Bioinformatics Free Essays

Full report on BIOINFORMATICS PURIFICACION, MARYNOLD V. CHEM 161. 1 3L 2nd Semester AY 2012-1013 GROUPMATES: Donato, Lualhati M. We will write a custom essay sample on Bioinformatics or any similar topic only for you Order Now Diaz, Manuelle Marie C. Date Submitted: March 8, 2013 Laboratory Instructor: Ms. Herra Grajo I. INTRODUCTION Bioinformatics is the branch of  biological  science which deals with the study of methods for storing, retrieving and analyzing biological data, such as  nucleic acid  (DNA/RNA) and protein sequence, structure, function,  pathways  and  genetic interactions. It is very important since it contains large amount of information regarding biomolecules that a human mind is not able to store and process such data. There are different data bases that can be used like National Center for Biotechnology Information (NCBI), European Molecular Biology Laboratory-European Bioinformatics Institute database (EMBL-EBI), GenBank (US-based), SwissProt/UniProt, DNA Data Bank of Japan (DDBJ), Entrez and PubMed. Basic  Local  Alignment  Search  Tool, or  BLAST, is an  algorithm  for associating  primary  biological sequence information, like amino-acid  sequences of various  proteins  or the  nucleotides  of  DNA sequences. A BLAST search allows a researcher to compare a query sequence with a library or  database  of sequences, and identify library sequences that resemble the query sequence above a certain threshold. The BLAST program was designed by  Stephen Altschul,  Warren Gish,  Webb Miller,  Eugene Myers, and David J. Lipman  at the  NIH  and was published in the  Journal of Molecular Biology  in 1990. On the other hand,ProtParam is a very useful softwarethat can compute various physico-chemical properties from a protein sequence. The parameters that can be computed by ProtParam include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY). At the end of this exercise, the student should be able to understand the concept and process of bioinformatics; to know the process on how to use computer programs related in biological information; and to apply these programs on different protein sequences and identify different informations using these programs. II. METHODOLOGY The FASTA sequence of the given proteins namely; Myk, Gi, Glean, Astara, Niko, SR, Joma, Melai, Danne, Jay, Annie and Hani were analyzed using BLAST and ProtParam. BLAST showed the protein with that given sequence and its function was researched. ProtParam, on the other hand, showed the amino acid composition of the given protein, its theoretical IpH, estimated molecular weight and other pertinent information. III. RESULTS AND DISCUSSION Bioinformatics is the branch of  biological  science which deals with the study of methods for storing, retrieving and analyzing biological data, such as  nucleic acid  (DNA/RNA) and protein sequence, structure, function,  pathways  and  genetic interactions. In this exercise, the computer program called Basic Local Alignment Search Tool (BLAST) was used to identify different protein sequences and determine the function of these proteins. Also, a computer program named ProtParam was used to determine the IpH and estimated molecular weight of the said proteins. Different sequences of proteins were analyzed using these 2 algorithms to study their identities, properties and purposes. Table 1 show the list of the given protein sequences, their identity, their theoretical IpH and estimated molecular weight. The FASTA sequences of the different codes are also shown below. PROTEIN SEQUENCES: Myk qavlslyasgrttgivldsgdgvthtvpiyegfalphailrldlagrdltdalmkiltergysftttaereivrdikeklayvaldyeqelesa Gi mftasqegdgmskshvhrsvwwswlvgvltvvglglglgsgvglapgsaapsglaldrfadrplapidps Glean mmvawwslflyglqvaapalaatpadwrsqsiyflltdrfartdgsttatcntadqkycggtwqgiidkldyiqgmgftaiwitpvtar Astara kkkslalvlatgmavttfggtgsafadsknvlstkkynetvqspefvsgdlteatgkkaesvvfdylnaakgdyklgeksaqdcfkvkqakkdavtdst Niko mgsigaasmefcfdvfkelkvhhanenifycpiaimsalamvylgakdstrtqinkvvrfdklpgfgdsieaqcgtsvnvhsslrdil SR ndfnlqdfnvgdyiqavldrnlaenisrvlypndnffegkelrlkqeyfvvaatlqdvirrfkaskfgskdgvgtvfdafpdqvaiqlndthpalaipel Joma vgeimnskrdaeavgpeafadedfderevrgigkflhsakkfgkafvgeimnskrdaeavgpeafadedlderevrgigkflhsakkf gk Melai tedskgghpfssetkeklnkeggafpgpsgslkfcpleiaqklwkenhseiypimktptrtrlaliicstdfqhlsrrvgadvdlremklllqdlgytvkvkenltale Danne kllravitcltypekhfekvlrlsinkmgtdewgltrvvttrtevdmerikeeyqrrnsipldraiakdtsgdyedmlvallghgda Jay sltafndlklgkkykfilfglndakteivvketstdpsydafleklpendclyaiydfeyeingnegkrskivfftwspdtapvrskmvyasskdalrr Annie kakyltemprasellshgipykankravpdridwresgyvtevkdqggcgscwafsttgamegqymknektsisfseqqlvdcsgpfgnygcngglmena Hani valkgfakffkessdeerehaeklmeyqnkrggrvrlqsivtpltefdhpekgdalyamelalaleklvneklhnlhgvatrcndpqltdfieseflee Table 1. Identity, IpH and molecular weight of different protein sequences. Name| Identity| IpH| Molecular weight, g/mol| Myk| NBD_sugar-kinase_HSAP70_actin superfamilyActin| 4. 