User talk:Apdang

Chaperones are known as helpers that supporting protein folding. Recently, researchers demonstrate that chaperones and co-chaperones contribute to all aspects of the cell. Researchers promote that in the cell, the cellular chaperones are divided into many small branches such as net, and each branch would involve in particular functions. Chaperones are not only supporting for proteins, but also support for RNA called RNA chaperones. Many molecular chaperons of the living organisms reflect to the aging process and disease. In fact, the relationship between separating chaperon network and their functions had been known in Eukaryote cells such as “de novo protein", and a specific mitochondrial chaperon network holds the role in the cancer cells. In addition, scientists conduct many experiment sets showed abundance of chaperones and co-chaperones in nucleoli regulates to the functions of the cell.  Through experiment sets, researchers propose that nuclear chaperones and multiple task protein are composed of a unique set of the folding factors that we can detect basing on the combination.  That would open a new future to develop medicine so that aging cells and diseases would be curved. Reference: "Chaperones and multitasking proteins in the nucleolus: networking together for survival." Trends in Biochemical Sciences 35. Department of Physiology, McGill University, 3655 Promenade Sir William Osier, Montreal, Quebec, H3G 1Y6, Canada. Apdang (talk) 21:20, 15 October 2010 (UTC)

Enzyme and its model of participate in a reaction: Enzyme participates in a reaction following two models that are Lock and Key model and induced fit model. In the lock and key model, enzyme and its active site are rigid. Since the substrates come in, they fit the active site of the enzyme very tightly; therefore, they are very specific fit. In the other hand, Induced Fit model allows the enzyme reacts more frequently due to the active site less tightly, less specific than Lock and Key. However, enzymes are either Lock and Key or Induced Fit, but that the two model is extremes of a continuum. References: “Microbiology.” Ed 9. Benjamin Cumming: 2009. apdang (talk) 04:42, 23 October 2010 (UTC)

Function of the enzyme: Antibody: IgG antibody accounts for 80% of all types of antibody serum in a body. They are monomers and ready cross blood vessel walls to enter tissue fluids. Structure of IgG has Y shape molecules that are composed of two light chains and two heavy c

hains. Two heavy chain linked by the disulfide bridge. Most of the molecules are made up of constant regions, which are the same for all antibodies of the same class. The amino acid sequence of the variable regions forms the two antigen-biding sites. Antigen biding sides are bound to the antigen determinant. In a region of inflammation, these monomer antibodies ready cross the walls of a blood vessel and enter tissue fluids. IgG antibodies, for ex, can cross the placenta and confer passive immunity to the fetus. IgG antibody protects against circulating bacteria and virus, neutralize a bacteria toxin, trigger the complement system, and when bound to the antigen, enhance the effectiveness of phagocytic cell. IgG is in late stage infection that plays a role as immune clearance, the most important antibodies in disease recovery. IgG antibodies are the most prevalent in serum. They provide naturally acquired passive immunity, neutralize bacterial toxins, participate in complement fixation and enhance phagocytosis. Therefore, it used to transfer from a mother to the fetus or to a newborn in colostrum results in naturally acquires passive immunity in the newborn. This type of immunity can last up to a few months. Reference: Campbell, Reece, and et. “Biology.” Ed 8. San Francisco: 2009. 900-1063. apdang (talk) 05:22, 23 October 2010 (UTC)

Scientists use bioinformatics to analyze genomes, their functions, and application of systems biology to medicine: The cancer genome Atlas is another example of system biology in which a large group of interaction gene products are analyzed together. Three types of cancers such as lung cancer, ovarian cancer, and glioblastoma of the brain are being analyzed by comparing gene sequences and patterns of gene expression in cancer cells with those of normal cells. A set of approximately 2000 genes from cancers cells will be sequenced at several different times during the progression of the disease to monitor changes due to mutations and rearrangements. Silicon and glass “chip” have already been developed that hold a microarray of most the known human genes. Those chips are being used to analyze gene expression pattern in patients suffering from various cancers and other diseases. References: “Genomes and their evolution.” Biology. Campbell and Reece. Ed 8th. 2007.400-450. apdang (talk) 06:07, 11 November 2010 (UTC)

