A Second Look to the Nature of Science and a Revisit to the World of the Cell

Kamusta mga kaibigan! :) Its been months since I created this site but haven't started out a single thread of my own. :( I got loaded with officework and homeworks hehe. :(. Well, I would like to share an interesting TMA (Teacher-Marked Assignment as they call it in UP Open University) in my Biology class which I think you will find interesting as well. Let us explore the intriguing processes of Science, and the immense possibilities it offers us. A revisit to the world of the cell is particularly inspiring for many of the basic functions we associate with organs can be traced back to the cell itself, the fundamental unit of which all of life's characteristics are manifested. Enjoy reading. :)

Julius

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On the Scientific Enterprise

1. What is science? Is science a process? Is it an endpoint? Is it a frame of mind? Is it Science that uncovers or explains? Who creates Science? Who decides what is Science and what is not? What is the scope of Science? How is Science created?

What is Science?

According to JP Siepmann, “Science is the field of study, which attempts to describe and understand the nature of the universe in whole or part.” It’s pretty nice a definition for science J. This definition is very important because it provides us with understanding and viewpoint regarding the nature and scope of science. Science as we know it seeks to explain everything but as we try to unravel the mystery behind everything, the more we get to question things that constitutes a thing until we come to a point that we will realize that everything cannot be explained by science. The scientists’ business is to find answers to the basic phenomena of nature but much of what is happening in nature are not explainable in terms of processes employed by scientists in Science but we do get credit to gaining noble information for the fundamental identity of a certain entity in nature and influence its working on a limited scale.

In a Worldbook Encyclopedia entry, it’s stated that,” Science covers the broad field of knowledge that deals with observed facts and the relationships among those facts. The word science comes from the Latin word scientia, which means knowledge.” If science is knowledge how can we describe subject areas that are categorized under Arts? What makes a certain subject Science and others not? If the prime language of Science is mathematics, ergo it’s the prime knowledge by which Science operates. How can we define subject areas that do not fall under this category? Can we say that subject areas that fall under Humanities have no knowledge at all? Questions like these usually arise because Science is limited to explaining the details of nature and its origin. The very origin of life itself cannot be deduced solely on its workings because the processes that motivate a certain thing to function will never explain its evolution and origin.

In his biology textbook, Neil Campbell expounded further the meaning of Science. He contradicted the idea of providing a concrete definition of science for Science is better understood by observing it than by trying to create a precise definition of it. There is no exact, single statement by which we can define Science for the facts and activities that involve Science far exceed the amount of knowledge of all men put together and their efforts to delineate a satisfactory definition of it through our concerted action.

Mathematics and logic are not based on experimental testing. Yet, they are categorized under Science. But they can be considered part of science because they are essential tools in almost all-scientific study. Mathematics enables scientists to prepare exact statements of their findings and theories and to make numerical predictions about what will happen in the future. Logic provides the basis for all scientific reasoning.1

Science can never be a frame of mind for its processes are purely knowledge-based and follow a logical flow. Science can be someone else’s frame of mind if it is manipulated to suit the current intellectual biases of a certain scientist. Thus, pseudoscience develops.
Most books mentions about the tool by which people propagate Science and most of them points mathematical language as its medium of communication by which Science can be best understood. Just like any other languages, the general population may not be able to speak and at the same time understand it unless a leader (which sometimes is the teacher which can be qualified as a scientist himself) has the courage to teach its semantics and syntax to decipher its very meaning. In this way, a common dialect is used to direct the path of our thinking towards the understanding of Science and more often than not, the so-called hypothetico-deductive approach is most effective as proposed by the famous philosopher Karl Popper. In this method, a true Science can be tested by the use of the approach by which the process of deduction is applied using the hypothesis, an educated guess as we usually call it, synthesized at hand. One strong point of this testing is that, it aims to falsify a certain hypothesis laid out to explain the behavior of a certain natural phenomenon. As mentioned in Dela Paz’s book, a hypothesis, to become effective, should be falsifiable so that it could undergo further testing through experimentation and confirm its validity.

The question concerning the creator of science is humans themselves. Humans created Science because they want to know God. Science was founded to study nature (God's works) to better know God1 as what Stanley White stipulated in one of his articles. The founding fathers of science were deeply religious men. They believed in monotheism, a single creator of the universe. These great men did not live in one place, but were scattered [over all of Europe.] They communicated mostly by letter. These early men of science believed that to better know God, one must study his works.

