Ribosome Quotes

When I started reading the literature of molecular biology, I was stunned by certain descriptions. Admittedly, I was on the lookout for anything unusual, as my investigation had led me to consider that DNA and its cellular machinery truly were an extremely sophisticated technology of cosmic origin. But as I pored over thousands of pages of biological texts, I discovered a world of science fiction that seemed to confirm my hypothesis. Proteins and enzymes were described as 'miniature robots,' ribosomes were 'molecular computers,' cells were 'factories,' DNA itself was a 'text,' a 'program,' a 'language,' or 'data.' One only had to do a literal reading of contemporary biology to reach shattering conclusions; yet most authors display a total lack of astonishment and seem to consider that life is merely 'a normal physiochemical phenomenon.

When we have a clear goal in mind, we think we are struggling to reach a summit. But there is no summit. When we get there, we realize we have just climbed a foothill, and there is an endless series of mountains ahead still to be climbed.

Well, the human genome has massive redundancy - that means that two per cent of the DNA does all the work of instructing the ribosomes that build the proteins that make up the cells of your body. Ninety-eight per cent of your DNA just sits there doing nothing. Taking up space in the gene.

Ricin is classed as a ribosome-inhibiting protein, which is abbreviated to RIP.

The ribosomes, for instance, which manufacture proteins, rival in complexity any chemical factory. The mitochondria are power plants which extract energy from food by a complicated chain of chemical reactions involving some fifty different steps: a single cell may have up to five thousand such power plants. Then there are the centrosomes, with their spindle apparatus, which organises the incredible choreography of the cell dividing into two; and the DNA spirals of heredity, coiled up in the inner sanctum of the chromosomes, working their even more potent magic.

Consider the genesis of a single-celled embryo produced by the fertilization of an egg by a sperm. The genetic material of this embryo comes from two sources: paternal genes (from sperm) and maternal genes (from eggs). But the cellular material of the embryo comes exclusively from the egg; the sperm is no more than a glorified delivery vehicle for male DNA—a genome equipped with a hyperactive tail. Aside from proteins, ribosomes, nutrients, and membranes, the egg also supplies the embryo with specialized structures called mitochondria. These mitochondria are the energy-producing factories of the cell; they are so anatomically discrete and so specialized in their function that cell biologists call them “organelles”—i.e., mini-organs resident within cells. Mitochondria, recall, carry a small, independent genome that resides within the mitochondrion itself—not in the cell’s nucleus, where the twenty-three pairs of chromosomes (and the 21,000-odd human genes) can be found. The exclusively female origin of all the mitochondria in an embryo has an important consequence. All humans—male or female—must have inherited their mitochondria from their mothers, who inherited their mitochondria from their mothers, and so forth, in an unbroken line of female ancestry stretching indefinitely into the past. (A woman also carries the mitochondrial genomes of all her future descendants in her cells; ironically, if there is such a thing as a “homunculus,” then it is exclusively female in origin—technically, a “femunculus”?) Now imagine an ancient tribe of two hundred women, each of whom bears one child. If the child happens to be a daughter, the woman dutifully passes her mitochondria to the next generation, and, through her daughter’s daughter, to a third generation. But if she has only a son and no daughter, the woman’s mitochondrial lineage wanders into a genetic blind alley and becomes extinct (since sperm do not pass their mitochondria to the embryo, sons cannot pass their mitochondrial genomes to their children). Over the course of the tribe’s evolution, tens of thousands of such mitochondrial lineages will land on lineal dead ends by chance, and be snuffed out. And here is the crux: if the founding population of a species is small enough, and if enough time has passed, the number of surviving maternal lineages will keep shrinking, and shrinking further, until only a few are left. If half of the two hundred women in our tribe have sons, and only sons, then one hundred mitochondrial lineages will dash against the glass pane of male-only heredity and vanish in the next generation. Another half will dead-end into male children in the second generation, and so forth. By the end of several generations, all the descendants of the tribe, male or female, might track their mitochondrial ancestry to just a few women. For modern humans, that number has reached one: each of us can trace our mitochondrial lineage to a single human female who existed in Africa about two hundred thousand years ago. She is the common mother of our species. We do not know what she looked like, although her closest modern-day relatives are women of the San tribe from Botswana or Namibia. I find the idea of such a founding mother endlessly mesmerizing. In human genetics, she is known by a beautiful name—Mitochondrial Eve.

I recently asked more than seventy eminent researchers if they would have done I their work differently if they had thought Darwin's theory was wrong. The responses were all the same: no. I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome: the mapping of genomes; research on medications and drug reactions: improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.

