Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

From DNA to Protein03:06

From DNA to Protein

24.6K
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...
24.6K
Transfer RNA Synthesis02:36

Transfer RNA Synthesis

13.7K
One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
13.7K
The Central Dogma01:25

The Central Dogma

145.5K
Overview
145.5K
The Central Dogma01:20

The Central Dogma

35.4K
The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...
35.4K
DNA as a Genetic Template02:05

DNA as a Genetic Template

28.9K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
28.9K
Leaky Scanning02:28

Leaky Scanning

5.9K
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...
5.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.

PLoS genetics·2026
Same author

Quantification of the coupled dynamics of marine microbes and reactive oxygen species in laboratory batch culture experiments.

Microbiology spectrum·2026
Same author

Polygenic risk scores improve CAD risk prediction in individuals at borderline and intermediate clinical risk.

NPJ cardiovascular health·2026
Same author

An Evolving View of Species Tree Inference.

Systematic biology·2026
Same author

Potential impact of social media and COVID-19 restrictions on adult attention-deficit rates.

BJPsych bulletin·2025
Same author

Evaluating single-cell variability in proteasomal decay within Saccharomyces cerevisiae.

Biophysical journal·2025

Related Experiment Video

Updated: Apr 4, 2026

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System
11:47

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

Published on: August 1, 2016

16.5K

A codon model of nucleotide substitution with selection on synonymous codon usage.

Laura Kubatko1, Premal Shah2, Radu Herbei3

  • 1Department of Statistics, The Ohio State University, Columbus, OH 43210, United States; Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, United States.

Molecular Phylogenetics and Evolution
|September 12, 2015
PubMed
Summary

We developed a new codon substitution model for protein-coding genes that improves phylogenetic inference. This model better fits yeast gene data and provides insights into protein production rates.

Keywords:
Codon substitutionMutation–selectionPhylogeneticsProtein productionSynonymous substitution

More Related Videos

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
10:41

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

8.9K
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.4K

Related Experiment Videos

Last Updated: Apr 4, 2026

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System
11:47

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

Published on: August 1, 2016

16.5K
Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
10:41

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers

Published on: June 24, 2019

8.9K
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

Published on: February 3, 2023

1.4K

Area of Science:

  • Molecular Evolution
  • Phylogenetics
  • Computational Biology

Background:

  • Accurate phylogenetic inference from protein-coding genes relies on realistic models of codon substitution.
  • Existing models like M0 do not fully capture the complexities of codon evolution, including selection pressures on synonymous sites.

Purpose of the Study:

  • To propose and test a novel mechanistic codon substitution model.
  • This model integrates the standard M0 model with selection on synonymous substitutions influenced by nonsense error rates.

Main Methods:

  • Developed a new codon substitution model combining Yang's M0 with Gilchrist's synonymous selection model.
  • Applied the model to 104 protein-coding genes from brewer's yeast.
  • Compared model fit using the Akaike Information Criterion (AIC) against M0 and the Yang-Nielsen mutation-selection model.

Main Results:

  • The new model significantly outperformed the basic M0 model in ~85% of cases and M0 with estimated codon frequencies in ~25% of cases.
  • Model fit was comparable to the mutation-selection model in a few instances.
  • A model parameter correlated strongly with independent measures of protein production rate in yeast.

Conclusions:

  • The proposed codon substitution model offers improved accuracy for phylogenetic analysis of protein-coding genes.
  • The model's parameter provides a useful proxy for protein production rates.
  • Substitution model choice can influence estimated phylogenies, highlighting the importance of realistic modeling.