Posts Tagged ‘amino acids’
Origins of life? Here we go again with new evidences
In the beginning, there were simple chemicals. And they produced amino acids that eventually became the proteins necessary to create single cells. And the single cells became plants and animals.
Recent research is revealing how the primordial soup created the amino acid building blocks, and there is widespread scientific consensus on the evolution from the first cell into plants and animals.
But it’s still a mystery how the building blocks were first assembled into the proteins that formed the machinery of all cells.
Now, two long-time University of North Carolina scientists – Richard Wolfenden, PhD, and Charles Carter, PhD – have shed new light on the transition from building blocks into life some 4 billion years ago.
“Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene,” said Carter, professor of biochemistry and biophysics at the UNC School of Medicine.
“This close interaction was likely the key factor in the evolution from building blocks to organisms.”
Their findings, published in companion papers in the Proceedings of the National Academy of Sciences, fly in the face of the problematic “RNA world” theory, which posits that RNA – the molecule that today plays roles in coding, regulating, and expressing genes – elevated itself from the primordial soup of amino acids and cosmic chemicals to give rise first to short proteins called peptides and then to single-celled organisms.
Wolfenden and Carter argue that RNA did not work alone; in fact, it was no more likely that RNA catalyzed peptide formation than it was for peptides to catalyze RNA formation.
The finding adds a new layer to the story of how life evolved billions of years ago.
Its name was LUCA
The scientific community recognizes that 3.6 billion years ago there existed the last universal common ancestor, or LUCA, of all living things presently on Earth. It was likely a single-cell organism. It had a few hundred genes. It already had complete blueprints for DNA replication, protein synthesis, and RNA transcription.
It had all the basic components – such as lipids – that modern organisms have. From LUCA forward, it’s relatively easy to see how life as we know it evolved.
Before 3.6 billion years, however, there is no hard evidence about how LUCA arose from a boiling caldron of chemicals that formed on Earth after the creation of the planet about 4.6 billion years ago. Those chemicals reacted to form amino acids, which remain the building blocks of proteins in our own cells today.
“We know a lot about LUCA and we are beginning to learn about the chemistry that produced building blocks like amino acids, but between the two there is a desert of knowledge,” Carter said. “We haven’t even known how to explore it.”
The UNC research represents an outpost in that desert.
“Dr. Wolfenden established physical properties of the twenty amino acids, and we have found a link between those properties and the genetic code,” Carter said. “That link suggests to us that there was a second, earlier code that made possible the peptide-RNA interactions necessary to launch a selection process that we can envision creating the first life on Earth.”
Thus, Carter said, RNA did not have to invent itself from the primordial soup. Instead, even before there were cells, it seems more likely that there were interactions between amino acids and nucleotides that led to the co-creation of proteins and RNA.
Complexity from simplicity
Proteins must fold in specific ways to function properly.
The first PNAS paper, led by Wolfenden, shows that both the polarities of the twenty amino acids (how they distribute between water and oil) and their sizes help explain the complex process of protein folding – when a chain of connected amino acids arranges itself to form a particular 3-dimensional structure that has a specific biological function.
“Our experiments show how the polarities of amino acids change consistently across a wide range of temperatures in ways that would not disrupt the basic relationships between genetic coding and protein folding,” said Wolfenden, Alumni Distinguished Professor of Biochemistry and Biophysics. This was important to establish because when life was first forming on Earth, temperatures were hot, probably much hotter than they are now or when the first plants and animals were established.
A series of biochemical experiments with amino acids conducted in Wolfenden’s lab showed that two properties – the sizes as well as the polarities of amino acids – were necessary and sufficient to explain how the amino acids behaved in folded proteins and that these relationships also held at the higher temperatures of Earth 4 billion years ago.
The second PNAS paper, led by Carter, delves into how enzymes called aminoacyl-tRNA synthetases recognized transfer ribonucleic acid, or tRNA. Those enzymes translate the genetic code.
“Think of tRNA as an adapter,” Carter said. “One end of the adapter carries a particular amino acid; the other end reads the genetic blueprint for that amino acid in messenger RNA. Each synthetase matches one of the twenty amino acids with its own adapter so that the genetic blueprint in messenger RNA faithfully makes the correct protein every time.”
Carter’s analysis shows that the two different ends of the L-shaped tRNA molecule contained independent codes or rules that specify which amino acid to select. The end of tRNA that carried the amino acid sorted amino acids specifically according to size.
The other end of the L-shaped tRNA molecule is called the tRNA anticodon. It reads codons, which are sequences of three RNA nucleotides in genetic messages that select amino acids according to polarity.
Wolfenden and Carter’s findings imply that the relationships between tRNA and the physical properties of the amino acids – their sizes and polarities – were crucial during the Earth’s primordial era.
In light of Carter’s previous work with very small active cores of tRNA synthetases called Urzymes, it now seems likely that selection by size preceded selection according to polarity. This ordered selection meant that the earliest proteins did not necessarily fold into unique shapes, and that their unique structures evolved later.
Carter said, “Translating the genetic code is the nexus connecting pre-biotic chemistry to biology.”
