What is Mad Cow Disease

Bovine spongiform encephalopathy (BSE), commonly known as mad-cow disease (MCD), is a fatal, neurodegenerative disease in cattle, that causes a spongy degeneration in the brain and spinal cord. BSE has a long incubation period, about 4 years, usually affecting adult cattle at a peak age onset of four to five years, all breeds being equally susceptible.

It is believed by most scientists that the disease may be transmitted to human beings who eat the brain or spinal cord of infected carcasses.[3] In humans, it is known as new variant Creutzfeldt-Jakob disease (vCJD or nvCJD)

Infectious agent
The infectious agent in BSE is believed to be a specific type of misfolded protein called a prion. Those prion proteins carry the disease between individuals and cause deterioration of the brain. BSE is a type of transmissible spongiform encephalopathy (TSE).[10] TSEs can arise in animals that carry an allele which causes previously normal protein molecules to contort by themselves from an alpha helical arrangement to a beta pleated sheet, which is the disease-causing shape for the particular protein. Transmission can occur when healthy animals come in contact with tainted tissues from others with the disease. In the brain these proteins cause native cellular prion protein to deform into the infectious state, which then goes on to deform further prion protein in an exponential cascade. This results in protein aggregates, which then form dense plaque fibers, leading to the microscopic appearance of "holes" in the brain, degeneration of physical and mental abilities, and ultimately death.

"Bovine spongiform encephalopathy." Wikipedia, The Free Encyclopedia. 16 Jul 2009, 20:16 UTC. 16 Jul 2009 <http://en.wikipedia.org/w/index.php?title=Bovine_spongiform_encephalopathy&oldid=302477785>.

Protein Recycling

Recycling is important not only on a global scale, but also at the cellular level, since key molecules tend to be available in limited numbers. This means a cell needs to have efficient recycling mechanisms.Certain intercellular proteins are needed to respond to specific extracellular signals. This movie covers how such proteins can be stored, recycled and kept available during the periods of time in between the arrival of such extracellular signals.

img height="5" src="http://i4.ytimg.com/vi/sJo0Eso-a3A/2.jpg" width="10" />

Ribosome Ratchet

Comparison of two states of bacterial ribosome, either with fMet - tRNA bound or with elongation factor EF-G bound reveals the significant conformational change that ribosome thought to undergo during each elongation cycle, The Ratchet like rearrangement at interphase between two ribosomal sub unit may help to move the mRNa and tRna through the ribosome during protein synthesis

What is Polyribosome

Polyribosomes (or polysomes) are a cluster of ribosomes, bound to a mRNA molecule, first discovered and characterized by Jonathan Warner, Paul Knopf, and Alex Rich in 1963.Polyribosomes read one strand of mRNA simultaneously, helping to synthesize the same protein at different spots on the mRNA, mRNA being the "messenger" in the process of protein synthesis. They may appear as clusters, linear arrays, or rosettes in routine

Laser Tweezers

An Laser tweezer is a scientific instrument that uses a focused laser beam to provide an attractive or repulsive force (typically on the order of piconewtons), depending on the refractive index mismatch to physically hold and move microscopic dielectric objects. Optical tweezers have been particularly successful in studying a variety of biological systems in recent years.

One of the more common cell-sorting systems makes use of flow cytometry through fluorescent imaging. In this method, a suspension of biologic cells is sorted into two or more containers, based upon specific fluorescent characteristics of each cell during an assisted flow. By using an electrical charge that the cell is "trapped" in, the cells are then sorted based on the fluorescence intensity measurements. The sorting process is undertaken by an electrostatic deflection system that diverts cells into containers based upon their charge.

In the optically-actuated sorting process, the cells are flowed through into an optical landscape i.e. 2D or 3D optical lattices. Without any induced electrical charge, the cells would sort based on their intrinsic refractive index properties and can be re-configurability for dynamic sorting. Mike MacDonald, Gabe Spalding and Kishan Dholakia, Nature 426, 421-424 (2003)[1] made use of diffractive optics and optical elements to create the optical lattice. An automated cell sorter was described at the University of Toronto in 2001, but made use of mechanical parameters as opposed to spatial light modulation

"Optical tweezers." Wikipedia, The Free Encyclopedia. 15 Jul 2009, 07:52 UTC. 15 Jul 2009 <http://en.wikipedia.org/w/index.php?title=Optical_tweezers&oldid=302188066>.

