In C4 the co2 compensation point is zero OR nearly zero whats the reason ?

In C4 plants, the CO2 compensation point is zero or nearly zero, reflecting their very low levels of photorespiration. In C4 plants, photosynthetic rates saturate at internal concentration values of about 15 Pa, reflecting the effective CO2-concentrating mechanisms operating in these plants.

Leaves release CO2 by photorespiration and day respiration, but CO2 is also converted into carbohydrate by photosynthesis. Assimilation is therefore the difference in the rate of these processes.

The intracellular concentration of CO2 affects the rates of photosynthesis and photo respiration. At higher carbon dioxide concentrations, the photosynthesis rate is higher, while at low CO2 concentrations, photo respiration is higher.
The atmospheic concentration at which photosynthesis just compensated for respiration is referred to as the CO2 compensation point. in C4 plants is lower, as C4 plasnts have high CO2 levels in the bundle sheath of chloroplasts and high pools of CO2 in the mesophyll cells. The CO2, absorbed by C4 leaves is fixed into organic acids, which thus maintain high levels of CO2. The mesophyll of C3 plants has no such mechanism of fixing CO2.

In c4 plants, the high levels of CO2 inhibit photorespiration , because, at high concentrations, CO2 competes better than O2 for the Rubisco caboxylase site and is therefore fixed at a greater rate than O2.

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SOME IMPORTANT POINTS ABOUT PLANT HORMONES

ABA -

DREB1 and DREB2 are two independent families of DREB proteins, which function as
trans-acting factors in two separate signal transaction pathways under low temperature
and dehydration. The ABA-responsive element (ABREs) contains the palindromic motif CACGTC with the G-box ACGT core element and A 9-bp conserved sequence,TACGACAT,termed dehydration responsive element (DRE), is essential for regulation of dehydration-responsive gene expression. The DRE has been reported to function as a cis- acting element involved in the induction of rd29A expression by low temperature stress.

GIBBERLLIN-

 Gibberllin (GA) regulate gene expressions by promoting degradation of the transcriptional regulator DELLA proteins, is essential for GA action that form a subgroup of the GRAS family of proteins. DELLA proteins are named for a conserved domain within the N terminus that is unique to this
subgroup and is necessary for GA-induced degradation.Binding of GA to its soluble, nuclear receptor,GID1, causes a conformational change in the protein that promotes its association with the
N-terminal domain of the DELLA protein, enabling, in turn, interaction with an SCF ubiquitin ligase, such that the DELLA is ubiquitinated, and thus targeted for degradation via the 26S proteasome.

ETHYLENE -

 There are many different types of receptor for ethylene like ETR1, ETR2, and ETHYLENE
INSENSITIVE4 (EIN4). ETR1 show the histidine kinase activity.  Any mutation in EIN2 will
lead to the loss of ethylene responsiveness throughout plant development.

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TOR PROTEINS

The TOR proteins were first identified in Saccharomyces cerevisiae, where rapamycin is growth-inhibitory.The rapamycin/FKBP12 complex binds directly to TOR, and the TOR mutations that confer rapamycin resistance in situ result in a loss of rapamycin/FKBP12 binding . The role of TOR as the rapamycin target responsible for inhibition of p70 S6 kinase .Rapamycin is an immunosurpressive whose cellular receptor is the cytosolic 12-kDa FK506-binding protein (FKBP12). Rapamycin binds to FKBP12  are immunosurpressive through inhibition of T-cell proliferation.  

PROTEINS SENSITIVE TO RAPAMYCIN-

1.The proteins eIF-4E BP1 and p70 S6 kinase each undergo an insulin/mitogen-stimulated phosphorylation in situ that is partially inhibited by rapamycin. mTOR mutants also protect eIF-4E BP1 against rapamycin-induced dephosphorylation, and for both p70 S6 kinase and eIF-4E BP1, such protection requires that the rapamycin-resistant mTOR variant retains an active catalytic domain. In contrast, mutants of p70 S6 kinase rendered intrinsically resistant to inhibition by rapamycin in situ are not able to protect coexpressed eIF-4E BP1 from rapamycin-induced dephosphorylation. We conclude that mTOR is an upstream regulator of eIF-4E BP1 as well as the p70 S6 kinase; moreover, these two mTOR targets are regulated in a parallel rather than sequential manner.