Our search for knowledge has never ended. People tend to ask questions of all the things happening in his environment. With the many questions left unanswered, curiosity pervades every human mind. From time to time, we see philosophers and scientists laid out their theories: explanations to a not well understood natural phenomenon. They may be accepted momentarily but since experimentation, which is one of the chief tools of Science, time will come that a rather comprehensive and scientifically accurate explanation will replace the pervading theory. When new information is discovered, the conclusion must be looked at again. If the new knowledge gives support, fine, but if not, what looked like an answer must be discarded or modified. That means scientific ideas may change. The changing attitudes and practices in medicine throughout history illustrates that science is a process.3 This is probably brought about by our deductive way of thinking and our ever application of the scientific method, the main tool by which scientists test the validity of a certain scientific supposition. As a learner of science we must keep our foot always on the ground by adhering to the basic rules of science otherwise our experiments will fail, although we can see how some scientists do away with some process in scientific method to better portray how their hunches greatly agrees with an observed phenomenon or fact which is not a healthy way of dealing with science.

2. Prepare a model of the cell. Choose a certain specific cell type and work on uncovering/discovering what is in that cell. Explain your model by answering these questions:

What is the cell? What is its purpose?

The cell has been referred to as the simplest unit that is capable of living and assuming all the functions of a living being. The cell in terms of structure is simple - being the smallest unit that is viewed as a dynamic machine that exhibits all the properties that define a living entity as a whole and complex since each structures that make up the entire cell is composed of complex substances intertwined to produce a highly complex organelle that performs varied task that cannot usually identified in a non-living entity. I recalled one instance in our conversations in the discussion board where the phrase “anything that metabolizes and self-perpetuates” was used by Dr. Dela Paz in his/her book which I responded in a reply below: “The problem with the phrase “any structure that metabolizes and self-perpetuates is that metabolism is not just inclusive (a feature) to living beings alone and self-perpetuation connotes something that a living being can reproduce without the aid of environmental instruments and raw materials. I think that the cell itself does not reproduce or “self-perpetuates” but the individual structures that makes up an entire cell and from the raw materials in the environment…thus, a living being cannot “self-perpetuate” without raw materials from its immediate environment. Therefore, a cell is not an independent, basic structure of all living things since it cannot exist alone. To illustrate this, Mitochondria has its own method of metabolism and so do other organelles. They also have their own genome, metabolizes and double during cell division “self-perpetuate” ika nga ni Dr. Dela Paz. If we are to use “self-perpetuation” as a basis in our definition for the word “life” does that gives mitochondrion a license to survive alone outside a host species? Definitely not although it is “a widely accepted belief that mitochondria and plastids (photosynthetic organelles in plant cells) evolved from bacteria that were engulfed by nucleated ancestral cells. As a relic of this evolutionary past, both types of organelles contain their own genomes, as well as their own biosynthetic machinery for making RNA and organelle proteins? (Molecular Biology of the Cell :Bruce Alberts, et. al.)4 Mahirap talagang humanap ng naaangkop na panaguri sa mga bagay na buhay. But as time goes by we can perhaps formulate a meaning that encompasses and clearly identifies a living being.

Surely, the purpose of the cell is to provide life the necessary mechanism to “self-perpetuate” and differentiate to pave the way for the production of a different living unit more complex and better adapted to its present habitat. The environment provides the necessary raw materials for the organism to metabolize, reproduce, and acquire the appropriate skills to survive. Without it, the organism dies due its failure to learn and to unlearn. This might come intrinsically as an organism cannot learn or unlearn without a brain or a primary motor that regulates all of life’s activities. Nonetheless, the environment provides the indispensable training ground for an organism to acquire the best learning equipment there is to survive.

What are found inside the cell? What are their purposes?

Model of a Eukaryotic Animal Cell

Although the animal cell vary differently from the plant cell in terms of shape, size, function and contents, both types of cells actually share many of the same features and organelles that can be found on both cells.

The animal cell is composed of several organelles that make up the entire unicellular entity and these I have enumerated below.

· Cell Membrane/Plasma Membrane/Cell coat

The cell membrane is pictured as a bilayer of phospholipids molecule with embedded protein and enzymes. Its membranes act as a discriminating barrier against unwanted substances that may harm or delimit the ability of the cell to perform its varied functions. Its primary function is to separate the vital chemicals and contents present inside the cell from the outside environment but permit other molecules, which the cell deemed appropriate, to pass through due to its selectively permeable property. Thus, it regulates the amount and type of material that must pass through the membrane of the cell either for cell-to-cell-communication or nutrition.

The cell membrane along with the cell coat promotes intimate contact among cells and plays a very important role in cell-to-cell recognition and thus advancing the organization among the adjacent cells. Some part of a multicellular animal’s body and other unicellular organisms there appears to be thickly distributed (in one part of the cell) cell membrane extensions that plays an important role in increasing the amount of available area (surface area) for additional gateway for the passage of materials into and out of the cell (microvilli). The cell membrane also provides the needed barrier that separates the content of one cell to another and supplies a communication satellite with other cells as in the case of tight junctions, desmosomes and gap junctions.

