DNA DAMAGE AND REPAIR

Dna damage would be due to to mismatch base pairing , catalyzed by environmental agents(ionizing radiation ,certain chemicals and uv radiation ) and  may be spontaneously .

TYPES OF REPAIR                        PROTEINS/ENZYMES                                       EFFECTS

1.MISMATCH REPAIR                   Dam methylase, MUT -H                              Results in mismatch
                                                          MUT-L AND MUT-S proteins,                                   Bases
                                                          Dna helicase II, SSB,Dna pol III,
                                                          Exonuclease I,Exonuclease VII,
                                                          Recj nuclease ,Exonuclease X,
                                                          Dna ligase

2.BASE  
EXCISION REPAIR                         Dna glycosylase ,Ap endonuclease ,            A.  Abnormal bases
                                                             Dna polymerase -I ,Dna ligase                         (Uracil,xanthine,
                                                                                                                                        Hypoxanthine )
                                                                                                                                 B.Pyrimidine dimers

3.NUCLEOTIDE 
EXCISION REPAIR                          ABC exonuclease,DNA POL-I,                  Pyrimidine dimers
                                                            Dna ligase 


4.DIRECT REPAIR                          DNA photolyase                                          Pyrimidine dimers 
                                                      
                                                     correction of    O6 methyl guanosine 7 
                                                                    nucleotide                                          methyl transferase  
                                                               Repair of alkylated bases                               By AlkB(Alpha                                                                                                                                        keto glutarate                                                                                                                            Fe2+ dependent deoxygense )
5.Recombinant repair                             Repair of Double stranadard breaks. It utilise the homologos chromosomes by exonuclease.


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AMES TEST

(USED TO SCREEN CARCINOGENS AND MUTAGENS )
                                       Discovered by Bruce Ames

• Histidine auxotroph (mutated ones)Salmonella typhimurium were taken which requires presence of histidine to grow.
• It is mixed with rat liver enzymes and plated in a media which is devoid of histidine .
• Liver enzymes are required to detect the mutagens that are converted to carcinoogenic form by the liver .
• Test chemical (mutagenic) is then added to the medium .
• Control plates lack the test chemical shows a small number of bacterial cells or colony growing without histidine .
• Plated innoculated with mutagens (test chemical )show a larger number of revertants which implies the auxotroph converted to prototrophs by the presence of histidine which acts as a selectable marker .

(ALL CARCINOGENS ARE MUTAGENS BUT ALL MUTAGENS ARE NOT CARCINOGENS)

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TYPES OF ECOLOGICAL EFFICIENCY

Ecological efficiency describes the efficiency with which energy is transferred as biomass from one trophic level to the next. It is determined by a summation of all the  efficiencies relating to organismic resource acquisition and assimilation in an ecosystem.

NOTE -Biodiversity is directly proportional to ecological efficiency .

1.Net production efficiency (NPE) measures how efficiently each trophic level uses and incorporates the energy from its food into biomass to fuel the next trophic level.

2.(A/I) The efficiency by which animals convert the food they ingest into energy for growth and reproduction is called assimilation efficiency. (Proportion of ingested biomass that consumers assimilate ).

JUNE 2017 CSIR NET ONE QUESTION WAS BASED ON THIS -

Herbivores assimilate  15 -80 percent of the plant material they ingest.

Carnivores have higher assimilation efficiency (about 80 percent) than do terrestrial herbivores (5 to 20 percent).

3.Consumption efficiency -Proportion of available biomass that is ingested by consumers .

4.(P/A) Production Efficiency-Production efficiency is the amount of energy that is allocated to animal production, including growth of the animal and animal reproduction. It is determined primarily by the metabolism of the animal.

5.Production to Consumption Index: ( Production/consumption; P/I) A measure of the efficiency with which energy is made available to the next group of consumersIndicates how much energy consumed by the animal is converted into production

Note-1.In case of insects =High production efficiency,Low assimilation efficiency
          2.HUMANS=Low production efficiency and high assimilation efficiency 
          3.Homeotherms: assimilation (A/I) is high: low production (P/A); very low (P/I) production to consumption ratio
            Poikilotherms: assimilaiton (A/I) :production (P/A); much higher (P/I) than that of homeotherms

(Homeotherms have a very poor production efficiency (P/A) giving a very low production to consumption ratio (P/I), and this is the opposite for poikilotherms )

Note- Endotherms have high DE( digestion efficiency) that is assimilation/consumption .

Ectotherms have low EE( ecological efficiency)
That is production/ consumption.

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KLENOW FRAGMENT (DNA POL I -LARGE FRAGMENT )

The Klenow fragment is a large protein fragment  produced when DNA polymerase I from E. coli is enzymatically cleaved by the protease subtilisin. 

