Saturday, June 9, 2018

Monday, June 4, 2018

Quantitative Reasoning

Quantitative Reasoning

  • Fundamental Operations (mostly arithmetic)
  • Word problems (work, power, probability, profit and loss, area, surface area, volume, percentage, basic trigonometry)
  • Data Interpretation (Statistics)

Physics

PHYSICS:

  1. Fluids and fluid dynamics
  2. Linear Motion
  3. Circular Motion
  4. Vectors
  5. Optics
  6. Simple Pendulum
  7. Sound
  8. Light
  9. Gravitation
  10. Centripetal and centrifugal force
  11. Electromagnetics
  12. Nuclear Force
  13. Friction
  14. Projectile Motion
  15. Rotational Motion
  16. Thermodynamics
  17. Mechanics
  18. Efficiency
  19. Waves (electromagnetic, mechanical)
  20. Circuits
  21. Air resistance

Chemistry

CHEMISTRY:

  1. Organic Chemistry basics
  2. Kinetics
  3. Periodic Table
  4. Thermodynamics
  5. Solutions
  6. Gases and Gas Laws
  7. Hybridization
  8. Bonds
  9. Biological Compounds: DNA, RNA, Sugar, Proteins, Fats
  10. Acids and Bases
  11. Equilibrium
  12. Concentration (molarity, molality,moles,..)
  13. Radioactivity and nuclear chemistry
  14. Solubility

Biology

BIOLOGY

  1. Osmosis
  2. Cell
  3. Plant tissues
  4. Animal tissues
  5. Cell Division (mitosis, meiosis)
  6. Cell Respiration
  7. Scientific Names
  8. Reproduction
  9. Embryology
  10. Genetics
  11. Circulatory System
  12. Nervous System
  13. Muscles
  14. Digestive System
  15. Immune System
  16. Endocrine System
  17. Ecosystem, community and population interaction

Sunday, June 3, 2018

Biology: Microbes in Human Welfare



Microbes in Household products:
  • A common example is the production of curd from milk.  Micro-organisms such as Lactobacillus and others commonly called Lactic Acid Bacteria (LAB) grow in milk and convert it to curd.  During growth, the LAB produces acids that coagulate and partially digest the milk proteins. It also improves its nutritional quality by increasing vitamin B12.  In our stomach too, the LAB play very beneficial role in checking disease causing microbes.
  • The dough, which is used for making bread, is fermented by using baker’s yeast (Saccharomyces cerevisiae).
  • “Toddy”, a traditional drink of some parts of southern India is made by fermenting sap from palms.
  • Microbes are also used to ferment fish, soya bean and bamboo-shoots to make foods.  Cheese, is one of the oldest food items in which microbes were used. The large holes in ‘Swiss cheese’ are due to production of a large amount of CO2 by a bacterium named Propionibacterium sharmanii. The ‘Roquefort cheese’ is ripened by growing a specific fungus on them for a particular flavour.

Microbes in Industrial products:
                Production on an industrial scale requires growing microbes in very large vessels called Fermentors.

a)  Fermented Beverages:
                The yeast Saccharomyces cerevisiae used for bread making and commonly called brewer’s yeast, is used for fermenting malted cereals and fruit juices to produce ethanol. Wine and beer are produced without distillation whereas whisky, brandy and rum are produced by distillation of the fermented broth.

b) Antibiotics:
                Antibiotics are chemical substances, which are produced by some microbes and can kill or retard the growth of other disease causing microbes.
                Pencillin was the first antibiotic to be discovered and it was a chance discovery.  Alexander Fleming while working on Staphylococci bacteria, once observed a mould growing in one of his unwashed culture plates around which Staphylococci could not grow.  He found out that it was due to a chemical produced by the mould and he named it Pencillin after the mould Pencillium notatum. Later, Ernest Chain and Howard Florey made its full potential effective antibiotic.

c) Chemicals, Enzymes and other Bioactive Molecules:
  • Aspergillus niger (fungus) – Citric acid
  • Acetobacter aceti (bacterium) – Acetic acid
  • Clostridium butylicum (bacterium) – Butyric acid
  • Lactobacillus (bacterium) – Lactic acid
  • Saccharomyces cerevisiae – Ethanol

Enzymes:
  • Lipase – used in laundry detergents
  • Pectinase and protease – used in bottled juices
  • Streptokinase (Streptococcus bacterium) – used as clot buster (to remove clots)

Bioactive molecules:
  • Cyclosporin A (Trichoderma polysporum fungi) – used as immunosuppressive agent (for organ transplant patients).
  • Statins (Monascus purpureus yeast) – used as blood cholesterol lowering agents.
Microbes in Sewage Treatment:
                Treatment of waste waster is done by heterotrophic microbes naturally present in the sewage.  This treatment is carried out in two stages;
Primary treatment / Physical treatment:                 It involves physical removal of particles from the sewage through filtration and sedimentation.
  • Sequential filtration – to remove floating debris
  • Sedimentation – to remove grit (soil and small pebbles)
                All solids that settle form the primary sludge, and the supernatant forms the effluent. The effluent from the primary settling tank is taken for secondary treatment.

Secondary treatment / Biological treatment:
  • The primary effluent is passed into large aeration tanks, this allows vigorous growth of aerobic microbes into flocs.  While growing, these microbes consume the major part of the organic matter in the effluent.  This significantly reduces the BOD (biochemical oxygen demand) of the effluent. BOD is a measure of the organic matter present in the water.  The greater the BOD of waste water, more is its polluting potential.
  • Once the BOD of sewage water is reduced significantly, the effluent is then passed into a settling tank where the bacterial ‘flocs’ are allowed to sediment. This sediment is called Activated sludge.
  • A small part of this sludge is pumped back into the aeration tank to serve as the inoculum.
  • The remaining major part of the sludge is pumped into large tanks called anaerobic sludge digesters.
  • During this digestion, bacteria produce a mixture of gases such as methane, hydrogen sulphide and carbon dioxide.  These gases form biogas.
  • The effluent from the secondary treatment plant is generally released into natural water bodies like rivers and streams.

