Microorganisms as cells

The cell is the basic unit of life, and microorganisms are cellular entities. A single cell is a unit, isolated or secluded from other cells by a membrane, and many cells also contain a cell wall outside the membrane. For example, bacteria are grouped into two main types based on their cell walls, viz: Gram positive bacteria and Gram negative bacteria. A cell contains different chemicals and cellular structures including cytoplasm, ribosomes and cell wall to mention but a few. The membrane is semi-permeable and it forms a compartment which maintains the internal constituents of the cell and protects it from external forces while allowing important nutrients and wastes to enter and leave the cell. Cells communicate and exchange materials with their environments, and they are constantly undergoing change, and they also show a high degree of metabolism. Cells can be considered as both chemical and coding devices because they can take up nutrient from their environment and chemically transform same for their upkeep or growth, and in turn can undergo reproduction. Thus, microorganisms are living things because they all show the fundamental characteristics of living things.

Prokaryotes are cells or organisms that lack a nucleus and other membrane-enclosed organelles like mitochondrion, chloroplast and so on. They usually have their DNA in a single circular molecular known as the nucleoid (the aggregated mass of DNA that makes up the chromosome of prokaryotic cells). Members of microorganisms that are prokaryotes are the Archaea and bacteria. Prokaryotes do not have a nucleus, mitochondria or other cell membrane-bound organelles. Thus everything inside the cell of a prokaryote is openly accessible within the cell, and some of them are free-floating inside the cell. Prokaryotes have a larger surface-area-to-volume ratio giving them a higher metabolic rate, a higher growth rate, and, as a consequence, a shorter generation time compared to eukaryotes.

A typical structure of a prokaryotic cell (bacterium)

Eukaryotes are distinct group of cells or organisms that have a unit membrane-enclosed nucleus and usually other organelles. It is an organism whose cells contain complex structures enclosed within membranes. Nucleus or nuclear envelope within which the genetic material of the eukaryotes is carried or enclosed is the membrane-bound structure that differentiates prokaryotes from eukaryotes. Most eukaryotic cells also contain other membrane-bound organelles such as mitochondria, chloroplasts and the Golgi apparatus. Microorganisms under this group of organisms called eukaryotes include protozoa, fungi, algae, plants and animal cells.

A typical eukaryotic cell (animal cell)

ECONOMIC IMPORTANCE OF MICROORGANISMS

Microorganisms which existed on planet earth for billions of years even before plants and animals appeared are microscopic and independently living cells that, like human beings, live in communities known as microbial communities. The diversity and abundance of a particular group of microorganisms in a given microbial community is largely controlled by the resources (e.g. food) and environmental conditions (pH, temperature, and oxygen content and water/humidity level) that exist in the environment or microbial community. Many illnesses are caused by infection with microbes and understanding these infections has lead to cures and better treatments.

The emergence of new infectious agents will spur continued interest in microbiology. Many more microbes grow harmlessly in the environment, taking advantage of chemicals and/or sunlight to grow. Research into these microbes has also helped us understand the basic framework of life and revealed the basic fundamental rules that govern living systems. In the past microbes have been used in experiments to answer many scientific questions and they will continue to serve as excellent tools of inquiry in the future. A significant number of these discoveries have lead to important applications in many areas of human endeavor.

Microorganisms are important to our lives in countless number of ways. Sometimes, the influence of microorganisms on both human and animal live can be advantageous, but in other cases, they can be detrimental – as they are implicated in a number of diseases that affect man and animals including plants. Beneficially, microorganisms are used for the production of drugs (e.g. antibiotics), bread, yoghurt, cheese, wine, beer, and alcohol/ethanol, vitamins and many other enzymes used in both industrial and medical practices. In an ecosystem, microorganisms play important roles in the cycling of important nutrients in plant nutrition particularly those of nitrogen, carbon and sulphur.

For example, nitrogen-fixing bacteria (e.g. Rhizobium, Nitrosomonas and Nitrobacter) which live in the soil work by converting huge amounts of nitrogen in the atmosphere into a form that plants can use. Methane (a type of natural gas) is a product of methanogenic bacteria, and in this way microorganisms play important roles in energy production. Microorganisms (e.g. those in the Pseudomonads family) are natural cleaners of the environment. They are use to clean up pollution caused by oil spills and other chemicals in a process called bioremediation (the introduction of microorganisms to restore stability to polluted environments).

Harmfully, microorganisms have over the years harmed humans, plants and animals in diverse ways, and they have played historical roles in shaping the cause of things in terms of the diseases they cause. Only in 1347 in Europe, when “plague” or “black death” hit Europe, 25 million people (which represent one third of the population of Europe as at the time) were killed within four (4) years. The “Black Death” was one of the most devastating pandemic in the human history. After careful DNA analysis of ancient plague victims in Europe, it was discovered that this disease was caused by a microorganism called Yersinia pestis.

