The Concept of free Energy

The Concept of free Energy

                Gibbs free energy is a thermodynamic property that was defined in 1876 by Josiah Willard Gibbs to predict whether a process will occur spontaneously at constant temperature and pressure. Gibbs free energy G is defined as,

                                                        G = H- TS

              Where H, T and S are the enthalpy, temperature and entropy.

                Changes in the Gibbs free energy G correspond to changes in free energy for processes at constant temperature and pressure. The change in Gibbs free energy change is the maximum non-expansion work obtainable under these conditions. G is negative for spontaneous processes, Positive for non-spontaneous processes and Zero for processes at equilibrium. Change in a system which is available for doing work it is the useful energy. 

                    

                  Some exergonic and endogonic reactions in biologic systems are coupled in this way. This type of systems has a built-in mechanisms of the rate control at which oxidative processes are allowed to occur since since the existence of a common obligatory intermediate or both exogonic and endogonic reactions allows the rate of utilization of the product of the synthetic path  (D) to determine by mass action the rate at which A is oxidized. Indeed , these relationships supply a basis for the concept of respiratory control, the process that prevents an organism from burning out of control. An extension of the coupling concept is provided by hydrogenation reactions, which are coupled to hydrogenation by an intermediate carrier.

Coupling of dehydrogenation and hydrogenation reactions by and intermediate carrier molecule.

An alternative method of coupling of an exergonic to an endergonic process is to synthesize a compound of high - energy potential in the exergonic reaction, thus affecting transference of energy from the exergonic to the endogonic pathway.

Transference of free energy from and exergonic to an endogonic reaction through the formation of a high-energy intermediate compound.

             In this image E is a compound of high potential energy and E is corresponding compound of low potential energy . The biologic advantage of this mechanism is that E, unlike in the previous system, need not to be structurally related to A, B, C, Or D. This would allow E to serve as a transducer of energy from a wide range of endergonic reactions or processes, as shown in next image.

In the living cell, the principal high-energy intermediate of carrier compound is adenosine troposphere or ATP.

Transaction of energy through a common high energy compound to energy-requiring biological process.

The Laws of thermodynamics in Biological systems

              The first law of thermodynamic states that "the total energy in a system, plus its surroundings remains constant." This is also the law of conservation of energy it implies that within a total system, energy is neither lost nor gained during any change. However, within the total system, energy may be transferred in to another form in to another form of energy. For example, chemical energy may be transformed into heat, electrical energy or mechanical energy.

                    The second law of thermodynamics states, " the total entropy of a system must be increase if a process is to occur spontaneously". Entropy represents the extent of disorder or randomness of the system and becomes maximum in a system as it approaches true equilibrium. Under the conditions of constant temperature and pressure, the relationship between the free energy (∆G) of a reacting system and the change in the entropy ( ∆S) is given by the following equations which combines the two laws of thermodynamics.


                           Where delta H is the change in enthalpy and T is the absolute temperature. Under the condition of biochemical reactions, because delta H is approximately equal to delta E, the total change in the internal energy of the reaction, the above relationship may be expressed in the following way.


If delta G is negative in sign, the reaction proceeds spontaneously, it is exogonic. If in addition, delta G id of great magnitude, the reaction goes virtually to completion and is essentially irreversible. On the other hands if (∆G) is positive, the reaction proceeds only if free energy can gain, it is endogonic . If in addition, the magnitude of (∆G) is great, the system is stable with little or no tendency for a reaction to occur. If (∆G) is zero , the system is at equilibrium and no net change takes place.

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Posted at 9:13 PM |  by Unknown

Main Categories Of Heterotrophic Nutrition Part I

Main Categories Of Heterotrophic Nutrition

                    The   heterotrophic mode of nutrition is found in all animals, Fungi, some protista, many bacteria and some non-green plant like Cuscuta. They consume ready made organic food from other dead or living plant and animals. Therefore, they depend on either autotrophs or other   heterotrophs for their nutrition.

                    When we consider   heterotrophs there are diverse types of organism which depend on a huge variety of food materials. These organisms can be categorized in to three basic groups according to their food type. Now, we shall have a brief idea about the three categories of   heterotrophic nutrition. 

Image : Mode of nutrition of organisms

1. Holozoic nutrition : This mode of nutrition involves the ingestion of liquid or solid organic material. The main steps in holozoic nutrition process include ingestion, digestion, absorption, assimilation and finally ejection. These holozoic animals can be divided in to the three major categories depending on the relative size of the food they intake and their feeding mechanisms, namely Macrophagous feeders, Fluid feeder and Macrophagous feeders.