Microbes in Production of Biogas:
                Biogas is mixture of gases produced by the microbial activity and which may be used as fuel.  Certain bacteria, which grow anaerobically on cellulosic material, produce large amount of methane along with CO2 and H2.  These bacteria are collectively called Methanogens (Methanobacterium).

                These bacteria are also present in the rumen of cattle.  A lot of cellulosic material present in the food of cattle is also present in the rumen.  In rumen, these bacteria help in the breakdown of cellulose and play an important role in the nutrition of cattle. Thus, the excreta (dung) of cattle, commonly called Gobar, is rich in these bacteria.  Dung can be used for generation of biogas commonly called gobar gas.

Biogas Plant:
  • The technology of biogas production was developed in India mainly due to the efforts of Indian Agricultural Research Institute (IARI) and Khadi and Village Industries Commission (KVIC).
  • The biogas plant consists of a concrete tank in which bio-wastes are collected and slurry of dung is fed.
  • A floating cover is placed over the slurry, which keeps on rising as the gas is produced in the tank due to the microbial activity.
  • The biogas plant has an outlet, which is connected to a pipe to supply biogas to nearby houses. 
  • The spent slurry is removed through another outlet and may be used as fertilizer.
  • The biogas thus produced is used for cooking and lighting.

Microbes as Biocontrol Agents:

Biological control of pests and diseases:
  • Lady bird – to control aphids
  • Dragon fly – to control mosquitoes
  • Bacillus thuringiensis (Bt Cotton)  – to control wide range insects
  • Trichoderma (fungi) – protects root system and control plant pathogens.
  • Baculoviruses (Nucleopolyhedrovirus) – to attack insects and other arthropods.
 
Microbes as Biofertilisers:                 Biofertilizers are organisms that enrich the nutrient quality of the soil.  The main sources of biofertilisers are bacteria, fungi and cyanobacteria.

Bacteria:
  • Symbiosis – Rhizobium with root nodules of leguminous plants
  • Free living (in the soil) – Azotobacter and Azospirillum.

Fungi:
  • Symbiosis – Mycorrhiza with root system of genus Glomus and absorb phosphorus and water from the soil for the plant growth.

Cyanobacteria:
  • Symbiosis – Anabaena in Azolla
  • Free living – Nostoc, Oscillatoria and Blue green algae.

Biology: HUMAN HEALTH AND DISEASE

 HUMAN HEALTH AND DISEASE


Health:- 
It can be defined as a state of complete physical, mental and social well-being.  When people are healthy, they are more efficient at work.
Health is affected by –
  • Genetic disorders – inheritable defects of parents to offspring.
  • Infections and
  • Life style including food and water we take, rest and exercise we give to our bodies, habits that we have or lack etc.

Diseases can be broadly grouped into infectious and non-infectious.  Diseases which are easily transmitted from one person to another, are called infectious diseases.  Among non-infectious diseases, cancer is the major cause of death.

Common Diseases in Humans:
Pathogen :- Disease causing organisms.

Typhoid:
  • Pathogen: Salmonella typhi.
  • Symptoms: High fever, weakness, stomach pain, constipation, headache and loss of appetite, intestinal perforation and death may occur in severe cases.  Typhoid fever could be confirmed by Widal test.
  • Mode of transmission: These pathogens generally enter the small intestine through contaminated food and water and migrate to other organs through blood.


Pneumonia:
  • Pathogen: Streptococcus pneumoniae and Haemophilus infuenzae.
  • Symptoms: the alveoli get filled with fluid leading to severe problems in respiration. Symptoms include fever, chills, cough and headache, in severe cases the lips and finger nails may turn gray to bluish in colour.
  • Mode of transmission: transmitted through droplets of infected persons.

Common Cold:
  • Pathogen: Rhino viruses.
  • Symptoms: nasal congestion and discharge, sore throat, hoarseness, cough, headache, tiredness.
  • Mode of transmission: through droplets of infected persons.



DISEASES CAUSED BY PROTOZOANS.
Malaria.(means bad air)
  • Pathogen. Protozoan Plasmodium.  
  • Vector.  Female Anopheles mosquito
  • Symptoms. Head aches, muscle pain, high fever.  During fever the patient feels chill and shivering.
  • Prevention.  Eradication of vector and keeping the surrounding clean.
  • Treatment. It involves the use of medicine like quinine and protection of patients from the mosquitoes.
  • Mode of spread. This disease spreads by the bite of infected Anopheles mosquito.  Only the female Anopheles is capable of spreading the disease because it sucks the blood of man.
 
Amoebiasis.  
  • Pathogen.  It is due to an intestinal protozoan parasite Entamoeba histolytica.
  • Symptoms. This parasite lives in the large intestine and destroys the mucus membrane.  This may cause bleeding and ulcer that produce dysentery.  Hence patient passes out blood and mucus with the stool.  There will be severe pain in abdomen, fever, nausea and nervessness.
  • Mode of transmission:  As the cysts of pathogen are found in the intestinal discharge the possibility of infection to healthy persons is through contaminated water or improperly washed or cooked vegetables and fruits.  The pathogen can also be transmitted through dirty hands.
  • Prevention.  Proper disposal of faecal matter of the patient.  Vegetables and fruits when used raw, should be thoroughly washed.  Water should be boiled before drinking. 
 

DISEASE CAUSED BY HELMINTHES WORM.