The major causes of death at the twentieth century were infectious diseases which are caused by microorganisms called pathogens. Children and the aged in particular succumbed to microbial diseases in large numbers. But today, infectious diseases are much less lethal due to their control as a result of an increased understanding of disease processes, improved sanitary and public health practices and the use of antimicrobial agents which were all lacking prior to the discovery of microorganisms. Nevertheless, microorganisms can still be a major threat to the survival of both humans and animals, and this can be seen in the case of AIDS (acquired immunodeficiency syndrome) and multiple drug-resistant pathogens in infected patients.

CHARACTERISTICS OF MICROORGANISMS

  1. Microorganisms are ubiquitous. That is to say that microorganism is present everywhere on the bodies of humans and animals, in the air, in water, in dust, in the soil, in the intestinal canals of humans, birds and animals.
  2. Microorganisms have a very small size.
  3. They have no cellular differentiation.
  4. They are unicellular and one cell is capable of performing all the functions.
  5. Some microorganisms are multicellular with little or no cell differentiation.

 TAXONOMIC GROUPS OF MICROORGANISMS

Taxonomy is simply defined as the scientific system of classifying biological organisms. It is the science of identifying and naming species of organisms and arranging same into a classification. Taxonomy is divided into 3 main groups including identification, classification and nomenclature. Microorganisms have wide taxonomic distribution and this includes organisms such as viruses, bacteria, protozoa, algae, Archaea and fungi.

 

Taxonomic distribution of microbial cells

Bacteria: Bacteria are single-celled or unicellular microorganisms. They are present in the air, soil, water and even on human and animal bodies. Bacteria are prokaryotic organisms. Their size varies from 1-5µm and they have varying shapes including rod, coccus and spiral shapes when viewed under a microscope. Spherical bacteria are called cocci while those that are rod-like are called bacilli. Some bacteria move by means of a hair-like structure called flagella – which is attached on their body surfaces. They reproduce by binary fission. Some bacteria have mycelial morphology (e.g. Actinomycetes), and this type of bacterium is very important in the production of antibiotics. Bacteria play tremendous roles in our everyday life. In food industry, they are important in food spoilage, fermentation processes and food preservation and poisoning. In agriculture, bacteria play important roles in the cycling of important nutrients like sulphur and nitrogen. Medically, they cause a range of both human and animal diseases. The study of bacteria is known as bacteriology.

Viruses: Virus is a genetic element that contains either an RNA or DNA as its genome. It replicates only in living cells and it has an extracellular form. They are non-cellular obligate parasites of animals, humans and plants including bacteria and some protists. Their sizes vary from 0.015µm-0.2µm. viruses unlike bacteria can only be seen under an electron microscope. They only contain one type of nucleic acid (DNA or RNA) which is surrounded by a protein coat. Viruses also have different shapes including spherical, icosahedron, rod and flexuous shapes. Because they are deficient of cellular components necessary for independent reproduction or metabolism, viruses only replicate or multiply on living cells like animal and human cells. Viruses cause large number of human diseases example AIDS which is caused by human immunodeficiency virus (HIV), and some animal diseases (example: foot-and-mouth disease caused by Aphtovirus of the Picornaviridae family) and plant diseases (example: tobacco mosaic disease caused by tobacco mosaic virus). The study of viruses is called virology.

Fungi: Fungi are members of eukaryotic organisms that include microorganisms such as yeast, moulds and mushrooms. They are non-phototrophic eukaryotic microorganisms that contain rigid cell walls that are made up of chitin unlike bacteria cell wall that contains cellulose. They form characteristic structure called mycelium, and they also form fruiting structures called conidia (or endospores and exospores). The spores of fungi are ubiquitous in the air, soil and dust, and they serve as source of contamination to both humans and animals. The size of fungi ranges from 2.0-1.0µm (for moulds) and 5-10µm (for yeasts). Fungi have beneficial importance as they are usually used for the production of some antibiotics like penicillin. And they also cause a range of diseases in both animals and humans. Yeasts are also used in the food industry to produce beverages like bread, wine and beer. The study of fungi is called mycology.

Protozoa: Protozoa are unicellular eukaryotic microorganisms that lack cell wall. They are motile and move by means of cilia, flagella and pseudopodia. Their size vary from 5-200µm, and they usually live in moist environments like soil, water and marshy environments. Protozoa are animal-like in that they eat food. They do not contain chlorophyll, and they are differentiated from other microorganisms on the basis of their morphological, physiological and nutritional characteristics. Protozoa have varying importance in nature including those that are found in the stomach of animals and helps in their digestion, and plasmodium parasites which are the best known protozoa because they cause disease in humans (e.g. malaria). Typical examples of protozoa include amoeba, plasmodium and trypanosome parasites. The study of protozoa is called protozoalogy.

