Cytoskeleton
Free online life science study material. Made up of actin filaments or microfilaments, intermediate filaments and microtubules.
Intermediate filaments are absent in plants except for lamins because they have rigid cell wall.
Microfilaments
7nm in diameter, filamentous and smallest among the three.
Mainly involved in muscle contraction, locomotion and cell migration, cytoplasmic streaming, cell attachment to extra cellular matrix, cell cell attachment for tissue formation etc.
Free online life science study material. Made up of actin filaments or microfilaments, intermediate filaments and microtubules.
Intermediate filaments are absent in plants except for lamins because they have rigid cell wall.
Microfilaments
7nm in diameter, filamentous and smallest among the three.
Mainly involved in muscle contraction, locomotion and cell migration, cytoplasmic streaming, cell attachment to extra cellular matrix, cell cell attachment for tissue formation etc.
Actin protein is basic unit of microfilament. It is a globular protein with ATP/ADP binding site. It is U shaped protein. The individual subunits are called G- actin and polymer is called F- actin.
The F actin is a polar structure with pointed and barbed ends.
The initial polymerisation is called nucleation. During nucleation three monomers should fit in right manner to form the filament.
Once three monomers are correctly allighned the subsequent monomers can be added through reversible addition.
At the pointed end there is ADP and at barbed end there is ATP present.For polymerisation hydrolysis of ATP is not required.
It only enhances the rate of asembly.
Actin binding proteins:
The F actin is a polar structure with pointed and barbed ends.
The initial polymerisation is called nucleation. During nucleation three monomers should fit in right manner to form the filament.
Once three monomers are correctly allighned the subsequent monomers can be added through reversible addition.
At the pointed end there is ADP and at barbed end there is ATP present.For polymerisation hydrolysis of ATP is not required.
It only enhances the rate of asembly.
Actin binding proteins:
1. Formin: These are barbed end tracking proteins which nucleate the actin monomers.Also move along growing polymers.
2.Arp 2/3 : Causes branching of actin filament. Branching is important for cell migration and cell movement.
3.Cofilin: This is required for remodeling of existing actin filament. ADP actin gets bound to cofilin so reassembly is prevented.
Profilin:Causes exchange of ADP for ATP.The subunit can no longer bound to cofilin and reassembly can take place
2.Arp 2/3 : Causes branching of actin filament. Branching is important for cell migration and cell movement.
3.Cofilin: This is required for remodeling of existing actin filament. ADP actin gets bound to cofilin so reassembly is prevented.
Profilin:Causes exchange of ADP for ATP.The subunit can no longer bound to cofilin and reassembly can take place
Lysosomal disease
Free online life science study material.
Lysosomal disease:
1. Type II glycogenosis: The lysosomal enzyme alpha- 1,4 glycosidase is defected. This enzyme when present breakdown glycogen.
2.Hunter's Syndrome: Due to accumulation of glycoamino glycans. These are major polysaccharide in extra cellular matrix. It is basically X linked recessive disease in which iduronate 2 sulphatase enzyme gets defected.
3. Hurler's syndrome: Autosomal recessive disorder. Enzyme alpha L idurodinase is defected. it is also glycoamino glycan accumulating disease.
Tay Sach's disease: Beta N acetyl hexoseaminidase A enzyme is defective. The ganglioside gets accumulated.
I cell disease: NAG phosphotransferase enzyme is non functional.
1. Type II glycogenosis: The lysosomal enzyme alpha- 1,4 glycosidase is defected. This enzyme when present breakdown glycogen.
2.Hunter's Syndrome: Due to accumulation of glycoamino glycans. These are major polysaccharide in extra cellular matrix. It is basically X linked recessive disease in which iduronate 2 sulphatase enzyme gets defected.
3. Hurler's syndrome: Autosomal recessive disorder. Enzyme alpha L idurodinase is defected. it is also glycoamino glycan accumulating disease.
Tay Sach's disease: Beta N acetyl hexoseaminidase A enzyme is defective. The ganglioside gets accumulated.
I cell disease: NAG phosphotransferase enzyme is non functional.
Peroxisomes:
These are very small, ubiquitous, variable and single membrane bodies.
These have crystalline core made up of urate oxidase.
In animals the catalase enzyme is present in periphery along with core.
It metabolises hydrogen peroxidase by help of catalase enzyme.
It also detoxicate various harmful substances such as methanol, ethanol, phenol etc.
In animals fatty acid oxidation takes place in it.
Some fats and lipids are also synthesies in peroxisomes.
Disorders:
Single enzyme defect includes X-ALD(X- linked adrenoleuco dystrophy). In this, one of the transport protein found in membrane of peroxisome is defective.
This protein is involved in transport of long fatty acid chain inside peroxisome.As a result long fatty acid chain accumulates in cytoplasm.
Another type of disease result from defect in mechanism involved in biosynthesis of peroxisome.Zellweger's syndrome is fatal genetic disease. The defect lies in numerous membrane transporters involved in transport of peroxisomal enzymes inside peroxisomes. So, peroxisomes without enzymes are called empty ghosts.PEX genes are found to be responsible of such disease.
These are very small, ubiquitous, variable and single membrane bodies.
These have crystalline core made up of urate oxidase.
In animals the catalase enzyme is present in periphery along with core.
It metabolises hydrogen peroxidase by help of catalase enzyme.
It also detoxicate various harmful substances such as methanol, ethanol, phenol etc.
In animals fatty acid oxidation takes place in it.
Some fats and lipids are also synthesies in peroxisomes.
Disorders:
Single enzyme defect includes X-ALD(X- linked adrenoleuco dystrophy). In this, one of the transport protein found in membrane of peroxisome is defective.
This protein is involved in transport of long fatty acid chain inside peroxisome.As a result long fatty acid chain accumulates in cytoplasm.
Another type of disease result from defect in mechanism involved in biosynthesis of peroxisome.Zellweger's syndrome is fatal genetic disease. The defect lies in numerous membrane transporters involved in transport of peroxisomal enzymes inside peroxisomes. So, peroxisomes without enzymes are called empty ghosts.PEX genes are found to be responsible of such disease.
Friday, November 7, 2014
Golgi Bodies
Golgi Bodies
Final processing of proteins take place in Golgi bodies.
Lipid synthesis takes place in it.
The mannose-6-Phosphate tagging of N- linked glycosylated protein takes place in Golgi. This tagged glycoprotein is directed to lysosome only.
Sulphation of tyrosine residue of proteins takes place here.
Proteolytic cleavage of certain protein also takes place in it.
Golgi has glycerol based phospholipid (Phosphatidyl choline), the choline group is transferred to ceramides to form sphingiomyelin in Golgi.
The Golgi release carbohydrate during cell plate formation in cell division.
Lysosomes
These are single membrane organelle.
They consist of variety of hydrolytic enzymes and function at acidic pH.
The membrane on the inner side of lysosome has carbohydrate coating which protect it from enzymes present inside it.
Many membrane proteins function as H+ ATPase to pump H+ inside lysosome.
It contains different phosphatase, protease, peptidase, nuclease, lipase etc variety of enzymes for degradation of complex molecules.
When a cell engulf a foreign material by endocytosis it forms early endosomes(fused product of plasma membrane and trans golgi).
When more content is delivered from Golgi to early endosome it becomes late endosome.
The enzymes of endosomes are inactive as they require acidic environment for activation, the acidic environment can be achived by two mechanisms: 1. Late endosome fuse with already existing lysosome or 2. The lumen can be made acidic by H+ATPase pump activity.
Lysosome can be heterophagic: containing extracellular material or autophagic: containing own cell material.
Free life science study material.
Final processing of proteins take place in Golgi bodies.
Lipid synthesis takes place in it.
The mannose-6-Phosphate tagging of N- linked glycosylated protein takes place in Golgi. This tagged glycoprotein is directed to lysosome only.
Sulphation of tyrosine residue of proteins takes place here.
Proteolytic cleavage of certain protein also takes place in it.
Golgi has glycerol based phospholipid (Phosphatidyl choline), the choline group is transferred to ceramides to form sphingiomyelin in Golgi.
The Golgi release carbohydrate during cell plate formation in cell division.
Lysosomes
These are single membrane organelle.
They consist of variety of hydrolytic enzymes and function at acidic pH.
The membrane on the inner side of lysosome has carbohydrate coating which protect it from enzymes present inside it.