How Depression is caused

Depression is one of the most common psychiatric disorders. Symptoms of depression are often subtle and unrecognized both by patients and physicians. The brain contains a network of interconnected nerve cells called neurons. The junction between the neurons is called the synaptic junction. Chemicals called neuro-transmitters facilitate the transmission of impulses from one neuron to another. The impulse triggers the release of neurotransmitters from one neuron, which cross the synaptic junction and attach themselves to the receptors in adjacent neurons sending the messages through.Later the neuro-transmitter returns to initial neuron the other reuptake channel.One of the causes of depressions believed to be the depletion of neuro transmitter called serotonin and noradrenaline.Antidepressant drugs increase the availability of neuro transmitters at the synaptic junction by blocking the re-uptake channel

Aspartate Transcarbamylase

Aspartate carbamoyltransferase (also known as ATCase or aspartate transcarbamoylase) catalyzes the first step in the pyrimidine biosynthetic pathway.

Enzyme is a multi-subunit protein complex composed of 12 subunits (300 kDa in total). The composition of the subunits is C6R6, forming 2 trimers of catalytic subunits (34 kDa) and 3 dimers of regulatory subunits (17 kDa). The particular arrangement of catalytic and regulatory subunits in this enzyme affords the complex with strongly allosteric behaviour with respect to its substrates. The enzyme is an archetypal example of allosteric modulation of fine control of metabolic enzyme reactions.

ATCase does not follow Michaelis-Menten kinetics, but lies between the high-activity, high-affinity "relaxed" or R and the low-activity, low-affinity "tense" or T states. The binding of substrate to the catalytic subunits result in an equilibrium shift towards the R state, whereas binding of CTP to the regulatory subunits results in an equilibrium shift towards the T state. Binding of ATP to the regulatory subunits results in an equilibrium shift towards the R state.


ATCase is a highly regulated enzyme that catalyses the first committed step in pyrimidine biosynthesis, the condensation of aspartate and carbamyl phosphate to form N-carbamyl-L-aspartate and inorganic phosphate. ATCase controls the rate of pyrimidine biosynthesis by altering its catalytic velocity in response to cellular levels of both pyrimidines and purines. The end product of the pyrimidine pathway, CTP, induces a decrease in catalytic velocity, whereas ATP, the end product of the parallel purine pathway, exerts the opposite effect, stimulating the catalytic activity.

Early studies demonstrated that ATCase consists of two different kinds of polypeptide chains which have different roles. The catalytic subunits catalyze the carbamylation of the amino group of aspartate, but do not have regulatory properties, while the regulatory subunits do not have any catalytic activity, but contain the regulatory sites for effector binding. The ATCase holoenzyme is made of two catalytic trimers that are in contact and held together by three regulatory dimers, so the native form of the enzyme contains six chains of each type, with a total molecular weight of 310 kDa.

Each of the catalytic domains is composed of two structural domains, the aspartate domain that contains most of the residues responsible for binding aspartate, and the carbamoyl phosphate domain, which contains most of the residues that bind to carbamoyl phosphate. Each regulatory domain is also composed of two domains, the allosteric domain that has the binding site for the nucleotide effectors, as well as the zinc domain, consisting of four cysteine residues clustered in its C-terminal region. These residues coordinate a zinc atom that is not involved in any catalytic property, but has been shown to be absolutely essential for the association of regulatory and catalytic subunits.

The three-dimensional arrangement of the catalytic and regulatory subunits involves several ionic and hydrophobic stabilizing contacts between amino acid residues. Each catalytic chain is in contact with three other catalytic chains and two regulatory chains. Each regulatory monomer is in contact with one other regulatory chain and two catalytic chains. In the unliganded enzyme, the two catalytic trimers are also in contact.