72| 10344. 7| Gi| Pepsin A trypsin| 5. 97| 7144. 1| Glean| AmyAC_family superfamilyAmylase A| 5. 93| 10002. 4| Astara| Protease| 8. 97| 10595. 0| Niko| SERPIN superfamilySerpin ovalbumin| 6. 24| 9899. 4| SR| Glycosyltransferase_GTB_type superfamilyGlycogen phosphorylase| 4. 65| 11336. 7| Joma| Magainin| 5. 21| 9931. 1| Melai| CASc superfamilyCaspase| 7. 73| 12230. 0| Danne| Annexin superfamilyAnnexin| 6. 14| 10022. 5| Jay| ADF_gelsolon superfamilyCofilin| 5. 47| 11504. 0| Annie| Peptidase_C1ACathepsin| 5. 80| 10982. 2| Hani| Euk_FerritinFerritin_like superfamilyFerritin| 5. 06| 11519. 9| Actin forms  microfilaments  which are typically one of the most dynamic of the three subclasses of the eukaryotic  cytoskeleton. In turn, this gives actin major functions in cells: * To form  microfilaments  to give mechanical support to cells, and provide trafficking routes through the cytoplasm to support signal transduction. * To allow  cell motility  in cells which undergo  amoeboid  motion using  pseudopods and  phagocytosis, for example of bacteria by  macrophages. * In  metazoan  muscle  cells, to be the scaffold on which  myosin  proteins generate force to support muscle contraction. In nonmuscle cells, to be a track for cargo transport myosins (nonconventional myosins) such as myosin V and VI. Nonconventional myosins use ATP hydrolysis to transport cargo, such as  vesicles  and organelles, in a directed fashion much faster than diffusion. Myosin V walks towards the barbed end of actin filaments, while myosin VI walks toward the pointed end. Most actin filaments are arranged with the barbed end toward the cellular membrane and the pointed end toward the cellular interior. This arrangement allows myosin V to be an effective motor for export of cargos, and myosin VI to be an effective motor for import. Pepsin  is an  enzyme  whose  zymogen  (pepsinogen) is released by the  chief cells  in the  stomach  and that degrades food  proteins  into  peptides. The ? -amylases (EC  3. 2. 1. 1  ) (CAS# 9014-71-5) (alternative names: 1,4-? -D-glucan glucanohydrolase; glycogenase)are  calcium  metalloenzymes, completely unable to function in the absence of calcium. By acting at random locations along the starch chain, alpha-amylase breaks down ling-chain carbohydrates, ultimately yielding maltotriose and maltose from amyloase, glucose and â€Å"limit dextrin† from amylopectin. It can act anywhere on the  substrate, ? amylase tends to be faster-acting than ? -amylase. In  animals, it is a major  digestive  enzyme, and its optimum pH is 6. 7-7. 0. In human physiology, both the salivary and pancreatic amylases are ? -amylases. A  protease  (also termed  peptidase  or  proteinase) is any  enzyme  that conducts  proteolysis, that is, beg ins  protein  catabolism  by  hydrolysis  of the  peptide bonds  that link  amino acids  together in thepolypeptide  chain forming the protein. Serpins  are a group of  proteins  with similar structures that were first identified as a set of proteins able to  inhibit  proteases. Glycogen phosphorylase catalyzes the rate-limiting step in  glycogenolysis  in animals by releasing  glucose-1-phosphate  from the terminal alpha-1,4-glycosidic bond. Ovalbumin  (OVA) is the main  protein  found in  egg white, making up 60-65% of the total protein. Ovalbumin displays sequence and three-dimensional  homology  to the  serpin  superfamily, but unlike most serpins it is not a  serine protease  inhibitor. The function of ovalbumin is unknown, although it is presumed to be a  storage protein. Ovalbumin is an important protein in several different areas of research, including:general studies of protein structure and propertiesbecause it is available in large quantities; studies of serpin structure and function since ovalbumin does not inhibit proteases which means that by comparing its structure with that of inhibitory serpins, the structural characteristics required for inhibition can be determined; in proteomics  where it is used as a molecular weight marker for calibrating  electrophoresis  gel; and in immunology where it is commonly used to stimulate an  allergic reaction  in test subjects likean established model allergen for  airway hyper-responsiveness, AHR. Caspases, or  cysteine-aspartic or  cysteine-dependent  aspartate-directed proteases  are a family of  cysteine proteases  that play essential roles inapoptosis  (programmed cell death),  necrosis, and  inflammation. Caspase 1/interleukin-1 converting enzyme is an  enzyme  that  proteolytically  cleaves other proteins, such as the  precursor  forms of the inflammatorycytokines  interleukin 1-? and  interleukin 