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Related Concept Videos

From DNA to Protein03:06

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...
Leaky Scanning02:28

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...
Initiation of Translation02:33

Initiation of Translation

Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
Initiation of Translation02:33

Initiation of Translation

Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
Improving Translational Accuracy02:07

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...
Improving Translational Accuracy02:07

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...

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Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation
12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

A role for codon order in translation dynamics.

Gina Cannarozzi1, Gina Cannarrozzi, Nicol N Schraudolph

  • 1Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland.

Cell
|April 21, 2010
PubMed
Summary
This summary is machine-generated.

Gene expression is influenced by codon choice. This study reveals that cells favor using the same transfer RNA (tRNA) for repeated amino acids, impacting translation speed and leaving a genomic signature.

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Last Updated: Jun 13, 2026

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Published on: July 6, 2012

Area of Science:

  • Molecular Biology
  • Genomics
  • Biophysics

Background:

  • The genetic code is degenerate, with multiple codons encoding a single amino acid.
  • Codon choice is known to affect gene expression levels.
  • The precise mechanisms and genomic implications of synonymous codon usage remain an active area of research.

Purpose of the Study:

  • To investigate whether synonymous codon usage is random or biased within coding sequences.
  • To determine if codon usage patterns correlate with transfer RNA (tRNA) availability and usage.
  • To elucidate the impact of codon correlation on translation dynamics and genomic signatures.

Main Methods:

  • Analysis of codon usage patterns in S. cerevisiae coding sequences.
  • Correlation analysis of synonymous codon occurrences and their associated tRNAs.
  • Comparative translation speed assays for correlated versus anticorrelated codon sequences.

Main Results:

  • Synonymous codon usage is non-random; subsequent codons for the same amino acid favor the same tRNA.
  • This codon-tRNA correlation is more pronounced in rapidly induced genes.
  • Codon correlation significantly accelerates translation speed compared to anticorrelated sequences.
  • Evidence suggests slower tRNA diffusion and potential tRNA channeling at the ribosome.

Conclusions:

  • The dynamics of translation leave a significant, non-random signature within the genome.
  • Codon usage bias is actively regulated to optimize translation efficiency.
  • Ribosome-associated tRNA dynamics play a crucial role in gene expression regulation.