Catalytic center
The catalytic site of ATCase is located at the interface between two neighboring catalytic chains in the same trimer and incorporates amino acid side chains from both of these subunits. Insight into the mode of binding of substrates to the catalytic center of ATCase was first made possible by the binding of a bisubstrate analogue, N-(phosphonoacetyl)-L-aspartate (PALA). This compound is a strong inhibitor of ATCase and has a structure that is thought to be very close to that of the transition state of the substrates. Additionally, crystal structures of ATCase bound to carbamoylphosphate and succinate have been obtained. These studies, in addition to investigations using site-directed mutagenesis of specific amino acids have identified several residues that are crucial for catalysis, such as Ser52, Thr53, Arg54, Thr55, Arg105, His134, Gln137, Arg167, Arg229, Glu231, and Ser80 and Lys84 from an adjacent catalytic chain. The active site is a highly positively charged pocket. One of the most critical side chains is from Arg54, which interacts with a terminal oxygen and the anhydride oxygen of carbamoyl phosphate, stabilizing the negative charge of the leaving phosphate group. Arg105, His134, and Thr55 help to increase the electrophilicity of the carbonyl carbon by interacting with the carbonyl oxygen.In general, the rate enhancement of ATCase is achieved by orientation and stabilization of substrates, intermediates, and products rather than by direct involvement of amino acid residues in the catalytic mechanism.

Allosteric site
The allosteric site in the allosteric domain of the R chains of the ATCase complex binds to the nucleotides ATP, CTP and/or UTP. There is one site with high affinity for ATP and CTP and one with 10- to 20- fold lower affinity for these nucleotides in each regulatory dimer.ATP binds predominantly to the high-affinity sites and subsequently activates the enzyme, while UTP and CTP binding leads to inhibition of activity. UTP can bind to the allosteric site, but inhibition of ATCase by UTP is possible only in combination with CTP. With CTP present, UTP binding is enhanced and preferentially directed to the low-affinity sites. Conversely, UTP binding leads to enhanced affinity for CTP at the high-affinity sites and inhibits enzyme activity by up to 95% while CTP binding alone inhibits activity to 50% to 70%. Comparison of the crystal structures of the T and R forms of ATCase show that it swells in size during the allosteric transition, and that the catalytic subunits condense during this process. The two catalytic trimers move apart along the threefold axis by 12 Å, and they rotate about this axis by 5° each, ultimately leading to a reorientation of the regulatory subunits around their twofold axis by 15°. This quaternary structure change is associated with alterations in inter-subunit and inter-domain interactions. The interaction between subunits C1-C4 and R1 is extensively modified during this conversion. In particular, there is large movement of amino acid residues 230-254, known collectively as the 240s loop. These residues are located at the cleft between the carbamoyl phosphate and aspartate domains at the C1-C4 interface. The overall outcome of these structural changes is that the two domains of each catalytic chain come closer together, ensuring a better contact with the substrates or their analogues.

During this structural transition, some side chain-side chain interactions are lost and some others are established. Studies have confirmed that the position of the 240s loop directly affects substrate binding in the corresponding active site.Earlier studies using site-directed mutagenesis of the 240s loop showed that interactions between Asp271 and Tyr240, and between Glu239 of C1 and Tyr165 of C4 would stabilize the T-state, while interactions between Glu239 of C1 and both Lys164 and Tyr165 of C4 would stabilize the R-state.

Located close to the 240s loop and the active site, the loop region encompassing residues 160-166 play a role in both the internal architecture of the enzyme and its regulatory properties. In particular, the residue Asp162 interacts with Gln231 (known to be involved in aspartate binding), and binds the same residues in both the T and R states. A mutant that had this residue mutated to alanine showed a huge reduction in specific activity, a two-fold decrease in the affinity for aspartate, a loss of homotropic cooperativity, and decreased activation by ATP. It was suggested that the change in the overall structure caused by the introduction of this residue affects other residues in the R1-C1, R1-C4 and C1-C4 interfaces, which are involved in the quaternary structure transition.

"Aspartate carbamoyltransferase." Wikipedia, The Free Encyclopedia. 2 Jun 2009, 13:35 UTC. 2 Jun 2009 <http://en.wikipedia.org/w/index.php?title=Aspartate_carbamoyltransferase&oldid=293941261>.

