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Monday, August 30, 2010

RNA, its Structure and Kinds

Monday, August 30, 2010 - 0 Comments

RNA is Ribo nucleic acid. It occurs in the nucleolic, chromosomes and cytoplasm. About 90% of cells RNA occurs in the cytoplasm. RNA consists of 5 – carbon ribose sugar and phosphate. RNA is macro molecule and is single stranded.
RNA is chemical messenger and plays key role in the process of protein synthesis.
RNA is the other nucleic acid. It is high molecular weight polynucleotide. It differs from DNA in having Pentose sugar ribose in place of deoxyribose and in that pyrimidine thymine is here replaced by uracil. Other three bases are the same as in DNA. The nucleotides (combination of ribose and base molecules) of RNA are called ribo-sides and its nucleotides are called ribotides. RNA is therefore described as polycribotide. Various ribotides are joined together by their phosphate groups to form an un-branched linear chain containing hundreds of ribotide (nucleotide) units. RNA molecule is single strand structure and not double strand structure. Its molecule is smaller and has lower molecular weight than DNA. There are three kinds of RNA which play important roles in the translation of genetic information contained in DNA. RNA is formed in the Nucleus by nuclear DNA. A part of it is present in the chromatin and nuclear ribosomes in the form of ribo-nucleoprotein. Most of it however is located in the cytoplasm, particularly in the cytoplasmic ribosomes. RNA formed in the nucleus is stored in the nucleolus from where it passé out through nuclear membrane into the cytoplasm.

Structure of RNA:

Kinds of RNA:
A cell contains many kinds of RNA. There are three major kinds:

(1)        Ribosomal RNA:
RNA found in ribosomes is called ribosomal RNA or rRNA. During polypeptide synthesis, rRNA molecules provide the site on ribosome where polypeptide bond is assembled.













(2)        Transfer RNA:
Second type of RNA is called Transfer RNA or tRNA which is much smaller. Human cells contain more than 40 different kinds of tRNA molecules which float free in the cytoplasm. During polypeptide synthesis tRNA molecules transport the amino acids present at their one end to the ribosome for use in building the polypeptide and position each amino acid at the correct place on elongating polypeptide chain.






(3)        Messenger RNA:
Third of RNA is messenger RNA. Each mRNA molecule is long, single strand of RNA that passes from the nucleus to the cytoplasm. During polypeptide synthesis mRNA molecules bring information from the chaeomosomes to ribosomes to direct the assembly of amino acids into a polypeptide.
These molecules together with ribosomal proteins and certain enzymes constitute a system that carries out the task of reading the genetic message and producing the polypeptide that the particular message specifies.

Replication of DNA

Essential property of genes is self duplication or replication. DNA possesses this property. Two strands of DNA molecule are complementary to each other. First step is relication is breaking of hydrogen bonds that bind together two strands of DNA. Two strands thus separate from each other and unwind. Each strand then directs the synthesis of new strand complementary to itself out of free deoxyribo nucleotides present as tri-phosphates in the environment of DNA. In this process each strand acts as a model or template to which free nucleotides are linked by hydrogen bonds with their complementary deoxyribo-nucleotides in the strand under the catalytic influence of the enzyme DNA polymerase: Thus an adenine base in free nucleotide would pair with thymine in DNA strand, a cytosine base in free nucleotide with guanine base in DNA strand and so on. This is followed by the formation of sugar phosphate bonds between successive nucleotides which arrive on the template. The result would be that each single strand of original DNA molecule would form double stranded DNA molecule in which new strand is complementary to and specified by the old strand. Further, new strand that is added to an old DNA strand is equivalent to other strand of the parental DNA molecule. Two daughter DNA molecules are thus formed which are identical to parental molecule. It should be noted that every daughter molecule is half old, half new. Each daughter molecule contains one newly synthesized strand and one strand belongs to old parental molecule which is entirely conserved. For this reason the replication of DNA is describe as Semi-conservative. It may noted that the breaking of parental DNA molecule and the unwinding of two strands occur in small segment of DNA molecule at a time. The synthesis of new strands starts at one end of old molecule and proceeds step by step to other end. This property of replication of DNA is called autocatalysis. There are three main hypothesis to explain the replication of DNA.


(A) Dispersive hypothesis (B) Conservative (C) Semi-conservative
(A)       Dispersive hypothesis: During the early stages of development of biochemical history of DNA some bio-chemists proposed that replication of DNA follows a dispersive mechanism. According to these both of the strands of daughter DNA have some parts new and some parts from parental DNA. Due to lack of experimental evidence dispersive mechanism of DNA replication was rejected very early.
(B)       Conservative replication: Some of the biochemists have also suggested conservative mechanism for DNA replication. According to this view both parental strands are retained by the parent DNA molecule and both the strands of daughter DNA are synthesized new under the guidance of parental strands. This was also rejected due to lack of evidence.
(C)       Semi-conservative replication: In E. Coli cells DNA is replicated in semi conservative manner. Each daughter DNA receives one strand from its parent and synthesize its second strand from its cell’s raw material. After replication both daughter DNA molecules appear as haploid of old (parental and new strands. This view is accepted by almost every biochemist as the only mechanism of DNA replication.

