Central dogma: the story of life RNA DNA Protein

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

DNA structure Atomic structure Double helix

The basic unit in DNA A T GC

From DNA to Protein 1. Transcription 2. Translation

Step1: Transcription, generation of mRNA

Amino acid carrier: tRNA Step2: Translation, protein assembly

Peptide bond formation Peptide Chain

Protein structure Primary Secondary Tertiary Quaternary

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

Proteins are the molecule tools for most cellular functions

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

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.

Bioinformatics - History 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….

Introduction to proteomics

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

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

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

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.

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)

Why Proteomics?

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

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

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.