Three stage approach to genome sequencing The initial stage: Cytogenetic maps based on this type of information provided the starting point for more detailed mapping. With these cytogenetic maps of chromosomes in hands, the initial stage in sequencing the human genome was to construct a linkage map of several thousand genetic markers spaced throughout the chromosomes. On the stage, the order of the markers and the relative distances between them on such a map are based on recombination frequencies. The markers can be genes or any other identifiable sequences in the DNA. It was also valuable as a framework for organizing more detailed maps of particular regions. The second stage: This stage was the physical mapping of the human genome. In a physical map, the distances between markers are expressed by some physical measure, usually the number of base pairs along the DNA. The key is to make fragments that overlap and then use probes or automated nucleotide sequencing of the ends to find the overlap. In this way, fragments can be assigned to a sequencing order that corresponds to their order in a chromosome. In working with large genome, researchers carry out several rounds of DNA cutting, cloning, and physical mapping. After such long fragments are put in order, each fragment is cut into smaller pieces, which are cloned in plasmids or phages, ordered in turn, and finally sequenced. The last stage: The ultimate goal in a mapping a genome is to determine the complete nucleotide sequence of each chromosome. For the human genome, this was accomplished by sequence machines, using chain-termination method. References: “Genomes and their evolution.” Biology. Campbell and Reece. Ed 8th. 2007.500-600. apdang (talk) 19:55, 13 November 2010 (UTC)

Biosynthetic enzymes of unusual microbial sugars Carbohydrates not only play roles in energy storage and plant cell wall structure, but also involved in such processes as fertilization, the immune respond and cell adhesion. Recently, researchers explored and understood the dideoxysugar and trideoxysugars, which are synthesized by the variety of bacteria, fungi, and plants. Many of the unusual sugars produced by microbes are formed from simple monosaccharides such as glucose-6-phosphate. The diversity of the dideoxysugars and trideoxysugars observed in the natural world seem to be huge, but there are seven enzymatic reaction types that ultimately lead to the production of these unusual sugars, which are acetylation, aminations, dehydrations, epimerization, isomerizations, ketoreductions, and methylations. The pathways for the biosynthesis of most dideoxysugars and trideoxysugars can be catalyzed by N-acetyltransferases that transfer of an acetyl group from acetyl-CoA to primary amino receptors. The first X-ray structure determined for an LβH super family member was that of UDP-N-acetylglucosamine acyltransferase. This enzyme has been known as the key role in Lpid A biosynthesis by catalysing the transfer of hydroxymyristic acid from an acyl carrier protein to the UDP-N-acetylglucosamine. Recently, three-dimensional structure of a second N-acetyltransferase belongs to the LβH super family member and functioning on a nucleotide-linked sugar was reported. Another enzyme has been classified is PLP-dependent aminotransferase. Adding of an amino group to the sugar rings occurs through the action of aminotransferases that require pyridoxal 5’-phosphate or PLP for activity. PLP-dependent aminotransferase structure was solved the last several years. Those enzymes are involving in the production of colitose, found in the O-antigens of some Gram negative and marine bacteria. Understanding the structure and functions of these sugars and the enzyme required for the biosynthesis of these sugars. It should be possible to design them to produce carbohydrates that are important for development of new therapeutics. References: “Biosynthetic enzymes of unusual microbial sugars.” Holden, Hazel M. Paul D Cook and Jame B Thoden. Current Opinion in Structural Biology. 2010, 20: 543-550. apdang (talk) 07:28, 17 November 2010 (UTC)

CO2 affects hemoglobin’s oxygen transport: CO2 affects Hb’s oxygen binding property in two ways; at high CO2 level carbonic anhydrase to forms bicarbonate and proton. High proton concentration reduces favors release of oxygen from HbO. CO2 also directly interacts with Hb altering the affinity of Hb for oxygen. CO2 modulates O2 binding to hemoglobin by combining reversibily with the N-teminal amino groups of blood protein to form carbamates:

R-NH2 + CO2  R-NH-COO- + H+ BPG binds to hemoglobin and affect oxygen binding: BPG binds in the central cavity of T-state hemoglobin. The anion groups of BPG are within Hb-bonding and ion-paring distances of the N-terminal amino group of both b subunits. BPG binds to and stabilizes only the T-state hemoglobin. This shifts the T  R equilibrium toward the T state, which lowers the O2 binding affinity. BPG is really important for O2 transport in our body. One example is high altitude adaptation. High altitude will induce a rapid increase in the amount of BPG synthesized in erythrocytes. The increased amount of BPG will shift the oxygen binding curve from sea-level position to a lower affinity position (shift to right). This decreases the amount of O2 binding in the lungs, but, to a greater extent, increases the amount of O2 released at tissues. So hemoglobin can deliver more O2 from lungs to tissues.

