That Fundamental Unit of Life, Cells

 




Life, in all of its diverse forms, are present in the biosphere and wherever we look, whether it is a natural habitat such as a coral reef, a tropical rainforest, an arboretum or even in your own backyard, one cannot help but notice the diversity that is life. As different as life appears , there is something that all life have in common. What is that common denominator that all of life share? What is that fundamental unit of life and would it share all of the attributes that life has as was explained in my last post on a scientific definition and if it does how do the definition of life apply to that biological fundamental unit? What is this universal attribute of life? It is that biological structure called cells and with cells, all characteristics  of biological life are present and not only will I talk about what a cell is but more importantly I will describe how the definition of life as a dynamic process as part of NET (see my blog on life and NET under the title “What is Life, Really?”) applies to cells.

 

 

This is an example of a eukaryotic cell or cell with a nucleus and internal structures called organelles. A cell such as this one displays all the attributes of life. (LECA)

This is an example of a eukaryotic cell or cell with a nucleus and internal structures called organelles. A cell such as this one displays all the attributes of life. (LECA)

 

 

In my previous post “What is Life, Really?” I talked about 7 defining characteristics of life, which are homeostasis, metabolism, growth, adaptation, organization, response to stimuli, and reproduction. I gave a general description of each biological fact as part of my argument on the nature of life. Let’s see how each separate definition applies to cells, which form the basis of both unicellular and multicellular organisms. Also, in my last blog, I argued that life is a process that is made possible by the second law of thermodynamics and I will show how the cell, as the fundamental unit of life, conforms to the broaden definition of life as an energy requiring process that evolves into more complex forms which processes energy and matter allowing it to avoid equilibrium.

 

                                                                      Homeostasis

 

The inside of the living cell as well as its outside is an intricately arranged structure that is dynamic and inside the cell, there are large complex molecules such as the variety of proteins, or molecules that carry out a variety of functions such as enzymes and transport proteins to name a few and all proteins, lipids, and carbohydrates are synthesized from small molecules and the bulk of the cell, the cytoplasm, is not a homogenous fluid but a heterogenous fluid with water, minerals such as cobalt and iron, enzymes which catalzye varieties of biochemical reactions and in the case of bacteria or prokaryotes generally, a cytoplasm with the DNA arranged in chromosomes, ribosomes where protein molecules are synthesized, enzymes throughout the cytoplasm as well as enzymes in the cell membrane and surrounded by an outer rigid structure called a cell wall, whereas in the eukaryotic cells, there are a variety of internalized membrane bound structures called organelles, the largest organelle being the nucleus where the DNA is arranged in linear structures called chromosomes, like in prokaryotes but in the eukaryotes, the DNA is wound around in small spherical proteins called histones which organize the DNA into chromosomes which tend to readily show under the microscope when the eukaryote cell undergo mitosis or cell division. Living cells must be able to maintain that internal structure in whatever environment it is in, and to live is to expend energy in maintaining the internal structure such importing food in the form of monomers like sugars, amino acids, fatty acids, and oxygen and giving off wastes such as carbon dioxide, water, and heat, which is applicable to some species of protists such as paramecia and all animal cells. There is a process that allows cells to keep its vital physiological functions within narrow limits in order to survive in its own native environment and that process is homeostasis.

 

Homeostasis is the process by which life forms such as cells keep all the vital and necessary biological functions constant and within narrow limits. It must be able to do this since whatever is present in the cell’s environment is constantly fluctuating and the cell must be able to keep up if it is to survive accordingly. There are three related components that make homeostasis possible and there is the sensor which monitors any changes in the environment which is usually the cell’s outside environment as well as the inside of its environment. The other two components are both positive and negative feedback mechanisms and the former if an input is receive through the sensor causes an increases in any internal mechanism resulting in a change in behavior such as movement towards a food source, and the latter, if that same set of internal mechanisms reaches a limit, is then shut off. All three worked interdependently to keep the integrity of the cell constant which is homeostasis.

 

To function as a whole, there is a single structure common to all cells, whether unicellular and multicellular,  and allow the cell’s vital integrity to be maintained and that is the cell membrane. The cell membrane is composed of a lipid or fat molecule called a phospholipid. This is a molecule that has two parts, a hydrophilic or water loving part that consists of a single phosphate atom bonded to three oxygen atoms and both oxygen and phosphate atoms are negatively charged and since cells can only function in an aqueous or water based environment, each water molecule bonded to two hydrogen atoms to a single oxygen atom with the oxygen atom with an excess negative charge and two positive charges on the two hydrogens. The other part of the lipid molecule consists of carbon and hydrogen and it is hydrophobic or water hating and when the phospholipid is immersed in water, the hydrophilic part is attracted towards the water on the outside as well as on the inside while the hydrophobic part avoids the water and so with a dual ability to seek out and avoid water, a cell membrane , which in living cells is double layered is formed and there results in a distinct separation between the outside which is inaminate and the inside which defines all the dynamic living activities which is the cell.

