BIOL 2025 Lab #9 Name_______________
Proteomics: Protein Profiles of Fish Muscle Tissue
In this lab you will use protein gel electrophoresis, the technique most widely used in
Biotechnology research, to examine muscle proteins from closely and distantly related fish
species, and to identify similarities and differences in these organisms’ protein profiles
(fingerprints). Muscle protein consists mainly of actin and myosin, but numerous other proteins
also make up muscle tissue. While actin and myosin are highly conserved across all animal
species, the other proteins are more diverse, varying even among closely related species.
Proteomics and Evolution
Proteomics is the study of proteins, particularly their structures and functions. This term
was coined to make an analogy with genomics, and while it is often viewed as the "next
step", proteomics is much more complicated than genomics. Most importantly, while the
genome is a rather constant entity, the proteome differs from cell to cell and is constantly
changing through its biochemical interactions with the genome and the environment. One
organism will have radically different protein expression in different parts of its body, in
different stages of its life cycle, and in different environmental conditions. The entirety of
proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of
proteins found in a particular cell type under a particular type of stimulation, are referred to as
the proteome of the organism or cell type, respectively.
Variations in an organism’s proteins may reflect physiological adaptations to an ecological
niche and environment, but they originate as chance DNA mutations. Such random mutation
events, if favorable, persist through the natural selection process and contribute to the
evolution of new species – with new specialized functions. The discovery of the chemical
structure of DNA by Watson, Crick, Wilkins, and Franklin and our understanding of how the
triplet code of nitrogen bases leads to the synthesis of proteins (which is the phenotypic
expression) convinced us that adaptations are the result of changes in the DNA code
(mutations). However, current research in the field of proteomics is leading some scientists to
question whether or not DNA is the final determining factor in the synthesis of proteins and thus
the determining factor in evolution.
Proteomics was initially defined as the effort to catalog all the proteins expressed in all cells
at all stages of development. That definition has now been expanded to include the study
of protein functions, protein-protein interactions, cellular locations, expression levels, and
posttranslational modifications of all proteins within all cells and tissues at all stages of
development.
Protein Electrophoresis and SDS - PAGE
Polyacrylamide gel electrophoresis (PAGE) can be used to separate small molecules such
as proteins. Understanding protein structure is important to understanding how we can use
PAGE for protein analysis. Proteins are made of smaller units (monomers) called amino acids.
There are 20 common amino acids. The sequence and interaction between these different
amino acids determine the function of the protein they form. Amino acids are joined together by