2.PHAS-1 is another rapamycin-sensitive protein; this 12-kDa polypeptide binds to the 7-methylguanosine cap-binding protein, eIF-4E, and prevents eIF-4E binding to p220/eIF-4G. 

PART -C QUESTION 
Insulin and other growth factors stimulates a pathway involving protein kinase m-TOR which in its turn augments protein synthesis .m-TOR  essentially modifies proteins which in their unmodified form act as inhibitors of protein synthesis .The following proteins are possible candidates -
A.eEF-1
B.eIF-4E-BP1
C.eIF-4E
D.PHAS-1
Which of the following sets are correct 
a. A & B                        c.A A& C 
b.B & D                         d.B & C 

ANSWER - b (B& D)

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NON STANDARD AMINO ACIDS

Apart from the 20 standard amino acids, all the rest amino acids are called as ‘non-standard’ amino acids. These include both proteinogenic as well as non-proteinogenic amino acids.  

Amino acid derivatives as proteins (Proteinogenic)

• 4-hydroxyproline = found in plant cell wall proteins, also  in collagen.
• 5-hydroxylysine= found in collagen
• 6-N-methyllysine= found in myosin, a muscle protein
• γ-carboxyglutamate = found in prothrombin  and certain other proteins that bind Ca₂⁺ ions.
• Desmosine= found in fibrous protein elastin
• N-Formylmethionine= It is initially the N-terminal residue of all prokaryotic proteins.

 D-amino acid residues form polypeptides that are generally found to constitute bacterial cell walls. Apart from this, certain bacterially produced peptide antibiotics also contain D amino acids like valinomycin, gramicidin A and actinomycin D. 

Other amino acids (Non-proteinogenic) 

Besides their role in protein synthesis, amino acids also serve various other important functions.

• Some amino acids act as neurotransmitters like γ-aminobutyric acid (GABA) that’s formed as a result of glutamate decarboxylation and dopamine that’s a tyrosine derivative.
•          Histamine which is formed as a result of decarboxylation of histidine is a local mediator of allergic reactions
•  Tyrosine derivative thyroxine is a thyroid hormone.
• Ornithine and citrulline are intermediates in the biosynthesis of arginine and urea cycle.
•  Homocysteine is an intermediate in amino acid metabolism.
• S-adenosylmethionine is a biological methylating reagent.
• Azaserine is a medically useful antibiotic.

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SEX DETERMINATION IN DROSOPHILA

Sex determination in Drosophila-
( By the ratio of x chromosomes to autosomes)

If X/A= 1 (female) XX:2A
If X/A =0.5 (male)XY:2A

1.XX genotyes-

In such embryos the Sxl Gene activated and produces a protein called Sxl protein.Which cause the splicing of tra pre mRna at a downstream 3' splice site and the termination codon is spliced out with the intron, which leads to production of tra protein. Tra protein interacts with Tra-2 proteins and together they direct the female specific splicing of dsx pre-mRNA ,which produces proteins that cause the embryo into a female .
( It is regulated in post transcriptional level).

2. XY genotyes-

In such embryos the sxl Gene is not activated and the sxl protein is not produced. So,tra premRNa spliced at an upstream site resulting in the inclusion of a premature stop codon in the mRNA producing a non functional Tra protein .

Without functional Tra the male specific splicing of dsx pre-mRNA takes place which produces male Dsx proteins that cause the embryo to develop into a male .

(Sxl- sex lethal 

Tra -Transformer
dSX-Double sex )

IMAGE SOURCE CREDIT-http://www.biocyclopedia.com/index/genetics/images/figure/f17.12.jpg

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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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