Central dogma: the story of life

RNA

DNA

Protein

Proteomics

Lecture 1Introduction to Proteomics and

Protein ChemistryBy Ms Shumaila Azam

DNA structure

Atomic structure Double helix

The basic unit in DNA

AT 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

SecondaryTertiary

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

TYPE FUNCTION EXAMPLE Structural proteins Support Collagen, Elastin,

Keratin Storage proteins Storage of amino acid Ovalbumin,

Casein Transport proteins Transport of other

substrate Hemoglobin

Hormonal proteins Coordination of and organism’s activities

Insulin

Receptors proteins Response of cell to chemical stimuli

Receptor in nerve transmit route

Contractile proteins Movement Actin, Myosin Defensive proteins Protecton against

disease Antibodys

Enzymatic proteins Selective acceleraton of chemical reactions

Trypsin, ATPase, GAPDH

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

1980

2005

2000

1990

1985

1995

Single StructuresModeling & GeometryForces & SimulationDocking

Sequences, Sequence-Structure Relationships

AlignmentStructure PredictionFold recognition

GenomicsDealing with many sequencesGene finding & Genome Annotation Databases

Integrative AnalysisExpression & Proteomics DataData miningSimulation 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 RNA Protein

Transcription Translation

x1 x4

DNA RNA Protein

Transcription Translation

x3

Stimulus

DNA RNA Protein

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.