- Which structural elements make up the secondary structure of proteins?
- What can you do using the Swiss Protein data bank viewer?
- Which structural elements are often represented as only slightly curved yellow arrows?
- In the binding of the NAG inhibitor to the catalytic site of lysozyme, do hydrophobic, non-polar interaction contribute to substrate binding?
- How many histones form the core of the nucleosome?
Are all of these identical? Are all of these homologous?
How would you expect the ancestral nucleosome to have looked like? - Are all nucleotide binding sites homologous? (E.g. consider the one in F-ATPases and the one in the carbamoyl phosphate synthetase?)
- Are the beta and the alpha chains of the hemoglobin molecule homologous, paralogous and/or orthologous to each other?
(As these terms are not mutually exclusive, more than one of the alternatives might be correct.) 
a) What tree does the dataset corresponding to point 1 support? How reliable is the support?
b) What tree does the dataset corresponding to point 2 support? How reliable is the support?- In SPDBV the three point alignment tool allows (check all that might be appropriate):
A) Align two 3D structures contained in two separate layers based on the selection of corresponding points.
B) Align three structures based on their centers of gravity, which are considered as points in 3-D space.
C) Automatically run through the three steps Magic Fit, Iterative Magic Fit and Improve Fit. - In the MrBayes program, the sampling process explores tree-space in a biased manner. What measure does the program use to decide, if one tree is “better” than the tree last examined?
- How does the heated chain in a Metropolis Coupled Monte Carlo Markov Chain exploration differ from the chain that is not heated?
- Why is it a good idea to include a heated chain in an analysis?
Under which conditions are heated chains most useful? (Think about the hills and valleys in the likelihood landscape.) - How does MrBayes approximate the posterior probability of a bipartition (i.e. a branch in a tree)?
- What does the term “posterior probability” in the above question denote?
A) the probability of the data given the model
B) the probability of an aspect of the model given the data
C) the probability of aspects of the model before one has looked at the data - Likelihood based phylogenetic reconstruction aims to find the tree under which the data set (e.g., aligned sequences) are most probably. To calculate this probability, a model describing the evolutionary process is used. Which model assumption(s) would correspond to a normal parsimony analysis?
A) Gaps (-) in the sequence alignment are treated as a 5th nucleotide or as the 21st amino acid.
B) All types of substitutions occur with the same probability.
C) The ratio between probability for transition and transversion is described by a parameter kappa that is estimated from the data
D) A-D is correct
E) All answers are incorret - 100 bootstrap data-sets are created for a set of sequences. The Parsimony method is applied to these data-sets to give 100 trees. The consensus tree of this set of 100 trees is given below with bootstrap percentages indicated to the left of the branch to which the support value pertains. It has been rooted by assuming that U is the outgroup. Which of the four conclusions can be drawn?
/----------- W
/--------| 87
| \------------ X
|
/-----| 91
| | /----------- Y
| \---------| 100
/---| 100 \----------- Z
| |
| \-------------------------- V
|
-------------------------------- U• A. The clade X+Y+Z never occurs in the set of 100 trees.
• B. The clade W+X+V never occurs in the set of 100 trees.
• C. The clade W+X+V could occur in up to 9 of the 100 trees.
• D. The clade W+V could occur in up to 13 of the 100 trees.
- A new mutant allele has just arisen in a population. Which statement is true?
A. If the mutant is neutral with respect to the original allele, there is a 50% probability that the mutant allele will replace the original allele.
B. It is very likely to disappear in a few generations due to random drift.
C. It will only become fixed in the population if there is a strong selective advantage.
D. If the mutant allele reaches a frequency of 50%, it will almost always go on to fixation. - (Bonus) What does MCMCMC or MC-cubed stand for? For each of the Ms give a one sentence explanation on what this refers to.
- (For Graduate Students) It is believed that all present-day copies of human mitochondrial DNA descended from a single person, ‘Eve’, living in Africa around 200,000 years ago.
Assuming that the African Eve hypothesis is correct, draw a tree depicting mitochondrial evolution that includes African Bushman, African Nubian (assuming that these represent two of the most divergent African lineages), Western European, Eastern European, and Asian mitochondrial lineages.
Where in this tree would the lineage branching off to the mitochondria of the Neanderthal humans be placed?
Which of the following is true?
A. Differences in mitochondrial DNA sequences between different African populations are larger than differences between non-African populations.
B. There are no fossil human remains prior to 200,000 years ago.
C. Mitochondrial sequences in present day African populations have changed less since the time of Eve than have the sequences in non-African populations.
D. Mitochondrial sequences in present day African populations have changed more since the time of Eve than have the sequences in non-African populations