Ascariasis.
  • Pathogen.  A round worm Ascaris lumbricoides.
  • Symptoms.  This parasite is found in the small intestine of man and is of world wide distribution.  It  causes a lot of stomach ache, nausea and cough.
  • Mode of transmission:  Through food, when soil consist of cyst and eggs, it will be transmitted through vegetables growing on it or through dirty hands or by ingestion of soil.
  • Prevention: The disposal of human faeces by underground sewer canals is an efficient measure to prevent the spread.  Washing of vegetables and fruits before eating help of keep away the eggs of the worm.

Filariasis.  
  • Pathogen.  Wuchereria bancrofti. 
  • Vector.  Culex mosquito.
  • Symptoms. The worm lives in the lymph vessels and  block them, this causes swelling of the body parts like, legs scrotum, foot, etc.  This enlargement of legs gives the disease its name as Elephantiasis.  
  • Prevention.  Eradication of vector.


DISEASE CAUSED BY FUNGI

Ringworms:
  • Pathogens: Trichophyton and Epidermophyton
  • Symptoms: appearance of dry, scaly lesions on various parts of the body such as skin, nails and scalp with intense itching.


Measures for prevention and control of infectious diseases –
  • Personal hygiene: It includes cleanliness of body, drinking of clean water, etc.
  • Public hygiene: It includes cleaning of water reservoirs, proper disposal of sewage, etc.
 
Immunity 
  • Ability of the body to fight infectious agents
  • On the basis of the immunity possessed by the body, immunity can be innate immunity and acquired immunity.

1.  Innate immunityis a non-specific type of defense mechanism.
It has four types of barriers – 
  • Physical barrier: Example, skin covering of the body, secretion of mucous in the respiratory tract
  • Physiological barrier: Example, acid in the stomach, tears from the eyes
  • Cellular barrier: Example, monocytes and lymphocytes in blood
  • Cytokine barrier: Example, interferon

2. Acquired immunity: itis a specific type of defense mechanism. It shows two types of responses: primary response and secondary response. It involves two types of lymphocytes – 
  • B lymphocytes: Show humoral immune response (HI)
  • T lymphocytes: Show cell mediated immunity (CMI)

Structure of an Antibody:
  • The antibodies are protein molecules called immunoglobulins and are of various types like IgA, IgM, IgE, IgG.
  • Each antibody molecule consists of four polypeptide chains, two are long called heavy chains and other two are short called light chains. Both are arranged in the shape of ‘Y’, hence an antibody is represented as H2L2.

On the basis of production of antibodies, immunity can be further categorised as –
  • Active immunity: Body produces its own antibodies against antigens
  • Passive immunity: Readymade antibody is transferred from one individual to another
  • Colostrum (contains antibodies IgA) is an example of passive immunity provided by the mother to her child.

Auto immunity: 
Production of antibodies against the tissues of its own cells. Example – Rheumatoid arthritis.

Lymphoid organs:
It acts as the sites of formation and maturation of lymphocytes.
Primary lymphoid organ – where lymphocytes are produced and matured. Example – Bone marrow and Thymus.

Secondary lymphoid organ– where lymphocytes fight with antigens. Example - Spleen, lymph nodes, tonsils, Peyer's patches Mucosal Associated Lymphocyte Tissues (MALT).


Vaccination: 
It is the protection of the body from communicable diseases by administration of agents (called vaccines) that mimic the microbes. Vaccines are available against tetanus, polio, etc.

 
Allergies:
 Hypersensitivity to a particular allergen (such as pollens, dust) is termed as allergy. IgE is an antibody responsible for allergy.  Symptoms include, sneezing, watery eyes, running nose and difficulty in breathing. Allergy is due to secretion of histamine and serotonine by mast cells. Allergy is treated with anti-histamine, adrenaline and steroids.

  AIDS (Acquired immunodeficiency syndrome) :

It can spread –
  • through sexual contact with the infected person
  • from the mother to her child, through the placenta
  • infected blood transfusion
  • by the use of infected syringe
It is caused by HIV virus (a retro virus) and has RNA as genetic material. HIV stands for Human Immunodeficiency Virus.

When HIV virus enters the host cell, the virus enters into macrophages, where RNA replicates and forms viral DNA by the help of enzyme reverse transcriptase. The viral DNA gets incorporated into the host cell’s DNA and directs the infected cells to produce daughter viruses.  The macrophages continue to produce virus that enters the helper T-lymphocytes.  Thus the number of helper T-lymphocytes progressively decreases in the body and weaken the immune system.

Diagnostic test for AIDS: ELISA (enzyme-linked-immuno-sorbent assay)

Cancer
  • Tumour caused by abnormal and uncontrolled cell division. It is of two types –
  • Benign tumour: Remains confined to a particular location and does not spread
  • Malignant tumour: Cells divides and invades new locations by getting transported through blood to distant sites
  • Metastasis: Property of malignant tumour to invade the distant body parts, thereby initiating formation of new tumours.
  • Carcinogen: Cancer-causing agents; e.g., X-rays, UV rays
  • Cancer detection and diagnosis: Techniques involved are radiography, computed tomography and magnetic resonance imaging

Treatment of cancer:
  1. Surgical – cancerous tissues are surgically removed.
  2. Radiotherapy – tumor cells are irradiated lethally by radiation.
  3. Chemotherapy – drugs are used to kill cancerous cells, but shows side effects like hair loss, anemia, etc.
  4. Immunotherapy – patients are given with alpha-interferon which activate their immune system and help in destroying the tumor.


Drugs and Alcohol 

Drugs and alcohol abuse includes – 
  • Opioids:  Morphine is obtained from Poppy plant. It is a sedative (depressant) and pain killer. Heroin is chemically diacetylmorphine.  It slows down body functions. Example, Heroin (extracted from Papaver somniferum)
  • Cannabinoids: Itis obtained from Cannabis sativa. These are taken by inhalation and oral ingestion, they affect the cardiovascular system of the body. Example, marijuana, hashish, charas, ganja (obtained from Cannabis sativa),
  • Coca alkaloids / Cocaine: it is obtained from Erythroxylon coca.  It is taken by smoking.  It is a stimulant and activates central nervous system.
  • Hallucinogens: It is obtained from Atropa belladonna and Datura sp. LSD (Lysergic acid Diethylamide) is obtained from fungus.
  • Tobacco: it contains nicotine, which is stimulant. It stimulates adrenaline and increases the secretion of adrenaline. Smoking of tobacco leads to lung cancer, bronchitis, emphysema, coronary heart diseases.