Many membrane proteins function as H+ ATPase to pump H+ inside lysosome.
It contains different phosphatase, protease, peptidase, nuclease, lipase etc variety of enzymes for degradation of complex molecules.
When a cell engulf a foreign material by endocytosis it forms early endosomes(fused product of plasma membrane and trans golgi).
When more content is delivered from Golgi to early endosome it becomes late endosome.
The enzymes of endosomes are inactive as they require acidic environment for activation, the acidic environment can be achived by two mechanisms: 1. Late endosome fuse with already existing lysosome or 2. The lumen can be made acidic by H+ATPase pump activity.
Lysosome can be heterophagic: containing extracellular material or autophagic: containing own cell material.
Thursday, October 30, 2014
To continue with ER..
Free online life science study material.
Modification of added sugar residue.
It always start in ER but continues to Golgi bodies.
It start witnremoval of 3 glucose and 1 mannose unit.
Enzyme glucosidase remove it.
Before removal of sugars calnexin and calreticulin (chaperons) bind to incompletely folded protein and retain that in ER. These chaperons form disulphide bond in newly formed protein.The disulphide bond formation provides stability to secretory protein outside where extreme environment is present.
An enzyme protein disulphide isomerase also help in disulphide bond formation.
Also lumen of ER has oxidising environment which favors disulphide bond formation.
When 3rd glucose is removed the chaperons are also removed and the protein is folded and transported to Golgi.
Removal of improper protein
Proper confirmation and sugar residues are monitored by UGGT(UDP glucose glycoprotein glucotransferase).
UGGT will interact with folded protein.
If UGGT find improper protein it adds back a glucose molecule, this brings the chaperons calnexin and calreticulin to bind and break the disulphide bond and the reaction is repeated till proper protein is formed.
Another mechanism to get rid of misfolded protein
When protein gets misfolded the hydrophobic regions are exposed.
Due to hydrophobic interaction these protein aggregate and cause other properly folded protein to disrupt their structure and interact with these aggregates.
These misfolded protein themselve act as catalyst.
So, these misfolded proteins are transported to cytoplasm and ubiquitinised by proteosome.
Cystic fibrosis, Alzeimer's disease are examples of misfolded proteins.
It always start in ER but continues to Golgi bodies.
It start witnremoval of 3 glucose and 1 mannose unit.
Enzyme glucosidase remove it.
Before removal of sugars calnexin and calreticulin (chaperons) bind to incompletely folded protein and retain that in ER. These chaperons form disulphide bond in newly formed protein.The disulphide bond formation provides stability to secretory protein outside where extreme environment is present.
An enzyme protein disulphide isomerase also help in disulphide bond formation.
Also lumen of ER has oxidising environment which favors disulphide bond formation.
When 3rd glucose is removed the chaperons are also removed and the protein is folded and transported to Golgi.
Removal of improper protein
Proper confirmation and sugar residues are monitored by UGGT(UDP glucose glycoprotein glucotransferase).
UGGT will interact with folded protein.
If UGGT find improper protein it adds back a glucose molecule, this brings the chaperons calnexin and calreticulin to bind and break the disulphide bond and the reaction is repeated till proper protein is formed.
Another mechanism to get rid of misfolded protein
When protein gets misfolded the hydrophobic regions are exposed.
Due to hydrophobic interaction these protein aggregate and cause other properly folded protein to disrupt their structure and interact with these aggregates.
These misfolded protein themselve act as catalyst.
So, these misfolded proteins are transported to cytoplasm and ubiquitinised by proteosome.
Cystic fibrosis, Alzeimer's disease are examples of misfolded proteins.
Monday, October 27, 2014
Endomembrane system
Endomembrane system
Endoplasmic reticulum, golgi bodies, lysosome and peroxisomes.
To start with Endoplasmic reticuum ER.
There are two types of ER. Smooth ER or SER and Rough ER or RER.
RER made up of cisternae with ribosomes attached and SER are tubular and lack ribosomes.
Important function of RER:
Glycosylation of protein.
Folding of protein.
Removal of mis folded protein.
Assembly of multi subunit protein.
When protein is made on ribosomes attached to ER and is transported into ER simultaneously then this movement is caled cotranslational translocation.
When protein is made on free ribosomes and then it is translocated in ER then the movement is called post translational translocation.
Glycosylation of protein or addition of carbohydrates on protein.
All N linked glycosylation of protein takes place in RER.
In this the carbohydrate will attach to NH2 of asparagine always.
All asparagine which are part of Asp-X-Ser will be N linked glycosylated. X can be any amino acid except proline and Ser is serine.
O linked glycosylation always takes place in Golgi body.
N linked glycosylation is of two types 1. Core glycosylation or initial glycosylation and 2. modification of added sugar.
Core Glycosyalation:
It always start with addition of N acetyl glucose amine or NAG by the help of enzyme oligosaccharyl transferase. This enzyme add 15-16 sugars to protein.
ER membrane has Dolichol phosphate and NAG and mannose are added to it towards cytosol.
So two NAG and 5-7 mannose are added towards cytosolic side of ER.
Then translocation of oligosaccharide from cytosol to ER lumen takes place with the help of Flippase.
Desired number of saccharides including mannose, glucose are added in luminal side of ER.
With the help of enzyme oligosaccharyl transferase completed core of oligosaccharide is transffered to asparagine residue of protein.
Finally certain sugar residues are added or removed for final processing.
Endoplasmic reticulum, golgi bodies, lysosome and peroxisomes.
To start with Endoplasmic reticuum ER.
There are two types of ER. Smooth ER or SER and Rough ER or RER.
RER made up of cisternae with ribosomes attached and SER are tubular and lack ribosomes.
Important function of RER:
Glycosylation of protein.
Folding of protein.
Removal of mis folded protein.
Assembly of multi subunit protein.
When protein is made on ribosomes attached to ER and is transported into ER simultaneously then this movement is caled cotranslational translocation.
When protein is made on free ribosomes and then it is translocated in ER then the movement is called post translational translocation.
Glycosylation of protein or addition of carbohydrates on protein.
All N linked glycosylation of protein takes place in RER.
In this the carbohydrate will attach to NH2 of asparagine always.
All asparagine which are part of Asp-X-Ser will be N linked glycosylated. X can be any amino acid except proline and Ser is serine.
O linked glycosylation always takes place in Golgi body.
N linked glycosylation is of two types 1. Core glycosylation or initial glycosylation and 2. modification of added sugar.
Core Glycosyalation:
It always start with addition of N acetyl glucose amine or NAG by the help of enzyme oligosaccharyl transferase. This enzyme add 15-16 sugars to protein.
ER membrane has Dolichol phosphate and NAG and mannose are added to it towards cytosol.
So two NAG and 5-7 mannose are added towards cytosolic side of ER.
Then translocation of oligosaccharide from cytosol to ER lumen takes place with the help of Flippase.
Desired number of saccharides including mannose, glucose are added in luminal side of ER.
With the help of enzyme oligosaccharyl transferase completed core of oligosaccharide is transffered to asparagine residue of protein.
Finally certain sugar residues are added or removed for final processing.
Signal transduction
Hi All
To continue with signal transduction...
Another pathway includes PIP2 which is phosphatidyl inositol biphosphate. It exist in inner plasma membrane.
Phospholipase C acts on PIP2 and convert it into DAG(diacyl glycerol) and IP3(inositol 1,4,5 triphosphate).
DAG remain attach to plasma membrane and IP3 is diffused in cytosol.
DAG activate PKC protein kinase C.
DAG controls cell differentiation, cell growth and cell death.
It serve as transcriptional activator.
DAG can be further cleaved to give arachidonic acid.
IP3 acts as a signal which binds to IP3 gated calcium release channel on endoplasmic reticulum.It releases calcium in cytoplasm from endoplasmic reticulum.
Calcium is secondary messanger and can activate several protein kinase.
One target of calcium is calmodulin.
Calmodulin has two arms and each arm has two calcium binding sites.
When calcium level are lower than calcium is released from calmodulin but when calcium is higher (as in reponse to IP3) calcium binds to calmodulin and its confirmation gets changed and gets activated.
Calmodulin is also known as CaM kinase or calcium dependent protein kinase.
CaM is present in nervous system of most animals and is involved in learning and memory.
CaM also regulate gene expression.
