Information about Proteome
The term proteome was coined by Mark Wilkins first in 1994 in the symposium: "2D Electrophoresis: from protein maps to genomes" in Siena, Italy, and was subsequently published in 1995 (1), which was part of his PhD thesis. The term proteome is a blend
of proteins and genome and Wilkins used it to describe the entire complement of proteins expressed by a genome, cell, tissue or organism. Subsequently this term has been specified to contain all the expressed proteins at a given time point under defined conditions.
The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome.
The proteome is larger than the genome, especially in eukaryotes, in the sense that there are more proteins than genes. This is due to alternative splicing of genes and post-translational modifications like glycosylation or phosphorylation.
Moreover the proteome has at least two levels of complexity lacking in the genome. When the genome is defined by the sequence of nucleotides, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins.
Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis. In the first dimension, the proteins are separated by isoelectric focusing, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight using SDS-PAGE. The gel is dyed with Coomassie Blue or silver to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.
The mass spectrometer has augmented proteomics. Peptide mass fingerprinting identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a non-reactive gas, and then cataloguing the fragment ions produced.
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The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organism's complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term "proteome" has also been used to refer to the collection of proteins in certain sub-cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome.
The proteome is larger than the genome, especially in eukaryotes, in the sense that there are more proteins than genes. This is due to alternative splicing of genes and post-translational modifications like glycosylation or phosphorylation.
Moreover the proteome has at least two levels of complexity lacking in the genome. When the genome is defined by the sequence of nucleotides, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of (1) the structure of the proteins in the proteome and (2) the functional interaction between the proteins.
Proteomics, the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis. In the first dimension, the proteins are separated by isoelectric focusing, which resolves proteins on the basis of charge. In the second dimension, proteins are separated by molecular weight using SDS-PAGE. The gel is dyed with Coomassie Blue or silver to visualize the proteins. Spots on the gel are proteins that have migrated to specific locations.
The mass spectrometer has augmented proteomics. Peptide mass fingerprinting identifies a protein by cleaving it into short peptides and then deduces the protein's identity by matching the observed peptide masses against a sequence database. Tandem mass spectrometry, on the other hand, can get sequence information from individual peptides by isolating them, colliding them with a non-reactive gas, and then cataloguing the fragment ions produced.
See also
External links
- The Proteome Society
- Bioinformatics Journal
- Grid Computing of the Human Proteome
- Databases: PIR | Swissprot | Pfam
Proteins |
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19th century - 20th century - 21st century
1960s 1970s 1980s - 1990s - 2000s 2010s 2020s
1992 1993 1994 - 1995 - 1996 1997 1998
Year 1995 (MCMXCV
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1960s 1970s 1980s - 1990s - 2000s 2010s 2020s
1992 1993 1994 - 1995 - 1996 1997 1998
Year 1995 (MCMXCV
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Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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hormone (from Greek όρμή - "to set in motion") is a chemical messenger that carries a signal from one cell (or group of cells) to another. All multicellular organisms produce hormones (including plants - see phytohormone).
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In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA.
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In biology the genome of an organism is its whole hereditary information and is encoded in the DNA (or, for some viruses, RNA). This includes both the genes and the non-coding sequences of the DNA.
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Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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For a non-technical introduction to the topic, see .
A gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions...... Click the link for more information.
Alternative splicing is the RNA splicing variation mechanism in which the exons of the primary gene transcript, the pre-mRNA, are separated and reconnected so as to produce alternative ribonucleotide arrangements.
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Post-translational modification (PTM) is the chemical modification of a protein after its translation. It is one of the later steps in protein biosynthesis for many proteins. A protein (also called a polypeptide) is a chain of amino acids.
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Glycosylation is the process or result of addition of saccharides to proteins and lipids. The process is one of four principal co-translational and post-translational modification steps in the synthesis of membrane and secreted proteins and the majority of proteins synthesized in
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Phosphorylation is the addition of a phosphate (PO4) group to a protein molecule or a small molecule. Another way to define it would be the introduction of a phosphate group into an organic molecule.
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A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. In the most common nucleotides the base is a derivative of purine or pyrimidine, and the sugar is the pentose (five-carbon sugar) deoxyribose or ribose.
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Protein structure, from primary to quaternary structure.]] Biochemistry refers to four distinct aspects of a protein's structure:
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- Primary structure - the amino acid sequence of the peptide chains.
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Proteomics is the large-scale study of proteins, particularly their structures and functions.[1][2] Proteins are vital parts of living organisms, as they are the main components of the physiological pathways of cells.
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DNA electrophoresis apparatus - An agarose gel is placed in this buffer-filled box and electrical current is applied via the power supply to the rear. The negative terminal is at the far end (black wire), so DNA migrates towards the camera.
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Isoelectric focusing, also known as electrofocusing, is a technique for separating different molecules by their electric charge differences. It is a type of zone electrophoresis, usually performed in a gel, that takes advantage of the fact that a molecule's charge changes
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molecular mass (abbreviated Mr) of a substance, formerly also called molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal to 1/12 the mass of one atom of carbon-12).
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SDS-PAGE, officially sodium dodecyl sulfate polyacrylamide gel electrophoresis, is a technique used in biochemistry, genetics and molecular biology to separate proteins according to their electrophoretic mobility (a function of length of polypeptide chain or molecular weight
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Coomassie (also known as Coomassie Blue, Brilliant Blue, Brilliant Blue G, Acid Blue 90, C.I. 42655, or Brilliant Blue G 250) is a blue dye commonly used in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE).
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Silver (IPA: /ˈsɪlvə(ɹ)/) is a chemical element with the symbol Ag (Latin: argentum) and atomic number 47.
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Mass spectrometry (previously called mass spectroscopy ()[1] or informally, "mass-spec" and MS) is an analytical technique used to measure the mass-to-charge ratio of ions.
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Peptide mass fingerprinting (PMF) (also known as protein fingerprinting) is an analytical technique for protein identification that was developed 1993 by several groups independently.
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In the field of bioinformatics, a sequence database is a large collection of DNA, protein, or other sequences stored on a computer. A database can include sequences from only one organism, as in databases including all the proteins in Saccharomyces cerevisiae, or it can include
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ion is an atom or molecule which has lost or gained one or more electrons, making it positively or negatively charged. A negatively charged ion, which has more electrons in its electron shells than it has protons in its nuclei, is known as an anion
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Proteomics is the large-scale study of proteins, particularly their structures and functions.[1][2] Proteins are vital parts of living organisms, as they are the main components of the physiological pathways of cells.
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Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically, the study of their small-molecule metabolite profiles.
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Cytomes are the cellular systems, subsystems, and functional components of the body. The cytome is the collection of the complex and dynamic cellular processes (structure and function) underlying physiological processes.
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