Adolescence and Drug abuse 
  • Adolescence is the period during which the child becomes matured.
  • It is between 12 – 18 years of age.
  Causes of drug abuse – 
  • Curiosity
  • Adventure
  • Excitement
  • Experimentation
  • Stress or pressure to excel in examination

Effects of drug/alcohol abuse – 
  • Reckless behaviour
  • Malicious mischief
  • Violence
  • Drop in academic performance
  • Depression, isolation, aggressiveness, etc.
 
Prevention and control – 
  • Avoid peer pressure
  • Counselling and education
  • Take help from teachers, parents and peers
  • Take professional and medical help.

Biology: PRINCIPLES OF INHERITANCE AND VARIATION

 PRINCIPLES OF INHERITANCE AND VARIATION

Heredity is the transfer of character from parents to their offsprings. These hereditary characters are present on the chromosomes in the form of genes.  These gene combinations express characters which may be more similar to one of its two parents.

The differences in characters of offspring mainly depend upon unique process of crossing over that occurs during meiosis.  This is one of the main reasons of producing recombinations.

Gregor Johann Mendel was born in 1822 in Heinzendorf, which was a part of Czechoslovakia.  He began his genetic experiments on garden pea in 1856 in the garden at the monastery.

Selection of pea plant:  The main reasons for adopting garden pea (Pisum sativum) for experiments by Mendel were – 
  • Pea has many distinct contrasting characters.
  • Life span of pea plant is short.
  • Flowers show self pollination, reproductive whorls being enclosed by corolla.
  • It is easy to artificially cross pollinate the pea flowers.  The hybrids thus produced were fertile.

Working method:  Mendel’s success was also due to his meticulous planning and method of work – 
  • He studied only one character at a time.
  • He used all available techniques to avoid cross pollination by undesirable pollen grains.
  • He applied mathematics and statistics to analyse the results obtained by him.

Mendel’s work and results:
The results obtained by Mendel were studied and on their basis he proposed certain laws known as “Laws of heredity”.  These laws are discussed below:

1)  Law of dominance:
This law states that when two contrasting genes for a character come together in an organism, only one is expressed externally and shows visible effect.  It is called dominant and the other gene of the pair which does not express and remains hidden is called recessive.
2)  Law of segregation or Purity of gametes:
This law states that both parental alleles (recessive and dominant) separate and are expressed phenotypically in F2 generation.  When F2 generation was produced by allowing F1 hybrid to self pollinate, to find out segregation or separation it was observed that both dominant and recessive plants appeared in 3:1 ratio. 

3)  Law of Independent assortment:
The law of independent assortment states that when inheritance of two or more genes occur at one time, their distribution in the gametes and in the progeny of subsequent generations is independent of each other.  To prove this, he did a dihybrid cross.  He crossed homozygous dominant smooth and yellow seeded (YYRR) with homozygous recessive wrinkled and green seeded (yyrr) plants. The F1 hybrid was self pollinated and F2 generation was obtained with the phenotypic ratio of 9:3:3:1 and genotypic ratio of 1:2:1:2:4:2:1:2:1.

Test Cross:
A cross between F1 hybrid (Aa) and its homozygous recessive parent (aa) is called Test Cross. This cross is called test cross because it helps to find out whether the given dominant phenotype is homozygous or heterozygous.

Incomplete dominance:
When neither of the alleles of a character is completely dominant over the other and the F1 hybrid is intermediate between the two parents, the phenomenon is called incomplete dominance.

The most common example of incomplete dominance is that of flower colour in 4’O clock plant.  Homozygous red (RR) flowered variety was crossed with white (rr) flowered variety.  F1 offspring had pink flowers (Rr).  This is called incomplete dominance.  Incomplete dominance is also known to occur in snapdragon.  The phenotypic ratio and genotypic ratio in F2 generation in case of incomplete dominance is 1:2:1.

Multiple Allelism / Codominance:
When a gene exists in more than two allelic forms, it shows the phenomenon of multiple allelism.  A well known example is the inheritance of A, B and O blood groups in human being.  The gene for blood group occurs in three allelic forms  IA, IB and i.  A person carries any two of these alleles.  The gene IA produces glycoprotein (sugar) A and the blood group is A.  The gene IB produces glycoprotein B and the blood group is B.  The gene ‘i’ is unable to produce any glycoprotein and so the person homozygous for it , has O group blood. The genes IA and  IB are dominant over ‘i’.   When IA and  IB are present together, both are equally dominant and produce glycoproteins A and B and the blood group is AB.  They are called codominant alleles. 

 Phenotypic (Blood group)                        Genotype
 A                                                               IAIA  /  IA IO
 B                                                               IBIB  /  IB IO
 AB                                                             IAIB
 O                                                               IOIO  (ii)
Chromosome theory of Inheritance:
Chromosome theory of inheritance was proposed by Sutton and Boveri independently in 1902.  The two workers found a close similarity between the transmission of hereditary characters and behaviour of chromosomes while passing from the one generation to the next through agency of gametes.  
Salient features of chromosome theory:
  • Both chromosomes as well as genes occur in pairs in the somatic or diploid cells.
  • A gamete contains only one chromosome of a type and only one of the two alleles of a character.
  • The paired condition of both chromosomes as well as Mendelian factors is restored during fertilization.

