Setting up Shop: RNA to Proteins

Ribonucleic acid (RNA to its friends, including us) is a sibling to DNA. You may have noticed from the name that RNA is really just DNA without the "deoxy". Much of what has been said about DNA applies to RNA as well. RNA contains genetic instructions, is made up of an alphabet, can base pair with DNA or other RNA strands. However, there are some crucial differences. The alphabet is different—instead of T, RNA uses a U (for Uracil). While DNA is usually found as a double-stranded molecule, RNA is almost always single stranded.  You can think of RNA as a working copy of the DNA, a copy that is intended to be recycled after use. RNA is disposable, because it's main purpose is to serve as a template for protein machinery and protein machinery is a huge part of biotechnology.

Transcription

To create a working protein, DNA is first transcribed into an RNA copy. Transcription is performed by a protein called RNA polymerase. Its job is to follow a single strand of DNA, all the while stringing together complementary bases in a strand of RNA. I'll use the DNA sequence from before as an example:

AUGCCAUGA RNA

||||||||| ---

TACGGTACT DNA

Once there's a working RNA copy of a piece of DNA, many things can happen. RNA is a versatile molecule with many functions including gene regulation, molecular sensing, enzyme structure, among other things. However, a very central function of RNA (the first thing anyone learns in molecular biology 101) is that RNA acts as a template to create proteins. 

Translation

Decoder Pin from "A Christmas Story"

Proteins are translated from an RNA template by a hotshot molecule called a Ribosome. Every living creature on earth needs ribosomes to survive because of its central role in translating genetic code into useful protein machines. The process of translation is just like translating a secret code with a Little Orphan Annie Secret Decoder Pin. In one end of the ribosome goes the RNA template. Out the other end comes a long string of amino acids, nicely linked together in a chain that will eventually fold into a unique 3D structure and perform a function for the cell. 

Sound like magic? I think it is, but that answer never worked on my molecular biology midterms. Here's roughly how it works: the RNA template (also known as the messenger RNA or mRNA) is divided into codons, which are a three-letter code. There are start codons, stop codons, and codons for each amino acid. Our example DNA strand would translate like this:

AUG  CCA  UGA mRNA

|    |    |    --

    M    P   Stop Protein

M stands for Methionine, an amino acid (the start codon AUG codes for Methionine). P stands for Proline, another amino acid, and UGA is the stop codon, which doesn't code for any amino acid. The key to the code is another type of RNA called transfer RNA (tRNA for short). tRNAs are keys that fit the ribosomal lock. On the tip, they are connected to an amino acid, and the butt is the complimentary three-letter sequence for the codons in the mRNA. As the mRNA is read through the ribosome, tRNAs flow in and out, unloading their amino acids into the growing protein chain. If the three letters on the tRNA don't fit the codon in the mRNA, that tRNA won't physically be able to enter the ribosome and deposit the amino acid. All in all, there are 20 common amino acids that most organisms on earth need to survive, and corresponding tRNAs for each one. Translation can't start until a start codon is encountered. All proceeding codons are said to be "in frame" with the first start codon. A gene generally refers to a stretch of DNA that codes for a complete protein, from start codon to stop.  In the image to the left you can see a "jean", he he. Excuse the pun. But seriously, the cotton fiber used to make jeans is the result of cotton plants making good use of proteins, and scientists have been quick to genetically modify cotton. Biotech at work, from genes to jeans.

For You Visual Learners

This video is not particularly humorous (unless you find tRNA amusing, which is certainly within the realm of possibility), but it does explain the whole protein synthesis process very well.

 Central-Dogma Voila

Spiffy, right? But so what? Proteins are the industrial machinery of our cellular factories. Proteins maintain our DNA, make new RNA, act as sensors so that cells can interact with the outside world and each other, provide energy, provide physical structure, fight disease, cause fluorescence, allow photosynthesis... You're reading this book because of proteins in your muscles that provide tension and movement, proteins in your eye that capture light, and proteins in your brain that allow your brain cells to uptake fatty acids. Proteins are everywhere, and are a key part of biotechnology. Engineers and scientists are interested in discovering new proteins in nature that catalyze interesting chemical reactions, in fixing proteins in our bodies that are broken and cause disease, and in discovering new artificial proteins that will improve health or serve as new biomaterials (so much cooler that just "materials", right?).

Here's a glowing example of proteins in biotechnology:

Our little two-amino acid protein is pretty dinky by most standards. On average, proteins are about one thousand amino acids long, but can be smaller, or much, much larger. One protein, called Titin (which is found in muscle cells) is over 20,000 amino acids long! When a protein catalyzes a chemical reaction (a very common role for proteins), it's called an enzyme. Most enzyme names end in "-ase" as in "polymerase". You'll see more "_ase" molecules throughout the blog, and now you know what that means. 

The Central Dogma

You are now familiar with what is fondly known as the Central Dogma of molecular biology. DNA codes for RNA, RNA codes for protein. With the central dogma under your belt, you are prepared to appreciate not only the outcomes of biotech research, but the underlying methods as well. Over the years, molecular biologists have created a large toolkit for working with DNA.