Biological system

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Biological system can be understood at different level such as molecular, cellular, tissue and organs level and be divided into different categories such as prokaryotic , eukaryotic( fungi, plants, and animals ). The design principles depend on such level or categories.

We focus on bacterial system at a molecular level and try to extract its design principles. In bacteria, all reactions including cell division, metabolism and stress responses are performed in the creosol, different from eukaryotes that consist of many organelles.


The branch of chemistry which deals with the rates of chemical reactions and factors which influences the rates of reaction is called chemical kinetics. The study of the rates of reaction also helps us to understand the pathways from reactants to products called mechanism of the reaction.

Chemical kinetics is the branch of chemistry which addresses the question: "how fast do reactions go?" Chemistry can be thought of, at the simplest level, as the science that concerns itself with making new substances from other substances. Or, one could say, chemistry is taking molecules apart and putting the atoms and fragments back together to form new molecules. (OK, so once in a while one uses atoms or gets atoms, but that doesn't change the argument.) All of this is to say that chemical reactions are the core of chemistry.

If Chemistry is making new substances out of old substances (i.e., chemical reactions), then there are two basic questions that must be answered:

  1. Does the reaction want to go? This is the subject of chemical thermodynamics.
  2. If the reaction wants to go, how fast will it go? This is the subject of chemical kinetics.

Here are some examples. Consider the reaction,

H2(g) + O2(g) → 2 H2O(l).

We can calculate ΔrGo for this reaction from tables of free energies of formation (actually this one is just twice the free energy of formation of liquid water). We find that ΔrGo for this reaction is very large and negative, which means that the reaction wants to go very strongly. A more scientific way to say this would be to say that the equilibrium constant for this reaction is very very large.

However, we can mix hydrogen gas and oxygen gas together in a bulb or other container, even in their correct stoichiometric proportions, and they will stay there for centuries, perhaps even forever, without reacting. (If we drop in a catalyst - say a tiny piece of platinum - or introduce a spark, or even illuminate the mixture with sufficiently high frequency uv light, or compress and heat the mixture, the mixture will explode.) The problem is not that the reactants do not want to form the products, they do, but they cannot find a "pathway" to get from reactants to products.

Another example: consider the reaction,

C(diamond) → C(graphite).

If you calculate ΔrGo for this reaction from data in the tables of thermodynamic properties you will find once again that it is negative (not very large, but still negative). This result tells us that diamonds are thermodynamically unstable. Yet diamonds are highly regarded as gem stones ("diamonds are forever") and are considered by some financial advisors as a good long-term investment hedge against inflation. On the other hand, if you were to vaporize a diamond in a furnace, under an inert atmosphere, and then condense the vapor, the carbon would come back as graphite and not as diamond.

How can all these things be?

The answer is that thermodynamics is not the whole story in chemistry. Not only do we have to know whether a reaction is thermodynamically favored, we also have to know whether the reaction can or will proceed at a finite rate. The study of the rate of reactions is called chemical kinetics.

We can also explain the concept of kinetics as:

the branch of physical chemistry that is concerned with understanding the rates of chemical reactions. It is to be contrasted with thermodynamics, which deals with the direction in which a process occurs but in itself tells nothing about its rate. Thermodynamics is time's arrow, while chemical kinetics is time's clock. Chemical kinetics relates to many aspects of cosmology, geology, biology, engineering, and even psychology and thus has far-reaching implications. The principles of chemical kinetics apply to purely physical processes as well as to chemical reactions.

One reason for the importance of kinetics is that it provides evidence for the mechanisms of chemical processes. Besides being of intrinsic scientific interest, knowledge of reaction mechanisms is of practical use in deciding what is the most effective way of causing a reaction to occur. Many commercial processes can take place by alternative reaction paths, and knowledge of the mechanisms makes it possible to choose reaction conditions that favour one path over others.

A chemical reaction is, by definition, one in which chemical substances are transformed into other substances, which means that chemical bonds are broken and formed so that there are changes in the relative positions of atoms in molecules. At the same time, there are shifts in the arrangements of the electrons that form the chemical bonds. A description of a reaction mechanism must therefore deal with the movements and speeds of atoms and electrons. The detailed mechanism by which a chemical process occurs is referred to as the reaction path, or pathway.