The cell membrane itself is made of phospholipids bilayer material (tail) and a phosphate group (head). These layer are oriented in such a way that the water loving head portion of the bilayer is situated towards the watery environment (hydrophilic) and its water-fearing portion away from it (hydrophobic) in such a away that the layer will look like a sandwich.

The cell membrane can be perfectly conceptualized using the fluid-mosaic model by Singer and Nicholson. Under this principle, the cell membrane is pictured as a two-dimensional bilipid “fluid” layer where the hydrophobic region of the molecules of the membrane is directed within the layer with integral proteins embedded in it. The word “mosaic” (a surface decoration made by inlaying small pieces of variously colored material to form pictures or patterns-Merriam Webster) is used since majority of the substances found in the bilipid layer are a conglomerate of different molecules such as cholesterol, proteins (integral and peripheral). The picture may represent the material as immobile but theoretically or when observed under a powerful electron microscope, the proteins are lying freely and can move around the sea of molecule created by lipids.

· Nucleus

The nucleus is usually the most prominent organelle in a cell. Most biology books picture it as the center organelle of the cell but most of the time found on one side of the cell under a light microscope. This organelle contains the genetic materials of the cell (DNA) in the form of chromosomes that is conspicuous during cell division. Its content, the nucleoplasm houses another distinct structure, which is called nucleoli, a mass of granular structures in nucleus, not bound by membrane. It is thought to be involved in ribosomal RNA synthesis and ribosome precursor function. We can also see pores surrounding the membranous nuclear envelope. This double membrane structure separates the contents of the nucleus to the rest of the cytoplasm. At the tip of each pore, the inner and outer membranes are fused. The pore, which contains proteins, only allows only a specific type of RNA molecule in and out of the nucleus, which has a direct involvement in the production of other types of protein needed by the cell to maintain life.
Inside the nucleus a dark region of chromatin, involved in making ribosomes called nucleolus can be found. This structure is involved in the production of particles called ribosomes, an organelle which functions in protein synthesis.

· Endoplasmic Reticulum

The Endoplasmic Reticulum (ER) is an extensive network of tubular channels and sacs whose primary function is to transport materials from the nucleus to the plasma membrane and vice versa. It functions much like that of a highway where products from one end of the highway are transported to the other end or to areas along its path. The amount of visible endoplasmic reticulum in the cell varies from one cell type to another depending on the activity and function of the cell as its presence is attributed to a certain function, which I will discuss later. There are two distinct types of ER, which depends on the presence, or absence of another organelle termed ribosomes, which are the primary sites of protein synthesis. These are discussed in more detail in the next section.

· Rough endoplasmic reticulum (RER)

Rough Endoplasmic Reticulum (RER) was so named due to the presence of ribosomes, a protein factory of the cell. They synthesize protein and are transported right into the ER to where they are stuck that is why RER shows to produce protein. It is these same organelles that make the RER unique in a sense that is able to perform protein production from nascent polypeptide.

· Smooth endoplasmic reticulum (SER)

Smooth ER, on the other hand, is NOT covered with ribosomes and processes LIPIDS and CARBOHYDRATES. Being devoid of ribosomes does not make SER devoid of its functions as well. In fact, there several of its various functions are critical for the maintenance of life as a whole when the body or the cell itself is confronted with toxins present in small or considerably large amounts in the food we eat. Many of the important functions of the ER are performed by the SER of which are listed below:

· synthesis of steroids in gland cells
· the regulation of calcium levels in muscle cells
· breakdown of toxic substances by liver cells

From the functions enumerated above, we can summarize that most of Smooth ER’s function is fundamentally related to detoxification since the liver and kidney cells are the most prominent organs in the human body in which most Smooth ER can be located. The abundance of smooth ER among liver cells only indicates an active detoxification effect of the said organs. I believe that it is interesting to note that one spectacular function of the smooth ER is its ability to separate or sequester calcium from the cell’s fluid medium, the cytosol. The lumen of the SER, which is the internal cavity of the endoplasmic reticulum, with its powerful calcium-binding particles allows the continuous influx of calcium ions from the cytosol to the smooth endoplasmic reticulum. A specialized smooth endoplasmic reticulum called sarcoplasmic reticulum is present in muscle cells and performs almost similar functions. An enzyme called CaATPase regulates the process done by this organelle type. From here on, it is but safe to assume that the ability of the muscle cells to regulate the contraction and relaxation of the myofibrils of muscle cell relates to the function of the SER above.

