nterest5ng Factz!!

3 interesting facts about Windows

1. You can’t create a folder named “con”, without d help of any code!!

2. Write following text into notepad:

“bush hid the facts”

save file & re-open & see magic

3. Open Microsoft Word & type:

=rand(200, 99)

Biotechnology questionz!!

Today's SET 1 questions are:

1. What do you understand by endosperm culture? What is its significance? How it can help combat the problem of deforestation?

Q1. Endosperm is the tissue produced under the seeds of most flowering plants during fertilization. It surrounds the embryo and provides nutrition in the form of starch, oils and protein. Tissue culture methods used for culturing endosperm are known as endosperm culture, the basic steps involved in tissue culture are:

1. The immature seeds are dissected under aseptic conditions and endosperms along with embryos, are excised;
2. The excised endosperms are cultured on a suitable medium and embryos are removed after initial growth;
3. The initial callus phase is followed by 'embryogenesis' or 'shoot bud differentiation'
4. The shoots and roots may subsequently develop and complete triploid plants can be established for further use.

Significance:

1. Endosperm culture has been used to produce triploid plants as they are useful for production of seedless fruits (apple, banana, watermelon)
2. Endosperm culture has been used for the production of of trisomics for cytogenetic studies
3. Triploid plants produced by endosperm culture were found to be more vigorous than the parents for e.g. Petunia axillaris
4. Endosperm provides an experimental system for studying biosynthesis and metabolism of natural products e.g. Endosperm of coffee was shown to sysnthesize caffine
5. Triploid production by conventional method is laborious and may be unsuccesful. In such cases, endosperm culture is the only feasible technique

Deforestation refers to the cutting, clearing, and removal of rainforest or related ecosystems into less bio-diverse ecosystems such as pasture, cropland, or plantations. Endoperm culture can combat the problem of deforestation in the following ways:

1. Generally for afforestation seedling are planted but it may happen that the seeds may be destroyed by the insects rodents etc. Using Endosperm culture afforestation can be achieved without seeds ensuring 100 percent accuracy.
2. The time period for growth of plants is shortned using endosperm culture
3. Propagation of species which are on the verge of extinction can be brought about by the endosperm culture.

1. How the overexpression of a transgene be enhanced in a transformed cell?

Q2. A transgene is a gene that is introduced into a cell or animal from an external source.The over expression of transgene can be achieved by two ways:

1. Using inducible promoters: The transgene is placed is under the control of a inducible promoter for its experssion. These inducible promoters used to control transgene expression respond to chemicals. These chemical are added in the culture medium of the transfected cell. The chemical stimulation brings about activation and expression of the transgene. Thus more the amount of chemical more expression of the transgene will occur.

2. Using regulatory transcription factor: For the activation of the transgene certain transcription factors are required. Thus the trangene is said to be regulated by that transcription factor. Transcription factor's activity is controlled by the external stimulus or chemical. Since the chemical stimulus can activate only a particlar transcription factor which is required by that transgene no coincidental activation of other genes can occur. Thus when the concentration of the chemical or the stimulus increases in the surrounding overexpression of the transgene can be achieved.

Biotechnika Questions3

What is Protein Splicing? How it is different from AutoProteolysis? 

How Functional Complementation is used for Screening of Transformed cells from untransformed cells?

Describe Gubler-Hoffman Method?     

Answers:


 Protein splicingis an intramolecular reaction of a particular protein in which an internal protein segment (called an intein) is removed from a precursor protein with a ligation of C-terminal and N-terminal external proteins (calledexteins) on both sides.  The protein splicing reactions which are known now do not require exogenous cofactors or energy sources such as ATP, GTP. 
Autoproteolysis is a self degradation process in which protein (intein and extein) lysis occur without further ligation while in protein splicing intiens are removed and extiens are ligated back.  
 
2) Some vectors contain a gene which complements a function missing in their host cells eg. Gene lacZ alpha in pUC vector, whch complement such lacZ- E. coli strain in which lacZ alpha is deleted. in such case the DNA insert is so placed that it disrupt the function of lacZ alpha in the recombinant DNA.therefor E.coli  cells containing the r-DNA are deficient in B-galactosidase and produse white colony on X-gal containing media, while other cell producing blue colonies.this is we can differentiate them.
 
