Systems Biology Overview Dr. Shaila C. Rssle 1 Topics to be - - PowerPoint PPT Presentation
Systems Biology Overview Dr. Shaila C. Rssle 1 Topics to be discussed What is Systems Biology? History the officially start point Impact and Potential of Systems Biology Properties of Systems Biology
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Molecular cell biology. Lodish, Harvey 5 ed
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ISB website in 2003
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Proceedings of the International Syposium on Systems Theory and Biology (1968)
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– Growing influence of enginnering approaches in biology “Synthetic biology is concerned with applying the engineering paradigm of systems design to biological systems in order to produce predictable and robust systems with novel functionalities in nature” ( NEST 2008).
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– Concurrency theory methods to biological systems
approach to Systems Biology – Evolutionary computing
(Chou and Voit 2009) – Information mining approaches
– Information systems supporting various forms of collaboratories (Olson et al 2008)
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Protein in living organismsGenerally speaking, proteins do everything in the living cells. All functions of the living
That is why in bacterial cells, proteins make about a half of the dry weight of cells.Classification by protein functionsProteins are responsible for many different functions in the living cell. It is possible to classify proteins on the basis of their functions. Very often, proteins can carry few functions and such proteins can be placed into different groups, but despite this, it is possible to assign main group for each protein.Enzymes - proteins that catalyze chemical and biochemical reactions within living cell and outside. This group of proteins probably is the biggest and most important group of the proteins. Enzymes are responsible for all metabolic reactions in the living cells. Well known and very interesting examples are: DNA- and RNA-polymerases, dehydrogenases etc.Hormones - proteins that are responsible for the regulation of many processes in organisms. Hormones are usually quite small and can be classifies as peptides. Most known protein hormones are: insulin, grows factor, lipotropin, prolactin etc. Many protein hormones are predecessor of peptide hormones, such as endorfine, enkephalin etc. It is possible to increase this group of proteins by adding of all protein venoms.Transport proteins - These proteins are transporting or store some other chemical compounds and ions. Some of them are well known: cytochrome C - electron transport; haemoglobin and myoglobin - oxygen transport; albumin - fatty acid transport in the blood stream etc. It is possible to classify trance membrane protein channels as a transport proteins as well.Immunoglobulin or Antibodies - proteins that involved into immune response of the organism to neutralize large foreign molecules, which can be a part of an infection. Sometimes antibodies can act as enzymes. Sometimes this group of proteins is considered as a bigger group of protective proteins with adding such proteins as lymphocyte antigen-recognizing receptors, antivirals agents such as interferon, tumor necrosis factor (TNF). Probably the clotting of blood proteins, such as fibrin and thrombin should be classified as protective proteins as well.Structural proteins - These proteins are maintain structures of other biological components, like cells and tissues. Collagen, elastin, α-keratin, sklerotin, fibroin - these proteins are involved into formation of the whole organism body. Bacterial proteoglycans and virus coating proteins also belongs to this group of
chemical energy into mechanical energy. Actin and myosin are responsible for muscular motion. Sometimes it is difficult to make a strict separation between structural and motion proteins.Receptors These proteins are responsible for signal detection and translation into other type of signal. Sometimes these proteins are active only in complex with low molecular weight compounds. Very well known member of this protein family id rhodopsin - light detecting protein. Many receptors are transmembrane proteins.Signalling proteins - This group of proteins is involved into signalling translation process. Usually they significantly change conformation in presence of some signalling molecules. These proteins can act as enzymes. Other proteins, usually small, can interact with receptors. Classical example of this group
processes in the organism. Egg ovalbumin and milk casein are such proteins. Almost all proteins can be digested and used as a source of energy and building material by other organisms.Classification of proteins by location in the living cellProtein classification can be based on their appearance in the living cell. According to this, it is possible to classify all proteins into four main groups.Membrane or transmembrane proteins - these proteins are located within cell membrane lipid bi-layer. These proteins can be completely or partially burred in membrane.Internal proteins - these proteins are located within living cell and all functions are related with intercellular needs.External or secret proteins - these proteins are functions outside the cell they produced. Such type of proteins is more common for multicells
particle.Classification of proteins by posttranslational modificationAfter protein translation some of them are subjected to posttranslational modification. This modification can be related with many different aspects of changes. Again this classification split all proteins into overlapped groups.Native proteins - these proteins are not changed after translation.Glico-proteins - these proteins are modified by covalent binding with linear or branched
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