 

 

The cell membrane of a chloroplast or the organelles in plant cells that carry out photosynthesis. Light, in the form of photons or quanta of electromagnetic radiation strikes a chlorophyll molecule and the energy of the photon is converted into a series of chemical reaction with oxygen being released as a waste product and ATP, the universal donor of energy being created. The chlorophyll is an example of a receptor protein which detects a stimulus and starts a response. (Blue Ridge Kitties)

The cell membrane of a chloroplast or the organelles in plant cells that carry out photosynthesis. Light, in the form of photons or quanta of electromagnetic radiation strikes a chlorophyll molecule and the energy of the photon is converted into a series of chemical reaction with oxygen being released as a waste product and ATP, the universal donor of energy being created. The chlorophyll is an example of a receptor protein which detects a stimulus and starts a response. (Blue Ridge Kitties)

 

 

How does the cell membrane play a part in the cell’s homeostasis? The cell membrane, although it may be impermeable mainly because the inside of the membrane has hydrophobic molecules, substances do get in an get out and that is possible because of specialized protein molecules called transport proteins.

 

Transport proteins allow certain molecules, such as sugar, amino acids, and oxygen in, and wastes like water and carbon dioxide out. In addition, there are other proteins that  play a role in cellular homeostasis, and these are receptor molecules which respond to stimuli such as visible light and hormone and both cause an internal change in the cells. The receptor molecules define the sensor component of homeostasis and as sensor, allows the cell to change its action such as moving towards a light source if the cell is an Euglena or in more complex organisms like our selves and other animals, if there is food, our eyes will pick up the sight of food which is a complex organ consisting of various types of cells for different tasks such as the retinal cells for processing light and converting that light into a series of nervous impulses and with the nose, the smell of food is picked up by the olfactory nerves which alerts us to the smell of food and together with the sight, those stimulate the hunger response and so we walk towards the food, powered by our muscles along with the motor neurons that stimulate the muscles that contract and relax resulting in a pattern of directed movement, all of which is possible for multicellular organisms, the result of specialized types of cells all coordinating towards the common goal of finding food. For unicellular organisms it is the same but with only a single cell, there is still the purpose of finding food and movement is made possible by specialized structures called flagella which are the whiplike structures found in most species of bacteria allowing for movement as well as in some species of protists like Euglena but much more sophisticated. Like the cell types that form the sensor component, the only sensors are the receptor proteins which can discriminate easily between the molecules that are nutrients and so the cell will respond to them and the molecules that are poison and the cell will move away.

 

The other two process of homeostasis , the feedback mechanisms, consists of both positive feedback, or if the input is a nutrient molecule, it must be broken down into a series of intermediates and in the process bits of biochemical energy is transferred into specialized molecules such as ATP. One of the intermediates may act to further enhance production of one core intermediates , furthering enhancing more production and that is the positive feedback and as long as there is a flux of a given reactant such as a glucose molecule, then positive feedbacks are possible. Of course there is a limit to an increase in whatever intermediate metabolism and if that increase were to pass some threshold, then the opposite of positive feedback which as you would guess correctly is negative feedback and that prevents any further growth of any intermediate metabolite.

 

Sensors, positive, and negative feedback are all part of the cell’s organization and all three act to keep the cell alive but to stay alive is to input high quality energy in and low quality energy out and since homeostasis is one of the functions of physiology, and like all processes of energy, that too requires energy and that energy is derived from another process, metabolism.

 

 

                                                                            Metabolism

 

Life is a process, a specialized dynamic pattern of organization and to be a dynamic pattern  requires energy and the flow of energy, as well as the flow of matter, is what powers life in order to carry out the criteria listed. The universe is full of energy, which according to the first law of thermodynamics, can change into many forms but life has evolved ( at least the life we are familiar on this planet) to use two forms of energy, electromagnetic energy, in the form of visible light, and chemical energy in the form of ATP, an universal energy donor present in all life forms, carbohydrates, proteins, and certain minerals emitted from hydrothermal vents. Those two forms of energy must be utilized in a specific way to keep life away from thermal equilibrium which is equivalent to death.

Cells use these two forms of energy to avoid equilibrium and to do so, an influx or flow of energy, whether in the form of light, sugars, amino acids, water, and minerals, and a flow of wastes out such as carbon dioxide, water, and heat. It is this pattern of inflow and outflow, that allows the cell to not only avoid equilibrium but to reproduce, to synthesize molecules out of small molecules, and to evolve and this is made possible by the coupled set of reactions called metabolism.

 

Since staying alive is an energy requiring process, metabolism is that set of processes that makes life possible for the cell. Metabolism is composed of two biochemical reactions. One that is a breaking apart process called catabolism and the opposite of catabolism is a building up process called anabolism. The former releases energy and the latter requires energy.

 

Molecules like carbohydrates, proteins, and lipids, must be broken down into glucose, amino acids, and fatty acids and glycerols respectively. This is accomplished by a set of protein molecules called enzymes and these kinds of molecules facilitate the process of catabolism or breakdown by splitting the bonds between the monomers or building blocks without the enzymes themselves being affected not by one bit. There are many different kinds of enzymes, each specific like a given lock to a given key, and it this “lock and key” mechanism that allows enzymes to break down molecules so the cell can utilize them for the process of biosynthesis or the buildup of cells in order to make more cells.