18, into active mature peptides. It belongs to a family of  cysteine proteases  known as  caspases  that always cleave proteins following an  aspartic acid  residue. Caspase 1 has been shown to induce cell  necrosis  or  pyroptosis  and may function in various developmental stages. Studies of a similar protein in mouse suggest a role in the pathogenesis of  Huntington’s disease. Alternative splicing  of the gene results in five transcript variants encoding distinct isoforms. Annexins have been observed to play a role along the  exocytotic  pathway, specifically in the later stages, near or at the plasma membrane. Annexins have been found to be the later stages, near or at the plasma membrane. Annexins have been found to be involved in the transport and also sorting of endocytotic events. Annexin one is a substrate of the EGF (epidermal growth factor)  tyrosine kinase  which becomes phosphorylated on its N terminus when the receptor is internalized. Cofilin is a ubiquitous actin-binding factor required for the reorganization of actin filaments. ADF/Cofilin family members bind G-actin monomers and depolymerize actin filaments through two mechanisms: severing and increasing the off-rate for actin monomers from the pointed end. Older† ADP/ADP-Pi actin filaments free of tropomyosin and proper pH are required for cofilin to function effectively. In the presence of readily available ATP-G-actin cofilin speeds-up actin polymerization via its actin- severing activity (providing free barbed ends for further polymerization and nucleation by the Arp2/3 complex). As a long-lasting  in vivo  effect, cofilin recycles older ADP-F-actin, helping cell to maintain ATP-G-actin pool for sustained motility. pH, phosphorylation and phosphoinositides regulate cofilin’s binding and associating activity with actin The  Arp2/3 complex  and cofilin work together to reorganize the actin filaments in the  cytoskeleton. Arp 2/3, an actin binding proteins complex, binds to the side of ATP-F-actin near the growing barbed end of the filament, causing nucleation of a new F-actin branch, while cofilin-driven depolymerization takes place after dissociating from the Arp2/3 complex. They also work together to reorganize microtubules in order to traffic more proteins by vesicle to continue the growth of filaments. Cofilin also binds with other proteins such as  myosin,  tropomyosin,  ? -actinin,  gelsolin  and  scruin. These proteins compete with cofilin for actin binding. ?ofilin also play role in innate immune response. Cathepsins have a vital role in mammalian cellular turnover, e. g. bone resorption. They degrade  polypeptides  and are distinguished by their  substrate  specificites. Ferritin serves to store iron in a non-toxic form, to deposit it in a safe form, and to transport it to areas where it is required. Knowing the protein sequence gives many advantages in studies especially dealing with medicine. The protein of interest whether it is the cause of the abnormality or the cure for abnormality can be identified with just few clicks. The reasons behind similarity of protein sequences despite diversity of source organism is because even though all protein families have distinct functional compositions across different species, some conserved functional features among family members included a shared reaction mechanism, cofactor usage, and/or ligand specificity. IV. SUMMARY AND CONCLUSION Bioinformatics is the branch of  biological  science which deals with the study of methods for storing, retrieving and analyzing biological data, such as  nucleic acid  (DNA/RNA) and protein sequence, structure, function,  pathways  and  genetic interactions. It is very important since it contains large amount of information regarding biomolecules that a human mind is not able to store and process such data. Basic  Local  Alignment  Search  Tool (BLAST), an  algorithm  for associating  primary  biological sequence information, like amino-acid  sequences of various  proteins  or the  nucleotides  of  DNA sequences; and ProtParam, a very useful software that can compute various physico-chemical properties from a protein sequence. Such parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, How to cite Bioinformatics, Essay examples Bioinformatics Free Essays Full report on BIOINFORMATICS PURIFICACION, MARYNOLD V. CHEM 161. 