I have research in biology about cells and bacteria.

I have research in biology about cells and bacteria. I need help to make it sophisticated.

Chapter 1: Cell Mechanics: Principles, Practices, and Prospects

1. Motivation

Mechanical forces are normal physiological functions which are generated and sustained by biological cells. Cells are always active and are capable of detecting mechanical stimuli via mechanosensitive signaling pathways which are activated and in turn respond physical signals by reorganizing the cytoskeleton and generating the appropriate forces. Various cell mechanical properties such as viscosity, elasticity and adhesiveness are susceptible to change as a result of mutation and pathogen-induced cytoskeletal disruption. Conversely, cell behavior can be influenced by perturbations in the mechanical environment. Such transformations are indicative of various pathological states. As such, there are multitudes of hypothetical and experimental models which have been used to characterize the mechanical properties of cells, which are drawn from soft matter physics and mechanical engineering. Human knowledge of cell mechanics and its associated roles in the disease, physiology and development has been furthered by interdisciplinary studies which amalgamate research in contemporary molecular biology and advanced techniques for mechanical cellular characterization. Comment by Rashid, Bazlur: Please explain Comment by Rashid, Bazlur: define Comment by Rashid, Bazlur: grammar check: too many ‘which’

1.2 Cell Mechanics

Modern biomechanical research is at an intriguing stage whereby more is being discovered about the influence of mechanical cellular functions and characteristics both as a regulating factor and as a direct result of cellular architecture. Contemporary biomechanical research is aimed at combining the experimental, theoretical and computational approaches in order to develop an elaborate description of the mechanical behaviors of cells. This information can then be used to develop new perspectives on the correlation of cellular mechanics and disease, and the procedures which are used to pursue such research avenues are becoming increasingly complex. One of the greatest challenges facing such endeavors is the requirement for the reconciliation of physical and biological research, which requires a lot of expertise.

1.3 Physiological Forces

All living organisms need to interact with the physical forces that exist within their environments. This is one of the fundamental requirements for life and survival, and it is one of the main influencing factors of biological design. Various body parts in human beings are designed structurally to serve specific physiological functions in order to mitigate natural physical forces, such as the skeleton which poses a barrier to gravitational force. Even the most minor body functions are based on the generation of force, such as in breathing and exhaling for respiratory purposes. In recent times, biomechanical research has been focused on understanding this phenomenon at more basic organism and organ levels. New experimental techniques have made it possible to evaluate the effects of physical interactions in physiology, development, and disease, via advancements in surface and cell culture sciences. The sustenance, detection, and generation of physical forces at unicellular levels is an important step which is necessary for understanding mechanical sensitivity, and organ and tissue-level physiology. Comment by Rashid, Bazlur [2]: be more specific

1.4 Cellular Mechanical Properties

The mechanical properties of a material are the traits which dictate a material’s response to mechanical stimuli. Essentially, the cellular mechanical properties define a cell’s deformation reaction to applied stress, and the manner in which this deformation changes over time. The unit of measurement for a solid material’s strain and stress is known as Young’s modulus. This is a basic property of solids since it relates their ability to resist stress by retaining their shapes under mechanical pressure. Unlike elastic solids, fluids flow do not store elastic energy, and instead flow when they are exposed to mechanical stress. The viscosity of a fluid is the measure of its rate of flow under a specific stress load. Still, many materials are viscoelastic; they exhibit both elasticity and viscosity when exposed to mechanical stress. Such materials concurrently undergo deformation while storing and dissipating mechanical energy. Over time, mechanical stress in viscoelastic materials relaxes while deformation continues increasing over time.

One of the biggest challenges in cell mechanics lies in explaining the origins of the structures of measured mechanical properties in cells. It is generally understood that cells are complicated and heterogeneous structures which contain a variety of proteins, sub-cellular structures, filaments and organelles, all of which have different physical properties and thus contribute variedly towards the viscosity and elasticity of the cell. The nucleus in particular is much stiffer than the other cytoplasmic constituents of the cell. In cell compression procedures, the cortex and cell membrane have always been observed to undergo deformation within the first 200 nm of force. Increasing the force applied in the cell causes a larger contribution from the nucleus, which implies that there is no simple, linear relationship between the stress applied and the strain on the cell. Still, mechanical models can be used to compare the characteristics of cell mechanics under pharmacological and genetic perturbations, which can reveal a lot of interesting information about the interpretations of cell mechanics.

1.5 The Context of Cell Mechanics

Cells have interiors which are fluid and packed with organelles, structures and macromolecules which have specific functions. The cytoskeleton, a network of sub-cellular filaments, makes up higher order meshes which enable cells to invariably sustain mechanical stress. With regards to cell mechanics, there are three particular cellular cytoskeletal filaments which draw interest: the actin microfilaments, microtubules, and intermediate filaments. Actin forms polarized filaments which in turn interact with a variety of ancillary proteins. Actin is also among the most abundant eukaryotic proteins. The mechanical properties of actin include semi-flexibility, persistence of length, and dynamicity. Actin filaments can quickly reorganize themselves and migrate in order to change their shapes. Individually, actin filaments may not necessarily have a lot of influence on the mechanics of a cell. However, by forming complex structures and interacting with polymerizing and crosslinking factors, actin filaments contribute a great deal towards the overall mechanical properties of a cell.

