RNA is a Piece of Cake

Have you heard words like gene, DNA, and RNA thrown around, but aren’t quite sure what they mean? Are you fuzzy on the difference between a genome and transcriptome? Read on then. This post is for you, and I promise by the end, you will find that all those fancy sounding science terms are a piece of cake—or at least a recipe for cake.

Before we talk about DNA, we need to talk about proteins. You’ve probably seen proteins listed on the nutrition information of your cereal box and know you need to eat them to be healthy. But what exactly are proteins? You can kind of think of them as the chemical machinery that keeps things running in cells. Need to move nutrients into a cell? There’s a protein for that. Need to stick parts of a cell together? There’s a protein for that. Need to let your cell know it’s under attack by a virus? There’s a protein for that. Need to signal to another cell that it needs to grow differently? There’s — well, you get the picture.

Each cell contains a recipe book for all the proteins that it can make. That recipe book is DNA. In simplest terms, a gene is a piece of DNA that contains one “recipe” for one type of protein. When a cell needs a particular protein, the cell goes to the relevant gene to get instructions, like you looking up a recipe when you want to make a certain dish. But DNA has a problem: it’s stuck inside an envelope called the nucleus, and the cell makes new proteins outside the nucleus. It’s the same kind of issue you run into when you want to make your aunt’s Famous Italian Cake, but the recipe is in her binder three states away.

So if you want to make that Famous Italian Cake, you have to figure out a way to get a copy of the recipe from your aunt’s binder to your countertop. You could do this by asking your aunt to photograph the recipe card and text it to you. Cells do the same thing with RNA. Messenger RNA (aka mRNA) makes copies of the DNA and takes them out of the nucleus.

Once outside the nucleus, the mRNA takes recipes to the ribosome, the “protein kitchen” of the cell. In the ribosome, other kinds of RNA (tRNA and rRNA) help bring and hold the “ingredients” that make up proteins. Think of them as the “measuring cups” and “mixing bowl” of the cell, respectively.

For my space botany project, I’m interested in the changes going on with certain signaling proteins when plants are grown floating “weightless” in space. I get a snapshot of what is going on inside the cell by measuring the mRNA. It’s like figuring out what is for dinner by glancing at the recipes on the counter.

Why not measure the proteins directly? The short answer is: proteins are messy. They are big complex chemicals, and the process of taking proteins apart to measure them is time consuming, expensive, and error prone. mRNA is a simple chemical that is easy to take apart, make copies of, and measure.

DNA and mRNA are so easy to measure, that scientists can now measure all the DNA or RNA in a plant (or animal) relatively easily. When we measure all the DNA which contains all the genes in a living thing, it’s called the “genome”. Knowing a plant’s genome lets us know all the potential protein recipes a plant can make—similar to getting an idea of someone’s food preferences by perusing their family cookbook collection.

Notice the genome just tells the potential of a cell. The genome doesn’t tell what proteins a given cell or plant is actually making. Just like you only make certain dishes for certain occasions, roots make different proteins than leaves, and stressed plants make different proteins than healthy plants. To find out what proteins are being made—the so-called “proteome”—scientists can cheat a bit and look at all the mRNA recipes a plant has made copies of to use. These copies are called the “transcriptome”. The transcriptome contains all the recipes for proteins that the plant is “cooking” at any given time. If we know what recipes the plant is using and how many copies it has made of them, we have a strong hint as to what is going on inside the plant cells.

Prior to my ground based project, other folks in my lab compared the transcriptomes of plants grown weightless in space with plants exposed to normal gravity forces. They saw that plants had more mRNA recipes out for certain signaling proteins when the plants didn’t feel gravity than when they did feel gravity. Those experiments are the basis of my project.

Transcriptomics, the ability to easily measure all the RNA in a living thing, has transformed biology in ways that were science fiction when I was a kid. We can now use transcriptomics to figure out how to keep plants healthy even when they are stressed by drought or pests, and we can figure out better ways to treat human diseases, too. I hope my space biology project will lead to discoveries that help understand how plants respond to their environment in spaceflight—and on earth. I also hope that this blog post has demystified some of the language you may hear scientists throwing around. If anything is unclear, feel free to comment with further questions.

Oh, and if my aunt with the truffle and the whipped cream dessert recipe reads this blog, could she please text me? I need better mRNA—I mean copies of those recipes.

For more information

I’ve simplified some things about mRNA, DNA, and various “omics” for the sake of brevity and clarity in this post. If you are interested in these topics, here’s some good resources for you to learn more:

I’m a big fan of the educational videos by the Amoeba Sisters. They have several great ones on genetics and biotech on their YouTube Channel. The first few videos on their Heredity playlist are especially relevant.