AKT pathway.
It involves PI3 kinase(phosphatidyl inositol-3 kinase).It converts PIP2 into PIP3.
AKT is serine threonine kinase and is activated by PIP3.
IGF insulin growth factor signal AKT pathway.
IGF bind to receptor tyrosine kinase and activate PIP3 kinase.
PIP3 is kinase and it recruit AKT and PDK-1.So AKT gets activated.
Target of AKT is FOXO protein which is a transcription factor.
When FOXO is unphosphorylated, it enters nucleus and cause transcription of those genes which are required in cell deat etc.
But when phosphorylated by AKT, FOXO becomes inactive and cannot translocate to nucleus hence no response.
Another target of AKT is GSK3 beta kinase.
GSK 3 beta is active when unphosphorylated. It phosphorylate target and regulates cell proliferation and cell survival.
When signal comes or AKT phophorylate GSK3 beta it becomes inactive.
MAP or ERK pathway
It is also known as mitogen activator protein because it involves Ras protein.
ERK extra cellular signal regulated kinase.
ERK can be activated by GPCR or tyrosine kinase receptor.
In case of receptor tyrosine kinase, when signal activates receptor tyrosine kinase, it dimerizes and autophosphorylation.
Then ovel sites are exposed and they recruit Ras Guanine nucleotide exchange factor or Ras GEF.
Ras GEF has SH2 domain which is called Grb2 domain.
Cytoplasm has Raf protein. And Raf is activated by Ras GEF.
Target of Raf are another protein kinase called MEK or MAP/ERK kinase.
MEK phosphorylate MAP.
To continue with signal transduction...
Another pathway includes PIP2 which is phosphatidyl inositol biphosphate. It exist in inner plasma membrane.
Phospholipase C acts on PIP2 and convert it into DAG(diacyl glycerol) and IP3(inositol 1,4,5 triphosphate).
DAG remain attach to plasma membrane and IP3 is diffused in cytosol.
DAG activate PKC protein kinase C.
DAG controls cell differentiation, cell growth and cell death.
It serve as transcriptional activator.
DAG can be further cleaved to give arachidonic acid.
IP3 acts as a signal which binds to IP3 gated calcium release channel on endoplasmic reticulum.It releases calcium in cytoplasm from endoplasmic reticulum.
Calcium is secondary messanger and can activate several protein kinase.
One target of calcium is calmodulin.
Calmodulin has two arms and each arm has two calcium binding sites.
When calcium level are lower than calcium is released from calmodulin but when calcium is higher (as in reponse to IP3) calcium binds to calmodulin and its confirmation gets changed and gets activated.
Calmodulin is also known as CaM kinase or calcium dependent protein kinase.
CaM is present in nervous system of most animals and is involved in learning and memory.
CaM also regulate gene expression.
AKT pathway.
It involves PI3 kinase(phosphatidyl inositol-3 kinase).It converts PIP2 into PIP3.
AKT is serine threonine kinase and is activated by PIP3.
IGF insulin growth factor signal AKT pathway.
IGF bind to receptor tyrosine kinase and activate PIP3 kinase.
PIP3 is kinase and it recruit AKT and PDK-1.So AKT gets activated.
Target of AKT is FOXO protein which is a transcription factor.
When FOXO is unphosphorylated, it enters nucleus and cause transcription of those genes which are required in cell deat etc.
But when phosphorylated by AKT, FOXO becomes inactive and cannot translocate to nucleus hence no response.
Another target of AKT is GSK3 beta kinase.
GSK 3 beta is active when unphosphorylated. It phosphorylate target and regulates cell proliferation and cell survival.
When signal comes or AKT phophorylate GSK3 beta it becomes inactive.
MAP or ERK pathway
It is also known as mitogen activator protein because it involves Ras protein.
ERK extra cellular signal regulated kinase.
ERK can be activated by GPCR or tyrosine kinase receptor.
In case of receptor tyrosine kinase, when signal activates receptor tyrosine kinase, it dimerizes and autophosphorylation.
Then ovel sites are exposed and they recruit Ras Guanine nucleotide exchange factor or Ras GEF.
Ras GEF has SH2 domain which is called Grb2 domain.
Cytoplasm has Raf protein. And Raf is activated by Ras GEF.
Target of Raf are another protein kinase called MEK or MAP/ERK kinase.
MEK phosphorylate MAP.
Tuesday, October 14, 2014
Signal transduction continue..
Hi All
To continue with signal transduction...
Signal cGMP
GTP is converted to cGMP by enzyme guanyl cyclase. NO,CO gases activates guanyl cyclase.
In the retina rhodopsin is linked to G protein. Rhodopsin is G protein coupled receptor and is part of rod cells of retina.
The G alpha protein of rhodopsin are called transducin.
Initially rhodopsin has 11 cis retinal molecule.
When light falls on retina, the 11 cis retinal is converted to all transretinal.
It changes the conformation of receptor opsin and G alpha or transducin dissociates and binds to cGMP phophodiesterse.
Phosphodiesterse breaks cGMP.
Decrease in the level of cGMP in rod cells initiates a nerve impulse. Since cGMP acts on sodium channels in plasma membranes of neurons, the sodium channels get closed in response to decrease in cGMP level.
So basically the role of CGMP is conversion of visual signal into electrical stimulus.
Point to be noted here is I have not discussed the dissociation of alpha beta nad gamma of G protein as already discussed in earlier blog.
JAK/STAT pathway or Janus Kinase pathway
This is very short and very fast pathway which directly involves interaction with transcription factors with receptors on membrane.
It is cytokine receptor pathway.
STAT signal transducers and activators of transcription.
When the cytokine binds the receptor it dimerises and recruit STAT on both at cytosolic domain.
JAK are cytosolic kinase on cytosolic sides of receptor dimer.
As STAT are recruited JAK phosphorylate STAT ad STAT after phosphorylation released from JAK and form STAT dimer in cytoplasm.STAT dimer's nuclear localising signal is exposed as they dimerise and now they can go to nucleus.
They pass to nucleus and interact with genes and cause change in gene expression.
Thankyou for reading.
To continue with signal transduction...
Signal cGMP
GTP is converted to cGMP by enzyme guanyl cyclase. NO,CO gases activates guanyl cyclase.
In the retina rhodopsin is linked to G protein. Rhodopsin is G protein coupled receptor and is part of rod cells of retina.
The G alpha protein of rhodopsin are called transducin.
Initially rhodopsin has 11 cis retinal molecule.
When light falls on retina, the 11 cis retinal is converted to all transretinal.
It changes the conformation of receptor opsin and G alpha or transducin dissociates and binds to cGMP phophodiesterse.
Phosphodiesterse breaks cGMP.
Decrease in the level of cGMP in rod cells initiates a nerve impulse. Since cGMP acts on sodium channels in plasma membranes of neurons, the sodium channels get closed in response to decrease in cGMP level.
So basically the role of CGMP is conversion of visual signal into electrical stimulus.
Point to be noted here is I have not discussed the dissociation of alpha beta nad gamma of G protein as already discussed in earlier blog.
JAK/STAT pathway or Janus Kinase pathway
This is very short and very fast pathway which directly involves interaction with transcription factors with receptors on membrane.
It is cytokine receptor pathway.
STAT signal transducers and activators of transcription.
When the cytokine binds the receptor it dimerises and recruit STAT on both at cytosolic domain.
JAK are cytosolic kinase on cytosolic sides of receptor dimer.
As STAT are recruited JAK phosphorylate STAT ad STAT after phosphorylation released from JAK and form STAT dimer in cytoplasm.STAT dimer's nuclear localising signal is exposed as they dimerise and now they can go to nucleus.
They pass to nucleus and interact with genes and cause change in gene expression.
Thankyou for reading.
More On Signal Transduction
Hello Friends
to continue with signal transduction
The first signal transduction pathway to discuss today is cAMP pathway.
High level of epinephrine induce or stimulate this pathway.
In this pathway epinephrine is primary messanger and cAMP is secondary messanger.
When epinephrine bind to G protein coupled receptor, the GDP is exchanged with GTP and alpha subunit of trimeric G protein is released from it and interacts with adenyl cyclase and starts producing cAMP.
cAMP activates protein kinase A. Protein kinase A is a tetramer of two regulatory and two catalytic subunits.So when cAMP binds to regulatory subunit it gets confirmation change in regulatory subunit and separates from catalytic subunit which results in activated protein kinase A.