Parallelism of behaviour between chromosomes and Mendelian factors:
  • Both the chromosomes as well as Mendelian factors (whether dominant or recessive) are transmitted from generation to generation in an unaltered form.
  • A trait is represented by only one Mendelian factor inside a gamete.  A gamete similarly contains a single chromosome out of a pair of homologous chromosomes due to meiosis that occurs before the formation of gametes.
  • An offspring contains two chromosomes of each type, which are derived from the two parents through their gametes that are involved in fusion and formation of zygote.  It also contains two Mendelian factors for each character.  The factors come from two different parents through their gametes.

Linkage and Recombination:
Linkage is the phenomenon, where two or more linked genes are always inherited together and their recombination frequency in a test cross progeny is less than 50%.

A pair of genes may be identified as linked, if their recombination frequency in a test cross progeny is lower than 50 percent.  All the genes present on one chromosome form a linkage group and an organism possesses as many linkage groups as its haploid number of chromosomes.  If the two genes are fully linked, their recombination frequency will be 0%.

Sex Determination by chromosomes:
Those chromosomes which are involved in the determination of sex of an individual are called sex chromosomes while the other chromosomes are called autosomes.

1) XX – XY type:  In most insects including fruit fly Drosophila and mammals including human beings the females possess two homomorphic sex chromosomes, named XX.  The males contain two heteromorphic sex chromosomes, i.e., XY. Hence the males produce two types of gametes / sperms, either with X-chromosome or with Y-chromosome, so they are called Heterogamety.

2) ZZ – ZW type:  In birds and some reptiles, the males are represented as ZZ (homogamety) and females are ZW (heterogamety).

3)  XX – XO type:  In round worms and some insects, the females have two sex chromosomes, XX, while the males have only one sex chromosomes X. There is no second sex chromosome. Therefore, the males are designated as XO.  The females are homogametic because they produce only one type of eggs.  The males are heterogametic with half the male gametes carrying X-chromosome while the other half being devoid of it.

Sex determination in Humans:
Human beings have 22 pairs of autosomes and one pair of sex chromosomes.  All the ova formed by female are similar in their chromosome type (22+X).  Therefore, females are homogametic.  The male gametes or sperms produced by human males are of two types, (22+X) and (22+Y).  Human males are therefore, heterogametic. The two sexes produced in the progeny is 50:50 ratio.

Mutation:
It is a phenomenon which results in alteration of DNA sequences and consequently results in changes in the genotype and phenotype of an organism.  
Gene / Point mutation:
Due to change in a single base pair of DNA. Ex. Sickle cell anemia (GAGàGUG).
Chromosomal mutation:
Due to change in structure or number of chromosomes. Ex. Down’s syndrome.
Mutagens: 
The chemical and physical factors that induce mutations are known as Mutagens. Ex. UV rays.
Genetic Disorders:
Pedigree analysis:  It is a system to analyse the distribution and movement of characters in the family tree.

Mendelian Disorders: 
These are mainly determined by alteration or mutation in the single gene.  These disorders are transmitted to the offspring on the same line as the principle of inheritance.
Examples : Haemophilia, Cystic fibrosis, Sickle cell anemia, Colour blindness, Phenylketonuria, Thalesemia, etc.

Haemophilia: 
It is a sex linked recessive disease, which shows its transmission from unaffected carrier mother to some of the male progeny.  Haemophilia is a disorder in which a vital factor for clotting of blood is lacking.  So clotting of blood is abnormally delayed and it can be fatal.  Bleeding can be checked by transfusion of the entire volume of blood or the clotting factor in concentrated form.

Sickle cell anemia: 
It is an autosome linked recessive trait.  It is due to a mutant allele on chromosome 11 (autosome), that causes change of glutamine (GAG) to valine (GUG) at the sixth position of  β-chain of haemoglobin.  The disease is controlled by a single pair of allele, HbA HbA (normal) ; HbA HbS (carrier)  and HbS HbS (diseased). The patient has sickle shaped RBCs with defective haemoglobin.  They are destroyed more rapidly than normal RBCs.

Phenylketonuria: 
It is due to a recessive mutant allele on chromosome 12 (autosome).  The affected individual lacks an enzyme (phenylalanine hydroxylase) that converts the amino acid phenylalanine into tyrosine.  As a result, this phenylalanine and its derivatives accumulate in the cerebrospinal fluid leading to mental degeneration (retardation) and are excreted in the urine due to its poor absorption by kidney.

Chromosomal Disorders: Due to absence or excess or abnormal arrangement of one or more chromosomes. 
A change in the number of chromosomes in an organism arises due to non-disjunction of chromosomes, during gamete formation.

Aneuploidy:  This arises due to loss or gain of one or more chromosomes during gamete formation. Example: Down’s syndrome (47) and Turner’s syndrome (45).

Polyploidy:  In this, the number of chromosomes is the multiple of the number of chromosomes in a single set (haploid).  Accordingly, these may be haploid, diploid and polyploid.
Down’s Syndrome:  It was first described by Langdon Down (1866). It is due to trisomy of 21st chromosome, arising from non-disjunction of chromosomes during gamete formation.  As the maternal age increases, the instances of non-disjuction increase.  When such an ovum containing two 21st chromosomes (24) is fertilized by a normal sperm (23), the zygote (47) comes to possess three copies of 21st chromosome.

Symptoms:  Short statured with small round mouth, palm is broad with characteristic palm crease, physical, psychomotor and mental development is retarded.

Klinefelter’s syndrome:  It arises due to non-disjunction of X-chromosomes during ova formation.  When an ovum containing two X-chromosomes is fertilized by a Y-carrying sperm, XXY individual (47) appears.

Symptoms:  A male with underdeveloped breasts (gynaecomastia), sparse body hair, mentally retarded and sterile.

Turner’s Syndrome:  It arises due to non-disjunction of X-chromosomes during ova formation. When an ovum carrying no X-chromosome is fertilized by a sperm carrying X- chromosome, a zygote with XO appears.