3) It is a simple method for generating cDNA libraries from sub microgram quantities of mRNA. This procedure considerably simplifies the establishment of cDNA libraries and thus the cloning of low-abundance mRNAs.
Following are the stages:-
Stage1: Synthesis of First-strand cDNA Catalyzed by Reverse Transcriptase
Stage2: Second-strand Synthesis
Stage 3: Methylation ofcDNA
Stage 4: Attachment of Linkers or Adaptors
Stage5: Fractionation of cDNA by Gel Filtration through SepharoseCL-4B
Stage 6: Ligation of cDNA to Bacteriophage Arms
This  describes the conversion of poly(A)+ mRNA into first-strand cDNA in a reaction catalyzed by a murine RNaseH- reverse transcriptase and primed by oligo(dT), random hexamers,or prime-adapters.

Answers :

otein splicing is defined as the excision of an intervening protein sequence (the INTEIN) from a protein precursor and the concomitant ligation of the flanking protein fragments (the EXTEINS) to form a mature extein host protein and the free intein . Protein splicing results in a native peptide bond between the ligated exteins.

Extein ligation differentiates protein splicing from other forms of autoproteolysis

Q2. Functional Complementation is helpful in screening of transformed cells from untransformed cells can be explained with an example of blue/white colony screening in Ecoli. Strains of Ecoli like JM109, DH5α have a mutation in LacZ that deletes part of the β-galactosidase (lacZ) gene. By using a plasmid that contains the deleted portion, or α-fragment, the function of the β-galactosidase gene can be restored once the plasmid has been incorporated into the bacterium.
For blue/white colony screening, the plasmids have a multiple cloning region within the coding sequence of the α-fragment. When a sequence is inserted into this cloning region, the reading frame is disrupted, and a non-functional α-fragment is produced. This fragment is incapable of α-complementation. Growing the transformed bacteria on a plate containing 5-bromo-4-chloro-3-indoyl-β -D-galactopyranosidase (X-gal) will allow you to distinguish between bacterial colonies formed from cells that contain plasmid with insert from those containing plasmid without insert. Any colony containing the plasmid (and therefore the functioning β-galactosidase gene) will turn blue, a result of the β-galactosidase activity. This is called α-complementation (Functional Complementation)

Q3. The Gubler-Hoffman method, is a  simplified version of Okayama and Berg's method used for non directional cDNA cloning.

1. The cDNA first sysnthesis is primed by oligo(dt) and catalaysed by reverse transcriptase.
2. The second strand synthesis is achieved by nick translation repair of the cDNA:mRNA hybrid, mediated by E.coli DNA polymerase I, RNase H, and E.coli DNA ligase.
3. Methylate cDNA
4. Attach linkers or adaptors for cloning
5. Fractionate cDNA by size (select 2-8 kb)
6. Ligate cDNA into bacteriophage arms

Biotechnika Questions 2

1. Which amino acid forms disulphide bond & why?
2. Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type of covalent bond.What is meant by the term "residue" in this context?
3. What is Molten Globule?
4. How are the properties of an alpha helix different from a beta strand? How are they similar? How do each of these secondary structure affect theproperties of a protein, such as silk?

Answers :-

1-Cysteine amino acid can form disulphide bond because it contain –SH (sulphahydral) group. Disulphide bond form between two cysteine amino acid by removal of one H2 molecule by oxidation.


 2-In this context a ‘residue’ means an amino acid molecule that has lost a water molecule by becoming joined to a molecule of another amino acid. 