     2. Saprophytic nutrition :   "Sparos" refers to rotten and 'trophic' refers to food. In this mode of 

         nutrition the organisms feed on dead and decaying organic matter. These organisms secrete   

         digestive juices which contain enzymes to digest the food and then absorb soluble end products 

         into the body.

     3. Symbiotic nutrition :  This is the mode of nutrition in which individuals of two (or more ) 

         different species share their shelter and nutrition. Depending on the degree of benefit and harm, 

         there are 5 types of symbiotic relationships. 

• Mutualism            -  both species benefit
• Commensalism    -   one species benefits, the other is unaffected
• Parasitism            -   one species benefits, the other is harmed 
• Competition         -   neither species benefits
• Neutralism           -   both species are unaffected

Image:   Graphical Representation of the 5 types of symbiotic relationships

         Now you have a brief idea about different types of heterotrophic nutrition. In order to get a broader knowledge about each type in heterotrophic nutrition, Let's have a detailed look to each category.

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Posted at 10:30 PM |  by Unknown

Distinction Between Heat And Temperature

DISTINCTION BETWEEN HEAT AND TEMPERATURE

                    When we place a lighted burner under a beaker of water, an amount of heat is transferred to the water. As the internal energy of the water increases, we observe a difference in sensation when we touch it. Internal energy is the total kinetic and potential energies of all the molecules. The energy that is transferred by the source of heat (bun son flame) is hear energy and the sensation of hotness or coldness experienced by the fingers corresponds to high or low temperature. In other words temperature  is the degree of hotness of a body. The increase in the kinetic energy of the molecules of the body is proportional to increase in temperature.

               

                    Suppose we keep a hot body in contact with a cold body. Let us try to explain what happens in terms of temperature and heat. The temperature of the hot body is higher than that of the cold body. When they are kept in contact energy is transferred from the hot body to the cold body in the form of heat. 

THERMAL EQUILIBRIUM ZEROTH LAW OF THERMODYNAMICS

                      When there is no flow of heat between bodies kept in contact they are said to be in thermal equilibrium. Consider three bodies A, B, and C. suppose that the body C is in  thermal equilibrium with A and also B. Then it is found experimentally that the bodies A and B are also in thermal equilibrium. That fact is sometime knows as the Zero law of Thermodynamics. This law enables us to use a thermometer (T) to find out whether two bodies A and B are in thermal equilibrium. Bring T into thermal equilibrium with A and note the reading in T. Repeat it for the body B. If the thermometer reading are the same in both cases, we can deduce that A and B are in thermal equilibrium . Using that law, temperature can also be defined as that property of a body which decides whether it is in thermal equilibrium with another body or not.

THERMOMETERS

                    Differences of temperature may be estimated roughly by our sense of touch. These sensations are not reliable enough for scientific work. Therefore, We make use, of a device which indicates a change in the reading when it is subjected to a change in temperature. Such a device is know as a thermometer.

THERMOMETRIC PROPERTIES

                        In General, all thermometers make use a measurable property of a substance which in sensitive to changes in temperature. Such a property is know as a "thermometric property".

                        "Mercury-in-glass thermometer" is the most common of all, the thermometers. In this type of thermometer the apparent expansion of a volume of mercury is used as the thermometric property. Here a change in  temperature is measured by observing the change in length of mercury column of uniform area of cross-section. In some other type of thermometers, change of pressure with temperature of a gas at constant volume is used as the thermometric property. This is known as the constant volume gas thermometer. Similarly, a constant pressure gas thermometer makes use of the volume of a gas at constant pressure as this property.

TEMPERATURE SCALES

                         In order to assign a number to specify a particular temperature, a "temperature scale" has to be defined. To establish a temperature scale we need to know the followings.

1. Physical Property of a substance should change in such a manner as to increase continuously with increase in temperature and to be constant at constant temperature. This condition is fulfilled if we use a good thermometric property such as the volume of gas or the electrical resistance of pure platinum. 
2. It should be always possible to reproduce certain chosen temperature' accurately whenever we require. These are known as fixed points. 

FIXED POINTS 

Temperature Scale were defined by making use of two fixed points. They are as follows.

1. Ice point : The temperature of ice in equilibrium with air saturated with water at 1 atmospheric pressure.
   
   
2. Steam point : The equilibrium temperature of pure water and pure steam at 1 atmospheric pressure.

                 However, the use of two fixed points was found to be unsatisfactory, partly due to the difficulty of achieving the equilibrium between pure ice and saturated water. When ice melts, it surrounds itself with pure water and this prevents intimate contact of Ice with air saturated water. Also, the steam point is extremely sensitive to a change in pressure. Thus , the temperature scale now in use is based on one fixed point only.  This fixed point is called the "triple point of water."

