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.

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RADIOACTIVE DECAY

• Every  Element has One or More Isotopes that have Unstable Nuclei that are Subject to radioactive decay, causing the Nucleus to emit particles or Electromagnetic radiation.
• Radioactivity can occur when the Radius of a Nucleus is large compared with the radius of the Strong forces, which only acts over distances on the order of 1fm.  

• THE MOST COMMON FORMS OF RADIOACTIVE DEACY ARE: 

•  ALPHA decay is caused when the nucleus emits an alpha particle, which is a helium nucleus consisting of two protons and two Neutrons.
• The result of the emission is a new element with a lower atomic number.
•  BETA decay (and electron capture) are regulated by the weak forces, and result from a transmission of neutron into a proton, or a proton into a neutron.
• The first is accompained by the emission of an electron and an antineutrino. 
• while the second causes the emission of a position and a neutrino.
• The Electron or positron emission are called beta particles.
• Beta  decay either incerases or decreases  the atomic number of the nucleus by one.
• An analog of  positron beta decay in nuclei that are proton-rich is electron capture, a process even more common than positron emission since it requires less energy.
• In this type of decay an electron is absorbed by the nucleus, rather than a positron emitted.
• A neutrino is still emitted in this process, and a proton again changes to a neutron.
• GAMMA decay results from a change in the energy level of the nucleus to a lower state, resulting in the emission of electromagnetic radiation.
• This can occur following the emission of an alpha or a beta particle form radioactive decay.

• Other more rare type of radioactive decay include ejection of neutrons or protons or clusters of nucleons from a nucleus, or more than one beta particle, or result (through internal conversion) in production of high-speed electrons that are not beta rays, and high-energy photons that are not gamma rays.
• A few large nuclei explode into two or more charged fragments of varying  masses plus several neutrons, in a decay called spontaneous nuclear fission. 
• Each radiactive isotope has a characteristic decay time period - the half-life - that is determined by the amount of time needed for half of a sample to decay.
• This is an exponential decay process that steadily decreases the proportion of the remaining isotope by 50% every half-life.
• Hence, after two half-lives have passed only 25% of the isotope is present, and so forth.

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WHAT DOES AN ATOM LOOKS LIKE ?

 

 WHAT DOES AN ATOM LOOKS LIKE ?

• Protons and Neutrons are held together rather closely in the centre of Atom.
• Together they make up the Nucleus,which accounts for Nearly all of the Mass of the Atom.
• Electrons move rapidly around the Nucleus and constitute almost the entire volume of atom.
• Quantum mechanics are required to explain the motion of an electron about the nucleus, we can say that the Distribution of Electrons about an atom is such that the distribution of electrons about an atom is such that the atom has a spherical shape.                  

• Atoms have sizes on the order of 1-5 Armstrong(1 armstrong = 1A = 1 x 10 power -10 m) and Masses on the order of 1-300 Armstrong(a.m.u)
• The Mass and dimension of the Atoms into perspectively consider the following analogies.
• If an only be the size of ohion stadium,the nucleus would only be the size of small marble.however, the mass of that marble would be ~115 million tons.               

 WHAT HOLDS AN ATOM TOGETHER?

• The Negatively charged electron is attracted to the positively charged nucleus by a columbic Attraction.
• The Proton and Neutrons are held together in the Nucleus by the Strong Nuclear Forces.

HOW MANY ELECTRONS,PROTONS AND NEUTRONS ARE CONTAINED IN AN ATOM?

• Atoms in their nautral state have no charge that is they are neutral. Therefore, in a neutral atom the Number of Protons and Electrons are the Same.If this condition is voilated the Atom has a Net charge and is called an Ion.
• The Number of Protons in the Nucleus determines the identity of the  Atom. For example, All Carbon Atoms contain six protons, all gold Atoms Contains 79 Protons, and  all leads atoms contain 82 protons.
• Two atoms with the Same Number of Protons, but different numbers of Neutrons  are called Isotopes.

HOW DOES THE STUCTURE OF THE ATOM RELATED TO ITS PROPERTIES?

