Planet Earth/7b. What is Life?

What is Life?
Growing up in a large family in North Carolina, Kizzmekia Corbett took an interest in understanding microbiology. She enjoyed working in science labs during her undergraduate education, where she specialized in the study of the organic chemistry and the study of some of the simplest organisms that live on Earth today in the field of microbiology. Tiny, nearly invisible, these simple organic molecules reside within the gray area of what is commonly defined as life, but to Corbett, these tiny complex organic molecules were especially important because they are responsible for large numbers of deaths. Corbett studies viruses, the simplest form of life on Earth, which sit in the weird gray area of what scientists define as life. Her research would catapult her to the international stage, as she specialized in a group of viruses called corona viruses. Her research into their chemical structure would become vital, when a pandemic of a new novel corona virus spread internationally in the spring of 2020, a lethal virus affecting hundreds of thousands of people, many in the United States and Europe; closing schools, destroying economies, resulting in the most significant threat to civilization since World War 2. At the young age of 34, Corbett found herself racing to find a vaccine during the summer of 2020 at the National Institute of Allergy and Infectious Diseases.

What is life? And are viruses, such as the novel 2019 corona virus (Covid-19 virus), living creatures? Chemically defined viruses are complex arrangements of carbon atoms bonded to a series of hydrogen, oxygen, nitrogen, and phosphorus atoms. This complexity of carbon-based molecules form the discipline of organic chemistry.

Organic Chemistry
Carbon typically covalently bonds to four, three or two other atoms, by having 4 valance electrons in the orbitals. In inorganic molecules this is typically hydrogen forming methane (CH4) or oxygen forming carbon dioxide (CO2), or could be other carbon atoms, like in graphite and diamonds. Although another common carbon molecule is the carbonate anion (CO3-2) where three oxygen atoms are bonded with carbon, with an extra two electrons (giving it a negative charge, as an -2 ion) allowing for an ionic bonding with calcium, magnesium or other cations. Hydrocarbon molecules are where carbon atoms form a short chain, surrounded by hydrogen found in common fuels such as ethane (C2H6), propane (C3H8), butane (C4C10), pentane (C5H12), hexane (C6H14), heptane (C7H16), and octane (C8H18) used in cooking, heating and automobiles, each with an addition carbon atom, forming increasingly longer and longer chains of carbon surrounded by hydrogen atoms. In complex organic molecules, carbon can form very long chains of carbon atoms into what is called a polymer. A polymer is complex molecule composed of many simple sets of molecules that are repeated, forming a chain. Unlike a crystalline lattice structure found in rocks and crystals, polymers are repeating chains or long strings of atoms, rather than structural blocks of molecules bonded on all sides. An example of a polymer is polyethylene plastic, which is composed of repeating carbon to carbon bonded atoms, surrounded by hydrogen atoms. Most plastics are composed of repeating structures of carbon atoms forming polymer chains, which makes them a very useful material, as they can be stringy and flexible when heated, but strong, like bound fiber when cooled. These chains of carbon can also fold in on themselves and can be bonded to other elements. Polymers can also be made up of six-membered carbon rings, individually called benzene rings, which can be bonded into polymers, forming even more complex molecules called phenyl. Pyridine is when one of the six carbons in the ring is replaced by another element, like nitrogen. Ringed organic molecules are often called aromatic as they often have odors or aromas, and some are used in artificial flavoring. While others like benzene if inhaled in large amounts can cause cancer.

The field of organic chemistry is the study of these complex organic carbon molecules formed by chains of carbon bonds with various elements. Such complex organic molecules of carbon are found in organic matter that are naturally produced by living organisms, but these molecules are not living on their own, and most can be synthesized in a lab.