Figure 1: Actin Filaments

Cells are active materials which exhibit essential pre-stress characteristics that are formed by myosin motors. When myosin proteins crosslink and process along filaments, they create stress between the neighboring filaments which are not aligned in parallel. The best illustration of pre-stress is in contractile actin formations, which includes structures like intercellular junctions and stress fibers. The transaction of chemical signals between cells spans a wide range of scales, from inter-organ hormonal traverses to pancrineparacrine signals transfer among groups of cells, and even intracellular signals cascading. Research conducted in recent times in the field of cell mechanics has indicated that cells have ways of sensing mechanical impetuses within their immediate environment.

The vitality of sustaining, sensing and generating cellular mechanical forces is evident in the analysis of cytoskeletal diseases. Some genetic disorders have been known to interrupt cellular actin cytoskeletal formations and actin-erythrocyte binding. This causes red blood cells to develop abnormal shapes and compromises their function, as is evident in cases of sickle-cell anemia and malaria. Establishing links between cellular mechanosensitivity and other factors such as underlying molecular mechanisms in cells is one of the most exciting prospects for future cell mechanics. Comment by Rashid, Bazlur [3]: Can you clarify?

1.6 Cellular structure

Cells are basic units orfundamental building blocks of all living organismslife. Eukaryotes such as humans contains trillions of cells in their body while prokaryotes such as bacteria contain fewerare single cells cell creatures compared to eukaryotesic, lack the nuclear membrane and do not possess membrane –bound organelles such as mitochondrion. The cell is made up of many parts with distinct functions; these organelles are highly specialized structures that can perform specific tasks in vivo (within the cell).

The fundamental organelles in the eukaryotic cell include: mitochondrion that is the powerhouse of metabolism, generating energy by process of respiration in the form of Adenosine Triphosphate (ATP) . It has its own stranded DNA hence able to self-replicate itself and multiply to replace the worn out cells during process of respiration . The mitochondrion is sac-like in its structure. The cell membrane is an organelle with the ability to select permeable substances into the cell hence able to transport desired material into the cell. In prokaryotic cells, the cell membrane is made up of glycolipid and glycoprotein thus providing mechanical resistance to the cell by being the base of attachment for cytoskeleton in some organisms. The proteins in cell membrane provide chemical climate required by the cell while the lipids can offer flexibility. Cell membrane is a lipid bBilayer in its composition. Cytoplasm is made up of all the contents outside the nucleus and enclosed by the cell membrane. These contents it includes the cytosol and in eukaryotic cells; mitochondria and ribosome are contained; cytoskeleton fibers are also in the cytoplasm. The cytoplasm is gel-like and is clear in color, and the main constituents are enzymes, water, organelles and organic salts. The role of cytoplasm is to move materials along the cell and dissolve the cellular materials within the cell. The endoplasmic reticulum is found near the nucleus and has flat sacs called Cisternae continuous with nuclear envelope. The rough endoplasmic reticulum has a lot of ribosome on its surface. However, smooth endoplasmic reticulum lacks ribosome. Rough endoplasmic reticulum transports proteins synthesized by the ribosome while smooth synthesizes lipids. (Cabello, 1988). Comment by Rashid, Bazlur: Reference for what?

The An eukaryotic cell is also made up of other organelles with sacs. Golgi apparatus contains flattened sacs with a protein and handles modifying the proteins received from the endoplasmic reticulum. The vesicle then transports these proteins to the desired region of the body. Lysosome has a spherical sac containing the enzymes necessary for breaking down cellular materials in the cell such as microorganisms that are engulfed by the cell. The nucleus of the cell carries genetic information, it contains DNA and RNA, which are important in transcription and translation during genetic decoding. DNA sequence is transcribed into the messenger RNA controlling the manufacture of proteins by the ribosome during growth and reproduction. The nucleus control every cellular activity of the cell since it handles sending a blueprint of proteins required to be synthesized by the ribosome. The nucleus contains nucleolus responsible for synthesizing DNA and ribosome and controls all activities of the cell. Comment by Rashid, Bazlur: Not correct. Please write functions for nucleus and nucleolus separately.

1.7 Bacterial Cell Structure

Bacteria are the large microscopic group of organisms found in Kingdom Monera and are prokaryotic, unicellular living freely or as parasites. They are single celled lacking nucleus reproducing by spore formation or fission. They can live in other organisms and normally cause diseases (harmful) but there are other bacteria beneficial to humans, these include bacteria located in the stomach and those aiding in digestion. Comment by Rashid, Bazlur: Fragment

1.8 Shape1.8 Shape of Bacteria

There are many kinds of bacteria classified according to the physical characteristics. They can also be classified according benefits to humans or those causing diseases. Bacteria are also be differentiated by morphology, nutritional requirements or the chemical composition of cells. Biochemical pathways and the source of energy also classify bacteria. There are three basic shapes of bacteria; coccus (spherical), bacillus (rod-shaped) and spiral (twisted).However, there exist a pleomorphic bacterium that assumes no definite shape. Most bacteria are about 0.2 µum in diameter and about 2-8 µum in length. The arrangement of cocci is oval, elongated of flattened on one of its side. However, they remain attached after cell division. Diplococci remain in pairs after dividing, streptococci remain in chains after division, tetrads are cocci that divide in two planes and remain in groupin-group. Sarcinae are divided into three planes and form cubes with eight groups and staphylococci that divide into multiple planes and form grape-like structures.