1 3L 2nd Semester AY 2012-1013 GROUPMATES: Donato, Lualhati M. We will write a custom essay sample on Bioinformatics or any similar topic only for you Order Now Diaz, Manuelle Marie C. Date Submitted: March 8, 2013 Laboratory Instructor: Ms. Herra Grajo I. INTRODUCTION Bioinformatics is the branch of  biological  science which deals with the study of methods for storing, retrieving and analyzing biological data, such as  nucleic acid  (DNA/RNA) and protein sequence, structure, function,  pathways  and  genetic interactions. It is very important since it contains large amount of information regarding biomolecules that a human mind is not able to store and process such data. There are different data bases that can be used like National Center for Biotechnology Information (NCBI), European Molecular Biology Laboratory-European Bioinformatics Institute database (EMBL-EBI), GenBank (US-based), SwissProt/UniProt, DNA Data Bank of Japan (DDBJ), Entrez and PubMed. Basic  Local  Alignment  Search  Tool, or  BLAST, is an  algorithm  for associating  primary  biological sequence information, like amino-acid  sequences of various  proteins  or the  nucleotides  of  DNA sequences. A BLAST search allows a researcher to compare a query sequence with a library or  database  of sequences, and identify library sequences that resemble the query sequence above a certain threshold. The BLAST program was designed by  Stephen Altschul,  Warren Gish,  Webb Miller,  Eugene Myers, and David J. Lipman  at the  NIH  and was published in the  Journal of Molecular Biology  in 1990. On the other hand,ProtParam is a very useful softwarethat can compute various physico-chemical properties from a protein sequence. The parameters that can be computed by ProtParam include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY). At the end of this exercise, the student should be able to understand the concept and process of bioinformatics; to know the process on how to use computer programs related in biological information; and to apply these programs on different protein sequences and identify different informations using these programs. II. METHODOLOGY The FASTA sequence of the given proteins namely; Myk, Gi, Glean, Astara, Niko, SR, Joma, Melai, Danne, Jay, Annie and Hani were analyzed using BLAST and ProtParam. BLAST showed the protein with that given sequence and its function was researched. ProtParam, on the other hand, showed the amino acid composition of the given protein, its theoretical IpH, estimated molecular weight and other pertinent information. III. RESULTS AND DISCUSSION Bioinformatics is the branch of  biological  science which deals with the study of methods for storing, retrieving and analyzing biological data, such as  nucleic acid  (DNA/RNA) and protein sequence, structure, function,  pathways  and  genetic interactions. In this exercise, the computer program called Basic Local Alignment Search Tool (BLAST) was used to identify different protein sequences and determine the function of these proteins. Also, a computer program named ProtParam was used to determine the IpH and estimated molecular weight of the said proteins. Different sequences of proteins were analyzed using these 2 algorithms to study their identities, properties and purposes. Table 1 show the list of the given protein sequences, their identity, their theoretical IpH and estimated molecular weight. The FASTA sequences of the different codes are also shown below. PROTEIN SEQUENCES: Myk qavlslyasgrttgivldsgdgvthtvpiyegfalphailrldlagrdltdalmkiltergysftttaereivrdikeklayvaldyeqelesa Gi mftasqegdgmskshvhrsvwwswlvgvltvvglglglgsgvglapgsaapsglaldrfadrplapidps Glean mmvawwslflyglqvaapalaatpadwrsqsiyflltdrfartdgsttatcntadqkycggtwqgiidkldyiqgmgftaiwitpvtar Astara kkkslalvlatgmavttfggtgsafadsknvlstkkynetvqspefvsgdlteatgkkaesvvfdylnaakgdyklgeksaqdcfkvkqakkdavtdst Niko mgsigaasmefcfdvfkelkvhhanenifycpiaimsalamvylgakdstrtqinkvvrfdklpgfgdsieaqcgtsvnvhsslrdil SR ndfnlqdfnvgdyiqavldrnlaenisrvlypndnffegkelrlkqeyfvvaatlqdvirrfkaskfgskdgvgtvfdafpdqvaiqlndthpalaipel Joma vgeimnskrdaeavgpeafadedfderevrgigkflhsakkfgkafvgeimnskrdaeavgpeafadedlderevrgigkflhsakkf gk Melai tedskgghpfssetkeklnkeggafpgpsgslkfcpleiaqklwkenhseiypimktptrtrlaliicstdfqhlsrrvgadvdlremklllqdlgytvkvkenltale Danne kllravitcltypekhfekvlrlsinkmgtdewgltrvvttrtevdmerikeeyqrrnsipldraiakdtsgdyedmlvallghgda Jay sltafndlklgkkykfilfglndakteivvketstdpsydafleklpendclyaiydfeyeingnegkrskivfftwspdtapvrskmvyasskdalrr Annie kakyltemprasellshgipykankravpdridwresgyvtevkdqggcgscwafsttgamegqymknektsisfseqqlvdcsgpfgnygcngglmena Hani valkgfakffkessdeerehaeklmeyqnkrggrvrlqsivtpltefdhpekgdalyamelalaleklvneklhnlhgvatrcndpqltdfieseflee Table 1. Identity, IpH and molecular weight of different protein sequences. Name| Identity| IpH| Molecular weight, g/mol| Myk| NBD_sugar-kinase_HSAP70_actin superfamilyActin| 4. 72| 10344. 7| Gi| Pepsin A trypsin| 5. 97| 7144. 1| Glean| AmyAC_family superfamilyAmylase A| 5. 93| 10002. 4| Astara| Protease| 8. 97| 10595. 0| Niko| SERPIN superfamilySerpin ovalbumin| 6. 24| 9899. 4| SR| Glycosyltransferase_GTB_type superfamilyGlycogen phosphorylase| 4. 65| 11336. 7| Joma| Magainin| 5. 21| 9931. 1| Melai| CASc superfamilyCaspase| 7. 73| 12230. 