1. Which of the following is incorrect regarding pair wise sequence alignment?
a) The most fundamental process in this type of comparison is sequence alignment
b) It is an important first step toward structural and functional analysis of newly determined sequences
c) This is the process by which sequences are compared by searching for common character patterns and establishing residue-residue correspondence among related sequences
d) It is the process of aligning multiple sequences
Explanation: Pair wise sequence alignment is the process of aligning two sequences and is the basis of database similarity searching and multiple sequence alignment. As new biological sequences are being generated at exponential rates, sequence comparison is becoming increasingly important to draw functional and evolutionary inference of a new protein with proteins already existing in the database
2. Which of the following is incorrect about evolution?
a) The macromolecules can be considered molecular fossils that encode the history of millions of years of evolution
b) The building blocks of these biological macromolecules, nucleotide bases, and amino acids form linear sequences that determine the primary structure of the molecules
c) DNA and proteins are products of evolution
d) The molecular sequences barely undergo changes
Explanation: During this time period, the molecular sequences undergo random changes, some of which are selected during the process of evolution. As the selected sequences gradually accumulate mutations and diverge over time, traces of evolution may still remain in certain portions of the sequences to allow identification of the common ancestry.
3. The presence of evolutionary traces is because some of the residues that perform key functional and structural roles tend to be preserved by natural selection; other residues that may be less crucial for structure and function tend to mutate more frequently.
a) True
b) False
Explanation: The residues that perform key functional and structural roles tend to be preserved by natural selection. For example, active site residues of an enzyme family tend to be conserved because they are responsible for catalytic functions. Therefore, by comparing sequences through alignment, patterns of conservation and variation can be identified.
4. The degree of sequence variation in the alignment reveals evolutionary relatedness of different sequences, whereas the conservation between sequences reflects the changes that have occurred during evolution in the form of substitutions, insertions, and deletions.
a) True
b) False
Explanation: The degree of sequence conservation in the alignment reveals evolutionary relatedness of different sequences, whereas the variation between sequences reflects the changes that have occurred during evolution in the form of substitutions, insertions, and deletions. Identifying the evolutionary relationships between sequences helps to characterize the function of unknown sequences. When a sequence alignment reveals significant similarity among a group of sequences, they can be considered as belonging to the same family.
5. If the two sequences share significant similarity, it is extremely ______ that the extensive similarity between the two sequences has been acquired randomly, meaning that the two sequences must have derived from a common evolutionary origin.
a) unlikely
b) possible
c) likely
d) relevant
Explanation: Sequence alignment provides inference for the relatedness of two sequences under study. Regions that are aligned but not identical represent residue substitutions; regions which residues from one sequence correspond to nothing in the other represent insertions or deletions that have taken place on one of the sequences during evolution.
6. Sometimes, it is also possible that two sequences have derived from a common ancestor, but may have diverged to such an extent that the common ancestral relationships are not recognizable at the sequence level.
a) true
b) false
Explanation: There are examples of such paralogous genes that have distinct functions but similar origin. In that case, the distant evolutionary relationships have to be detected using other methods.
7. Which of the following is incorrect regarding sequence homology?
a) Two sequences can homologous relationship even if have do not have common origin
b) It is an important concept in sequence analysis
c) When two sequences are descended from a common evolutionary origin, they are said to have a homologous relationship
d) When two sequences are descended from a common evolutionary origin, they are said to share homology
Explanation: Homologous relationships are more certain when the sequences have common evolutionary origin. A related but different term is sequence similarity, which is the percentage of aligned residues that are similar in physiochemical properties such as size, charge, and hydrophobicity.
8. Sequence similarity can be quantified using ________ homology is a ______ statement.
a) percentages, quantitative
b) percentages, qualitative
c) ratios, qualitative
d) ratios, quantitative
Explanation: Similarity is a direct result of observation from the sequence Alignment. For example, one may say that two sequences share 40% similarity. It is incorrect to say that the two sequences share 40% homology. They are either homologous or nonhomologous.
9. Shorter sequences require higher cutoffs for inferring homologous relationships than longer sequences.
a) True
b) False
Explanation: For determining a homology relationship of two protein sequences, for example, if both sequences are aligned at full length, which is 100 residues long, an identity of 30% or higher can be safely regarded as having close homology. If their identity level falls between 20% and 30%, determination of homologous relationships in this range becomes less certain.
10. Sequence similarity and sequence identity are synonymous for nucleotide sequences and protein sequences as well.
a) true
b) false
Explanation: Sequence similarity and sequence identity are synonymous for nucleotide sequences. For protein sequences, however, the two concepts are very different. In a protein sequence alignment, sequence identity refers to the percentage of matches of the same amino acid residues between two aligned sequences. Similarity refers to the percentage of aligned residues that have similar physicochemical characteristics and can be more readily substituted for each other.