Proline Kinks

Integral membrane proteins often contain proline residues in their presumably alpha-helical transmembrane segments. This is in marked contrast to globular proteins, where proline is rarely found inside alpha-helices. Proline residues cause kinks in helices, and, in addition to leaving the i-4 backbone carbonyl without its normal hydrogen bond donor, also sterically prevent the (i-3)-carbonyl-(i + l)-amide backbone hydrogen bond from forming. Here, some structural aspects of proline kinks in transmembrane helices are discussed on the basis of an analysis of Pro-kinked helices in the photosynthetic reaction center and bacteriorhodopsin.


Glucose (Glc), a monosaccharide (or simple sugar) also known as grape sugar, blood sugar, or corn sugar, is a very important carbohydrate in biology. The living cell uses it as a source of energy and metabolic intermediate. Glucose is one of the main products of photosynthesis and starts cellular respiration in both prokaryotes (bacteria and archaea) and eukaryotes

Glucose (C6H12O6) contains six carbon atoms, one of which is part of an aldehyde group and is therefore referred to as an aldohexose. In solution, the glucose molecule can exist in an open-chain (acyclic) form and a ring (cyclic) form (in equilibrium). The cyclic form is the result of a covalent bond between the aldehyde C atom and the C-5 hydroxyl group to form a six-membered cyclic hemiacetal. At pH 7 the cyclic form is predominant. In the solid phase, glucose assumes the cyclic form. Because the ring contains five carbon atoms and one oxygen atom (like pyran), the cyclic form of glucose is also referred to as glucopyranose. In this ring, each carbon is linked to a hydroxyl side group with the exception of the fifth atom, which links to a sixth carbon atom outside the ring, forming a CH2OH group. Glucose is commonly available in the form of a white substance or as a solid crystal. It can also be dissolved in water as an aqueous solution.

Lymphocyte Homing

Lymphocyte "homing" process disperses the immunologic repertoire, directs lymphocyte subsets to the specialized microenvironments that control their differentiation and regulate their survival, and targets immune effector cells to sites of antigenic or microbial invasion. Recent advances reveal that the exquisite specificity of lymphocyte homing is determined by combinatorial "decision processes" involving multistep sequential engagement of adhesion and signaling receptors. These homing-related interactions are seamlessly integrated into the overall interaction of the lymphocyte with its environment and participate directly in the control of lymphocyte function, life-span, and population dynamics. In this article a review of the molecular basis of lymphocyte homing is presented, and mechanisms by which homing physiology regulated the homeostasis of immunologic resources are proposed.

Neutrophil Chase

Neutrophils are white blood cells, which hunt and kill bacteria In this video neutrophil can be seen in the mist of red blood cells.Bacteria releases chemo-attractine that is sensed by the neutraphils, the neutrophil becomes polarized and starts chasing the bacteria.The bacteria bounce around by thermal energy move in a random path, avoiding neutrophils. Eventually the neutrophill catches the bacteria and engulfs them by phagocytosis

Cytokine Signaling

Cytokines are a category of signaling molecules that are used extensively in cellular communication. They are proteins, peptides, or glycoproteins. The term cytokine encompasses a large and diverse family of polypeptide regulators that are produced widely throughout the body by cells of diverse embryological origin.

Cytokines typically consists of two chains each having extra-cellular Cytokines binding domain and intracytoplasmic domain, which binds member of family protein tyrosine kinases called Janus kinases or JAK kinase. In the absences of cytokine the two chain do not remain associateded.the cytokine binding to the receptors stabilize the hetero dimer and brings together the JAKs that are bound to the cytoplasmic portions of each chain.

JAKS kinases those are able to phosphoralate cytoplasmic tails of the cytokine receptors.

Signal trasduction and transcription or STAT molecules bind to the phosphorated cytokine receptor chains and phosphorated by JAKS.

The addition of phosphate to the STATs enables them to dimerise and migrate to the nuclues,where the directly activate gene transcription.

Lipids and Membranes

Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules.

Membrane is an enclosing or separating amphipathic layer that acts as a barrier within or around a cell. It is, almost invariably, a lipid bilayer, composed of a double layer of lipid (usually phospholipid) molecules and proteins that may constitute close to 50% of membrane content.