0| Danne| Annexin superfamilyAnnexin| 6. 14| 10022. 5| Jay| ADF_gelsolon superfamilyCofilin| 5. 47| 11504. 0| Annie| Peptidase_C1ACathepsin| 5. 80| 10982. 2| Hani| Euk_FerritinFerritin_like superfamilyFerritin| 5. 06| 11519. 9| Actin forms  microfilaments  which are typically one of the most dynamic of the three subclasses of the eukaryotic  cytoskeleton. In turn, this gives actin major functions in cells: * To form  microfilaments  to give mechanical support to cells, and provide trafficking routes through the cytoplasm to support signal transduction. * To allow  cell motility  in cells which undergo  amoeboid  motion using  pseudopods and  phagocytosis, for example of bacteria by  macrophages. * In  metazoan  muscle  cells, to be the scaffold on which  myosin  proteins generate force to support muscle contraction. In nonmuscle cells, to be a track for cargo transport myosins (nonconventional myosins) such as myosin V and VI. Nonconventional myosins use ATP hydrolysis to transport cargo, such as  vesicles  and organelles, in a directed fashion much faster than diffusion. Myosin V walks towards the barbed end of actin filaments, while myosin VI walks toward the pointed end. Most actin filaments are arranged with the barbed end toward the cellular membrane and the pointed end toward the cellular interior. This arrangement allows myosin V to be an effective motor for export of cargos, and myosin VI to be an effective motor for import. Pepsin  is an  enzyme  whose  zymogen  (pepsinogen) is released by the  chief cells  in the  stomach  and that degrades food  proteins  into  peptides. The ? -amylases (EC  3. 2. 1. 1  ) (CAS# 9014-71-5) (alternative names: 1,4-? -D-glucan glucanohydrolase; glycogenase)are  calcium  metalloenzymes, completely unable to function in the absence of calcium. By acting at random locations along the starch chain, alpha-amylase breaks down ling-chain carbohydrates, ultimately yielding maltotriose and maltose from amyloase, glucose and â€Å"limit dextrin† from amylopectin. It can act anywhere on the  substrate, ? amylase tends to be faster-acting than ? -amylase. In  animals, it is a major  digestive  enzyme, and its optimum pH is 6. 7-7. 0. In human physiology, both the salivary and pancreatic amylases are ? -amylases. A  protease  (also termed  peptidase  or  proteinase) is any  enzyme  that conducts  proteolysis, that is, beg ins  protein  catabolism  by  hydrolysis  of the  peptide bonds  that link  amino acids  together in thepolypeptide  chain forming the protein. Serpins  are a group of  proteins  with similar structures that were first identified as a set of proteins able to  inhibit  proteases. Glycogen phosphorylase catalyzes the rate-limiting step in  glycogenolysis  in animals by releasing  glucose-1-phosphate  from the terminal alpha-1,4-glycosidic bond. Ovalbumin  (OVA) is the main  protein  found in  egg white, making up 60-65% of the total protein. Ovalbumin displays sequence and three-dimensional  homology  to the  serpin  superfamily, but unlike most serpins it is not a  serine protease  inhibitor. The function of ovalbumin is unknown, although it is presumed to be a  storage protein. Ovalbumin is an important protein in several different areas of research, including:general studies of protein structure and propertiesbecause it is available in large quantities; studies of serpin structure and function since ovalbumin does not inhibit proteases which means that by comparing its structure with that of inhibitory serpins, the structural characteristics required for inhibition can be determined; in proteomics  where it is used as a molecular weight marker for calibrating  electrophoresis  gel; and in immunology where it is commonly used to stimulate an  allergic reaction  in test subjects likean established model allergen for  airway hyper-responsiveness, AHR. Caspases, or  cysteine-aspartic or  cysteine-dependent  aspartate-directed proteases  are a family of  cysteine proteases  that play essential roles inapoptosis  (programmed cell death),  necrosis, and  inflammation. Caspase 1/interleukin-1 converting enzyme is an  enzyme  that  proteolytically  cleaves other proteins, such as the  precursor  forms of the inflammatorycytokines  interleukin 1-? and  interleukin 18, into active mature peptides. It belongs to a family of  cysteine proteases  known as  caspases  that always cleave proteins following an  aspartic acid  residue. Caspase 1 has been shown to induce cell  necrosis  or  pyroptosis  and may function in various developmental stages. Studies of a similar protein in mouse suggest a role in the pathogenesis of  Huntington’s disease. Alternative splicing  of the gene results in five transcript variants encoding distinct isoforms. Annexins have been observed to play a role along