The Theme of Structure and Function in Gene to Protein
Transcription and translation overcome a number of obstacles to produce functional RNAs and proteins. You've probably guessed by now that the structures of the factors involved are absolutely essential for the success for these processes. Are you beginning to feel a little déjà vu here? That's because the link between structure and function is such an important theme in biology.
Many of the common factors involved in transcription and translation show remarkable similarity across organisms (read: similar structures used for similar functions). These factors exploit common principles to fulfill their functions. First let's talk about proteins involved in transcription.
We've talked about how the proteins involved in transcription must recognize specific regions of DNA. The promoter. The regulatory regions. Proteins don't have eyes, but they can "read" DNA in a non-traditional way. In fact, the DNA helix can be read from the outside of the helix. Why is this observation surprising?
Look at the structure of the DNA helix below. The DNA helix has both minor and major grooves, but the base pairs hydrogen bond within the center of the helix. What does this mean? Basically the factors involved in transcription are reading a book by looking at its cover.
It is actually not quite as complicated as you might think. The DNA bases do expose an edge of the base, and this fact is enough for proteins to figure out the inner sequence. It is kind of like closing your eyes and trying to pick out a particular fruit from feeling along the edges of the fruit in the bowl. It is also easier for some sequences to be recognized because they generate a distinctive kink or bend in the helix. The proteins that bind to these regions must form complementary interactions with these exposed residues.
There are certain common DNA structural binding domains, or parts of a protein important for binding DNA, which are observed in many DNA binding and regulatory proteins. In other words, these domains look alike and share common functions. Imagine that!
Some common domains are helix-turn-helix and zinc fingers. Helix-turn-helix are formed by two protein α-helixes. Different helix-turn-helix proteins have unique amino acids sequences despite sharing a common protein structure, and these differences provide the specificity to recognize the specific DNA sequence. Zinc fingers motifs use amino acids and zinc to recognize specific DNA structures. Both helix-turn-helix and zinc fingers use α-helixes to recognize the major grove of the DNA. These groups of proteins also tend to function as dimers, or a pair of two molecules. Although less common, amino acids arranged into β-sheets can also contact the DNA helix through the major groove.
The importance of structure isn't unique to proteins. We've mentioned that even the nascent RNA strand can take on unique structures to aid in its release from the polymerase. Furthermore, the RNAs involved in the production of proteins take on elaborate structures, all of which are essential for their function. Like proteins, RNAs can form elaborate structures and even catalyze biological reactions.
RNA also has the unique advantage that they can base pair with DNA and other RNA structures. We've already talked extensively about how this base pairing allows for the codon/anticodon pairing required for translation. Base pairing is also how the RNA can take on higher order structures by base pairing to bases within the same molecules. Disruption of these interactions can be extremely disruptive, even leading to a tRNA that charges with an incorrect amino acid. Sound familiar? Yes, good. You've been paying attention. If not, click here for a little refresher—link to section on tRNAs.