L12 - Proteomics

Intro to Bioinformatics

bioinformatics - a scientific subdiscipline that involves computer tech to collect, store, analyze, and disseminate biological data and info such as DNA and amino sequences, etc.

Applications include:

  • id new drug targets

  • understanding disease mechanisms

  • designing new drugs

  • predicting interactions btwn compound and enzyme

  • predicting drug responses/safety

  • streamlining clinical trials

  • shortening timeline and reducing cost of drug development

  • reducing risk of side effects

  • fostering growth of personalized medicine

Bioinformatics Tools:

  • Databases - sequence storage

    • archival - genbank

    • curated - uniprot

  • computational models - mathematical models to describe biological systems

  • software

    • sequence alignment

    • function analysis

    • image analysis

    • clinical

  • machine learning

    • protein structure predictions

    • drug response predictions

UniProt - Knowledgebase has lots of info

Techniques used to determine protein conformation:

  • x-ray crystallography - uses diffracted x-rays from a protein crystal to generate electron density map, indicating the atomic positions of the protein (only for those that can readily crystallize)

  • NMR spectroscopy - reveals structure + dynamics of proteins in solution by iding protons in close proximity

  • Cryo-electron microscopy - a rapidly developing method that can elucidate the structures of large multimeric complexes at increasingly higher resolutions

Protein Structure Prediction

  • one the most important goals of computational biology (very challenging)

  • Approaches:

    • Ab initio - without prior knowledge; calculations that attempt to minimize the free energy of a structure

    • Knowledge-based - an unknown primary structure is examined for compatibility with known protein structures/fragments

Predictions + Analysis of 3D biomolecules

blah blah blah

Proteomics encompasses the large-scale study of proteins, particularly their functions and structures, utilizing advanced techniques such as mass spectrometry and bioinformatics to elucidate protein interactions and modifications.

Genomics is the study of a person’s genes

Methods for sequencing DNA

  • Sanger (Dideoxy) sequencing - uses DNA polymerase + chain-terminating nucleotides (dideoxyribonucleoside triphosphates) to block further elongation of a DNA strand once incorporated

    • does not have the 3’ OH that would have allowed extension

  • Next Generation Sequencing (NGS) - Illumina; allows sequencing of millions of DNA molecules simultaneously

    • high speed, reduced costs

    • whole genome can be broken into millions of fragments then sequences are amplified on a surface w/ covalently attached linkers

  • RNA-seq - detects the presence and quantitation of all the RNA molecules in a cell under specific conditions

    • step 1: isolate RNA from cell/tissue of interest

    • step 2: select for RNA by filtering for sequences containing poly(A) tails

    • step 3: synthesize cDNA using reverse transcriptase

    • step 4: sequence cDNA using NGS

    • step 5: using computational algorithms to assemble the sequencing data