It deals with the structures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules. The experiments included in Biochemistry Virtual Lab I are fundamental in nature, dealing with the identification and classification of various carbohydrates, acid-base titrations of amino acids, isolation of proteins from their natural sources, etc. Population ecology is the study of populations especially population abundance and how they change over time.
Crucial to this study are the various interactions between a population and its resources. Studies on simple models of interacting species is the main focus this simulation oriented lab. Studies based on models of predation, competition as seen in interacting species is the main focus this simulation oriented lab. Lab II focuses on applied principles of population ecology for PG students.
Sit-and-wait Predators that Maximize Energy Microparasite and Macroparasite - Host Dynamics Immunology Virtual Lab I The branch of biomedicine concerned with the structure and function of the immune system, innate and acquired immunity, the bodily distinction of self from no self, and laboratory techniques involving the interaction of antigens with specific antibodies. This includes eukaryotes such as fungi and, protists and prokaryotes.
Viruses, though not strictly classed as living organisms, are also studied. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry. Molecular biology chiefly concerns itself with understanding the interactions between the various systems of a cell, including the interactions between DNA, RNA and protein biosynthesis as well as learning how these interactions are regulated. It includes the study of the structure and organization, growth, regulation, movements and interaction of the cells.
Cell biology is closely related to other areas of biology such as genetics, molecular biology, and biochemistry. This virtual lab is an introductory course for undergraduate students and deals with the storage and retrieval of data from different biological databases like Gene, Pubmed, GEO, TAIR, Prosite etc. The exercises mainly deal with the different algorithms in sequence alignment and provides a computational exploration to the use of various tools used for sequence alignment.
This lab is targeted towards PG students with exercises that will allow one to learn visualising proteins in 3D, how to calculate distance among atoms, find active sites in protein structures and also delve into some structural analysis methods including docking and homology modeling.
However it is known that ancestral reconstruction is somewhat unreliable especially at sites with alignment gaps. Ancestral values are represented in grey. Despite the fact that the pH of other digestive compartments can show marked differences between mammals, we chose only to represent the stomach pH values, as this compartment is the main first barrier for milk proteins.
A review of the pH values is reported in Table 5 of the following reference [ 24 ] p , we could not find well-defined values for chimp, horse, cow, and guinea pig.
However mouse and guinea pig seem to be an exception to this observation. It is unclear how much this is due to real pI shifts or to and artifact of the method of pI calculation. Lactadherin has shifted at least twice on the tree. To investigate this, we considered all the orthologous proteins in the 13 mammals human, chimp, monkey, mouse, rat, guinea pig, rabbit, cow, horse, dog, cat, opossum, platypus.
We considered a shift in pI between human and mouse to be high if it was greater than 0. These large shifts seen for certain milk proteins are therefore unexpected for typical proteins that have conserved their function in evolution. Most proteins have a similar pI between species, with some exceptions lying out on both sides of the diagonal. The change in pI between the milk proteins may reflect amino acid replacement at a number of residues, or they might be due to large insertions or deletions that cause large changes in pI.
However, we observe noticeable changes in length between lactadherin and muc1. When the regions in mouse that are not aligned with those found in human are removed, the pI is 7. For muc1, the human protein is much longer than the mouse sequence. However, the pI of the human regions alignable with mouse muc1 was 7. These results show that for Lactadherin the change in pI is mainly due to the mouse insertion. Can selection have contributed to the change in pI?
A recent study of the pI of mammalian proteins argues that selection has contributed to some of the pI shifts between orthologous proteins [ 5 ]. SLR is a direct test of whether a particular site is evolving in a non-neutral fashion, inspecting the excess of non-synonymous over synonymous DNA changes; and indicates which sites in the protein have strong evidence of positive selection, which correspond to sites that are unusually variable.
Eleven of these sites change the pI of the protein, and 7 of those also change the overall charge of the protein at neutral pH. Only four positively selected sites have not affected the pI of the protein, and are not known to be implicated in any side modifications of the protein. We find that there are significantly more sites that affect the pI that have undergone positive selection compared to all other sites that do not affect the pI.
The sequences of casoxin peptides A, B, and C are in the pink colored boxes. Cleavage sites are to the right of the red residues, while green residues are the corresponding residues that are not cleavable by the same enzyme in human and mouse. Casoxin-A and C are cleaved by a pepsin-trypsin digest for the former, and a trypsin digest for the later [ 12 ].
Horizontal lines represent gaps. Stars indicate sites that were predicted to be under positive selection see results. Orange residues have been shown in the literature to undergo phosphorylation. Blue residues have been shown in the literature to undergo glycosylation. One potential phosphorylation site indicated in lavender in mouse. Under a random distribution of the positively selected sites detected in the human muc1 protein sequence, we will expect an average of 4.
Put together these results show that selection has played a part in the change of pI and consequently on the overall net charge of the protein. What is driving this selection on the pI? Can it be the important differences in pH and compartmentalization between the digestive systems of different mammals? Some, such as the caseins, get broken down in the highly acidic conditions of the stomach, whereas others such as lactadherin and lactoferrin [ 9 , 10 ] travel intact or partially intact to be broken down further down in the digestive tract.
Given the very large shifts in pI , we would anticipate that the processing and breakdown of milk proteins are likely to differ substantially.
