STORAGE POLYSACCHARIDE- STARCH

STORAGE POLYSACCHARIDE - STARCH 

• Starches are glucose polymers in which glucopyranose units are bonded by alpha-linkages.
• It is made up of a mixture of amylose(15%-20%) and amylopectin (80%- 85%).
• Amylose consists of a linear chain of several hundred glucose molecules and amylopectin is a branched molecule made of several thousand glucose units(every chain of 24-30 glucose units is one unit of amylopectin).Starches are insoluble in water.
• They can be digested by hydrolysis, catalysed by enzymes called amylases, which can break the alpha-linkages(glycosidic bonds).
• Humans and other animals have amylases, so they can digest starches. Potato, Rice, Wheat, and maize are major sources of starch in the human diet.
• It is exclusively formed in plants and not in Animals.

Figure: Amylopectin is a glucose polymer with mainly a(1-->4) linkages, but it also has branches formed by a(1--->6) linkages. The branches are generally longer than shown above. The branches produce a compact structure, and provide multiple chain ends at which enzymatic cleavage of the polymer can occur. 

Figure: Amylose is a linear polymers of glucose mainly linked with a(1-->4) bonds. It can be made of several thousands of glucose units. It is one of the two components of starch, the other being amylopectin.

POLYSACCHARIDES OR OLIGOSACCHARIDES

POLYSACCHARIDES OR OLIGOSACCHARIDES 

• Polysaccharide is an important class of biological polymers. Their function in living organisms is usually either structure- or storage-related.
• Starch is a polymer of glucose is used as a storage polysaccharide in plants, being found in the form of both amylose and the branched amylopetcin.
• In Animals, the structurally similar glucose polymer is the more densly branched glycogen, sometimes called 'animal starch'.
• Glycogen's properties allow it to be metabolized more quickly, which suits the active lives of moving animals.
• Structural Polysaccharides: Cellulose, Pectin and Chitin
• Cellulose is used in the cell walls of plants and other organisms, and is said to be the most abundant organic molecule on earth.
• It has many uses such as a significant role in the paper and textile industries, and is used as a feedback for the production of rayon (via viscose process),cellulose acetate, celluloid, and nitrocellulose.
• Chitin has a similar structure, but has nitrogen-containing side branches, increasing its strength. It is found in arthropod exoskeletons and in the cell walls of some fungi.
• Chitin is also has multiple uses, including surgical threads.
• Polysaccharides also include callose or laminarin, chrysolaminarin, xylan, arabinoxylan, mannan, fucoidan, and galactomannan.
• Monosaccharides can be linked together into polysaccharides(or Oligosaccharides)in a large variety of ways.
• Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed.
• Pectins are a family of complex polysaccharide that contain 1,4-linked α-D-galactosyluronic acid residues.
• They are present in most primary cellwalls and in the non-woody parts of terrestrial plants.

STORAGE POLYSACCHARIDE-GLYCOGEN

• Glycogen serves as the secondary long-term energy storage in animals and fungal cells, with the primary energy stores being held in adipose tissue.
• Glycogen is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach.
• Glycogen is the analogue of starch, a glucose polymer in plants, and is sometimes referred to as animal starch, having a similar structure to amylopectin but more extensively branched and compact than starch.
• Glycogen is a polymer of α(1--->4) glycosidic bonds linked, with α(1--->6)-linked branches.
• Glycogen is found in the form of granules in the cytosol/cytoplasm in may cell types, and plays an important role in the glucose cycle.
• Glycogen forms an energy reserves that can be quickly mobilized to meet a sudden need for glucose, but one that is less compact than the less immediately available energy reserves of triglycerides(lipids).
• In the Liver hepatocytes, glycogen can compose up to eight percent(100-120 g in an adult) of the fresh weight soon after a meal.
• Only glycogen stored in the liver can be made accessible to other organs. In the muscles, glycogen is found in the kidneys, and even smaller amounts in certain glial cells in the brain and white blood cells.
• The Uterus also stores glycogen during pregnancy, to nourish the embryo.
• Glycogen is composed of a branched chain of glucose residues. It is stored in liver and muscles.

