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.

 

What does DNA look like? Like, really?

Everyone talks about DNA.  And shows those lovely double helix cartoon images of DNA. But when you’re a researcher in a lab, what does DNA actually look like?  How in the world do we see it?

DNA-X-Ray

  1. X-Ray crystallography.  To be fair, this is an indirect way to see DNA but it is the way that the structure of DNA was determined (as described in our book club book The Double Helix) so it’s worth mentioning.  Remember when you were a kid and you made rock candy by hanging a string or stick in water that had a ton of sugar dissolved into it?  Well scientists can do the same thing with DNA or proteins – make crystals of them.  These crystals are much smaller than the crystals in rock candy.  Think microscopic.  When molecules are all lined up in the same direction, like they are when they form a crystal, scientists can hit the crystal with X-rays and what bounces around and through the crystal can be detected (this is called a diffraction pattern), measured and transformed to determine the 3D image of the molecule – that double helix structure you see pictures of all the time.  This process is called X-Ray crystallography and for the first images of DNA, the diffraction pattern looked like the picture to the left.
  2. dna_in_cellMost scientists do not look at DNA to the atomic level like in X-Ray crystallography, but rather want to see it inside of a cell. The DNA in a cell is inside the nucleus and certain dyes (such as the Hoechst dye) bind to DNA.  Under UV light, the Hoechst dye glows, showing exactly where the DNA is in the cell.  If you look at the picture to the right, you can see the outline of three cells and the blue DNA inside the nucleus of those three cells. Why would a scientist want to see where the DNA is and what it looks like? You can learn a lot from just looking at the DNA. For example, whether or not a cell is dividing or dying, which can be really important if you want to know whether or not the cancer cells you are studying die when you treat them with a drug.
  3. Scientists don’t always look at the DNA directly inside of a cell either.  For an experiment they may want to isolate the DNA (meaning, take the DNA out of a lot of cells to dna_in_eppendorfstudy it) and then manipulate it in some way (sequence it, amplify it, modify it, etc).  Once my mom asked me how big DNA is when you take it out of cells and work with it in the lab.  Well, the answer is that you need a LOT of it to even see it.  In the lab, we may grow bacteria in 5 ml of growth media, which after growing overnight contains 10,000,000,000 cells.  We then bust these cells open with a detergent (like soap, but not soap), spin out all of the extra bits of cells, and then force the DNA to show itself by adding an alcohol like ethanol in a process called precipitation (if you want to learn more about the details, check out this article).  How much DNA do you get in the end – well it depends, but it’s not a lot, visually at least.  And what does it look like?  See the whitish smear at the bottom of that tiny tube?  That’s the DNA.

Are there other ways to see DNA?  YES!  But many of them are based on dyes like the one described in #2 above.  At some point, we’ll definitely talk about them in the context of analyzing DNA sequence and running gels.  And I’m not talking at all here about “seeing” DNA by determining it’s sequence, even though that’s important too.

strawberry_dnaSo now that you know a few ways that scientists see DNA, it’s your turn.  Grab a lab partner, and isolate DNA on your own!!  Don’t know how?  No problem!  There are a number of different ways to isolate DNA at home, the most common being from the cells of an onion or the cells of strawberries.  The experiments for extracting DNA from ONIONS or STRAWBERRIES are linked. At the end of the experiment, what will you see?  Long strands of isolated DNA from all of the onion or strawberry cells. Enjoy and please share photos and stories of your DNA isolation adventures!