Bioinformatics Chapter 6 Exam Questions with Verified Answers Latest Update (Graded A+)
bioinformatics - Answers computational biology; application of computer programs and using biological
data to look at patterns and make predictions
structural similarity - Answers implies functional similarity regardless of species from which protein
came
homolog - Answers homology between 2 sequences is based on % identity and % similarity; 2 sequences
that are very similar
paralog - Answers homologous genes in single species resulting from a gene duplication event but may
have different biological functions
ortholog - Answers homologous genes in different species originating from common ancestor; have very
similar biological functions
how to determine if two proteins are homologous - Answers compare sequence and structure
sequence alignment - Answers line up two sequences in different ways to determine # of amino acids
that match
gaps - Answers space in one of the sequences that give more amino acids that line up
BLAST website - Answers can align nucleotides as well; we want Protein BLAST; can search through
genome databases to find sequence that will give information about function
shuffling - Answers approach to authenticate alignment and rule out that alignment has happened
randomly; takes first sequence and puts in every possible position and compares all of these alignments
with the second sequence; gives best alignment score and compares to all other alignments
Blosum-62 Matrix - Answers provides matrix for types of substitutions that occur between homologs;
large positive score means substitution occurs frequently - homologous
conservative substitution - Answers can have positive alignment scores for substitutions; similar amino
acid side chains with similar properties are considered conservative substitutions
repeated shuffling vs. alignment with Blosum 62 - Answers will get a higher alignment score using
Blosum 62
E-value - Answers how likely you could get that alignment randomly; want a smaller E-value which
means alignment is less likely to be random; want score LARGER than E-value
identities - Answers how many amino acids are same
positives - Answers same amino acids or similar amino acids (indicated by a +)
bioinformatics - Answers computational biology; application of computer programs and using biological
data to look at patterns and make predictions
structural similarity - Answers implies functional similarity regardless of species from which protein
came
homolog - Answers homology between 2 sequences is based on % identity and % similarity; 2 sequences
that are very similar
paralog - Answers homologous genes in single species resulting from a gene duplication event but may
have different biological functions
ortholog - Answers homologous genes in different species originating from common ancestor; have very
similar biological functions
how to determine if two proteins are homologous - Answers compare sequence and structure
sequence alignment - Answers line up two sequences in different ways to determine # of amino acids
that match
gaps - Answers space in one of the sequences that give more amino acids that line up
BLAST website - Answers can align nucleotides as well; we want Protein BLAST; can search through
genome databases to find sequence that will give information about function
shuffling - Answers approach to authenticate alignment and rule out that alignment has happened
randomly; takes first sequence and puts in every possible position and compares all of these alignments
with the second sequence; gives best alignment score and compares to all other alignments
Blosum-62 Matrix - Answers provides matrix for types of substitutions that occur between homologs;
large positive score means substitution occurs frequently - homologous
conservative substitution - Answers can have positive alignment scores for substitutions; similar amino
acid side chains with similar properties are considered conservative substitutions
repeated shuffling vs. alignment with Blosum 62 - Answers will get a higher alignment score using
Blosum 62
E-value - Answers how likely you could get that alignment randomly; want a smaller E-value which
means alignment is less likely to be random; want score LARGER than E-value
identities - Answers how many amino acids are same
positives - Answers same amino acids or similar amino acids (indicated by a +)