Algae: Algae are phototrophic eukaryotic microorganisms i.e. they are photosynthetic on nature like plants. They are simple organisms whose size ranges from 1µm to several feet. Algae are unicellular to multi-cellular and some are motile while others are not. They exhibit a wide range of reproductive strategies, from simple, asexual cell division to complex forms of sexual reproduction. Algae are autotrophic, and are usually found in aquatic environments and in damp soil. They exhibit some economic importance where they are found by clogging water pipes, releasing toxic chemicals into water and growing in swimming pools. Some also possess some useful importance as they serve as source of agar used as solidifying agents in microbial media and as anti-inflammatory drugs for ulcer treatment. The study of algae is called algology or phycology.

SPONTANEOUS GENERATION

Spontaneous generation is the hypothesis that living organisms can originate from non-living matter. This concept had existed since biblical times, and people had believed in this theory of spontaneous generation – that living things originated from non-living things. The ancient Greeks believed that living things could spontaneously come into being from non-living matter, and that the goddess Gaia as at the time could make life arise spontaneously from stones – a process they called Generatio spontanea. The great Aristotle (384-322) disapproved this concept of the Greeks, but he still believed that creatures could arise from dissimilar organisms or from the soil. The basic idea of spontaneous generation can easily be understood.

For example, if food is allowed to stand for a given amount of time, the food decays (or putrefies). Upon examination of the putrefied food using the microscope, it will be found to be swarming with bacteria and some higher organisms like maggots and worms. The question that “spontaneous generation” is trying to answer is: “where did the bacteria, worms and maggots which were not initially present in the food com from”? Some people said these organisms came from seeds or germs that entered the food from the air while others said that the organisms arose “spontaneously” from non-living materials. At this stage, people were left mystified as nobody knew who was right and who was wrong. This led many researchers including Louis Pasteur, Francesco Redi, John Needham, John Tyndall and others who all undertook different kinds of experimentation to try and unravel or end the mystery called “spontaneous generation”.

Louis Pasteur used his swan-necked flask experiment to prove the theory of spontaneous generation of living things from non-living things as invalid. But the first serious attack on the theory of spontaneous generation was made by Francesco Redi in 1668.  Francesco Redi disproved Spontaneous Generation by putting some decaying meat in 2 jars, and then covered one of them. When fly maggots appeared in only the uncovered jar, he had enough evidence to prove that the flies came from eggs and not the decaying meat because if the flies came from the meat, there would be flies in both jars. Redi showed in his experiments that rotten meat carefully kept from flies will not spontaneously produce maggots.

Though the theory of spontaneous generation was an attractive theory to many people as at the time, this concept was nevertheless disproven by a series of observations and arguments and experiments that finally laid this fallacy to rest.  The theory of spontaneous generation was held by many even till the late 19th century because the notion meshed satisfactorily with the prevailing religious views of how God created the universe – which until today is still being debated by some few people.

Abiogenesis: Abiogenesis or biopoiesis as some people call it, is the belief that living organisms arise from non-living matter. Abiogenesis is used synonymously with spontaneous generation because they both mean the same thing. It is the study of how biological life could arise from inorganic matter through natural processes. In particular, abiogenesis usually refers to the processes by which life on Earth may have arisen.  Belief in the ongoing spontaneous generation of certain forms of life from non-living matter goes back to ancient Greek philosophy and continued to have support in Western learning until the 19th century when the works of scientists like Francesco Redi and others proved all previous sentiments about spontaneous generation as false. Classical notions of abiogenesis, now more precisely known as spontaneous generation, held that certain complex living organisms are generated by decaying organic substances. Spontaneous Generation is thus believed by those who hold the philosophy of evolution, but scientifically it is a myth.

Biogenesis: Biogenesis is the belief that living things come only from other living things. It is the alternative of abiogenesis, and biogenesis is the fact that every living thing came from a pre-existing living thing. For example, a spider lays eggs, which develop into spiders. It may also refer to biochemical processes of reproduction in living organisms. Biogenesis can also mean “omne vivum ex ovo”, which is the Latin word for “every living thing is from an egg”. It is the contention that living matter can only be generated by other living matter, which is in complete contrast to the theory of abiogenesis which holds that life can arise from non-living matter under suitable conditions. In terms of real science, the Law of Biogenesis “Omne vivum ex ovo” – ”all life is from life” stands as a scientific law with no exceptions.

ATP

ATP is the acronym for “adenosine triphosphate”. ATP is a nucleotide molecule in which chemical energy is conserved and utilized in living cells. It is the major carrier of chemical energy in all living cells. ATP can also be referred to as the energy currency of the cell since it is the primary form in which chemical energy is stored in living cells. ATP is found in both prokaryotic and eukaryotic cells. ATP participates in a variety of metabolic processes and reactions in which energy is either conserved or expended. When ATP is broken down, adenosine diphosphate (ADP) and inorganic phosphate (Pi) will be produced.

