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

Amino acids03:42

Amino acids

105.3K
Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...
105.3K
Amino Acid Catabolism01:18

Amino Acid Catabolism

1.1K
Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...
1.1K
Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

1.2K
Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
1.2K
Factors Affecting Drug Biotransformation: Physicochemical and Chemical Properties of Drugs01:21

Factors Affecting Drug Biotransformation: Physicochemical and Chemical Properties of Drugs

752
A drug's physicochemical properties fundamentally influence its metabolism. For instance, a drug's molecular size and shape critically determine its interaction with enzymes and transporters — larger drugs may face difficulty reaching enzyme active sites, altering their metabolic pathways. The pKa of a drug, which establishes its ionization state, can impact its solubility and absorption, thereby influencing metabolism.
The drug's acidity or basicity is essential in...
752
Factors Affecting Renal Clearance: Drug's Physicochemical Properties and Plasma Levels01:31

Factors Affecting Renal Clearance: Drug's Physicochemical Properties and Plasma Levels

598
Renal clearance of a drug is influenced by various factors, including its physicochemical properties and plasma levels. These factors play a significant role in determining how efficiently the kidneys eliminate a drug.
One important factor is the drug's molecular size. The kidneys readily excrete smaller molecules below 300 Daltons (Da). On the other hand, molecules weighing between 300 and 500 Da are excreted through both urine and bile. Larger molecules above 500 Da tend to be excreted...
598
Physical Properties of Carboxylic Acids01:31

Physical Properties of Carboxylic Acids

6.3K
Carboxylic acids with lower molecular weight exhibit a sharp and unpleasant odor. They also have higher boiling and melting points than analogous compounds, such as aldehydes, ketones, and alcohols.
6.3K

You might also read

Related Articles

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

Sort by
Same author

Forty new genomes shed light on sexual reproduction and the origin of tetraploidy in Microsporidia.

PLoS biology·2025
Same author

Myxozoan parasite genomes assembled from contaminated host data reveal extensive gene order conservation and rapid sequence evolution.

G3 (Bethesda, Md.)·2025
Same author

Disentangling cobionts and contamination in long-read genomic data using sequence composition.

G3 (Bethesda, Md.)·2024
Same author

Automated Removal of Non-homologous Sequence Stretches with PREQUAL.

Methods in molecular biology (Clifton, N.J.)·2020
Same author

Ambiguity Coding Allows Accurate Inference of Evolutionary Parameters from Alignments in an Aggregated State-Space.

Systematic biology·2020
Same author

Estimating Phylogenies from Shape and Similar Multidimensional Data: Why It Is Not Reliable.

Systematic biology·2020

Related Experiment Video

Updated: Jan 30, 2026

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

3.1K

Physicochemical Amino Acid Properties Better Describe Substitution Rates in Large Populations.

Claudia C Weber1,2, Simon Whelan3

  • 1Center for Computational Genetics and Genomics, Department of Biology, Temple University, Philadelphia, PA.

Molecular Biology and Evolution
|January 23, 2019
PubMed
Summary

Codon substitution models better explain evolution by distinguishing radical and conservative amino acid changes. This approach is more effective for large populations, suggesting stronger selection against radical changes.

Keywords:
effective population sizemutation–selection modelphylogenomicsprotein evolutionsubstitution models

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

8.8K
Evaluation of Amino Acid Consumption in Cultured Bone Cells and Isolated Bone Shafts
06:32

Evaluation of Amino Acid Consumption in Cultured Bone Cells and Isolated Bone Shafts

Published on: April 13, 2022

2.1K

Related Experiment Videos

Last Updated: Jan 30, 2026

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

3.1K
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

8.8K
Evaluation of Amino Acid Consumption in Cultured Bone Cells and Isolated Bone Shafts
06:32

Evaluation of Amino Acid Consumption in Cultured Bone Cells and Isolated Bone Shafts

Published on: April 13, 2022

2.1K

Area of Science:

  • Evolutionary Biology
  • Molecular Evolution
  • Bioinformatics

Background:

  • Most codon substitution models do not account for the chemical differences between amino acids, treating all nonsynonymous changes equally.
  • Existing methods categorize substitutions as radical or conservative, but their impact on evolutionary models is not fully understood.

Purpose of the Study:

  • To develop and test a parametric codon model that differentiates between radical and conservative amino acid substitutions.
  • To assess whether this new model improves the description of sequence evolution, particularly regarding selection against radical changes.

Main Methods:

  • Proposed a parametric codon model incorporating distinctions between radical and conservative amino acid substitutions.
  • Applied the new model to diverse phylogenomic data from populations of varying sizes.
  • Compared the performance of the new model against simpler codon models and standard amino acid models.

Main Results:

  • The proposed model, distinguishing radical from conservative substitutions, significantly improved model fit for large populations.
  • No significant improvement was observed for smaller populations, where genetic drift may obscure selection effects.
  • For large populations, models incorporating amino acid exchangeability were favored, while smaller populations relied more on genetic code structure.

Conclusions:

  • Selection against radical amino acid substitutions is more pronounced in large populations.
  • The effectiveness of evolutionary models is linked to population size and the relative influence of selection versus genetic drift.
  • Life history traits of phylogenetic groups are crucial for selecting appropriate evolutionary models.