Although tryptophan contains a heterocyclic amine, it is considered a neutral amino acid.

(a) Explain why the indole nitrogen of tryptophan is more weakly basic than one of the imidazole nitrogens of histidine.

With respect to Vmax (biochemistry), specify whether changes in substrate or enzyme concentration will lead to changes and explain your reasoning using a biochemical description of enzymes/formulas.

Describe two specific catalytic mechanisms that enzymes may use to speed up a reaction and describe two molecular mechanisms which regulate enzyme activity

The very useful restriction enzyme SpoBob hydrolyses the phosphodiester bond between the guanylates in the sequence AGGACCA. Is SpoBob generating blunt or sticky ends? Please explain.

What is a tyrosine kinase receptor (RTK)? Describe how this type of receptor works. Once activated, what kind of enzyme is needed to deactivate the receptor? Explain

A real-estate agent claims that the average price of a condominium in Naples, Florida is different from $50000. A sample of 81 condominiums has an average selling price of $51500 with a sample standard deviation of $8500.

13. The standardized test statistic calculated for a hypothesis test which tests whether the sample mean is equal to the hypothesized population mean is equal to: a, 1.56   b. 1.57        c. 1.59

14. The probability value of the event that the standardized test statistic would assume a value as large as that calculated in part 12 is: a, 0.01   b 0.112        c. 0.116

15. By comparing the probability value calculated in question 13 with a level of significance of 0.01 in a hypothesis test, we cannot reject the statement that: a. the mean price of a condominium in Naples, Florida is not equal to $50000.    b. the mean price of a condominium in Naples, Florida is greater than $50000   c, the mean price of a condominium in Naples, Florida is equal to $50000.

16. The 99% confidence interval for the population mean price of condominiums in Naples, Florida will fall between a. (49000, 54000)          b. (49008, 53992)   c. (49067, 53933)

Calculate the conformational entropy associated with the folding of a 75 amino acid peptide into a protein. Assume there are 3 conformational states for each side chain.

Compute the energy associated with the entropy change required to reach the folded state.

Estimate the energy associated with the hydrophobic collapse of this peptide to the folded state and compare the two. What does this say about the role of the hydrophobic effect in protein folding?

Revise your answer for a for the transition from unfolded peptide to molten globule. Assume that the molten globule has 1/2 the number of conformational states available to each amino acid. Does this change your answer for b?

Please use pictures to illustrate your thinking.

Draw a transmembrane protein (as a cartoon) that functions in the Plasma Membrane. Draw the path for its production and deposition. The transmembrane protein must have 3 N- linked glycosylations and 2 O-linked glycosylations. For the N and O linked glycosylations the saccharide units should be cartoons – geometric shapes).Draw how the above transmembrane protein is bound by a receptor from another cell. The picture should include the structure of the terminal saccharide(s) that is /are contained on your transmembrane protein (above) and the few amino acid R groups of the receptor pocket which is binding the saccharides. Show how the amino acid R groups are interacting with (binding) the saccharides of the transmembrane protein.

4. This is a coding DNA : 5’ ATG AGT GAT CTA GAC AGA CTT GCA AGC CGG …3’

(a) Predict the complementary strand and identify the strand name of it. (3' --> 5’)

(b) Predict the mRNA sequence (5' --> 3’) for the given coding strand.

(c) Predict the amino acid sequence of the gene.

(d) Predict the amino sequence, if there is a base substitution from A to T at the 16^th base.

(e) Which type of mutation and protein will result from the base substitution?

(f) Identify the location(s) likely to be cut by the restriction endonuclease XbaI, whose recognition site is 5’…T^CTAGA…3’, and predict the digested DNA sequence (double stranded).