When the genetic code was solved, in the early 1960s, it turned out to be full of redundancy. Much of the mapping from nucleotides to amino acids seemed arbitrary—not as neatly patterned as any of Gamow’s proposals. Some amino acids correspond to just one codon, others to two, four, or six. Particles called ribosomes ratchet along the RNA strand and translate it, three bases at a time. Some codons are redundant; some actually serve as start signals and stop signals. The redundancy serves exactly the purpose that an information theorist would expect. It provides tolerance for errors. Noise affects biological messages like any other. Errors in DNA—misprints—are mutations.

Each ribosome had more than fifty different components. If you broke down a slew of them into their separate parts and thoroughly mixed them up in a suspending fluid, then Brownian movement—caused by encounters with molecules of the suspending medium—kept knocking them against one another until the fifty-some parts assembled into whole ribosomes.

It was the magnesium. The addition of the ion was critical: with the solution supplemented with magnesium, the ribosome remained glued together, and Brenner and Jacob finally purified a miniscule amount of the messenger molecule out of bacterial cells. It was RNA, as expected-but RNA of a special kind. The messenger was generated afreah when a gene was translated. Like DNA, these RNA molecules were built by stringing together four bases-A,G,C, and U (in the RNA copy of a gene, remember, the T found in DNA is substituted for U). Notably, Brenner and Jacob later discovered the messenger RNA was a facsimile of the DNA chain-a copy made from the original. The RNA copy of a gene then moved from the nucleus to the cytosol, where its message was decoded to build a protein. The messenger RNA was neither an inhabitant of heaven nor of hell-but a professional go-between. The generation of an RNA copy of a gene was termed transcription-referring to the rewriting of a word or sentence in a language close to the original. A gene's code (ATGGGCC...) was transcribed into an RNA code (AUGGGCC...).

The ribosome did not contain the recipe for the protein; it was a tape reader. It could make any protein so long as it was fed the right tape of “messenger” RNA.

in the minds of many genetic engineers at the time—there was no difference between cells and computers. Computers use a software code of 1s and 0s, whereas biology uses a code of As, Cs, Ts, and Gs. Computers use compilers and storage registries; biology uses RNA (ribonucleic acid) and ribosomes. Computers use peripherals; biology uses proteins.

The rest of the organism was as natural as any other ordinary cell. Indeed, Venter’s synthetic genome depended on the rest of the recipient cell’s natural and native apparatus for its expression: it depended on the cell’s molecular machinery of transcription, translation, and replication, its ribosomes, metabolic pathways, its energy supplies, and so on.

The actual mechanics of cell division, according to Dick McIntosh at the University of Denver, require significantly more instructions than it takes to build a moon rocket or supercomputer. First of all, the cell needs to duplicate all of its molecules, that is DNA, RNA, proteins, lipids, etc. At the organelle level, several hundred mitochondria, large areas of ER, new Golgi bodies, cytoskeletal structures, and ribosomes by the million all need to be duplicated so that the daughter cells have enough resources to grow and, in turn, divide themselves. All these processes make up the ‘cell cycle’. Some cells will divide on a daily basis, others live for decades without dividing. The cell cycle is divided into phases, starting with interphase, the period between cell divisions (about 23 hours), and mitosis (M phase), the actual process of separating the original into two daughter cells (about 1 hour). Interphase is further split into three distinct periods: gap 1 (G1, 4–6 hours), a synthesis phase (S, 12 hours), and gap 2 (G2, 4–6 hours). Generally, cells continue to grow throughout interphase, but DNA replication is restricted to the S phase. At the end of G1 there is a checkpoint. If nutrient and energy levels are insufficient for DNA synthesis, the cell is diverted into a phase called G0. In 2001 Tim Hunt, Paul Nurse, and Leeland Hartwell received the Nobel Prize for their work in discovering how the cell cycle is controlled. Tim Hunt found a set of proteins called cyclins, which accumulate during specific stages of the cell cycle. Once the right level is reached, the cell is ‘allowed’ to progress to the next stage and the cyclins are destroyed. Cyclins then start to build up again, keeping a score of the progress at each point of the cycle, and only allowing progression to the next stage if the correct cyclin level has been reached.

Ribosomes have an error rate of about one letter in 10,000, far lower than the defect rate in our own high-quality manufacturing processes. And they operate at a rate of about 10 amino acids per second, building whole proteins with chains comprising hundreds of amino acids in less than a minute.

(mRNA), in a process called transcription. This mRNA then leaves the nucleus to enter the cytoplasm, where it is translated into protein by large multiprotein complexes called ribosomes. The proteins resulting from translation are then folded and glycosylated correctly by various means and directed towards their required location in the cell

mitochondria and the ribosomes and the chloroplasts and the endoplasmic reticulum.

