A Set of Computer Methods for Analyzing Biological Data: Purification Essay Example

,Annie,and Hani), their FASTA sequences were subjected to BLAST and ProtParam. Through BLAST analysis,the corresponding protein for each sequence as well as its associated function was determined.

ProtParam provided information about the amino acid composition, theoretical IpH, estimated molecular weight, and other relevant details of the given protein. The results and discussion section presents the utilization of Bioinformatics in analyzing biological data including nucleic acid (DNA/RNA) and protein sequences, structure, function, pathways, and genetic interactions. For this exercise, the computer program BLAST was employed to identify protein sequences and determine their functions. Additionally, ProtParam was used to determine the IpH and estimated molecular weight of the proteins. Eukaryotic cytoskeleton subclass Dients are known for their dynamic nature.

Actin plays several important roles in cells. First, it forms microfilaments that provide mechanical support and create trafficking routes for signal transduction. Second, it allows cell motility through pseudopods and phagocytosis, such as bacteria engulfment by macrophages. Third, in muscle cells, actin serves as a scaffold for myosin proteins that generate force for muscle contraction. In nonmuscle cells, actin acts as a track for cargo transport by nonconventional myosins like myosin V and VI. These myosins use ATP hydrolysis to transport cargo, such as vesicles and organelles, in a directed manner faster than diffusion. Myosin V moves towards the barbed end of actin filaments, while myosin VI moves towards the pointed end. Typically, actin filaments are arranged with the barbed end facing the cellular membrane and the pointed end facing the cellular interior. This arrangement enables myosin V to effectively export cargo and myosin VI to efficiently import cargo. Pepsin is an enzyme released by chief cells in the

stomach that degrades food proteins into peptides.

Alpha-amylase is an enzyme that breaks down long-chain carbohydrates by randomly acting at different points along the starch chain. This process ultimately results in the creation of maltotriose and maltose from amylose, as well as glucose and "limit dextrin" from amylopectin. Amylase can act on any part of the substrate and is generally faster compared to amylase. In animals, it serves as a significant digestive enzyme with its optimal pH ranging between 6.7 and 7.0. In human physiology, both salivary and pancreatic amylases are considered amylases.

A protease, also known as peptidase or proteinase, is an enzyme that carries out proteolysis, which is the process of breaking down proteins by hydrolyzing the peptide bonds connecting amino acids within the polypeptide chain to form the protein.

Serpins are a group of proteins with similar structures and were initially identified as proteins capable of inhibiting proteases.

Glycogen phosphorylase plays a vital role in glycogenolysis in animals. It releases glucose-1-phosphate from the terminal alpha-1,4-glycosidic bond.

Ovalbumin makes up 60-65% of egg white's total protein content. It shares both sequence and three-dimensional similarities with the serpin superfamily but differs from most serpins as it does not act as an inhibitor of serine proteases.

The function of ovalbumin is not known, but it is believed to be a storage protein. Ovalbumin has significance in various areas of research, including: protein structure and properties studies because of its abundance; studies on serpin structure and function, as ovalbumin does not inhibit proteases, allowing for the determination of structural characteristics required for inhibition by comparing it with inhibitory serpins; proteomics, where it is used as a molecular weight marker for calibrating electrophoresis

gel; and immunology, where it is commonly used to induce allergic reactions in test subjects and serves as a model allergen for airway hyper-responsiveness (AHR). Caspases, a family of cysteine proteases, have crucial roles in apoptosis (programmed cell death), necrosis, and inflammation. Caspase 1/interleukin-1 converting enzyme is an enzyme that cleaves other proteins, including precursor forms of interleukin 1-? and interleukin 18, into active mature peptides.

It is a member of the caspases family, a type of cysteine proteases that cleave proteins after an aspartic acid residue. Caspase 1 induces cell necrosis or pyroptosis and may have various functions during development. Research on a similar protein in mice suggests its involvement in Huntington's disease pathogenesis. The gene undergoes alternative splicing, resulting in five transcript variants that encode distinct isoforms. Annexins have been found to have a role in the exocytotic pathway, particularly in the later stages near or at the plasma membrane.

Annexins are involved in the transport and sorting of endocytotic events. Annexin one is phosphorylated on its N terminus when the EGF tyrosine kinase receptor is internalized. Cofilin is a factor that binds to actin and is necessary for reorganizing actin filaments. Members of the ADF/Cofilin family depolymerize actin filaments by severing and increasing the off-rate for actin monomers. Cofilin requires older ADP/ADP-Pi actin filaments without tropomyosin and under the proper pH conditions to function effectively. When ATP-G-actin is present, cofilin accelerates actin polymerization by severing actin and providing free barbed ends for further polymerization by the Arp2/3 complex.

Cofilin plays a crucial role in the cell's sustained motility by recycling older ADP-F-actin, maintaining an ATP-G-actin pool. Its binding and associating activity with actin are

regulated by factors such as pH, phosphorylation, and phosphoinositides. Working in tandem with the Arp2/3 complex, cofilin aids in the reorganization of actin filaments within the cytoskeleton. The Arp2/3 complex, a complex of actin binding proteins, attaches to the side of ATP-F-actin near the growing barbed end, initiating nucleation for a new F-actin branch. Afterward, cofilin-driven depolymerization occurs following dissociation from the Arp2/3 complex. These two components also collaborate in reorganizing microtubules to facilitate protein trafficking via vesicles for filament growth continuation.

Cofilin has the ability to bind to various proteins, including myosin, tropomyosin, ?-actinin, gelsolin, and scruin. These proteins compete with cofilin for binding to actin. Additionally, cofilin plays a role in the innate immune response. Cathepsins also have an important function in cellular turnover in mammals.

Bone resorption involves the breakdown of polypeptides by proteases, enzymes responsible for this process. Proteases have various specificities towards different substrates. On the other hand, ferritin serves multiple purposes including safe storage of iron, formation of non-toxic deposits, and transportation to necessary areas. The study of protein sequences offers many advantages, particularly in medicine. By examining a particular protein, researchers can determine its role in abnormalities or its potential as a treatment. Despite coming from diverse organisms, protein sequences often display similarities due to shared features within the same protein family such as reaction mechanisms, cofactor usage, and ligand specificity.

Summary and conclusion

Bioinformatics is a vital branch of biology that focuses on storing, retrieving, and analyzing biological data, including DNA/RNA and protein sequence, structure, function, pathways, and genetic interactions. This field is essential because it contains extensive information about biomolecules that surpasses

human capacity for storage and processing. The Basic Local Alignment Search Tool (BLAST) is an algorithm used to associate primary biological sequence information, such as amino-acid sequences of proteins or DNA sequences. Additionally, ProtParam is a valuable software capable of calculating various physico-chemical properties from a protein sequence. These properties encompass molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, and instability index.