The  cleavage results in  1. Small fragment of  322 amno acids having 5'-3' exonuclease activity .
                                   2.Large fragment of 604 amino acids having DNA polymerization and 3'-5' exonuclease activity .

The larger fragment retains the 5' → 3' polymerase activity and the 3’ → 5’ exonuclease activity for removal of precoding nucleotides and proofreading, but loses its 5' → 3' exonuclease activity.

The other smaller fragment formed when DNA polymerase I from E. coli is cleaved by subtilisin retains the 5' → 3' exonuclease activity but does not have the other two activities exhibited by the Klenow fragment (i.e. 5' → 3' polymerase activity, and 3' → 5' exonuclease activity).

The elimination of exonuclease activity makes Exo- Klenow Fragment the enzyme of choice for isotopic or biotin labeling of DNA probes by the random primed method and for DNA sequencing by the sanger dideoxy method.

Applications -

DNA blunting - By filling-in 5'-overhangs with unlabeled or labeled dNTPs

cDNA strand synthesis 

Generate single-stranded DNA probes using random primers

Site-directed DNA mutagenesis using synthetic oligonucleotides

Dideoxy DNA sequencing of single- or double-stranded DNA templates

3’→5’ exonuclease activity can blunt a 3’-overhang.

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BIOCHEMISTRY FLASH CARD

1.GLYCOGEN AND STARCH ------- Alpha (1 -4)glucose (Branched and unbranched)

2.CELLULOSE--------Beta(1-4)glycosidic bond of  glucose (unbranched )

3.Insulin ---------------- 21 and 30 amino acids

4. Chitin ---------------------- N-acetyl glucosamine with alpha (1--4 ) linkage

5. Hemicellulose -------------D galactose

6.ADP ribosylation----------- Arginine

7. Uridylytion -----------------Tyrosine

8. Mg2+ is an inorganic activator of ---------Phosphatase enzyme

9. Zn2+ is an inorganic activator of ---------Carbonic anhydrase

10.Penicillin -------------Block the active site of enzyme that many bacteria used to make cell walls.

11. Phosphofructokinase allosterically regulated ---------------by ATP

12. Phosphorylation and Glycosylation---------Ser residue involved

13.Tyrosine --------------------------------Dopamine

14.Methylation and Acetylation ------------------------------lysine

15.Isocitrate lyase -------------------------------------------Synthesis of glucose from acetate

16.PEP  Carboxylase --------------------------------------Conversion of aminoacid into glucose

17.Pyruvate dehydrogenase complex-------------------Lipoic acid

18.Phosphofructokinase -------------------------------An allosteric enzyme

19.Pyruvate carboxylase ------------------------------Biotin

20.Uronic acid-----------------------------------------Dermatan sulphate ,Chondroitin sulphate ,Heparin sulphate

21.1,1-----Glucoside linkage -----------------------Trehalose

22.Invert sugar --------------------------------------Hydrolytic product of sucrose

23.Hyaluronic acid ---------------------------------Glucurnic acid and N- acetyl D- galactosamine

24.Diasteromers------------------------------------Isoleucine and threonine (Also have 2 chiral centers)

25.Non polar amino acids -----------------------In the core of proteins

26.Arginine--------------------------------------Imidazole group

27.Histidine-----------------------------------Guanidine group

28.Name of test - a. Histidine and tyrosine ----------------------Pauly
                             b.Tryptophan------------------------(glyoxylic acid reaction)Hopkins cole
                             c.Arginine---------------------Milon
                             d.Cysteine--------------------Nitroprusside
29.Spingosine------------------------------------Ceramide ,Cerebrosides,Gangliosides,Spingomyelin

30.Tay-Sachs disease -----------------------------Genetic defect in the metabolism of gangliosides

31.Alpha keratin -----------------------------Mammals and Beta keratin-------Birds and Reptiles

32.Major polysaccharide components of extracellular matrix----------------Glycosaminoglycans

33.Lipids -------------Fatty acid ,spingolipid,glycerophospholipid ,triglecerides,chlesterol

34.Transfatty acids--------------------By fermentation in the rumen of diary animals.