DNA replication mechanism: Replication DNA is possible only when the parent molecule uncoils and both of its strands get apart. For unwinding and separation of the strands of the parent molecule, at the time of replication, three types of enzymes are involved. These are (1) Gyrase or Helicase enzymes uncoil replicating DNA and force it to become straight and uncoiled. (2) DNA binding proteins (B – protein), or melting enzymes react with both strands of the parent DNA and by breaking hydrogen bonds gap both strands apart. (3) Helix destabilizing proteins react with single stranded DNA and do not allow them to recoil during replication. By the activity of enzymes Gyrase, DNA B – proteins and helix destabilizing proteins, origin site (single stranded region) is created at which replication starts bi-directionally.
Replication is catalyzed by numbers of enzymes called DNA polymerases and ligases. DNA polymerases are enzymes which are responsible for replication. These enzymes of DNA polymerases are known to exist. They are (1) DNA polymerase I (2) DNA polymerase II (3) DNA polymerase III

DNA, its Functions and Watson Crick Model of DNA

DNA is present in the chromosomes of the nucleus i.e. nuclear reticulum. DNA is double stranded molecule. DNA is controlling centre of vital activities of the cell. DNA is genetic or hereditary material migrating intact from generation to generation through reproductive units or gametes and is responsible for the development of specific characters. It also controls biosynthetic processes of cell including protein synthesis. DNA molecule is very large and complex (macromolecule) forming the backbone of each chromosome. In 1953 Watson and Crick worked out a model of DNA molecule and the model was named by their name i.e. ‘Watson Crick Model of DNA’. According to them DNA occurs as double stranded molecule with two strands profusely coiled and entwined about each other throughout their whole length. The structure is like a ladder twisted spirally. Each spiral strand is made of groups of deoxyribose sugar alternating with groups of phosphate. Besides there are infinite pairs of cross links connecting two strands. Each pair is made of two distinct nitrogenous bases Purines and Pyrimidines. Altogether there are two purines adenine and guanine and two pyrimidines thymine and cytosine. It is rule that specific Purine always pairs with specific Pyrimidine. The base molecule of two strands are joined together by weak Hydrogen bonds to form base pairs. Although hydrogen bonds between base pairs of two strands are weak, their large number ensures that two strands are held together by fair degree of firmness. This arrangement gives to DNA molecule ladder like appearance. The ride rails or longer banisters of ladder which form the backbone of DNA super-molecule are formed by alternating sugar and phosphate groups bound by strong chemical bonds. The base pairs form the rungs or horizontal steps of the ladder. This ladder is however not straight. As convinced by Watson Crick, two strands of DNA molecule are twisted about each other at intervals around a central axis to form double helix, something like a spiral circular stair case.

Structure of DNA:
There may be thousands of turns in the spiral. Two strands of DNA travel in opposite direction. In other words they are of opposite polarity. Purine Adenine is always paired with Pyrimidine thymine by two hydrogen bonds and Purine Guanine is always paired with Pyrimidine Cytosine by three hydrogen bonds. This means that Adenine is complimentary to thymine and guanine is complementary to cytosine. If the base sequence in one strand of DNA is known the sequence of bases in the other strand can be determined because two strands are complementary to each other. If at any point on one strand there is adenine, there is bound to be thymine at the corresponding point on the other strand. Total molar amount of adenine in DNA of given species is always equal to that of thymine (A = T) and the same 1:1 relation holds well between guanine and cytosine (G = C). As a corollary it is also true that A + G = T + C.
In other words total numbers of DNA Purines is always equal to total number of DNA Pyrimidines.

Watson Crick Model of DNA:

DNA of different species shows great variations in their A + T and G + C content. This due to the fact that different specimens of DNA vary greatly in the types or frequencies of the bases present along with length of the molecule. They also differ in the sequence of base pairs along great length of DNA double helix. Base pairs can be arranged in any sequence. The number of possible base sequences is equal to 4n where n equals to the number of nucleotides per strand. This gives infinite variety in DNA molecule, each different for different species. That is why there are many kind of DNA, each peculiar to a particular species. Each strand of DNA molecule completes one spiral in length of 34A and each complete spiral contains 10 base pairs. This means that each nucleotide occupies 3.4A along with the length of a strand. Two strands have diameter of about 20A (radius 10A)
A = Angestron = 1 / 10,000µ).

Tuesday, August 24, 2010

Nucleic Acids

Tuesday, August 24, 2010 - 1 Comment


22 years old, Swiss physician and chemist Friedrich Miescher isolated a substance from nuclei of Pus cells which was quite different from other biomolecules and named it as ‘nucleic’. Later it was found that nuclei has acidic properties and hence it was renamed and nucleic acids. Nucleic acids are present in all organisms from virus to man. These micro-molecules are present either in Free State or bound to proteins as nucleoproteins. Like proteins nucleic acids are biopolymers of high molecular weight with mononucleotide or their sub units (monomers). Nucleic acids are long chain of polynucleotide in which mononucleotides are linked with each other. There are two kinds of nucleic acids, deoxyribose nucleic acid (DNA) and ribonucleic acid (RNA). DNA is found mainly in chromatin of cell nucleus where as most of RNA (90%) is present in the cell cytoplasm and little 10% in the nucleolus. Nucleic acids is polymer of nucleotide. 


Nucleotide is molecule which consists of following three parts.
(i) Pentose sugar (5 carbon)
(ii) Phosphoric acid (H2Po4)
(iii) A nitrogenous base
Pentose sugar found in nucleotides either ribose (C5H10O5) or Deoxyribose (C5H10O4).
Ribose is found in RNA nucleotides while Deoxyribose sugar is found DNA nucleotides, both of them are distinguished primarily or the basis of this Pentose Sugar. This Sugar behaves as basic Skeleton Phosphoric acid common in all nucleotides. It is attached with 5th carbon of Pentose Sugar in each nucleotide. There are two basic types of nitrogenous bases i.e. Purine and Pyrimidine. Purine includes two nitrogenous bases named Adenine (A) and Ginine (G) while Pyrimidine includes three nitrogenous bases Cytosine (C), Thymine (T) and Uracil (U).
The nucleotides differ on basis of their nitrogenous bases.
Formation of Nucleotide takes place in two steps. At first step nitrogenous base combines with Pentose Sugar at its first carbon to form a nucleoside. At the second step Phosphoric acid combines with 5th carbon of Pentose sugar to form a nucleotide. Nucleotides are of three kinds.