the  exocytotic  pathway, specifically in the later stages, near or at the plasma membrane. Annexins have been found to be the later stages, near or at the plasma membrane. Annexins have been found to be involved in the transport and also sorting of endocytotic events. Annexin one is a substrate of the EGF (epidermal growth factor)  tyrosine kinase  which becomes phosphorylated on its N terminus when the receptor is internalized. Cofilin is a ubiquitous actin-binding factor required for the reorganization of actin filaments. ADF/Cofilin family members bind G-actin monomers and depolymerize actin filaments through two mechanisms: severing and increasing the off-rate for actin monomers from the pointed end. Older† ADP/ADP-Pi actin filaments free of tropomyosin and proper pH are required for cofilin to function effectively. In the presence of readily available ATP-G-actin cofilin speeds-up actin polymerization via its actin- severing activity (providing free barbed ends for further polymerization and nucleation by the Arp2/3 complex). As a long-lasting  in vivo  effect, cofilin recycles older ADP-F-actin, helping cell to maintain ATP-G-actin pool for sustained motility. pH, phosphorylation and phosphoinositides regulate cofilin’s binding and associating activity with actin The  Arp2/3 complex  and cofilin work together to reorganize the actin filaments in the  cytoskeleton. Arp 2/3, an actin binding proteins complex, binds to the side of ATP-F-actin near the growing barbed end of the filament, causing nucleation of a new F-actin branch, while cofilin-driven depolymerization takes place after dissociating from the Arp2/3 complex. They also work together to reorganize microtubules in order to traffic more proteins by vesicle to continue the growth of filaments. Cofilin also binds with other proteins such as  myosin,  tropomyosin,  ? -actinin,  gelsolin  and  scruin. These proteins compete with cofilin for actin binding. ?ofilin also play role in innate immune response. Cathepsins have a vital role in mammalian cellular turnover, e. g. bone resorption. They degrade  polypeptides  and are distinguished by their  substrate  specificites. Ferritin serves to store iron in a non-toxic form, to deposit it in a safe form, and to transport it to areas where it is required. Knowing the protein sequence gives many advantages in studies especially dealing with medicine. The protein of interest whether it is the cause of the abnormality or the cure for abnormality can be identified with just few clicks. The reasons behind similarity of protein sequences despite diversity of source organism is because even though all protein families have distinct functional compositions across different species, some conserved functional features among family members included a shared reaction mechanism, cofactor usage, and/or ligand specificity. IV. SUMMARY AND CONCLUSION Bioinformatics is the branch of  biological  science which deals with the study of methods for storing, retrieving and analyzing biological data, such as  nucleic acid  (DNA/RNA) and protein sequence, structure, function,  pathways  and  genetic interactions. It is very important since it contains large amount of information regarding biomolecules that a human mind is not able to store and process such data. Basic  Local  Alignment  Search  Tool (BLAST), an  algorithm  for associating  primary  biological sequence information, like amino-acid  sequences of various  proteins  or the  nucleotides  of  DNA sequences; and ProtParam, a very useful software that can compute various physico-chemical properties from a protein sequence. Such parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, How to cite Bioinformatics, Papers Bioinformatics Free Essays As the world has changed into computer based and more of technology based, so has the various fields changed. Molecular biology is concerned with how the systems of a cell interact which also includes the DNA and RNA interactions plus the protein biosynthesis. It therefore involves several techniques which include Polymerase Chain Reactions, Western Blotting, southern blotting, expression cloning, gel electrophoresis and so many other techniques. We will write a custom essay sample on Bioinformatics or any similar topic only for you Order Now Since it is mostly involved in the interactions of the cell systems, it requires means to be able to identify the DNA which are similar, if the DNA of some organism are evolving, if some mutation in a DNA can help in new inventions about how to deal with certain problems of the world among others. Determination of all these requires the use of information technology. There have been major advances in molecular biology and advances in technologies of genomic study too. This is the reason why there