          1. It is an energy reserves for animals.

          2. It is the chief form of carbohydrate stored in animal body.

          3. It is insoluble in water. It turns red when mixed with iodine.

          4. It also yields glucose on hydolysis.

 DISACCHARIDES

• When the alcohol component of a glycoside is provided by a hydroxyl function on another monosaccharide, the compound is called a Dissacharide.
• Ex. Cellulose : 4-O-β-D-Glucopyranosyl-D-Glucose(the beta-anomer is drawn)
• Maltose : 4-O- α-D-Glucopyranosyl-D-Glucose (the beta-anomer is drawn)
• Gentiobiose : 6-O-β-D-Glucopyranosyl-D-Glucose (the alpha-anomer is drawn)
• Trehalose : α-D-Glucopyranosyl-α-D-Glucopyranoside
• Although all the disaccharides shown here are made up of two glucopyranose rings, their properties differ in interesting ways.
• Maltose, sometimes called malt sugar, comes from the hydrolysis of starch. It is about one third as sweet as cane sugar(Sucrose),is easily digested by humans, and is fermented by yeast. 
•  Cellobiose is obtained by the hydrolysis of cellulose.
• It has virtually no taste, is indigestible by humans, and is not fermented by yeast.
•  Some bacteria have beta-glucosidase enzymes that hydrolyse the glycosidic bonds in cellobiose and cellulose. 
• The presence of such bacteria in the digestive tracts of cows and termites permits these animals to use cellulose as a Food. 
• Finally, it may be noted that trehalose has a distinctly sweet taste, but gentiobiose is bitter.

Figure. A four examples of disaccharides composed of two glucose units are shown

• Disaccharides made up of other sugars are known, but glucose is often one of the components. 
• Two important examples of such mixed disaccharides will be displayed above by clicking on the diagram.
• Lactose, also known as milk sugar, is a galactose-glucose compound joined as a beta-glycoside.

Figure. Lactose is a disaccharide found in milk.

• It is a reducing sugar because of the hemiacetal function remaining in the glucose moiety. Many adults, particularly those from regions where milk is not a dietary staple, have a metabolic intolerance for lactose.
• Infacts have a digestive enzyme which cleaves the beta-glycoside bond in lactose, but production of this enzyme stops with weaning.
• Cheese is less subject to the lactose intolerance problem, since most of the lactose is removed with the whey.
• Sucrose, or cane sugar, is our most commonly used sweetening agent. It is a non-reducing disaccharide composed of glucose and fructose joined at the anomeric carbon of each by glycoside bonds(one alpha and one beta).
• In the formula shown here the fructose ring has been rotated 180° from its conventional perspective.

Microbiology terms and definitions from Y

 MICROBIOLOGY TERMS AND DEFINITIONS FROM Y

Yaws definition

• A tropical disease caused by Treponema pertenue that produces granulomatous ulcers on the extremities and occasionally on the bone but does not produce a central nervous system or cardiovascular complications. (Foundation in Microbiology by Talaro and Chess)

Yeast definition

• (1) A type of unicellular, nonfilamentous fungus that resembles bacterial colonies when grown in culture. (2) A term sometimes used to denote the unicellular form of pathogenic fungi. (Alcamo’s Fundamentals of Microbiology)
• The single-celled growth form of various fungi. (Brock Biology of Microorganisms)
• Single-celled, budding fungi. (Foundation in Microbiology by Talaro and Chess)
• Nonfilamentous, unicellular fungi. (Microbiology: An Introduction by Tortora, Funke, and Case)
• A unicellular, uninuclear fungus that reproduces either asexually by budding or fission, or sexually through spore formation. (Prescott’s Microbiology)

