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Biochemistry-II - Protein Synthesis

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    Study Guide Biochemistry - II – Protein Synthesis 1. Fidelity in tRNA Aminoacylation Why Accuracy in Aminoacylation Matters Before protein synthesis can begin, each tRNA must be attached to the correct amino acid . This process is called aminoacylation . Accuracy here is critical because: • The ribosome does not check which amino acid is attached to a tRNA • If a tRNA carries the wrong amino acid, that mistake will be built directly into the protein • Even small errors can produce harmful or nonfunctional proteins Aminoacyl - tRNA Synthetases Aminoacylation is carried out by enzymes called aminoacyl - tRNA synthetases . Important points: • There are 20 different synthetases , one for each amino acid in the genetic code • Each enzyme recognizes: o One specific amino acid o One or more specific tRNAs for that amino acid These enzymes are responsible for maintaining the accuracy of translation . Step 1: Formation of Aminoacyl Adenylate In the first step: • The correct amino acid reacts with ATP • This forms an aminoacyl adenylate intermediate • Inorganic pyrophosphate ( PPi) is released

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    Study Guide The pyrophosphate is quickly broken down into phosphate by inorganic pyrophosphatase . This breakdown helps drive the reaction forward. The aminoacyl adenylate is a high - energy intermediate . Step 2: Transfer to tRNA In the second step: • The amino acid is transferred from the aminoacyl adenylate to the acceptor end of tRNA • The amino acid attaches to the terminal adenosine (A) of the CCA sequence • No additional ATP is required for this step The final product is a correctly charged aminoacyl - tRNA .

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    Study Guide Figure 1 Editing: Preventing Mistakes Even with careful recognition, errors can occur — especially with chemically similar amino acids . To prevent these errors: • Aminoacyl - tRNA synthetases have a second active site • This site performs an editing function

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    Study Guide If an incorrect amino acid is attached to a tRNA: • The enzyme recognizes the mistake • The incorrect aminoacyl - tRNA is cleaved • Free amino acid and free tRNA are released Figure 2 Why Editing Is Essential Because: • The ribosome treats all charged tRNAs the same • A mischarged tRNA would be used without question • This could lead to faulty proteins Editing ensures that only correctly charged tRNAs enter protein synthesis. Energy Cost vs Accuracy The editing process creates a “futile cycle” :

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    Study Guide • Energy is used to form a bond • That bond is then broken if it is incorrect This is similar to: • The 3′ – 5′ exonuclease proofreading activity of DNA polymerase during DNA replication Although energy is wasted: • The cost is small compared to the danger of errors • High fidelity in information processing is essential for survival Key Takeaways Fidelity in tRNA aminoacylation is ensured by: • Highly specific aminoacyl - tRNA synthetases • A two - step, ATP - dependent reaction • An editing mechanism that removes incorrect amino acids This accuracy protects the cell from dangerous mistakes and ensures reliable protein synthesis , even at the cost of extra energy. 2. Initiation of Protein Synthesis Choosing the Correct Starting Point Protein synthesis must begin at the correct position on mRNA . In most cases, the start codon is AUG , and almost all proteins begin with the amino acid methionine . However, AUG can also appear inside a gene . Therefore, cells need a way to: • Recognize which AUG starts translation • Distinguish it from AUG codons that appear later in the message

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    Study Guide 2.1 Ribosomes and Their Subunits In prokaryotes, ribosomes consist of two subunits : • 30S (small subunit) • 50S (large subunit) Together, they form a 70S ribosome . The “S” values refer to how fast particles sediment in a centrifuge; they are not additive . Functions of the subunits: • 30S subunit → decoding and mRNA – tRNA interactions • 50S subunit → peptide bond formation Before initiation begins, the ribosome exists as separate subunits . Where Initiation Begins Translation begins at the 5′ end of the mRNA . Because transcription occurs in the 5′ → 3′ direction , bacteria can: • Begin translating mRNA before transcription is finished This coupling of transcription and translation plays an important role in gene regulation in bacteria. Special Initiator tRNA Protein synthesis begins with a special initiator tRNA , called tRNA ᵐᵉᵗᴵ (I = initiator) Key features: • In bacteria, this tRNA carries N - formylmethionine (fMet) • The formyl group is added from formyl - tetrahydrofolate • This initiator tRNA: o Recognizes only start codons o Does not insert methionine at internal AUG codons

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    Study Guide The formyl group ensures that: • fMet can be placed only at the amino (N - terminal) end of the protein 2.2 Identifying the Correct Start Codon Shine – Dalgarno Sequence (RBS) To select the correct AUG, bacteria use an additional base - pairing step. • The mRNA contains a purine - rich sequence upstream of the start codon • This sequence is called the Shine – Dalgarno sequence or ribosome - binding site (RBS) • The RBS base - pairs with the 3′ end of 16S rRNA in the 30S subunit Figure 1 After this pairing: • Translation begins at the first AUG downstream of the RBS mRNAs with stronger complementarity between: • RBS and 16S rRNA are translated more efficiently This provides a mechanism for translational control .

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