Symptoms: A female with rudimentary ovaries, short stature, lack of secondary sexual characters, they are sterile.

IMPORTANT TERMS:
  1. Heredity: - It can be defined as the transmission of characters from one generation to successive generations of living organisms.
  2. Alleles: - The various forms of a gene are called alleles.
  3. Phenotype: - The external / observable characteristics of an organism constitute its phenotype.
  4. Genotype: - The genetic constitution of an organism is its genotype.
  5. Homozygote: - It is an individual organism in which the members of a pair of alleles for a character are similar.
  6. Heterozygote: - It is an individual organism in which the members of a pair of alleles of a character are different.
  7. Dominant character: - The form of the character which is expressed in the F1 hybrid is called dominant character.
  8. Recessive character: - The form of the character which is suppressed in the presence of the dominant character in a hybrid is called recessive character.
  9. Monohybrid cross: - It is a cross between individuals of the same species, in which the inheritance of contrasting pairs of a single trait is considered.
  10. Dihybrid cross: - It is a cross between two individuals of the same species, in which the inheritance of contrasting pairs of two traits is considered.

Biology: MOLECULAR BASIS OF INHERITANCE

MOLECULAR BASIS OF INHERITANCE


Structure of DNA:
Watson and Crick proposed a double helical model for DNA, based on X-ray crystallography of the molecule.  Each strand (helix) is a polymer of nucleotides, each nucleotide consisting of a deoxyribose sugar, a nitrogen base and a phosphate.  The sugar – phosphate chain is on the outside and act as back bone and the bases are on the inside (like in ladder).  The two strands are held together by weak hydrogen bonds between the nitrogen bases.  A purine base, always pairs with a pyrimidine base, i.e., adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C).  So the two strands are complementary to each other and run in antiparallel direction with one chain having 5’ – 3’ orientation and the other having a 3’ – 5’ orientation.  The purine and pyrimidine bases are stacked 0.34 nm apart in the chain and the helix makes a turn after ten base pairs, i.e., 3.4 nm. 

Central dogma of molecular biology:
Crick proposed the Central dogma in molecular biology, which states that the genetic information flows from DNA à RNA à Protein.  In some viruses like retroviruses, the flow of information is in reverse direction, that is from RNA à DNA à mRNA à Protein.

Packaging of DNA helix:
In prokaryotes, negatively charged DNA is held with some positively charged proteins and form as nucleoid. 

In eukaryotes, negatively charged DNA is held with positively charged proteins called Histones (octomer) and form a structure called Nucleosome. 

The search for Genetic Material:

1. Bacterial Transformation (Transforming Principle) :
Fredrick Griffith conducted his experiment onStreptococcus pneumoniae, the pneumonia causing bacterium.  He observed that there are two strains of this bacterium, one forming smooth colonies (S-type) with capsule (virulent) and the other forming rough colonies (R – type)  without capsule (avirulent).
Experiment:
a)         Smooth type bacteria were injected into mice. These mice died as a result of pneumonia caused by bacteria.

b)         Rough type bacteria were injected into mice.  These mice lived and pneumonia was not produced.

c)          Smooth type bacteria which normally cause disease were heat killed and then injected into the mice.  The mice lived and pneumonia was not caused.

d)         Rough type bacteria (living) and heat killed S-type were injected together into mice.  The mice died due to pneumonia and virulent smooth type living bacteria could also be recovered from their bodies.

This indicates that some factor from the dead S-cells converted the live R-cells into S-cells (transformation).

Later Avery, MacLeod and McCarty (1944) found out that when DNA isolated from the heat killed S-cells was added to R-cells in a culture, the R-cells changed into S-cells and pathogenic.

Evidence from experiments with bacteriophage:
This experiment was devised by Hershey and Chase with two different preparations of T2 phage.  In one preparation, the protein part was made radioactive and in the other, nucleic acid (DNA) was made radioactive.  These two phage preparations were allowed to infect the culture of E.coli. Soon after infection, before lysis of cells, the E.coli cells were gently agitated in a blender, to loosen the adhering phage particles and the culture was centrifuged.  The heavier infected bacterial cells pelleted to the bottom and the lighter viral particles were present in the supernatant.  It was found that when T2 phage containing radioactive DNA was used to infect E.coli, the pellet contained radioactivity.  If T2phage containing radioactive protein coat was used to infect E.coli, the supernatant contained most of the radioactivity.  This suggests that during infection by the virus, the viral DNA enters the bacterial cell and that has the information for the production of more viral particles.  It proves that DNA and not proteins, is the genetic material in bacteriophage.

Properties of Genetic Material:
a)      It should be able to generate its replica (replication)

b)      It should chemically and structurally be stable.

c)       It should provide the scope for slow changes (mutation) that are required for evolution.

d)      It should be able to express itself in the form of ‘Mendelian Characters’.

Replication:
The Watson – Crick model of DNA immediately suggested that the two strands of DNA should separate.  Each separated or parent strand now serves as a template (model) for the formation of a new but complementary strand.  Thus, the new or daughter DNA molecules formed would be made of one old or parental strand and another newly formed complementary strand.  This method of formation of new daughter DNA molecules is called semi-conservative method of replication. 
The Experimental Proof:
Meselson and Stahl conducted an experiment to prove that DNA replication is semi conservative.  They grew bacterium E. coli in a medium containing nitrogen salts (15NH4Cl)  labeled with radioactive  15N.  15N was incorporated into both the strands of DNA and such a DNA was heavier than the DNA obtained from E.coli grown on a medium containing 14N. Then they transferred the E.coli cells on to a medium containing 14N.  After one generation, when one bacterial cell has multiplied into two, they isolated the DNA and evaluated its density.  Its density was intermediate between that of the heavier 15N-DNA and the lighter 14N-DNA.  This is because during replication, new DNA molecule with one 15N-old strand and a complementary 14N-new strand was formed (semi-conservative replication) and so its density is intermediate between the two.

