Lecture 3 - Origins and Evolution of Life

Question 1

artificial selection

Answer 1

used as a model or analogy for natural selection

Question 2

antibiotic resistance

Answer 2

• natural resistance

- acquired resistance

Question 3

natural resistance

Answer 3

• lacks transport system
• lacks target
• thick cell wall

Question 4

acquired resistance

Answer 4

• mutations (including duplications)

- HGT

Question 5

horizontal gene transfer (HGT)

Answer 5

acquisition of DNA from individuals that are not an organism’s direct cellular progenitor

Question 6

outcomes of HGT

Answer 6

• novel acquisition
• loss and regain
• homologous replacement
• analogous replacement

Question 7

evolution of E. coli under artificial selection

Answer 7

• as E. coli hit a new barrier in the liquid agar, only those with mutations were able to continue to grow
• folA (encodes for DHFR, the target of Trimethoprim, the antibiotic) was mutated
• multiple substitutions occured independently (convergently)
• mutation in dnaQ gene, used in proofreading, resulted in some strains to increase their mutation rate
• some strains of E. coli were unable to develop resistance to high concentrations of antibiotic directly

Question 8

example experiment results

Answer 8

• selection acts on genetic changes over one or more generations
• HGT allows microbes to exchange info. (genetic material)
• mutations can be convergent
• one phenotype can be affected by many genetic changes
• lineages evolving in parallel can evolve at different rates

Question 9

homology

Answer 9

• similarity among a set of biological entities due to shared ancestry
• divergent evolution from a common ancestor

Question 10

analogy

Answer 10

• similarity among a set of biological entities that originated independently from different ancestors
• convergent evolution from different ancestors

Question 11

homology in hypothesis

Answer 11

additional similarities between organisms can be predicted if homology is supported in different organisms

Question 12

homology in sequence level

Answer 12

• gene homologues

- positional homology of basepairs in different sequences

Question 13

homology in ultrastructural level

Answer 13

• ribosomes

- cell membranes

Question 14

homology in organism level

Answer 14

• aerobic and anaerobic could be convergent

- antibiotic resistance could be convergent

Question 15

types of homology

Answer 15

• paralogs

- orthologs

Question 16

orthologs

Answer 16

divergence from each other after speciation event

Question 17

paralogs

Answer 17

divergence after gene duplication event

Question 18

xenologs

Answer 18

• divergence after lateral gene transfer events

- not used as often

Question 19

basic local alignment search tool (BLAST)

Answer 19

• method for sequence similarity

- amino acid and nucleotide databases are searched and those with similar/identical sequences are identified

Question 20

BLAST databases

Answer 20

• nucleotide
• protein
• reference sequence

Question 21

expect value (E-value)

Answer 21

• primary metric for ranking hits

- number of similar sequences to the query sequence that is expected to be found in the database by chance

Question 22

dissimilarity of homologous sequences

Answer 22

• ubiquitin in Homo sapiens and ThiS in E. coli had no/little nucleotide and a.a. sequence similarity
• homology was identified when 3D structure of both structures was shown