Bacilli are bacteria, which ivied across their axis and most appear as single rods. Diplobacilli appears in pairs after division, streptobacillus appear in chains after dividing while coccobacilli are short and flat hence look like cocci. Spiral bacteria are twisted in nature Vibrio as spiral has curved rods while spirillums have a rigid body that is helical in shape. Spirochetes have helical and flexible bodies; they move by using axial filaments. Bacteria also has other shapes including star-shaped Stella with about 0.5 µum in diameter, rectangular shaped Holoarcula with a diameter of about 0.5 µum and is from genus archaea.

1.9 Gram Classification

There are different types of bacteria grouped according to how useful or harmful to man. They are classified into gram-positive and gram-negative bacteria depending on their differences in their cell wall structure and staining. When crystal violet dye is used and is stained then the type of bacteria is gram-positive bacteria. However, gram-negative bacteria do not stain crystal violet but pink or red color appears. Comparing the resistance to antibiotics of both bacteria, gram-positive gram-negative have impenetrable cell wall hence are more resistance to antibiotics.

Gram-negative bacteria have thin or single layered peptidoglycan while gram-positive bacteria have thick or multilayered peptidoglycan. Teichoic acids are also absent in gram-negative bacteria but are present in most of gram-positive bacteria. Teichoic acid are polysaccharides of glycerol phosphates or ribitol phosphates found in bacteria and are linked by phosphodiester bonds.

Gram-negative bacteria have high lipid and lipoprotein content due to the high presence of the outer membrane; gram-positive bacteria have virtually no lipid and lipoprotein. Gram-negative bacteria have four rings in the basal body on the flagella while gram-positive bacteria have two rings of the basal body in the flagella. Gram-negative bacteria are endotoxins while the gram positive are exotoxins, toxigenesis is the process by which pathogenic bacteria produce toxins. Endotoxin is a polysaccharide found in gram-negative bacteria such as Escherichia coli; however, exotoxin is soluble proteins that act as an enzyme and catalyze biochemical reactions. The cell wall of gram-negative bacteria has 70-120 Angstromong thick two layers, the lipid content is very high at about 30% while murein content is very low at less than 10 percentage. In gram-positive bacteria, it has a single layer of 100-120 Armstrong Angstrom with very low lipid content and very high murein content at about 90%. There economic uses of bacteria depending on their benefits and harm it causes to man. Lactobacilli are Gram-positive bacteria located mostly in the human intestine, vagina and the mouth. It secretes lactic acid hence prevents overgrowth of harmful bacteria. These bacteria are also found in the fermented milk products such as yogurt and are taken to maintain the amount of the probiotics in the human body. Bifidobacteria are branched rod shape gram-positive bacteria that are important in humans since they maintain the concentration of probiotics in the human body. It also prevents yeast infection and diarrhea ; probiotics are the organism that improve health conditions when consumed. Escherichia coli is a gram negative bacteria which is rod-shaped; it is important because it breaks down undigested sugars in the intestine thus aid in the digestion. They also provide vitamin k and biotin that are crucial in cellular activities in the body. Streptomyces and cyanobacteria are other helpful bacteria found in the environment; they prevent the proliferation of harmful bacteria. There are also some of the harmful bacteria, which cause disease or adversely affect the health. Mycobacteria are rod-shaped and are neither gram-negative nor gram positive, they cause infection of primary organs of the body such as skin and lungs. Leprosy and tuberculosis are common diseases caused by mycobacteria. Other bacteria that cause harm are Clostridium tetani a Gram-positive bacteria that infect the gastrointestinal and skin ; as a result cause tetanus that can result in death. Yersinia pesitis is gram-positive bacteria infecting skin and lungs leading to bubonic and pneumonic plague. The terrorists can use these bacteria as a dangerous biological weapon. Helicobacter pylori is a common bacteria associated with ulcers of the gastric and peptic glands. Bacillus anthracis are gram-positive rods occurring in animals, such as goats, cattle and sheep and can cause abnormal problems such as diarrhea.

Bacteria are organisms that are found everywhere and therefore, there is a need for humans to develop methods of getting rid of the bacterial infections. Depending on the type of bacteria, different methods are available. The standard method is boiling water prior to drinking or any other commercial use, and heat can minimize the bacterial infections. Prescription drugs are used in the synthetizing of antibiotics such as methicillin and penicillin has effects on different species of bacteria. Doctors and pharmacists study the interaction of drugs to different strains of microbes. The potential side effects of these medicinal products in the body is also analyzed. Chlorination is also efficient method of eliminating bacteria in water; it is the most used method in public places but debate by scientists on the efficiency of the method is still on because of the safety concerns.

Chapter 2: Quantum Biology

2.1 Introduction

By the early twentieth century, it had already been established that electrons are the factors that are responsible for chemical bonding. Ernest Rutherford described atoms as miniature systems with electrons orbiting a central nucleus, much like the sun in the solar system. Niels Bohr suggested that electrons have specific energies which govern their activities, and that due to this limitation, electrons are only able to jump from an orbit to another by either expending or absorbing energy. This is referred to as a quantum jump, and it involves the absorption or splitting of a photon of light which has a specific wavelength associated with its energy.