Protein kinase A activates phosphorylase kinase A.
Activated Phosphorylase kinase A activates glycogen phosphorylase. Glycogen phosphorylase is enzyme used to convert glycogen to glucose.
Protein kinase A also phosphorylate glycogen synthase. Phophorylation of glycogen synthase inactivates this enzyme and inhibit glycogen synthesis.
Increase in cAMP leads to
Enhanced degradation of storage feuls, increase of acid secretion by gastric mucosa,
decrease in aggregation of blood platelets.
In odorant receptors of nose are coupled to G protein coupled receptors.
Stimulus leads to increase in cAMP level and cAMP directly act on sodium ion channel in plasma membrane and causes depolarisation of membrane and initiation of nerve impulse.
G protein are also involved in cholera and whooping cough.
In cholera, the part of cholera toxin has enzymatic activity and inhibits hydrolysis of GTP, So GTP is permanently bound which leads to constant salt secretion, water secretion and ultimately to dehydration.
Hope this will help you all. See you all with next topic.
Thankyou for reading.
to continue with signal transduction
The first signal transduction pathway to discuss today is cAMP pathway.
High level of epinephrine induce or stimulate this pathway.
In this pathway epinephrine is primary messanger and cAMP is secondary messanger.
When epinephrine bind to G protein coupled receptor, the GDP is exchanged with GTP and alpha subunit of trimeric G protein is released from it and interacts with adenyl cyclase and starts producing cAMP.
cAMP activates protein kinase A. Protein kinase A is a tetramer of two regulatory and two catalytic subunits.So when cAMP binds to regulatory subunit it gets confirmation change in regulatory subunit and separates from catalytic subunit which results in activated protein kinase A.
Protein kinase A activates phosphorylase kinase A.
Activated Phosphorylase kinase A activates glycogen phosphorylase. Glycogen phosphorylase is enzyme used to convert glycogen to glucose.
Protein kinase A also phosphorylate glycogen synthase. Phophorylation of glycogen synthase inactivates this enzyme and inhibit glycogen synthesis.
Increase in cAMP leads to
Enhanced degradation of storage feuls, increase of acid secretion by gastric mucosa,
decrease in aggregation of blood platelets.
In odorant receptors of nose are coupled to G protein coupled receptors.
Stimulus leads to increase in cAMP level and cAMP directly act on sodium ion channel in plasma membrane and causes depolarisation of membrane and initiation of nerve impulse.
G protein are also involved in cholera and whooping cough.
In cholera, the part of cholera toxin has enzymatic activity and inhibits hydrolysis of GTP, So GTP is permanently bound which leads to constant salt secretion, water secretion and ultimately to dehydration.
Hope this will help you all. See you all with next topic.
Thankyou for reading.
Friday, October 10, 2014
Types of receptors
Hello Friends
To continue with signal tranduction.
free life science study material. Types of receptors.
1. G protein coupled receptors: Largest family of receptors.
These are GTP coupled proteins and transmembrane protein.This receptor have 7 transmembrane segments alpha helical in nature.
G protein has three subunits alpha , beta and gamma (heterotrimeric).
GTP/GDP binding sites are present on alpha subunits.
When ligand bind the receptor the GDP gets exchanged with GTP on G alpha subunit.
When GTP binds to alpha the affinity of alpha decreases for beta and gamma and is free to interact with target.
Beta and gamma can also act as signals.
2. Protein tyrosine kinase receptor: are directly linked to enzyme activity.
It has three subunits: N terminus which is ligand binding site, transmembrane segment and C terminus which is cytosolic and has intrinsic tyrosine kinase activity.
When ligand bind to N terminus it causes dimerization of receptor.(ligand can be monomer or dimer).
After dimerization the kinase activity of C terminal gets activated and cross phosphorylates the opposite C Terminal and then autophosphorylation takes place.The protein that can bind to phosphorylated tyrosine are :
a) Which have SH2 (src homology) domain and
b) Which have PTB (phosphotyrosine binding domain). Either of them can bind to activated protein tyrosine kinase receptor.
3. Cytokine receptor: Similar to tyrosine kinase receptor. The only difference is it does not have intrinsic tyrosine kinase activity.
When ligand bind it causes dimerization and affinity for cytosolic kinase increases. The cytosolic kinase bind to c terminal and cross phosphorylate and become active.
4. Other receptors include receptor associated with tyrosine phosphatase, serine or threonine kinase and receptor associated with guanyl cyclase.
Secondary messanger will be discussed in next blog.
Thankyou.
To continue with signal tranduction.
free life science study material. Types of receptors.
1. G protein coupled receptors: Largest family of receptors.
These are GTP coupled proteins and transmembrane protein.This receptor have 7 transmembrane segments alpha helical in nature.
G protein has three subunits alpha , beta and gamma (heterotrimeric).
GTP/GDP binding sites are present on alpha subunits.
When ligand bind the receptor the GDP gets exchanged with GTP on G alpha subunit.
When GTP binds to alpha the affinity of alpha decreases for beta and gamma and is free to interact with target.
Beta and gamma can also act as signals.
2. Protein tyrosine kinase receptor: are directly linked to enzyme activity.
It has three subunits: N terminus which is ligand binding site, transmembrane segment and C terminus which is cytosolic and has intrinsic tyrosine kinase activity.
When ligand bind to N terminus it causes dimerization of receptor.(ligand can be monomer or dimer).
After dimerization the kinase activity of C terminal gets activated and cross phosphorylates the opposite C Terminal and then autophosphorylation takes place.The protein that can bind to phosphorylated tyrosine are :
a) Which have SH2 (src homology) domain and
b) Which have PTB (phosphotyrosine binding domain). Either of them can bind to activated protein tyrosine kinase receptor.
3. Cytokine receptor: Similar to tyrosine kinase receptor. The only difference is it does not have intrinsic tyrosine kinase activity.
When ligand bind it causes dimerization and affinity for cytosolic kinase increases. The cytosolic kinase bind to c terminal and cross phosphorylate and become active.
4. Other receptors include receptor associated with tyrosine phosphatase, serine or threonine kinase and receptor associated with guanyl cyclase.
Secondary messanger will be discussed in next blog.
Thankyou.
Signal transduction mechanism today
Online free life science study material.
Hello Friends
I will discuss signal transduction mechanism today.
All cells receive and respond to signals.
The signaling molecules are of various types and their receptors are also different, the receptors can also vary from cell to cell in same organism in different location.
Four types of signals are there:
1.Endocrine: act over very long distance and carried through circulatory system, eg. Hormones.
2.Paracrine: act locally on nearby cells, highly unstable, eg. NO, neurotransmitters etc.
3.Juxtacrine:also to very short distance, require physical contact of cells.
4.Autocrine:the signal produce by cell act on the same cell which produces the signal.
Types of signals
I will discuss signal transduction mechanism today.
All cells receive and respond to signals.
The signaling molecules are of various types and their receptors are also different, the receptors can also vary from cell to cell in same organism in different location.
Four types of signals are there:
1.Endocrine: act over very long distance and carried through circulatory system, eg. Hormones.
2.Paracrine: act locally on nearby cells, highly unstable, eg. NO, neurotransmitters etc.
3.Juxtacrine:also to very short distance, require physical contact of cells.
4.Autocrine:the signal produce by cell act on the same cell which produces the signal.
Types of signals
1. Steroids and steroidal hormones: small hydrophobic molecules which can diffuse through plasma membrane, their receptor are intracellular protein. (All the receptors of them are part of single superfamily called nuclear recepter superfamily).
2. Gaseous signals: NO, CO. They act locally on nearby cells, paracrine. They directly act on enzymes and modulate their activity.
Arginine is precursor of NO. Nitric oxide synthase( NOS) enzyme is required for NO production in animals. In plants nitric oxide synthase is absent so nitrate reductase synthesize it.
Action of NO: Acetyl choline released in endothelial cells (on stimulus)activates NOS which produces NO, it diffuses out and act on guanyl cyclase enzyme and activates it. Guanyl cyclase produces cGMP which causes muscle to relax and in turn vessel dilates.
CO is analogous to NO. It is very important signal in nervous system.It can also synthesize cGMP.