· Golgi Apparatus

Golgi bodies or apparatus are another series of flattened disks, which form channels all throughout the cell. It is manufactured by endoplasmic reticulum and its main function is to modify the contents of the vesicle produced by the endoplasmic reticulum. The Golgi bodies have two distinct faces, one forming a convex area where coalescing vesicles coming from the endoplasmic reticulum discharges its content to the internal content of the Golgi apparatus for modification and further processing (cis face). On the other side, the trans face area, is a place of increased budding activity where the substances modified by the Golgi bodies are packed and transported towards the cell membrane and excreted to the outside of the cell by means of exocytosis, the release of cellular substances (as secretory products) contained in cell vesicles by fusion of the vesicular membrane with the plasma membrane and subsequent release of the contents to the exterior of the cell. (Merriam-Webster Dictionary)

· Ribosomes

Among the organelles listed herein, ribosomes are the only one not bounded by a membrane. They are the primary sites of protein integration and synthesis and are found either attached with the endoplasmic reticulum or lying free in the cytoplasm. If lying free in the cytoplasm, they can be found in clusters called polysomes. Proteins produced by free ribosomes

On the next section, I will introduce you to two (aside from the Nucleus) of some of the most popular organelles high school students generally do not forget after finishing elementary biology which I regard to be true. Part of the reason, I can think of is probably due to giving these organelles the distinguishable phrase that describes their function and in turn aids memory retention.

· Lysosomes

Remember the phrase “suicidal pack of the cell”? Does that ring a bell? J Retention is made rapid when we associate an object to a word, phrase or a situation. In all cases, they employ sounds as a tool for communication. I can define this organelle even when sleeping. J Christian de Duve, a cell biologist discovered lysosomes, cell organelles specialized for recycling and waste disposal. The structures vary in size from 0.2 to 2 micrometers in diameter which is quite small. Most books usually dismiss lysosomes as indistinguishable under a microscope partly due to their varied sizes and appearances. Under a high-resolution microscope, most of these organelles appear black due to their high content of hydrolytic enzymes, which in chemistry translates a high-density electron region. Animal cells have numerous number of this organelle but found very seldom in plant cells. Like most eukaryotic organelles, this tiny organelle is membrane-bound. Its membrane is again a lipid bilayer and protects its content. The fact that the organelle is encased in a lipid membrane suggest one thing: more than protecting its content, this organelle protects the cell since its poisonous or digestive content harms the cell in any way or will result to its premature destruction. It has been identified that lysosome’s content can reach pH of 5 and lower making its content very dangerous in some way but beneficial for nutrition and also works in autolysis (self-destruction) during period of environmental stress and brings balance to the ecosystem. That provides the ecosystem the opportunity to replenish itself through the action of these substances. J They usually fuse with vacuoles and eventually digest its content with a cocktail of enzymes (around 40 different enzymes) present in the organelle’s interior bringing about nutrition to the cell in a way. I also believe that this action neutralizes any harmful substances present in the vacuole itself.

· Mitochondria (sing. Mitochondrion)

Another interesting organelle found in an animal cell is the mitochondrion, from the Greek, "mito-" meaning, "thread" and "chondrion" meaning "body” which probably explains the thread-like appearance of these minute structures in the cell. Just like the previous organelle mentioned, this structure is very popular for it was identified for decades using a phrase that depicts its main function: “The powerhouse of the cell.” Overused a phrase as it may seem but this very phrase provides a substantial overview of the organelle’s fundamental function in a living cell.

A mitochondrion is a double-membrane organelle. Their appearance varies from rod to ovoid structures but all of them share the same internal structures. My college cell biology teacher usually note in most of her discussions that “structure always relate to function” which is true in all circumstances as in the case of mitochondria’s internal structure which we will discuss as we go along. The organelle has an outer membrane, and an inner membrane, which envelopes the organelle. The Inner membrane is folded many times along its length to create a region called crista (sing. cristae) where mitochondrial respiration [energy-yielding oxidative (using oxygen) reactions in living matter] occurs. The inner membrane encloses the internal matrix, a region where the most important proteins needed for aerobic (containing oxygen) respiration are situated.

Mitochondria are the powerhouses, energy-generators, or in other words “power sources” of the cell. Whatever you call it, these distinct organelles’ function only boils down to one: to produce energy when the cell needs it. If we are to observe the structure as shown in the cartoon above, we can describe this organelle having a rod shaped appearance, although some of them are ovoid, and are long and having a distinct stripes inside which are found to be an inner membrane folded many times in several areas the length of the inner membrane. Knowing that the actual ATP (energy-currency/molecule produced by mitochondria that powers most of cell’s cytoplasmic activities) production occurs mostly in the inner membrane of the organelle, this structure is vital to the function of mitochondria for it increases the area by which this process occurs thereby increasing the number of by-products of the ATP production activity of the mitochondrion. One interesting fact about mitochondria is that it does have its own sets of DNA not similar to the one contained in the nucleus. Similarly, ribosomes can be found. During cell division, it divides independently and forms offspring mitochondrion, which are distributed and used by the forming cells. In short, it possesses its own genetic apparatus and mitotic (cell-division) behavior.