TRIPLE POINT OF WATER

                     Water can exist as solid, liquid and gas at the same time in the same vessel at one temperature and one pressure only. This temperature at which saturated water vapor, pure water and melting ice are all in equilibrium is known as "triple point of water".

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Posted at 2:25 AM |  by Unknown

Identification Of Organisms and Living Things

Identification Of Organisms and Living Things

      In thinking about identification of living things, the first question that comes to our mind is the need for identification of them. We know that we share the planet with at least 1.5 million other species. In order to communicate, retrieve store and accumulate information about our immediate neighbors like people , dogs, elephants, coconut trees and other plants, it is necessary to : (a). identify these organisms; (b) name them ; and (C) place these organisms into groups that reiect our current knowledge of their evolutionary relationships. As we know collectively these activities - identification, nomenclature and classification - make up the discipline of taxonomy .

Here we will focus only on identification

      Identification could be defined as comparing an unknown one with that is already known; or at least recognize that the unknown doesn't have a known counterpart. So what does this mean ? Let's give an example. Suppose you didn't know that the bird which one of your friends is carrying is a parrot. How could you identify this creature ? The answer is simple in theory. We could compare the '' unknown bird '' to other ''known'' or "reference" or "type" birds until we find one that matches. If, we don't find a perfect match, we may have to follow the process of matching the unknown organism to known ones in some other ways.

How can we do that ? 

A. Asking an expert or someone who knows.

                                     Consult an individual who has spent his/ her life studying birds (ornithologist). This method usually provides a reliable and accurate answer because it is based on the wisdom and years of experience of  a professional. "Experts" are typically found in botanical gardens, museums, herbaria, colleges , universities, etc.

B. Specimen Comparison.

                              In this case, we search through a field guide, museum or zoo for a bird that matches our mystery bird. If we were trying to identify a plant we could even search through the her barium. This can involve looking at pictures, actual specimens or descriptions. Although we may get lucky, this method is the least satisfactory because of the small probability that we will stumble upon the match.

C. Using a taxonomic key 

                                      A key is a device, which when properly constructed and used, enables a user to identify an organism. The most common and widely used type of key are dichotomous keys. 

      They consist of a series of paired statements, termed couplets, that describe some feature of the organism. The statements, or leads are in direct contrast. To use the key, begin with the first couplet and select the statement that best fits your specimen. this will direct you to another couplet and ultimately provide the identity of your specimen. 

        There are two types of dichotomous keys. They differ in the method by which the couplets are organized and how the user is directed to successive choices. They are Indented Keys and Bracketed Keys. At this point we are not discussing these two types and you will be studying them later.

A simple dichotomous key

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Posted at 6:01 AM |  by Unknown

States Of Matter

• States Of Matter

Matter exists in three physical states: gas, liquid and solid.

The three states of matter : gas, liquid and solid.

Let us now discuss the three states of matter in detail.

A gas which is also known as vapor has no fixed volume or shape. Rather, it takes up the volume and shape of its container. The particles in a gas are far apart and are moving at high speeds colliding repeatedly with each other and with the walls of the container.

A liquid has a definite volume independent of its container, but has no definite shape. It takes up the shape of the portion of the container that it occupies. The particles in a liquid are packed more closely together than in a gas, however, they move rapidly sliding over each other.

A solid has both a distinct volume and a shape. In a solid, the particles are packed tightly together to give a definite arrangement in which the particles move about a mean position.

• Classification of matter

Most forms of matter that we encounter are not chemically pure and can be separated into different substance. A pure substance can be either an element or a compound that have distinct properties and a composition that does not vary from sample to sample. Mixtures, however , are composed of different substance with varying composition. Therefore, matter can be classified according to its composition as an element, compound or mixture.

Elements

An element is a substance that consists of only one kind of atom. For example, magnesium is and element made up of magnesium atoms only. At present over one hundred elements vary widely in their abundance. For example, only five elements (Oxygen, silicon, aluminium, iron and calcium) account for over 90% Earth's crust. To refresh your memory look at table 1 that gives some common elements with their chemical symbols.