3. Neurotransmitters: convey signals between neurons, they are basically hydrophillic. They are produce on stimulus.Targets of neurotransmitters are ion channels, ligand gated, some targets are G protein coupled receptors.
4.Peptides and growt factors:includes peptides, polypeptides, growth hormones, neuropeptides.
5.Eicosanoids: these are certain lipids for which receptors are present on plasma membrane. These include prostaglandins, leukotrienes, thromboxanes etc.
2. Gaseous signals: NO, CO. They act locally on nearby cells, paracrine. They directly act on enzymes and modulate their activity.
Arginine is precursor of NO. Nitric oxide synthase( NOS) enzyme is required for NO production in animals. In plants nitric oxide synthase is absent so nitrate reductase synthesize it.
Action of NO: Acetyl choline released in endothelial cells (on stimulus)activates NOS which produces NO, it diffuses out and act on guanyl cyclase enzyme and activates it. Guanyl cyclase produces cGMP which causes muscle to relax and in turn vessel dilates.
CO is analogous to NO. It is very important signal in nervous system.It can also synthesize cGMP.
3. Neurotransmitters: convey signals between neurons, they are basically hydrophillic. They are produce on stimulus.Targets of neurotransmitters are ion channels, ligand gated, some targets are G protein coupled receptors.
4.Peptides and growt factors:includes peptides, polypeptides, growth hormones, neuropeptides.
5.Eicosanoids: these are certain lipids for which receptors are present on plasma membrane. These include prostaglandins, leukotrienes, thromboxanes etc.
The precursors is arachidonic acid which is derived from phospholipid.
6.Plant hormones: auxin, gibberlin, cytokinin,etc.
will continue ..
Hope this will help you all. See you all with next topic.
Thankyou for reading.
6.Plant hormones: auxin, gibberlin, cytokinin,etc.
will continue ..
Hope this will help you all. See you all with next topic.
Thankyou for reading.
Monday, October 6, 2014
Proteosome
Hello Friends
I will discuss proteosome today.
The function of lysosome organelle is to beakdown potein and other cellular and extracellular components. The pathway which is independent of lysosome is called ubiquitin proteosome pathway as it does not use lysosome for the above function.The pathway is ATP dependent.
Ubiquitin is a polypeptide which can either exist freely in cytoplasm or covalently conjugated with protein.
The molecule to be degraded is ligated to ubiquitin molecule and then it is recognised by proteosome for degradation.
Binding of ubiquitin to target protein is multistep process and is post translational modification.
Glycine is present at C terminal(carbxy) of Ubiuitin and it normally attch to NH2 group of lysine of target protein so an isopeptide bond is formed.
After ubiquitinisation they are identified by 26S proteosome.
For identification by proteosome at least 4 ubiquitin are required.
The 26S proteosome is composed of 19S and 20S subunits.
The 19S subunits have ATPase activity and identify ubiquitin tail attached to target. It forms the upper and lower subunits.
The 20S subunit are central to 19S subunits.
20S is barrel shaped made of 4 ring shaped layers and each layer has 7 protein.
Central 2 layer are called beta and peripheral are called alpha rings or layers.
The beta have catalytic sites and involved in degradation.
when 19S identify target, the alpha unit open and make ubiquitinised target to enter into core subunit beta and then the alpha closed.
The target is breakdown into peptides inside proteosome and released. Point to remember is the proteosome do not degrade target into aminoacid rather it breaks into peptides.
In cytoplasm the other enzymes(peptidases) act on these peptides and degrade target completely into aminoacids.
Ubiquitin tail is identified by deubiuitinating enzyme and cleaved into ubiquitin molecules to be reused.
Hope this will help you all. See you all with next topic.
Thankyou for reading.
I will discuss proteosome today.
The function of lysosome organelle is to beakdown potein and other cellular and extracellular components. The pathway which is independent of lysosome is called ubiquitin proteosome pathway as it does not use lysosome for the above function.The pathway is ATP dependent.
Ubiquitin is a polypeptide which can either exist freely in cytoplasm or covalently conjugated with protein.
The molecule to be degraded is ligated to ubiquitin molecule and then it is recognised by proteosome for degradation.
Binding of ubiquitin to target protein is multistep process and is post translational modification.
Glycine is present at C terminal(carbxy) of Ubiuitin and it normally attch to NH2 group of lysine of target protein so an isopeptide bond is formed.
After ubiquitinisation they are identified by 26S proteosome.
For identification by proteosome at least 4 ubiquitin are required.
The 26S proteosome is composed of 19S and 20S subunits.
The 19S subunits have ATPase activity and identify ubiquitin tail attached to target. It forms the upper and lower subunits.
The 20S subunit are central to 19S subunits.
20S is barrel shaped made of 4 ring shaped layers and each layer has 7 protein.
Central 2 layer are called beta and peripheral are called alpha rings or layers.
The beta have catalytic sites and involved in degradation.
when 19S identify target, the alpha unit open and make ubiquitinised target to enter into core subunit beta and then the alpha closed.
The target is breakdown into peptides inside proteosome and released. Point to remember is the proteosome do not degrade target into aminoacid rather it breaks into peptides.
In cytoplasm the other enzymes(peptidases) act on these peptides and degrade target completely into aminoacids.
Ubiquitin tail is identified by deubiuitinating enzyme and cleaved into ubiquitin molecules to be reused.
Hope this will help you all. See you all with next topic.
Thankyou for reading.
Saturday, October 4, 2014
FAQs
Hello Friends
In this blog I will write some few questions and their answer shall be given later.
MCQ
1.Choose the correct option
Transcriptionally inactive genes
a)Can be located within nucleosome
b) Can be located in heterochromatin
c)are always metylated
d)are sensitive to DNAse
2.Most human cells are diploid with total DNA content of 2N. The DNA content increases to 4N before onset of mitosis.At anaphase the DNA content of each cluster would be
a)4N b)2N c)1N d)3N
3.Microorganism that help in nitrification are
a)Nitrosomonas and nitrobacter
b)Nostoc and Anabeana
c)Clostridium and Pseudomonas
d)Rhizobium and Azotobacter
4. Which of the following class of seeds should have high content of moisture in order to remain viable are known as
a)Orthodox seeds
b)Recalcitrant seeds
c)Labirynth seeds
d)Ex albuminous seeds
5.The nitrate reductase has which of the following cofacter
a)Mo b)Cu c)Al d)Mn
6. The Nitrate reductase accepts electron from
a)FAD b)NADH c)FMN d)Ferrodoxin
Hope this will help you all. See you all with next topic.
Free online lifescience study material. Thnkyou for reading.
In this blog I will write some few questions and their answer shall be given later.
MCQ
1.Choose the correct option
Transcriptionally inactive genes
a)Can be located within nucleosome
b) Can be located in heterochromatin
c)are always metylated
d)are sensitive to DNAse
2.Most human cells are diploid with total DNA content of 2N. The DNA content increases to 4N before onset of mitosis.At anaphase the DNA content of each cluster would be
a)4N b)2N c)1N d)3N
3.Microorganism that help in nitrification are
a)Nitrosomonas and nitrobacter
b)Nostoc and Anabeana
c)Clostridium and Pseudomonas
d)Rhizobium and Azotobacter
4. Which of the following class of seeds should have high content of moisture in order to remain viable are known as
a)Orthodox seeds
b)Recalcitrant seeds
c)Labirynth seeds
d)Ex albuminous seeds
5.The nitrate reductase has which of the following cofacter
a)Mo b)Cu c)Al d)Mn
6. The Nitrate reductase accepts electron from
a)FAD b)NADH c)FMN d)Ferrodoxin
Hope this will help you all. See you all with next topic.
Free online lifescience study material. Thnkyou for reading.
Tuesday, September 30, 2014
Agrobacterium tumifaciens
Hello Friends
Topic of discussion is Agrobacterium tumifaciens
It is gram negative bacteria.
The agrobacterium causes crown gall disease and hairy root syndrome.
A. tumifaciens causes crown gall and A. rhizogenes causes hairy root syndrome.
The bacteria enter plant through cuts and wounds.
Most of these bacteria have plasmids. The size of plasmid is variable and the ability to synthesize the opines and virulence is plasmid borne traits.
This plasmid is called the Ti plasmid.
Only a segment (which is called t DNA) of this plasmid enters the plant on infection and integrated into host genome at non specific site.
The ends of tDNA are specialised as they are flanked by 25 bp repeats called as border sequence.