has been growth in biological information created by the scientists (Gibas and Jambeck, 2001). Because of these advances, genomic information has to be computerized and stored in databases in an organized manner for use. The databases are organized in a manner that scientists can retrieve information about a genome and more, add more information if need be and for future references (Gibas and Jambeck, 2001). It therefore means that the databases index the data for viewing and analysis purposes. Application of information technology in the field of molecular biology is what is known as Bioinformatics. It involves the creation of algorithms statistical techniques, databases and computational techniques in molecular biology. There are theories on how the biological data should be solved and how they should be managed. These are the theories that are the base of computation, data storage, data analysis and formation of algorithms (Letovsky, 1999). Bioinformatics This is a field of science, created due to the changing world enabling advances in molecular biology, that merge molecular biology, information technology and computer science together (Baxevanis and Ouellette, 2001). It is therefore a single discipline meant to make possible biological insight discoveries. It also creates an international perspective of biological principles discernation (Letovsky, 1999). As has been noted, this field was created due to the advances in molecular biology. At the beginning, as the world of computer began to take over, Bioinformatics was just meant for biological information storage. It was as simple as creation of the databases and maintaining them. Information stored at that time was amino acid sequences and nucleotide sequences. At this time though, the researchers could retrieve information and put in more either revised or new invention (Baxevanis and Ouellette, 2001). As time and more advances are being made and more information is needed about the interaction of the cell system, Bioinformatics is evolving too. It is getting more complex with more information and more activities on molecular biology. This is due to the need to comprehend the normal cellular activities so that any abnormalities can be easily detected. Bioinformatics currently provides options of analysis and interpretation of data. Most analyzed and interpreted data include amino acid sequences, nucleotide sequences, structures of protein and protein domains. This is what is referred to as computational biology (Baxevanis and Ouellette, 2001). There are two sub disciplines in Bioinformatics and computational biology. One is algorithm and statistics development for the assessment of large data sets. This includes data sets such as gene allocation from a specific sequence, formation of protein families from related protein sequences, protein structure prediction and protein function prediction (Westhead et al. , 2002). The other sub discipline is information management which requires development of tools that allow retrieval, use and management of information (Westhead et al. , 2002). Importance of Bioinformatics Since there is advancement in the world of technology, bioinformatics is to improve the understanding of the so many biological processes. This involves research areas of involvement such as evolutionary biology, gene expression analysis, analysis of cancer mutations, determination of biodiversity, analysis of sequences, comparative genomics, genome annotation and several others (Lesk, 2005). Gene Expression Analysis As this information technology system enables storage of information, analysis and interpretation, gene expression can be performed. This is done by the use of appropriate techniques which measure RNA levels such as sequencing of expressed complementary DNA, Serial Analysis of Gene Expression, micro arrays and so many other techniques. This is important in the determination of genes expressed in certain disorders (Lesk, 2005). Determination of such kinds of genes is important in the development of therapies, as developments have gone further in molecular biology so that disorders can be corrected using gene therapies. An example is gene replacement therapy. When a gene causing a specific disorder or disease is determined, a means of replacing it with a normal one could also be determined (Lesk, 2005). Evolutionary Biology Bioinformatics enables measurement of changes in the DNA of animals therefore determination of origins of evolution of animals from their ancestors. Other ways in which Bioinformatics has enabled researchers to study the origins of organism and animal species is through comparison of their genomes, hence classifying animals that originated from the same ancestor. Bioinformatics through computational models enable