Fluorescence Recovery After Photobleaching (FRAP)

Fluorescence recovery after photobleaching (FRAP) denotes an optical technique capable of quantifying the two dimensional lateral diffusion of a molecularity thin film containing fluorescent labeled probes, or to examine single cells. This technique is very useful in biological studies of cell membrane diffusion and protein binding. In addition, surface deposition of a fluorescing phospholipid bilayer (or monolayer) allows the characterization of hydrophilic (or hydrophobic) surfaces in terms of surface structure and free energy. Similar, though less well known, techniques have been developed to investigate the 3-dimensional diffusion and binding of molecules inside the cell; they are also referred to as FRAP.

What is IgG Antibodies

Immunoglobulin G (IgG) is a monomeric immunoglobulin, built of two heavy chains γ and two light chains. Each IgG has two antigen binding sites. It is the most abundant immunoglobulin and is approximately equally distributed in blood and in tissue liquids, constituting 75% of serum immunoglobulins in humans. IgG molecules are synthesised and secreted by plasma B cells.


IgG antibodies are predominately involved in the secondary antibody response, (the main antibody involved in primary response is IgM) which occurs approximately one month following antigen recognition, thus the presence of specific IgG generally corresponds to maturation of the antibody response. Pro-inflammatory cytokines particularly IL-4 and IL-2, have a crucial role in activation of the IgG antibody response.

This is the only isotype that can pass through the human placenta, thereby providing protection to the fetus in utero. Along with IgA secreted in the breast milk, residual IgG absorbed through the placenta provides the neonate with humoral immunity before its own immune system develops.

It can bind to many kinds of pathogens, for example viruses, bacteria, and fungi, and protects the body against them by agglutination and immobilization, complement activation (classical pathway), opsonization for phagocytosis and neutralization of their toxins. It also plays an important role in Antibody-dependent cell-mediated cytotoxicity(ADCC).

IgG is also associated with Type II and Type III Hypersensitivity.

IgG antibodies are large molecules of about 150 kDa composed of 4 peptide chains. It contains 2 identical heavy chains of about 50 kDa and 2 identical light chains of about 25 kDa, thus tetrameric quaternary structure. The two heavy chains are linked to each other and to a light chain each by disulfide bonds. The resulting tetramer has two identical halves which together form the Y-like shape. Each end of the fork contains an identical antigen binding site.


In humans, the three receptors for IgG are:
  • FcγRI (CD64) – 72kDa in size. Expressed on cells of mononuclear phagocyte lineage.
  • FcγRII (CD32) – 40kDa in size. Has 2 forms, alpha (with an ITAM receptor motif) and beta (with an ITIM receptor motif).
  • FcγRIII (CD16) – 50-80kDa in size. Has 2 forms, alpha (a transmembrane protein) and beta (expressed on neutrophils).

Glycosylation is essential for IgG binding to its receptors, regardless of its class

"Immunoglobulin G." Wikipedia, The Free Encyclopedia. 13 Jun 2009, 07:45 UTC. 13 Jun 2009 <http://en.wikipedia.org/w/index.php?title=Immunoglobulin_G&oldid=296129750>. 

Lecture on Myoglobin and Hemoglobin

Myoglobin is a single-chain globular protein of 153 amino acids, containing a heme (iron-containing porphyrin) prosthetic group in the center around which the remaining apoprotein folds. It has eight alpha helices and a hydrophobic core. It has a molecular weight of 16,700 daltons, and is the primary oxygen-carrying pigment of muscle tissues.

Uptake of Bacteria by Phagocytes

Uptake of bacteria by phagocytes is an active process, which requires triggering of specific receptors on phagocytes.Fc receptor, which binds antibody-coated bacteria, is one of the receptors capable of triggering phagocytosis.
In the case of LPS it is recognize by TLR4 receptor, which is expressed in the surface of dendritic cells.
LPS is transported by a soluble LPS binding protein (LBP) to the surface of dendritic cells, And it’s deposited in cell surface protein (CD14).The presence of LPS is detected by TLR4 though its interaction and recognition of the LPS bound CD14.The signal delivered by TLR initiates maturation of dendritic cell.
Dendritic cell can now migrate to regional lymph nodes and activate required immune response.

