Microbiology

                                      Transformation

 Involves uptake of short fragments of naked DNA by naturally transformable bacteria.

                                         Transduction

 Involves transfer of DNA from one bacterium into another via bacteriophages. 

                                 Conjugation 

Involves transfer of DNA via sexual pilus and requires cell –to-cell contact.  

Cell Biology

                             phosphatidylinositide 3-kinases

Family of enzymes involved in cellular functions such as cell growth, proliferation, differentiation, motility, survival and intracellular trafficking, and at last in cancer.

PI3Ks are intracellular signal transducer enzymes capable of phosphorylating the 3 position hydroxyl group of the inositol ring of phosphatidylinositol. The pathway, with oncogene and tumor suppressor is involved in insensitivity of cancer tumors to insulin and IGF1, in calorie restriction.

G protein–coupled receptors (GPCRs)

Other names:  seven-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptor, and G protein–linked receptors (GPLR).

They are from large protein family of receptors that sense molecule outside the cell and activate inside signal transduction pathways and cellular responses. They are called seven-transmembrane receptors because they pass through the cell membrane seven times.

G protein–coupled receptors are found only in eukaryotes, including yeast and animals. 

The ligands that bind and activate these receptors include light-sensitive compounds, odors, pheromones, hormones, and neurotransmitters. It varies in size from small molecules to peptides to large proteins. G protein–coupled receptors are involved in many diseases, and are also the target of approximately 40% of all modern medicinal drugs.

There are two principal pathways involving the GPCRs:

·          cAMP signal pathway and

·         Phosphatidylinositol signal pathway.  

When a ligand binds to the GPCR it causes a conformational change in the GPCR, which allows it to act as a guanine nucleotide exchange factor (GEF). The GPCR can then activate G protein by exchanging its bound GDP for a GTP. The G protein's α subunit, together with the bound GTP, can then dissociate from the β and γ subunits to further affect intracellular signaling proteins or target functional proteins directly depending on the α subunit type.

 Ryanodine receptors (RyRs)

They are class of intracellular calcium channel in muscles and neurons. It is the major cellular mediator of calcium induced calcium release (CICR) in animal cells.

There are multiple isoforms of ryanodine receptors:

• RyR1 is expressed in skeletal muscles.
• RyR2 is expressed in heart muscle.
• RyR3 is expressed more widely, but especially in the brain.

Ryanodine receptors mediate the release of calcium ions from the ER, an essential step in muscle contraction. In skeletal muscle it is thought that activation occurs via a physical coupling to the dihydrphyridin receptors, whereas, in cardiac muscle, the primary mechanism is calcium-induce calcium release from the sarcoplasmic reticulum.

Cell Biology

                                                 Oncogenes and tumor suppressor genes

Two of the main types of genes that play a role in cancer are oncogenes and tumor suppressor genes.

Oncogenes

Proto-oncogenes are genes that normally help cells grow. When a proto-oncogene mutates, it becomes a "bad" gene that can become permanently turned on or activated when it is not supposed to be. When this happens, the cell grows out of control, which can lead to cancer. This gene is called an oncogene. It may be helpful to think of a cell as a car. For it to work properly, there need to be ways to control how fast it goes. A proto-oncogene normally functions in a way that is much like a gas pedal. It helps the cell grow and divide. An oncogene could be compared with a gas pedal that is stuck down, which causes the cell to divide out of control.

A few cancer syndromes are caused by inherited mutations of proto-oncogenes that cause the oncogene to be turned on. But most cancer-causing mutations involving oncogenes are acquired, not inherited. They generally activate oncogenes by:

·          Chromosome rearrangements: Changes in chromosomes that put one gene next to another, which allows one gene to activate the other

·          Gene duplication: Having extra copies of a gene, which can lead to it making too much of a certain protein.

Tumor suppressor genes

Tumor suppressor genes are normal genes that slow down cell division, repair DNA mistakes, or apoptosis or programmed cell death. When tumor suppressor genes don't work properly, cells can grow out of control, which can lead to cancer. A tumor suppressor gene is like the brake pedal on a car. It normally keeps the cell from dividing too quickly, just as a brake keeps a car from going too fast. When something goes wrong with the gene, such as a mutation, cell division can get out of control.

An important difference between oncogenes and tumor suppressor genes is that oncogenes result from the activation (turning on) of proto-oncogenes, but tumor suppressor genes cause cancer when they are inactivated (turned off).

Inherited abnormalities of tumor suppressor genes have been found in some family cancer syndromes. They cause certain types of cancer to run in families. But most tumor suppressor gene mutations are acquired, not inherited.

For example, abnormalities of the TP53 gene (which codes for the p53 protein) have been found in more than half of human cancers. Acquired mutations of this gene appear in a wide range of cancers.

Microbiology

• 
  

                                                            Viral Replication 

   Lytic and lysogenic cycles are two different way of viral replication.

  At first, the virus has to infect the cell. So the virus attaches itself to the outer cell wall and releases enzymes that weaken the cell wall. Then, depending on whether it is a DNA virus or a RNA virus, the virus injects its double stranded DNA or its single stranded RNA into the cell.

  
  

  The Lytic Cycle

  It the main cycle in viral replication, once the viral DNA enters the cell it transcribes itself into the host cell's messenger RNAs and uses them to direct the ribosomes.

  The host cell's DNA is destroyed and the virus takes over the cell's metabolic activities.

  The virus begins using the cell energy for its own replication. The virus produces progeny phages. These replicate fast, and soon the cell is filled with 100-200 new viruses and liquid. As the cell starts getting overcrowded, the original virus releases enzymes to break the cell wall. The cell wall bursts (lysing) and the new viruses are released.