Mechanism of DNA replication:
The intertwined DNA strands start separating from a particular point called origin of replication (single in prokaryotes and many in eukaryotes).  This unwinding is catalysed by enzymes called Helicases.  Enzymes called Topoisomerases break and reseal one of the strands of DNA, so that the unwound strands will not wind back.  When the double stranded DNA is unwound upto a point, it shows a Y-shaped structure called Replication Fork.  Enzyme DNA dependent DNA polymerase catalyses the joining of Deoxyribonucleotides (A, G, C and T) in the 5’ – 3’ direction.  The enzyme forms one new strand in a continuous stretch (leading strand) in the 5’ – 3’ direction, on one of the template strands.  On the other template strand, the enzyme forms short stretches (discontinuous) strand of DNA also in the 5’ – 3’. The discontinuous fragments are later joined by DNA-ligase to form a leading strand.  The two strands are held together by hydrogen bonds between nucleotides.

Transcription:
Transcription is the process by which DNA gives rise to RNA. It can also be defined as, the process of copying genetic information from one strand of the DNA into RNA is termed as Transcription. 

Transcription Unit:
A transcription unit in DNA is defined primarily by the three regions in the DNA;
  • A Promoter
  • The Structural gene
  • A Terminator
 
Mechanism of Transcription:
Transcription involves the binding of RNA-polymerase at the promoter site on DNA.  As it moves along (through structural gene), the DNA unwinds and one of the two strands acts as template to synthesize a meaningful RNA and other strand act as non-coding.  A complementary RNA strand is synthesized with A, U, C and G as bases.  RNA synthesis is terminated when the RNA-polymerase falls off a Terminator sequence on the DNA.

Transcription Unit and the Gene:
A gene is defined as the functional unit of inheritance.  In eukaryotes, DNA consists of both coding and non-coding sequences of nucleotides.  The coding sequences / expressed sequences are defined as Exons.  Exons are said to be those sequence that appear in mature / processed RNA.  These exons are interrupted by non-coding sequences called Introns.  These introns do not appear in mature RNA.

Types of RNA:
In prokaryotes, a single RNA polymerase enzyme (composed of different subunits) catalyses the synthesis of all types of RNA(mRNA, tRNA and rRNA) in bacteria.

Where as in eukaryotes, there are three different RNA polymerase enzymes I, II and III, they catalyse the synthesis of all types of RNA.

                RNA polymerase I –    rRNAs

                RNA polymerase II -   mRNA

                RNA polymerase III – tRNA

Process of transcription in Prokaryotes:
RNA polymerase binds to promoter and initiates transcription.  RNA polymerase associates with initiation factor and termination factor to initiate and terminate the transcription respectively.  In prokaryotes, since the mRNA does not require any processing, the transcription and translation take place in the same compartment and can be coupled. 

Process of transcription in Eukaryotes:
In eukaryotes, the primary RNA contains both the exons and introns and is non-functional.  Hence, these non-coding introns will be removed by the process called Splicing. Then this mature RNA undergoes Capping (addition of unusual nucleotide methyl guanosine triphosphate at 5’ –end) and Tailing (addition of adenylate residues at 3’ –end).  Now, this fully matured RNA will be transported out of the nucleus for translation.
Genetic Code:
Genetic code refers to the relationship between the sequence of nucleotides (nitrogen bases) on mRNA and the sequence of amino acids in proteins.  Each code is known as Codon with three nucleotides (triplet). It has been deciphered by Nirenberg, Khorana, Severo Ochoa and Crick.

Salient features of Genetic code:
  • The codon is triplet.  61 codons code for 20 different amino acids and 3 codons do not code for any amino acids, hence they function as Stop codons (UAG, UGA and UAA).
  • One codon codes for only one amino acid, hence, it is unambiguous and specific.
  • Some amino acids are coded by more than one codon, hence the code is degenerate.
  • The codon is read in mRNA in a contiguous fashion.  There are no punctuations.
  • The code is nearly universal.  For example, from bacteria to human, UUU would code for Phenylalanine (phe) amino acid.
  • AUG has dual function. It codes for Methionine (met), and it also act as Initiator codon.

Mutations and Genetic Code:
Mutation caused due to insertion / deletion of single base pair is known as Point mutation.  Effect of point mutations that inserts or deletes a base in structural gene can be better understood by following simple example;

Consider a statement that is made up of the following words each having three letters like genetic code;

RAM      HAS       RED        CAP

If we insert a letter B in between HAS and RED and rearrange the statement, it would read as follows;

RAM      HAS       BRE        DCA       P

Similarly, if we now insert two letters at the same place, say BI’.  Now it would read,

RAM      HAS       BIR         EDC        AP

Now we insert three letters together, say BIG, the statement would read,

RAM      HAS       BIG         RED        CAP

The conclusion is, insertion or deletion of one or two bases changes the reading frame from the point of insertion or deletion.  Insertion or deletion of three or its multiple bases insert or delete one or multiple codon hence one or multiple amino acids, and reading frame remains unaltered from that point onwards.  Such mutations are referred to as Frame-shift insertion or deletion mutations.

Structure of t-RNA : The Adapter Molecule:

tRNA molecule appears like a clover leaf , but in actual structure, the tRNA is a compact molecule which looks like inverted L.

tRNA has three loops,

a)      an anticodon loop that has bases complementary to the codon.

b)      An amino acid accepter end to which it binds to amino acids.

c)       Ribosomal binding loop.

tRNAs are specific for each amino acid.  There are no tRNAs for stop codons.

Translation: It refers to the process of polymerization of amino acids to form a polypeptide.  The order and sequence of amino acids are defined by the sequence of bases in the mRNA.  The amino acids are joined by a bond which is known as a peptide bond.