These border sequence are involved in tDNA transfer but they themselves do no get transffered.
The genes which regulate the trasfer of tDNA are present at some other sites in plasmid DNA and are called vir genes.
vir A and vir G are important and constituvely expressed and their product are required for expression of other vir genes.
vir A product is a protein kinase.
The wounded plant also secrete acetosyringone for vir gene expression.
vir G product is soluble protein which is phosphorylated by vir A product.
vir G product is transcription factor required for activation of rest of vir genes.
vir B produces component of pilus.
virD1 encodes for endonuclease which act on border sequence to create nicks and initiate transfer of tDNA.
vir D2 remain attached to processed DNA.
vir C1 and C2 product act on enhancer sequence.
vir E codes a DNA binding protein which provide stability to DNA.The processed DNA is called "Fire Cracker Complex".
The vir D2 product are attached to processed tDNA and protect this DNA from host nucleases.
vir D2 protein also has nuclear localising signal and are required for recombination evennts.
The cell in which tDNA enters have high level of phytohormones, the genes called tms1 and tms2 synthesize auxin, tmr synthesize cytokinin, ocs synthesize octopine and nos synthesize nopaline.
This tDNA is also used as vector by removing tms1, tms2 and tmr region.
It is even used to express in eukaryotic system as promoter sequence and polyadenylation sites of tDNA are very similar to eukaryotic system.
Many monocots are not infected by this bacteria as they do not sectrete acetosyringone.
Hope this will help you all. See you all with next topic.
Thnkyou for reading.
Topic of discussion is Agrobacterium tumifaciens
It is gram negative bacteria.
The agrobacterium causes crown gall disease and hairy root syndrome.
A. tumifaciens causes crown gall and A. rhizogenes causes hairy root syndrome.
The bacteria enter plant through cuts and wounds.
Most of these bacteria have plasmids. The size of plasmid is variable and the ability to synthesize the opines and virulence is plasmid borne traits.
This plasmid is called the Ti plasmid.
Only a segment (which is called t DNA) of this plasmid enters the plant on infection and integrated into host genome at non specific site.
The ends of tDNA are specialised as they are flanked by 25 bp repeats called as border sequence.
These border sequence are involved in tDNA transfer but they themselves do no get transffered.
The genes which regulate the trasfer of tDNA are present at some other sites in plasmid DNA and are called vir genes.
vir A and vir G are important and constituvely expressed and their product are required for expression of other vir genes.
vir A product is a protein kinase.
The wounded plant also secrete acetosyringone for vir gene expression.
vir G product is soluble protein which is phosphorylated by vir A product.
vir G product is transcription factor required for activation of rest of vir genes.
vir B produces component of pilus.
virD1 encodes for endonuclease which act on border sequence to create nicks and initiate transfer of tDNA.
vir D2 remain attached to processed DNA.
vir C1 and C2 product act on enhancer sequence.
vir E codes a DNA binding protein which provide stability to DNA.The processed DNA is called "Fire Cracker Complex".
The vir D2 product are attached to processed tDNA and protect this DNA from host nucleases.
vir D2 protein also has nuclear localising signal and are required for recombination evennts.
The cell in which tDNA enters have high level of phytohormones, the genes called tms1 and tms2 synthesize auxin, tmr synthesize cytokinin, ocs synthesize octopine and nos synthesize nopaline.
This tDNA is also used as vector by removing tms1, tms2 and tmr region.
It is even used to express in eukaryotic system as promoter sequence and polyadenylation sites of tDNA are very similar to eukaryotic system.
Many monocots are not infected by this bacteria as they do not sectrete acetosyringone.
Hope this will help you all. See you all with next topic.
Thnkyou for reading.
Friday, September 26, 2014
Cell cycle Continued
Hello Friends
Free online life science study material. To continue with cell cycle
In the M or mitotic phase the CDK1 cyclin B complex also phosphorylate component of nuclear pore and some protein of inner nuclear membrane.so choromosome is unable to bind to inner nuclear membrane and whole structure gets disorganized.
Protein of nuclear pore are imbibed by endoplasmic reticulum and golgi bodies also get fragmented.
Endoplasmic reticulam remains intact.
Centrosome also gets phosphorylated and repell each other.
Microtubule associated proteins are target of CDk1-cyclin B compex, so microtubule also get disorganized.
Microtubule associated protein (MAP) are present on the cytoplasm periphery initialy prior to cell division.
At metaphase Anaphase promoting Complex (APC) is present, which is a ubiquitin ligase.
If APC is inactive, cell do not proceed to cell division and gets activated only when choromosmes are properly alligned to spindle fibre.
If they are not alligned properly, Mad and Bub protein bind to kinetocore and lead to inhibition of APC.
Active APC have two targets:
1. APC bind ubiquitin to securin and cohesin gets degraded by separase enzyme.The securin subunit is attached to separase enzyme and APC act on securin to detach from separase.
2. Cyclin B is target of APC and gets deactivated by APC.
APC inactivated in late G1 phase by Gi/S CDKs.
CDKs are regulated by phosphorylation and dephosphorylation. It is activating phosphorylation at some sites and activating dephosphorylation on the other sites.
A threonin of CDK at 160 position requires phosphorylation and is phosphorylated by CAK= CDK activating kinase.
At 14 and 15 th position threonina nd tyrosin are phosphorylated respectively, they require dephosphorylation for activation and this is done by cdc25 phosphatase.
At 14 and 15 th position during inactive state they are phophorylated by wee1 kinase to make them inactive.
This ends the topic cell cycle regulation.
Hope this will help you all. See you all with next topic.
Thnkyou for reading.
Free online life science study material. To continue with cell cycle
In the M or mitotic phase the CDK1 cyclin B complex also phosphorylate component of nuclear pore and some protein of inner nuclear membrane.so choromosome is unable to bind to inner nuclear membrane and whole structure gets disorganized.
Protein of nuclear pore are imbibed by endoplasmic reticulum and golgi bodies also get fragmented.
Endoplasmic reticulam remains intact.
Centrosome also gets phosphorylated and repell each other.
Microtubule associated proteins are target of CDk1-cyclin B compex, so microtubule also get disorganized.
Microtubule associated protein (MAP) are present on the cytoplasm periphery initialy prior to cell division.
At metaphase Anaphase promoting Complex (APC) is present, which is a ubiquitin ligase.
If APC is inactive, cell do not proceed to cell division and gets activated only when choromosmes are properly alligned to spindle fibre.
If they are not alligned properly, Mad and Bub protein bind to kinetocore and lead to inhibition of APC.
Active APC have two targets:
1. APC bind ubiquitin to securin and cohesin gets degraded by separase enzyme.The securin subunit is attached to separase enzyme and APC act on securin to detach from separase.
2. Cyclin B is target of APC and gets deactivated by APC.
APC inactivated in late G1 phase by Gi/S CDKs.
CDKs are regulated by phosphorylation and dephosphorylation. It is activating phosphorylation at some sites and activating dephosphorylation on the other sites.
A threonin of CDK at 160 position requires phosphorylation and is phosphorylated by CAK= CDK activating kinase.
At 14 and 15 th position threonina nd tyrosin are phosphorylated respectively, they require dephosphorylation for activation and this is done by cdc25 phosphatase.
At 14 and 15 th position during inactive state they are phophorylated by wee1 kinase to make them inactive.
This ends the topic cell cycle regulation.
Hope this will help you all. See you all with next topic.
Thnkyou for reading.
Wednesday, September 24, 2014
cell cycle
Hello All
to continue with cell cycle
When cyclins are complexed with CDKs they become activated.
The cyclinD CDK 4&6 has a target protein called Rb protein.
Rb is a tumor suppressor protein. It is found to be mutated in cancer patients.
In normal cell Rb protein remains under phosphorylated especialy during G0 and G1 phase.
Its activity can be changed by level of phosphorylation.
It has affinity towards E2F which is a transcription factor in under phosphorylated state.
So binding of Rb to E2F suppress the activity of E2F.
The cyclinD CDK 4&6 complex phosphorylate Rb and its affinity towards E2F decreases and E2F after separating from E2F becomes activated and since it is a transcription factor, after activation it helps expression of genes required in cell cycle progression.
Another target of CDK4&6 and cyclin D complex is Cyclin E.
Cyclin E binds with CDK 2 and target the MCM helicase.