 

The process of buildup is called anabolism, and unlike catabolism, requires an input of energy and that source of energy comes from the breakdown of that universal energy donor called adenosine triphosphate or ATP for short. This molecule stores chemical energy in the form of three phosphate bonds and the bonds are pretty unstable and if one of them is broken, energy is released and this released energy can be used to combine two monomers together, whether it is two glucose molecules, two amino acids, or two nucleotides together.

 

In order to make ATP, which is itself an energy requiring process (you can never get something for nothing all thanks to the laws of thermodynamics!) requires a coupling or combination of catabolism and anabolism. In both plant and animal cells, glucose undergoes a process called glycolysis where glucose, as well as amino acids are broken down into a compound called pyruvic acid. The pyruvic acid then goes through a cycle called the Krebs Cycle which takes place in the mitochondria and these are the organelles where nutrients such as  glucose are converted into pyruvic acid from glycolysis which takes place in the cytoplasm and once in the mitochondria, the pyruvic acid is converted first into acetyl-CoA and in a step by step series of reaction ( I will spare you the details) going back to acetyl-coA, energy is released but in the form of two carries FADH and NADH one of these  is involved in what is called electron transfer reactions and here with FADH from the Krebs cycle, electron flow through a set of proteins which provide chemical energy in the form of a gradient of protons, outside and inside the mitochondria and the flow of protons specifically go through an enzyme called ATP synthase and as the name suggest, this enzyme combines ADP or adenosine diphosphate and a single molecule of phosphate and as the protons flow through the enzyme, ADP and phosphate are combined together to form one molecule of ATP and for every flow of protons, one molecule of ATP is synthesized and each ATP can then be broken down to release energy for any anabolic process. All of this is the result of the flow of electrons but the electrons end up somewhere and each electron ends up in one molecule and that is oxygen. Oxygen or molecular oxygen accepts each electron and water forms while carbon dioxide is released from each turn of the Krebs cycle so both water and carbon dioxide are released as wastes. More simply and somewhat poetically, the power of life is the result of an electron coming to rest.

 

This process , known technically as oxidative phosphorylation , involves a final electron acceptor, such as oxygen where the flow of electrons towards oxygen produces the proton gradient between the membrane of a mitochondrion where the chemical energy produced is use to synthesize ATP. ATP is synthesized from ADP and inorganic phosphate as long as there is a flow of both electrons and protons and these flows are coupled to the cycle of the Krebs cycle making one revolution which depends on the flow of glucose and amino acids and with a flow of glucose and amino acids, this results in a full complete spin of the Krebs cycle and that ultimately produces the ATP while wastes such as carbon dioxide, water, and heat are released to the environment. From the perspective of non equilibrium thermodynamics, the cell remains a non equilibrium system because of the inflow and outflow of matter and energy and so results in the coupling of catabolism and anabolism that is metabolism.

 

In eukaryote cells, oxidative phosphorylation or respiration for short takes place in the mitochondria with glycolysis occurring in the cytoplasm whereas in prokaryote cells especially those prokaryotes that use oxygen, it occurs in the cell membranes using specialized enzymes for that particular kind of task of utilizing chemical energy for ATP synthesis. Also in those kinds of eukaryotic cells that carry out photoautrophy which is a fancy term for cyanobacteria, algae, and plants, whereas unicellular protists like amoebas, paramecia and the rest of the animal kingdom which is multicellular are organoheterotrophs and can survive by getting  complex organic compounds made by organisms such as carbohydrates and proteins.

 

A drawing of a plant cell and in this cell, in addition to the nucleus which carries genetic instruction on how that plant cell is made and ribosomes where DNA language is translated into protein language, there are the chloroplasts where photosynthesis occurs and mitochondria where energy is released into ATP. Photosynthesis also produces ATP and in the presence of energy flow in the form of light, glucose is produced from carbon dioxide and water. Not only is the plant cell capable of carrying out both photosynthesis and respiration but plant cells whether in the form of green plants and algae form the foundation of the biosphere.

A drawing of a plant cell and in this cell, in addition to the nucleus which carries genetic instruction on how that plant cell is made and ribosomes where DNA language is translated into protein language, there are the chloroplasts where photosynthesis occurs and mitochondria where energy is released into ATP. Photosynthesis also produces ATP and in the presence of energy flow in the form of light, glucose is produced from carbon dioxide and water. Not only is the plant cell capable of carrying out both photosynthesis and respiration but plant cells whether in the form of green plants and algae form the foundation of the biosphere.(Ambra Galassi).

 

With the synthesis of ATP, the breakdown of ATP releases energy and the released energy is channeled for specific biochemical reactions such as protein synthesis. This is a universal and vital process in all cells, and this involves instructions first in the form of a sequence of nucleotides which are the building blocks of DNA and another related molecule called RNA that copies the exact genetic information and carry that information to the ribosome where protein molecules are synthesized. In the ribosomes, RNA, in the form of a molecule called messenger RNA is placed through the ribosome where the ribosome reads each sequence in groups of three bases, as copied from DNA, and the ribosome takes in another set of RNA molecules called transfer RNA and each transfer RNA carries an amino acids. Amino acids and transfer RNA molecules are combined together with the breakdown of each ATP and with the breakdown of ATP both transfer RNA and amino acid combine together and with the ribosome reading each message , the amino acid from each transfer RNA then combines to the ribosome, one transfer RNA after another with each amino acid and so a chain of amino acids, in that process of protein synthesis results and protein synthesis is an anabolic process made possible not just by genetic instructions but by the release of energy from the breakdown of ATP.