· Microbodies

It’s hard to identify microbodies based on their appearance due to their diverse shape and sizes. It has been found out that these organelles are found everywhere in a fungal cell. Among the most common microbodies are peroxisomes (found in plants and animals) and glyoxysomes (found only in plants), although lysosomes are sometimes being included in the list of microbodies due to the similarities in basic functionalities with microbodies, that is, digestive properties. Despite of this similarity, the functions of lysosomes far outweigh that of the function of microbodies for they contain numerous enzymes, which aid them from performing varied functions aside from the one, which will be described later.

Microbodies are membrane bound vesicles (a membranous and usually fluid-filled pouch-Merriam-Webster Dictionary) present in cytoplasm in most animal and plant cells. Each cell possesses their unique microbodies and performs quite different function but share similar characteristics: all of them contain valuable enzymes for degradation of toxic macromolecules, which are intermediate products of cellular metabolism. One enzyme worth mentioning is the enzyme catalase present in animal peroxisomes. The role of this enzyme is critical to the survival of the cell due to its neutralizing effect on toxic hydrogen peroxide (H2O2), intermediate by-products of amino acid and fatty acid metabolism.

To give you a brief detail of the chemical reaction that culminates to the production of oxygen and liquid water in the metabolism of hydrogen peroxide, please refer to the diagram below.

2 H2O2 <-> O2 + 2H2O

As the cell metabolizes amino acid and fatty acids, it creates by-products, which are toxic to the cell itself and as these substances accumulates in the cytoplasm, their potential to damage the cell is enormous. The amount of these harmful substances is counterbalanced by the catalytic action of peroxisomes with the use of catalase enzyme, which breaks toxic hydrogen peroxide into a less toxic form - water and oxygen.

Analysis of enzymes in purified or partially purified microbodies from fungi indicates that they participate in the following biochemical functions8:

· Fatty acid degradation
· Glyoxylate cycle
· Purine metabolism
· methanol oxidation
· Assimilation of nitrogenous compounds
· Amine metabolism
· Oxalate synthesis

Glyoxysomes function in lipid, such as fatty acid, metabolism and its greatest glyoxysomic activity were found mostly in plants especially in fruits and seeds. It is in this organelle where chemical process known as glyoxylate cycle, where the start of the beta-oxidation (stepwise catabolism of fatty acids in which two-carbon fragments are successively removed from the carboxyl end of the chain) of fatty takes place, begins.

· Cilia and Flagella

Cilia and flagella are an important hallmark of a motile organism. Some types of cells may have evolved to become stationary but most of them retain one of these structures as in the case of ciliated cells of trachea and bronchioles of the lungs. They function in the movement of substances over their surface either for the distribution of substances for nutrition or moving particulate wastes out of the organism through its specialized excretory instrumentations. Our respiratory tract is kept clean by the actions made by these organelles especially when cilia present in the cells of trachea beat synchronously in one direction to move the foreign material trapped on the mucus (slippery secretions of the cell which moistens and protects) lining of the cell out towards the nose or the mouth to be swallowed.

Cilia and flagella are extra-cellular extensions that protrude from the cell. Although both structures are composed of the same material, which in this case are microtubules, one distinguishes the other from their length since flagella are longer than the cilia. Microtubules, the cytoskeleton that makes up cilia and flagella are composed of a globular protein tubulin. This globular protein is composed of alpha and beta tubulin dimer (a compound formed by the union of two radicals or two molecules of a simpler compound) suggesting its heterodimeric (composed of more than one dimer) structure. This dimer molecule connects to form a linear pattern called protofilament and these rows of globular proteins conjoin to frame a microtubule molecule.

