Download Genomic differences study questions

Review: can we distinguish foreign from
native genes?
GC-content
=
[G] + [C]
[total nucleotides]
SQ2: List the two triplets that code for Lys. What
proportion of each is used in Borrelia burgdorferi
compared to Mycobacterium tuberculosis? Is this finding
surprising? Why or why not?
Borrelia burgdorferi
AAU Asn 0.80
AAC Asn 0.20
AAA Lys 0.80
AAG Lys 0.20
29% GC content
Mycobacterium tuberculosis
AAU Asn 0.21
AAC Asn 0.79
AAA Lys 0.26
AAG Lys 0.74
65% GC content
Can we distinguish foreign
from native genes?
SQ4: The GC content of Bacillus anthracis is
33.97%. By analysis of codon use, would it likely
be easier to detect a foreign gene originating
from Borrelia burgdorferi or from
Mycobacterium tuberculosis?
Borrelia burgdorferi
AAU Asn 0.80
AAC Asn 0.20
AAA Lys 0.80
AAG Lys 0.20
29% GC content
Mycobacterium tuberculosis
AAU Asn 0.21
AAC Asn 0.79
AAA Lys 0.26
AAG Lys 0.74
65% GC content
How do genomic differences arise?
Point mutation revisted
organism 1 TTT TCT GAA TCC GTA GAC GTT
organism 2 TTT TCT GAA TCA GCA GAC GTG
GUU
GUC
GUA
GUG
Val
Val
Val
Val
GCU
GCC
GCA
GCG
Ala
Ala
Ala
Ala
How do genomic differences arise?
Addition/deletion of DNA
Point mutation
organism 1 TTT TCT GAA TCC GTA GAC GTT
organism 2 TTT TCT GAA TCA GCA GAC GTG
Silent mutation
GUU
GUC
GUA
GUG
Val
Val
Val
Val
GCU
GCC
GCA
GCG
Ala
Ala
Ala
Ala
Single base mutations
Transitions
Purine for purine
or
pyrimidine for pyrimidine
Transversions
Purine for pyrimidine
or
pyrimidine for purine
How do genomic differences arise?
Point mutation
organism 1 TTT TCT GAA TCC GTA GAC GTT
organism 2 TTT TCT GAA TCA GCA GAC GTG
Transition:
Transversion:
purine
pyrimidine
purine
pyrimidine
purine
pyrimidine
Tautomerization of bases
C
T
G
A
C* T*
A
G
DNA replication can “lock in” a mutation
Mutations can arise as a consequence of misincorporation during replication
How to distinguish foreign from native genes?
SQ7: There are two codons each for 9 of the amino
acids. Choose any one of these 18 codons.
• Create a transition mutation in the third position of
the codon. What is the result?
• Create a transversion mutation in the third position.
What is the result?
• In the third position, are transition mutations or
transversion mutations more likely to result in a
change in the amino acid encoded?
How do differences arise between genomes?
Addition/deletion of DNA
Point mutation
Keeping track of gene variants
– Concepts of ortholog / paralog
Orthologs, Paralogs, and Xenologs
Speciation event
leading to orthologs
Horizontal transfer
leads to xenologs
Gene duplication
gives rise to paralogs
Orthologs vs Paralogs
SQ5: Are genes B1
and C2 orthologs or
paralogs?
How to predict
orthology with
imperfect
information?
A1 AB1
Species A
B1
B2 C1 C2
Species B
C3
Species C