Yeast Artificial Chromosome (YAC) definition

• A genetically engineered chromosome with yeast origin of replication and centromere sequence. (Brock Biology of Microorganisms)
• Engineered DNA that contains all the elements required to propagate a chromosome in yeast and is used to clone foreign DNA fragments in yeast cells. (Prescott’s Microbiology)

Yeast infection definition

• Disease caused by the growth of certain yeasts in a susceptible host. (Microbiology: An Introduction by Tortora, Funke, and Case)

Yellow fever definition

• Best-known arboviral disease. Yellow fever is transmitted by mosquitoes. Its symptoms include fever, headache, and muscle pain that can proceed to oral hemorrhage, nosebleeds, vomiting, jaundice, and liver and kidney damage. (Foundation in Microbiology by Talaro and Chess)

 

MICROBIOLOGY TERMS AND DEFINITIONS FROM X

X-factor definition

• Substances from the heme fraction of blood hemoglobin. (Microbiology: An Introduction by Tortora, Funke, and Case)

X-ray definition

• The ionizing radiation that can be used to sterilize objects. (Alcamo’s Fundamentals of Microbiology)

Xenobiotic definition

• A synthetic compound not produced by organisms in nature. (Brock Biology of Microorganisms)
• Synthetic chemicals that are not readily degraded by microorganisms. (Microbiology: An Introduction by Tortora, Funke, and Case)

Xenodiagnosis definition

• A method of diagnosis based on exposing a parasite-free normal host to the parasite and then examining the host for parasites. (Microbiology: An Introduction by Tortora, Funke, and Case)

Xenograft definition

• A tissue graft between members of different species, such as between a pig and a human. (Alcamo’s Fundamentals of Microbiology)
• The transfer of a tissue or an organ from an animal of one species to a recipient of another species. (Foundation in Microbiology by Talaro and Chess)
• A tissue graft from another species. (Microbiology: An Introduction by Tortora, Funke, and Case)
• A tissue graft between animals of different species. (Prescott’s Microbiology)

Xerophile definition

• An organism adapted to growth at very low water potentials. (Brock Biology of Microorganisms)
• Microorganisms that grow best under low water activity (aw) conditions, and may not be able to grow at high aw values. (Prescott’s Microbiology)

STRUCTURE AND FUNCTIONS

 STRUCTURE AND FUNCTION

Formerly the name "carbohydrate" was used in chemistry for any compound with the formula Cm(H2O)n. Following this definition, Some chemists considered formaldehyde(CH2O) to be the simplest carbohydrate while other claimed that title for glyceraldehyde Today the term is generally understood in the biochemistry sense, which exclude compounds with only one or two carbons.

MONOSACCHARIODES

• Natural saccharide are generally built of simple carbohydrates called monosaccharides with general formula (CH2O)n where n is three or more.
• A typical monosaccharide has the structure H-(CHOH)x(C=O)-(CHOH)y-H, that is, an aldehyde or ketone with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group.
• Examples of monosaccharides are Glucose, Fructose and Glyceraldehyde. However, Some Biological Substances Commonly called "Monosaccharide" do not conform to this formula(e.g; Uronics Acids and  Deoxy-Sugars Such as fucose), and there are many chemicals that do conform to this formula but are not considered to be monosaccharides (e.g; Formaldehyde CH2O and inositol(CH2O)6)
• The open-chain form of a monosaccharide often coexists with a closed rong form where the aldehyde/ketone carbonyl group carbon(C=O) and hydroxyl group (-oh) react forming a hemiacetal with a new C-O-C bridge.

α-D-Glucopyranose

 HAWORTH PROJECTION

• The Three Dimensional structure of a monosaccharide in cyclic form is usually represented by its Haworth Porjections.
• In the Diagram, the α-isomer has the -OH of the anomeric carbon below the plane of the carbon atoms, and the β-isomer has the-OH of the anomeric carbon above the plane.

