Subject Code & Title : AY2020-21 Computational Biology
Computational Biology questions:-
1) Modern genomic sequencing has revolutionised the study of phylogeny. Discuss how sequences can be analysed to give produce phylogenetic trees. Your answer should include a description of sequence alignment methods.
• Basic description of sequence alignment – pairwise and multiple
• How does sequence alignment work
• Information from a sequence alignment
• Identical and conserved positions in a sequence
• Secondary structure sequence signatures
• expected conserved repeats for different secondary structure types.
• UPGMA methods to produce phylogenetic trees
• Advantages of whole genome sequences over individual genes
AY2020-21 Computational Biology Assignment – UK
2) Drug design is now based on structural hypotheses. Discuss this proposition making reference both to historical drug design methods and modern drug design concepts. Use at least one example to illustrate your argument
• Activity screening methods
• QSAR
• Molecular expansion
• Definition of pharmacophore
• Active analogue approach
• Assumption that everything binds in the same way a major shortcoming.
• Grid
• Relenza
3) Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the‘whole protein content’ of cells
• Origin of the Proteomics approach
• Problems compared to Genomics (no amplification etc; complexity of expression)
• Description of the methods
• How is data analysed in each case?
Computational Biology
1) Pairwise sequence alignment is good, but multiple alignment is better. Discuss this statement. Your should describe how a each type of alignment is carried out (20% of total mark) and describe their strengths and weaknesses in relation to understanding protein structure
2) Describe how Systems biology techniques can be used to study mechanisms of cell regulation Discuss the particular example of Transcriptional Control
3) Discuss how the pharmacophore approach has allowed structural hypotheses to be defined for drug discovery when no structural information is available about the receptor. Discuss the limitations of these studies.
4) Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the ‘whole protein content’ of cells
1) The majority of sequence alignment programmes are based upon the dynamic programming algorithm devised by Needleman and Wuntsch. Describe the steps in this method and discuss how it is used for both pairwise and multiple sequence alignments. Your answer should consider how secondary structure can be predicted from the results of alignments.
2) “The molecular mechanics method can be considered to disregard completely the quantum mechanical treatment of molecular energies.” Discuss this statement making reference to the physical origin of the different terms in the molecular mechanics representation. In what ways might such a molecular description be limited?
3) Discuss how the structural implications of evolutionary divergence can be used to model proteins of unknown structure.
4) “Microarrays have revolutionised the way that Biology is done.” Discuss this proposition making reference to the general principles that underpin microarray design and the scope of the results that they can provide.
5) Describe how the theory of the behaviour of networks can be used to provide systems’ models of biological processes.
AY2020-21 Computational Biology Assignment – UK.
1.Compare and contrast the global pairwise sequence alignment, as exemplified by the dynamic programming method, with local alignment methods like Smith Water man.
2. Describe how drug design can proceed both with and without a 3-D structure of the protein target. (50%) Discuss the importance of pharmacophores in each case.
3. Describe how Transcriptomics gives a different view, compared to genomic or proteomic analysis, of a cell’s activity. Include in your answer two different approaches to this kind of study. (70%) Compare and contrast the advantages and disadvantages of transcriptomics versus proteomics.
4. ‘With suitable models we can now predict the structures of almost all protein structures’.Discuss this proposition in relation to the homology modelling technique (50%). Describe the principal technical issues that need to be overcome when using homology-based approaches
5. Proteomic analyses are transforming our understanding of the cell. Discuss this statement outlining what proteomics is, and the data that comes from the principal techniques used in proteomic studies (90%). How has this changed our perspective on proteins within living systems?
1.Modern genomic sequencing has revolutionised the study of phylogeny. Discuss how sequences can be analysed to give produce phylogenetic trees. Your answer should include a description of sequence alignment methods(100%).
• Basic description of sequence alignment – pairwise and multiple
• How does sequence alignment work
• Information from a sequence alignment
• Identical and conserved positions in a sequence
• Secondary structure sequence signatures
• expected conserved repeats for different secondary structure types.
• UPGMA methods to produce phylogenetic trees
• Advantages of whole genome sequences over individual genes
2. Drug design is now based on structural hypotheses. Discuss this proposition making reference both to historical drug design methods and modern drug design concepts. Use at least one example to illustrate your argument
• Activity screening methods
• QSAR
• Molecular expansion
• Definition of pharmacophore
• Active analogue approach
• Assumption that everything binds in the same way a major shortcoming.
• Grid
• Relenza
3.Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the‘whole protein content’ of cells
• Origin of the Proteomics approach
• Problems compared to Genomics (no amplification etc; complexity of expression)
• Description of the methods
• How is data analysed in each case?