ATP      ↔     ADP ┼ Pi

Illustration of ATP hydrolysis

The above reaction in which ATP is hydrolyzed to ADP and Pi is a reversible reaction as shown. This is because ADP can be phosphorylated to ATP by the addition of Pi. The phosphorylation of ADP to ATP commonly occurs by oxidative phosphorylation, substrate level phosphorylation or by photophosphorylation

Oxidative phosphorylation is defined as the production of ATP using electron transport   chain (ETC). It us the non-phototrophic production of ATP at the expense of a proton motive force (PMF) formed by electron transport in mitochondria of the cell.

Substrate level phosphorylation does not rely on electrons from the ETC to synthesize ATP. It is the synthesis of ATP (high-energy phosphate bonds) through reaction of inorganic phosphate with an activated organic substrate as seen in fermentation.

Phosphorylation is defined as the synthesis of   ATP using light energy of sunlight. It occurs in the chloroplast of photosynthetic cells/organisms. Energy is obtained from sunlight or fuels by converting the energy from electron flow into chemical bonds of ATP

Structure of ATP

ATP is the major link between anabolic reactions (energy-requiring processes) and catabolic reactions (energy-yielding processes) in the cell. And ATP plays the same role that money plays the in the economy. ATP is earned or produced in exergonic reactions. Energy is produced and stored in living cells as ATP. And ATP is the main source of energy for the various cellular and metabolic activities going on in the cell. These activities include growth motility and reproduction. ATP is the most important energy-rich phosphate compound in living cells; and this is because the amount if energy released by the hydrolysis of ATP is far greater than the energy that could be generated when other phosphorylated compounds 9e.g. glucose-6-phosphate) are hydrolyzed or broken down. ATP is continuously being broken down drive anabolic reactions and re-synthesized at the expense of catabolic reactions. Electron transport system consist of a series membrane associated electron carriers (e.g. NADH, FADH2) that function in an integrated fashion to carry electrons from the primary electron donor (e.g. NADH) to a terminal electron acceptor such as oxygen (O2). Oxygen (O2) is the terminal or final electron acceptor of the electron transport chain or system.

ELECTRON TRANSPORT SYSTEM

Electron transport system (respiratory chain) is a respiratory chain composed of several component including   NADH and cytochromes in which electron flows from one molecule to another with the aim of producing ATP for the cell. Oxidation and reduction reactions in which electrons are lost and gained respectively in the cell occur in the electron transport system. The electron transport system can also be called electron transport chain (ETC) ort respiratory chain. ETC is located in the inner membrane of the mitochondrion. As fuel molecules such as carbohydrates or sugars are oxidized in the cell, the electrons they lose are usually used to make NADH and FADH2 (which are both electron carriers of the ETC).

The major function of the ETC is to take the electrons from these molecules (i.e. NADH and FADH2) and transfer them to oxygen (O2), thereby making ATP (the energy currency of the cell) in the process. Oxygen is the final electron acceptor of the ETC as they move down the ETC; the electron carriers (NADH and FADH2) become reduced. The next electron carrier in ETC oxidizes the previous electron carrier, thereby taking its electrons and transferring them to next electron carrier. This process continues until finally the electrons end up reducing oxygen to water. ETC occurs in the cell membrane of prokaryotic cells, but in eukaryotic cells, it occurs in the inner membrane of the mitochondria.

Illustration of the electron transport system

The electron transport chain is usually divided into four complexes that illustrate how electrons flow in system. These complexes are:

  1. Complex 1
  2. Complex 2
  3. Complex 3
  4. Complex 4

Complex 1 and complex 2 catalyze electron transfer from two different electron donors (NADH and succinate) to ubiquinone (CoQ). NADH is electron donor in complex 1 while succinate is the electron donor in complex 2. Complex 3 carries from reduced CoQ to cytochrome C (cyt C). Complex 4 is the final step of ETC; and it transfers electrons from cytochrome C to oxygen (O2), thereby producing huge amounts of ATP in the process. Complex 4 can also be called cytochrome oxidase and it signals the final stage of the ETC since it carries electrons from cyt C to molecular oxygen, thereby reducing it to H2O as shown in the above illustration.

ETC gets its substrate from the NADH and FADH2 as supplied by the TCA cycle and other metabolic sources. As they transfer of electrons in the ETC proceeds at the different complexes (1-4), protons are generated through a proton motive force (PMF). The protons are usually moved outward from the mitochondrion (i.e. they are pumped out of the mitochondria into the cytoplasm) while electrons are transported inwards into the mitochondrial matrix. PMF plays a critical role in the physiology of organisms especially in prokaryotic or bacteria cells where PMF facilitates motility in the bacteria and even the transport of important molecules across the cell membrane. ATPase is the enzyme that drives ATP synthesis and in the cell as the proton motive force proceeds. PMF drives their synthesis of ATP as protons flow passively back to the mitochondrial matrix. Another word for ATPase is ATP synthase.