prediction of system outcome over a specified period of time (Lesk, 2005). Analysis of Sequences There are so many sequences that decode different proteins. These sequences are made available in the databases. This provides sequences for analysis, for example if a scientist has a sequence of a gene obtained from a species of organism and would like to know the sequence, he/she would check with the sequences in the data bases. In these databases, the information helps determine the genes that encode specific polypeptides and regulatory sequences. Sequence analysis also enables comparison of genes of species hence determination of certain protein functions (Lesk, 2005). Biodiversity Measurement Bioinformatics is also important as it enables measurement of biodiversity of an ecosystem. Biodiversity is all the genomes of all the different species of organisms and animals in an ecosystem. The animals and organisms’ names have therefore to be collected, including their descriptions, genetic information and distribution in a specific ecosystem. There are so many other important information about the organisms that have to be noted alongside the genetic information. These are such as habitat needs, species and population size (Barnes and Gray, 2003). All this information is stored in the databases and is collected for a reason. Several studies that require animal genomic constitution in an ecosystem do take place, therefore need an information source. Information technology has enabled formation of specialized programs of software which are used by the scientists and researchers to retrieve, analyze and share information about their research. This leads to more progress in the field of molecular biology. The importance of this is that it helps in the conservation of the ecosystem. For example, in an ecosystem, there are always those species that are endangered, this can easily be determined by this information technology system of biodiversity determination. Computer simulations has enabled modeling of conservation, population dynamics and calculation of a breeding pool’s genetic health (Barnes and Gray, 2003). Cancer Mutation Analysis Since bioinformatics has enabled storage of sequences of several genes and provided means through which analysis can be carried out, cancer mutations can be detected. Sequences of normal genes are stored in the databases. Determination of a cancer mutation is therefore not difficult as the normal sequence can be compared to the abnormal one and the area of difference marked. This has been used to find out point mutations and other types of mutations. As noted earlier, this is important in cancer therapy (Higgins and Taylor, 2000; (Lesk, 2005). Conclusion Bioinformatics has lead to enormous discoveries due to the provision of information about the genomes of different species, their characteristics and other biological information in the databases. The main issue here is the biological information, how to retrieve it, provision of analysis methods and provision of interpretation methods thereby assisting many studies in many areas. Application of information technology in molecular biology has enabled discoveries of therapies and genetic information about disease causing organisms. This application of information technology is very important as with the changes in the world, evolution is taking place and several different organisms are coming up. Some of these organisms can cause diseases to human and can be a threat if nothing is done about them. Since genome sequences, analysis methods and other important biological information are provided in the programs and databases, determination of the origin of such an organism can be easy and ways of treating it can also be established, therefore eliminating the threat to humans. If for example HIV mutates, like it does, and there are no effective ways of determining the mutation, it means the virus will kill so many people as the new strain has no way to be controlled. Bioinformatics is therefore very important in molecular biology. References Barnes, M. R. and Gray, I. C. (2003). Bioinformatics for Geneticists. US: Wiley. Baxevanis, A. D. and Ouellette, B. F. (2001). Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. US: Wiley-IEEE. Gibas, C. and Jambeck, P. (2001). Developing Bioinformatics Computer Skills. Oreilly Associates Inc. Higgins, D. and Taylor, W. (2000). Bioinformatics: Sequence, Structure, and Databanks : a Practical Approach. UK: Oxford University Press. Letovsky, S. (1999). Bioinformatics: Databases and Systems. US: Springer. Lesk, A. M. (2005). Introduction to Bioinformatics. UK: Oxford University Press, 2005 Westhead, R. D. , Parish, J. H. and Twyman, M. R. (2002). Bioinformatics. UK: BIOS, 2002 How to cite Bioinformatics, Papers