35.The pentose sugar present mainly in the
heart muscle is                                              -------------------------------------- Lyxose

36.Dietary fats are transported as ----------------------------------------------------Chylomicrons

37.Neurotransmitters ----------------------------------------Dopamine, serotonin,GABA,epinephrine 

38.Energy related metabolites-----------------------------Creatine, citrulline ,carnitine 

39.Carboxyglutamate-------------------------------Blood clotting proteins and Ca 2+ binding proteins 

40.Methyllysine--------------------------constituent of  myosin

41.Pyroglutamate---------------------Bacteriorhodopsin

42.Ornithine and Citrulline--------------------Intermediates in biosynthesis of arginine and urea cycle

43.Ketogenic amino acids ---------------------leucine and lysine

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BLOCKS OF POLYSPERMY (DEVELOPMENTAL BIOLOGY )

Two mechanisms are used by animals to ensure that only one sperm will fertilize the egg to prevent the polyspermy condition .
1.FAST BLOCK - ( In sea urchins and Frogs) No fast block polyspermy are identified in mammals .

•  (It happens immediately after fertilization )Depolarization of membrane so it is the change in potential of the plasma membrane. Sperm binding causes Na+ influx. 
• STEPS-   a. Opening of Na+ channels in the egg plasma membrane .

                          b.Flow of Na+ into the egg cell (Na+ influx) .

                          c.Depolarization of the membrane .

                          d. As a result of that it prevents the additional sperm entry to the egg plasma membrane .

                          e. The egg plasma membrane restored to its normal -70 Mv resting potential within minutes of fusion as the Na+ channels  close  and Na+ is pumped out .

          (IF DEPOLARIZATION IS PREVENTED IT WOULD RESULTS IN POLYSPERMY )

2.SLOW BLOCK -(CHEMICAL AND MECHANICAL BLOCK)
Upon sperm entry the cortical granules fuse with the egg plasma membrane and  exocytosis of cortical granules occurs which  releases zonal inhibiting proteins like  serine proteases (which digest the connection between vitelline membrane and plasma membrane .) ,mucopolysaccharides ( It produce osmotic gradient and water rushes to perivitelline space), peroxidases ( oxidizes and cross links tyrosine )going to harden the fertilization envelope and in case of Humans it is zona Pellucida ) and hyaline which provides support during cleavage by formimg a coat around the egg called hyaline layer  .
STEPS - (In most of the species)

• Inositol triphosphate -(IP3) causes the release of  Ca2+ from intracellular stores in the egg Endoplasmic Reticulum .
• At the site of sperm entry ca2+ is released and it passes to the egg .
• This ca2+ results in the fusion of cortical vesices with the egg plasma membrane releasing their contents into the space surrounding the egg called the perivitelline space. which is presnt in between cell membrane and vitelline envelope .
• This raises the vitelline envelope and inactivates or destroys  the bindin receptor.
• So, any additional sperm cannot bind which in turn prevents polyspermy .  Image source credit -http://slideplayer.com/slide/6364295/

NOTE -SOME ORGANISMS DO NOT BLOCK POLYSPERMY MANY SPERM ENTER ONLY ONE SURVIVE AND THE REST ARE DEGRADED.


What would be the reason to block polyspermy ?
Ans.       It leads to polyploidy and eventually death ..

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BIOREMEDIATION ,BIOLOGICAL AUGMENTATION,PHYCOREMEDIATION ,MYCOREMEDIATION AND BIOFORTIFICATION

BIOREMEDIATION-

It is the use of organisms to detoxify ecosystem . Basically it is a waste management technique Organisms are mostly prokaryotes ,fungus and plants. They have the ability to take up and metabolize the toxic products. The removal or degradation of environmental pollutants or toxic materials by living organism is by bioremediation. Chelating agents may be used in bioremediation to bind toxic heavy metals to soil particles, a process known as sequestration.It is the integration of several sciences such as ecology and genetics to sustain biological diversity at all levels .

Example-  Shewanella oneidensis  It metabolize uranium into insoluble  form so that it cannot mix up with water .

BIOLOGICAL AUGMENTATION-
It uses organisms to add essential nutrients to the degraded ecosystem. It is also acts as strategy  for cleaning up soils which are contaminated with aromatic compounds .

Example- 1.The nitrogen fixing plants can increase the avalability of Nitrogen in soil.
                2.Mycorrhizal fungi can help plants  to access nutrients from soil .
               3.Addition of consortium or cocktail of micro-organisms to the polluted soil .
PHYTOREMEDIATION- 

Natural plants or transgenic plants are able to bioaccumulate toxins .The direct use of the green plants and their microorganisms used to balance or decrease the contaminated soils, sludges, sediments, surface water or ground water is called Phytoremediation.  Phyto means plant and remedian means restoring balance. This type of bioremediation explains a way of treating the environmental problems with the help of plants. The element of Phytoremediation consists of contaminated soil, water, and air which are polluted and the plants are able to contain and eliminate the metals, pesticides, solvents, explosives, crude oil.

MYCOREMEDIATION-It is a form of bioremediation in which fungi are used to decontaminate the area.