(1)        Mononucleotide:
Generally nucleotides are found in the nucleic acid as Polynucleotide but they are also found as mononucleotide and Di-nucleotide. Mononucleotides exist singly in the cell or as a part of other molecules. These are not the part of DNA or RNA. Some of these have extra phosphate groups e.g. ATP (Adenosine tri phosphate). It is most important among these nucleotides. It is an unstable molecule and carries energly from place to place within a cell. It is synthesized from ADP (Adenosine di-phosphate) and inorganic phosphate by capturing energy during photosynthesis. This energy is utilized to derive energy demanding reactions such as in synthesis of Proteins, Lipids, Carbohydrates, mechanical energy for Cyclosis, Contractility, Cell-division, movement of Flagella, active transport etc. ATP consists of Adenosine (Adenosine and ribose sugar) and three phosphate; among them two are energy rich phosphate bond. During conversion of ATP into ADP, free energy releases which is considerable large.

(2)        Di-nucleotide:
Sometimes two nucleotides are covalent by bounded together, these compounds are called di-nucleotide. One of the well known di-nucleotide is Nicotinamide adenine di-nucleotide (NAD). Nicotinanide is vitamin constituent. Two nucleotides are linked by phosphate of oen another. NAD is a coenzyme [Coenzymes are organic (molecule non protein) which bind to enzyme (Protein) and serve as a carrier for chemical groups or electrons] that carries electron and work with dehyrogenase enzyme. It removes tow hydrogen atom (2e- + 2H+) from its substrate, both electrons, but only one hydrogen ion is passed to NAD which reduces it to NADH.



(3)        Polypeptide:
Nucleic acids are informational macromolecules. They have a variety of role in living organisms. Inspite of all, unique and premiere service of nucleic acid is as repositories (store house) and transmitters of genetic information. They make it possible for cells to function according to specific patterns and give rise to new cells that either function similarly or develop new functions, according to plants encoded in nucleic acid molecule in a particular and simple fashion. Four different nucleotides make up each informational nucleic acid molecule. They are three letters in a genetic code.
Nucleic acid molecule is somewhat linear and the units (nucleotides) like letters on a printed page or digits magnetic signals on a computer tape. In the proper machinery these codes (nucleotides) can be interpreted. The cell interpretes the information present in many nucleic acid molecules as sequence of amino acid in protein and peptide molecules. The synthesis of protein with definite sequences of amino acids are controlled anounts of protein is observed as the expression of heredity of organisms which give physical appearance of that particular character.
DNA and RNA are basically similar structure because both of these are poly nucleotide chains but the nucleotide of both are different in following ways.
(i) DNA contains deoxyribose sugar (C5H10O4) while RNA contains ribose sugar (C5H10O5) in the nucleotides.
(ii) DNA contain Adenine Guanine, Cytosine and Thymine containing nucleotides where as RNA contains Adenine, Guanine, Cytosine and Uracil containing nucleotide.
(iii) DNA is double stranded helical structure while RNA is single stranded structure except RNA.
(iv) DNA is of just one kind while RNA is of three kinds rRNA, tRNA, and mRNA (r = ribosomal, t = transfer, m = messenger).

Proteins

Proteins are organic compounds of living organisms making 55 – 85% of dry weight of the cell.
Protein molecule has many different levels of structure and may be coiled and folded or it may interact with other protein molecules to form unique three dimensional structure.
Different kinds of protein molecules have different shapes related to their particular functions in life processes.


They are as under:
(1)        Primary Structure: It is the linear sequence of amino acids in polypeptide chains comprising the molecule.
(2)        Secondary Structure: It is repeating pattern of bonds (often Hydrogen bonds) between amino acids and it commonly takes the shape of alpha relize or pleated sheet.
(3)        Tertiary Structure: It results from the helix folding into three dimensional shape.
(4)        Quaternary Structure: In some instances two Protein chains join to form larger protein which is called quaternary structure.

(1)        Primary Structure of Proteins:
It is the linear structure of amino acids in polypeptide chains comprising the molecule. In primary structure in addition to peptide bonds, disulphide bonds (S – S) may link into peptide chains as in insulin where two amino acids chains are linked with one another. In ribonuclease single chain is folded and has disulphide bond – Single peptide chain is formed as a result of polymerization of 100 – 1000 or more amino acids in straight chain. This chain will always be having a carboxyl group on one end which is known as C-termed and an amino group on other end thus known as N-terminal. New amino acids can be added both at C or N terminals. New amino acid can be added both at C or N terminals. Proteins have specific primary structure due to
(i) Number of amino acids in Polypeptide chain
(ii) Types of amino acids present in polypeptide chain
(iii) Sequence of amino acids in polypeptide chain.
DNA template determines the specificity in number, size, type and arrangement of amino acids in Protein.

(2)        Secondary Structure of Proteins:
Polypeptide chain that shows folding due to the formation of hydrogen bonds and forms a stabilized structure is called secondary structure of protein. It may be of following types:
(i) α-Helix: It is formed when a polypeptide chain is twisted in such a way that every amide and carboxyl carbon is involved in hydrogen bonding. α-helix look like a helical spring α-helix is controlled by number of amino acids residues per turn, the pitch of single residue. α-helix protein chain is the structural protein of hair, wood, nails, claws, beaks, feathers, horns and vertebrate skin.
Amino acids have the ability to form hydrogen bonds and participate in helix formation. Such amino acids are called helix formers like Glutamic acid, Alanine, Leucine, Histidine.
(ii) β-Pleated sheets: In some cases torsion angles in polypeptide chains are so irregular that hydro bonding does not take place in extended peptide chain. Two of three such extended chains interact with one another by hydrogen bonding A form β-Pleated sheets.