 

Photosynthesis would be the opposite of oxidative phosphyorlation or more simply respiration. In this process which is an anabolic process the energy of sunlight is used to synthesize carbohydrates from water and carbon dioxide, both waste gases from respiration and using these wastes, photosynthesis is an efficient process occurring step by step in the synthesis of glucose molecules which will form starches and cellulose. Notice that photosynthesis uses the waste of respiration in order to make something vital such as glucose first as a source of energy needed to make ATP through respiration while serving as food for other organisms first in the herbivorous animals such as caterpillars, and carnivores such as birds. Both of these organisms only carry out respiration and release carbon dioxide and water while plants release oxygen as a waste products and the respiration is used both in plants and animals but more so in unicellular organisms which in the cell is where these two processes occur. Recycling was invented by life and that too involves the flow of energy. It occurs within and between cells and with such efficiency which persisted in the biosphere for 2 billion years and will continue to do so thanks to flow of visible light in and flow of infrared or heat energy out.

 

                                                                                Organization

 

I have argued that life is not only a dynamic system characterized by negative entropy, but it is a complex organization that carries out all the listed criteria for living. As I have said before, negative entropy as a rough measure of order and function depends on flow and outflow of matter and energy otherwise if such flows stopped then thermal equilibrium is inevitable and only the flows in and out keeps a complex system like cells alive. Cells, as you are probably aware come in two forms, prokaryotes and eukaryotes. Prokaryote cells such as bacteria are not only small but have an internal organization consisting of DNA wrapped in chromosomes in a cytoplasm but with no organelles other than ribosomes which are smaller than those in eukaryotes and the ribosomes carry out protein synthesis in both prokaryotes and eukaryotes. Both cell types have a membrane with both transport proteins and receptors and even enzymes but in prokaryotes, there is an additional layer outside the cell membrane in prokaryotes called a cell wall which is made up of a protein and carbohydrate complex called a peptidoglycan layer and that keeps the structural integrity intact.

 

In the prokaryote cells, there are ribosomes where protein synthesis takes place using transfer DNA and messenger RNA and the DNA is arranged in chromosomes carrying the information needed for the prokaryotes to live and reproduce. A variety of enzymes are in the cytoplasm for various tasks such as DNA replication and metabolism.

 

A population of bacteria under the microscope. Bacteria are typical examples of prokaryotes or cells without nuclei and organelles. Prokaryotes are presumably the first life forms to appear after the formation of the earth and had a profound effect in the evolution of the biosphere.

A population of bacteria under the microscope. Bacteria are typical examples of prokaryotes or cells without nuclei and organelles. Prokaryotes are presumably the first life forms to appear after the formation of the earth and had a profound effect in the evolution of the biosphere.(Umberto Salvignin)

 

 

This is in contrast to the eukaryote cells which have more internalized structures organelles which perform specific functions such as mitochondria for oxidative phosphorylation, chloroplasts for photosynthesis, a network of inner membranes called the endoplasmic reticulum , Golgi apparatus for export of cell synthesized materials, lysosomes for destroying old cell parts, and other microscopic structures for various other tasks, along with a defining feature present in all eukaryotic cells but lacking in prokaryotes and that is the nucleus, which is clearly visible under the microscope. In the nucleus, the DNA is arranged in units called genes. Genes are present in prokaryotic chromosomes but in eukaryotes, the genes are arranged differently. Eukaryotic genes tend to be separated into exons which are genes that code for proteins and by introns which do not code for any protein and in multicellular organisms introns tend to outnumber exons for reasons that are still obscure. Genes are arranged in chromosomes because of histones or proteins that associate with eukaryotic genes into chromosomes and in the process of mitosis or cell division specific to eukaryotes, chromosomes tend to be visible under the microscope.

 

 

A schematic drawing of an amoeba with its specialized organelles along with the nucleus, a characteristic feature of eukaryotic cells. This is an example of a dynamic form of organization.

A schematic drawing of an amoeba with its specialized organelles along with the nucleus, a characteristic feature of eukaryotic cells. This is an example of a dynamic form of organization.(Jim)

 

Every biochemical activity is performed differently in each organelle and depending on which cell since every cell is different, a variation on a common theme in all cells whether in unicellular or multicellular organisms mainly because of a common evolutionary heritage, some cells like paramecia are like predators and must eat in order to survive and possesse special kinds of organelles called digestive vacuoles for breaking down food for energy and also possese several nuclei since in addition to cell division, paramecia also undergo a kind of sex called conjugation where genes are exchanged between partners.

 

In both prokaryotes and eukaryotes, both have a cell membrane that can discriminate which molecules can enter because of specialized proteins called transport proteins and both have ribosomes for protein synthesis. Enzymes are crucial in both cell types since they catalyze a variety of biochemical reactions. The difference is that in prokaryotes , no nuclei and no organelles and the DNA is in the form of chromosomes but with no specialized proteins to associate with while in eukaryotes, a variety of organelles are present for each specific activity need for the eukaryotic cell, a nucleus with the DNA in combination with histones and with each gene consisting of exons and introns.