The vast amount of work done in chemical kinetics has led to the conclusion that some chemical reactions go in a single step; these are known as elementary reactions. Other reactions go in more than one step and are said to be stepwise, composite, or complex. Measurements of the rates of chemical reactions over a range of conditions can show whether a reaction proceeds by one or more steps. If a reaction is stepwise, kinetic measurements provide evidence for the mechanism of the individual elementary steps. Information about reaction mechanisms is also provided by certain nonkinetic studies, but little can be known about a mechanism until its kinetics has been investigated. Even then, some doubt must always remain about a reaction mechanism. An investigation, kinetic or otherwise, can disprove a mechanism but can never establish it with absolute certainty[4].


The main scientific interest of the "Kinetics in Biological Systems" group is to understand the effects that the physical characteristics of the biochemical systems have on the kinetics of simple reactions.

The physical constraints focused so far are the small number of reactants available per reaction compartment (Stochastic Effects), due to the compartmentalization of the system, and the bi-dimensionality of the biological membranes.

The objects of study are simple model systems where the physical properties in study are well known, like micelles for the study of compartmentalization or lipid bilayer membranes as bi-dimensional systems.

The methods used are mainly spectroscopic (steady state and time resolved fluorescence and fluorescence recovery after photo bleaching) and computational. Recently, the group has started a new but complimentary line of research, the development of nano-particles for use as sensors and/or actuators inside cells. The main objective of this project is to measure not only the concentration of metabolites but also their distribution. At the moment the nano-particles being used have a polyacrylamide matrix and are about 40 nm. We are currently at a stage of development of the nano particles.

Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multi-scale and stochastic nature of the biological processes.

This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multi-scale problems and the possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided[6].




In general, enzymes are proteins produced by living cells; they act as catalysts in biochemical reactions. A catalyst affects the rate of a chemical reaction. One consequence of enzyme activity is that cells can carry out complex chemical activities at relatively low temperatures.

In an enzyme-catalyzed reaction, the substance to be acted upon (the substrate = S) binds reversibly to the active site of the enzyme (E). One result of this temporary union is a reduction in the energy required to activate the reaction of the substrate molecule so that the products (P) of the reaction are formed.

Note that the enzyme is not changed in the reaction and can be recycled to break down additional substrate molecules. Each enzyme is specific for a particular reaction because its amino acid sequence is unique and causes it to have a unique three-dimensional structure. The active site is the portion of the enzyme that interacts with the substrate, so that any substance that blocks or changes the shape of the active site affects the activity of the enzyme. A description of several ways enzyme action may be affected follows.

1. Salt concentration.

If the salt concentration is close to zero, the charged amino acid side chains of the enzyme molecules will attract each other. The enzyme will denature and form an inactive precipitate. If, on the other hand, the salt concentration is very high, normal interaction of charged groups will be blocked, new interactions will occur, and again the enzyme will precipitate. An intermediate salt concentration such as that of human blood (0.9%) or cytoplasm is the optimum for many enzymes.


His a logarithmic scale that measures the acidity or H+ concentration in a solution. The scale runs from 0 to 14 with 0 being highest in acidity and 14 lowest. When the pH is in the range of 0-7, a solution is said to be acidic; if the pH is around 7, the solution is neutral; and if the pH is in the range of 7-14, the solution is basic. Amino acid side chains contain groups such as -COOR and -NH2 that readily gain or lose H+ ions. As the pH is lowered an enzyme will tend to gain H+ ions, and eventually enough side chains will be affected so that the enzyme's shape is disrupted. Likewise, as the pH is raised, the enzyme will lose H+ ions and eventually lose its active shape. Many enzymes perform optimumly in the neutral pH range and are denatured at either an extremely high or low pH. Some enzymes, such as pepsin, which acts in the human stomach where the pH is very low, have a low pH optimum.

3. Temperature.

Generally, chemical reactions speed up as the temperature is raised. As the temperature increases, more of the reacting molecules have enough kinetic energy to undergo the reaction. Since enzymes are catalysts for chemical reactions, enzyme reactions also tend to go faster with increasing temperature. However, if the temperature of an enzyme-catalyzed reaction is raised still further, a temperature optimum is reached; above this value the kinetic energy of the enzyme and water molecules is so great that the conformation of the enzyme molecules is disrupted. The positive effect of speeding up the reaction is now more than offset by the negative effect of changing the conformation of more and more enzyme molecules. Many proteins are denatured by temperatures around 40-500C, but some are still active at 70-800C, and a few even withstand boiling.