(3)        Tertiary Structure of Proteins:
Secondary proteins on extensive coiling or folding form compact structure called tertiary structure of protein. Tertiary structure determines the shape protein. Folding is held together due to interaction of R-group of different amino acids present in peptide chains. These interactions include ionic, hydrogen, disulphide bonds and hydrophobic interaction.
(4)        Quaternary Structure of Proteins: Sometimes more than two monomeric proteins are essential to make a structure or collectively perform a function; such bigger structures with more than two units form Quaternary structure of Protein. It is classified as monometric, dimeric, oligomeric depending upon the number of submits as one, two or many respectively. Different monomers are held together by ionic bonds, hydrogen bonds and hydrophobic interactions.

Functions of protein are
(1) Enzyme Catalysis: Chemical reaction occurring in enzymes, the specific proteins, controls the body.
(2) Coordinated Motion: Proteins like myosin, actin, troponin and tubulin are responsible for movement of animals, organs, chromosomes, flagella, cilia, cells etc.
(3) Mechanical Support: A fibrous protein, collagen provides mechanical support and strength to skin, bones, connective tissues, tendons and ligaments.
(4) Transport and storage: Haemoglobin and myoglobin present in RBC and muscles are responsible for transportation of oxygen to the cells and muscles. During starvation proteins present in body is used by process of autolysis for energy production.

Carbohydrates and their Classification

Carbohydrate literary means hydrated carbon. Carbohydrates are composed of carbon, hydrogen and oxygen and the ratio of hydrogen and oxygen is the same as in water. Carbohydrates polyhydroxy aldehydes or ketones or complex substances that on hydrolysis yield polyhdroxy aldehydes or ketones subunits. Hydrolysis involve break down of large molecules into smaller ones utilizing water molecules. Carbohydrate occurs abundantly in living organisms. They are found in all parts of the cell, cellulose of wood, cotton and paper starches present in cereals, root tubers, cane sugar and milk sugar are all examples of carbohydrate. The sources of carbohydrates are green plants. These are primary products of photosynthesis. Other compounds of plants are produced from carbohydrates by various chemical changes. Carbohydrates are animal’s major source of energy. Most animal cells have chemical machinery to breakdown the energy rich carbon hydrogen (C – H) bonds in sugars and starches. Carbohydrates in cell combine with proteins and lipids and the resultant compounds are called glycoproteins and glycolipids. Glycoproteins and glycolipids have structural role in extracellular matrix of animals and bacterial cell wall. Carbohydrates play structural and functional roles. Simple carbohydrates are main constituents of cell walls in plants and micro organisms.

Classification of carbohydrates:

They are also called saccharides which means sugar. They have three groups.
(1) Monosaccharides
(2) Disaccharides
(3) Polysaccharides

(1)        Monosacchrides:
They are single sugars and are simple sugars. They have following properties.
They are sweet in taste, they are easily soluble in water and they cannot be hydrolyzed into simple sugars. Chemically they are either polyhdroxy aldehydes or ketones. All carbon atoms in a monosaccharaide except one have a hydroxyl group. Remaining carbon atom is either a part of an aldehyde group or a keto group. The sugar with aldehyde group is called also sugar and with keto group as keto sugar e.g. Glucose, Fructose.



(2)        Disaccharides:
It is formed by removing a molecule of water from two monosaccharides. Disaccharides have the same molecular formula C12H22O11 e.g. Sucrose, lactose and maltose. A molecule of glucose combines with a molecule of fructose through 1 – 2 glycosidic bond to form sucrose, the table sugar. If a glucose molecule bonds to another monosaccharide galactose through 1 – 4 glycosidic bonds, the disaccharides formed is lactose, the milk sugar, when two glucose submits join together by 1 – 4 glycosidic bonds they form maltose that is present in seeds, especially it gives barley seeds a sweet taste. Beer brewers ferment barley into alcohol. Organic compounds having same molecular formula but different structural formulae are called isomers and each isomer has unique properties.

(3)        Polysaccharides:
They are most complex and abundant carbohydrates in nature. They are usually branched and tasteless. Several monosaccharide units linked by glycosidic bonds form polysaccharides. They are tasteless and insoluble in water and thus are responsible for making structural part of cell and organelles. On hydrolysis they produce large number of monosaccharides. Monosaccharides are bonded together with glycosidic bond. Polysaccharides may be in straight chain formed through 1 – 4 glycosidic bonds or have branched chain formed by 1 – 4 and 1 – 6 glycosidic bonds e.g. starch, glycogen, cellulose, dextrin, agar, pectin and chitin. Starch is main source of carbohydrate, for animals and on hydrolysis provides glucose molecules for animal. It is found in fruits, grains, seeds and tubers.
Glycogen is generally known as animal starch. It is stored in liver and muscles of animals. It is insoluble in water and converted into glucose on hydrolysis. Cellulose is most abundant carbohydrate in nature. Cotton is the pure form of cellulose. It is main constituent of cell walls of plants and is highly insoluble in water. On hydrolysis it also yields glucose molecules. In herbivores it is digested because of presence of micro organisms like bacteria, yeasts and protozoa in the digestive tract. It is not digested in human digestive tract.
Chitin is major component of exoskeleton of insects and crustaceans. The monomer of chitin is amino sugar comprising of glucose with a nitrogen containing appendage.