Figure 2: The Rutherford Atom

In nature and science, quantum mechanics has an alternative interpretation. Many effects and occurrences that cannot be explained using intuition are often ascribed to quantum mechanics. Quantum biology considers the prospects of such unusual occurrences happening in biological systems, and that such occurrences may actually be fundamentally important to the functioning of some biological systems. Whereas it is relatively easy to reconcile and examine the effects of quantum mechanics in physics, replicating the same procedures for biological systems is an extremely difficult feat which requires specialized expertise and machinery. The field of quantum biology is still in its infancy, although more research is being directed towards the field presently than ever before.

Figure 3: The Bohr’s Atom and an Illustration of Quantum Jumps

Quantum Biology can help explain processes by which the growth of bacteria in deep sites can be inhibited. For bacterial infections, tunneling and barrier potential are the two fundamental aspects that can help in the understanding of the time required to completely treat bacterial infection-related ailments. Tunneling works particularly effectively in situations whereby bacterial infections are hidden deep within a broth. Using tunneling approaches, researchers can successfully develop means of accessing bacterial locations that are heavily layered in various locations within the body. Bacterial growth is most commonly inhibited through the use of antibiotics. Antibiotics form virtual barriers which prevents bacteria from utilizing the broth that it needs to multiply. As such, ensuring that antibiotics are able to penetrate the broth is essential to their operations.

Despite the fact that there is limited evidence-based research in the field, it is imprudent to disregard the findings that have been established by the little research in quantum biology with respect to health sciences. Quantum biology is understood to have immense potential for application in various contexts. This is primarily why research in this field has often taken exceedingly long periods of time in order to first establish whether the results are legitimately verifiable. The results of such research will be the basis of future measures aimed at improving antibiotics performance. The barrier potential is a principle which provides insight into the factors that impede the optimal functioning of antibiotics. The principle of tunneling is generally understood to be based in the assumption that particles set in resonance with barriers. The particles will hence penetrate the barriers in order to ensure that the antibiotics are also able to pass through the protective membranes in order to reach the bacteria within.

2.2 The Significance of Quantum Biology

Researchers use models based on quantum biological principles to better understand the means by which bacteria develops resistance to antibiotics. This is one of the major problems in drug administration in the world today, since drug resistance would pose a dire threat to many people all over the world who rely on antibiotic treatment to treat their bacteria-related ailments. This also justifies the immensity and frenzy of efforts that are being directed towards understanding the process of combating bacteria as they develop more and more resistance to conventional antibiotic medication.

The general quantum biology equation is defined as:The general quantum biology equation is defined as: E0 = E + e.B E0 E + e.B

From the formula, the initial broth which contains the bacteria and the enzyme (E0), will yield a new bacterial count (E) and a new enzyme (e.B). In this setup, the addition of an antibiotic into an environment that contains bacteria is aided by the use of a virtual membrane in areas of the body which exhibit bacterial activity. A chemical is thus introduced to ensure that the bacteria does not multiply and continue affecting the environment in which it resides.

Tunneling refers to the ability of electrons to get transferred by enzymes, regardless of the preexisting energy barriers, hence moving in a way that is reminiscent of a tunnel. Research in this area utilizes knowledge of cell activities which feature the movement of electrons that is enhanced using natural light, especially in the case of photosynthesis. In human-related health control and research into the inhibition of microbial activity, researchers use laser light, which raises a lot of skeptic concerns.

Enzymatic activity is understood to be largely influenced by the phenomenon of quantum tunneling. In photosynthesis and cellular respiration, long distance electron transfers traversing various redox centers is dictated by quantum tunneling. Long range electron tunneling plays a major role in cellular respiratory enzymatic redox reactions. Despite the fact that there are relatively large distance separations between redox sites that exist within enzymes, there is a consistent, efficient, temperature independent, and distance dependent traversing of electrons that occurs. This implies that electrons are capable of tunneling in physiological environments. However, there is little research that conclusively illustrates that this manner of tunneling follows a coherent procedure.

The bacteria-related diseases that are extremely difficult to treat are known as the multivariate bacterial ailments because the resistance that the bacteria involved develop towards antibiotics leads the body to become more susceptible to unique infections. Tunneling is used in the treatment of such bacterial ailments to ensure that the antibiotics do not access other strains of bacteria. The means of operation for antibiotics is selective. In essence, the antibiotics eliminate the bacterial strains

Figure 4: Quantum Tunneling

The bacteria-related diseases that are extremely difficult to treat are known as the multivariate bacterial ailments because the resistance that the bacteria involved develop towards antibiotics leads the body to become more susceptible to unique infections. Tunneling is used in the treatment of such bacterial ailments to ensure that the antibiotics do not access other strains of bacteria. The means of operation for antibiotics is selective. In essence, the antibiotics eliminate the bacterial strains that are responsive to medicine, but leave behind the unresponsive, resistant strains. Some strains of Salmonella typhi have been reported to be responsible for thirty-five percent of antibiotic drug resistance in the U.K. This does not necessarily imply that the medication that is used for such cases is poor, rather, that there are some modifications that are necessary in order for the starting points of the bacteria to be eliminated in the future.