 3-A molten globule is a stable, partially folded protiene state found in mildly deaturing conditions such as low pH  mild denaturant, or high temperture. Molten globules are collapsed and generally have some native-like secodary sructure but a dynamic tertiary strcture as seen by far and near circular dichromism (CD) specroscopy, respectively. These traits are similar to those observed in the transient intermediate states found during the folding of certain proteins, especially globular protiens that undergo hydrophobic collapse, and therefore the term "molten globule" is also used to refer to certain  protien folding
intermediates corresponding to the narrowing region of the folding funnel higher in energy than the native state but lower than the denatured state. The molten globule ensembles sampled during protein folding and unfolding are thought to be roughly similar.
4-Alpha helix and beta-sheet conformations are the two main types of secondary structure of a protein molecule.
In the alpha-helix structure, the polypeptide curls longitudinally by the action of hydrogen bonds forming a spiral, or helix. In the beta-sheet conformation, the protein is more distended and the hydrogen bonds form a zig-zag-shaped protein structure called B-strand. Many assembled beta-strands make a beta-sheet.
Alpha helix and beta sheet both are secondary structure of protein and involve hydrogen bonds.
Silk is made up of the amino acids Gly-Ser-Gly-Ala and forms Beta pleated sheets. H-bonds form between chains, and side chains form above and below the plane of the H-bond network.
The high proportion (50%) of glycine, which is a small amino acid, allows tight packing and the fibers are strong and resistant to stretching. The tensile strength is due to the many interseeded hydrogen bonds. Since the protein forms a Beta sheet, when stretched the force is applied to these strong bonds and they do not break.

other answers for ques - 4 

Difference: (i) Alpha helix is formed by hydrogen bonds between carbonyl oxygen of first amino and amide N of fourth amino acid residues while beta sheet is formed when hydrogen bonds are formed between the carbonyl oxygens and amide hydrogens of two or more adjacent extended polypeptide chains.
(ii)alpha helix show intra chain hydrogen bonding and cross linking by disulphide bond is present while beta sheet show interchain hydrogen bonding.
(iii)alpha helix are tough, insoluble showing varying flexibility and hardness while beta sheets are soft, flexible filaments.
(iv)Alpha helix are right or left handed, while beta sheets are parallel or antiparallel.
(v)polar residues are found in beta sheet while is absent in former.
Proline occurs in beta-pleated sheet.
Similarity:Both are secondary structure of protein and are stabilized by hydrogen bond

The polypeptide chains of silk fibroin, a protein of silk worm are predominantly rich in the beta pleated conformation. Fibroin is rich in Ala and Gly residues, permitting a close packing of sheets and an interlocking arrangement of R groups. The overall structure is stabilized by extensive hydrogen bonding between all peptide linkages in the polypeptides of each sheet and by the optimization of van der Waals interactions between sheets. Silk does not stretch, because the conformation is already highly extended. However, the structure is flexible because the sheets are held together by numerous weak interactions rather than by covalent bonds in other proteins such as the disulfide bonds in alpha-keratins

Biotechnika Questions1

Name two nonpolar amno acids.

• 1a) Sickle cell anaemia results from a substitution of a valine for a glutamate. What do you expect the effect might be if mutation were to have placed a leucine at that site? Or an aspartate?

Which of the two photosystems operates at the most negative redox potential?

• 2a) Which among them generates the strongest reducing agent?
• 2b) Which among them must absorb 4 photons during each round of non cyclic photophosphorylation?
• 2c) Name some accessory pigments that surround each
  photosystem?

AnsWERS :-

1. There are eight amino acids with nonpolar side chains. Glycine, alanine, and proline have small, nonpolar side chains and are all weakly hydrophobic.
Phenylalanine, valine, leucine, isoleucine, and methionine have larger side chains and are more strongly hydrophobic.

1a. Sickle cell anemia results is caused due to substitution of charged amino acid i.e glutamate (at the 6th position ) by valine which is non polar in nature hence due to the charge variance in the molecule the structure of the hemoglobin molecule changes drastically making it sickle shaped.
Leucine also has a non polar nature hence it would also result in abnormality of haemoglobin molecule.
However when you have a charged counterpart like aspartic acid which has the same equivalent charge and polar nature present in the molecule, replacing glutamate, it would not cause any abnormality in the haemoglobin molecule but would decrease the chain length by one Ch2 group which is additional in glutamate

Q2. PSI generates the most negative redox potential because it involves NADP+-NADPH coupled reaction which has a standard redox potential of -0.32V as compared to PSII which involves o2-H20 coupled reaction having a standard redox potential of +0.82V

Q2. a *** very imp** The strongest reducing agent is generated by photosystem Iit produces NADPH from NADP+
(note by:strong oxidising is produced by Photosystem II since it produces oxygen from water)

Q2b.Both the photosystems must absorb four photons.
(Explanation: The production of one molecule of oxygen requires the removal of four electrons from two water molecules.The removal of electrons from water requires the absorption of four photons, one for each electron. At the same time the reduction of one molecule of NADP+ requires transfer of 2 electrons. Thus hypotectically if only one photosystem were able to transfer electrons from H2O to NADP+, four photons would be sufficient to produce two molecules of NADPH. Because two photosystems are utilized in the cell that number is doubled to eight four being utilised by PSII and four in PSI.)