The importance of water for life
The interaction of these long polymer chains of carbon atoms in an aqueous solution of water is an important physical consideration. Some ends of these chains can be hydrophilic (water loving), which means they are attracted to the polarized H2O molecules in water, while other ends of these chains are hydrophobic (water fearing) and are repelled from the polarized H2O molecule in water. If a polymer chain has one end that is hydrophilic and another end that is hydrophobic, it is what is called amphiphilic. Amphiphilic carbon molecules can form a micelle. A typical micelle in an aqueous solution forms when the hydrophilic ends of the molecule are attracted and contact the surrounding water, while the hydrophobic end of the molecule point inward toward regions in the micelle center and away from any contact with the water. This can result in spherical bubbles, that will form in the water. Many soaps are composed of long chains of carbon atoms, with one end that is hydrophilic, and the other hydrophobic. The hydrophilic end of the molecule of soap is most often a result of having sodium Na+ or potassium K+ ionically bonded to these ends of the molecule. One of the most common ingredients of soaps is sodium laureth sulfate, which is a long chain of carbon and hydrogen atoms, with a hydrophilic end composed of a sulfur atom bonded to oxygen (sulfate), with one of the oxygen atoms ionically bonded to a sodium ion (Na+). When this molecule is introduced to water, the sodium ion (Na+) dissolves, leaving behind an anionic negative charged end, that attracts the positive charged side of the surrounding water molecules (H2O). Many micelle will form, resulting in suds and bubbles, when agitated in water. Another type of soap, common in hand sanitizers is benzalkonium chloride, which has a hydrophilic end with a negative charged chloride atom, which will dissolve in water leaving a positive charged hydrophilic end or head and will attract surrounding polarized water molecules. These types of molecules are sometimes called salts of fatty acids, since they contain a salt (ionic bonds of sodium, potassium or chloride), as well as an acid (since they increase the amount of hydrogen ions in a solution), and have a fat, or a lipid end. A lipid is any long chain of carbon molecules that have hydrophobic ends, and will not dissolve in polarized liquid molecules, such as water. Many oils, fats, and cellular membranes of organisms are composed of lipids, as they repel water molecules. One of the reasons oil and water don’t mix, is that oil is composed of hydrophobic chains of carbon molecules. The reason that soaps work so well to wash oils and fats is because the hydrophobic end of a soap will dissolve into the lipid molecules, while the hydrophilic end will dissolve into the water, resulting in a micelle around the lipid molecules isolating and breaking them apart.

Phospholipid Membranes
Viruses such as the corona virus, have a lipid membrane, making them susceptible to breakage in the presence of soaps formed from these types of micelle forming molecules. The membrane will rupture, breaking apart the lipid membrane. Liberal use of soap when washing is important because it cleanses these dangerous particles away. Lipids are important however, as they are the group of molecules that typically form cellular membranes that protect the internal parts of cells in living organisms. Some cellular membranes are composed of amphiphilic molecules such phospholipids, which have hydrophobic and hydrophilic ends, with the hydrophilic end composed of a phosphate group molecule, often joined with a glycerol molecule into two tails. These phospholipids will form two layers, with the hydrophobic tails pointing inward, and hydrophilic phosphate group molecules on either side. Because most lifeforms use phospholipid cellular membranes, phosphorus is a required element for life, in addition to carbon, oxygen, and hydrogen

Amino Acids
One group of organic molecules that are important for life to exist are amino acids. Amino acids contain amine (-NH2), which is similar to ammonia (NH3), but with a covalent bond in the chain of carbon atoms, by having one less hydrogen atom. Amino acids also have a carboxyl group (-COOH), where carbon, which in addition to being bonded to the carbon chain, is also bonded to two oxygen -COO-, with one of those oxygen atoms bonded to a hydrogen atom -OH. These two key parts of amino acids indicate that carbon, hydrogen, oxygen, phosphorus and nitrogen are all elements necessary for life, but amino acids individually are not life, and can be synthesized in a lab as well as found in nature as isolated molecules. There are about 500 variable amino acids, although most lifeforms contain about 20 varieties of amino acids.

Amino acids can be linked together when the amine ends (-NH2) contributing a single hydrogen atom, while the carboxyl end (-COOH) contributes an oxygen and hydrogen atom, together these three atoms form a molecule of water (H2O) as well as linking these two amino acids together to form a chain. Such linking of strings of amino acids together can form very large molecules called proteins. This process is called peptide bonding, and is a type of polymerization. Proteins are gigantic macromolecules that contain chains of amino acids linked together by these peptide bonds. Amino acids don’t normally bond together to form proteins by themselves individually, instead they need a catalyst, or enzyme that helps bind these links together. This intermediate molecule is called RNA (Ribonucleic acid). RNA is an extremely complex group of molecules consisting of many different types of atomic bonds of carbon, hydrogen and oxygen (but also nitrogen and phosphorus). There are billions and trillions of different combinations of RNA molecules, but the major types of RNA can be viewed in their role in building proteins.

