Lecture 4 - Origins and Evolution of Life Flashcards
organism level mutation
mutation occurs as a single cell replicates itself
population level mutation
a new allele resulting from an organism level mutation becomes prevalent in a pop’n
fixed mutation
all individuals in a pop’n share the mutation
S values
- S values of ribosomal subunts and sub-complexes are Svedberg units
- higher number indicates a larger structure
functionality in orthologs and paralogs
orthologs are more likely to have similar functions that paralogs
positional homology
- chromosomes aligned
- gene segments
- specific codons in homologous proteins
- specific bps in homologous gene segments
- homology is inferred based on homology of adjacent bps, a.a residues, or gene segments
sequence identity
proportion of characters that are identical in an alignment of two or more sequences in nucleotide sequences
sequence similarity
proportion of characters that are similar in an alignment of two or more sequences in amino acids
high-scoring segment pairs (HSP)
pairwise alignment of a sequence segment of a BLAST query sequence and a BLAST subject (database) sequence which shows a high score (because of identity or similarity)
BLAST interpretation
- positional homology is used to infer the false-negative rate of typical BLAST searches
- gene homology is a hypothesis which can be supported/refuted by sequence comparison using BLAST
- additional forms of evidence can also be important: gene synteny, location of a particular segment withina gene, predicted higher-order structure of encoded RNA/proteins, function
principle of parsimony
things are connected in the simplest way
monoderms and diderms
monoderms (Gram-+) and diderms (Gram–) are polyphyletic
archaea discovered with small subunit rRNA
archaea was discovered based on sequence similarity between small subunit rRNA