Tuesday, August 17, 2010

Acids, Bases and Buffers

Tuesday, August 17, 2010 - 0 Comments

Electrolyte is a substrate that conducts electricity when in solution, such as sodium chloride (NaCl). Many fluids contain strong electrolytes that break down or ionize into ions. Most acid and bases are electrolytes. An acid is a substrate that releases hydrogen ions (H+), when dissolved in water. Hydrogen atom without its electron is only a proton, an acid can be described as a proton donor. One molecule of Hydrogen chloride dissolves in water to produce hydrochloric acid which dissociates into one Hydrogen ion and one chlorine ion.
HCl ====> H+ + Cl-
In contrast, a base (or alkali) is a substrate that releases hydroxyl ions (OH-) when dissolved in water one molecule of sodium hydroxide dissolves in water to produce one sodium ion and one hydroxyl ion.
NaOH ====> Na+ + OH-
When a base dissolves in water it removes free protons (H+) from water and it is proton acceptor
OH- + H+ ====> H2O
pH: Measuring acidity and alkalinity:
Hydrogen and hydroxyl ions often affect the chemical reactions involved with life processes. Therefore the concentrations of these ions in body fluids are important. Higher the concentration of hydrogen ions (H+), more acidic the solution be.
If the concentration of hydroxyl (OH+) ions is higher in a solution, more basic or alkaline the solution is. A solution is neutral when the number of hydrogen ions equals the number of hydroxyl ions.
The pH scale runs from 0 to 14, measures acidity and alkalinity. Acidic solutions have pH less than 7 and basic (alkaline) solutions have pH above 7. A pH of 7 is neutral. Each whole number on pH scale represents a tenfold change (logarithmic) in acidity; therefore a solution with pH of 3 is 10 times more acidic than a solution with pH of 4 and pH of 9 is 10 times more basic than a pH of 8. Actually pH value is equal to negative logarithm of hydrogen ion concentration.
pH = –log [H+] or pH = Log (1/[H+])

pH: Control with Buffers:
Maintenance of stable internal environment in an animal requires constant pH of body fluids. A strong acid or base can destroy cell stability. Like wise sudden change in pH, may also be destructive. Fluid systems of most animals contain chemical substances that help, regulate the acid base balance. These substances called buffers resist changes in pH by accepting H+ ions when they are in excess and donating H+ ions when they are depleted. Most important buffers are bicarbonates, phosphates and organic molecules such as amino acids and proteins.

Carbonic acid – Bicarbonate ion System:
It is important in buffering the blood of many vertebrates. Carbonic acid dissociates to form Hydrogen ion and bicarbonate ion.
H2CO3 <====> H+ + HCO3-
In this example if H+ ions are added to the system, they combine with HCO3 to form H2CO3. This reaction removes H+ ions and keeps pH from changing.

Molecules of animals:
The chemicals that enter into or are produced by metabolic reactions can be divided into two large groups, organic molecules that contain carbon and inorganic molecules without carbon atoms. Most important characteristics of organic molecules depend on properties of key element carbon, the indispensable element for all life. Carbon atom has four electrons in the outermost shell, also requires four electrons to fill its outer orbits. Carbon atoms may share one or two pairs of electrons. When they share one pair of electron, single covalent bond is formed and still leaving carbon atoms to bond with other atoms. In case of ethane C2H6, two Carbons form covalent bond among themselves and the remaining three electrons share with three hydrogen atoms to form additional three single covalent bonds. In case of ethane C2H4, two covalent bonds are formed between two carbons and the remaining two electrons are shared with two hydrogen atoms.

H – C = C
Acetylene

     H     H
       |      |
H - C = C
Ethylene

     H     H
       |      |
H - C - C - H
       |      |
      H    H
Ethane

The ability of carbon to bond with other carbon atoms helps to develop carbon chains or rings of variable length and sizes. Bonds between Carbon and Hydrogen are also source of energy for living organisms Hydrocarbons are organic molecules that contain only carbon and hydrogen. Carbons are bended with each other in a linear fashion. Hydrocarbons form the frame work of all organic molecules.
Carbon chain or ring of many organic molecules provides relatively inactive molecular backbone to which reactive group or atoms are attached. These functional groups of molecules are responsible for molecules unique chemical properties and behaviour.

Compounds and Molecules as Aggregates of Atoms

In addition to being an element, a substance can also be a compound. Compound is composed of atoms of two or more elements chemically united in fixed proportion. For example water has two H atoms and one O atom. This composition does not change that is a compound cannot be separated into its pure components, the atoms of the elements present, except by chemical methods. When atoms interact chemically, electrical forces called chemical bonds hold the atoms together and form molecules like H2, N2, H2O, CO2 etc.

Chemical Bonds:
There are three types of chemical bonds, Covalent, Hydrogen and Ionic which are responsible in making all types of molecules whether smaller or larger, organic or inorganic in nature.

Covalent bonds sharing electron pairs:
When atoms share outer shell electrons with other atoms, the chemical bond that forms is covalent bond. In covalent bonding electrons are always shared in pairs. When a pair of electron is shared from each atom, single bond forms as in hydrogen [H – H] molecule. When two pairs of electrons are shared, double bond forms as in oxygen [O O] molecule and when three pairs of electrons are shared, a triple bond forms e.g. nitrogen [N N] molecule. In a molecule like H2, the electrons spend as much time orbiting one nucleus as the other. The distribution of charges is symmetrical and the bond is called non polar covalent bond. Due to this equal sharing, the molecule is electrically balanced and the molecule as a whole is neutral.

Hydrogen Bonds:
In molecules in which hydrogen combines with certain other atoms like O, N or Fe, Hydrogen electron is drawn toward another atom leaving a proton behind. As a result, Hydrogen atom gains slight positive charge. Remaining proton is attracted to negatively charged atoms of oxygen in nearby molecules. When this happens a weak attraction called Hydrogen bond, forms. Hydrogen atom in one water molecule forms hydrogen bond with oxygen atom in another water molecule and so forth until many molecules bond.

Hydrogen bonds and water Droplets:
Hydrogen bonds form when oxygen atoms of different water molecules weakly join by the attraction of electronegative oxygen for the positively charged hydrogen. Because of the arrangement of electron orbital and the bonding angles between oxygen and hydrogen, the molecule as a whole is polar as it carries a slight negative charge at one end and slight positive charge at the other end. This polarity is responsible for many important properties of water. In other molecules such as H2O where two hydrogen atoms combine with one oxygen atom the electrons spend more time orbiting oxygen nucleus than Hydrogen nuclei. As the electrical charge from the cloud of moving electrons is asymmetrical, the bond is called Polar covalent bond. Such a bond leaves oxygen atom with slightly negative charge and Hydrogen with slightly positive charge, even though the entire molecule is electrically neutral. Shape of water molecule reflects this polarity; rather than the linear arrangement H – O – H, two hydrogen are at one end, a bit like the corners of a triangle. This shape and the polarity can lead to the formation of another kind of chemical bond – the hydrogen bond.