ATP synthesis in the cell is usually blocked by some inhibitors which stop the passage of electrons to O2. Carbon monoxide, cyanide and actimycin are typical examples of inhibitors that block ATP synthesis in the cell. Cyanide inhibits cytochrome oxidase and block the transfer if 4elecctrons to O2. Together with carbon monoxide, they both block at complex 4 and 3. Actimycin inhibits electron transfer from cyt B to cyt C1, and it blocks at complex 2. Rotenone inhibits the catalyses of NADH to CoQ and it blocks at complex 1. In summary, the flow of electrons through complexes 1-4 of the ETC results in the pumping of protons in inner mitochondrial membrane. A proton is generated via the PMF; and this proton gradient provides the energy (in the form of PMF) for the ATP synthesis from ADP and Pi by ATP synthase in the inner membrane of the mitochondria.

ROLES OF ATP

  1. The energy released during the hydrolysis of ATP is used to power biosynthesis processes in the cell.
  2. The energy from ATP hydrolysis is also used to prepare molecules for catabolism.
  3. Energy stored in ATP is used to drive anabolic reactions in the cell.
  4. When ATP is utilized, the terminal phosphate is removed to release energy and ADP is formed.
  5. Energy from ATP is used to activate individual subunits before they are linked together by enzymatic reactions.

BIOSYNTHESIS OF CARBOHYDRATE, LIPIDS, PROTEIN, PURINE AND PYRIMIDINES SYNTHESIS

Summary of macromolecules and their monomers

Macromolecules Monomers Biological function
1.      Polysaccharides

(carbohydrates)

Monosaccharide Energy storage, receptors, structure of plant cell wall
2.      Lipids/fats Fatty acid, glycerol Enzymes, structure, receptors, transport
3.      Proteins Amino acids Information storage and transfer
4.      Nucleic acids Nucleotides Membrane structure, energy storage, insulation

                                              CARBOHYDRATES

Carbohydrates are macromolecules that contain carbon, hydrogen and oxygen. Carbohydrates (CHO) are important source of the energy for all living organism including microorganisms. The monomers of CHO comprise of simple sugars known as monosaccharide, disaccharides (Oligosaccharides) and polysaccharides are the three major classes of CHO. Carbohydrates are the most abundant macromolecules on earth, and they are the source of immediate energy needs in living systems. Carbohydrates also participate in defining the structure of cells and living systems.

Carbohydrates include single sugars or multiple sugar molecules bonded together into polymers. Collectively, there are three types of carbohydrates. They are monosaccharides, disaccharides, and polysaccharides. Monosaccharides, also referred to as simple sugars, are made up of a single sugar molecule. The major example of a monosaccharide is glucose. Sugar molecules, such as the glucose molecule, contain many OH functional groups. For example, the molecular formula for glucose is C6H12O6. Other examples of monosaccharides include isomers of glucose, such as fructose and galactose.

Monosaccharides are transported in the blood of animals, broken down to produce chemical energy inside the cell, and can also be found in other macromolecules such as nucleic acids. Monosaccharides are known as simple sugars. Glucose (D-glucose) is the most abundant monosaccharide in nature. Glucose is the six-carbon structure.

Disaccharides are composed of two single monomers of sugar linked together. Examples of disaccharides are maltose (glucose + glucose) and sucrose (glucose + fructose). Disaccharides are broken down into their subunits for use inside living systems. Disaccharides also known as oligosaccharides are formed from two monosaccharides joined together by glycosidic bonds. Maltose, lactose and sucrose are examples of disaccharides.

Polysaccharides are made up of chains of sugar monomers linked together, and they are stored inside the cell for future energy use. Polysaccharides are sugar polymers that contain several monosaccharide units held together by glycosidic bond. Glycogen and cellulose are examples of polysaccharides. In plants, the major storage polysaccharide is starch, while in animals it is glycogen. Inside plants like the potato, starch is stored inside of granules throughout the winter until it is needed for growth in the springtime. In animals, glycogen is stored inside the liver and it released when the amount of glucose in the blood circulation is too low. At this time, glycogen is broken down chemically into monomers of glucose. Plants also contain cellulose, which is the most abundant of all carbohydrates. Cellulose is the found in the plant cell wall, where it provides structure and support to the plant cell.

The oxidation of carbohydrates in most living organisms including microbes is the central energy-yielding pathway via which energy for other cellular and metabolic activities of the cell are provided. CHO form an integral part of the cell components of microbes. For example the cell wall of bacteria is mainly made of CHO. CHO is also part of the nucleic acids of microorganisms as can be seen in deoxyribose and ribose sugars of DNA and RNA respectively. Certain marine red algae also have cell walls that are made of CHO. Agar, the solidifying agent of culture media also contains CHO.