Example- A plot of soil contaminated with diesel oil was inoculated with oyster mushrooms. After 4 weeks, more than 95% of the polycyclic aromatic hydrocarbons had been reduced to non-toxic compounds.

BIOFORTIFICATION-Breeding crops for improved nutritional quality or u can say Breeding of crops with high levels of minerals, vitamins and proteins by best conventional breeding practices and modern biotechnology .
As such, bio-fortification is seen as an upcoming strategy for dealing with deficiencies of micronutrients in the developing world. In the case of iron, WHO estimated that bio-fortification could help curing the 2 billion people suffering from iron deficiency-induced anemia.

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SYNAPOMORPHY ,SYMPLESIOMORPHY ,APOMORPHY ,PLESIOMORPHY AND HOMOPLASY

All these terms have to do with identifying organisms, called taxa, into "family trees", according to identifying traits or characteristics.

Synapomorphy: a trait share by 2 or more taxa and their most recent common ancestor.

Symplesiomorphy : A characteristic shared by 2 or more taxa also found in their earliest common ancestor.

Apomorphy: A characteristic believed to have evolved within a family tree; can be used to separate one group from the other.
Plesiomorphy-A plesiomorphy refers to the ancestral trait state, usually in reference to a derived trait state.

All these terms provide valuable information, depending on how one is constructing the family tree or taxa. The first two, synapomorphy and symplesiomorphy, provide evidence among similarities between recent taxa and their ancestors. Apomorphy distinguishes differences between recent taxa and their ancestors, providing a breaking-off point that could be used to establish new groups or sub-groups.

 Homoplasy is a character shared by a set of species but not present in their common ancestor. A good example is the evolution of the eye which has originated independently in many different species. When this happens it is sometimes called a convergence.

                               Image source credit goes to -http://slideplayer.com/slide/3525255/
CSIR PART C-QUESTION

CORRECT OPTION IS 2 As Synapomorphy: a trait share by 2 or more taxa and their most recent common ancestor in that case resin canal should be present  in the ancestor as it is pinacea  family .

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COMPARISION BETWEEN PIONEER(YOUNG) AND CIMAX(MATURE) COMMUNITY

ATTRIBUTES                      PIONEER                                           CLIMAX

1.Food chain                          Grazing                                            Detritous                                                                                                                    

2.Food web                            Simple                                              Complex 

3.Biomass                                Low                                                  High

4.Species diversity                     Low                                                  High

5.Stratification                           less                                                   More

6.Niche                                    Broad                                              Narrow 

7.Feeding relation                  Generalized                                     Specialized

8.Life cycle                                Short                                                long

9.Type of population control       Physical                                      Biological

10.Trophic relationship             Simple                                         Complex

11.Fluctuations                          More                                            less

12.Stability                                  Low                                               High

13.Net community                        Higher                                        Lower 

production 

14.Community                             Lower                                       Higher 

respiration 

15 P/ R RATIO                             p>R                                            P=R

16.Growth rate                              high                                             low

17.Dispersal                               High degree                                  low

18.Size                                           small                                          large

19. Timeperiod                    live for short period                              live longer 

20.Tolerance                Can tolerate extreme condition                   cannot 

21.Examples                    Moss ,Dune grass,Lichens                      Beech and maple 

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EQUILIBRIUM THEORY OF ISLAND BIO-GEOGRAPHY

Equilibrium theory of island biogeography -
Discovered by Robert Mcarthur and E.O. Wilson in 1967

This theory is based on species are relationship ,Species isolation relationship and species turn over .
Acc. to this theory the number of species inhabiting an island is based on the dynamic equilibrium between the immigration of new species  and extinction of species previously established .

So ,in simple words it would be the number of species in an island reflects the balance between the rate at which new species colonize it and the rate at which the populations of established species become extinct .The island will reach equilibrium when extinction rates equal immigration rates.

NOTE -The thoery explains about the patterns of species richness in island . It also explains the reason of lower number of species in an island .Over time, the countervailing forces of extinction and immigration result in an equilibrium level of species richness.

To understand their theory, take a look at the graph . The axis on the bottom of the graph is the number of species. If we follow the blue line, it shows that as the number of species increases, the rate of immigration begins to decrease. That's because as more and more species arrive, the chances grow that that species is already present.
Closer islands will have more species on them than far islands, just because closer islands are easier to reach. Extinction is lower on islands close to the mainland because of the likelihood of immigration. There is more of a chance that new immigrants will arrive and keep a species in existence on that island. 
Rates of immigration to an island are mainly determined by the distance from the mainland to the island, and rates of extinction on the island are mainly determined by island size.

Image source credit goes to -http://www.islandbiogeography.org/

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