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Amino acids

Amino acids

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...

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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...

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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...

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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...

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Proteins are polymers of amino acids linked together by peptide bonds. Proteins and polypeptides are interchangeably used to refer to long chains of amino acids. However, polypeptides have a molecular weight of fewer than 10,000 daltons, while proteins have greater molecular weight. Polypeptides with less than 20 amino acids are called oligopeptides or simply peptides. Interactions among the constituent amino acid side chains of proteins help them fold into a stable 3-dimensional...

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Related Experiment Video

Updated: Jul 29, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

aaHash: recursive amino acid sequence hashing.

Johnathan Wong¹, Parham Kazemi¹, Lauren Coombe¹

¹Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada.

Biorxiv : the Preprint Server for Biology

|May 22, 2023

Summary

This summary is machine-generated.

aaHash is a new hashing algorithm for amino acid sequences. It is ~10X faster than generic methods, improving bioinformatics applications for protein sequences.

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Published on: February 6, 2020

Area of Science:

Bioinformatics
Computational Biology
Biochemistry

Background:

Generic string hashing algorithms are not optimized for bioinformatics, particularly for complex amino acid sequences.
Existing methods fail to capture the biochemical similarities and context inherent in protein sequences.
There is a need for domain-specific hashing algorithms to enhance bioinformatics tools for protein analysis.

Approach:

We developed aaHash, a recursive hashing algorithm specifically designed for amino acid sequences.
aaHash employs multiple hash levels to encode biochemical similarities between amino acids.
This approach allows for more sensitive and efficient representation of protein sequence data.

Key Points:

aaHash significantly accelerates the hashing of adjacent k-mers, achieving approximately 10X speed improvement over generic algorithms.
The algorithm's multi-level hashing effectively represents biochemical properties of amino acids.
This specialized hashing enhances the performance of bioinformatics applications dealing with protein sequences.

Conclusions:

aaHash offers a substantial performance improvement for k-mer hashing in protein sequence analysis.
The algorithm's ability to represent biochemical similarities enhances sensitivity in bioinformatics tasks.
aaHash provides a valuable tool for accelerating and improving protein sequence-based research.