• Pyranose typically adopt a chair Conformation,similar to cyclohexane. In this conformation, the α-isomer has the -OH of the anomeric carbon in an axial position, whereas the β-isomer has the OH- of the anomeric carbon in equatorial position.

COMPOSITION,STRUCTURE AND FUNCTION OF BIOMOLECULES

 1.2 COMPOSITION,STRUCTURE AND FUNCTION OF BIOMOLECULES 

BULLET POINTS

• There are four major classes of biomolecules - Carbohydrates, Proteins, Nucleotides and Lipids.
• carbohydrates, or Saccharides, are the most abundant of the four. Carbohydrates have several roles in living organisms, including energy transportation, as well as being structural components of plants and arthropods.
• Carbohydrate derivatives are actively involved in fertilization, immune systems, and the development of diseases, blood clotting and development.
• Carbohydrates are called carbohydrates because the carbon, oxygen and hydrogen they contain are generally in proportion to form water with general formula Cn(H2O)n.
• Carbohydrates (saccharides)- Molecules consist of carbon, hydrogen and oxygen atoms. 
• A major polymers, carbohydrates can function as long term food storage molecules, as protective membranes for organisms and cells, and as the main structural support for plants and constituents of many cells and their contents.
• Lipids (fats) - Molecules consist of carbon, hydrogen and oxygen atoms. 
• The main constituents of all membranes in all cells (cell walls), food storage molecules, intermediaries in signalling pathways, vitamin A,D,E and K, cholestrol.
• Proteins - molecules contain nitrogen, carbon, hydrogen and oxygen. They act as biological catalyst (enzymes), form structural parts of organisms, participate in cell signal and recognition factors, and act as molecules of immunity. proteins can also be a source of fuel.
• Nucleic Acids(Nucleotides) - DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid).These molecules are involved in genetic information, as well as forming structure within cells.
• They are involved in the storage of all heritage information of all organisms, as well as the conversion of this data into proteins. 

1.2.1 CARBOHYDRATES

    Carbohydrates are one of the main types of nutrients. They are the most important source of energy for your body. Your digestive system changes carbohydrates into glucose( Blood Sugar). 

Your body uses this sugar for energy for your cells, tissues and organs. It stores any extra sugar in your liver and muscles for when it is needed.

Carbohydrates are called simple or complex, depending on their chemical structure. Simple Carbohydrates include Sugars found naturally in foods such as Fruits, vegetables, Milk and Milk products.

They also include Sugars added during food processing and refining. Complex Carbohydrates include whole grain breads and cereals, Starchy vegetables and Legumes.

Many of the complex Carbohydrates are good sources of Fibre. For a Healthier Diet, limit the amount of added Sugar that you eat and choose whole grains over refined grains.

The Term is Most common in Biochemistry, it is called Saccharide. The Carbohydrates (Saccharides) are divided into four chemical grouping:

1. Monosaccharide

2. Disaccharide

3. Oligosaccharide

4. Polysaccharide

In general, the Monosaccharides and disaccharides,  which are smaller ( lower molecular weight). Carbohydrates, are commonly reffered to as sugars. while the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix-ose. For example, grape sugar is the monosaccharide glucose, cane sugar is the dissacharide sucrose, and milk sugar is the disaccharide lactose.

CHEMICAL BONDS 

A Chemical bond is an attraction between atoms. This attraction may be seen as the result of different  behaviours of the outermost electrons of atoms. Although all of these  behaviours merge  into each other seamlessly in various bonding situations so that there is no clear line to be drawn between them, nevertheless behaviours of atoms become so qualitatively different as the character of the bond changes quantitatively, that it remains useful and customary to differentiate between the bonds that cause these different properties of condensed matter.

'Covalent Bond' : one or more electrons (often a pair of electrons) are drawn into the space between the two atomic nuclei.

Here, the negatively charged electrons are attracted to the positive charges of both nuclei, instead of just their own. This overcomes the repulsion between the two positively charged nuclei of the two atoms, and so this overwhelming attraction holds the two nuclei in a fixed configuration of equilibrium, even though they will still vibrate at equilibrium position. 