Ribonucleic acid (RNA)
Transfer RNA (tRNA) is a molecule that has a distinctive folded structure in the shape of a three-leaf clover, with one end that corresponds to a particular type of amino acid, which it will bond to, while the other end called the anticodon will be attracted to a messenger RNA (mRNA) molecule and will bind to a corresponding codon, in the presence of a third molecule called ribosome RNA (rRNA). Depending on the expression of the messenger RNA molecule, the produced protein is made by linking amino acids together, and will be different depending on the expression of the messenger RNA molecule. RNA is formed by ribose (which is a sugar or carbohydrate). A carbohydrate is a molecule that has carbon atoms (C), which in addition to being bonded to other carbon atoms are also bonded to hydrate, which is oxygen bonded to hydrogen atoms (-OH). RNA also has four types of base pairs named guanine (G), cytosine (C), uracil (U) and adenine (A), the codons, which dictate the order of amino acids paired. RNA forms an extremely complex tangle of strings of atoms bonded together, which fold in upon itself, and is sometimes supported by a protein.

Where does RNA come from?
In the modern biological rich Earth, mRNA is synthesized by DNA in the cells of all living organisms. RNA is littered in every cell in every living organism on Earth. But can RNA form from inorganic chemical ingredients? This is one of the central scientific investigations into the origin of life on Earth, and it is actively being researched. Scientists have focused on a type of RNA called ribozyme. Ribozyme is a molecule of RNA that can splice or break apart other RNA molecules. They can also catalyze their own synthesis from these fragmentary molecules. Ribozyme RNA can break apart RNA and bind those fragments into copies that resemble itself. Messenger RNA can also make copies of itself by making mirror images of the long chains of codons of nucleic acids, with reverse positive and negative copies. Since this type of replication is possible without the presence of DNA, researchers have proposed that the earliest life on Earth was composed of self-replicating RNA molecules, envisioning an RNA-world during Earth’s early history. But are these self-replicating RNA molecules life?

Are self-replicating RNA molecules life?
Many viruses, like the Covid-2019 virus that was killing so many people during 2020 and 2021, is a self-replicating RNA molecule that is packaged in a lipid membrane and bound by spike proteins. Spike proteins project from the lipid membrane giving the virus a crown when viewed under a scanning electron microscope, where the name corona, meaning crown comes from. The spike protein is unique in its chemistry to be able to enter certain cells in the respiratory tract of various mammals. Once inside the cell, the lipid breaks apart, and the protected RNA molecule is released into the cell. This molecule slices up the host cell’s RNA and DNA molecules, killing it, and using these fragmentary molecules to replicate copies of the virus RNA and spike proteins. Once a replicated copy of the virus RNA is synthesized it is expelled from the dead cell, using the dying cells lipids to form a membrane, with an arrangement of spike proteins (and other proteins) produced by the RNA molecule encircling it. Each infected cell can produce many millions of copies of the virus, which can over run the respiratory system, killing the person who becomes inflected, or making them very ill until their body can fight off the viral infection. RNA viruses exhibit two key characteristics of life. First, viruses can reproduce (make copies of themselves). Second, viruses can evolve through the heredity of traits encoded in the RNA. Each time a virus reproduces by making a copy of the RNA, it introduces a probability of novel changes in the copied RNA molecule. This process allows RNA to introduce and maintain variability in its chemical structure, this is very different than what happens in inorganic molecules like water (H2O). Despite differences in the isotopic composition of water (say in a chemical reaction), each molecule of water will be identical. RNA molecules on the other hand, because they are so large and complex each one can be chemically very unique. This is due to minor changes that are introduced into the RNA molecule. RNA molecules are like a large stack of playing cards, with a nearly endless series of different ways of ordering the position of each card in the deck. The origin of the COVID-19 virus appears to have occurred in bats, where a copied RNA strain had a new novel feature of having codons that replicate a spike protein that would allow the virus to infect human respiratory epithelial cells. Once the virus is able to infect a new host, these RNA molecules are copied, and can quickly spread from cell to cell, and from person to person. If the RNA strain produced a novel feature that prevents its entrance into a living cell, it would not replicate copies and would not spread. This ensures that RNA that successfully replicates is the type of molecule that will persist in an environment. In the unlucky case of COVID-19 the novel virus found success in being highly able to infect cells in the lungs of humans, but also produce asymptomatic cases that allowed them to spread between human individuals sharing a close physical spacing.

