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Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...

From DNA to Protein

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

tRNA Activation

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...

tRNA Activation

tRNA Activation

Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...

Translation

Translation

Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life

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Related Experiment Video

Updated: Jun 7, 2026

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

Published on: August 1, 2016

Translationally optimal codons associate with aggregation-prone sites in proteins.

Yaelim Lee¹, Tong Zhou, Gian Gaetano Tartaglia

¹Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.

|November 4, 2010

Summary

Optimal codons associate with aggregation-prone residues across diverse organisms. This suggests optimal codon usage may reduce translation errors or speed up protein synthesis at these sites.

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Last Updated: Jun 7, 2026

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

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Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

Area of Science:

Genomics
Molecular Biology
Biophysics

Background:

Codon usage bias influences protein synthesis efficiency.
Amino acid properties like aggregation propensity affect protein folding and function.
Previous studies linked translationally optimal codons to buried residues.

Purpose of the Study:

To investigate the relationship between codon usage bias and residue aggregation propensity.
To determine if optimal codons are associated with aggregation-prone sites in various organisms.
To explore the combined influence of aggregation propensity and solvent accessibility on codon usage.

Main Methods:

Analysis of genomic data from Escherichia coli, yeast, fly, mouse, and Halobacterium species NRC-1.
Application of the Mantel-Haenszel procedure to assess codon-residue associations.
Integration of aggregation propensity and solvent accessibility data.

Main Results:

Translationally optimal codons were found to associate with aggregation-prone residues.
This association was observed in both buried and exposed sites.
Aggregation propensity and solvent accessibility appeared to have independent, comparable effects on codon usage.

Conclusions:

Optimal codon usage may be linked to managing aggregation-prone sites during translation.
This could involve reducing translation errors or facilitating rapid synthesis of aggregation-prone regions.
Further research is needed to fully elucidate the functional implications.