Enzymes lecture

Protein Structure Lecture

Innate Recognition of Pathogens

In the initial stage of immune response, the innate immune system recognizes the presence of pathogens and provides the first line of defense.Dendritic cells which are circulating through the tissue has the ability to recognize presence of pathogen associated molecular patterns or PAMPs.PAPMs are conserved features of pathogens such as lipopolysaccharides (LPS) that are components of the cell membrane of all gram-negative bacteria.Dendritic cells have the ability to recognize PAMPs through the expression of family of Toll like receptors (TLRs).

In the case of LPS it is recognize by TLR4 receptor, which is expressed in the surface of dendritic cells.
LPS is transported by a soluble LPS binding protein (LBP) to the surface of dendritic cells, And it’s deposited in cell surface protein (CD14).The presence of LPS is detected by TLR4 though its interaction and recognition of the LPS bound CD14.The signal delivered by TLR initiates maturation of dendritic cell.
Dendritic cell can now migrate to regional lymph nodes and activate required immune response.

Induction of Apoptosis

Apoptosis in T cells and other cells can be activated through cell surface receptors called FAS,Fas are member of TNF receptor family and binds to TNF family member. FasL (FAS ligand) expressed on the surface of other cells, usually activated T cells.
FASL ligands like other TNF family members are a trimmer, and when FAS receptors bind trimmer ligands, three receptors chains are brought together to form a other trimmer.Bringing together the intercellular domains of Fas, which contains adapter molecules called death domains, allows them to bind other intercellular death domains containing protein such as FADD.

A FADD act has an adapter linking FAS to caspase 8;a member of intercellular protease called Caspases.It cleaves at the C terminal side of the aspartic acid residues.Initially Caspase 8 binds as a inactive precursor, but once bound pro-caspase molecule are able activate each other by cleavage and by second cleavage to release the protease domain from the complex proteins assembled around the Fas receptors.
Caspase 8 proteolytic domain activates other pro-caspases, which can in turn activates other pro-caspases in a proteolytc cascade.At the end of the cascade is a important effector caspase called caspase 3,which cleaves the protein called I-CAD the inhibitor of caspase activated DNA.By cleaving I-CAD inhibitor, the caspase3 releases active DNA, which is able to migrate to nucleus.In the nucleus the caspase activated DNA degrades chromatin, cutting the DNA into small pieces and ultimately killing the cell

MAP kinase pathway, MAPK

The Mitogen activated Protein kinase pathway or MAP kinase pathway is a key signaling pathway by which cell responds to external stimuli,There are number of such MAP kinase Pathways which involves different proteins each step, but they share some common features.

Generic Pathway
  • Each MAP kinase Pathway starts with activation of Guanine Nucleotide Exchange Factor or GEF.In this example we see activation of GEF by T cell Adapter protein LAT,which links the ligand binding to the T cell receptor with MAP kinase pathways.
  • GEF proteins activates small G protein by exchanging GDP bound G protein for GTP.In the GTP bound state the G protein is active and can activate other proteins.
  • In the MAP kinase pathways the protein activated by small G protein is the MAP Kinase kinase kinase or MAPKKK.
  • The activated MAPKKK now phosphorylates a second kinase MAP kinase kinase or MAPKK.
  • MAPKK is a dual function kinase able to phosphorylate both tyrosine and serine on its target
  • MAPKK phosphorylates and activates third kinase called MAP kinase or MAPK.
  • Activated MAP kinase now migrates to the nucleus where its able activate transcription factors.

Activated T Cell

In this video, we can see a T cell becomes activated when its interact with Dendritic cells (DCs).The T cell is labeled with a dye that fluoresce when its bind calcium ion. As the T cell contacts the surface of dendritic cells we can see suddenly fluoresce a bright green when it gets activated.However it still continues to move crawling over the surface of dendritic cells.Eventully the T cell loses interest,while it still contacting the dendritic cells you can see floresence starts to fade.the T cell then migrates away from dendritic cells

Reversible Inhibition

Kinetics of Bi substrate Enzyme

TCR Signaling Pathway

T cell receptor is a complex of antigen specific alpha and beta chains associated in membrane CD3 gamma and CD3 delta,epsilon and zeta chains .

Each of the cd3 chains have at lest one copy of signaling motif immunoreceptor tyrosine activation motif or ITAMs in the cytoplasmic domain .various short family tyrosine kinase will associate with cytoplasmic domains in the Tcell receptor complex.

