What is a protein?

I keep mentioning proteins.  When I use this word, are you thinking of steak? or eggs? or protein shakes?  I am not talking about nutritional protein (though steak and eggs and protein shakes do all have protein in them), but rather the molecules in a cell that perform a ton of different functions in the cells.  Before we talk about what proteins are made of, let’s take a minute to think about what proteins do. They do a lot.  Proteins are how the cells of your body stay connected together, why and how you are able to digest food, why you are able to fend off disease, why you’re able to build up muscle and why you have energy.

protein_function

But what ARE proteins you ask?  Remember how DNA is made from a macromolecule called a nucleotide? Proteins are made from a macromolecule called an amino acid.  There are 20 different amino acids that each have different sizes and properties.  Some are hydrophobic (meaning they dislike water – like oil) some are hydrophilic (they are attracted like water – like wine).  Some are acidic (like lemon juice) or basic (like soap).  On average, a human protein has 500 of these amino acids strung together in a row, though some can be as small as just a few amino acids whereas the biggest protein called titin is 34,350 amino acids long.

Protein-structureIf you represent proteins as a string of amino acids, this is called their primary structure.  If this is all that proteins were, they wouldn’t do anything at all in the cell. Proteins need STRUCTURE to function.  It’s like rolling out a string of clay.  Until you coil the clay into the shape of a cup or a pot or a vase, it doesn’t have a function.

So what shapes do proteins make?  the two shapes are a sheet and a helix.  These sound exactly like you imagine them to look like.  The beta sheet is a flat piece of protein and the alpha helix looks like a spiral staircase.  However even at this secondary structure, the protein isn’t functional.  It needs to coil up even more into the tertiary structure, making a functional protein.

GFPWe can actually determine the shape of proteins in the same way that the double helix of DNA was determined : X-ray crystallography. Here is an example of what a protein looks like at the atomic level.  The flat parts are the beta sheets and that one tiny blue coil in the middle is an alpha helix.  This structure is of the GFP protein we talked about in a previous post.  So to bring it back to what proteins are made of, depending on the number, and properties of the amino acids in a protein, the protein will have a different structure and therefore will have a different function.

Here are some examples of proteins whose shape helps define its function

  • Cellular channels.  The size and shape of these proteins determines if large or small molecules can be let in and whether or not a key is needed to “unlock” the protein to open up the channel.  As an analogy, think about connecting two rooms to one another.  You have choices – you can choose to connect them with a door, which is much bigger and can let larger items through, or you can put in a window, which will let smaller items though. And either can be unlocked or locked.
  • Enzymes are another type of protein that often function by binding to another molecule or protein and doing something to it (for example, cutting it, in the case of digestion).  The shape of the protein will determine what it can bind to and what type of activity it can have.
  • And then there are structural proteins, like actin, that are long and stringy and help cells keep their shape, as you can see in the images below.

actin

When you think about proteins, just remember that depending on what they look like, they will do different things.  And if the shape of a protein is changed (say, by changing the DNA blueprint) the protein may not function as intended and could result in disease.

 

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