  The lytic cycle occurs in virulent viruses. The symptoms from a viral infection occur when the virus is in a lytic state.

  The Lysogenic Cycle

  The viral DNA or RNA enters the cell and integrates into the host DNA as a new set of genes called prophage. That is, the viral DNA becomes part of the cell's genetic material. No progeny particles, like in the lytic phase, are produced. Each time the host cell DNA chromosome replicates during cell division, the passive and non-virulent prophage replicates too. This may alter the cell's characteristics, but it does not destroy it.

  There are no viral symptoms in the lysogenic cycle; it occurs after the viral infection is over. But the viral DNA or RNA remains in the cell and it may remain there permanently. However, if the prophage undergoes any stress or mutation or is exposed to UV radiation, the viral lysogenic cycle can change into the viral lytic cycle. In which case, there will be symptoms of a new viral infection. Some viruses first replicate by the lysogenic cycle and then switch to the lytic cycle.

  Differences between Lytic and Lysogenic Cycles

                                                 In the Lytic Cycle:

  Viral DNA destroys Cell DNA, takes over cell functions and destroys the cell.

  The Virus replicates and produces progeny phages.

  There are symptoms of viral infection.

  Virtulant viral infection takes place.  

                                                 In the Lysogenic Cycle:

  Viral DNA merges with Cell DNA and does not destroy the cell.

  The Virus does not produce progeny.

  There are no symptoms of viral infection.

  Temperate viral replication takes place.

• 
  
• 
  
• 
  
• 
  
• 
• 
  
• 
  
• 
  
• 
  
• 
  

Cell Biology

                Translocon (translocator, translocation channel):

A complex of proteins associated with the translocation of polypeptide across membranes. In eukaryotes:  transports polypeptides with a targeting signal sequence into the luminal space of ER from the cytosol. The same complex is also used to integrate proteins into the membrane itself.

In prokaryotes: a similar protein complex transports polypeptides across the plasma membrane or integrates membrane proteins.  Bacterial pathogens can also assemble other translocons in their host membranes, allowing them to export virulence factor into their target cells.

SEC 62/63

Translocation protein SEC63 homolog is a protein that in humans is encoded by the SEC63 gene.Translocation protein SEC62 is a protein that in humans is encoded by the SEC62 gene.

The Sec61 complex is the central component of the protein translocation apparatus of the endoplasmic reticulum (ER) membrane. The protein encoded by this gene and SEC62 protein are found to be associated with ribosome-free SEC61 complex. It is speculated that Sec61-Sec62-Sec63 perform post-translational protein translocation into the ER. The Sec61-Sec62-Sec63 complex might also perform the backward transport of ER proteins that are subject to the ubiquitin-proteasome-dependent degradation pathway. The encoded protein is an integral membrane protein located in the rough ER.

Mutations of this gene have been linked with autosomal dominant polycystic liver disease.

The mammalian Sec61 complex consisting of Sec61α, Sec61β, and Sec61γ has been identified as a crucial membrane component involved in the signal recognition particle (SRP)1-dependent co-translational protein translocation across the endoplasmic reticulum (ER) membrane. The Sec61 complex forms the hydrophilic pore in the membrane through which the nascent polypeptide is translocated.

Signal recognition particle (SRP) receptor

Signal recognition particle (SRP) receptor, also called docking protein, and is a dimer composed of 2 different subunits that are associated exclusively with the rough ER in mammalian cells.

Its main function is to identify the SRP units. SRP (signal recognition particle) is a molecule that helps the ribosome-mRNA-polypeptide complexes to settle down on the membrane of the endoplasmic reticulum.

The eukaryotic SRP receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain,while the prokaryotic SRP receptor comprises only the monomeric loosely membrane-associated SR-alpha.

Binding immunoglobulin protein (BiP)

Binding immunoglobulin protein (BiP) also known as 78 kDa glucose-regulated protein (GRP-78) or heat shock 70 kDa protein 5 (HSPA5) is a protein that in humans is encoded by the HSPA5 gene.

BiP is a HSP70 molecular chaperone located in the lumen of the endoplasmic reticulum (ER) that binds newly synthesized proteins as they are translocated into the ER, and maintains them in a state competent for subsequent folding and oligomerization. BiP is also an essential component of the translocation machinery, as well as playing a role in retrograde transport across the ER membrane of aberrant proteins destined for degradation by the proteasome. BiP is an abundant protein under all growth conditions, but its synthesis is markedly induced under conditions that lead to the accumulation of unfolded polypeptides in the ER.

Microbiology

                                                     Prion disease


        A group of conditions that affect the nervous system in humans and animals. All are currently untreatable and universally fatal. 
         
        In people, these conditions impair brain function, causing changes in memory, personality, and behavior, dementia, and abnormal movements and ataxia.

        It is very rare and the conditions affects one person per million worldwide each year. Approximately 350 new cases are reported annually in the United States.

          A Prion is an infectious agents and specifically a protein in a misfolded form. Prion protein (PrP) are responsible for mammalian transmissible spongiform encephalopathies, including bovine spongiform encephalopathy and scrapie in sheep. In humans, cause Creutzfeldt - Jakob disease (CJD), variant Creutzfeldt - Jakob disease (vCJD), Gerstmann–Sträussler–Scheinker syndrome, Fatal Familial Insomnia and kuru.

       Prions are not considered living organisms but are misfolded protein molecules.  If a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the disease-associated, misfolded prion form; the prion acts as a template to guide the misfolding of more proteins into prion form. These newly formed prions can then go on to convert more proteins themselves; as a result; produces large amounts of the prion form. This altered structure is stable and are resistant to denaturation by chemical and physical agents; as a result; accumulates in infected tissue, causing tissue damage and cell death.