2 H2O + 2 NADP ----4Photons---> 1 O2 + 2 NADPH (Overall light reaction)

Q2c. Accessory Pigments are chlorophyll b (also c, d, and e in algae and protistans), xanthophylls, and carotenoids or phycobiliproteins (beta carotenoids)

vaccancy!!

Make your career at Cryobanks international as relationship Exec | B.Sc/B.Tech Biotech can apply

Cryobanks International India a JV between Cryobanks International USA and RJ Corp founded in 2006. Cryobanks International is a leader in the collection, processing and banking of umbilical cord blood stem cells.

Current vacancy:

Post: Relationship Executive

Job Description:

• Lead generation from OPDs and Clinincs
• Giving Home presentation
• Counseling regarding the concept of banking ones cord blood
• handling anti natal Classes
• Daily MIS

Required Skills:

• Good communication skill
• Comfprtable with home presentation
• Can do attitude
• Preferably from biotech background

Qualification & Experience

• exp- 0-2yrs
• qualification- MBA (Marketing)/B.Pharma/ B.Sc/B.Tech(biotech).
• In case of any other graduation stream then the person must be an MBA

Send your resume to: Nayantara@cryobanksindia.com

Freshers can join Aptara Corporation as Editors | B.Tech/M.Sc Biotech, Life Sciences can apply

Aptara Corporation- Transforming Content into Knowledge

Aptara is an American company in providing electronic content solutions through the integration of technology & global resources.Our clients include publishers, information aggregators, professional societies, government agencies, universities presses.

Current vacancy:

• Post: Editor/Trainee Editor
• Experience: 0 - 3 Years
• Location: DehradunQualification: B.Tech/M.Sc Life Sciences

Desired Candidate Profile

• Graduate or Post graduate in Science / Biotechnology/ Microbiology.Extreme attention to detail, Avid reader , Thirst for knowledge, Meticulous

Job Description

• Excellent knowledge of English grammar and good communication skills, Check spelling, grammar and punctuation are correct .Read and edit for sense, accuracy and clarity.good eye for detail and grammatical accuracy .

Interested candidates can apply to Bishwajeet Kumar atBishwajeet.kumar@aptaracorp.com with reference id: Aptara.Bishwajeet.CE/DDN/MB

Website: http://www.aptaracorp.com

Biotechnika Questions

1. 
   What are Secondary Metabolites? How they are Produced ? Give 2 Examples of Secondary Metabolite & Elaborate their role. How do they differ from Primary Metabolite.?

Secondary metabolite are mainly found in plant and microorganisms. They are formed along with specialized pathways from primary metabolites such as amino acid, nuclis acids, carbohydrate etc.The secondray metabolites has no role in primary functions like photosynthesis, growth or reprodution.Human usese some this metabolites as medicine, flavouring and recreational drug.Some of these Nitrogeh cotaining(alkaloids) and remainings are non nitrogenous.
     Secondary metabolites are produced from the intermediate productes of primary metabolism pathways.
         Classification of secondary metabolites:
           1.Polyketides and Fatty acid- Formed by accetate and derived from accetyl coenzyme A
           2. Terpenoids and Steroids- isoprenoid C5 unites derived from Isopentyl phosphate
           3. Phenyl propanoids
           4.Alkaloids
           5.Specialized amino acid and peptides
           6.Specialized carbohydrate
Example: Alkaloids- Resarpin- Found in Rauvolifa sepentia "Sarpagandha" Plant used for High blood pressure medicine
              Niccotin- Found in Tobacco plant- interfer with neurotranmission .
Diffrence between Primary and secondary metabolites:
1.Secondary metabolites are mainly found in plant and some microorganisms where primary metabolites are largly distributed among living thigs.
2. Secondary metabolites are non essentials to primary fuctions in plant body where as primary metabolites are essential.
3. secondary metabolites are produced from intermediate of primary mebolite synthesis pathways.
4. secondary metabolites are caracteristics of some plant depending on whichs a taxonomic classification of plant can possible.

