Evolution Biochemistry

Question 1

speciation

Answer 1

evolution of a new gene/protein that is genetically independent of the ancestral gene from which it arose

Question 2

homolog

Answer 2

actually a variant of a gene/protein (may be due to post-transcriptional/translational modifications)

• same species
• fewer genes needed to do jobs

Question 3

ortholog

Answer 3

evolve, but retain the same function (in different species)

- common ancestor is indicated by sequence similarities

Question 4

paralog

Answer 4

related by duplication of a common ancestral gene that evolves new functions (even if related to that of the ancestor)

Question 5

convergent evolution

Answer 5

evolution of similar features or properties in genes/proteins of different genetic lineages

Question 6

Divergent evolution

Answer 6

speciation

Question 7

Convergent

Answer 7

found the same solution to a common problem not necessarily from the same ancestral gene

Question 8

Mutation

Answer 8

single point changes in genetic material due to environmental damage, radiation, replication errors, viruses, transposable elements.

Question 9

Molecular Clock

Answer 9

rate of mutations - constant - 10^-8 or 10^-9 mutations per base per generation - leads to genetic drift

Question 10

Recombination

Answer 10

transfer of genetic material between chromosomes (basis for new proteins and things)

Question 11

gene duplication

Answer 11

one copy of the gene continues to serve the same function while the other is free to speciate and potentially develop new functions

Question 12

retrotransposition

Answer 12

mRNA is used to insert sequences into DNA at new locations (with different expression patterns)

Question 13

Dendrogram

Answer 13

tree that shows evolutionary relationships between proteins by matching them to their most closely related sequences (or something like that)

Question 14

multiple sequence alignments

Answer 14

lining up different DNA/RNA/protein sequences to identify similarities.

• may look at the local level (investigating smaller portions of a large sequence such as domains to look for similarities)
• global level - looking for similarities within a larger region of the sequence (compare similar sequences of similar lengths)

Question 15

scoring matrix

Answer 15

used to quantify the level of similarity between sequences

Question 16

clustal

Answer 16

global alignment algorithm for performing multiple sequence alignments

1. pairwise comparison
2. pairwise comparison used to make guide tree
3. guide tree used to do final alignment

Question 17

PAM

Answer 17

percent acceptable mutation - scoring matrix

• derived from global alignments
• measures the percent that something has changed.
• baseline is 20% identity
• there is about a 5% chance that sequence will be the same in any given position

Question 18

BLOSUM

Answer 18

block substitution matrices - local alignments

• looking at % difference
• use BLOSUM 80 for sequences that have no more than 80% identity
• higher blosum, more identity, while higher pam, more distantly related

Question 19

gap penalties

Answer 19

penalty for introducing gap and smaller penalty for each time the gap is widened

Question 20

filtering

Answer 20

filtering out repeated sequences

Question 21

e-value

Answer 21

lower e value means that the two things are related. 10^-70 means that there is a one in 10^-70 chance that they are not related.