Biological Information and Intelligent Design: the curious world of RNA (continued)

| By on Letters to the Duchess

From left to right: leadzyme, hammerhead ribozyme, twister ribozyme. By Lucasharr - Own work, CC BY-SA 4.0, via Wikimedia.

EDITOR’S NOTE: A scientific glossary is provided below this article for those who are unfamiliar with the scientific terms and concepts.

Is “biological information” merely an analogy of convenience for biologists, or does the cell contain information in the sense of a language or code? In this series we explore the science behind this question and its implications for the arguments of the Intelligent Design movement. 

Is the process by which cells use the information stored in DNA to form proteins complex organic chemistry, an indicator of a designing intelligence, or both? The Intelligent Design movement claims that it is very much both, stating that the genetic code found in cells is in fact a genuine code, like what a human might create. In this series we’re taking a tour through the complex chemistry that cells use to process information in order to understand and evaluate this claim.

In yesterday’s post, we looked at the role of messenger RNA (mRNA) as a means to prepare a gene’s DNA sequence for conversion into an amino acid sequence – a process known as translation. Translation, as we have seen, is the process whereby a nucleotide sequence in mRNA is converted – three nucleotides (one codon) at a time – into an amino acid sequence. This process is accomplished by two other types of RNA - let’s examine their roles.

Bridging the two languages: tRNA

Once the codon “code” was worked out, the next question was how each amino acid was specified by a particular codon. One hypothesis was that some sort of adaptor molecule existed for each codon - a molecule that would both recognize the codon sequence and be physically connected to an amino acid. It was known that the enzyme complex that connected amino acids together was the ribosome, so these adaptors, if they existed, would have to work with the ribosome and the mRNA it was using as a template. Eventually it was shown that these adapter molecules are a different kind of RNA: transfer RNAs, or "tRNAs" for short". In a literal way, they act as a bridge between the “language” of nucleic acids and the “language” of amino acids.

Though mRNA molecules may have some three-dimensional structures important for their function, the structure of tRNA molecules is essential to their role within the cell. Though tRNAs are single-stranded molecules, their nucleotide monomers can still pair up with other monomers using hydrogen bonds - except that they bond with other monomers on their same strand. The result is a single stranded molecule that folds up through base-pairing within itself – producing something that resembles a cloverleaf with three “leaves” protruding from it:

In the image above, the small right hand image shows a line diagram of the single RNA strand that makes up a tRNA. The larger image shows the actual structure of the molecule. The blue “leaf” contains the anticodon: the nucleotide sequence that recognizes and binds to its corresponding codon on the mRNA with hydrogen bonds. The end of the short, single-stranded section (shown in yellow) is where an amino acid will be physically joined to the tRNA. The loading of the proper amino acid onto the correct tRNA is what gives the code its specificity. Amino acid loading is accomplished by protein enzymes that recognize the shape of a particular tRNA, the shape of its corresponding amino acid, and join them together with a chemical bond. Amino acids are present in the cell, floating around, and available for these enzymes to grab and bind on to their correct tRNA molecule. Interestingly, this process, along with the entire transcription / translation system, depends on random, chaotic motion within the cell, a type of motion known as Brownian motion

Once loaded with amino acids, tRNA molecules can interact with the ribosome. This enzyme complex is where mRNAs and tRNAs meet, and the third class of RNA molecules does its work: ribosomal RNAs, or rRNAs. 

The ribosome: a massive rRNA enzyme complex 

Let’s look at a “cartoon” version of the ribosome to help us understand its function:

The ribosome serves as a platform for the mRNA, and provides two places where tRNA molecules can enter “slots” and interact with it. An incoming tRNA (brought in through Brownian motion) is stabilized by its anticodon attraction to the codon on the mRNA, and once stabilized, the amino acid it bears is bonded to the amino acid attached to the tRNA on the adjacent slot. This reaction breaks the bond of this amino acid with its tRNA, ejecting that “spent” tRNA from the ribosome. The ribosome then ratchets over one codon, and the process repeats until the amino acid chain – a mature protein – is completed. In this way the ribosome translates the nucleic acid sequence of the mRNA into a specified sequence of amino acids.


This 3D animation (which was also embedded in yesterday’s post) shows how proteins are made in the cell from the information in the DNA code.


It has long been known that the ribosome is a complex of RNA molecules (named “ribosomal RNA” or “rRNA”) and some associated proteins. What was suspected was that the ribosome might in fact be an RNA enzyme, or “ribozyme” and not a protein. Though most enzymes (molecules that favor specific chemical reactions) are proteins, some are RNA molecules. 

