2/6/2012

Organizing Protein Function

Gene Ontology

Level of Biological Function

Ecosystem Societal Organism Organ System Organ Tissue Cellular Biochemical Mechanistic

Controlled vocabulary for describing genes and gene products (http://www.geneontology.org/) 3 hierarchies of terms: Biological Process (B) - cellular to societal functions. Cellular Component (C) - part of the cell or its extracellular environment. Molecular Function (F) - biochemical functions like binding or catalysis.

Enzyme Commission (EC) Numbers

Numerical classification scheme for enzymes, based on the chemical reaction catalyzed. Describes biochemical and some mechanistic functions. 6 categories (hierarchies): 1. Oxidoreductases 2. Transferases 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases

Description of Function Mechanistic Biochemical

Structure Configuration and conformation Conformational Change Interactions (with matter and energy) Noncovalent Specific to particular site Nonspecific Transformations Energy and chemical Chemical Transformations (enzymes) Energy Transformations Binding Signal Transduction Allosteric interactions Changes in Concentration

Cellular & Above

Component Location Transport Pathways Signaling Metabolic

Trypsin Example
Mechanistic Serine protease with a catalytic triad of H57,D102, and S195. See SCOP Classification. D189 attracts and stabilizes positively charged K and R, SCOP Classification creating the specificity of the active site. Class: all Optimal pH of 8 and temperature of 37C. Fold: Trypsin-like serine proteases Biochemical barrel, closed; n=6, S=8; greek-key Endopeptidase (EC 3.4.21.4) that cleaves proteins/peptides duplication: consists of two domains of the same fold. at the carboxyl side of K and R, except when followed by P. Superfamily: trypsin-like serine Organ proteases Produced in the pancrease and released as a zymogen. Family: Eukaryotic proteases Organ system (digestive) Protein: Trypsin(ogen) Secreted in duodenum to hydrolize proteins/peptides into Species: Human (Homo sapiens) more absorbable units for digestion. PDB: 1H4W