to bacteria where the lipid tails are long and simple (fatty acids). These side groups might make the membranes less leaky and more resistant to extreme conditions. Even more strangely, in some archaea the bilayer is replaced by a monolayer where the tails from two lipids are fused together (Figure 5.8). This is the case in Ferroplasma, an archaeon (member of the archaea) that lives in acidic environments. It is thought that this adaptation might make the membranes more resistant to extreme conditions, preventing the membranes from falling apart.
Figure 5.8 The structure of archaeal cell membrane lipids compared to bacterial lipids. The lower diagram also shows how, in some organisms, archaeal lipids can be joined in the middle.
These membrane differences between archaea and bacteria have astrobiological significance. Preserved membrane lipids can be used to tell the identity of long-dead organisms. For example, archaea are often the dominant microorganisms in salty environments. Membrane isoprenoids preserved in salts are diagnostic of archaea and can be used to infer information on the microbial communities that once lived in the salts. Different membrane lipids preserve differently. In other words, their taphonomic potential is different. To be able to interpret which organisms lived in ancient environments, preserved in salt or rock, we need to know about cell membrane components, their ability to be preserved, and which ones might be more quickly degraded, leaving no trace.
5.6 The Information Storage System of Life
We now have a membrane containing the molecule of life. But obvious questions arise: How is the biochemistry of life controlled? What is the way in which instructions are read and directed to make molecules required for the cell to function and eventually to reproduce itself? The key information storage molecule of life is deoxyribonucleic acid, DNA. We briefly explored the structure of this molecule in the previous chapter. We learned about the four bases, guanine, adenine, cytosine, and thymine, which comprise the information code within the DNA, the bases strung together in a long sequence of different combinations. Here, we investigate how the code is turned into useful proteins.
The information storage system is crucial to the cell, since from this information, all cell instructions and coordinated biological patterns emerge. Instructions for the cell to replicate itself and interact with its environment are provided. Within complex multicellular organisms, this information coordinates cells, allowing them to communicate with each other and create differentiated cell structures, with each cell playing a dedicated role in the whole.
5.6.1 Transcription – DNA to RNA
The question arises: How do we go from the DNA information storage system to making proteins and other molecules needed by the cell for growth and reproduction?
This extraordinary transformation is accomplished in two stages. First, DNA is used to make a similar molecule called ribonucleic acid, RNA, the structure of which was described in the last chapter. This process is called transcription. RNA is similar to DNA except for three features: (i) the thymine base is replaced by uracil (U), (ii) it has a ribose sugar with a hydroxyl group (–OH) in the 2′ position, which is not present in DNA (DNA is deoxy-ribose), (iii) it generally (but not always) is single-stranded. DNA and RNA are similar in that they both contain a base, sugar, and phosphate in each structural unit.
The first step in reading the DNA is to make a copy of the sequences of the bases, or a “complementary” copy of the DNA. This copy is made out of RNA. The DNA molecule unwinds along a small part of its length (about 15 base pairs long) called the transcription bubble (Figure 5.9). At this point on the DNA, an RNA polymerase binds. RNA polymerase is a protein with five subunits and a sigma factor, a small specialized protein that recognizes particular promoters on the DNA. Promoters are sequences of DNA that correspond to the beginning of the sequences of DNA that are to be decoded. In colloquial language, the promoters tell the RNA polymerase: “Start decoding the DNA into an RNA strand here.” The RNA polymerase reads along the DNA strand, generating an RNA molecule, called messenger ribonucleic acid or mRNA. This mRNA molecule is sometimes called the mRNA transcript or primary transcript. The production of the mRNA strand occurs from the 3′ to the 5′ end of the DNA strand.
Figure 5.9 The transcription of DNA into mRNA.
In prokaryotes, this process occurs in the cytoplasm of the cell. In eukaryotes, it occurs in the cell nucleus. In eukaryotic cells, the RNA transcript must be transported out of the cell nucleus into the cytoplasm. The mRNA strand so produced can then act as the template for protein synthesis.
5.6.2 Translation – RNA to Protein
Another question now follows: How do we read the mRNA into protein? This is achieved in the next process called translation.
In translation, a new set of molecular apparatus binds to the mRNA to read the code into protein. A central part of this machinery is yet another type of RNA that is folded into a ribosome (sometimes called ribosomal ribonucleic acid or rRNA). The ribosome binds to the mRNA strand. The ribosome provides a scaffold on which other pieces of RNA called transfer ribonucleic acid (tRNA) can bind. tRNAs are the molecules that bring in the amino acids to allow for the assembly of proteins. They can be considered to be adaptor molecules that bind to the mRNA and bring amino acids into alignment to add to a growing polypeptide chain.
Let's go through this process in a simplified way and consider what is happening. You can follow this text and cross-refer to Figure 5.10. We have an mRNA strand, just transcribed from DNA. Around this strand the ribosome forms, made up of subunits which provide the assembly point around which protein synthesis occurs. The ribosome is an impressive structure. In bacteria, it is made up of a large subunit of RNA, consisting of two folded strands of RNA and no fewer than 31 specialized proteins. There is also a small subunit, made up of one folded piece of RNA, called the 16S rRNA, together with another 21 proteins. Remember the 16S rRNA, as it will become important in Chapter 8 when we explore the diversity of life on Earth. This whole apparatus is now ready to make protein.
Figure 5.10 The translation of the genetic code. The protein synthesis apparatus around the mRNA.
The ribosome provides a protected environment in which the tRNA can bind. The tRNA has an amino acid at one end, and each amino acid has its own tRNA molecule associated with it. At the other end is an anticodon. The anticodon is a three-letter sequence of bases that matches three bases on the mRNA molecule (called the codon). Thus, each codon or triplet code on the mRNA corresponds to a specific amino acid (Figure 5.11).
Figure 5.11 The structure of t-RNA. The amino acid is attached at the top of the molecule. The diagram also illustrates the codon-anticodon binding occurring at the bottom of the molecule.
Source: Reproduced with permission of John Wiley & Sons, Ltd.
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