Bioinformatics

Question 1

Homologs

Answer 1

Proteins derived from a common ancestor

Question 2

Orthologs

Answer 2

Homologs from different organisms

Usually similar function

Question 3

Paralogs

Answer 3

Homologs within same organism

May have similar or different functions

Question 4

Sliding scales

Answer 4

Proteins are aligned at different positions (sliding past each other) and number of amino acid matches are counted
Problems: splicing differences and mutations

Question 5

Introducing gaps when comparing homologous proteins

Answer 5

Allows for more matches in sliding scale

Problem: if there are too many small segments, there can be an artificially high number of alignments

Question 6

Scoring sliding scales

Answer 6

Add up identities (matches) and subtract number of gaps introduced

Question 7

Testing for significance

Answer 7

Compare sequence to a scrambled sequence

If actual sequence has higher alignment score than “noise,” it is statistically significant

Question 8

Blosum-62 matrix

Answer 8

Method of scoring substitutions in protein sequences
High points are given if substituted amino acid is similar to original (highest points if no substitution)
Points are taken away if substituted amino acid isn’t like original

Question 9

Positives versus identities

Answer 9

Positive: amino acids that are related to each other (accounting for everything that aligns)
Identities: identical amino acids
Positives are always greater than or equal to identities

Question 10

How to find harder to see relationships between proteins

Answer 10

Use an alignment scoring system that accounts for both positives and identities: alignment score should be higher than noise

Question 11

Most important area of comparison between proteins

Answer 11

Protein folding is most important: amino acid sequence doesn’t always reveal structural similarity (many individual amino acid mutations can be made that don’t change the structure much)