While addressing quantum biology, it is necessary to understand the concepts which can demonstrate the progression of resistance, and the development of antibiotics which can successfully traverse the barriers. Various strains of bacteria undergo a diversity of mutations which ultimately result in their resistance to antibiotics. As more antibiotics invade the ecology of the bacteria, it actually makes it more favorable for the bacteria to survive since it enhances the adaptability of the bacteria. Initial efforts aimed at evaluating the potential applications of the principles of tunneling and barrier potential were directed towards existing radiological methods. The efforts successfully illustrated that the fission of radioactive elements and radioactivity successfully bore through the barriers, regardless of their thickness. Likewise, adapting the same principles for quantum biological applications can aid the development of treatments which can overcome potential barriers and access layered bacteria.

2.3 The Density Matrix

The density matrix is a matrix that serves to describe quantum systems in mixed states. In contrast, a single state vector serves to describe quantum systems in their pure states. A mixed state occurs when the particular state that is under manipulation in an experiment is not fully understood. This may include situations such as those whereby the experiment involves a quantum system with two or more entangled subsystems. In such a case, each subsystem must be treated as a mixed state regardless of the pureness of the complete system.

Many biological systems are capable of remaining in quantum coherent states at room temperature for extended periods of time. By maintaining the optimal balance between chaos and regularity, systems can successfully increase their time spent in coherent states by orders of magnitude.

2.4 The Hartree-Fock Computational Model

Hartree-Fock is among the most important and efficient quantum biological techniques since it recovers nearly 99% of the aggregate electronic energy. The method has seen more widespread application in physics and chemistry compared to biological adaptations. Still, the Hartree-Fock model is understood to be quite unreliable and offers a weak approximation in many cases. However, the model has been refined and customized into more sophisticated post-Hartree-Fock models which are more accurate in their depiction of the Hartree-Fock wave function. In addition, the Hartree-Fock computational model offers mathematical structures upon which molecular orbits can be studied and interpreted in detail.

The basis of the Hartree-Fock computational model is the evaluation and manipulation of O(M4) integrals with two electrons. The algorithm then scales in the interval between O(M2) and O(M3) for all instances in which the computation dominates the runtime. However, given that the Hartree-Fock method is based on the solution of nonlinear Eigenvalue sequences of equations via iteration, there are some key hindrances which prevent worst-case scaling from forming polynomials. The main hindrance is the convergence of implementations which are self-consistent. As a result of the complexity of the results, the worst-case scaling can only be a polynomial when P=NP. P=NP.

Figure 5: Algorithmic Illustration of the Hartree-Fock Method

2.5 Interpretations of Quantum Biology

Quantum biology can be interpreted using sets of statements which are aimed at describing the influences of quantum mechanics on human understanding of nature. Still, even though quantum mechanics theories have largely held up to rigorous testing and experimentation, there are various interpretations that can be deduced from quantum mechanical phenomena. Among the sources of contention and divisive interpretations of quantum mechanics is the lack of clarity over which facets of quantum mechanics can be interpreted as deterministic, and which ones can be considered real. This likewise affects the applications of quantum mechanics in biology, since this is a field which is heavily dependent on the influence of non-trivial quantum phenomena.

Quantum biology is a very intriguing subject because it presents the answers to some of the most fundamental concerns and questions regarding basic operations in nature. At a more specific and practical level, quantum biology presents immense opportunities for resolution of impending problems related to human health, and the development of new solutions to issues which have bugged mankind for a very long time. In antibiotics, for instance, the development of medication that is able to combat resistant strains of bacteria depends greatly on the prospects of quantum biology theory to come up with ways of handling such issues. Currently, mankind is facing a serious problem in the near future which may result from the development of super resistant strains of Salmonella typhi and other bacteria. Quantum biology presents people with opportunities to better understand the fundamental functioning of cell-level structures, which in turn informs the best procedures to utilize for the solution of problems such as hard antibiotic resistance. In the case of antibiotic resistance, the solution is through tunneling. With the wide array of applications of quantum biology currently in various stages of research, one can only ponder what the future holds for humanity as a result of such research.

2.3 Tunneling in Quantum Biology

The application of theoretical chemistry and quantum mechanics to biological problems and objects is referred to as the quantum biology. The biological process involves various transformations that are chemical in nature and apply the nature of quantum mechanics (Lambert, Chen, Cheng, Li, Chen & Nori, 2013). Tunneling in quantum biology is defined as the ability of the mass particles that are small in nature to travel and pass through various energy barriers. It is therefore the metaphorical name given to the process, possible in quantum mechanics, but not in classical mechanics, whereby a particle can disappear from one side of a potential-energy barrier and appear on the other side without having enough kinetic energy to overcome the obstacle. Quantum tunneling in biology is an important factor that plays major role in processes that involve enzymatic reactions such as photosynthesis and cellular respiration example is the redox reaction.

The following is a demonstration of a Quantum tunneling through a barrier. The energy of the tunneled particle is the same but the probability amplitude is decreased.

