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.

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.





 

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.

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.

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.

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.

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

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.

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.

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.

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.