· Vault

A decade ago (1992, although first reported in mid1980s but was not attributed a function), Leonard Rome and Nancy Kedersha of the UCLA School of Medicine recently discovered these subcellular organelle under a rat liver cell, although it has been observed that such particles/organelles exist in all nucleated cells observed so far. Among its properties are octagonal in structure, composed of RNA, and looks more like a cathedral vaults because of obvious multiple arch-type structure. They are believed to be nuclear pore complex plugs due to their shape although such assumptions alone were not yet verified due to lack of experimental evidence. These structures are usually found in a location where fiber precursors are building up to make actin protein. In that instance, Rome assumed that vaults are responsible for transporting , "mail trucking"as one of my classmate in UPOU calls it, the actin RNA templates in such actin-organizing region of cells. What scientists are trying to do today is that, they are attempting to disable the gene that is responsible for the production of vault protein. If paralyzation is complete and the cells show signs of failure for actin production then scientists are right that such organelles are responsible for actin protein assembly by providing templates for the production of actin (RNA templates). That confirms the "Mail Truck Theory" stipulated for the mobility of these subcellular organelles. They are not only found near the nucleus but througout the cytoplasm, probably due to their transporting ability from the nuclear pore through the rest of the cytoplasm. Additonally, another interesting fact to note here is that vaults are visibly abundant in multi-drug resistant cancer cells. This discovery lead to the hypothesis that these organelles participates in interceding drug resistance conferring the cell its ability to reject medication.

All the characteristics of living things, as outlined in the Module, can be traced back to the cell. Show, using examples, how your cell…

Metabolizes

Nearly all living things share certain basic characteristics. These characteristics include (1) reproduction; (2) growth; (3) metabolism; (4) movement; (5) responsiveness; and (6) adaptation. Not every organism exhibits all these features, and even nonliving things may show some of them. However, these characteristics as a group outline the basic nature of living things.5

Metabolism is one of the unique characteristics of a living thing. It is able to assimilate a component of its environment and transform it into a form that can be used to power the many processes undergone for its continued existence. Almost all books mention at least once in its entire content the more popular meaning of the word: “metabolism involves all the chemical processes by which an organism converts molecules and energy into forms that it can use.”5 All of the biological substrates needed by metabolism come from the environment although the energy that powers this process comes from sunlight, which is the ultimate source of energy of all living beings. Moreover, metabolism offers the organism’s body the opportunity for growth, and repair of damaged parts. It is interesting to note that metabolism is driven by a high-energy molecule (Adenosine Triphosphate) that is unique to living species. It stores and releases energy trapped between the bonds of phosphate that makes up the entire molecule.

Reproduces

Reproduction is a process by which living creatures uses to perpetuate their kind, which is better, or in worst cases, inferior to the parent living creature. All organisms reproduce or use some other mechanisms, which helps them to complete the process, even though some of them cannot reproduce by themselves (as in the case of viruses) and influences others to do it for them. Reproduction can be in many ways but primarily are classified as asexual or sexual, depending on the type of biological tool used (gamete or part of the body of the organism). Humans for example, reproduce by sexual means. This is performed using gametes as a tool to perpetuate its own kind. Major forms of individuals distinguishable among sexually reproducing species includes male or females. Both of these forms bear their own respective sexually active gamete ready to produce a viable offspring by fertilization from one of the other counterpart gamete. Asexual reproduction are usually performed by lower forms of animals such as bacteria where a new organism is produced by budding which is a characteristic of a hydra (small-bodied, freshwater polyps), releasing special kind of cells within the body of the organism which develops into a new, but identical individual as in the case of Sponges [any of a phylum (Porifera) of aquatic chiefly marine lower invertebrate animals that are essentially double-walled cell colonies that are permanently attached as adults(Merriam Webster Dictionary)], fragmentation (body of the parent organism breaks into two forming new individual) and regeneration (formation of a new individual using a lost or detached part) , which are characteristics of planarians and various echinoderms.

This process is an indispensable tool to counteracting the effect of death of an individual species. Reproduction itself is a major characteristic that sets living organisms apart from non-living entities and is a direct manifestation of an organism’s ability to violate the effect of the second law of thermodynamics, to put it simply, the “law of disorder” which is the fate of all matter in the universe.

There are two types of sexual reproduction. It comes in two forms: mitosis and meiosis. Mitosis produces two daughter cells with equal number of genetic material with 2 copies (diploid) of them in each cell while meiosis produces offspring (daughter cells) with half the number of chromosomes or genetic material (haploid) as the parent cell. While mitosis produces two cells during replication meiosis produces 4 daughter cells carrying half the number of genetic material the original cell has.

Responds

All living organisms respond in various ways depending on their learned evolutionary differences but I believe that organisms respond in many ways due to their internal and conscious willingness to survive. Last week when I watched the movie “The Island”, I can’t help but agree with Ewan McGregor’s line, “I will do everything to survive” where he used his ability to pretend in order to mask his true identity and the bad guys from the cloning facility mistook someone else’s as he (in this regard, his source since he is a clone).

In the October 4, 2001 issue of the National Geographic News Online [I kept this one in my mailbox for a year!:-) ] a Swedish scientist named Arne Öhman, a psychologist at the Karolinska Institute and Hospital in Stockholm, Sweden has conducted experiment on the sources of fear of humans and further extrapolated the role of evolution itself from its development and survival use. He stated that, “individuals who have been good at identifying and recruiting defense responses to predators or aggressors have left more offspring than individuals with less efficient defense systems."6

Living species of plants and animals continue to survive because of their continued responsiveness to objects that hinders their survival and perpetuation. Size sometimes does not equate to less efficient in managing the effects of predation but good response mechanisms helps a certain species to be aware of what is happening in its environment and react on how to avoid threats.