CHO are majorly biosynthesized from the activated forms of their monomers (i.e. the simple sugars known as monosaccharide). Photosynthetic cells such as plants utilize the suns energy to degrade or make energy rich nutrients in their environment. But this is not the case for known phosynthetic cells such as microbes. Microorganisms make their glucose (CHO) from simpler precursor molecules in a process known as gluconeogenesis. Gluconeogenesis is the production of glucose from non sugar precursors such as uridine diphosphoglucose (UDPG) and adenosine diphosphoglucose (ADPG). ADPG and UDPG are activated forms of glucose and they needed for the synthesis of other CHO molecules in the cell of a microbe. Organisms that do not have access to glucose from other sources must synthesize it. If a bacterium is growing on a sugar medium or substrate, it will not have problem sourcing for glucose to make CHO.

But when the bacterium is growing on other carbon sources of compounds, it must biosynthesize glucose in other to make pother CHO molecules, such as its peptidoglycan cell wall. To this it uses phosphophenolpyruvate (an intermediate of glycolysis as its starting material to synthesize glucose molecule for the cell through the process of gluconeogenesis. Once glucose is provided in the growth medium air in the environment of the organism, the bacterium can have access to carbon sources it requires to synthesize other important cell molecules apart from CHO. For example E coli growing in a glucose medium can obtain from glucose carbon skeleton from every amino acid, fatty acids, coenzyme, nucleotide and other metabolic intermediates it requires for its growth.

LIPIDS

Lipids are water insoluble organic molecules. They serve a wide variety of functions in living organisms including microorganisms. Lipids are macromolecules that are all insoluble in water. They include oils and fats, phospholipids, and steroids. Oils are found in plants, where they are used for long term energy storage. Fats are found in animals where they also provide long term energy storage, as well as insulation. Fats and oils are composed of glycerol and fatty acids. A fatty acid is a long chain of carbon-hydrogen (C-H) bonds, with a carboxyl group (-COOH) at one end. On average, a fatty acid contains sixteen to eighteen carbon atoms per molecule. Based on the number of carbons and the number of double bonds that are present, fatty acids can be classified as saturated or unsaturated. Fatty acids are saturated when they do not contain any double bonds between the carbons, and unsaturated when they contain double bonds.

An example of a saturated fat is butter, while an example of an unsaturated fat is vegetable oil. Fats and oils are formed in a dehydration reaction in which, three fatty acids react with the -OH group in glycerol. Triglycerides, which are the major component of vegetable oil as well stored fat in animals, are composed of three fatty acids and glycerol. Phospholipids are found primarily in the cell membranes of living systems, of which they are the major component. Structurally, a phospholipid contains a hydrophilic head and a hydrophobic tail. The head of the phospholipid contains a phosphate group, while the tail is typically a diglyceride. The cell membrane is a double layer of phospholipids, in which the tails are turned inwards and the heads are exposed to the intracellular and extracellular environments.

Phospholipids are also used inside biological systems for cell to cell signaling. Steroids are also lipids; however they are the most unique category in the group. Steroids are typically made up of fused hydrocarbon rings. Each type of steroid is different in the type of chemically active functional groups that it contains. Examples of steroids include cholesterol, estrogen, and testosterone. Cholesterol in found in the cell membrane of animals, where it provides structural support. Cholesterol is also the precursor for other steroids, such as testosterone and estrogen. Some vitamins, such as Vitamin D, are also classified as steroids.

Lipids are the main integral part o0f the cell membranes. They are found in the cell wall of some bacteria e.g., Mycobacterium species. Lipids are carbon and energy reserves of the cell. They are found in the outer membrane of Gram negative bacteria. Fatty acids are the monomers from which fatty acids are formed. Fatty acids are synthesized into two-carbons at a time and then attached to glycerol to form lipids. They synthesized with the help of a protein called acyl carrier protein (ACP). The ACP molecule holds the growing fatty acids as it is being synthesized. ACP releases the growing fatty acid once it has reached its final length. Fatty acids are carboxylic acids with hydrocarbon chains ranging from 4 to 36 carbon long (C4 to C36 ). When the fatty acid is saturated, it contains no double bonds and are the malonate (a three carbon compound). Malonate is attached to ACP to form malonyl-ACP. And as each malonyl is donated for the synthesis of fatty acid, one molecule of CO2 is released. In the final assembly of lipids, fatty acids are added to glycerol to form lipids in bacteria and eukaryotic cells.

PROTEINS

Proteins are polymeric molecules or macromolecule that consists of polypeptides. A given protein molecule consists of one or more polypeptides-formed by amino acids that are held together by peptide bonds. Amino acids are the monomers of proteins. Organisms that cannot obtain some or all of their amino acids preformed from their environment must synthesize them from other sources. While some organism must ingest amino acids from protein synthesis, others synthesize them from glucose and other intermediates from the Kreb cycle or glycolytic pathway. The amino group of amino acids is derived from inorganic nitrogen sources in the environment, such as ammonia (NH3). When NH3 is present in high amount, glutamate dehydrogenase catalyzes the reaction.  But at low levels of NH3, glutamine synthethase will catalyze the reaction.