Thus, covalent bonding involves sharing of electrons in which the positively charged nuclei of two or more atoms simultaneously attract the negatively charged  electrons that are being shared between them.

These bonds exist between two particular identifiable atoms, and have a direction in space, allowing  them to be shown as single connecting lines between atoms in drawing , or modelled as sticks between sphere in models. In a polar covalent bonds, one or more electrons are unequally shared between two nuclei.

Covalent bonds often result in the formation of small collection of better -connected atoms called  molecules, which in solids and liquids are bound to other molecules by forces that are often much weaker than the covalent bonds that hold the molecules internally together.

Such weak intermolecular bonds give organic molecular substances, such as waxes and oils, their soft bulk character, and their low melting points (in liquids, molecules must cease most structured or oriented contact with each other).

When covalent bonds link long chains of atoms in large molecules, however (as in polymers such as nylon), or when covalent bonds extend in networks though solids that are not composed of discrete molecules (such as diamond or quartz or the silicate minerals in many types of rock) then the  structures that result may be both strong and tough, at least in the direction oriented correctly with networks of covalent bonds. Also, the melting points of such covalent polymers and networks increase greatly.

Ionic bonds: the bonding electron is not shared at all, but transfered . In this type of bond, the outer atomic orbital of one atom has a vacancy which allows addition of one or more electrons. These newly added electrons potentially occupy a lower energy-state (effectively closer to more nuclear charge) than they experience in different atom.

Thus, one nucleus offers a more tightly bound position to an electron than does another nucleus, with the result that one atom may transfer an electron to the other.

This transfer causes one atom to assume a net positive charge, and the other to assume  a net negative charge. The bond then result from electrostatic attraction between atoms, and  the atoms become positive or negatively charged ions. 

Ionic bonds may be seen as  extreme examples of polarization in covalent bonds. often, such bonds  have no particular orientation in space, since they result from equal electrostatic attraction of each ion to all ions around them.

Ionic Bonds are strong (and thus ionic substances require high temperature to melt) but also brittle, since the forces between ions are short-range, an do not easily bridge cracks and fractures.

This type of bond gives a characteristic physical  character to crystals of classic minerals salts, such as table salt.

Metallic Bond:  

In this type of bonding, each atom in a metal donates one or more electrons to a "Sea" of electrons that reside between many metals atoms. In this sea, each electron is free (by virtue of its wave nature) to be associated with a great many atoms at once.

The bond results because the metal atoms become somewhat positively charged due to loss of their electrons, while the electrons remain attracted to many atoms, without being part of any given atom.

Metallic Bonding may be seen as an extreme example of delocalization of electrons over a large system of covalent bonds, in which every atom participates. This type of bonding is often very strong (resulting in the tensile strength of metals).

However, metallic bonds are more collective in nature than other types, and so they allow metal crystals to more easily deform, because they are composed of atoms attracted to each other, but not in any particularly-oriented ways.

This results in the malleability of metals. The sea of electrons in metallic bonds causes the characteristically good electrical and thermal conductivity of metals, and also their "shiny" reflection of most frequencies of white light.

Aromatic (aryl) compounds:

• An aromatic (or aryl) compound contains a set of covalently bound atoms with specific characteristics
• A delocalized conjugated π system, most commonly an arrangement of alternating single and double bonds.
• Coplanar structure, with all the contributing atoms in the same plane 
• contributing atoms arranged in one or more rings.
• A number of  π delocalized electrons that is even, but not a multiple of 4.That is, 4n+2 number of  π electrons, where n=0,1,2,3, and so on. This is known as Huckel's Rule.

All bonds can be explained by quantum theory, but, in practice, simplification rules allow chemist to predict the strength, directionality, and polarity of bonds.

The octet rule and VSEPR theory are two examples. More sophisticated theories are valence bond theory which includes orbital hybridization an d resonance, and linear combination of atomic orbitals molecular orbital method which includes ligand field theory. 