MCM helicases after activation unwinds the DNA for replication.
The DNA is scanned by ATM and ATR protein for any DNA damage. They are kinases.
ATM is activated if it find double strand damage and ATR activates by single strand damage.
ATM and ATR phosphorylate p53 protein and phosphorylation of p53 stabilizes it. after stabilization the level of p53 increases and they expresses cip and kip family of protein as p53 is transcription factor for them, which are discussed in earlier blog. Cip and Kip activation leads to cell cycle arrest in G1 phase.
CDK1 and cyclin B target is condensin protein which are required for chromosome activation in the S phase.
Lamins are also phosphoryated by CDK1 and cyclin B and they get depolymerised after phosphorylaton.
Microtubule associated protein are also the targets of this complex and get depolymerised.
Rest I will discuss in next blog.
to continue with cell cycle
When cyclins are complexed with CDKs they become activated.
The cyclinD CDK 4&6 has a target protein called Rb protein.
Rb is a tumor suppressor protein. It is found to be mutated in cancer patients.
In normal cell Rb protein remains under phosphorylated especialy during G0 and G1 phase.
Its activity can be changed by level of phosphorylation.
It has affinity towards E2F which is a transcription factor in under phosphorylated state.
So binding of Rb to E2F suppress the activity of E2F.
The cyclinD CDK 4&6 complex phosphorylate Rb and its affinity towards E2F decreases and E2F after separating from E2F becomes activated and since it is a transcription factor, after activation it helps expression of genes required in cell cycle progression.
Another target of CDK4&6 and cyclin D complex is Cyclin E.
Cyclin E binds with CDK 2 and target the MCM helicase.
MCM helicases after activation unwinds the DNA for replication.
The DNA is scanned by ATM and ATR protein for any DNA damage. They are kinases.
ATM is activated if it find double strand damage and ATR activates by single strand damage.
ATM and ATR phosphorylate p53 protein and phosphorylation of p53 stabilizes it. after stabilization the level of p53 increases and they expresses cip and kip family of protein as p53 is transcription factor for them, which are discussed in earlier blog. Cip and Kip activation leads to cell cycle arrest in G1 phase.
CDK1 and cyclin B target is condensin protein which are required for chromosome activation in the S phase.
Lamins are also phosphoryated by CDK1 and cyclin B and they get depolymerised after phosphorylaton.
Microtubule associated protein are also the targets of this complex and get depolymerised.
Rest I will discuss in next blog.
Thursday, September 18, 2014
Hello Friends
The Regulation of Cell Cycle
The cell cycle is under the control of various cdks and Cyclins.These control the cell cycle progression to varoius phases of cell cycle.
Here I am dealing with the G or growth phase and M.or mitotic Phase.
The cell cycle is divided into four phases
1. G0 Phase and G1
2. S or synthesis phase wherein synthesis of DNA takes place
3 G2 Phase
4. M or mitotic Phase.
There are check points in the cell cycle which requires CDK-cyclin activity to pass them.
One check point at G1 phase. To pass this CDK4&6 and cyclin D is required.
Another check point is at G1-S transition this require CDK2 and cyclin E.
CDK2 and Cyclin E is also required for initiation of DNA replication and chromosome replication.
For progression through S phase CDK2 and cyclin A is required.
Another check point is at S-G2 transition which requires CDK 1 and cyclinA.
For G2 - M transition CDK 1 and cyclin B are required.
Some mechanism regulate CDKs.
Several inhibitors bind to CDK at specific sites for its activation and deactivation.
1. Ink 4 family of protein: These protein are prominent for CDK 4& 6. when they bind to them they stop cell cycle from G1-S progression and the cell will remain in G1 phase.
2. Cip/Kip Family of proteins: Act on CDK 2 and can also bind to cyclin A and E and stop cell cycle in S or G1 phase. These also hep in association of CDK 4& 6 with cyclinD and in G2 M transition phase it also enhance association of CDK 1 with cyclin B.
All external factors such as erk, ras, Raf, MEK signal the cell externally for cell division and these finaly led to the formation of cyclin D.
Cyclin D is only synthesised as long as external signals are available.
Cyclin D mutation also led to several cancer.
Hope this will help you all. See you all in next blog.
Thnkyou for reading.
The Regulation of Cell Cycle
The cell cycle is under the control of various cdks and Cyclins.These control the cell cycle progression to varoius phases of cell cycle.
Here I am dealing with the G or growth phase and M.or mitotic Phase.
The cell cycle is divided into four phases
1. G0 Phase and G1
2. S or synthesis phase wherein synthesis of DNA takes place
3 G2 Phase
4. M or mitotic Phase.
There are check points in the cell cycle which requires CDK-cyclin activity to pass them.
One check point at G1 phase. To pass this CDK4&6 and cyclin D is required.
Another check point is at G1-S transition this require CDK2 and cyclin E.
CDK2 and Cyclin E is also required for initiation of DNA replication and chromosome replication.
For progression through S phase CDK2 and cyclin A is required.
Another check point is at S-G2 transition which requires CDK 1 and cyclinA.
For G2 - M transition CDK 1 and cyclin B are required.
Some mechanism regulate CDKs.
Several inhibitors bind to CDK at specific sites for its activation and deactivation.
1. Ink 4 family of protein: These protein are prominent for CDK 4& 6. when they bind to them they stop cell cycle from G1-S progression and the cell will remain in G1 phase.
2. Cip/Kip Family of proteins: Act on CDK 2 and can also bind to cyclin A and E and stop cell cycle in S or G1 phase. These also hep in association of CDK 4& 6 with cyclinD and in G2 M transition phase it also enhance association of CDK 1 with cyclin B.
All external factors such as erk, ras, Raf, MEK signal the cell externally for cell division and these finaly led to the formation of cyclin D.
Cyclin D is only synthesised as long as external signals are available.
Cyclin D mutation also led to several cancer.
Hope this will help you all. See you all in next blog.
Thnkyou for reading.
Friday, September 12, 2014
Hello Friends
to continue
Lambda repressor is under tight regulation.
Two types of regulation
1. Positive Autoregulation
2.Negative Autoregulation
1. Positive Autoregulation:
It activates its own expression.
It makes level do not reach so low.
2.Negative Autoregulation:
PRM being activated by repressor at OR2 to make more repressor but if concentration increases too high repressor will bind to OR3 also and repress PRM.
This act decreases concentration of repressor.
On new infection the phage has to chose between lytic and lysogeny.
cII and cIII products decide this step.
cII transcribed from PR and cIII from PL.
cII is transcriptional activator it binds to a site called PRE(Repressor Establishment)
PRE stimulate transcription of cI(repressor).
Thus, repressor can be transcribed from PRE and PRM.
PRE is weak promoter so cII product help polymerase bind to PRE.
Once, sufficient repressors are made from PRE, they can bind to OR1 and OR2 and directs their own synthesis from PRM.
Thus repressor synthesis established from one promoter and maintained by other promoter.
Thus, upon infection transcription immediately initiate from PR and PL.
PR synthesise both cro and cII.
cro favours lytic phase. Once cro product is at certain level of concentration it will bind OR3 and block PRM activity.
cII favours lysogeny by directing transcription of repressor gene and for successful lysogeny repressor must bind to OR1 and OR2 and activate PRM before cro inhibit that promoter.
So, phage favous lytic in good bacterial growth environment and lysogeny in poor conditions.
For diagrams you can consult books or diagrams online.
Hope this will help you all. See you all in next blog.
Thnkyou for reading.
to continue
Lambda repressor is under tight regulation.
Two types of regulation
1. Positive Autoregulation
2.Negative Autoregulation
1. Positive Autoregulation:
It activates its own expression.
It makes level do not reach so low.
2.Negative Autoregulation:
PRM being activated by repressor at OR2 to make more repressor but if concentration increases too high repressor will bind to OR3 also and repress PRM.
This act decreases concentration of repressor.
On new infection the phage has to chose between lytic and lysogeny.
cII and cIII products decide this step.
cII transcribed from PR and cIII from PL.
cII is transcriptional activator it binds to a site called PRE(Repressor Establishment)
PRE stimulate transcription of cI(repressor).
Thus, repressor can be transcribed from PRE and PRM.
PRE is weak promoter so cII product help polymerase bind to PRE.