Ionic Bonds: When an atom either gains or loses electrons, it acquires electrical charge and is called an ion. When atom loses one or more electrons, it becomes positively charged because more positively charged protons are now in the nucleus than negatively charged electrons surrounding the nucleus. This positive charge is shown as ‘plus’ sign and is known as cation e.g. Sodium (Na+), Potassium (K+), Hydrogen (H+), Calcium (Ca2+) and iron (Fe3+).
When atom gains one more electrons it becomes negatively charged and is shown as one or more ‘minus’ signs and such charged particle is called anion e.g. chlorine (Cl-), Hydroxyl (OH-), Bicarbonate (HCO3-), Sulphate (So42-), Phosphate (Po43-) and Carboxyl (CO3-).

Ionic Bonds: Ionic bonds form when an atom or group of atoms develop on electrical charge due to loss or gain of electrons. Due to opposite charges these atoms or group of atoms attract each other. A molecule of sodium chloride, the common table salt is formed charge when sodium atom and chlorine atom come together, sodium atom donates an electron to chlorine atom. This electron transfer changes the balance between protons and electrons in each of the two atoms. Sodium atom ends up with one more proton than it has electrons and chlorine atom with one more electron than it has Protons. Sodium atom is left with net charge of +1 (Na+) and net charge of chlorine atoms is -1 (Cl-). These opposite charges attract each other and form ionic bonds.

Atoms and Elements as Building Blocks

Matter occupies space and has mass. It includes solid, liquids and gases of the environment as well as those in the bodies of all forms of life. Mass is the amount of matter in an object. Matter is composed of elements; chemical reactions cannot break down into simpler units. O is symbol for element oxygen, H is symbol for hydrogen, and Na is symbol for sodium. Recently scientists recognise 92 elements occurring in nature. Fifteen elements are found in large quantity in most animals and four of these (carbon, hydrogen, oxygen and nitrogen) account for the majority (97%) of animals’ body weight. Remaining 3% of animals’ weight consists primarily of calcium, phosphorus and potassium. Elements present in trace amount include sodium, sulphur, manganese, magnesium, copper, iodine, iron and chlorine. Elements are composed of units of matter called atoms. Atom is smallest part of an element that can enter into chemical reaction. Atoms vary in size, weight and the diverse ways they interact with each other. For example some atoms can combine with atoms like themselves or with dissimilar atoms, others lack this ability.

Structure of Atom: Atoms have two main parts, a central core called a nucleus and the surrounding electron cloud. Nucleus contains two major particles, positively charged protons (P+) and uncharged neutrons (n). Surrounding the nucleus are negatively charged particles called electrons (e-). Any one electron moves so rapidly around the nucleus that it cannot be found at any given point at any particular movement in time. Therefore its location is given as an electron cloud. Because the number of negatively charged electrons outside the nucleus is equal to the number of positively charged protons, the atom is electrically uncharged or neutral.
Atomic number: The number of protons and neutron in the nucleus and the number and arrangement of electrons in the electron cloud determine an atoms’ chemical and physical properties. The atomic number of an element is the number of protons in the nucleus of one of its atoms. Elements are identified by their atomic number. For example, if an atom has one proton, it is hydrogen; if it has six it is carbon; if it has seven, it is nitrogen and if an atom has eight protons it is oxygen.

Valence: Another measure of an atom is its valance. The valance is the number of bonds an atom will usually form equal to the number of electrons required to complete the outermost that is the valence electron shall.
Atomic mass: Another measure of an atom is its atomic mass. Atomic mass is equal the number of neutrons and protons in the atoms nucleus. Because carbon contains six protons and six neutrons, its atomic mass is 12 and is symbolized with a super script preceding the elements. Symbol 12C and is read as “Carbon – 12”.
Isotopes: All atoms of given element have same number of protons in the nucleus but some have different number of neutrons and thus different atomic masses. These different form with the same atomic number but different atomic masses are isotopes. Most common form of carbon atom has six protons and six neutrons in the nucleus and atomic mass of 12 (12C). A carbon isotope with six protons and seven neutrons has atomic mass of 12 (12C) while carbon isotope with six protons and eight neutrons has atomic mass of 14(14C). Some isotopes like 12C and 13C are stable and do not break down. Other isotopes like 14C are unstable and tend to break down, decay or decompose by periodically emitting small particles and energy. These unstable isotopes are named as radio isotopes or radio active isotopes. Hydrogen has three isotopic forms, each isotope has one proton in each nuclear but have no, one or two neutrons. Hydrogen with no neutron is denoted by 1H; Hydrogen with two neutrons is deuterium and represented by 3H and is radio isotope. Oxygen, iron, cobalt, iodine and phosphorus are examples of elements that have radio active isotopes.
Energy level shells: Electrons of an atom are distributed around its nucleus in orbital called energy level shells or clouds of electrons and are numbered as K, L, M, N. Seven Energy level shells are possible. Each shell can hold only certain number of electrons. The shell nearest to nucleus never has more than two electrons. Second and third shells can each have not more than 8 electrons. Larger number fills the more distant shells. When the shell of an atom holds the maximum number of electrons possible, the shell is complete and stable.

Thursday, August 12, 2010

Scientific Method

Thursday, August 12, 2010 - 2 Comments

Science is an organized and systematic knowledge which is gathered through observations inquiry and experiments. Since function in the realm if matter and energy. The methods of science cannot be applied in areas of investigation involving the aspects of human mind and spirit. Scientific knowledge is neither inherently good nor bad. Same scientific knowledge that gave the nuclear energy and nuclear medicines also gave the nuclear wastes problems for the workers and environment.

