So, you’re interested in learning more about proteomics!?
Maybe you heard the term on the news or in a lecture hall and you would like to learn more about proteomics? Or maybe you ran across the topic in a google search while researching something entirely different? Either way, welcome to our Proteomics 101 for everyone blog post series! Our first post will start with some basics for those of you who are not trained in science, but future posts will quickly ramp up to help everyone understand proteomic concepts. If you have questions, suggestions or comments, please contact us at email@example.com.
What is a proteome?
It basically means all the proteins that are found in a cell, tissue or organism. The term “proteome” was coined in the 1990s to describe the full set of proteins expressed in a cell by a genome (DNA in the nucleus of a cell).
What does “proteomics” mean?
Proteomics is a way of identifying which proteins are in a sample and often how much of each protein is present. Although proteomics first meant the study of all proteins in a proteome, it is now used more generally to include the identification and/or quantitation of a set of proteins from cells, tissues, affinity purifications (where a subset of proteins are purified in some way), and/or subcellular structures, etc.
Ok, what are proteins again?
Proteins are basically long strings of amino acids (building blocks that your body makes or you eat). Proteins are large biological molecules that perform many functions in cells. They are built from amino acids which are put together in a specific sequence and with directionality; you can think of them like a beads on a string for now (although proteins fold into more complex structures in cells). The sequence of amino acids is determined by messenger RNA, which is encoded by the DNA in cells (See figure). Short strings of amino acids are called peptides and longer ones are called proteins. Proteins have many functions in the cell including structural and active roles, i.e. proteins are sometimes building blocks and other times they are enzymes (proteins that can perform chemical reactions on other proteins or small molecules in the cell).
Figure key. Left: DNA sequence is transcribed to messenger RNA sequence which is translated to a sequence of amino acids in a protein. The DNA, RNA and protein all have directionality, i.e. one end of the sequence is chemically distinguishable from the other end (like the ends of an arrow are distinguishable). Middle: Cartoon of DNA and protein structures. Right: Analogy of car design, engineer and car manufacturing (see below).
Proteins are designed and produced in cellular factories, much like cars are designed and produced in car factories. If you’re new to thinking about proteins and proteomics, it might help to think about proteins being like cars. The protein amino acid sequence is defined by the cell’s DNA, much like cars are imagined by designers. Engineers then translate the car design to the factory, much like messenger RNA carries the protein design to the ribosome (place in cell where proteins are made). The amino acids are assembled into a sequence at the ribosome, like a car frame is built in an assembly line in a factory. We’ll come back to this analogy later after we explain more about proteins.
What happens after a protein is made?
Proteins are processed in different ways depending on their job in the cell. After proteins are made (translated from messenger RNA to protein), they are processed in a few different ways depending on their ultimate function in the cell. Proteins can be trimmed or cut into smaller pieces by enzymes called proteases. Second, enzymes can modify the ends (termini) of proteins and/or individual amino acid residues within proteins, creating modified proteins. These modifications are called post-translational modifications (PTMs). Proteins that are modified with different PTMs typically have specific functions in the cell, e.g. PTMs can determine whether a protein is destroyed, whether it becomes active, where it localizes in the cell or any number of other signals. You can think about protein modifications like flags on a protein, deciding protein fate and function. PTMs create broad diversity, expanding the proteomic world by creating new protein forms (We will expand on PTMs in a future Proteomics 101 for everyone blog post).
Proteins are changed by processing and modification like cars are customized for specific functions. There are different kinds of cars and each of them can be customized, much like there are many different proteins in the cell and each of them can be modified. In the case of proteins, diversity comes from the many different protein sequences and customization can mean cutting into smaller pieces or some kind of PTM that affects how the protein works. Analogously, cars come in all shapes and sizes and can be customized in lots of ways (specific paint color, sunroof, leather seats, snow tires, etc). Car customization impacts how a car looks and what a car can do just like protein modifications and processing affect how a protein works. For example, a car equipped with snow tires can handle snowy road conditions much better than a car without snow tires, much like a protein with a specific PTM is better able to do a specific job in the cell.
What makes proteomics exciting?
Proteins and protein forms are involved in disease, making proteomics a hotbed for biomarker identification, directly impacting human health. The sheer number of proteins (tens of thousands) produced in each cell is amazing and each of these proteins has specific work to do in the cell. Loss or gain of protein function due to changes in protein modification state, cellular localization, protein abundance or enzyme activity can lead to disease. So, understanding what proteins and protein forms are present in a cell, tissue or organism is an important foundation for development of novel therapeutic drugs and better diagnostic tools.
-Proteomics is the study of proteins (often all proteins in a cell, tissue or organelle) -Proteins are a sequence of amino acid residues (dictated by DNA) -Proteins can be processed and modified (PTMs) -Proteomics is a challenging, but rewarding field that impacts human health
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