Life has the ability to change with time
This ability to change, or evolve is one of the key aspects of life, yet many scientists view viruses as more a chemical particle than a true living organism. This is because viruses lack many of the other characteristics of life. For example, living organisms grow. Viruses only make copies of their molecular make up, they don’t grow or change once they are produced or formed. In other words, there are no baby viruses or adult viruses. Furthermore, viruses don’t metabolize by gaining energy from chemical reactions, they only form from an initial chemical reaction, and require broken species of organic material found only in living cells. Once formed they don’t maintain homeostasis with stable inner conditions, rather viruses can easily be destroyed by heat, oxidation, or soaps that break open their lipid membrane. They are unable to respond to these events (such as swim away), and are unable to respond to changing environmental conditions. Most importantly viruses don’t have a cellular make up, most are simply formed from RNA molecules that are encased in a lipid and protein coat. Biologists however have suggested that these complex replicating molecules might be the precursors to life; imagining an early RNA World.

The origin of life, also came with the origin of death
Life at its basic level is simply self-organizing systems. That is the process of replication that favors an outcome, which in turn favors the continuation of that replication in a cycle. Imagine a deck of red and black cards, if a red card is dealt the card is discarded, if a black card is dealt, the card is kept, and a second card can be dealt, if that card is red, then both cards must be discarded, however if the first two cards are black the pile is kept, even if the next card is red. Each pile of successful cards is returned to the deck randomly. This process would over time slowly decrease the number of red cards, and increase the number of black cards in the deck. This is an example of a self-organizing system. For this to work, there must be the continued recycling of material, with short durations in regard to the molecules themselves. If RNA did not break apart easily, and instead remained for millions of years, like a crystalline structure of silicate minerals, these molecules would go from one state to another and then just stay there for long periods of time like a crystal.

One of the basic tenets for life at its simplest level is that these complex molecules must be easily broken so they can be recycled and reused for new molecules. In other words, for life to exist, it must do so alongside death. This means that the formation of these complex molecules must require the input of energy into the system, with the inevitable conclusion that these complex molecules will break apart in the environment they were created within after a short length of time. Every living creature must die at some point in its life, this short duration between the production (birth) of the molecule and its destruction (death) is short. This will ensure that the complex molecule will self-organize, but it also requires the constant input of energy.

Are viruses really life?
Not everyone agrees that viruses are living, and an alternative origin of viruses suggests that viruses originated from bacteria. Bacteria, unlike viruses have all the characteristics of life. They exhibit growth and development, reproduce (asexually and/or sexually), they pass on genetic information with the heredity of traits, the genetic information within the cells is variable and able to evolve and change through each generation, they exhibit homeostasis with stable conditions inside the cell, and can metabolize food by gaining energy from chemical reactions, including in some bacteria a very clever way of gaining energy from photons (photosynthesis), they have cellular bodies, and they respond to the external environment. Furthermore, they have very short lifecycles between birth and death, able to rapidly reproduce, but also quickly perish. And maybe most importantly they don’t depend on a host for reproduction, like viruses do.

Strains of RNA if they were to exist before the appearance of life on Earth, would need to be able to replicate from inorganic molecules, like amino acids. This is an active field of research, with some theories regarding how this might be possible early in Earth’s history. One idea is that amino acids were bonded together by ligase ribozyme RNA strains, which joins strands together by a phosphate ester linkage. This method has been used in laboratories to synthase RNA strands, where the ends of RNA molecules are held in proximity to one another by a splint, until they become linked together. The other idea is that RNA forms a template, which in the presence of RNA polymerase ribozyme attracts theses subunits to the RNA template to form a copy of the molecule, a primitive but similar way in how messenger RNA works in living cells to make proteins, but making copies of the RNA itself instead.