 

For eukaryotes there are either the photoautrophs which use sunlight as a source of energy for photosynthesis and there are the organoheterotrophs which use organic compounds for the energy source. Prokaryotes, on the other hand can exploit a variety of chemical sources such as oxidation of sulfur in addition to visible light and chemical compounds and not surprisingly they can be found in a variety of inhospitable environments such as boiling hot springs, saline lakes, and even near nuclear reactors!

 

 

                                                                Stimuli and Response

 

To survive, a cell must have some level of awareness of what is present in the surroundings. For a bacterium such as E.coli if there is a concentration of sugar in its environment then the E.coli must be able to sense that sugar is present and so make a set of complex interrelated set of changes in it’s interior to prepare to move towards the sugar. That set of actions in which the cell such as the E.coli moves towards the food is called the response and the sugar is the stimuli. All cells, whether prokaryote or eukaryote must have this ability to tell the difference between food and poison and elicit the series of appropriate responses; for the former it would be to swim towards the food and in the later, move away.

 

 

An amoeba changing in response in the presence of a ciliate organism. Even at the level of a single cell are cells capable of stimulus and response. (Picture Pest)

An amoeba changing shape in response to the presence of a ciliate organism. Even at the level of a single cell  they are capable of stimulus and response. (Picture Pest)

 

 

Recall that an important criteria of life, homeostasis, is to keep the internal environment of a cell constant, and that there are three components, the sensor, positive and negative feedback. For the sensor, that could be in the form of chemical receptor proteins for detecting sugar and if sugar is found, bacteria such as E.Coli undergo a directed movement called chemotaxis and the bacteria will move in response to the sugar. There is a set of response that the prokaryotes execute which one can call “behavior” and that is part of the response allowing the prokaryote to sense what it needs which is sugar and move , for the purpose of seeking out the sugar for sources of carbon and energy and indeed there is a purpose that animate systems like prokaryotes display that inaminate systems lack. The process of seeking nutrients is also present in eukaryotes but with more complex set of molecular senses to detect and utilize nutrients but the process of stimuli and response is the same.

 

                                                                     Growth and Reproduction

 

Of all the biological processes that are necessary for survival of organisms, one of the most vital for the survival is when either cells divide into two cells both of which inherit the same structure and function as the original while two cells unite as one producing another cell or two or more that has characteristics of both cells. Both of these whole cell making processes are both asexual and sexual and collectively are called reproduction or the making of a new cell or new organism from a previous cell, organism or from two cells and two organisms respectively.

 

If you have read my blog “What is life, really?” You will realize that life is a process that is both active and dynamic because of the second law of thermodynamics where  both total and system level entropy is increasing towards a maximum but only in the small scale system there can be an increase, decrease, or the system can reach negative entropy. A fully functional cell with metabolism and homeostatic mechanisms such as networks of enzymes, define a biological system that is the cell with low entropy and only if there is a flow of usable energy and matter in and flow of wastes out, can the cell remain in that low entropy state, and having an internal structure with various kind of biochemical functions, a low entropy state can not only be maintained but can make two identical copies from one cell. To do that, the cell membrane must be flexible enough to divide, the cytoplasm must be divided in between each dividing membrane and the DNA in the chromosomes, whether prokaryotic or eukaryotic must undergo careful replication with one DNA molecule duplicated into two DNA molecules. There are two forms of asexual reproduction , binary fission and that kind of reproduction is present in prokaryotes and in a single step, a bacterium divides in two with molecular duplication of DNA, partitioning of the cytoplasm , and synthesis of two cell walls. In mitosis, indicative of eukaryotes, this is not a single step but a step by step process where a single eukaryote cell or cells of a specific type in multicellular organisms undergo cell division such as preparation of the specific set of proteins for mitosis, duplication of DNA molecules, condensation of chromosomes, identical chromosomes moving in two opposite directions, and the division of a mother cell into two daughter cells.

 

In asexual reproduction cells are identical to the original,more or less, but there is still imperfections such as an occasional mutant that will either cope with new changes in its environment or if the mutant has a genetic defect then it will likely die out. For species of unicellular organisms such as paramecium which can not only undergo cell division but can also mate with other paramecia and exchange genes. Bacteria can also undergo what is called conjugation and that is when a donor bacterium gives its genes to a recipient bacterium. In more complex multicellular organsims a specific set of cells called germ cells undergo a process called meiosis where the total amount of genes is reduced in half and in two special cell divisions that is different from mitosis, genes on chromosomes are swapped between chromosomes and after the second division the germ cells will either become a sperm or an egg, each with a unique combination of genes and when sperm and egg unite in what is called fertilization, a fully formed organism results. This kind of process where two cells become one is sexual reproduction. It is a characterstics of unicellular eukaryotes, and of course it is more prevalent in multicellular eukaryotic organisms.