He and Wolfenden believe that the intermediate stage of genetic coding can help resolve two paradoxes: how complexity arose from simplicity, and how life divided the labor between two very different kinds of polymers: proteins and nucleic acids.
“The fact that genetic coding developed in two successive stages – the first of which was relatively simple – may be one reason why life was able to emerge while the earth was still quite young,” Wolfenden noted.
An earlier code, which enabled the earliest coded peptides to bind RNA, may have furnished a decisive selective advantage. And this primitive system could then undergo a natural selection process, thereby launching a new and more biological form of evolution.
“The collaboration between RNA and peptides was likely necessary for the spontaneous emergence of complexity,” Carter added. “In our view, it was a peptide-RNA world, not an RNA-only world.”
“A short history of nearly everything” by Bill Bryson (written on September 25, 2007)
This is a voluminous book of 575 pages that describes and explains the scientific achievements that tried to comprehend Earth and the life processes.
I will try to summarize the discoveries chronologically, each discipline taken separately such as physics, chemistry, and geology and so forth. It is a long undertaking but it would be useful for me in this assimilation process and quick review of science on the march, to explain, and to conquer.
The manuscript is divided into 6 parts: lost in the Cosmos, the size of the earth, the new age, dangerous planet, life itself, and the road to us. I am including a few quotations of scientists that preface each main part.
Hans Christian von Baeyer in “Taming the atom“: “The physicist Leo Szilard announced to Hans Bethe that he was thinking of keeping a diary: “I don’t intend to publish. I am merely going to record the facts for the information of God” Bethe asked him: “Don’t you think God knows the facts?” Szilard replied: “God knows the facts, but not this version of the facts”
The Astronomer Geoffrey Marcy describing the solar system: “They’re all in the same plane. They’re all going around in the same direction. It’s perfect, you know. It’s gorgeous. It’s almost uncanny”.
Alexander Pope in an epitaph intended for Sir Isaac Newton: ” Nature and nature’s laws lay hid in night; God said: “Let Newton be!” and all was light”
An anonymous: “A physicist is the atoms’ way of thinking about atoms”
The British geologist Derek V. Alger: “The history of any one part of the Earth, like the life of a soldier, consists of long periods of boredom and short periods of terror”
Freeman Dyson: “The more I examine the universe and study the details of its architecture, the more evidence I find that the universe in some sense must have known we were coming”
Remark of the wife of the Bishop of Worcester after Darwin’s theory of evolution was explained to her: “Descended from the apes! My dear, let us hope that it is not true, but if it is, let us pray that it will not become generally known”
Byron in “Darkness”: “I had a dream which was not all a dream
The bright sun was extinguish’d, and the stars
Did wander…”
Lonely planet
Earth is not the easiest place to be an organism, even if it is the only place in our nearest galaxies. The portion of land mass or continental area we are able to live in is only about 12% because we are not adaptable to hot or very cold weather. Apparently, the most recent super volcano eruption occurred at Toba in Northern Sumatra, about 74,000 years ago and almost annihilated human kind; maybe a thousand human survived, which account for the lack of our genetic diversity.
Greenland ice cores show that the Toba blast was followed by at least six years of “volcanic winter” and many poor growing seasons after that. There are currently 13 active super volcanoes and Yellowstone in the USA is the only continental one. Yellowstone is estimated to erupt every 600, 000 years and is ready for another of his monstrous feat; the last eruption was estimated to spew enough ash to bury the State of California under 6 meters of ash; ash covered the whole western states of the USA and a large part of Canada.
We belong to the portion of living things that decided 400 million years ago to crawl out of the sea and become land-based and oxygen-breathing creatures. We abandoned the vast seas for a more restricted area with the advantage that we can climb over 7000 meters and live at very high altitude while the feat of the Italian Umberto Pelizzari recorded 72 meters under water. We cannot bear the pressure of the water; for every 10 meters of depth we add one atmosphere.
A few professional divers, aided by weight to descend up to 150 meters, their lungs are compressed to the dimensions of a Coke can. Since our body is mostly water and water cannot be compressed by water, it is the gases in our body that is fatal in the depths. At a specific depth, Nitrogen in our system starts to bubble and enter our blood stream and obstruct the tiny blood vessels, depriving cells of oxygen.
Human technology was able to send a diving vessel to the deepest point in the Mariana Trench in the Pacific at 11.3 kilometers down; they discovered a type of crustacean similar to shrimp but transparent. There are particular microbes that strive in water at temperature over 70 degrees Celsius.
Observers have identified two dozen fortunate breaks we have had on Earth to create the living organism. If the Sun was larger it would have exhausted its fuel before Earth could be formed because the larger the star the more rapidly it burns. If we were two light minutes closer to the Sun we would be like planet Venus that cannot sustain life; Venus surface temperature is 470 degrees Celsius and all its water has evaporated driving hydrogen away into space.
If we were 1% further from the Sun we would be like frozen Mars. If our core didn’t contain molten liquid we would not have magnetism to protect us from cosmic rays. If our tectonic plates didn’t collide to produce more gases and continually renew and rumple the surface with mountains then we would be under 4,000 meters of water.