4.Activations and Inhibitors.

Many molecules other than the substrate may interact with an enzyme. If such a molecule increases the rate of the reaction it is an activator, and if it decreases the reaction rate it is an inhibitor. These molecules can regulate how fast the enzyme acts. Any substance that tends to unfold the enzyme, such as an organic solvent or detergent, will act as an inhibitor. Some inhibitors act by reducing the -S-S- bridges that stabilize the enzyme's structure. Many inhibitors act by reacting with side chains in or near the active site to change its shape or block it. Many well-known poisons such as potassium cyanide and curare are enzyme inhibitors that interfere with the active site of critical enzymes.

The enzyme used in this lab, catalase, has four polypeptide chains, each composed of more than 500amino acids. This enzyme is ubiquitous in aerobic organisms. One function of catalase within cells is to prevent the accumulation of toxic levels of hydrogen peroxide formed as a by-product of metabolic processes. Catalase might also take part in some of the many oxidation reactions that occur in all cells.

The primary reaction catalyzed by catalase is the decomposition of H2O2 to form water and oxygen.

In the absence of catalase, this reaction occurs spontaneously, but very slowly. Catalase speeds up the reaction considerably. In this experiment, a rate for this reaction will be determined.

Much can be learned about enzymes by studying the kinetics (particularly the changes in rate) of enzyme-catalyzed reactions. For example, it is possible to measure the amount of product formed, or the amount of substrate used, from the moment the reactants are brought together until the reaction has stopped.

If the amount of product formed is measured at regular intervals and this quantity is plotted on a graph, a curve like the one that follows is obtained.

Study the solid line on the graph of this reaction. At time 0 there is no product. After 30 seconds, 5 micromoles (µmoles) have been formed; after one minute, 10 µmoles; after two minutes, 20 µmoles. The rate of this reaction could be given as 10 µmoles of product formed per minute for this initial period. Note, however, that by the third and fourth minutes, only about 5 additional ttmoles of product have been formed. During the first three minutes, the rate is constant. From the third minute through the eighth minute, the rate is changing; it is slowing down. For each successive minute after the first three minutes, the amount of product formed in that interval is less than in the preceding minute. From the seventh minute onward, the reaction rate is very slow.

In the comparison of the kinetics of one reaction with another, a common reference point is needed. For example, suppose you wanted to compare the effectiveness of catalase obtained from potato with that of catalase obtained from liver. It is best to compare the reactions when the rates are constant. In the first few minutes of an enzymatic reaction such as this, the number of substrate molecules is usually so large compared with the number of enzyme molecules that changing the substrate concentration does not (for a short period at least) affect the number of successful collisions between substrate and enzyme. During this early period, the enzyme is acting on substrate molecules at a nearly constant rate. The slope of the graph line during this early period is called the initial rate of the reaction. The initial rate of any enzyme-catalyzed reaction is determined by the characteristics of the enzyme molecule. It is always the same for any enzyme and its substrate at a given temperature and pH. This also assumes that the substrate is present in excess.

The rate of the reaction is the slope of the linear portion of the curve. To determine a rate, pick any two points on the straight-line portion of the curve. Divide the difference in the amount of product formed between these two points by the difference in time between them. The result will be the rate of the reaction which, if properly calculated, can be expressed as µmoles product/sec. The rate then is:

The rate of a chemical reaction may be studied in a number of ways, including the following:

  1. measuring the rate of disappearance of substrate (in this example, H2O2);
  2. Measuring the rate of appearance of product (in this case, O~, which is given off as a gas); and
  3. Measuring the heat released (or absorbed) during the reaction.