1) Pairwise sequence alignment is good, but multiple alignment is better. Discuss this statement.Your should describe how a each type of alignment is carried out and describe their strengths and weaknesses in relation to understanding protein structure
2) Describe how Systems biology techniques can be used to study mechanisms of cell regulation Discuss the particular example of Transcriptional Control
3)Discuss how the pharmacophore approach has allowed structural hypotheses to be defined for drug discovery when no structural information is available about the receptor. Discuss the limitations of these studies.
4) Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the ‘whole protein content’ of cells
1.The majority of sequence alignment programmes are based upon the dynamic programming algorithm devised by Needle man and Wuntsch. Describe the steps in this method and discuss how it is used for both pairwise and multiple sequence alignments. Your answer should consider how secondary structure can be predicted from the results of alignments.
2.“The molecular mechanics method can be considered to disregard completely the quantum mechanical treatment of molecular energies.” Discuss this statement making reference to the physical origin of the different terms in the molecular mechanics representation. In what ways might such a molecular description be limited?
3.Discuss how the structural implications of evolutionary divergence can be used to model proteins of unknown structure.
4.“Microarrays have revolutionised the way that Biology is done.” Discuss this proposition making reference to the general principles that underpin microarray design and the scope of the results that they can provide.
5.Describe how the theory of the behaviour of networks can be used to provide systems’ models of biological processes.
1) Compare and contrast the global pairwise sequence alignment, as exemplified by the dynamic programming method, with local alignment methods like Smith Water man
2) Describe how drug design can proceed both with and without a 3-D structure of the protein target. (50%) Discuss the importance of pharmacophores in each case.
3) Describe how Transcriptomics gives a different view, compared to genomic or proteomic analysis, of a cell’s activity. Include in your answer two different approaches to this kind of study. Compare and contrast the advantages and disadvantages of transcriptomics versus proteomics.
1.‘With suitable models we can now predict the structures of almost all protein structures’.Discuss this proposition in relation to the homology modelling technique (50%). Describe the principal technical issues that need to be overcome when using homology-based approaches
2. Proteomic analyses are transforming our understanding of the cell. Discuss this statement outlining what proteomics is, and the data that comes from the principal techniques used in proteomic studies (90%). How has this changed our perspective on proteins within living systems?
1.Modern genomic sequencing has revolutionised the study of phylogeny. Discuss how sequences can be analysed to give produce phylogenetic trees. Your answer should include a description of sequence alignment methods.
• Basic description of sequence alignment – pairwise and multiple
• How does sequence alignment work
• Information from a sequence alignment
• Identical and conserved positions in a sequence
• Secondary structure sequence signatures
• expected conserved repeats for different secondary structure types.
• UPGMA methods to produce phylogenetic trees
• Advantages of whole genome sequences over individual genes
2.Drug design is now based on structural hypotheses. Discuss this proposition making reference both to historical drug design methods and modern drug design concepts. Use at least one example to illustrate your argument
• Activity screening methods
• QSAR
• Molecular expansion
• Definition of pharmacophore
• Active analogue approach
• Assumption that everything binds in the same way a major shortcoming.
• Grid
• Relenza
3. Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the ‘whole protein content’ of cells
• Origin of the Proteomics approach
• Problems compared to Genomics (no amplification etc; complexity of expression)
• Description of the methods
• How is data analysed in each case?
1) Pairwise sequence alignment is good, but multiple alignment is better. Discuss this statement.Your should describe how a each type of alignment is carried out (20% of total mark) and describe their strengths and weaknesses in relation to understanding protein structure
2) Describe how Systems biology techniques can be used to study mechanisms of cell regulation Discuss the particular example of Transcriptional Control
3) Discuss how the pharmacophore approach has allowed structural hypotheses to be defined for drug discovery when no structural information is available about the receptor. Discuss the limitations of these studies.
4) Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the ‘whole protein content’ of cells
1) The majority of sequence alignment programmes are based upon the dynamic programming algorithm devised by Needle man and Wuntsch. Describe the steps in this method and discuss how it is used for both pairwise and multiple sequence alignments. Your answer should consider how secondary structure can be predicted from the results of alignments.
2) “The molecular mechanics method can be considered to disregard completely the quantum mechanical treatment of molecular energies.” Discuss this statement making reference to the physical origin of the different terms in the molecular mechanics representation. In what ways might such a molecular description be limited?
3) Discuss how the structural implications of evolutionary divergence can be used to model proteins of unknown structure.
4) “Microarrays have revolutionised the way that Biology is done.” Discuss this proposition making reference to the general principles that underpin microarray design and the scope of the results that they can provide.