Fyn along with other short kinase family members are important for t cell activation,other molecules involved in T cell activation includes CD45 whose cytoplasmic domain contains tyrosine phosphatase enzyme and the T cell co receptor either CD4 or CD8.In this example the co receptor is CD4 ,the co receptor molecules have bound to cytoplasmic domains tyrosine kinase Lck,the cytosol enzyme ZAP70 also plays a essential role t cell activation.

Lipid Rafts

Lipod rafts are specialised regions of the cell membrane,that are rich lipids and cholestrol and more rigid than rest of membrane ,tehese regions are first discovered because the remain intact when certains detergents are used to solubilise the cell membrane.Sometypes of cellular proteins are associated with the lipid rafts,protein with GPI anchors and proteins like src-family kinases,which are modified by the addition of fatty acids that allow them to bind the cell membrane are both found to associated with lipid rafts.

The rafts are dynamic structures and they can move in the membrane joining to form large rafts are breakingdown into smaller ones .other membrane proteins may not associate with lipid rafts.
Lipid rafts are specialized regions of the cell membrane that are enriched for particular lipids and cholesterol, and consequently more rigid than the rest of the membrane.

Viral Evasions

When virusus infect a cell ,the proteins produced in the cytosol by the virus can be degraded by proteosome and trasported into ER though the TAP transporter ,the presence of these peptide in the ER allows them to loaded on to MHC class 1 molecules and evetully trasported to surface of the cell where it can be recognised by CD8 T cells .

Certain viruses are developed a stargeries to prevent their detection by cytotoxic t cells,Many of the statergies involve in preventing peptide derived from the virus from entering the ER and being loaded in MHC Class I molecules.

For example herpes simplex virus 1 codes a protein IPC47 that has ability to block peptide binding to the cytosol surface of the TAP transporter,In this way transport of viral peptides into the ER is prevented ,consequently these peptides cannot be loaded into MHC class I molecules.This results in reduced expression of peptide loaded MHC on surface of the infected cell.Cell is not killed and therfore virus can replicate sucessfully.

Gene Recombination

Immunoglobin genes are composed of separated segments of DNA that become join together in the process called somatic recombination to make a functional gene.In heavy chain genes there are 3 gene segments the Variable or V segment, the diversity or D segment and joining the J segment.Light chain genes have only 2 gene segments V and J segments

Gene segments that can be recombined has specific sequence motifs adjacent to them called Recombination Signal sequence or RSS motifs .The protein complex containing the products of the recombination activated genes RAG1 and RAG2 binds specifically to the RSS motif.
The individual gene segments to whose flanking RSS motif the RAG protein complex binds are selected at random from the number of copies present in each gene locus .The RAG protein complex brings together the gene segments to be recombined and cleave the DNA exactly at the junction of gene segments and adjoining RSS motifs .The cleavage creates a Hair pin of DNA at the end of the gene segments and double stranded breaks at the end of RSS motifs.
Additional proteins DNA -dependent protein kinase(DNA-PK),Ku,Artemis and dimer of DNA ligase/XRCC4 dimer are incorporated into larger complex with RAG proteins. These RSS ends are joined forming signal joints to create closed circular DNA that plays no further role in the recombination process.
DNA hairpins at the end of the gene segments are cleaved, an additional enzyme Terminal deoxynucleotidyltransferase (TdT) is recruited and adds additional nucleotide to ends of nucleotide strands, The other enzymes in the complex ligate together the two ends of the DNA segment completing the recombination process.

Leukocyte Extravasation

Activated vascular endothelium cell express E-selectin and ICAM-1 and display chemokines on extracellular matix.leukocytes initiatly adhere by binding to selectins which recognise S-lex.these allows other molecules to bind,LFA-1 binds to ICAM-1,chemokine signalling converts this weak binding to tight adhesion.

  • The tightly bound leukocytes now migrates across the endothelium squeezing between adjacent endothelial cells.
  • Chemokine binding now signals leukocytes to migrate along the chemokine concentration gradient .
  • The site of information is the source of chemokine gradient .hence leukocytes are attracted from the blood towards sites of infection.