NH3 can also be used to form other nitrogenous compounds because it contains nitrogen (N). The amino acids formed are held together by peptide bonds to form polypeptides. The polypeptide molecules self-fold into the different protein structure. Proteins are polymers that are made up of amino acids. Amino acids are small molecules that contain an amine (-NH2), a carboxyl acid (-COOH), and a side chain (R). There are twenty naturally occurring amino acids, and each amino acid has a unique side-chain or R-group. Amino acids are connected by peptide bonds to form protein polymers. This gives rise to different levels of structure for proteins. The primary (1°) structure of a protein is a made up of a string of connected amino acids. The secondary (2°) structure of a protein is formed by the coiling and folding of the 1° structure. At this level, structures called alpha-helices and beta-sheets are visible.

The tertiary (3°) structure of a protein is formed by interactions between the components of the 2° structure. Some proteins have quaternary (4°) structure, which includes the assembly of multiple individual subunits to form the functional protein. Proteins have numerous biological functions. The common types of proteins that are found in biological systems are enzymes, antibodies, transport proteins, regulatory proteins, and structural proteins. Structural proteins provide support, and examples included keratin that is found in hair and fingernails and collagen that is found in human skin. Proteins such as enzymes are actively involved in metabolism, in which they speed up or accelerate chemical reactions in the body. Enzymes are temperature sensitive, and most are optimal at the body temperature of the living system.

Transport proteins are important for carrying compounds or chemicals that are important for survival throughout living systems. Examples of transport proteins include hemoglobin that carries oxygen through the blood, and pores in the cell’s membrane that allows substances to enter and leave the cell. Proteins, such as antibodies, are a part of the immune system or defense mechanism in living systems. Antibodies bind to particles or cells that are foreign to the system and aid in their elimination. Regulatory proteins ensure that physiological processes are carried out in the correct manner inside living systems. Examples of regulatory proteins are hormones that control processes such as growth (growth hormone) and metabolism (insulin and glucagon).

NUCLEIC ACIDS

Nucleic acids are the molecules inside the cell that store and process genetic or hereditary information. The two types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). These macromolecules are called nucleic acids, because they were first found inside the nucleus of the cell. The monomers that make up nucleic acids are called nucleotides. Each nucleotide contains a sugar, a base, and a phosphate group. DNA contains the genetic or hereditary information. It is made up four nucleotides: adenine (A), cytosine (C), guanine (G), and thymine (T). These nucleotides organize themselves to form a double helical structure that is often compared to a ladder. In the double helix, A pairs with T and C pairs with G forming the centre or rungs of the ladder. The nucleotide pairs are held together by hydrogen bonds.

The backbone of the double helix is made of up the sugar and phosphate groups, which are held together by phosphodiester bonds. The base pairing in DNA is important, because it allows the DNA molecule to copy itself during DNA replication. Functionally DNA can be organized into three groups. Exons are the coding regions of DNA (gene) that contain the genes for proteins and other genes. Introns are the segments of the DNA (gene) that are not used in making genes. Like DNA, RNA is made up of monomers of nucleotides. RNA is very similar in content to DNA. The major differences are: (1.) the sugar used in RNA is ribose, which contains one less oxygen atom than the deoxyribose in DNA, and: (2.) the base thymine is replaced by uracil (U) in RNA. As a result, in RNA A pairs with U and C still pairs with G. Structurally, RNA differs from DNA in that it does not form a double stranded molecule.

Rather, it is a single stranded molecule that forms many different secondary structures. There are three major types of RNA. The first, messenger RNA (mRNA) is involved in the interpretation of the genetic information stored in DNA. During the production of proteins for example, DNA is copied and translated into mRNA. The second type of RNA is ribosomal RNA (rRNA). rRNA is found in the ribosome, the site of protein synthesis in the cell. As a part of the ribosome, rRNA is responsible for the accurate production of proteins inside the cell. The third type of RNA is transfer RNA (tRNA). tRNA is also involved in protein synthesis. As the name implies, it transfers amino acids to the ribosome so that they can be assembled to form polymers of proteins during protein synthesis. Some RNA molecules also function as enzymes.

PURINE AND PYRIMIDINE SYNTHESIS

The synthesis of purine and pyrimidines is critical to every living cell because the molecules are critical to the biosynthesis of DNA and RNA- which are both formational macromolecules.

Purine includes adenine (A) and guanine (G), and their structure is composed of double rings. The synthesis is a complex process, and purine is synthesized from several carbon and nitrogenous sources-including CO2.

Purines are synthesized as nucleotides. The first compound in the purine synthesis to have a completely formed purine ring system is inosine monophosphate (IMP). IMP is the precursor of the purine nucleotides, adenosine monophosphate (GMP). Adenosine and guanine are derived from IMP as well as AMP and GMP are synthesized in their triphosphate forms and have been attached to their correct pentose sugar, they are ready to be incorporated into DNA or RNA.

The structure of purine is that of cyclohexane (pyrimidines group) and cyclopentane (imidazole group) attached to one another.

Purines (adenine and guanine) are biologically significant because they are involved in the construction of the backbone of DNA and RNA.