 

Because, whether of asexual or sexual reproduction, cells have the ability to make copies that are either identical or genetically distinct from its parents. Think about this for a moment; a cell, using nothing but nutrients and water can use these nutrients to organize a fully functioning cell and that cell will have the potential to reproduce using both protein molecules of all kinds and cell membrane along with the instructions encoded in its DNA on how to replicate the DNA molecule and on how the cell will divide. Also recall that a cell is dynamic organization or a system of interacting components that catalyze reactions such as protein synthesis and ATP synthesis and that since this is a form of order and that order can beget order despite being a physical system with a higher degree of complexity as was duly noted by Schrodinger in his book What is Life? and since life is a dynamic process that has an ability to make more copies of itself despite the second law or that law of thermodynamics about increasing disorder , a cell like any physical system is not violating any law of thermodynamics and the reason why is because it imports matter and energy in the form of minerals, organic compounds, and visible light, while useless compounds such as carbon dioxide and oxygen are released into the environment along with heat and both inflow and outflow are crucial for the organization of the dynamic system that is the cell and also it is possible for the cell to undergo reproduction which is also an energy requiring process.

 

There is a special quality that cells possesse because of its ability to make more cells of itself and it is a characteristic of those systems that are in far from equilibrium. That quality is called autopoesis and autopoesis is indicative of those class of systems called dissipative structures and those are the systems that are far from thermodynamic equilibrium, and coexist with the second law, where dissipative systems of any degree of complexity can have low or negative entropy as long as there is an increase of positive entropy anywhere in its environment, and have an organization which is implies purpose and the purpose of a cell is to make more cells.  Autopoetic systems such as the cell have that ability to synthesize more cells from the level of the membrane to the DNA molecule. Information on how to divide is in the DNA, the enzymes needed to catalyze those sets of reactions for cell division is also present in the DNA so nothing outside is needed to make more cells and as long as the cell is away from thermodynamic equilibrium, a cell such as a single bacterium if placed in a nutrient medium such as agar will divide into many cells just like the original bacterium wherever there is space to reproduce and availability of vital nutrients are present.

 

The ability to undergo reproduction is in stark contrast to man made machines such as automobiles where combustion of fuel is what powers automobiles so in a sense, the movement of automobiles is the result of a kind of metabolism but if a part of the car breaks down then it will likely to impair its function so you have to take your car to a repair shop which requires the skills of auto technician to repair your car. Notice that it takes an outside influence such as trained technicians to fix a car whereas if part of a cell is damaged then it will repair itself or when a cell needs to divide, the two cells will inherit the internal structures. Also notice for the dividing cell, there is nothing and no one outside that can make two cells from one, only the cell itself makes more copies of itself. That is the essence of autopoesis and it applies to the process or reproduction as well as growth.

 

                                                                     Adaptation

 

Living things must not only be able to behave in a certain way such as finding shelter, food, or mates but must possese characterstics allowing them to survive in their own habitat and must have the ability to inherit those particular kind of characterstics from their parents to not only to survive in its habitat but if the habitat where to change in both biotic or living aspects such as the presence of a parasite that was not present in its habitat as before and abiotic or nonliving aspect such as change in water temperature from warm to cool. If the organisms cannot cope with such changes , then it is likely to die but if an organism inherited a change in its characteristic or phenotype that allowed it to survive then it will prosper and as each generation inherits what was present in its ancestors along with a capacity to change as a result of changes in the genotype or set of genetic instructions after each round of reproduction, then that change will allow it to either survive with such new phenotypes or if the phenotypes does nothing at all, then it is likely that the offspring with a lower chance of survival if its habitat changes. Such inherited changes are what is called adaptations and for a population of organisms such as prokaryotes and eukaryotes, with the ability to inherit any novel changes and if these changes prove beneficial in its altered environment, then through a non random process called natural selection, those organisms will because of these new phenotypes will either survive or perish and through adaption and natural selection evolution is inevitable.

 

A hot spring in Yellowstone National Park. The green colors indicate the presence of a microbial community adapted to near boiling temperatures. Like all life forms, these microbes need water, carbon, and energy to survive and reproduce but because of certain characteristics that these kinds of cells possesse, makes them able to adapt to the hot temperatures.

A hot spring in Yellowstone National Park. The green colors indicate the presence of a microbial community adapted to near boiling temperatures. Like all life forms, these microbes need water, carbon, and energy to survive and reproduce but because of certain characteristics that these kinds of cells possesse, makes them able to adapt to the hot temperatures. (James St. John).

 

 

