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Central dogma: the story of life

Central dogma: the story of life. DNA. RNA. Protein. Proteomics. Lecture 1 Introduction to Proteomics and Protein Chemistry By Ms Shumaila Azam. Atomic structure. Double helix. DNA structure. A. C. T. G. The basic unit in DNA. From DNA to Protein. 1. Transcription. 2. Translation.

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Central dogma: the story of life

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  1. Central dogma: the story of life DNA RNA Protein

  2. Proteomics Lecture 1 Introduction to Proteomics and Protein Chemistry By Ms Shumaila Azam

  3. Atomic structure Double helix DNA structure

  4. A C T G The basic unit in DNA

  5. From DNA to Protein 1. Transcription 2. Translation

  6. Step1: Transcription, generation of mRNA

  7. Step2: Translation, protein assembly Amino acid carrier: tRNA

  8. Peptide bond formation Peptide Chain

  9. Primary Secondary Tertiary Quaternary Protein structure

  10. 1. Hydrogen bond 2. Hydrophobic interaction 3. Ionic bond 4. Disulfide bond The bonds contribute to protein structure

  11. Proteins are the molecule tools for most cellular functions

  12. What is “bioinformatics”? Let’s take minutes to see the hot topic” bioinformatics

  13. What is “bioinformatics”? • (Molecular)Bio – informatics • One idea for a definition? • Bioinformatics is conceptualizing biology in terms of molecules (in the sense of physical-chemistry) and then applying “informatics” techniques (derived from disciplines such as applied math and statistics) to understand and organize the information associated with these molecules, on a large-scale. • Bioinformatics is “MIS” for Molecular Biology Information. It is a practical discipline with many applications.

  14. Bioinformatics - History 1980 1985 1990 1995 2000 2005 • Single Structures • Modeling & Geometry • Forces & Simulation • Docking • Sequences, Sequence-Structure Relationships • Alignment • Structure Prediction • Fold recognition • Genomics • Dealing with many sequences • Gene finding & Genome Annotation • Databases • Integrative Analysis • Expression & Proteomics Data • Data mining • Simulation again….

  15. Introduction to proteomics

  16. What’s “proteomics” ? "The analysis of the entire protein complement expressed by a genome, or by a cell or tissue type.“ Two most applied technologies: 1. 2-D electrophoresis: separation of complex protein mixtures 2. Mass spectrometry: Identification and structure analysis

  17. Why proteomics becomes an important discipline • Significant DNA sequencing results: • 45 microorganism genomes have been sequenced and 170 more are in progress • 5 eukaryotes have been completed • Saccharomyces cerevisiae • Schizosaccharomyces pombe • Arabodopsis thaliana • Caenorhabditis elegans • Drosophilia melanogaster • Rice, Mouse and Human are nearly done However, 2/3 of all genes “identified” have no known function

  18. Only DNA sequence is not enough • Structure • Regulation • Information • Computers cannot determine which of these 3 roles DNA play solely based on sequence (although we would all like to believe they can) Those are what we need to know about proteins

  19. Introduction to Proteomics • Definitions • 1. Classical - restricted to large scale analysis of gene products involving only proteins(small view) • 2. Inclusive - combination of protein studies with analyses that have genetic components such as mRNA, genomics, and yeast two-hybrid(bigger view) • Don’t forget that the proteome is dynamic, changing to reflect the environment that the cell is in.

  20. 1 gene = 1protein? • 1 gene is no longer equal to one protein • The definition of a gene is debatable..(ORF, promoter, pseudogene, gene product, etc) • 1 gene=how many proteins? (never known)

  21. Why Proteomics?

  22. Differential protein expression Stimulus Stimulus RNA Protein DNA Transcription Translation x4 x1 Scenario 1: can be analyzed by microarray technology RNA Protein DNA Transcription Translation x3 Scenario 2: can be solved by proteomics technology RNA Protein DNA Transcription Translation x3

  23. What proteomics can answer • Protein identification • Protein Expression Studies • Protein Function • Protein Post-Translational Modification • Protein Localization and Compartmentalization • Protein-Protein Interactions

  24. General classification for Proteomics • Protein Expression comparison (beginning) • Quantitative study of protein expression between samples that differ by some variable • Structural Proteomics(simulation) • Goal is to map out the 3-D structure of proteins and protein complexes • Functional Proteomics(everything) • To study protein-protein interaction, 3-D structures, cellular localization and PTMS in order to understand the physiological function of the whole set of proteome.

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