Once, sufficient repressors are made from PRE, they can bind to OR1 and OR2 and directs their own synthesis from PRM.
Thus repressor synthesis established from one promoter and maintained by other promoter.
Thus, upon infection transcription immediately initiate from PR and PL.
PR synthesise both cro and cII.
cro favours lytic phase. Once cro product is at certain level of concentration it will bind OR3 and block PRM activity.
cII favours lysogeny by directing transcription of repressor gene and for successful lysogeny repressor must bind to OR1 and OR2 and activate PRM before cro inhibit that promoter.
So, phage favous lytic in good bacterial growth environment and lysogeny in poor conditions.
For diagrams you can consult books or diagrams online.
Hope this will help you all. See you all in next blog.
Thnkyou for reading.
Thursday, September 11, 2014
Hello Friends
To continue with the Lysogenic and Lytic cycle of Lambda Phage..
PRM transcribes only cI and it is a weak promoter and efficient only when activator is bound just upstream.
PL and PR are stong promoter and do not require any activator.
For lytic phase PL and PR remains on PRM is off and for lysogeny PRM is on and PL and PR are off.
cI encodes Lambda repressor which is dumbbell shaped and join to DNA as a dimer.
Lambda repressor and cro can each bind with 6 operators. 3 operator on left and 3 on right side of cI.
OR1 OR2 OR3 are three operators on the right side of cI. PR overlaps OR1 and OR2 and PRM overlaps OR2 and OR3.
For lytic cycle single cro dimer bind to OR3 which overlap PRM and repress it. No repressor and no cro on OR1 and OR2 therefore PR binds RNA polymerase and transcribes lytic genes. so does PL.
For lysogeny PRM is on. Repressor is bound cooperatively at OR1 and OR2. RNA Polymerase bind at PR and its transcription is repressed.
Induction to lytic phase.
Eg. E. coli sense and respond to DNA damage by activating Rec A protein. Rec A cleaves Lex A protein during DNA damage repair mechanism. Lambda repressor resemble Lex A hence Lambda repressor is also cleaved by Rec A protein.The cleavage of repressor removes C terminal domain of repressor and its dimerization and cooperativity is lost.
Loss of dimer triggers transcription PR and PL which induces lytic phase.
I will continue with it in the next blog.
Thank you for reading.
To continue with the Lysogenic and Lytic cycle of Lambda Phage..
PRM transcribes only cI and it is a weak promoter and efficient only when activator is bound just upstream.
PL and PR are stong promoter and do not require any activator.
For lytic phase PL and PR remains on PRM is off and for lysogeny PRM is on and PL and PR are off.
cI encodes Lambda repressor which is dumbbell shaped and join to DNA as a dimer.
Lambda repressor and cro can each bind with 6 operators. 3 operator on left and 3 on right side of cI.
OR1 OR2 OR3 are three operators on the right side of cI. PR overlaps OR1 and OR2 and PRM overlaps OR2 and OR3.
For lytic cycle single cro dimer bind to OR3 which overlap PRM and repress it. No repressor and no cro on OR1 and OR2 therefore PR binds RNA polymerase and transcribes lytic genes. so does PL.
For lysogeny PRM is on. Repressor is bound cooperatively at OR1 and OR2. RNA Polymerase bind at PR and its transcription is repressed.
Induction to lytic phase.
Eg. E. coli sense and respond to DNA damage by activating Rec A protein. Rec A cleaves Lex A protein during DNA damage repair mechanism. Lambda repressor resemble Lex A hence Lambda repressor is also cleaved by Rec A protein.The cleavage of repressor removes C terminal domain of repressor and its dimerization and cooperativity is lost.
Loss of dimer triggers transcription PR and PL which induces lytic phase.
I will continue with it in the next blog.
Thank you for reading.
Friday, September 5, 2014
Overview of Lambda Phage genome
Hello Friends
Free online life science study material.
The topic I am going to brief about is Lambda Phage
lysogenic and lytic phase gene regulation introduction.
It is a Bacteriophage which is consist of a capsid, a tail
and tail fiber.
It has double stranded, linear DNA as genetic material, 50Kb
genome with 50 genes.
The linear genome has 12bp cohesive ends which are
complementary and it gets circularize as soon as it infects the bacterium.
Now, gene regulation of lytic and lysogenic phase takes
place with the help of regulatory proteins.
A region of genome of Lambda has sequence like this
PL
|
cI
|
PRM
|
PR
|
cro
|
All other genes are
outside this region except one and are transcribed directly from PL
and PR or from other promoters whose activities are controlled by
their products.
PRM transcribes only cI . It is repressor maintenance
promoter. It is weak promoter and efficient only when activator bind just
upstream.
PL and PR are strong promoters and do
not require activator.
PL and PRM codes towards left and PR codes towards right.
PL and PRM codes towards left and PR codes towards right.
For lytic phase PL
and PR are switched on and PRM is switched off and for lysogenic phase PRM
and rest two are off.
cI encodes Lambda repressor which can act as both repressor
and activator.
As a repressor it s target is σ subunit of RNA Ploymerase , the
adjacent to the part of σ which recognize -35 region on DNA.
As activator it works like CAP as in Lac operon.
The cI and cro are functional in dimeric form.
Rest I will discuss in next blog.
Hope this will help you all. See you all in next blog.
Thankyou for reading.
Thursday, September 4, 2014
Hello Friends
I am Sakshi Garg, I would like to share my notes with you which I have prepared for preparation. These might be useful for you.
I would also like to know your views regarding each topic, any queries regarding the notes and also if you would like to share any information with me I will be highly thankful.I will be writing breifly and in a very simple language.
Today, the topic that I am going to discuss is Tranduction.
Transduction is transfer of bacterial genes by virus.
Transduction are of two types:
1. Generalized Transduction
2.Specialized Transduction
Generalized Transduction:
This occurs during lytic cycle of virulent and temperate phage and can transfer any part of bacterial genome.
During packaging of capsids in lytic phase random fragments of bacterial DNA can also be packed by mistake in some capsids.
Since viral capsid can contain limited amount of DNA, the viral DNA is left behind. These virus can inject DNA of bacteria into other bacteria after infection but does not initiate lytic cycle.
Double stranded DNA remain Double stranded during transfer and integrates into host bacterium or endogenote.
Specialized Transduction:
also known as restricted Transduction.
When prophage leaves the bacterial genome the cleavage or excision of viral DNA is improper.
Phage may contain portion of bacterial DNA next to integration sites.
This type of transducing phage is defective and cannot reproduce without assistance.
This can be explained with this example: phage att site or attachment site and bacterial att site are similar and can recombine with each other.
Since viral att site are next to bacterial gal and bio sites these can be carried by lambda phage due to mistake in excising.
Stable transduction may arise through recombination of bacterial genome nad phage chromosome.
Hope this will help you all. See you all in next blog.
Thnkyou for reading.
I am Sakshi Garg, I would like to share my notes with you which I have prepared for preparation. These might be useful for you.
I would also like to know your views regarding each topic, any queries regarding the notes and also if you would like to share any information with me I will be highly thankful.I will be writing breifly and in a very simple language.
Today, the topic that I am going to discuss is Tranduction.
Transduction is transfer of bacterial genes by virus.
Transduction are of two types:
1. Generalized Transduction
2.Specialized Transduction
Generalized Transduction:
This occurs during lytic cycle of virulent and temperate phage and can transfer any part of bacterial genome.
During packaging of capsids in lytic phase random fragments of bacterial DNA can also be packed by mistake in some capsids.
Since viral capsid can contain limited amount of DNA, the viral DNA is left behind. These virus can inject DNA of bacteria into other bacteria after infection but does not initiate lytic cycle.
Double stranded DNA remain Double stranded during transfer and integrates into host bacterium or endogenote.
Specialized Transduction:
also known as restricted Transduction.
When prophage leaves the bacterial genome the cleavage or excision of viral DNA is improper.
Phage may contain portion of bacterial DNA next to integration sites.
This type of transducing phage is defective and cannot reproduce without assistance.
This can be explained with this example: phage att site or attachment site and bacterial att site are similar and can recombine with each other.
Since viral att site are next to bacterial gal and bio sites these can be carried by lambda phage due to mistake in excising.
Stable transduction may arise through recombination of bacterial genome nad phage chromosome.
Hope this will help you all. See you all in next blog.
Thnkyou for reading.
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