If our moon was not large enough, one fourth the size of Earth, then Earth would be wobbling like a dying top with unstable climate and weather. It is to be noted that the Moon is slipping away at a rate of 4 centimeters a year, relinquishing its gravitational hold. If comets didn’t strike Earth to produce the Moon or asteroid to wipe out the Dinosaurs or if we didn’t enjoy enough stability for a long time human would not be what they are.
Earth contains 92 naturally occurring elements and barely 6 of them are of central importance to life.
Of every 200 atoms in our body, 126 are hydrogen, 51 are oxygen, 19 are carbon, 3 are nitrogen and the remaining atom is divided among all the other elements such as iron to manufacture hemoglobin, Cobalt for the creation of vitamin B12, Potassium and Sodium for the transmission of electrical charges in the nerves, Molybdenum, manganese and vanadium to keep the enzymes purring and Zink to oxidize alcohol.
Oxygen is the most abundant element on Earth crust of about 50%, then silicon, and aluminum the fourth. Carbon is only the 15th most common element or 0.05% of Earth crust, but is the most promiscuous since it adheres to almost every atom and holds extremely tight, and is the very trick of nature to build proteins and DNA.
What we marvel at is not that Earth is suitable to life but that it is suitable to our life. A big part that Earth seems so miraculously accommodating is that we evolved to suit its severe conditions. When elements don’t occur naturally on earth, like plutonium, we have evolved zero tolerance for them. Selenium is vital to all of us but is toxic at a little higher level; even tiny dozes of arsenic, lead, copper and other natural elements we have managed to tolerate but industrialization is not allowing the natural tolerance process in evolution to absorb these huge amounts of noxious elements in our artificial environment.
The building blocks of life might be the 20 amino acids that combine in certain sequences to form the 700,000 kinds of proteins in our body; the number of proteins discovered is increasing and might be in the range of one million kinds.
Hemoglobin is only a chain of 146 amino acids long, a runt by protein standards in length, and yet it offers 10 at an exponent of 190 possible amino-acid combinations in order to have the exact sequence of the different kinds of amino acids.
To make the protein called “collagen” you need to arrange 1,055 amino acids in precisely the right sequence which means you need 1,055 spinning wheels with 20 symbols in each wheel to coincide exactly for the jack pot! Thus, the odd that any protein was formed by hazard is nil.
Any protein cannot reproduce itself and it needs DNA, which is a whiz in replicating itself.
DNA can do nothing but replicate proteins and proteins which are useless without DNA. Are we to assume that these two organisms arose simultaneously with the purpose of supporting each other?
No atom or molecule has achieved life independently; it needs some sort of membrane to contain them so that they come together within the nurturing refuge of a cell. Without the chemicals, the cell has no purpose. It is little wonder that we call it the miracle of life. Forming amino acids is not the problem because if we expose water to ammonia, hydrogen sulphide and methane gases and introduce some electrical sparks, as a stand-in for lighting, then within days you will have amino acids, fatty acids, sugar and other organic compounds.
What was needed is a process of a few of these amino acids to procreate and then cluster to discover some additional improvement.
What do we know about cells so far?
A single cell splits to become two and after 47 doublings you have 10 thousand trillion cells and ready to spring forth as a human being. Each cell carries a copy of the complete genetic code, the instruction manual for your body, and it knows far more about you that you do, and is devoted in some intensively specific way to your overall well-being.
The human body has at least a few hundred types of cells and they vary in shape, size, and longevity; we have nerve cells, red blood cells, photocells, liver cells that can survive for years, brain cells that last as long as we live and they don’t increase from the day we are born but 500 die every single hour, and so forth. The components within a cell are constantly renewed so that everything in us is completely renewed every nine years.
The outer casing of a cell is made up of lipid or light grade of machine oil but on the molecular level it is as strong as iron, then the nucleus wherein resides the genetic information and the busy space called cytoplasm. The cell contains about a thousand power plants or mitochondria that convert processed food and oxygen into ATP molecules or battery packs.
A cell would use up one billion ATP molecules in two minutes or half the body weight every day. The electrical energy activities in a cell is about 0.1 volts traveling distances in the nanometers; or when this number is scale up it is the equivalent of 20 million volts per meter or the amount of what a thunderstorm is charged.
Each strand of DNA is damaged 10,000 times a day and swiftly repaired, if the cell is not to perish by a command received from a hormone. When a cell receives the order to die then it quietly devour its components. For example, nitric oxide is a formidable toxin in nature but cells are tremendous manufacturers of this substance which control blood flow, the energy level in cells, attacking cancerous cells, regulating the sense of smell, and penile erection among other things.
Our body contains 200,000 different types of protein and we barely understand a tiny fraction of them.
Enzymes are a type of protein with tasks to rebuild molecules and marking the damaged pieces and other protein for processing.
A cell might contain 20,000 different types of protein.
In the 1860s, Louis Pasteur showed that life cannot arise spontaneously, but come from pre-existing cells.
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Adonis Diaries 