Cells particularly do that by way of releasing chemicals or moving away from the location where the threat was detected (chemotaxis). This is dictated by the nucleus to counteract any effect the environment has to its survival and continued stability. For unicellular organisms such as bacteria, the chemicals surrounding them motivate their motility. This behavior is employed to find food in the environment or flee from the source of threat, which comes in form of predator or poison.

Adapts

Perhaps the most popular among the characteristics of living things is adaptation. This is because this topic is hotly debated in almost every biology class I have attended since high school, even when I was still teaching. J The main reason I can think of is our varied and sometimes irreconcilable beliefs as to the origin and diversity of life around us. Our religious belief sometimes gets in the way of our scientific thinking. We often ask questions like, “How did humans evolve?” “Is evolution really true, if yes, is it acceptable according to our own religious belief that we evolve from monkey’s (literally)?” “Is there a God who authored all these things?” Things like that sometimes interferes our scientific understanding and judgment as to what is true and what is not but basically there are evidences that supports evolution where vitalists, people who believe that living things are not governed solely by the laws of physics and chemistry but by which a potent life force present in all living things, fails.

All organisms have a knack on adapting to its environment. This ability helps the organism to survive under extreme environmental conditions and as when surrounded by environmental threats. Throughout the course of an organism’s evolution, organisms change due to internal need to suit their structure to the current environment. They may develop certain structures (modifications), or features not characterized by an organism’s physique such as stamina and endurance, that is employed to adapting to its niche (function in the ecosystem) or environment.

Species of organisms that shows the characteristics necessary to survive in an environment from which it functions most of the time reproduces offspring with similar abilities. They may reproduce more organisms that can survive but the organisms that are able to withstand the stress in the environment are able to pass on their desirable characteristics using reproduction mechanism and contribute to the fitness of the organisms to which their genes will be passed on. This what best describes natural selection; a natural process that results in the survival and reproductive success of individuals or groups best adjusted to their environment and that leads to the perpetuation of genetic qualities best suited to that particular environment (Merriam-Webster Dictionary).

Cells adapt to the environment by manipulating its internal machineries, producing proteins necessary for its survival and moving away from the source of danger by its unique locomotive ability. The cell particularly uses mRNAs to create proteins which direct the cell’s activity and in turn alter its behavior.

3. Define an Enzyme.

Putting it simply, an enzyme is protein biocatalyst, which lowers the amount of time a certain substance be modified (or digested) and provides the necessary venue for the chemical reaction to occur rapidly that would proceed otherwise at room temperature. The name enzyme was taken from the Greek énsimo, formed by én = in and simo yeast. This was due to the fact that many of the enzymes studied by scientists during the 1800s were of yeast in origin. Almost all enzymes are proteins. The basic structure and functionalities of enzymes are fully discussed in the next question. As early as 1800, scientists like Louis Pasteur (1822-1895 French chemist & microbiologist) and Hans and Eduard Buchner (1860-1917 German Chemists; awarded 1907 Nobel prize for chemistry for research on alcoholic fermentation) working on the fermentation of sugar to alcohol by yeast cells, were able to conclude that something which Pasteur called “ferments”, were aiding the digestion and eventual degradation of sugar to alcohol and were thought to happen only in living organisms. With our knowledge in basic inorganic chemistry, we can now conclude that such assumption is incorrect since some inorganic substances (and organic substances) can act as much like the workings of an enzyme. Similar experiments were conducted by Buchner in 1897 and observed the same phenomenon though their purpose was purely medical. It was in the year 1926 when James B. Summer, an American Biochemist, confirmed that enzymes present in living systems are protein molecules. He was also the first person to isolate a pure enzyme in the form of crystals. 7

In terms of its composition.

Enzymes are structurally and functionally diverse just as animals are in a certain ecosystem. Diverse as they are, enzymes do share a common structure. An enzyme has an active site where a substrate, a molecule that binds to and acted upon by biological catalysts, fits snugly into the enzyme. The lock and key hypothesis is the most intelligible model by which we can understand the workings of an enzyme. In this model, the substrate, the reacting molecule, binds with an enzyme in the active site producing what we call a reaction intermediate, which also shows how an enzyme-substrate complex forms. This reaction intermediate is important for it provides a way for enzymes to lower the activation energy, the minimum amount of energy required to convert a normal stable molecule into a reactive molecule, of a substance when reacting to another substance than done otherwise. This way, a reaction that usually occurs years to complete is expedited to a minute or seconds upon the intervention of an enzyme molecule. Upon contact with a substrate, it was observed that an enzyme changes its shape to accommodate the shape of the entire substrate. This behavior is a characteristic of a covalent bond that connects the molecules of an enzyme and confers the molecule its apparent flexibility. This discovery led to the formulation of a new model for enzyme activity, which is known as Induced Fit Hypothesis in 1959 by Maxi Koshland. Under this hypothesis, active sites changes shape as substrates interact with it. The amino acids making up the active site is a flexible material, which fits the substrate snugly into the active site and performs the normal catalytic function.