Electrostatics are used to describe bond polarities and the effects they have on chemical substances.

Understanding Biochemistry

There are two common ( and equivalent ) ways to describe molecular mass; both are used. The first is molecular weight , or relative molecular mass, denoted Mr.

The Molecular weight of a substance is defined as the ratio of the mass of a molecule of that substance to one-twelfth the mass of carbon-12(12C).Since Mr is a ratio, it is dimensionless- it has no associated units.

The second is molecular mass, denoted m. This is simply the mass of one molecule, or the molar mass divided by Avogadro's number.

The molecular mass, m, is expressed in daltons(abbreviated as Da). one Daltons is equivalent to one-tweflth the mass of carbon-12; a kilodalton (kDa) is 1000daltons; a megadaltons (MDa) is 1 million daltons.

Consider, for example, a molecule with a mass 100 times that of water. we can say of this molecule either Mr=18,000 or m= 18,000 daltons is incorrect.

Another convenient unit for describing the mass of a single atom or molecule is the atomic mass unit (formerly amu, now commonly denoted u). 

One atomic mass unit (1u) is defined as one- twelfth the mass of an atom of carbon-12.Since the experimentally measured mass of an atom of carbon-12 is 1.9926 x 10power 23 g, 1u= 1.6606 x10-24 g, The atomic mass unit is convenient for describing the mass of a peak observed by mass spectrometry.

Table-1.3: Typical biond lenghths in pm and bond energies inkj/mol.Bond lengths can be converted to Armstrong by division by 100 (1Armstrong = 100 pm)

figure1.7: Benzene the most widely recognized aromatic compound with six (4n+2,n=1) delocalized electrons

 

 STRUCTURE OF MOLECULES

The Three dimensional shape or configuration of a molecule is an important characteristics. This shape is dependent on the preferred spatial orientation of covalent bonds to atoms having two or more bonding partners.

Three dimensional configurations are best viewed with the aid of models. In order to represent such configurations on a two-dimensional surface (paper, blackboard or screen), we often use perspective drawing in which the direction of a bond is specified by the line connecting the bonded atoms. In most cases, the focus of configuration is a carbon atom so the lines specifying bond directions will originate there. 

As defined in the diagram on the right, a simple straight line represents a bond lying approximately in the surface plane. The two bonds to substituents A in the structure on the left are of this kind. A wedge shaped bond is directed in front of this plane (thick end towards the viewer), as shown by the bond to substituent B and a hatched bond is directed in back of the plane ( away from the viewer), as shown by the bond to substituents D.

Some texts and other Sources may use a dashed bond in the same manner as we have defined the hatched bond, but this can be confusing because the dashed bond is often used to represent a partial bond(i.e. a covalent bond that is partially formed or partially broken).

The following examples make use of this notation, and also illustrate the importance of including non-bonding valence shell electron pairs when viewing such configurations.

Bonding configurations are readily predicted by valence-shell  electron-pair repulsion theory common referred to as VSEPR in most introductory chemistry texts.

This simple model is based on the fact that electrons repel each other, and that it is reasonable to expect that the bonds and non-bonding valence electron pairs associated with a given atom will prefer to be as far apart as possible. 

The bonding configurations of carbon are easy to remember, since there are only three categories.

In the three examples shown in table 1.2, the central atom (carbon) does not have any non-bonding valence electrons; consequently the con figuration may be estimated from the number of bonding partners alone. For molecules of water and ammonia, however, the non-bonding electrons must be included in the calculation.

In each case there are four regions of electron density associated with the valence shell so that a tetrahedral bond angle is expected. The measured bond angles of these compounds (H2O 104.5° & NH3 107.3°) show that they are closer to being tetrahedral than  trigonal or linear. Of course, it is the configuration of atoms (not electrons) that defines the shape of a molecule, and in this sense ammonia is said to be pyramidal (not tetrahedral). The compound boron trifluoride, BF3, does not have non-bonding valence electrons and the configuration of its atoms is trigonal.