2.4 Proton Tunneling in DNA

Proton tunneling is an example of quantum tunneling that involves disappearance of a proton instantaneously and its appearance in an adjacent site that is separated by a potential barrier.it is a fundamental factor in spontaneous mutation of DNA which occurs when a normal DNA replicates after an important proton has taken advantage of quantum tunneling. Hydrogen bond is associated with proton tunneling. The DNA strand is made up of hydrogen bond and it’s subject to proton tunneling (Ball, 2011). The arrangement of the hydrogen bond is unique in a DNA strand and it defines the genetic code. Basically there exists a double well potential along hydrogen bond separated by a potential barrier. The potential well is usually asymmetric and one of the well is deeper than the other. The proton usually lies on the deeper well. During the replication of a DNA strand, proton tunneling takes place that is responsible for the changes and the configuration of the hydrogen bond. At times the tunneling will depend on height and form of barrier in DNA, the form of the double-well potentials regulating the hydrogen bonds depends on both base and neighboring pairs involved, their net charges and the entire electric environment. Proton tunneling is of great importance since it controls the occurrences of tumors. The growth of a person is a highly refined balance between the factors that enhance the cell duplication and that limits the duplication so that an organism takes a desired shape.

In a quantum mechanical system the proton can be represented by a wave packet which allow the proton to penetrate into hindered areas in the classical system. This enables the proton to move from one equilibrium state to another by means of tunneling through the potential barrier. The figure below shows quantum tunneling effect allows a quantized wave packet to penetrate the barrier and move from one potential well to another.

 2.5 Electron Transfer

Electron transfer is defined as the relocation of electrons from a molecule or an atom to another chemical entity.it involves the movement of an electron transfer from one molecular species known as donor to another known as the acceptor. It is an important and essential step in biological photosynthesis where the electron transfer initiates downstream process such as the proton pumping through the membrane and the production of glucose. The chemical reactions such as the oxidation or redox involve the movement of electrons from one atom to another (Karreman, 1962). Various numerous processes that are biological in nature involve the electron transfer reactions. They include respiration, oxygen binding and detoxification. Electron transfer in quantum biology can be considered and viewed in terms of quantum mechanical and semi-classical models (shown in the figure below). In biological systems we base on a specific example of plant cryptohrome, where electrons are essential for functioning. In this case proteins and electrostatics play a significant role in the transfer of electrons. The polarization forces also are crucial in propelling the electrons through the cryptochrome. Consequently, the quantum mechanical of electron transfer is applicable in variety of biological systems including, DNA photolyase.

The two state model of electron transfer

43. Antibiotics interaction with bacteria

34.1 Antibiotics

Antibiotics are antimicrobial type of drug used in the treatment and prevention of bacterial infections. Antibiotics kill or stop bacterial growth; however they are not effective against viruses such as influenza or common cold. Antibiotics use has nearly led to the eradication of deadly diseases like tuberculosis. At times, the term antibiotic is mostly used to refer to any substance used against microbes. The revolutionary of antibiotic medicine occurred in the 20th century. Conversely, their easy access and effectiveness have led to their overuse stimulating bacteria to gain resistance (Bobone, 2014). Alexander Fleming, a Scottish researcher and botanist began the modern antibiotics use and his penicillin discovery in 1928.

Antibiotics can be classified based on the system they affect or cellular component. Antibiotics successfully work by bacterial microorganisms’ elimination, referred to as bactericidal or by hindering bacterial microorganisms’ development known as bacteriostatic. Since the penicillin discovery, other and more effective antimicrobials have been developed and discovered by elucidation by drug molecule modification and by drug target interactions. The increasing drug resistant bacteria prevalence, resistance gaining means, has significantly made it clear of the multilayered mechanisms through which available antibiotics eliminate bacteria and also find alternative therapies of antibacterial. Antibiotic induced cell death has been linked with formation of breaks of double-stranded DNA following DNA inhibitor treatment. Most current bacterial antimicrobials inhibit RNA synthesis, DNA synthesis, protein synthesis, metabolic pathway, cell membrane disorganizing and cell wall synthesis (Berlatsky & Thomson, 2011).

34.2 Method of action

The method of action or mechanism of action for antimicrobial drugs is the means by which they kill or inhibit bacterial colonies. There should be three conditions for an anti-microbial to powerfully be against microscopic organisms. These include; the antibiotic need to reach the objective in adequate amount, the anti-infection must not be altered/in activated and a vulnerable target of anti-microbial should exist in the cell. They fall generally into the following categories: inhibition of protein synthesis, inhibition of nucleic acid, inhibition of cell wall synthesis, inhibition of metabolic activity and alteration of cell membranes.

Cell wall synthesis interference; the bacterial cell is enclosed by murein or, peptidoglycan layers which is polymer matrix covalently cross linkedcross-linked. The mechanical strength managed by this layer of the cell wall is crucial to the ability of bacteria to survive conditions of the environment that may alter osmotic pressure prevailing. Glycopeptides and ß-lactams are among the antibiotic classes that interfere with specific steps in homeostatic biosynthesis of cell wall. Effective treatment with an inhibitor of cell wall synthesis can results in cell changes of size and shape, culminate in cell lysis and induce cellular stress response. In Staphylococcus aureus , an extra holing-like system was discovered in S. aureus and found to activate autolysins making S. aureus more prone to β-lactam facilitated killing.

Protein synthesis inhibition; cellular structures and enzymes are primarily made of primarily proteins. Protein synthesis is a critical process necessary for the survival and multiplication of all bacterial cells. The process of mRNA translation process into protein occurs over three phases of sequence that is initiation, elongation and termination involving the ribosome. Ribosome organelle contains two ribonucleoprotein subunits the 30S and 50S. Erythromycin, a 50S ribosome inhibitors, e.g. erythromycin works by physically blocking physically either initiating exit of growing protein translation or peptidyl tRNA translocation. The 30S ribosome inhibitor which include aminocyclitol and tetracycline families of antibioticsinhibitors that include aminocyclitol and tetracycline families of antibiotics work by blocking the access of aminoacyl-tRNAs to the ribosome. This activity then leads to disruption of normal bacterial cellular metabolism and subsequently leads to the inhibition of multiplication or death of the organism.