The idea that the ribosome is a ribozyme was first suggested by proponents of the “RNA world” hypothesis. This hypothesis suggests that present-day, DNA-based life is a modified descendent of RNA-based life. In this proposed model, RNA was both a hereditary molecule and a source of functional, 3-D structures that did enzymatic functions. Only later, so the hypothesis goes, did DNA get added on to act as a hereditary molecule, and proteins take over most enzymatic functions.

One prediction of the RNA world hypothesis was that the ribosome might have retained its RNA-based enzymatic structure. This was spectacularly confirmed in the year 2000, by careful analysis of ribosome structure. These researchers showed that although the proteins in the ribosome stabilize the rRNA molecules, they do not have an enzymatic role.

ID, the ribosome, and the RNA world hypothesis

Those who follow the Intelligent Design literature will know that philosopher and historian of science Stephen Meyer discusses transcription and translation at length in his 2009 book Signature in the Cell. In this book, Meyer attempts to build a case that the “information” we see in living organisms is in fact information in the same sense as a human code or a language. Part of his case involves casting doubt on the RNA world hypothesis, since this hypothesis suggests a material, chemical origin for the genetic code, even if an incomplete one. One of Meyer’s critiques in Signature is that such a hypothesis would have to explain how ribosomes transitioned from using RNA enzymes to using protein ones: Meyer erroneously claims that the enzyme in the ribosome that joins amino acids together is a protein. This is, of course, incorrect, since present-day ribosomes are ribozymes. As we have seen, proponents of the RNA world hypothesis suspected that the ribosome might still be a ribozyme, since its function may have been difficult to transition from an RNA enzyme to a protein one. When, in 2000, the ribosome was definitively shown to be a ribozyme, it was widely seen as a successful prediction for the RNA world position. That Meyer was unaware of this widely-cited and highly-influential work (it would garner the 2009 Nobel Prize in Chemistry, the same year that Meyer’s book appeared) came as quite a surprise to biologists reading Signature, especially given its import for Meyer’s claims.

Despite this blunder, the ID community continues to use the “argument from information” as a key plank in its platform. In the next post in this series, we’ll begin to sketch out that argument, and discuss its strengths and weaknesses in light of our understanding of how transcription and translation work at the molecular level.


Notes

Citations

MLA

Venema, Dennis. "Biological Information and Intelligent Design: the curious world of RNA (continued)"
https://biologos.org/. N.p., 29 Jul. 2016. Web. 22 November 2017.

APA

Venema, D. (2016, July 29). Biological Information and Intelligent Design: the curious world of RNA (continued)
Retrieved November 22, 2017, from /blogs/dennis-venema-letters-to-the-duchess/biological-information-and-intelligent-design-the-curious-world-of-rna-continued

References & Credits

Glossary

DNA: deoxyribonucleic acid. Chromosomes are made of two strands of DNA, wound around each other in a double helix. The two strands are held together with weak attractions between nucleotides called hydrogen bonds. Each nucleotide bonds with a pairing partner: A with T, and C with G.

Enzyme: a molecule that acts to make a chemical reaction require less energy - and thus allow it occur. Enzymes can be made of protein or RNA. rRNA molecules that make up the ribosome are the enzymes that connect individual amino acids together to form proteins. Since rRNA molecules are both RNA and enzymes, they are called ribozymes.

Ribosome: the enzyme complex that joins amino acids together to make protein - a process called translation. The ribosome uses mRNA as a template and tRNA molecules to align the correct amino acids in sequence along it.

Ribozyme: an enzyme made up of RNA. Ribosomal RNA (rRNA) is an example of a ribozyme.

RNA:  ribonucleic acid. RNA, like DNA, is made from nucleotides strung together. RNA, however, is single stranded, and uses a nucleotide “U” instead of “T” U can bind to A with hydrogen bonds just as a T does . There are three classes of RNA: mRNA, tRNA, and rRNA:

mRNA (messenger RNA): the single-stranded, “working copy” of a gene sequence copied from the DNA sequence in a process called transcription.

tRNA (transfer RNA): tRNA molecules carry amino acids and have a section that recognizes and binds to a codon on mRNA. tRNAs bring amino acids to the ribosome, the large enzyme that connects amino acids together to form proteins - a process called translation.

rRNA (ribosomal RNA): rRNA molecules make up the enzyme portion of the ribosome. Since rRNA molecules are both RNA and enzymes, they are called ribozymes.

About the Author

Dennis Venema

Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia and Fellow of Biology for BioLogos. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. 

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