Mitochondria are strange organelles in the sense that they have their own DNA and ribosomes.Therefore, mitochondria are able to make some of their own proteins

In DNA, the alphabetic instructions are adenine, thymine, cytosine, and guanine. One way to recognize mRNA in the cell is that it does not contain thymine, but substitutes uracil instead. The mRNA is then composed of a collection of these four bases (a, u, c, and g). It takes only three bases to form what is called a “codon.” This codon corresponds to an amino acid. A large protein called a ribosome works like a tiny machine, moving along the mRNA strand, while transfer RNA (tRNA) units attach, encoding one of twenty amino acids. The string of amino acids form into a protein.[353]

Like a strand of DNA, the mRNA is a chain of letters, and its sequence matches the sequence of the DNA it copied (the only major exception being that T gets replaced by U). The mRNA is exported out of the cell’s nucleus and delivered to a protein-synthesizing factory called a ribosome, which translates the four-letter language of RNA (A, G, C, and U) into the twenty-letter language of proteins (the twenty amino acids). This translation proceeds according to the genetic code, a cipher in which every three-letter RNA combination, called a codon, instructs the ribosome to add one specific amino acid.

Here’s an example: DNA stores information very nicely, in a durable format that allows for exact duplication. A ribosome turns that stored information into a sequence of amino acids, a protein, which folds up into a variety of chemically active shapes. The combined system, DNA and ribosome, can build all sorts of protein machinery. But what good is DNA, without a ribosome that turns DNA information into proteins? What good is a ribosome, without DNA to tell it which proteins to make? Organisms don’t always leave fossils, and evolutionary biology can’t always figure out the incremental pathway. But in this case we do know how it happened. RNA shares with DNA the property of being able to carry information and replicate itself, although RNA is less durable and copies less accurately. And RNA also shares the ability of proteins to fold up into chemically active shapes, though it’s not as versatile as the amino acid chains of proteins. Almost certainly, RNA is the single A which predates the mutually dependent A* and B. It’s just as important to note that RNA does the combined job of DNA and proteins poorly, as that it does the combined job at all. It’s amazing enough that a single molecule can both store information and manipulate chemistry. For it to do the job well would be a wholly unnecessary miracle. What was the very first replicator ever to exist? It may well have been an RNA strand, because by some strange coincidence, the chemical ingredients of RNA are chemicals that would have arisen naturally on the prebiotic Earth of 4 billion years ago. Please note: evolution does not explain the origin of life; evolutionary biology is not supposed to explain the first replicator, because the first replicator does not come from another replicator. Evolution describes statistical trends in replication. The first replicator wasn’t a statistical trend, it was a pure accident. The notion that evolution should explain the origin of life is a pure strawman—more creationist misrepresentation.

Much of the mapping from nucleotides to amino acids seemed arbitrary—not as neatly patterned as any of Gamow’s proposals. Some amino acids correspond to just one codon, others to two, four, or six. Particles called ribosomes ratchet along the RNA strand and translate it, three bases at a time. Some codons are redundant; some actually serve as start signals and stop signals. The redundancy serves exactly the purpose that an information theorist would expect. It provides tolerance for errors. Noise affects biological messages like any other.

Sets of three deoxyribonucleic acids in a specific order encode a specific amino acid, and the proteins are manufactured on those very old nanomachines, the ribosomes. The proteins are themselves used to make the nanomachines that allow the organism to generate energy and reproduce. The reproduction of cells is dependent on replication of the genes, and the replication of genes is dependent on the ability of the organism to generate energy, survive, and grow.

A, C, G, T for short. A cell carries out a series of chemical reactions to translate a gene’s sequence of bases into a protein. A cell first makes a copy of the gene, creating a single-stranded series of bases called ribonucleic acid, or RNA. That RNA molecule is taken up by a molecular factory called a ribosome, which reads the sequence of RNA and builds a corresponding protein.

Life relies on digitally coded instructions, translating between sequence and structure (from nucleotides to proteins), with ribosomes reading, duplicating, and interpreting the sequences on the tape. But any resemblance ends with the different method of addressing by which the instructions are carried out. In a digital computer, the instructions are in the form of COMMAND (ADDRESS) where the address is an exact (either absolute or relative) memory location, a process that translates informally into “DO THIS with what you find HERE and go THERE with the result.” Everything depends not only on precise instructions, but also on HERE, THERE, and WHEN being exactly defined. In biology, the instructions say, “DO THIS with the next copy of THAT which comes along.” THAT is identified not by a numerical address defining a physical location, but by a molecular template that identifies a larger, complex molecule by some smaller, identifiable part. This is the reason that organisms are composed of microscopic (or near-microscopic) cells, since only by keeping all the components in close physical proximity will a stochastic, template-based addressing scheme work fast enough. There is no central address authority and no central clock. Many things can happen at once. This ability to take general, organized advantage of local, haphazard processes is the ability that (so far) has distinguished information processing in living organisms from information processing by digital computers.