Basic Traits of Life

 * 1) Exhibit growth and development
 * 2) Reproduce
 * 3) Heredity of traits between generations
 * 4) Variable and individually unique characteristics
 * 5) Evolve and change through time
 * 6) Exhibit homeostasis
 * 7) Metabolize food or energy
 * 8) Exhibit cellular bodies
 * 9) Respond to the external environment
 * 10) Expire or die with time

Viroids
RNA to RNA replications have been observed both in nature and in the laboratory. In nature RNA to RNA replication has been found in a type of infectious pathogen that effects plants, called viroids. Viroids are short strands of circular, single-stranded RNA molecules that lack a protein coat. The RNA in viroids does not code for proteins, instead they are able to replicate RNA using RNA polymerase enzyme found in a host cell to synthesis new RNA. This is done by using the original viroid’s RNA as a template within a plant’s cell. Some viroids are ribozyme RNA, which can also use cleavage or split larger molecules in a host cell and use ligation to bring those fragments together to aid in replication of new strands of RNA. In a laboratory setting, the work of Tracey Lincoln and Gerald Joyce have demonstrated that RNA enzymes can self-replicate in a laboratory by RNA-template joining in perpetuity as long as they have an active supply of subunits for which to synthesize that RNA.

Vaccines
In the spring of 2020, Kizzmekia Corbett watched the head of National Institute of Allergy and Infectious Diseases give daily briefings of the rising death toll as the new virus spread across the United States. By May of that year, nearly 60,000 American citizens had died of the novel corona virus, by June it had doubled to 120,000, in September it rose to 200,000 dead and two years later nearly 1 million Americans had died of the virus, a rate more rapid than many other countries in the world. The streets of New York City were parked with refrigerated trucks filled with dead bodies, waiting to be claimed by their loved ones. At no other point in the history of the United States of America have its citizens been so dependent on a clear understanding of the life sciences. The spread of the virus was a humbling reminder of the importance of science for the health of a nation. All this death, caused by an extremely tiny self-replicating particle of RNA, that scientists debate whether is a life-form or not.

The race was on to find a vaccine, a cure. Kizzmekia Corbett and her fellow scientists published a paper in the spring 2020 detailing the atomic structure of the virus spike protein, and how it gained entrance into human cells in the respiratory system using a protein in the cellular membrane called angiotensin-converting enzyme-2 (ACE2). The spike protein would allow the virus RNA to gain entry through this cellular door, like a key in a lock. In developing a vaccine or cure, one idea proposed by scientists was to synthesize the spike protein and inject it into a person. The spike protein would open cellular membranes, but without the RNA portion of the virus, the cell would not become infected and result in new copies of viral RNA. This would allow the cell to respond by building antibodies to prevent further holes opening in the membrane due to these spike proteins. If the person would later be exposed to the virus, the antibodies would help prevent the virus infecting cells, and prevent its replication by building a resistance to the virus. This is how vaccines often work. Such inoculations work as long as the protein spike does not change or evolve through new generations of the virus, and often needs to be updated, or followed up with booster shot of those proteins. Another more radical idea was proposed that involves injecting messenger RNA that codes for the spike protein instead. This would allow the RNA to replicate the spike protein and result in immunity to the virus for a longer time, since it would be synthesized by the body using RNA. This novel technology lead to the Moderna and Pfizer RNA vaccines that proved more successful in fighting this disease.

How we define Life
One of the key aspects of life is the rapid recycling of complex molecules, building them up and breaking them down, which results in a self-replicating cycle that becomes self-organizing toward successful modes of replication. Simplistically, life is a complex set of molecules that is continually formed and destroyed, through a system that promotes self-replication, matched with trial and error. We can think of life as anything that is born, loves (reproduces), and dies over a short time scale. You share the same cycle as the simplest virus; birth, love, and death. The reason a crystal is not living, is that it may be created through chemical reactions, but it does not reproduce itself, and only changes due to chemical, temperature and pressure change to its structure over millions of years. The rock cycle is immensely slow. Life, on the other hand, is fleeting, oscillating between life and death, and rebirth, hourly, daily, and yearly. Life gains its essence through its fragility.