• Chemical Reactions involve either the Transfer or the Sharing of Electrons between Atoms.
• Therefore, the chemical reactivity/properties of an element is primarily dependent upon the Number of Electrons in an atom of that Element .
• Protons Also play a Significant Role because the Tendency for an atom to either Lose or Gain or Share electrons is dependent upon the charge of the Nucleus.
• Therefore,we can say that the Chemical Reactivity of an atom id dependent upon the Number of Electrons and Protons, and independent of the Number of Neutrons.
• The Mass and Radioactive properties of an atom are Dependent upon the Number of Proton and Neutrons in the Nucleus.

NOTE: The Number of protons, Neutrons and Electrons in an Atom completely determine its properties and identity, regardless of how and where the atom was made. So, it is inaccurate to speak of synthetic atoms and natural atoms. In other words, A lead Atom is lead Atom, it does not matter if was mined from the Earth, produced in a Nuclear Reactor, or came to the Earth on an Asteroid.

SYMBOLISM

• There is a Symbolism or shorthand for Describing atoms which is Universally used across all Scientific Disciplines
• Atomic Number (Z) The # of Protons
• Mass Number (A) [The # of Protons]+[The # of Neutrons]
• The number of Protons, Neutrons and Electrons in an Atom are Uniquely specified by the Following symbol example diagram

• where X = The Element symbol (i.e; C,N,Cr) defines the # of Protons. 

•  A = The Mass Number [# of protons]+[# of neutrons]

•  Z = The Net Charge [# of Protons]+[# of Electrons]

 

MOLECULAR AND THEIR INTERACTION RELAVENT TO BIOLOGY

BIOCHEMISTRY NOTES  

MOLECULAR AND THEIR INTERACTION RELAVENT TO BIOLOGY

1. STRUCTURE OF ATOMS,MOLECULES AND CHEMICAL BONDS.

BULLET POINTS:

• ATOMS ARE SMALLEST MOLECULES WHICH WE COME ACROSS OFTEN.
• AN ATOM CONTAINS  PROTON, NEUTRONS AND ELCTRONS.
• MOLECULES AGGREGATES THE ATOMS IN A PARTICULAR MANNER.
• THE AGGREGATION CALLS FOR BONDING: CHEMICAL BONDS
• THERE ARE MANY TYPES OF BONDS,NAMELY COVALENT BONDS,ELECTROSTATIC BONDS,COORDINATE BONDS,IONIC BONDS,VANDERWAAL FORCES ETC.

1.1 STRUCTURE OF ATOMS:

• The Atom is a basic unit of matter that consist of dense nucleus surrounded by cloud of negatively charged electrons.
• The Atomic Nucleus contains postively charged protons and electrically neutral Neutrons(except Hydrogen).
• The electrons of an Atom are bound to the nucleus by the Electromagnetic forces.
• An Atom containing An equal number of proton and Electrons is Electrically Neutral, otherwise it is Positively or Negatively charged and is known as an ion.
• An atom is classified According to the Number of protons and Neutrons in its Nucleus.
• The Number of protons determines the chemical element, and the number of neutrons determines the isotopes of the element.
• Chemical atoms, which carry simple name of"Atom" are minuscule objects with diameters of a few tenths of a nanometre and tiny masses proportional to the Volume implied by these dimensions.
• Atoms can only be observed individually using special instruments such as the scanning tunnelling microscope.
• Over 99.94% of an atom's mass is concentrated in the Nucleus. protons and neutrons having roughly equal mass.
• Each element has atleast one isotope with an unstable nucleus that can undergo radioactive decay.
• This results in transmutation that changes the Number of protons and neutrons in a nucleus.
• Electrons that are bound to atoms possess a set of stable energy levels, or orbitals and can undergo transition between them by absorbing or emitting protons that match the energy difference between the levels.
• The electron determine the chemical properties of an element, and strongly influence an atom's magnet properties.
• The Principle of quantum mechanics have been successfully used to model the observed properties  of the atom.

Table 1.1: Charge and Mass of Subatomic Particles

• In the Table, we have used a unit of mass called the Atomic Mass Unit (AMU).This unit is much more convenient to use than grams for describing masses of atoms.
• It is defined so that both protons and neutrons have a mass of approximately 1 amu.