     How does the conditions of natural selection apply to cells? Starting with Darwin’s theory of evolution by natural selection, natural selection is the process that chooses in a population which organisms live or perish. There are three basic processes that are the essence of natural selection and the first is the ability of organisms such as cells to grow exponentially or to reproduce without limits but in reality there are limits that stop runaway growth. A relevant example is a single E.coli bacterium that is transferred on the surface of agar in a petri dish. Within 24 to 48 hours, that single cell will have reproduced into over a billion cells but since all cells not only utilize nutrients and through metabolism produce wastes and with the small size of the petri dish will never expand beyond the borders of the dish so the growth is constrained by both a limited space and accumulation of wastes which can poison the E.coli. From single cells to elephants, every population will expand but cannot do so because of limited natural resources and many offspring do not survive but only a small number will survive. What about the survivors in each generation?   It is because of reproduction that the copying process of DNA into daughter DNA molecules and remember that DNA carries the instructions needed for the cell’s survival and also remember that like all physical systems, cells and life in general are also subjected to the second law ( consider the process of aging in organisms) that sooner or later, a slightly different DNA molecule may result. That change in the sequence of nucleotides in the new DNA molecule may not affect the entire cell, or would be known as a neutral mutation, but a changed DNA sequence may be harmful so the cell dies but if that new DNA sequence results in a new protein such as a new transport protein with an ability to block out poisonous substances is present and if in its environment there is such a poison which killed most of it’s ancestors but with that new protein it can resist the poison, then that mutation will confer a benefit which will be passed on to its descendants. This can occur in asexual reproduction but the process of producing new genetic environments is further enhanced through sexual reproduction ranging from conjugation in prokaryotes and unicellular eukaryotes to meiosis and recombination or the exchange of genes between two chromosomes followed by fertilization which further accelerates genetic diversity. With a population where no two individuals are alike, the chances of survival are increased with whatever mechanism there is to generate genetic diversity and with variations in a population and in each reproducing generations each organism will either survive or die in its changing environment so with reproduction, population growth, along with a process to generate novel forms that will allow it to adapt, a population evolves into new forms possibly resulting in new species. The environment, with both biological and non biological components then chooses the survivors in each population and that is natural selection, as was first defined by Darwin and has been confirmed by countless experiments ever since.

 

In addition to evolving into new forms that can survive in its environment made possible through heredity, organisms also have a history and each organism alive is the descendant of ancient and ancestral which have gone extinct and each one adapted to its own habitat where there are a variety of habitats that are part of the biosphere ranging from cold artic lands, the surface of sunlight waters, in soils of humid forests, and even in near inhospitable places like hot springs and in the abysmal deep near hydrothermal vents under oceans. Throughout the dynamic geological history of the planet, and starting at the origin of life which is presumed to have been estimated about 3.8 billions of years, at first life was indeed simple but with all the necessary qualities and as new niches begin to form, ranging frome extreme to mild, sometimes going from mild to extreme, the ability to adapt has served life well and through natural selection and other evolutionary mechanisms such as genetic drift, life diversified as new environments where created from a restless earth and life, when it survived took opportunity to use whatever resource it get use. This was done whether it was bacteria, the ancestor of all eukaryote cells and so on.

 

How can the history of life ever be found ? There are two methods for constructing the natural history of life as related through heredity or phylogenetics as it is called. One is find fossils and they range from the well known fossils you find in museums in the form of bones or imprint made by extinct animals. From the use fossils along with dating of the rocks and in relation to each sediment from which a fossil is found, a sequence of past histories of what ancient life was like can be reasonably inferred. The other method is to determine the sequence of molecules such as proteins and nowadays , DNA, along with RNA which can give an accurate relationship to which species are related to one another and even the single common ancestor to all forms of life, large and small.

 

I have spoke about the unity of life and indeed from cell biology to molecular biology, all of the diverse forms of life ranging from all the many kinds of microbial life to the familiar animals and plants do share everything in common at the cellular level along with the two main divisions of cell structure, prokaryotes and eukaryotes. All cells use the same genetic code or instructions on which three base nucleotide or codon codes for one amino acid or several and there is one way information flow from DNA to RNA to protein, called the Central Dogma which is universal in all life, more or less. Biology now recognizes that all of life can divided into three categories or domains which are the Prokarya domain or the domain of bacteria, the Archaea domain (formerly called archeabacterica) which includes those prokaryotes that can adapt to extreme conditions such as high heat and zero oxygen, and the Eukarya or the domain that includes all the eukaryotes, the protists, fungi, plants, and animals.

 

 

All of life that make sup the biosphere of planet earth are related through what Darwin called "descent with modification" or evolution. In this diagram, all of life is organized into three domains, the prokarya and archae domains which share the prokaryote structure and the eukarya domain. This reveals that the ancestor or LUCA is the ancestor of all three domains and that the eukarya domain evolved through endosymbiosis also revealed in this chart. (Phylogeny Figures)

All of life that makes up the entire biosphere of planet earth are related through what Darwin (1859) called “descent with modification” or evolution. In this diagram, all of life is organized into three domains, the prokarya and archae domains which share the prokaryote structure and the eukarya domain. This reveals that the ancestor or LUCA is the ancestor of all three domains and that the eukarya domain evolved through endosymbiosis also revealed in this chart. (Phylogeny Figures)

 

Organisms can compete for natural resources, where on may win and the other loses but organisms can form partnerships in which both partners benefit from one another, and in what is called co-evolution. Recall that the definition of an eukaryote cell is a cell with a nucleus and organelles but investigations of the two most important organelles in cells, mitochondria and chloroplasts which carry out respiration and photosynthesis respectively are like prokaryotes in that both have circular DNA and ribosomes. How is that possible? The currently accepted theory , endosymbiosis, a form of coevolution was that the ancestor of all eukaryotes ended up taking in a fully functional prokaryote, the ancestor of either a mitochondrion and/chloroplasts was once a free living independent cell which somehow got acquired in a large cell. Gradually, both cells begin to benefit where the two cells, the mitochondria and the chloroplasts begin to provide biochemical energy to the host cell as it would been called and the host cell offered protection for those trapped prokaryotes. Both the organelles and cell begin to surive and because of natural selection favored that cooperation where both entities benefited from one another and it was this mutual partnership that is believed to have been the ancestor of all unicellular and multicellular prokaryotes which because of that acquisition resulted in new characteristics specific to eukaryotes such as mutlicellulularity, meiosis, aging, and the gradual transition of life in water to land.