            Make Observations
            Formulate a hypothesis
            Design a controlled experiment
            Collect data
            Interpret data
            Draw conclusions
            Consult prior knowledge

Biological method of study: In order to resolve a specific biological problem certain scientific method is adopted in which conclusion or answers to various related questions of biological problem are drawn from observation and experiments. Summary of this method is explained in the flow chart. Here malaria is being considered as an example of biological problems.
(1) Observations: After determination of specific biological problem observations are made to collect relevant information or data. Malaria is dreadful disease whose history goes back to pre birth time of Christ. In ancient days there was no treatment of malaria and large number of people used to die due to this disease. Some historians have attributed the downfall of Greek and Roman empires to this disease. The scientists were struggling to know the cure or treatment of this disease from ancient times. In those days back of cinchona tree was considered to be effective remedy against malaria. At the same time the bad air coming from stagnant ponds was considered to be possible cause of malaria. Some volunteers drank dirty water from the ponds to find the cause but failed. In 1878 French army physician Lavern found small microscope thread like organisms in the blood of malaria patients. These thread like organisms were not present in the blood of healthy person. He called this micro-organism as malarial parasite that was later described and given the name Plasmodium. By this time four major observations for malaria were recorded.
(i) Malaria and marshy places were some how associated. (ii) Quinine from cinchona bark was an effective remedy for malaria. (iii) Malaria parasites always have malarial parasite in their blood. (iv) Drinking marshy water did not cause malaria.
(2) Hypothesis: Observations alone do not usually provide solution to scientific problems. In most of the cases one or more suitable propositions are made on the basis of the observations. These propositions are called hypothesis. The hypothesis are tested by scientific method and the scientific hope that one of the hypothesis would turn out to be the solution of scientific problem under study good hypothesis has the following merits:
(i) It is close to the observed facts.
(ii) The deductions can be drawn from it.
(iii) Deduction should be suitable for testing experimentally.
(iv) Results whether positive or negative should be reproducible.
Every year about 200 million people get malaria and about two million die of it in which most of them are children and pregnant women. Main hypothesis is “Plasmodium is the cause of malaria”. Hypothesis can not be directly tested. Some deductions are made from the hypothesis which is put to test through experimentation.
(3) Deduction: Many deductions may be drawn from hypothesis. Testing one deduction and finding it correct does not mean the hypothesis is correct. The validity of hypothesis is more supported if many deductions confirm the hypothesis. Symptoms of deductions are (i) High fever (106°F) with shivering (ii) Headache and nausea (iii) High breathing rate with increased heart beat (iv) Heavy sweating sometime after high fever leading to normal or below normal temperature (v) Person feels fatigued and exhausted (vi) Recurrence of all above symptoms after specific intervals in absence of proper treatment. Deduction can be tested by experiment.
(4) Experiment: Experimental group is the group of those people who are affected but the real cause is now known e.g. group of malarial patient on the other hand a group of un affected people is called control group e.g. group of healthy people. Both groups are kept in identical conditions. In order to find out the real cause of malaria, experts examined the blood of about 100 malaria patients termed as experimental group, and examined blood of 100 healthy persons known as control group.
(5) Results: Most of the malarial patients had plasmodium in their blood where as the blood of healthy persons was free of plasmodium. These results verified the deduction and thus the hypothesis i.e. the plasmodium is the cause of malaria was proved to great extent. AF. A King in 1883 suggested “Mosquitoes are involved in spreading the malaria”. His observations are (i) People who slept out doors in open spaces suffered more frequently from malaria than those who slept indoors (ii) People who slept under mosquito net did not suffer from malaria. (iii) Persons who slept near smoke fire also did not suffer from malaria.
Opinions of King were further tested by Ronald Ross in 1880 who performed different experiments in order to establish relationship between the work of Lavern and King. After discovery that plasmodium is the cause of malaria, Ronald Ross tried to find out how plasmodium entered the blood of man. He observed that plasmodium was growing and multiplying in the stomach of female. Anopheles mosquito that had bitten a person ill with malaria Ross selected sparrow instead of man for experiments. Malarial parasite (plasmodium) completes its life cycle in two steps. Asexual reproduction is completed in human body and sexual reproduction completed in the body of female Anopheles mosquito. Ross proved that mosquito is the cause of malaria that transferred plasmodium from the blood of one sparrow to the other.

Environment and World Resources

Common environment unites life. In some parts of the world, the land is recovering from decades of abuse. We can compare polluted lake Eric of 1960s to much cleaner lake of 1990s. A lake once unfit for fishing and other recreational uses is now used for these purposes. Tracts of land have been set aside for use as natural and wilderness areas. Many non biodegradable (the substances that cannot be broken down by biological processes) substances have been taken out of market place. These developments and others like them offer hope. Some societies are beginning to realise that all life shares dependence on earth’s resources. Even though there is hope many societies have not abandoned those values that treat land, water and air commodities that can be brought and sold or neglected and abused. The problems are most acute in the developing counties that are striving to attain the same wealth as industrialized nations. In the process the land suffers, population growth goes unchecked, tonic wastes are dumped plant and animal species becomes extinct and deserts and famine expand. Government and private agencies like world watch institute have undertaken large-scale evolution of environmental health of the world. The results of such studies deserve the serious attention of every concerned citizen.
Population:
Global over population in some cause of global problems. Among these human population growth is expected to continue in twenty first century that is around 92% in less developed countries.
Since majority of population will be of child bearing age, growth could even be faster in 21st century. As the human population grows, the disparity between wealthiest and poorest nations will increase.
World Resource: Human over population is stressing world resources. Although new techniques continue to increase food production, most food is produced in industrialized countries that already have high per capita food consumption. Maximum oil production is expected to continue into new millennium to meet the ever increasing needs of energy. Continued use of fossil food adds more carbon dioxide to the atmosphere, contributing to the green house effect and global warning.
Deforestation: The process of cutting or removing the forests of large areas of the world results from continued demand for forest products and fuel. Thus trend contributes to the green house effect causes severe regional water shortage and results in the extinction of many plants and animal species especially in tropical forests. Forest presentation would result in the identification of new species of plants and animals that could be important human resources, new foods and drugs, building material and predators of the pests. Nature also has intrinsic value that is first important as its provision of human resources.
Solution: Above mentioned problems cannot be easily solved, famine and other problems, that accompany over production steps should also be taken towards improved social and economic conditions and better resource management.