References: Berg, Jeremy M. Biochemistry. Ed 6th. 2007. 205-300. “Genomes and their evolution.” Biology. Campbell and Reece. Ed 8th. 2007.400-450. apdang (talk) 19:31, 26 November 2010 (UTC)

The Bohr effect: The Bohr effect says increasing [H+] will decrease O2 binding. The Bohr effect has important physiological functions in transporting O2 from the lungs to respiring tissue and in transporting the CO2 produced by respiration back to the lungs. The CO2 produced by respiring tissues diffuses from the tissue to the capillaries. This dissolved CO2 form bicarbonate by the reaction CO2 + H2O ⇔   H+ + HCO3 - In the capillaries, where pO2 is low, the H+ generated by bicarbonate formation is taken up by hemoglobin in forming the ion pair of the T-state, thereby inducing hemoglobin to unload its bound O2. Also, this H+ uptake, facilitates CO2 transport by stimulating bicarbonate formation. In the lungs, where pO2 is high, O2 binding by hemoglobin disrupts the T-state ion pairs to form the R state, thereby releasing the Bohr protons, which recombine with bicarbonate to drive off CO2. These reactions are closely matched, so they cause very little change in blood pH.

References: Berg, Jeremy M. Biochemistry. Ed 6th. 2007. 205-300. “Genomes and their evolution.” Biology. Campbell and Reece. Ed 8th. 2007.400-450.

Molecular Clock and mitochondrial DNA. 1. The Molecular Clock is based on idea that we assume we know the mutation rate in DNA. 2. Populations from around the planet were sampled for their mitochondrial DNA. This DNA was sequenced. As the results certain genotypes were found only in certain 	populations or 	more prevalently in some populations and not in others. 3. Determining ancestry and migration of human populations based on Genetic Variation in mitochondrial DNA. SNP’s occur at a more or less known rate in mitochondrial DNA of man. Since mitochondrial are haploid and inherited directly from Mom, then any changes in the mitochondrial DNA must be due to SNP mutations. Once a SNP occurs, all descendents of that person will have that particular SNP. If a particular SNP occurred early in the history of man, all persons from that region will have that same SNP. If a particular SNP occurred early in the history of man, all persons from that region will have that same SNP. This allows scientists to postulate the migration patterns of early man. If a person in a particular family acquires a SNP, all her descendants will also have that SNP. This allows scientists to determine familial and ethnic relatedness.

References: Berg, Jeremy M. Biochemistry. Ed 6th. 2007. 205-300. Biology. Campbell and Reece. Ed 8th. 2007.400-450. apdang (talk) 05:17, 2 December 2010 (UTC)

Specific Immunity: Invasion by pathogen: pathogen Cells are infected pathogen by inhaled: Ag is moved to lymphoid respiratory mucosa, parenteral: Ag is carried to regional lymph nodes by lymph, in blood stream: Ag is carried to spleen by circulation, and digestive system: Ag is picked up by Peyer’s patches of small intestine. Once in lymphoid tissue, the Ag is phagocytized by 	macrophages or neutrophil. In this instance, the macrophages or neutrophil is acting as an antigen presenting cell (APC). APC chops up the Ag into small pieces and “decorates” its cell membrane with the Ag along with self Ag (MHC II). APC’s then contacts a variety of B cells (i.e. it shows the Ag to the total population of B cells). A few B cells out of the total pop of B cells have receptors that fit the Ag. These few B cells are contacted by APC’s, are stimulated into mitosis and mature into plasma cells (clonal selection & expansion) apdang (talk) 05:45, 2 December 2010 (UTC)

Clonal selection: T helper cells are involved in clonal selection in a regulatory role and make a lot of the activation factors (like cytokines) that tell the B cells to complete the maturation process. That started in the bone marrow The selected B cells differentiate into plasma cells: large, short lived cells, and churn out IgM and then switch to making IgG later in the recovery process. A few of the selected B cells become B memory cells. The Anamnestic response: Memory B cells are produced in the late stages of disease recovery. Memory B cells are very long lived, are specific to a particular Ag, and very quick to respond to that Ag upon 2nd exposure. Upon a second exposure to the same Ag, the anamnestic response kicks in. APC present Ag to B cell pop, but there are lots of these particular B memory cells and they are ready to go. After clonal selection, mitotic expansion occurs rapidly. 3) Ag is cleared so rapidly that patient usually is totally unaware that they were exposed to the 	disease causing agent. apdang (talk) 05:47, 2 December 2010 (UTC)