 

Incredible as it is, something as small as a cell does display all characteristic of life, making it one of the most potent force in the history of the cosmos. Nothing compares in the degree of complexity and our growing technology has yet to catch up in terms of the cell’s ability to reproduce and harness energy. Next time you see a living cell under the microscope, reflect that this wondrous entity has a complexity that is unrivalled by anything inaminate in the universe and with a history that can be traced when the earth was very young and full of future possibilities.

 

 

A species of Phacus, an unicellular algae and example of a photoautroph or organism capable of photosynthesis. Don't let its small size fool you. Organisms like Phacus and other life forms that carry out photosynthesis have had a profound impact on the evolution of the biosphere. Without such microbes to carry out photosynthesis, and to recycle elements like carbon, oxygen, and nitrogen, earth would be as lifeless as the moon. (Picturepest)

A species of Phacus, an unicellular algae and an example of a photoautroph or organism capable of photosynthesis. Don’t let its small size fool you. Organisms like Phacus and other life forms that carry out photosynthesis have had a profound impact on the evolution of the biosphere. Without such microbes to carry out photosynthesis, and to recycle elements like carbon, oxygen, and nitrogen, earth would be as lifeless as the moon. (Picturepest)

 

 

 

 

 

 

 

 

 

             

 


 

References:

 

Atkins, P (2007) Four Laws that Drive the Universe. Oxford, England: Oxford University Press

 

Chaisson, E (2000) Cosmic Evolution: The Rise of Complexity in Nature Cambridge, MA: University of Harvard Press

 

Darwin, C (1859) On the Origin of Species By Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life. London, England: Murray London

 

de Duve, Christian (1983) A Guided Tour of the Living Cell New York, NY: Scientific American Library

 

Goodsell, D.S (2009) The Machinery of Life: New York, NY: Springer Verlag

 

Harold, F.M (2001) The Way of the Cell: Molecules, Organisms, and the Order of Life New York, NY: Oxford University Press

 

Jantsch, E (1980) The Self Organizing Universe: Scientific and Human Implications of the Emerging Paradigm of Evolution New York, NY: Pergamon Press

 

Life (n.d). Retrieved August 20 2015 https://en.wikipedia.org/wiki/Life

 

Mayer, E (2001) What Evolution Is New York, NY: Basic Books

 

Morowitz, J (1963) Life and the Physical Sciences: Introduction to Biophysics New York, NY: Holt Library of Science

 

Sagan, D Schneider. E (2005) Into the Cool: Energy Flow, Thermodynamics, and Life Chicago, IL: The University of Chicago Press

 

Schrödinger, E  (1944) What is Life? The Physical Aspect of the Living Cell Cambridge, England:Cambridge University Press

 

Photos:

 

LECA – last eukaryotic common ancestor https://www.flickr.com/photos/ajc1/8056113172/in/photolist-hVg7hD-afov6u-dgTFLY-83bzYP CC BY-SA 2.0

 

Blue Ridge Kitties Photosynthesis light reaction diagram https://www.flickr.com/photos/blueridgekitties/4619809768/in/photolist-p5HRD-9FGf8L-eMKXQg-aafkCC  CC BY 2.0

 

Ambra Galass Untitled https://www.flickr.com/photos/a-g/2498324151/in/photolist-4NLyJk-84g73c-8yTeDk-84jaGQ CC BY-ND 2.0

 

Jim backbone_illustration https://www.flickr.com/photos/jim68000/3234294469/in/photolist-5VNB4K-PgupA-CbSjC-CbSiM CC BY 2.0

 

James St. John Morning Glory Pool 1 https://www.flickr.com/photos/jsjgeology/8275354016/in/photolist-ettS6G-5dopRY CC BY 2.0

 

Umberto Salvignin Bacteria https://www.flickr.com/photos/kaibara/2234750993/in/photolist-4ptFBx-9y4sD6-a4RLq5-97dMAf-8QYufp CC BY 2.0

 

Phylogeny Figures  pgen.1000497.g001 https://www.flickr.com/photos/123636286@N02/14144001125/in/photolist-nxRGLn-akgEFV-akjsfh-akgECv-cZcVyf-ovZaTW CC BY 2.0

 

PicturePest Phacus sp. – 400x https://www.flickr.com/photos/picksfromoutthere/10388386126/in/photolist-gPZcgC-nxUMAW-orS6XN-gQ19BA CC BY 2.0

 

Picture Pest Pseudocohnilembus pusillus und Amöbe – 400x https://www.flickr.com/photos/picksfromoutthere/8999991915/in/photolist-eHij3p-eHigcH-eHpiHS-eHi7i8 CC BY 2.0

 

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