Sunday, March 30, 2014

Electromagnetic Radiation

Spectroscopy
The ways in which the measurements of radiation frequency (either emitted or absorbed) are made experimentally and the energy levels deduced from these comprise the spectroscopy. It gives qualitative and quantitative information.
Spectroscopy deals with interaction of electromagnetic radiation with any compound or atoms.  The interaction is measured as energy which is either absorbed or emitted by the matter in discrete amount called quanta.
Spectroscopy was originally the study of the interaction between radiation and matter as a function of wavelength (λ).
Spectrometry is the spectroscopic technique used to assess the concentration or amount of a given species. In those cases, the instrument that performs such measurements is a spectrometer or spectrograph.
Spectroscopy/spectrometry is often used in physical and analytical chemistry for the identification of substances through the spectrum emitted from or absorbed by them.
Spectroscopy/spectrometry is also heavily used in astronomy and remote sensing. Most large telescopes have spectrometers, which are used either to measure the chemical composition and physical properties of astronomical objects or to measure their velocities from the Doppler shift of their spectral lines.

There are two types of spectroscopy
1. Atomic spectroscopy
It deals the interaction of electromagnetic radiation with atoms which are most commonly in their lowest energy state called the ground state level.
DE = h g                                 here     h = Planck's constant
                                                g = Frequency of radiation    
2. Molecular spectroscopy
It deals the interaction of electromagnetic radiation with molecules which includes rotational, vibrational and election transitions of the molecule. It gives the information regarding molecular structure (molecular symmetry, bond distances and angles, and chemical properties such as electronic distribution, bond strength and intra or inter molecular processes)

Properties of electromagnetic radiation
Electromagnetic radiation is a form of energy that is transmitted through space at an enormous velocity which is equivalent to the velocity of light in the space. It requires no supporting media and can travel in vaccum. They have dual nature exhibiting both wave and particle like properties.
A. Wave properties
Wave properties of electromagnetic beam are an alternating electrical and associated magnetic force in space. They possess both the electric component and magnetic component. Both of these oscillate in plane perpendicular to each other and perpendicular to the direction of propagation of the radiation. They are coherent and plane polarized. Phase of one is related to that of other. Velocity of it is independent of frequency on vaccum (c= 3 x 108 m/s). Some of the wave properties are:
1. Wavelength
It is a distance between two successive maxima on an electromagnetic wave.
Figure: Electromagnetic beam showing wavelength, l
It is denoted by ' l' lambda (Greek letter). The units of wavelength are m, cm, mm, mm, nm and A°. The beam carrying only one discrete wavelength is said to be monochromatic beam.

2. Frequency
The number of complete wavelength units passing through a given point in unit time is called frequency of radiation. It is denoted by 'g' Gamma (Greek letter).Its unit is hertz or Fresnel which means per second (s-1). Further they can be measured in terms of KHz, MHz or GHz etc.
3. Wave number
Frequency is more fundamental than the wavelength. So it is cumbersome to use in practice because of large number of frequency in calculation. Therefore in practice, it expresses frequency in wave number. It is defined as the numbers of waves per centimeter in vaccum which is denoted by 'n' (Greek v letter) or bar in frequency.
n = 1 / l
Its unit is Kaiser or Kilokaiser (Per centimeter or cm-1).

4. Velocity
It is defined as distance travelled by electromagnetic radiation per unit time. It is denoted by 'c'.
Velocity= wavelength x frequency
c = l x g
5. Relationship between frequency, velocity and wave number
c = l x g
or        n = g / c                                   here:   n = 1 / l
\        g = c x n  ………………….equ i
i.e. The frequency of radiation is mathematically equal to the product of velocity of radiation and its wave number.
The examples of wave properties of electromagnetic radiations are refraction, reflection etc.

B. Particle Properties
Electromagnetic radiation consists of a stream of discrete packets (particles) of pure energy called photons or quanta. They have definite energy and travel in the direction of propagation of the radiation beam with the velocity equal to that of light.
E = h . g          Where h = 6.626 x 10-34  J. s (Planck's constant )
The example of particle property of electromagnetic radiation is photoelectric effect.
1. Relationship between wave and particle properties
We  have,        E = h . g 
            Or        E = h . c . n                 Where c is velocity and n is wave number of electromagnetic radiation
            Or        E = h . c . 1/ l             here; n = 1/ l
            \        E  µ 1/ l                     since both h and c are constant terms

Velocity is independent of frequency on vaccum. Finally the above relation shows that the energy carried by an electromagnetic beam is inversely proportional to the wavelength of the beam. It means lower the wavelength, higher the energy of the beam and vice versa. For example: The wavelength for ultraviolet rays and visible rays ranges from 190-390 nm and 400-750 nm respectively. Since the wavelength of ultraviolet rays are smaller than that of visible rays the energy carried by the UV rays are comparatively higher than that of visible rays.