=> Secondary metabolites (SM) are organic compounds not directly involved in the normal growth, development or reproduction of organisms, their absence results in mild impairment for the organisms such as lowered survivality/fecundity, aesthetic differences, or else no change in phenotype at all.

• Most SMs are products of primary metabolic pathway (viz. photosynthesis), originally thought to be the waste products shunted into the dumping ground of the vacuole.
• SMs often accumulate in a  restricted range of species, sometimes in a single species or genus, and often within a specific organ or tissue or at a specific stage of development within a single species.        

Example of two secondary metabollites:

1. Alkaloid used as drug: Quinine from Cinchona barkas anti-malarial.
2. As Flavour:  Saffron from Crocus sativus (dried stigma).

Primary vs. Secondary Metabolisms:

While primary metabolim consists of biochemical pathways that are in general common to all cells, secondary metabolisms consist of a large number of diverse processes that are specific to certain cell types. Plant pigments, alkaloids, isoprenoids, terpenes, and waxes are some examples of secondary products. The role of many of the secondary products has been rather ambiguous, and initially they were thought to be just waste materials. However, considering their non-motile nature and the lack of sophisticated immune system that we have, plants had to develop their own defence system against pathogens and predators, and systems to lure motile creatures for fertilization and dissemination. Indeed, many of the secondary products are bacteriocidal, repellent (by bad tastes, etc), or even poisonous to pests and hervibores. Pigments of flowers would give attractive colors for insects that help with fertilization, or warning colors against predators. Plant pigments also provide protection against environmental harms, such as free radiacls and UV irradiation. Some of the secondary products perform signalling function as plant hormones.

Many of these secondary products are originally meant for defence against herbivores such as insects which would soon come up with metabolic pathways todetoxify and even utilize these defence compounds. During eveolutionary processes, animals developed a variety of dependencies to phytochemicals, including the secondary products that are, with or without modification, used as procursors for the synthesis of vital or benefitial molecules in animal body.

Secondary plant products have for thousands of years played an essential role in medicine. Traditionally, they have been directly used as food and herbs. Nowadays, they are used either directly or after chemical modification. Plant secondary metabolites represent a tremendous resources for scientific and clinical researches and new drug development. Overall, their pharmacological value not only remains undeminished until today, but is increasing due to constant discoveries of their pontential roles in healthcare and as lead chemicals for new drug development.


Ques:-
If you were to add HCl to water , what effect would this have on the hydrogen ion concentration? On the pH? On the ionic charge of any protein in solution? What is the relationship between a conjugate acid & its base?

When HCl is added to water, HCl donates a hydrogen ion to water to form a hydronium ion. HCl acts as a Bronsted Acid and water as a bronsted base here.Both the hydrogen ion concentration and the pH of the solution remains the same and hence, even the charge of any protein inside the solution remains unchanged.
HCl ------> H+ + Cl-
H2O <------> H+ + OH-
__________________________
HCl + H2O ------> H3O+ + Cl-
__________________________

Conjugate acid and its base are related to each other by donating and accepting a single proton to and from each other respectively.

=> 

water has a buffering capacity. most of the water molecules remain intact but small amount of it reacts to produce hydronium ion(H3O+) which accounts for the acidic property of water. when HCl is added to water, hydronium ion concentration increases resulting in decrease of pH. so, HCl is used to decrease pH, however, the exact quantity needed depends upon water buffering capacity. as the pH of solution decreases due to addition of HCl, the amino and carboxyl groups of protein  will be protonated and the molecule will be in the acidic form. generally mineral acids are used for isolelectric precipitation of protein in solution. when an acid donates a proton, it forms a conjugate base. HCl + H2O.......Cl- +  H3O+  HCl and chloride ion as well as H2O and H3O+ are conjugate acid base pairs.