system (ER→Golgi→plasma membrane or lysosome)

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Regulation: Controlling Protein Output

Cells don't make all proteins at all times. Regulation at multiple levels allows cells to respond to environmental signals and maintain homeostasis.

Regulation of Protein Synthesis

• Transcriptional control (activators, repressors, enhancers) determines which genes are expressed—the primary regulation point
• miRNA and siRNA bind mRNA to block translation or trigger degradation, providing rapid post-transcriptional control
• Feedback inhibition—end products can inhibit enzymes in their own synthesis pathway or repress their own gene transcription

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Quick Reference Table

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Self-Check Questions

1. What structural features must mRNA have before it can be exported from the nucleus, and what is the function of each?

2. Compare and contrast the roles of RNA polymerase and ribosomes in protein synthesis—what does each "read" and what does each produce?

3. A mutation changes a codon from UGG to UGA. What type of mutation is this, and how would it affect the resulting protein?

4. How do chaperone proteins and post-translational modifications both contribute to protein function, and at what stage of protein synthesis does each act?

5. If an FRQ asks you to explain how a cell could increase production of a specific protein in response to a hormone signal, what three levels of regulation could you discuss?