Interference with nucleic acid synthesis; RNA and DNA are keys to the replication of all living organisms with even inclusion of bacteria. Chromosomal modulation supercoiling through catalyzed strand breakage and reactions of rejoining is required for synthesis of DNA, cell division and mRNA transcription. Exploitation of the reactions is done by the synthetic quinolone, a class of antimicrobials. The inhibition of synthesis of RNA byyrifamycinrifamycin has a disastrous effect on prokaryotic metabolism of nucleic acid and it’sit is an effective way of inducing death of bacterial cells. The antimicrobial class of quinolone interferes with the chromosomal topology maintenance targeting DNA topoisomerase and gyrase preventing strand rejoining. Comment by Rashid, Bazlur: Rewrite, not clear.

Inhibition of a metabolic pathway; some antibiotics act on selected processes of cells essentially for the bacterial pathogens survival. An example is a case whereby trimethoprim and sulfonamides disrupt the pathway of folate whichfolate that is important step for production of precursors by bacteria for DNA synthesis. Sulfonamides bind to dihydropteroate synthase while trimethoprim inhibits enzyme dihydrofolate reductase.

Cell membrane disorganizing; cell membranes are significant barriers that regulate and separate the extracellular and intracellular flow of substances. Damage or leakage to this structure may result in important solutes crucial for survival of cells leaking. Polymyxins apply inhibitory impacts by expanding the penetration power of bacterial layer hence causing bacterial substance spillage. Most of the clinical use is limited to topical applications. Also, daptomycin indicates fast action of bacteria to the cytoplasmic film thus encouraging efflux of potassium from the cells of bacteria.

34.3 Erythromycin

In this investigation, the antibiotic utilized is erythromycin. Erythromycin was isolated from Saccharopolyspora erythraea. The drug has been listed by the World Health Organization as a crucial medicine and has been given title as one of the safest medicine. Erythromycin is relatively inexpensive range of antimicrobial indicating that it is effective for an extensive variety of disease causing microorganism. Erythromycin can be used to treat skin contaminations, tract infections, inflammation of pelvic, syphilis and contaminations by chlamydia (Dakhel & University of Alberta, 2005). Due to its slight adverse reactions, the drug is generally prescribed to the pregnant ladies and women who are nursing.

Figure 34.3.1: Erythromycin structure

Erythromycin method of activity is restraint of protein synthesis by binding to the 23S rRNA molecule of the bacterial ribosome therefore blocking the sensitive microorganism growing peptide chain exit. This produces bacteriostatic cell response which stops replication. Certain resistant microorganisms with changes in mutation in components of the subunit of the ribosome fail to fix the drug. The ribosome and erythromycin association is reversible and takes place only when the 50S subunit is free from tRNA molecules bearing emerging peptide chains. Erythromycin interferes with translocation of aminocyl, keeping the tRNA exchange bound at the A-site of the rRNA complex to the P-site of the complex rRNA.

A time that the translocation cannot take place due to the A-site as yet being used, at that event protein synthesis ends. Any approaching tRNA and its attached amino corrosive to the incipient polypeptide chain are restrained from moving further along the chain of mRNA .This prevents the creation of practical proteins used as a part of replication of cells (Bobone, 2014). Erythromycin is assimilated immediately through layers of tissue and equally diffuses between phagocytes. For this, the high phagocytes number show in circulatory system takes into account the irritable erythromycin dissemination to the diseased area. The larger erythromycin part is utilized by the liver using hepatic catalysts. Erythromycin contains mycrocyclic center, which is a ring made out of an extensive moderate molecule number. The rRNA chain assumes a critical part in the blend of protein. On the erythromycin account, of which ties to 50S site of ribosomes, the anti-toxin viability

Figure 34.3.2: Action method of erythromycin

blend of protein. On the erythromycin account, of which ties to 50S site of ribosomes, the anti-toxin viability is controlled by the anti-infection ties amount. Resistance of antibiotics on account of erythromycin sometimes originates from many alterations in the structure and conduct of cells. Anti-infection resistance can progress through the rRNA inactivation in the cell. The protein methylation would reduce the medication adequacy because of the other rRNA groupings being bound to the sites of 50S. This allows the cells of bacteria to deliver the basic protein needed for replication by passing the 50S viably. The drug would lose its effectiveness if a place to bind the drug is not available. The process of taking carbon and hydrogen to form methyl group is called methylation. This group is applied in cellular functions like turning on & off genes, getting rid of environmental toxins, repairing DNA and fighting infections. Comment by Rashid, Bazlur: Unclear, Rephrase. Comment by Rashid, Bazlur: Unclear. Comment by Rashid, Bazlur: Please clarify.