Aside from the aforementioned main structure of an enzyme, an auxiliary molecule that aids the enzymes from performing their catalytic function called co-factors which includes co-enzymes (organic compound like vitamins or any derivative molecule of vitamins), and activators (trace elements such as copper, iron, or magnesium) are worth mentioning in this TMA. Co-factors can come in different shapes, sizes, forms, and kinds. If co-enzymes are firmly associated with an enzyme, they are called prosthetic groups.

In terms of its purpose in the cell

Enzymes function primarily to maneuver chemical reaction rapidly. Without them, a chemical reaction that usually last for a seconds will take years to complete. The presence of enzymes is critical to our biological existence for it helps the organism from performing its varied functions while supplying the correct form of molecule unique to a particular process. Most chemical reactions occur very slowly under ordinary temperature conditions but an enzyme speeds up this process and helps the production and modification of biological molecules by which the cell can readily use for its diverse functionalities. We have seen several cases of diseases where a defective enzyme is involved. One perfect example is for people with Phenylketonuria. Patients suffering from this disease suffer from mild to severe mental retardation, depending on the severity of the condition and blood phenylalanine levels. This condition manifests in patients who lacks the necessary enzyme to initiate the degradation of the essential amino acid phenylalanine, which in this case, the phenylalanine hydroxylase (hydroxylase: any of a group of enzymes that catalyze oxidation reactions in which one of the two atoms of molecular oxygen is incorporated into the substrate and the other is used to oxidize NADH or NADPH – Merriam-Webster’s Dictionary). In phenylketonuric patients, the enzyme responsible for the metabolism of the essential amino acid phenylalanine is completely or partially non-functional or in other cases, the lack of other enzymes necessary for the catabolistic process of the same is absent. Consequently, knowing that the amino acid cannot be metabolized, the unmonitored intake of phenylalanine causes an increase in phenylalanine in the blood and saturates the blood vessels causing organ damage especially the brain. Through genetic screening, it was found that this condition is genetic in origin and was due to a mutation in both alleles coding for the enzyme phenylalanine hydroxylase and can be located in chromosome 12. Patients exhibiting these symptoms and found to be inflicted with this disease are kept in strict dietary supervision to control the intake of dietary phenylalanine thereby avoiding the consequences this disease portends.

Give a metaphor that will allow you to describe an enzyme to a fourteen year old. Explain your metaphor.

Using the descriptions provided above for enzymes, we could use the child eating a lollipop as an analogy to better understand the province of enzymes with the “lollipop” logically substituting the substrate and “saliva” as enzymes to a fourteen-year-old child. I can somehow illustrate to a novice learner of science how saliva acts as a destabilizing agent towards the partial digestion of the lollipop and better prepare it to further digestion in the stomach using the digestive juices (hydrochloric acid and other enzymes) as secondary agent for further enzymatic action. In this way, the basic foundation for the concept of enzymes is established using simple activity that is rather comprehensible to a juvenile pupil.

Find out where the enzymes are in the Central Dogma of Molecular Biology.

DNA <-> RNA > PROTEIN

In the above illustration, it describes the flow of genetic information starting from DNA as the template material for the production of succeeding molecules left of the diagram. According to this tenet, RNA molecules are arranged from the intricate structure of DNA by a process called transcription. In turn, the production of RNA from the DNA template will provide a new pattern to yield another product by translating the information contained in RNA to produce proteins, a process popularly known as translation. To every reaction that is taking place in the process of replication (DNA synthesis from DNA template), transcription (RNA production from DNA template) and translation (protein synthesis from RNA template), enzymes are always involved. Enzymes can be located in the arrows connecting each molecules produced by every reaction. In fact, the skeleton of this doctrine is quite so simple for many enzymes are involved in each reaction as represented by these arrows.

Enzymes are the catalyst of change that aids molecule to be created from one form to another. They provide the proper avenue in order for the chemical modification to takes place. A biochemical reaction cannot move on without the aid of chemical modifiers such as enzymes for they possess the necessary biochemical machinery to process a molecule in a form that an organism can readily use.


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