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Stanford CS 374 - Biological Background for Computer Scientists

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CS 374 Fall 2005 Lecture 1Lecture 1: Introduction to Algorithms in Biology.Lecturer: Prof. Serafim BatzoglouTeaching Assistant: Relly BrandmanScribe: Abhishek RathodTable of Contents1.>Biological Background for Computer Scientists1.1>Cell and its Components1.2.>The nucleic acids DNA and RNA.2.>The two ideas that drove Biology of the 20 th century 2.1>Evolution2.2>Central Dogma3.>Experimental Methods3.1>Gene Mapping and Sequencing3.2>Microarray technology and clustering3.2.1>Technology3.2.2>Applications4.>Computational Biology4.1> Protein related problems4.1.1>Determining Protein Structure and its classification4.1.2>Levels of protein structure:4.1.3>Computational Problems in Protein structure4.2> DNA related problems4.2.1>What is sequence alignment?4.2.2> Types of Sequence Alignment4.2.3>Methods of Pair-Wise Sequence Alignment4.2.4>Multiple Sequence Alignment4.2.5>Motifs and Profile Analysis4.2.6>Gene Finding4.2.7>Evolution at the DNA level4.3>Protein Interaction networks related problems4.3.1>Introduction to Protein-protein interaction network4.3.2>Computational Methods for predicting PPI5.>Applications of Computational Biology6.>References1.>Biological Background for Computer Scientists1.1>Cell and its componentsThe above image is from http://www.biosci.uga.edu/almanac/bio_103/notes/may_15.html.A>Nucleus: The nucleus occurs only in the eukaryotic cells and does not occur in theprokaryotic cells. The nucleus contains the genetic material of the cell in the form ofchromatin. Chromatin contains long stretches of DNA in a variety of conformations,surrounded by nuclear proteins. The nucleus is separated from the rest of the cell by anuclear envelope. RNA is formed in the nucleus by transcription of the DNA. Thenucleolus is the area of the nucleus where the ribosomes are constructed. Nuclear poresoccur in the nucleus allowing RNA and other molecules to pass but block the DNA frompassing.B>Cytoplasm: Cytoplasm is the name for the gel-like collection of substances inside thecell. In eukaryotic cells cytoplasm is the material between plasma membrane and nuclearenvelope. In Bacteria and Archaea, the cytoplasm contains all of the materials in the cell. Fibrous proteins that occur in the cytoplasm, referred to as the cytoskeleton maintain theshape of the cell as well as anchor organelles, moving inside the cell and control internalmovement of structures. Microtubules function in cell division and serve as a "temporaryscaffolding" for other organelles. Actin filaments are thin threads that function in celldivision and cell motility.C>Vacuoles and Vesicles: Vacuoles are single-membrane organelles that are part of theoutside of the cell. Many organisms use vacuoles as storage areas. Vesicles are muchsmaller than vacuoles and function in transport within and to the outside of the cell.D>Ribosomes; Ribosomes are large molecular complexes, composed of several proteinsand RNA molecules. The function of ribosomes is to assemble proteins. All cells,including Bacteria and Archaea have ribosomes. Ribosomes are the location where theprocess of translation of genetic information into protein occurs. Biochemically, theribosome consists of ribosomal RNA (rRNA) and some 50 structural proteins.E>Endoplasmic Reticulum: Endoplasmic Reticulum is a mesh of interconnectedmembranes that serve a function involving protein synthesis and transport. Roughendoplasmic reticulum (Rough ER) is so-named because of its rough appearance due tothe numerous ribosomes that occur along the ER. Rough ER connects to the nuclearenvelope through which the messenger RNA (mRNA) that is the blueprint for proteinstravels to the ribosomes. Smooth ER; lacks the ribosomes characteristic of Rough ER andis thought to be involved in transport and a variety of other functions.F>Mitochondria and Chloroplasts: Mitochondria and Chloroplasts are cellularorganelles involved in the production the energy that powers the cell. Mitochondria arefound in all eukaryotic cells, and their job is respiration: using oxygen to efficiently turnfood into energy the cell can use. Some bacteria and archaea get their energy by a processcalled glycolysis. This process creates two energy-carrying molecules for every moleculeof sugar consumed. As oxygen became more abundant, some organisms found a methodfor using it (called oxidative phosphorylation) to make an order of magnitude increase intheir ability to extract energy from food, getting 36 energy-carrying molecules for everysugar. These originally free living organisms were engulfed by early eukaryotes. Thissymbiosis gradually became obligatory as eukaryotes came to depend on theirmitochondria for energy, and the mitochondria came to depend on the surrounding cellfor many vital functions and materials. Mitochondria still have their own genetic materialhowever, and, in sexually reproducing organisms, are inherited only via the cytoplasm ofthe egg cell. As a consequence, all mitochondria are maternally inherited. Like themitochondria, chloroplasts appear to have originated as free-living bacteria thateventually became obligatory symbionts, and then parts of eucaryotic plant cells. Theirtask is to convert sunlight into energy-carrying molecules.G>Golgi Apparatus: The Golgi apparatus are elongated sacs that are involved in thepackaging of materials that will be exported from the cell, as well as segregatingmaterials in the cell into the correct intracellular compartment.H>Lysosomes: Lysosomes contain substances that are used to digest proteins; they arekept separate to prevent damage to other cellular components.1.2>Nucleic acids: DNA and RNADNA(The information in this section is borrowed from Online Biology Book by M J Farabee)DNA or deoxyribonucleic acid is the physical carrier of inheritance.DNA is a polymer that contains deoxyribose sugar, phosphate group and four nitrogenousbases: cytosine C, thymine T, adenine A, and guanine G. A single monomer in thispolymer is called nucleotide which is composed of a base attached to sugar and thephosphate also attached to sugar. The structure of DNA: DNA is in the form of a double helix. The helix consists of 2polydeoxynucleotide chains. Each chain is an alternating polymer of deoxyribose sugarsand phosphates that are joined together via


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Stanford CS 374 - Biological Background for Computer Scientists

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