                                                                          

Element	Symbol
Carbon	C
Oxygen	O
Aluminium	Al
Calcium	Ca
Nickel	Ni
Copper	Cu
Antimony	Sb
Mercury	Hg
Bismuth	Bi
Plutonium	Pu

                                                                             

Compounds

When two or more different element are combined chemically, a compound is formed. In a compound, the atoms of the constituent elements are in a definite characteristic ratio. There are only over one hundred elements, but millions of compounds are known to date. The symbol for a compound is called its chemical formula. As you already know, it is made up from chemical symbols of the elements and numbers indicate the number of atoms present in each element for a particular compound.

For example, consider water. It is a compound made two elements, hydrogen and oxygen in a fixed ratio of 2 : 1 and the chemical formula is given as H₂O.

Similarly the formula for carbon dioxide is give as CO₂ where elements, carbon and oxygen are combined in a 1 : 2 ratio.

Mixtures

Most of the matter we encounter are mixtures of different substance. In a mixture, the substances are not chemically joined. The substances making up a mixture are called components of that mixture. For example, consider a cup of coffee. It is a mixture of the following composition: water , coffee, milk and sugar. Some mixtures have the same composition, properties and appearance throughout and are called homogeneous mixtures. For example, a solution of copper sulfate is a homogeneous mixture. Mixtures which are not universal throughout are called is a homogeneous mixtures. Soil is a good example of a heterogeneous mixture. 

The classification of matter in to elements, compounds and mixtures that we discussed in this section is summarized in  image.

• Properties of matter

Every substances a unique set of properties and these properties can be categorized as physical or chemical. Physical properties can be measured without changing the identity and composition of the substance. For example color, odor, melting point, boiling point and hardness are physical properties. Chemical properties describe how substances undergo change or react to form other substances. For example, flammability, the ability of a substance to burn in the presence of oxygen is a chemical property.

The changes that substance undergo can also be categorized as either physical or chemical. During a physical change, a substance changes its physical its physical appearance but not its composition. A good example of a physical change is the evaporation of water. When water evaporates, it changes from the liquid state to the gas state but it is still composed of water  molecules. In a chemical change, a substance is transformed into a chemically different substance. Consider burning of hydrogen in air to form water. In this case, hydrogen undergoes a chemical change, as it has combined with oxygen to form water.

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Posted at 1:52 AM |  by Unknown

Atomic Structure of Matter

              In the study of electricity, positive and negative electricity were regarded as two types of fluids and that were present in equal quantities in neutral bodies. It was considered that when two bodies are rubbed, this fluid is separated, so that one body obtained an excess of the positive fluid and the other an excess of the negative fluid. 

             Modern theory of electricity is somewhat similar to this. When Dalton presented his atomic theory about the year 1810, all matter was considered to be composed of some elementary particles called "atoms" these being. Identical for each element, these atoms were regarded as indivisible. 

             It is now know that atoms are divisible and a number of different kinds of particles, many of which are electrically charged, exist and are formed by the breaking up of the atom. There are three main kinds of elementary particles. They are the electron, the proton and the neutron. The mass of an electron is about 1/1840th of the mass of a hydrogen atom which was considered to be the lightest atom . Also, the electron carries a negative charge of electricity. This charge is considered to be the smallest charge and all other charges are considered as multiples of this elementary charge. The mass of the proton is equal to that of the hydrogen atom, While it carries a charge of positive electricity equal in size to the charge of an electron. neutron has nearly the same mass as a proton but is electrically neutral. The atom is regarded as being built up of these three kinds of particles. The protons and neutrons together form a heavy center called the "nucleus" around which the electrons continuously revolve somewhat like a miniature solar system. 

             Practically, all the mass of an atom Is concentrated in the nucleus. Because of the protons, the nucleus, the nucleus has a positive charge. But the number of protons in the nucleus is equal to the number of electrons around it. So, the complete atom Is electrically neutral. For instance, let us consider an atom which has three protons in the nucleus, as shown in this image.

            The nucleus has positive charge numerically equal to that of three electrons. Since this atom is neutral, three electrons are associated with it, and these electrons revolve in orbits around the nucleus. The presence of neutrons in a nucleus will add to its mass but not affect its electrical charge. It may be mentioned that a nucleus with three protons may contain three or four neutrons. When electrons of an atom are transferred to another atom they both become electrically charged.

             For example let us consider two neutral atoms each having three protons in the nucleus and three electrons around the nucleus image . They are both neutral.

Now, suppose that one electron from the left hand atom is transferred to the right hand one , as shown image .

            Then , left hand one now has a bigger positive charge on its nucleus than the negative charge around it. So, the charge on the atom is positive and the atom is said to be positively charged . Also, the right hand atom Is negatively charged by its excess electron. When an atom gained or lost electrons, it is referred to as an ion.

