Cycle 2 - Molecular Evolution

Question 1

Compare the GlsA gene in volvox vs. chlamy

Answer 1

• GslA in chlamy is very similar to the volvox gslA gene
• When the gslA is knocked out in chlamy, nothing happens, but in volvox, the cell dies –> it is essential for asymmetric cell division
• When the chlamy gene is extracted and put in volvox, it work well
• Bioinformatics (blast) is used to confirm the idea that the gene originated from a common ancestor

Question 2

Differences between global versus local sequences

Answer 2

Two types of algorithms are used by the computer

1. Global: matches all sequences to form global alignment (attempts to align end to end)
   
   • Computationally more demanding, therefore slower
2. Local: the computer uses small, local regions of matching (builds alignment out from local matches)
   
   • Still end up with a complete alignment

Question 3

Distinguish between the BLAST score and the E-value

Answer 3

• BLAST gives you the probability that the two proteins are similar purely by chance.
• E value is how likely they are to be homologous
• E < 0.00001 = homologous
• E value for volvox and chlamy GslA gene = 0; they are related

Question 4

Define synonymous vs nonsynonymous mutations

Answer 4

• Synonymous mutations are point mutations that, like a synonym in grammar, still have the same meaning as the original codon and therefore does not change the amino acid
• Non-synonymous mutations affect the amino acids that are coded for and change the resulting protein that is expressed

Question 5

Describe neutral theory and selection theory

Answer 5

• Selection theory: all mutations affect fitness, and most mutations cause bad things
• Neutral theory: many changes to the gene sequence have no affect (gene evolution without any natural selection)

Question 6

State the relationship between frequency of amino acid substitutions in given proteins vs. time since common ancestor (molecular clock)

Answer 6

• If the neutral theory is correct, then the number of mutations acquired should be clocklike; i.e., they just enter the population at a constant rate.
• So, the number of mutations (differences from common ancestor) would be proportional to the number of time since the species last diverged

Question 7

Relative rates of accumulation of synonymous vs. non-synonymous mutations: why the difference?

Answer 7

Synonymous mutations have a higher rate because they are neutral, so they are always passed on and eventually become fixed in the population

Non-synonymous mutations have a lower rate because they are on average harmful, and so are less likely to be passed on due to lowering fitness

Exception: any type mutation in introns and pseudogenes has a high rate of accumulation because it can never affect the phenotype regardless

Question 8

State the variables that affect the rate of evolution for a particular protein

Answer 8

• Rates of evolution differ for proteins due to selection pressures
  
  • Ex., cytochrome C is very important, we don’t want a lot of mutations in this area
  • Thus, cytochrome C is more constrained in tis structure because mutations in this area are likely to be severely negative due to its critical function for respiration

Question 9

Define contigency and convergence evolution

Answer 9

• Contingency (Gould) states that each step in evolution is dependent on the step before it
• Convergence (Morris) states that the evolutionary routes are many, but the destinations are limited.

Question 10

Describe the two types of opsin

Answer 10

Type 1: ex., channelrhodopsin, homologous to bacterial opsin

Type 2: rhodopsin, functions in sight and smell as well (called GPCR G-protein coupled receptors)

Question 11

State the characteristics of ruminant organisms that enable them to extract energy from cellulose

Answer 11

• Ruminant organisms: mammals that are able to acquire energy from cellulose
• They have lysozyme enzyme which functions to digest grass/cellulose
• They have a rumen: section of the stomach where fermentation occurs
• The rumen consist of microbes which release the cellulase

Question 12

Distinguish between digestive lysozyme and non-digestive lysozyme.

Answer 12

• Digestive lysozyme is more pH resistant than non-digestive forms, due to having amino acids at specific residues that are capable of protecting against degradation.
• It can exist in the stomach
• Non-digestive forms unfold at low urea/extreme pH