Wednesday, March 5, 2014

Introduction to Biochemistry

BIOCHEMISTRY

·         What is the Biochemistry?
·         History and development
·         How to study Biochemistry?


Definition: The chemistry of life;
·         The science concerned with the chemical basis of life.
·         The science concerned with the various molecules that occur in living cells and organisms and with their chemical reaction.
·         Anything more than a superficial comprehension of life – in all its diverse manifestation - demands knowledge of biochemistry.
Organic Chemistry: It is a science that deals with the organic compounds found in the nature. Biochemistry is thus a branch of organic chemistry which deals with the organic compounds within the living systems. Biochemistry deals with the structural, functional and dynamic roles of biomolecules in depth.
Definition: Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level. It emerged as a distinct discipline around the beginning of the 20th century when scientists combined chemistry, physiology and biology to investigate the chemistry of living systems by:
A.    Studying the structure and behavior of the complex molecules found in biological material and
B.     the ways these molecules interact to form cells, tissues and whole organism
Aim of Biochemistry:
Biochemistry describes structure, function and organization of cell in molecular terms, and explains all chemical processes of living cells
·         Structure-function
·         Metabolism and Regulation
·         Molecular Genetics
History of Development of Biochemistry:
·         Vital forces in early part of 19th century: The vital force stated that the vital forces exist only to living organisms. According to the theory, the compounds found in living organisms cannot be synthesized in the lab. They are only found in living systems. The theory existed for a longer period and was disproved in half of 19th century.

·         1828 Friedrich Wohler: F. Wohler in1828 disproved the vital force theory. Urea was synthesized by heating the inorganic compound ammonium cyanate (1828). This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances

Ammonium cyante + heat           ®        Urea
  • 1897 Eduard Buchner: E. Buchner fermented alcohol from glucose and dead yeast in lab in 1897. It showed that living organisms are not required for fermentation. The products from living organisms are sufficient to carry out chemical reactions. He showed the role of enzymes in fermentation.
Glucose + Dead Yeast           ®        Alcohol
·         1903, Neuberg (German): He defined the term “Biochemistry” as the “Chemistry of Life”
  • Two notable breakthroughs in history of Biochemistry are;
1. Discovery of the role of enzymes as catalysts
2. Identification of nucleic acids as information molecules 
  • Flow of information from nucleic acids to proteins: The flow of information from nucleic acids to proteins take place by transcription and translations processes.
      Transcription                       Translation
DNA               ®        RNA               ®        Protein
  • Krebs in 1937: In 1937 Krebs for the discovery of the Citric Acid Cycle-won the Nobel Prize in physiology or Medicine in 1953.
  • 1944 Avery, MacLeod and McCarty: They identified DNA as information molecules
  • In 1953Watson & Crick: Watson and Crick proposed the “DNA Double Helix” model by X-ray crystallography and won the Nobel Prize in Physiology or Medicine in 1962.
  • In 1955Sanger: Sanger determined the insulin sequence and won the Nobel Prize in Physiology or Medicine in 1956 
  • In 1980 Sanger & Gilbert: They discovered the methods for sequencing of DNA and won the Nobel Prize in Chemistry in 1980.
  • In 1993,  Kary B. Mullis: Kary B. Mullis invented PCR method  and won the Nobel Prize in Chemistry in 1993
Evolution of Earth
  • Big bang theory
         Cataclysmic explosion
         All the matter in the universe was originally confined to a comparatively small volume of space.
         Late started explosion and spread
         Volume expanded and exploded into many pieces in the universe
         Early universe contains only H, He and Le
  • Rest of the chemicals are thought to have been formed in three ways
1. the thermonuclear reactions in stars
2. explosion of stars
3. action of cosmic rays outside the stars
  • Radioactive dating
         The age of the Earth=4-5 billion
         No free 02 in the early stages
         UV irradiation
         No 03 layer in the Earth
         Only the gases present are NH3, H2S, CO, CO2, CH4, N2, H2
Structural hierarchy of an organism:
Elements
¯
Simple organic compounds (monomers)
¯
Macromolecules (polymers)
¯
Supramolecular structures
¯
Organelles
¯
Cellss
¯
Tissues
¯
Organisms
Figure: Structural hierarchy of an organism
Biomolecules
  • Just like cells are building blocks of tissues likewise molecules are building blocks of cells.
  • Animal and plant cells contain approximately 10, 000 kinds of molecules (bio-molecules)
  • Water constitutes 50-95% of cells content by weight.
  • Ions like Na+, K+ and Ca+2 may account for another 1%
  • Almost all other kinds of bio-molecules are organic (C, H, N, O, P, S)
  • Infinite variety of molecules contain carbon, C.
  •  Most bio-molecules considered to be derived from hydrocarbons.
  • The chemical properties of organic bio-molecules are determined by their functional groups. Most bio-molecules have more than one.
  • Organic compounds are compounds composed primarily of a Carbon skeleton.
  • Carbon is more abundant in living organisms than it is in the rest of the universe.
  • What makes Carbon Special?  Why is Carbon so different from all the other elements on the periodic table?
  • The answer derives from the ability of Carbon atoms to bond together to form long chains and rings.
Small molecules:
         Lipid, phospholipid, glycolipid, sterol, 
         Vitamin
         Hormone, neurotransmitter
         Carbohydrate, sugar
Monomers:
         Amino acids
         Nucleotides
         Monosaccharides
  • Polymers:
         Peptides, oligopeptides, polypeptides, proteins
         Nucleic acids, i.e. DNA, RNA
         Oligosaccharides, polysaccharides (including cellulose) 
Different functional groups in Biomolecules:


All cells share some common characteristics:
  • All cells use nucleic acids (DNA) to store information
    • Except RNA viruses, but not true cells (incapable of autonomous replication) .
  • All cells use nucleic acids (RNA) to access  stored information
  • All cells use proteins as catalysts (enzymes) for chemical reactions
    • A few examples of RNA based enzymes, which may reflect primordial use of RNA
  • All cells use lipids for membrane components
    • Different types of lipids in different types of cells
  • All cells use carbohydrates for cell walls (if present), recognition, and energy generation

Scope of Biochemistry: It is essential to all life sciences as the common knowledge
·         Genetics; Cell biology; Molecular biology
·         Physiology and Immunology
·         Pharmacology and Pharmacy
·         Toxicology; Pathology; Microbiology
·         Zoology and Botany

Clinical Biochemistry:
Medical students who acquire a sound knowledge of Biochemistry will be in  a strong position to deal with two central concerns of the health sciences:
            (1) The understanding and maintenance of health
            (2) The understanding and effective treatment of disease
·         Causes of cancers
·         Molecular lesions causing various genetic diseases
·         Rational design of new drugs
Industrial Biochemistry:
Fermentation technology and many food industries require knowledge on Biochemistry. They are working as quality controller in many industries. Without knowledge on Biochemistry, no good quality of products can be obtained. E.g. wine and alcohol production
·         Beverage: breads and CO2
·           Drug and food supplements
·         Organic compounds used as substrate
Nutritional Biochemistry:
·         Calculation of energy
·         Balanced diet
·         Diet for patients:
§  enzymes for gastric patients or metabolic disorder problems
§  Insulin for Diabetic patients
§  HDL foods for heart disease patients

Agricultural Biochemistry:
·         Livestock and animal husbandry
·         Animal feeds
·         Peculiarities in metabolism of Plant
§  E.g. Golden rice (Beta carotene-Vitamin A)
§  Genetically modified plants and products
§  Hybridization
§  Virus free plant/Tissue culture

Space Biochemistry:
·         Composition of space atmosphere
·         Utilization of cosmos rays
·         Alternate source of energies from the space
·         Protection of Foods for Space

Radiation Biochemistry:
·         Estimate the changes in chemical composition of compounds
·         X-rays, Gamma rays
·         Scanning by NMR-MRI
Others
·         Pure sciences-botany, zoology

·         Applied  sciences- Microbiology, Biotechnology, Genetic Engineering etc.

Bacteria in Photos

Bacteria in Photos