IMPORTANT POINT TO NOTE:

• PROTON AND NEUTRONS HAVE ALMOST THE SAME MASS,WHILE THE ELECTRON IS APPROXIMATELY 2000 TIMES LIGHTER.
• PROTONS AND NEUTRONS CARRY CHARGES OF EQUAL MAGNITUDE, BUT OPPOSITE CHARGE.NEUTRONS CARRY NO CHARGE(THEY ARE NEUTRAL).

It was once that proton,neutrons and electrons were spread out in a rather uniform fashion to form the atom.

J.J.THOMPSON'S PLUM PUDDING MODEL OF THE ATOM,but we know actual structure of the atom to be quit different.

                            THANK YOU...

          

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DISEASES - 1.2 KOCH'S MOLECULAR POSTULATES

 DISEASES - 1.2 KOCH'S MOLECULAR POSTULATES 

• Although the criteria that Koch developed for proving a causal relationship between a microorganism and a specific disease have been of great importance in medical microbiology, it is not always possible to apply them in studying human diseases.

• For example, some pathogens cannot be grown in pure culture outside the host; because other pathogens grow only in humans, their study would require experimentation on people.

• The identification, isolation, and cloning of genes responsible for pathogen virulence have made possible a new molecular form of Koch’s postulates that resolves some of these difficulties. 

• The emphasis is on the virulence genes present in the infectious agent rather than on the agent itself. 

• The molecular postulates can be briefly summarized as follows:             

                 1. The virulence trait under study should be associated much more with                                pathogenic strains of the species than with nonpathogenic                                                  strains.

                  2. Inactivation of the gene or genes associated with the suspected

                        virulence trait should substantially decrease pathogenicity.

                  3. Replacement of the mutated gene with the normal wild-type gene

                        should fully restore pathogenicity.

                  4. The gene should be expressed at some point during the infection

                       and disease process.

                  5. Antibodies or immune system cells directed against the gene

                      products should protect the host

• The molecular approach cannot always be applied because of problems such as the lack of an appropriate animal system. It also is difficult to employ the molecular postulates when the pathogen is not well characterized genetically.
     

KOCH'S POSTULATES

KOCH'S  POSTULATES 

• First Direct Demonstration of the Role of Bacteria in causing disease came from the study of anthrax by the German physician Robert Koch (1843–1910).

Figure 1.6 Robert Koch. Koch (1843–1910) examining a

specimen in his laboratory

• Koch used the criteria proposed by his former teacher, Jacob Henle (1809–1885), to establish the relationship between Bacillus anthracis and anthrax, and published his findings in 1876 (Techniques &Applications 1.1 briefly discusses the scientific method)

 

.

• Koch injected healthy mice with material from diseased animals, and the mice became ill.
  
• After transferring anthrax by inoculation through a series of 20 mice, he incubated a piece of spleen containing the anthrax bacillus in beef serum. The bacilli grew, reproduced, and produced endospores.
• When the isolated bacilli or their spores were injected into mice, anthrax developed.
• His criteria for proving the causal relationship between a microorganism and a specific disease are known as Koch’s postulates (table 1.1).
  
• Koch’s proof that B. anthracis caused anthrax was independently confirmed by Pasteur and his coworkers.
  
• They discovered that after burial of dead animals, anthrax spores survived and were brought to the surface by earthworms. Healthy animals then ingested the spores and became ill.
  
• Although, Koch used the general approach described in the postulates during his anthrax studies, he did not outlined them fully until his work on the cause of tuberculosis (table 1.1).
  
• In 1884, he reported that this disease was caused by a rod-shaped bacterium, Mycobacterium tuberculosis; he was awarded the Nobel Prize in Physiology
  or Medicine in 1905 for his work.
  
• Koch’s postulates quickly became the cornerstone of connecting many diseases to their causative agent. However, their use is at times not feasible (Disease 1.2).
• some organisms, like Mycobacterium leprae, the causative
  agent of leprosy, cannot be isolated in pure culture
  

CONTINUEDD....NEXT  (DISEASE 1.2)