Pyrimidines consist of cytosine(C), thymine (T) and uracil (U). Pyrimidines have a single structure. Carbamoyl phosphate is the first intermediate in the synthesis of pyrimidines. The pyrimidine ring like the purine ring is also synthesized from various carbon and nitrogen sources. Uridylate is the first key pyrimidines from which other pyrimidine cytosine. Uracil and thymine are derived. Urydylate is the precursor of all pyrimidine nucleotide including uridine monophosphate (UMP), cytosine monophosphate (CMP) and thymidine monophosphate (IMP). Pyrimidines are significant because they are involved in the construction of the backbone of DNA and RNA.

REGULATION OF METABOLISM

Metabolism is the sum total of chemical reactions occurring in a living cell at any given time. It encompasses all the chemical reactions and physical workings of the cell. Metabolism is important for the management of cellular materials and energy resources. Metabolism reactions are organized into different pathways of enzymes controlled chemical reactions. While some of these pathways are responsible for the building up of the important cell molecules, others like the glycolytic   pathway are mainly responsible for the breakdown of substrate like glucose, so that   chemical energy( in the form of ATP) will be released ion sufficient amount for the cellular and metabolic works going on in the cell. Each metabolic reactions or pathway going on in living cell require enzyme- which help to speed up the chemical  reaction and thus lower the energy required for the process, so that energy can be efficiently conserved for the cell.

Anabolism and catabolism are the two types of metabolism occurring in every living system.

ANABOLISM

Anabolism is the metabolic reaction or pathway that results in the synthesis of new cell molecules or structures. It can also be called anabolic reaction. Anabolism is an energy requiring process because it requires the input of energy required to form or build larger macromolecules from smaller ones. Many component of glycolysis and kreb cycle are the starting points to make amino acids, fatty acids and nucleotides- which are building blocks used for the biosynthesis of proteins, fat/lipids and nucleic acids respectively. ATP is used in anabolic reactions. The biosynthesis of macromolecules is examples of anabolic reactions in the cell.

CATABOLISM

Catabolism is the metabolic process that results in the breakdown of bond in larger molecules (macromolecules) into smaller molecules. It can also be called catabolic reactions. In catabolic reactions, the energy stored in the complex molecules is made available to do work or transformed into ATP. The energy stored in ATP can be used to perform cellular work including movement of substances across cell membranes and for movement of cell organelles. Cellular respiration and fermentation are examples of catabolic reactions. ATP is produced in catabolic pathways reactions.

REASONS FOR REGULATING METABOLISM

  1. Cells need a regular supply of molecules and energy.
  2. Cells need to get rid of waste products once produced.
  3. Cells need to conserve energy and biosynthetic materials.
  4. To function properly, cells need to maintain metabolic balance.
  5. Regulation of metabolism allows cells to respond to environmental changes.
  6. Regulation of metabolism help cells to maintain appropriate concentration for each metabolite.

The regulation of metabolism is carried out by enzymes that regulate the different anabolic and catabolic pathways of living organisms; and these enzymes carry out this function of regulation via a feedback mechanism. The main reason of regulating metabolism in living cells is to achieve balance of molecules and other cellular materials in the cell. This implies that both macromolecules and their monomers are only synthesized when they are needed. The regulation of metabolism including anabolism and catabolism also ensures that no molecule is over synthesized or under synthesized. The synthesis of carbohydrates, proteins, lipid/fats and nucleic acids only occur in precise proportions required by the cell under any given circumstance. When cells are growing, the monomers of CHO, proteins, lipids and nucleic acids are synthesized in large quantities so that cell growth can occur at an exponential level. But in non-growing cells, the requirements for these building blocks are much reduced. The reason is because the cell is not growing or actively metabolizing. Each sequence is regulated during metabolism in order to provide what the cell needs at a given time and to expend energy when necessary.

REFERENCES

Willey J.M, Sherwood L.M and Woolverton C.J (2008). Harley and Klein’s Microbiology. 7th ed. McGraw-Hill Higher Education, USA.

Talaro, Kathleen P (2005). Foundations in Microbiology. 5th edition. McGraw-Hill Companies Inc., New York, USA.

Singleton P and Sainsbury D (1995). Dictionary of microbiology and molecular biology, 3d ed. New York: John Wiley and Sons.

Ryan K.J and Ray C.G (2004). Sherris Medical Microbiology. 4th edition. McGraw Hill Companies Inc., New York, USA.

Brooks G.F., Butel J.S and Morse S.A (2004). Medical Microbiology, 23rd edition. McGraw Hill Publishers. USA.

Prescott L.M., Harley J.P and Klein D.A (2005). Microbiology. 6th ed. McGraw Hill Publishers, USA.

Madigan M.T., Martinko J.M., Dunlap P.V and Clark D.P (2009). Brock Biology of Microorganisms, 12th edition. Pearson Benjamin Cummings Inc, USA.

 

 

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