01:694:301 Lecture Notes - Lecture 6: Gene Duplication, Cell Nucleus, Railways Act 1921

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Chapter 6‘Exploring Evolution and Bioinformatics’
Evolutionary Links b/w Species, Proteins, etc.
This short chapter shows how various kinds of biochemical info (DNA sequences,
amino acid sequences, and structural info about proteins) can be used to learn about
the evolutionary relationships b/w species
o Also possible to learn about evo relationships b/w proteins within species
o Ex: Hb is a tetramer !2"2; Mb is a monomer
! The proteins have different roles in the body but obviously have common
o Refer Fig. 6.15
Homologs are proteins that come from a common ancestry
o They are divided into orthologs and paralogs
o Paralogs derive from a gene duplication event; often differ in their detailed
biochemical functions (evolve new functions)
o Orthologs derive from a speciation event; have similar/identical functions
o Thus Hb (human) is an ortholog of Hb (chimpanzee), but a paralog of human (or
chimpanzee) Mb
! Here the duplication event (Hb/Mb) too place 100s myo, but speciation event
(human/chip) took place 6 myo
o Homology is often detectable by significant similarity in nucleotide or amino acid sequence
and almost always manifested in three-dimensional structure
Analyzing Sequence Alignment to Determine Homology
Understand the discussion of sequence alignment, looking for identities, with and
without gaps
o Sequence similarity may imply " same evo origin " similar 3D structure,
functions, and mechanisms
o Nucleic acids and protein sequences can be compared to detect homology; protein
more effective due to more arrangement possibilities (4 bases vs. 20 aa)
o During sequence alignment, two sequences are systematically aligned with respect
to each other to identify regions of significant overlap
! Slide one sequence past another one amino acid at a time, count the # matched
residues ‘sequence identities’
! Insertion of gaps compensates for insertions or deletions of nucleotides for one
gene not the other over evo
! Scoring systems are used to compare alignments and avoid inserting
unreasonable about of gaps (penalized)
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