           In general, atoms of metals tend to lose electrons and become positive ions and atoms of non-metals tend to gain electrons and become negative ions. 

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Posted at 9:30 AM |  by Unknown

What is Chemical Analysis?

       In Simple words chemical analysis is finding out the substance present and the amount of the substance present in a sample. Finding out the substances present is called qualitative analysis and the amount of the substances presence is called qualitative analysis.

Example : Look at a water bottle available for sale.

                  Does the label give the composition of the ions/elements present as percentages ?

                  Yes. The manufacture of this water brand has done a sample testing for quality and 

                  qualitative analysis. 

       If you consider the above example , each and every bottle carries this label. Do you think he has checked each and every water bottle ? No. It is practically impossible (Although it should been done.) What must have he done ? He must have checked some water bottles (samples) of the production. This is called sampling. He has taken few samples from a batch of bottles or a population of bottles. Let us see what these terms really mean. 

Population and Sample

What is a population ?

      It is an actual or conceptual collection of individual items/ observations /  measurements , which may be finite of infinite.

Example :  1. Students in a university

                   2. Inland waters of Sri Lanka

                   3. Soil in the Anuradhpura District area 

                   4. The effluent of a paint factory 

                   5. Blood of a patient

                   6. Results of a tit-ration

What is a Sample ?

       

        A sample is a small part of the population, taken for analysis.

Example : A water sample of a well be of about 1 L.

       When the size of the sample or number of samples is large, its properties will be very much closer to the population. Therefore, if you want test your well water it is better to take at least about three samples of 1 L each.

Population and a sample

        In the determination of a characteristic of  population, taking measurements of the whole  population is not possible. Therefore, we have take samples from the population for the determination.

Let's explain this more by trying to answer the following question. 

        Can you find the average weight of children of age five in the Colombo district?

You can . What should you do in Oder to find out the average weight ? You have to take the weight of each child and average it. Is it an easy task? How much of time and how many people should be employed for this ? Here, the population is the total number of children of age five in the district of Colombo. It is not an easy task. This is because we can't take measurements form all units/ individuals of due to various reasons. It may be due to lack of time, energy, money  etc.... If so, is there another way to find the average weight of children of age five in the Colombo district ? 

       Yes. There is . We have to take a sample of children having a number we can cope with. then we can take the weight of the children in the sample and take the average. The sample should not be biased. What does this mean? Samples should be randomly selected in order to be true representatives of the population. 

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Posted at 11:28 PM |  by Unknown

Occurrence and isolation

          Alkali metals are reactive and they are not found in nature as free metals.Sodium and potassium are relatively more abundant than the metals in this group. Na is present as a salt (sodium chloride, NaCl) in huge quantities in underground deposits (salt mines), in seawater and other natural waters. Potassium salts are found naturally in seawater, and as carnality, KCl-MgCl₂-6H₂O or ptash (KOH). The concentrations of Na⁺ and K⁺ions in seawater are 10,800 and 590ppm, respectively.

Sodium and lithium are obtained by the electrolysis of their molten chloride. For example.

During electrolysis Na⁺ ions are reduced to Na metal and chloride ions are oxidised to chlorine gas.

Potassium is made by the reaction of sodium vapour with molten/fused KCl at 850⁰C.

Rubidium and cesium are made by the reduction of their chlorides with calcium metal at 800⁰C.

All isotopes of francium are radioactive.

Some properties of alkali metals

           In this session, we will mainly concentrate on the chemistry of Na, K, and Li. The elements of Group 1 are soft metals and they conduct electricity and heat. Table 1 provides you with some of the physical data of Group 1 elements. As one would expect the ionic radius, r(M⁺), increases as you go down the group. The melting point (m,p) decreases from Li to Cs. Alkali metals have low densities and the densities (d) of Li, Na, and K are less than that of water thus these metals float on water. 

Some properties of group 1 elements

	R(M+)/pm	En Configuration	m.p./0C	d/gcm-3	E0	IE1 kjmol-1	IE2 kjmol-1
Li (Litium)	60	2s1	181	0.53	-3.04	520	7590
Na (Sodium)	95	3s1	98	0.97	-2.71	496	4560
K (Potasium)	133	4s1	63	0.86	-2.94	418	3060
Rb (Rubidium)	148	5s1	39	1.53	-2.94	401	2630
Cs (Caesium)	169	6s1	29	1.90	-3.03	376	2430

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Posted at 12:07 AM |  by Unknown