Chapter 6 Evolution and bioinformatics Flashcards
paralogs and orthologs
paralogs are homologous proteins found within the same species (have different functions)
orthologs are homologous proteins found between different species and have the same functions
which ones have more likelihood of getting random similarity
nucleic acids (4 nucleotides) amino acids (20 amino acids)
sequence alignment
the two sequences are symmetrically aligned with respect to each other to identify regions of significant overlap
sequence identities
number of matched residues
why are gaps used to sequence allignments
to compensate for the insertions and deletions tha have taken place in one of the molecules but not the other
Describe the scoring system in sequence alignment
gaps are -25 points each regardless of size
each sequence identity +10 points
statistical significance of alignement sequences
using shuffling.
If the new scores are not quite different. Then we can not rule out the possibility that identity sequences generated in the original alignment was a mere chance
Amino acid changes in terms of structure
Conservative: changes produce the same structural features
non-conservative: changes that produce different structural differences
less frequently occuring amino acids
cystein tryptophan
gap penalty in blosum-62
-12 per single residue gap and then the extenstion by each single residue costs -2
rules of thumb in sequence analysis
above 25% homology is highly possible
between 15% and 25 % further tests are necessary for the determination of the statistical significance
less than 15 %: lacks statistifical significance
The lack of a statistically significant degree of sequence similarity does not rule out ……
homology
…… structure is more evolutionary conserved than….. structure
tertiary
primary
how can internally repeated sequences be found
by aligning it with itself
convergent evolution
very different evolutionary pathways lead to the same solution