Macrolides are actinomycetes products (soil bacteria) or semi-synthetic derivatives of actinomycetes. Antifungal and antimicrobial properties of substances rise from macrocyclic ring structures. Some of the molecules exhibiting properties of antimicrobial include; azithromycin, erythromycin and clarithromycin. The role of macrolides is to specifically inhibit synthesis of protein. This occurs by preventing the tRNA from binding to the active sites on the rRNA. Erythromycin hinders the amino acids from changing into a functional complex of protein by preventing peptidyl-transferase from adding the growing peptide in the tRNA to the amino acid next. This in turn hinders translation of ribosomes along the sequence of rRNA. Comment by Rashid, Bazlur: Is this correct statement? Where are the references.

34.4 Magnetic Fields, Bacteria, and Antibiotics.

Magnetic fields are characterized by attraction impact delivered by magnetic materials or electrical currents. A wide variety of magnetic fields are vectors, this means they have both direction and magnitude with them. Magnetic field cooperation changes when separation occurs. Magnetic field strength has a 1/r2 dependence on its size indicating that the further one moves from the magnetic field source, the field drops away inverselywith the square of the distance. The distribution of magnetic fields is similar to that of electric fields. The bar magnet fields resembles scattered lines that on top of one other get stack. To find out the magnetic fields effect on the biological system behavioral field uniform is applied to the system. If, on the system a gradient of field is applied, then it would be difficult to find out if the observed effect is solely due to the fields’ gradient or magnetic field.

Figure 34.4:1: Magnetic field lines

Staphylococcus aureus is a major pathogen that produces super antigens and toxins causing skin and soft tissue infections in communities or hospitals. Antibiotic therapy is not greatly proficient because the intensive and routine usage has led to emergence of both community and hospital linked methicillin resistant staphylococcus aureus. A study conducted on the effect of paused intensity of magnetic field and th4e pulse number on bactericidal property of pulsed magnetic field in sterilization of fresh juice of watermelon. The results showed that the overall effect of the bactericidal was reinforced as the pulse number and magnetic field intensity was 21 and 2.52 respectively. Effects of electromagnetic field on bacteria study are important not only for environmental stress influences investigating on biological systems but also to discover the possibility of controlling the sensitivity of bacteria toward environmental antibiotics.

Magnetic field effect on growth and antibiotic susceptibility of bacteria Staphylococcus aureus was tested. This was aimed to examine the exposure effect of different magnetic fields that is; 400, 800, 1200 and 1600 Gauss for 2 to 24 hours on the rate of growth and antibiotic sensitivity of Staphylococcus aureus. The bacteria were isolated from the medical case and identified using a system known as API STAPH. The vulnerability of the antibiotic of staphylococcus aureus measured according to the technique of diffusion. The results exhibited an important logarithm reduction in the number of staphylococcus aureus treated with high frequency magnetic field. The sensitivity of staphylococcus aureus to antibiotic increase during a short period of 4 to 6 hours and increase its resistance to the same antibiotic at a long term exposure of 18-24 hours.

Also, sSome biochemical tests results also indicated positive effects of magnetic fields on the biochemical properties. The enzymes bacterial lactose, trehalose, sucrose, mannitol, acetyl-glucosamine and maltose were affected by magnretic field at 24 hours of incubation. From the research, it is concluded that the cellular membrane of the microorganism had been affected by the fields of magnet (Lister and Horswill, 2014). Furthermore, the response amplified when the intensity of the magnetic fields increased. According to this, the effects of magnetic field on bacteria are considered bactericidal and thus a change in the number of cells or the change measured in the sensitivity of membrane to antibiotic demonstrated the change in the structure of the cells internally.

Figure 34.4.2: Absorbance at 600 nm of S.aureus cells with different exposure periods.

It was found that magnetic fields increased the phase of logarithm of staphylococcus aureus growth within 4 hours of treatment but reduced growth curve after 8 hours period.

There was a change which was considerable in the rate of growth of S. aureus. A decrease in the colony forming units started instantly after the magnetic field effect on the bacteria could be deliberated as bactericidal. These results are concurring with

Figure 34.4.3: Growth rate of S. aureus for each group.

others who reported the exposure of salmonella typhi, E. coli and S. aureus to the magnetic field has the same effects (Kim et al, 2013).

on the bacteria could be deliberated as bactericidal. These results are concurring with others who reported the exposure of salmonella typhi, E. coli and S. aureus to the magnetic field has the same effects (Kim et al, 2013).

Antibiotic test of exposed and unexposed S.aureus to magnetic field. 

R: Resistance, M.F: magnetic field, S-R: Subunit-Ribosome.

The above table showed the antibiotics susceptibility test at various exposure periods 2,4,6,8 and 24 hours which estimated according to the action mode. The results indicated that S. aureus were sensitive for ceftazidiumceftazidime, gentamycin, rifampcin, chloramphenicol, ceftriaxone and tetracycline where else resistant to metronidazole (Kobayashi et al, 2015). The diameters of the stimulation or inhibition zone of the different forces of magnet were measured after 24 hours from the process of exposure compared with samples unexposed. These results concurred with a study which found that moderate intensity static fields were able to lead to a reduction in resistance of E. coli and sensitivity. In addition, found that the possibility of magnetic field interfering with the charge on the antibiotic molecule or surface charges of the membrane altering the antibiotic penetration rate may exist.

Also it was exhibited that magnetic field can affect functions of membrane however, the magnetic field could relate with other specific process that help the bacteria adapt to the new environment (Carrey et al, 2013). Due to this, the bacteria are able to retort to stresses of environment by initiating suitable inducible systems like DNA repair system and in turn destroy processes which increase the variability of genes.


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