It involves four steps namely
  • Activation of amino acids (charging of tRNA / aminoacylation of tRNA)
  • Initiation of polypeptide synthesis
  • Elongation of polypeptide synthesis
  • Termination of polypeptide synthesis

a)       Activation of amino acids:  In this process, a particular amino acid binds to a specific tRNA molecule. 

b)       Initiation of polypeptide chain:  The initiator methionyl-tRNA charged with amino acid methionine and anticodon UAC interacts with the initiation codon by codon-anticodon interaction.  With the initiator methionyl-tRNA at P site, the larger subunit binds to the smaller subunit, thus forming an initiation complex.

c)        Elongation of polypeptide chain:  A second tRNA charged with an appropriate amino acid enters the ribosome at the A site, close to the P site.  A peptide bond is formed between the first amino acid and the second amino acid.  Then the first tRNA is removed from the P-site and the second tRNA at the A site, now carrying a dipeptide, is pulled along with mRNA to the P-site (translocation).  Now the A-site is occupied by a third codon and an appropriate aminoacyl tRNA will bind to it.  This process of peptide bond formation and translocation will be repeated and the polypeptide chain grows in length.

d)       Termination of polypeptide chain:  When untranslated regions / termination codons come at the A-site, no amino acid would be added, as it is not recognized by any tRNA.  So protein synthesis will stop.  At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome.

Regulation of Gene Expression:
All the genes are not needed constantly.  The genes needed only sometimes are called regulatory genes and are made to function only when required and remain non-functional at other times.  Such regulated genes, therefore required to be switched ‘on’ or ‘off’ when a particular function is to begin or stop.

The Lac operon:

                Jacob and Monod (1961) proposed a model of gene regulation, known as operon model.  Operon is a co-ordinated group of genes such as structural genes, operator genes, promoter genes, regulater genes and repressor which function or transcribed together and regulate a metabolic pathway as a unit.

                There are three structural genes, lac Z, lac Y and lac A, coding for galactosidase, permease and transacetylase respectively.  These three genes are controlled by a single switch called operator.  The operator switch is controlled by the repressor protein which coded by the regulator gene.

                When the repressor binds to the operator, the genes are not expressed (switched off).  When the operator switch is on, the three structural genes transcribe a long polycistronic mRNA catalysed by RNA – polymerase.

                A few molecules of lactose (inducer) enter the cell by the action o enzyme permease.  They are converted into an active form of lactose which binds to the repressor and changes its configuration and prevents it from binding to the operator.  Beta-galactosidase breaks lactose into glucose and galactose.  (Fig. Text book p.117).

Human Genome Project:

Goals of HGP:
  • Identify all the approximately 20,000-25,000 genes in human DNA;
  • Determine the sequences of the 3 billion chemical base pairs that make up human DNA
  • Store this information in databases;
  • Improve tools for data analysis;
  • Transfer related technologies to other sectors, such as industries.

Methodologies:
The methods involved two major approaches.  One approach focused on identifying all the genes that expressed as RNA referred asExpressed Sequence Tags (ESTs). The other approach is blind approach of simply sequencing the whole set of genome that contained all the coding and non-coding sequence, and later assigning different regions in the sequence with functions, referred asSequence Annotation.
Steps involved in sequencing:
a)      Isolation of total DNA from a cell and converted into random fragments.

b)      Cloning of DNA fragments can be performed by using cloning vectors like BAC (Bacterial Artificial chromosomes) and YAC (yeast artificial chromosomes).

c)       The fragments were sequenced using automated DNA sequencers that worked on the principle of a method developed by Frederick Sanger.

d)      These sequences were then arranged based on some overlapping regions present in them.


Salient features of Human Genome:
a)      The human genome contains 3164.7 million nucleotide bases.

b)      The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.

c)       Less than 2 per cent of the genome codes for proteins.

d)      Repeated sequences make up very large portion of the human genome.

e)      Repetitive sequences are stretches of DNA sequences that are repeated many times, sometimes hundred to thousand times.

f)       Chromosome 1 has most genes (2968), and the Y has the fewest (231).

g)      Scientists have identified about 1.4 million locations where single base DNA differences (SNPs – single nucleotide polymorphism) occur in humans.

  DNA Fingerprinting:
                DNA fingerprinting involves identifying differences in some specific regions in DNA sequence called as repetitive DNA, because in these sequences, a small stretch of DNA is repeated many times.  These repetitive DNA are separated from bulk genomic DNA as different peaks during density gradient centrifugation.  The bulk DNA forms a major peak and the other small peaks are referred to as satellite DNA.  These sequence show high degree of polymorphism (variation at genetic level) and form the basis of DNA fingerprinting.

                Polymorphism can be defined as, an inheritable mutation is observed in a population at high frequency, it is referred to as DNA polymorphism.

                The technique of DNA fingerprinting was initially developed by Alec Jeffreys.  He used a satellite DNA as probe that shows very high degree of polymorphism.  It was called Variable Number of Tandem Repeats (VNTRs).

Mechanism of DNA fingerprinting :
Extraction:  DNA is extracted from the small amounts of blood, semen or hair bulbs available.

Amplification:  Many copies of this DNA are made by a technique called Polymerase Chain Reaction (PCR).

Restriction Digestion:  DNA is cut into desired reproducible segments using restriction enzymes.

Separation:  These DNA sequences (restriction fragments) are separated by Gel Electrophoresis.

Southern Blotting:  The separated DNA sequences are transferred from Gel onto a nitrocellulose membrane.

Hybridisation with probe, the DNA sequence complementary to VNTR sequences.

Exposure of the membrane to X-ray film, whose specific bands are developed.

Applications:

It is used effectively in forensic science for identifying;

a)      the biological father (in case of paternity disparity)

b)      the criminals such as murderers and rapists.
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