Chapter 6 Exploring Evolution and Bioinformatics 6 4 How are sequence alignments made? Ans:Two sequences are aligned and the best matches determined for all possible juxtapositions.In some cases,gaps are introduced to maximize the number of possible matches.Statistical formulas are used to determine the best fit according to defined parameters. Section:6.2 5 What is a substitution matrix? Ans:A substitution matrix is deduced from aligned sequences,and scores correlate to how often an amino acid is substituted. Section:6.2 6 What is the difference between a simple scoring system for alignment and the Blosum-62 matrix? Ans:The Blosum-62 allows an examination of substitutions that considers mutations that are conservative.Thus,conservative substitutions can be considered in the scoring used to determine the significance of the change in the alignment and allow more significant conclusions about evolutionary relationships. Section:6.2 7 How are three-dimensional structures useful in evolutionary comparisons? Ans:The structural details can be correlated with specific functions.Enough of the structure must be maintained to retain the function,thus sequence changes occur that do not disrupt the structure.It is difficult to determine which amino acids are critical to the structure without evaluation of the three-dimensional structure.Thus,comparisons of proteins with similar structures reveal more critical information than sequence alignments. Section:6.3 8 If a protein contains a repetitive region,what might be assumed,and what should be done next to test the hypothesis? Ans:Similar sequences imply a gene duplication event,which may indicate that that region of the protein has an important functional or structural role.The next steps would be to determine if the region of repetition is statistically significant and to examine the three- dimensional structure of the region. Section:6.3 9 In addition to examining the base sequence,what other features of RNA are useful in determining evolutionary patterns? Ans:Changes to bases that retain the ability to form base-pairs with partner bases in other sections of the sequence imply that the base pair is important.These conservative changes will retain the three-dimensional shape of the RNA molecule Section:6.3 10 What evidence exists for a duplication event that led to the a and B hemoglobin? Ans:Lamprey is a fish that diverged from bony fish long ago.It has hemoglobin that contains a single type of subunit. Section:6.4Chapter 6 Exploring Evolution and Bioinformatics 6 4 How are sequence alignments made? Ans: Two sequences are aligned and the best matches determined for all possible juxtapositions. In some cases, gaps are introduced to maximize the number of possible matches. Statistical formulas are used to determine the best fit according to defined parameters. Section: 6.2 5 What is a substitution matrix? Ans: A substitution matrix is deduced from aligned sequences, and scores correlate to how often an amino acid is substituted. Section: 6.2 6 What is the difference between a simple scoring system for alignment and the Blosum-62 matrix? Ans: The Blosum-62 allows an examination of substitutions that considers mutations that are conservative. Thus, conservative substitutions can be considered in the scoring used to determine the significance of the change in the alignment and allow more significant conclusions about evolutionary relationships. Section: 6.2 7 How are three-dimensional structures useful in evolutionary comparisons? Ans: The structural details can be correlated with specific functions. Enough of the structure must be maintained to retain the function, thus sequence changes occur that do not disrupt the structure. It is difficult to determine which amino acids are critical to the structure without evaluation of the three-dimensional structure. Thus, comparisons of proteins with similar structures reveal more critical information than sequence alignments. Section: 6.3 8 If a protein contains a repetitive region, what might be assumed, and what should be done next to test the hypothesis? Ans: Similar sequences imply a gene duplication event, which may indicate that that region of the protein has an important functional or structural role. The next steps would be to determine if the region of repetition is statistically significant and to examine the three- dimensional structure of the region. Section: 6.3 9 In addition to examining the base sequence, what other features of RNA are useful in determining evolutionary patterns? Ans: Changes to bases that retain the ability to form base-pairs with partner bases in other sections of the sequence imply that the base pair is important. These conservative changes will retain the three-dimensional shape of the RNA molecule. Section: 6.3 10 What evidence exists for a duplication event that led to the  and  hemoglobin? Ans: Lamprey is a fish that diverged from bony fish long ago. It has hemoglobin that contains a single type of subunit. Section: 6.4