The best way to study the three-dimensional shapes of molecules is by using molecular models. Many kinds of model kits are available to student and professional chemists. Some of the useful features of physical models can be approximated by the model viewing applet Jmol. This powerful visualization tool allows the user to move a molecular structure in any way desired. Atom distances and angles are easily determined.

To measure a distance, double-click on two atoms. To measure a bond angle, do a double-click, single-click, double-click on three atoms. To measure a torsion angle, do a  double-click, single-click, single-click, double-click on four atoms.

A pop-up menu of commands may be accessed by the right button on a PC or a control-click on a mac while the cursor is inside the display frame.

One way in which the shapes of molecules manifest themselves experimentally is through molecular dipole moment. A molecule which has one or more polar covalent bonds may have a dipole moment as a result of the accumulated bond dipoles. 

In the case of water, we know that the O-H covalent bond is polar, due to the different electronegativities of hydrogen and oxygen. Since there are two O-H bonds in water, their bond dipoles will interact and may result in a molecular dipole which can be measured. The following diagram shows four possible orientations of the O-H bonds.

In the Linear configuration (bond angles 180°) the bond dipoles cancel, and the molecular dipoles is zero. For the other bond angles(120 to 90°) the molecular dipole would vary in size, being largest for the 90° configuration.

In a similar manner the configurations of methane (CH4) and carbon dioxide (CO2) may be deduced from their zero molecular dipole moments. Since the bond dipoles have cancelled, the configuration of these molecules must be tetrahedral (or square- planar) and linear respectively.

The case of methane provides insight to other arguments that have been used to confirm its tetrahedral configuration. For purpose of discussion we shall consider three other configurations for CH4, square-planar, Square-pyramidal and triangular-pyramidal.

Substitution of one hydrogen by a chlorine atom gives a CH3Cl compound. Since the tetrahedral, Square-planar, and Square-pyramidal configurations have structurally equivalent hydrogen atoms, they would each give a single substitution product.

However, in the trigonal-pyramidal configuration one hydrogen( the apex) is structurally different from the other three ( the pyramid base). Substitution in this case should give two different CH3Cl compounds if all the hydrogen react. In the case if di-substitution, the tetrahedral configuration of methane would lead to a single CH2Cl2 product, but the other configurations would give two different CH2Cl2 compounds. These substitution possibilities are shown in the above insert.

MOLECULES

 1.1.2 MOLECULES

A molecule is an electrically neutral group  of two or more atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their lack of electrical charge. However, in quantum physics, organic chemistry and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions.

In the kinetic theory of gases, the term molecule is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules despite being composed of a single non-bonded atom.

• A molecule may be homonuclear, that is, it consists of atoms of a single chemical element, as with water (H2O).
• Atoms and complexes connected by Non-covalent bonds such as Hydrogen Bonds or Ionic Bonds are generally not considered single molecules
• Molecules as components of matter are common in organic substances( and therefore biochemistry).
• They also make up most of the oceans and atmosphere. However, the majority of Familiar Solid Substances on Earth, including most of the minerals that make up the Crust, Mantle, and Core of the Earth, Contain many Chemical Bonds, But are not made of identifiable molecules.
• Also, no typical molecule can be defined for ionic crystals (salts) and Covalent Crystals (Network Solid),although these are often composed of repeating unit cells that extend either in a plane (Suchas in Graphene) or three-dimensionally (Such as in Diamond. Quartz, or Sodium Chloride).
• The theme of Repeated Unit-Cellular-Structure also holds for most condensed phases with metallic bonding, which means that Solid metals are also not made of molecules.
• In glasses (Solids that exist in a vitreous disordered state), atoms may also be held together by chemical bonds without presence of any  definable molecule, but also without any of the regularity of repeating units that characterises crystals.

                                                    NEXT PAGE