Genetic Unity, Evolutionary Oneness and Diversity of Life

All life is based on fundamental molecule Deoxyribose nucleic acid (DNA). This molecule carries genetic codes from all proteins that make up the structural and functional components of life and is passed from generation to generation. Study of DNA molecule is important to know different aspects of life. DNA molecule controls activities of life which bears hydrogen, oxygen, carbon, nitrogen and phosphorus; cell is the fundamental unit of life.
Animals are united at all levels because of their evolutionary origin and shared forces that influence their history. Evolutionary processes are remarkable for their relative simplicity, yet they have some effects on life forms. Evolutionary processes have resulted in an estimated 4 to 30 million species of organisms living today. Out of these 1.4 million species have been described, many existed in the past and have become extinct.
They of organic evolution are the concept that population of organisms change over time.
Charles Darwin (1809 – 1892) described evidence for his theory in the origin of species by means of Natural selection in 1859. By 1900 most biologists were convinced that evolution takes place through natural selection evidences.
Evidences of Evolution:
A number of evidences in favour of evolution are available some of these are as follows:
(1) Biogeography: It is the study of geographical study of plants and animals. Biogeographers try to explain why organisms are distributed as they are. Biogeographic studies show that life forms in different parts of the world have distinctive evolutionary histories. One of the distribution patterns that biogeographers try to explain is how similar groups of organisms can live in places separated by seemingly impenetrable of most continents of the earth, yet they cannot cross wide open oceans. Similarities in morphology suggest common ancestry but similarly obvious differences result from millions of years of independent evolution. Geographers also try to explain why plants and animals separated by geographical barriers like ocean, sea, rivers, streams, mountains, deserts and forests etc are often very different inspite of similar environments e.g. animals living in Australia and Tasmania are very different from animals in any other part of the world. Major native herbivores of Australia and Tasmania are many species of Kangaroo. Tasmania wolf known as tiger now considered being extinct was predatory marsupial that was unlike any other large predator.
(2) Paleontology: It is based on study of fossil record, provides direct evidences for evolution. Fossils are the evidences of plants and animals that existed in the past have become incorporated into earth’s crust in the form of rocks or minerals. Paleontologists estimate that the earth is about 4.6 billion years old. They have also used the fossil record to describe the history of life on the earth.
(3) Comparative anatomy: A structure in one animal may resemble a structure in another animal because of common evolutionary origin. Structures or organs derived from common ancestry are called homologous organs and its study is known as homology. Homologous organs have same or similar origin and perform same functions e.g. vertebrate appendages have common arrangements of similar bones even though the function of appendages may vary. This indicates that vertebrates have evolved from common ancestor convergent evolution occurs when two unrelated organisms adapt to similar conditions e.g. wing of a bird and wing of an insect are both adapted for flight but they are not homologous. Being homologous these structures are analogous that is having similar function but dissimilar origin.
Organisms often retain structures that have lost their usefulness. These structures are poorly developed and are called vestigial structures e.g. boa constrictors have minute remnants of hind limbs bones left over from appendages of their reptilian ancestors. Such remnants of once useful structures are clear indications of evolution.
(4) Molecular biology: It has provided important information on evolutionary relationships. Structure and function are based on genetic blue print found in all living animals in the form of DNA molecule related animals have similar DNA derived from common ancestor. Because DNA carries the codes for proteins that make up each animal, related animals have similar proteins. Evolutionary theory has impressed biologist to believe with fundamental unity of all of biologists.

Tuesday, August 10, 2010

Parallel Axis Theorem

Tuesday, August 10, 2010 - 0 Comments

Parallel Axis Theorem:
In physics, the parallel axis theorem or Huygens-Steiner theorem can be used to determine the moment of inertia of a rigid body about any axis, given the moment of inertia of the object about the parallel axis through the object’s center of mass and the perpendicular distance between the axes.
The moment of inertia about the new axis z is given by:
Iz = Icm + md2
Where:
Icm is the moment of inertia of the object about its center of mass;
m is the object’s mass;
d is the perpendicular distance between the two axes.
This rule can be applied with the stretch rule and perpendicular axis theorem to find moments of inertia for a variety of shapes.
The parallel axes rule also applies to the second moment of area (area moment of inertia) for a plane region D:
Iz = Ix + Ad2,
Where:
Iz is the area moment of inertia of D relative to the parallel axis;
Ix is the are amoment of inertia of D relative to its centroid;
A is the area of the plane region D;
d is the distance from the new axis z to the centroid of the plane region D.
Note: The centroid of D coincides with the center of gravity (CG) of a physical plate with the same shape that has constant density.
In classical mechanics
In classical mechanics, the Parallel axis theorem (also known as Huygens-Steiner theorem) can be generalized to calculate a new inertia tensor Jij from an inertia tensor about a center of mass Iij when the pivot point is a displacement a from the center of mass:
Jij = Iij + m (a2δij – aiaj)
where
a = a1x + a2y + a3z (where x, y, and z are unit vectors)
is the displacement vector from the center of mass to the new axis, and
δij
is the Kronecker delta.
We can see that, for diagonal elements (when i=j), displacements perpendicular to the axis of rotation results in the above simplified version of the parallel axis theorem.

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