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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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proteomics

Proteomics

Lecture 1

Introduction to Proteomics and Protein Chemistry

By Ms Shumaila Azam

from dna to protein
From DNA to Protein

1. Transcription

2. Translation

step2 translation protein assembly
Step2: Translation, protein assembly

Amino acid carrier: tRNA

protein structure

Primary

Secondary

Tertiary

Quaternary

Protein structure
the bonds contribute to protein structure

1. Hydrogen bond

2. Hydrophobic interaction

3. Ionic bond

4. Disulfide bond

The bonds contribute to protein structure
what is bioinformatics
What is “bioinformatics”?

Let’s take minutes to see the hot topic” bioinformatics

what is bioinformatics1
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.
slide14

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….
what s 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
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
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 proteomics1
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 = 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)
differential protein expression
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

what proteomics can answer
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
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.