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Proteomics


Published on Mar 12, 2016

Abstract

Proteomics is something new in the field of biotechnology. It is basically the study of the proteome, the collective body of proteins made y a person's cells and tissues. Since it is proteins, and to a much lesser extent, other types of biological molecules that are directly involved in both normal and diseaseassociated biochemical processes, a more complete understanding of the disease may be gained by directly looking at the proteins present within a diseased cell or tissue and this is achieved through the study of the proteome, Proteomics.

For, Proteomics, we need 2-D electrophoresis equipment ot separate the proteins, mass spectrometry to identify them and x-ray crystallography to know more of the structure and function of the proteins. These equipments are essential in the study of proteomics.

From The Genome To The Proteome

Genomics has provided a vast amount of information linking gene activity with disease. It is now recognized that gene sequence information and pattern of gene activity in a cell do not provide a complete and accurate profile of a protein's abundance or its final structure and state of activity. The day of spotlight of the human genome is now coming to an end. Researchers are now concentrating on the human proteome, the collective body of all the proteins made by a person's cells and tissues.

The genome- the full set of information in the body-contains only the recipes for making proteins; it is the proteins that constitute the bricks and mortar of cells and that do most of the work. Moreover it is the proteins that distinguish the various types of cells: although all cells have essentially the same genome, they can vary in which genes are active and thus in which proteins are made. Likewise diseased cells often produce proteins that healthy cells don't and vice versa. Proteome research permits the discovery of new protein markers for diagnostic purposes and of novel molecular targets for drug discovery.

Proteins

All living things contain proteins. The structure of a cell is largely built of proteins. Proteins are complex, three-dimensional substances composed of one or more long, folded polypeptide chains. These chains, in turn, consist of small chemical units called amino acids. There are twenty kinds of amino acids involved in protein production, and any number of them may be linked in any order to form the polypeptide chain. The order of the amino acids in the polypeptide chain is decided by the information contained in DNA structure of the cell's genes.

Following this translation, most proteins are chemically changed through post-translation modification (PTM), mainly through the addition of carbohydrate and phosphate groups. Such modification plays an important role in modulating the function of many proteins but the genes do not code it. As a consequence, the information from a single gene can encode as many as fifty different protein species. It is clear that genomic information often does not provide an accurate profile of protein abundance, structure and activity.

PROTEOMICS: A DESCRIPTION OF THE METHODOLOGY

The exact definition of proteomics varies depending on whom you ask, but most of the scientists agree that it can be broken into three main activities: identifying all the proteins made in a given cell, tissue or organism; determining how these proteins join forces to form networks akin to electrical circuits; and outlining the precise three-dimensional structure of the proteins in an effort to find their Achilles’ heels-that is, where drugs might turn their activity on or off. Though the task seems straightforward, it is not as simple as it seems.

The critical pathway of proteome research includes:

Sample collection

Protein separation

Protein identification

Protein characterization

Bioinformatics

SAMPLE COLLECTION, HANDLING AND STORAGE

Access to relevant body fluid and tissue samples is fundamental to proteome research. Proteome sciences has collected a large bank of clinical samples for its cancer, neurological disease, cardiovascular disease, transplant rejection and diabetes research areas through its ongoing access to the leading hospitals where its collaborative scientists practice. All clinical samples are pathology-authenticated and are accompanied by details medical records to allow the correlation of proteome changes with disease pathology.

PROTEIN SEPARATION

The sample we have collected will have many proteins included in it. We need to separate these in order to study them. One of the main technologies used is two-dimensional gel electrophoresis. Electrophoresis is a technique used in laboratory that results in separation of charged particles and proteins in general are charged particles. Electrophoresis may be in general defined as the movement of a solid phase (the proteins in sample) with respect to a liquid (the buffer solution). The main function of the buffer is to carry the current and to keep the pH of the solution constant during migration. A solid substance called the medium supports buffer solution. Here we use a gel as the substrate.

A common material is agarose which is prepared from common seaweed. Purified agarose is in powdered form, and insoluble in water at room temperature, but is soluble in boiling water. When it starts to cool, it undergoes polymerization. The polymers crosslink and form the gel. If more agarose is added, the gel will become more firm. While solution is still hot, we pour it into a mould called casting tray so that it will assume the shape we want. For setting, gel body is immersed in deionised water. Deionised water, an insulator, prevents massive heat generation. Much higher voltage, such as 280 volts can be applied to derive rapid sample migration. Scientists add a mixture of proteins to an edge of the gel.

An electric field is applied across the gel. The gel is in the form of a mesh network. In two-dimensional electrophoresis, separation is done according to mass in one direction an according to electric field in the perpendicular direction. Each protein has an individual mass and charge. So they will separate out as individual dots in the gel. Researchers can then isolate each of these proteins for further analysis.

PROTEIN IDENTIFICATION

Mass spectrometry is a method of protein identification. The instrument used is a mass spectrometer. A mass spectrometer is an apparatus that produces a stream of charged particles from the substance being analyzed, separates the ions into a spectrum according to their mass-to-charge ratios, and determines the relative abundance of each type of ion present. Components of a mass spectrometer Functionally, all mass spectrometers perform three basic tasks: (1) creating ion fragments from sample, (2) sorting ions according to mass-tocharge ratio (3) measuring relative abundance of ion fragments of each mass. Once the ions are formed, they can be sorted based on their energy, momentum or velocity. A measurement of any two of these gives mass-tocharge ratio. Conventionally the method is to use energy and momentum:

Sample

Inlet system Ion source Mass

analyzer on collection system

Vacuum system

Data handling system











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