5) Describe how the theory of the behaviour of networks can be used to provide systems’ models of biological processes.
1.Compare and contrast the global pairwise sequence alignment, as exemplified by the dynamic programming method, with local alignment methods like Smith Water man
2.Describe how drug design can proceed both with and without a 3-D structure of the protein target. Discuss the importance of pharmacophores in each case.
3.Describe how Transcriptomics gives a different view, compared to genomic or proteomic analysis, of a cell’s activity. Include in your answer two different approaches to this kind of study.Compare and contrast the advantages and disadvantages of transcriptomics versus proteomics.
AY2020-21 Computational Biology Assignment – UK.
1.‘With suitable models we can now predict the structures of almost all protein structures’.Discuss this proposition in relation to the homology modelling technique (50%). Describe the principal technical issues that need to be overcome when using homology-based approaches
2. Proteomic analyses are transforming our understanding of the cell. Discuss this statement outlining what proteomics is, and the data that comes from the principal techniques used in proteomic studies (90%). How has this changed our perspective on proteins within living systems?
1.Modern genomic sequencing has revolutionised the study of phylogeny. Discuss how sequences can be analysed to give produce phylogenetic trees. Your answer should include a description of sequence alignment methods.
• Basic description of sequence alignment – pairwise and multiple
• How does sequence alignment work
• Information from a sequence alignment
• Identical and conserved positions in a sequence
• Secondary structure sequence signatures
• expected conserved repeats for different secondary structure types.
• UPGMA methods to produce phylogenetic trees
• Advantages of whole genome sequences over individual genes
2.Drug design is now based on structural hypotheses. Discuss this proposition making reference both to historical drug design methods and modern drug design concepts. Use at least one example to illustrate your argument
• Activity screening methods
• QSAR
• Molecular expansion
• Definition of pharmacophore
• Active analogue approach
• Assumption that everything binds in the same way a major shortcoming.
• Grid
• Relenza
3.Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the ‘whole protein content’ of cells
• Origin of the Proteomics approach
• Problems compared to Genomics (no amplification etc; complexity of expression)
• Description of the methods
• How is data analysed in each case?
1) Pairwise sequence alignment is good, but multiple alignment is better. Discuss this statement. Your should describe how a each type of alignment is carried out (20% of total mark) and describe their strengths and weaknesses in relation to understanding protein structure
AY2020-21 Computational Biology Assignment – UK.
2) Describe how Systems biology techniques can be used to study mechanisms of cell regulation Discuss the particular example of Transcriptional Control
3) Discuss how the pharmacophore approach has allowed structural hypotheses to be defined for drug discovery when no structural information is available about the receptor. Discuss the limitations of these studies.
4) Describe how Mass Spectrometry and 2-D SDS-PAGE gels have applied to the study of the ‘whole protein content’ of cells
1.The majority of sequence alignment programmes are based upon the dynamic programming algorithm devised by Needle man and Wuntsch. Describe the steps in this method and discuss how it is used for both pairwise and multiple sequence alignments. Your answer should consider how secondary structure can be predicted from the results of alignments.
2.“The molecular mechanics method can be considered to disregard completely the quantum mechanical treatment of molecular energies.” Discuss this statement making reference to the physical origin of the different terms in the molecular mechanics representation. In what ways might such a molecular description be limited?
3.Discuss how the structural implications of evolutionary divergence can be used to model proteins of unknown structure.
4.“Microarrays have revolutionised the way that Biology is done.” Discuss this proposition making reference to the general principles that underpin microarray design and the scope of the results that they can provide.
5.Describe how the theory of the behaviour of networks can be used to provide systems’ models of biological processes.
AY2020-21 Computational Biology Assignment – UK.
1.Compare and contrast the global pairwise sequence alignment, as exemplified by the dynamic programming method, with local alignment methods like Smith Water man
2.Describe how drug design can proceed both with and without a 3-D structure of the protein target. (50%) Discuss the importance of pharmacophores in each case.
3.Describe how Transcriptomics gives a different view, compared to genomic or proteomic analysis, of a cell’s activity. Include in your answer two different approaches to this kind of study. Compare and contrast the advantages and disadvantages of transcriptomics versus proteomics.
1.‘With suitable models we can now predict the structures of almost all protein structures’.Discuss this proposition in relation to the homology modelling technique (50%). Describe the principal technical issues that need to be overcome when using homology-based approaches
AY2020-21 Computational Biology Assignment – UK.
2. Proteomic analyses are transforming our understanding of the cell. Discuss this statement outlining what proteomics is, and the data that comes from the principal techniques used in proteomic studies . How has this changed our perspective on proteins within living systems?
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