General Procedure :

In this experiment the disappearance of the substrate, H2O2, is measured as follows:

  1. A purified catalase extract is mixed with substrate (H2O2) in a beaker. The enzyme catalyzes the conversion of H2O2 to H2O and O2 (gas).
  2. Before all of the H2O2 is converted to H2O and 02, the reaction is stopped by adding sulfuric acid (H2SO4). The H2SO4 lowers the pH, denatures the enzyme, and thereby stops the enzyme's catalytic activity.
  3. After the reaction is stopped, the amount of substrate (H2O2) remaining in the beaker is measured. To assay (measure) this quantity, potassium permanganate is used. Potassium permanganate (KMnO4), in the presence of H2O2 and H2SO4 reacts as follows:

5H2O2+2KMnO4+3H2SO4 forms K2SO4+2MnSO4+8H2O+5O2

Note that H202 is a reactant for this reaction. Once all the H2O2 has reacted, any more KMnO4 added will be in excess and will not be decomposed. The addition of excess KMnO4 causes the solution to have a permanent pink or brown color. Therefore, the amount of H2O2 remaining is determined by adding KMnO4 until the whole mixture stays a faint pink or brown, permanently. Add no more KMnO4 after this point. The amount of KMnO4 added is a proportional measure of the amount of H2O2 remaining (2 molecules of KMnO4 reacts with 5 molecules of H2O2 as shown in the equation).

EXERCISE 2A: Test of Catalase Activity

  1. To observe the reaction to be studied, transfer 10 mL of 1.5% (0.44 M) H2O2 into a 50 mL beaker and add 1 mL freshly made catalase solution. The bubbles coming from the reaction mixture are O2, which results from the breakdown of H2O2 by catalase. Be sure to keep the freshly made catalase solution on ice at all times.
  2. The effect of boiling on enzyme activity was demonstrated in a previous lab (Biol 121).
  3. The presence of catalase in living tissue was demonstrated in a previous lab (Biol 121).

EXERCISE 2B: The Baseline Assay

To determine the amount of H2O2 initially present in a 1.5% solution, one needs to perform all the steps of the procedure without adding catalase to the reaction mixture. This amount is known as the baseline and is an index of the initial concentration of H2O2 in solution.

  1. Place 10 mL of 1.5% H2O2 in a beaker.
  2. Add 1 mL of H2O.
  3. Add 10 mL of H2SO4 (1.0 M).
  4. Mix well.
  5. Remove a 5 mL sample (called an aliquot) and place it in a beaker to assay the amount of H2O2. To do this, place the beaker over a white surface. Use a burette to add KMnO4 dropwise until a persistent pink or brown color is obtained.
  6. Baseline Calculation:Baseline (mL KMnO4) = Final Burette - Initial Burette
  7. Perform the baseline assay three times to obtain a meaningful average.

EXERCISE 2C: The Uncatalyzed Rate of H202 Decomposition

To determine the rate of spontaneous conversion of H2O2 to H2O and 02 in an uncatalyzed reaction, put a small quantity of 1.5% H2O2 (about 15mL) in a beaker. Store it uncovered at room temperature for approximately 24 hours. Repeat steps 2-5 from Exercise 2B to determine the proportional amount of H2O2 remaining (for ease of calculation assume that 1 mL of KMnO4 used in the titration represents the presence of 1 mL H2O2 in the solution).
Calculate the amount of H2O2 spontaneously decomposed (ml baseline - mL KMnO4).
Calculate the percent of the H2O2 that spontaneously decomposes in 24 hours? [(mL baseline - mL 24 hours)/mL baseline] x 100

EXERCISE 2D: An Enzyme-Catalyzed Rate of H202 Decomposition

In this experiment, you will determine the rate at which a 1.5% H2O2 solution decomposes when catalyzed by the purified catalase extract. To do this, you should determine how much H2O2 has been consumed after 10, 30, 60, 120, 180, and 360 seconds.

If a day or more has passed since you did Exercise 2B, you must reestablish the baseline by determining the amount of H202 present in your 1.5% solution. Repeat the assay procedure (steps 1 through 5, page 24) and record the results below. The baseline assay should be approximately the same value for all groups. Check with another team before proceeding[7].


In such a task of term paper named as kinetics in biological system,

We have studied about the biological system, chemical kinetics, and relation between the chemical system and biological system. We also have studied that how can we use the concept of chemical kinetics in biological system i.e. the bio reactions and mechanism.

We have studied that kinetics plays a vital role in biological system reactions. We have taken an example of the enzyme catalysisand some of its experiment. We can be noticed that kinects can also easily explain the biochemical reaction mechanism.