We might imagine that the greatest shifts during evolution might occur when animals shift between largely carnivorous or omnivore diets and herbivore diets, since the more complex stomachs of some herbivores, and the more acid stomach pH s of some carnivores might alter functional constraints. This suggests that the shifts in functional constraints may be associated with factors that are not linked with the gross morphology or diet of major clades.
It is interesting to speculate on how extrinsic factors, such as commensal and pathogenic bacteria, may exert selection pressures on milk protein function, but also of interest to consider how alterations in intrinsic milk protein functions may relate to adaptive changes. Milk proteins are known to yield many bioactive peptides that modulate and participate in various regulatory processes in the body [ 11 ].
These peptides are usually cleaved by digestive enzymes such as trypsin, pepsin, and chymotrypsin. Some proteases cleave near positively charged residues, such as trpysin, while others avoid positive charge in their substrate region pepsin , and the adaptive requirements for the gain and loss of proteolytic cleavage sites in certain regions of the gut e. Thus, the shift in pI may be associated with divergence in functional requirements for either rates of digestion, or for functional components of the milk.
We observe that all the proteins that have shifted dramatically are ones that also happen to be highly glycosylated and phosphorylated. Also, there are 9 referenced phosphorylations in human muc1, while there are 6 and 7 by similarity in cow and mouse respectively.
Our analyses of pI did not take into account these post-translational modifications. To examine if post-translational modifications can reduce the difference in the isoelectric point, we used experimentally validated phosphorylation and glycosylation sites, which are defined in cow, human and to a weaker extent in mouse.
The phosphorylation sites for muc1 in both cow and mouse are potential sites found with similarity rather than experimentally validated sites. For muc1, experimental validation is only available for human that has 4 O-linked, and 5 N-linked glycosylations.
These might also narrow down the gap in the muc1 pI between the different species. Nonetheless, both cases where the pI difference is reduced or not are interesting. Indeed if the pI difference is reduced and becomes very close between both species, this reflects that the protein has adapted its pI so that the final product with the different number of glycosylations and phosphorylations becomes the same. Indeed, if the pI was initially not different, the addition of glycosylation will then further the gap between the pI s.
Although the production of milk is conserved between mammals for over MA, our results argue that common proteins that have been shared by mammals are functionally diverging. We have shown that selection has acted on the residues that affect the protein's pI.
The simplest explanation was the adaptation of the protein to the different digestive systems to accommodate reactions to changes in pH of the different compartments.
However, we found the pattern of change did not correlate strongly with the greatest shifts in compartmentalization and pH during evolution, suggesting that other factors, potentially including milk proteins' functional features, may be associated with the adaptive changes.
It is not clear if this is merely coincidental, or whether glycosylated proteins play a particular role in the gut that is subjected to shifting selection pressures over evolutionary time.
Exactly how shifting the pI of these milk proteins might benefit the neonate is not entirely clear. However, given the ability of pathogens such as H. In addition the 8 species needed to include human, chimp, cow, and mouse. We used the 9 major milk proteins defined in human and cow to detect their orthologs in the 13 other genomes, defined by reciprocal hits. To find orthologous non-milk proteins, we identified way mutual best BLASTP hits among human, chimp, monkey macaque, mouse, rat, guinea pig, rabbit, cat, dog, horse, cow, opossum, and platypus.
This method resulted in sets of putative orthologs that were present among all 13 species. Each set of 13 proteins was aligned using ClustalW [ 19 ]. Send the link below via email or IM Copy. Present to your audience Start remote presentation. Do you really want to delete this prezi? Neither you, nor the coeditors you shared it with will be able to recover it again. Comments 0 Please log in to add your comment. P, maximum precipitation can be obtained at the isoelectric point by addition of some reagents such as, ethanol which dehydrates the molecule and allow neutralization of charge.
The approximate position of the isoelectric point of casein can be obtained by determining the PH of minimum solubility. Creating downloadable prezi, be patient.
Determination of isoelectric point of protein (casein). Introduction: Casein is a globular colloidal protein. Globular proteins are hydrophobic proteins which in certain external condition are soluble in eater. The ph at which the protein is electrically neutral is known as the isoelectric point.
That pH value is known as the isoelectric point (IEP) of the protein and is generally the pH at which the protein is least soluble. For casein, the IEP is approximately and it is the pH value at which acid casein is precipitated.
Determination of the Isoelectric Points of Casein. Certain proteins e.g. gelatin are relatively soluble in water even at their I.E.P. BUT maximum precipitation can be obtained at the the isoelectric point by addition of some reagents such as, ethanol which dehydrates the . 2 Determination of the Isoelectric Points of Casein Certain proteins e.g. gelatin are relatively soluble in water even at their I.E.P. BUT maximum precipitation can be obtained at the the isoelectric point by addition of some reagents such as, ethanol which dehydrates the .
Transcript of Determination of the isoelectric point of Casein. Determination of Isoelectric point of Casein L.A. Alaa Alahmadi BIOC, Lab 6 1. Introduction Casein 2. Principle 3. Protocol position of the isoelectric point of casein can be obtained by determining the PH of minimum solubility. The precise determination of the isoelectric point of proteins is time- ISOELECTRIC POINT OF PROTEINS checked with the quinhydrone electrode. SUMMARY The isoelectric points of soluble proteins can be roughly determined by noting the lowest pH level at which precipitates are formed with cationic detergents.