Amino acids are the building blocks of proteins, and can act as both a Brønsted acid and a Brønsted base through intramolecular proton transfer (see Chapter 16, pg. 709 of the textbook). The simplest amino acid known is glycine, NH2CH2CO2H (Ka = 4.5 ×10–3 and Kb = 6.0 ×10–5 ), and it can exist in three forms in equilibrium with one another:

H2N––CH2––COOH +H3N––CH2––COOH +H3N––CH2––COO– H2N––CH2––COO–

Glycine cation zwitterion anion

(a) Write the equilibria corresponding to Ka and Kb of glycine.

(b) Estimate the value of the equilibrium constant, K, for the intramolecular proton transfer to form the zwitterion in glycine: H2N––CH2––COOH (aq) K ? +H3N––CH2––COO– (aq)

(c) If the pH of an aqueous solution containing glycine is 7.2, in what form is glycine most abundant?

Researchers have described the “binary patterning” of polar and nonpolar amino acids in the sequences of proteins. In their code, polar and charged residues like D, N, E, Q, K, H, and R are represented as open circles (○) and nonpolar residues like F, L, I, M, and V as closed circles (●). Thus, a polypeptide with the sequence asp-ile-his-phe-gln would be represented as ○●○●○. Researchers analyzed the binary patterns of isolated secondary structure elements (short pieces) from native proteins. A sequence with the pattern ○●●○○●●○○●●○ forms an amphipathic alpha helix that has a nonpolar face and a polar face. A sequence with the pattern ○●○●○● forms an amphipathic beta strand. Explain these observations by discussing the structures of helices and sheets.

For each question, explain how you got the answer.

Which of the following have a net charge of +2 at pH of 1?

A. Asparagine

B.Arginine

C.Glutamine

D.Lysine

E.More than one of the above

2. A 200-amino acid polythreonine protein would have a net charge of _____ at pH 10.9

A.+200

B.-1

C.0

D.-200

E.+199

3. Which of the following amino acids has a side chain that is neutral at pH10?
A. Lysine

B. Aspartate

C. Histidine

D. Cysteine

E. None of the above

4. The net charge of the tripeptide Asn-Asn-Asn at pH=4.5 will be:

A. +2

B. +1

C. 0

D. -3

E. None of these answers are correct

a) Three nucleotides are inserted into a protein-encoding gene. The insertion occurs such that the mRNA transcript has an additional 3 bases (NOT a stop) right next to the stop codon (on the 5’ side). Which of the following will be the result?

b) Which of the following are consequences of encoding each amino acid using 3 nucleotides in the Genetic Code? (mre than one)

Your project should be on temperature adaptation or thermostability of proteins.

For a temperature adaptation project select an ectothermic organism with sub-species living in different climates. You will then focus on one protein, preferably an enzyme, for which you need to find amino acid sequences (one for each sub-species). You also need at least one crystal structure of this protein with enough sequence similarity to your selected amino acid sequences to make it feasible to create homology models. Finally, you will make comparisons between the structures or homology models while focusing on structural features that promote protein stability.

OR

For a thermostability project select a thermophilic organism (for example a bacterium thriving in a hot spring) and one protein, preferably an enzyme for which a crystal structure is already available. Next, you will need to search for crystal structures and/or amino acid sequences of your selected protein in other non-thermophilic organisms so that you can make comparisons between the crystal structures (or homology models). Aim to identify structural features that promote the thermostability of the protein from the thermophilic organism.

State the parameters of your project:

Species:

Protein(s):

PDB ID:

Confirm that you will have access to protein sequences and at least one protein structure (as a template for homology modeling) so that you can carry out your project. Post the access codes for the sequences and the PDB-ID(s) here:

Make a list of structural features that promote protein stability:

Note: Except the isocitrate dehydrogenase protein.

example like in the below articke

. For each of the restriction enzymes listed below: (i) Approximately how many restriction fragments would result from digestion of the human genome (3 x 109 bases) with the enzyme? (ii) State whether the fragments produced by digestion with each enzyme would have sticky ends with a 5’ overhang, sticky ends with a 3’ overhang, or blunt ends. (The recognition sequence for each enzyme is given in parentheses, where N means any of the four nucleotides. ^ marks the site of cleavage.)

a. EcoRV (GAT^ATC)

b. HpaII (C^CGG)

c. DrdI (GACNNNN^NNGTC)

NAD+ -dependent Glyceraldehyde-3-phosphate + Dehydrogenase from Thermoproteus tenax.

1. Name the three enzymes that catalyze irreversible, regulated reactions in glycolysis as studied in class.

2. What is the significance of the GAPDH reaction in E. coli to glycolysis?

3. How does the reaction catalyzed by GAPDH from T. tenax presented here differ from the reaction carried out in E. coli?

4. The activity of the GAPDH enzyme was assayed in the presence of a constant amount of glyceraldehyde-3-phosphate and an increasing amount of NAD . The activity of the control was + compared to the activity in the presence of various metabolites. The results are shown in Figure 20.2. Additional data are given in Table 20.2.

a. Use the data in Figure 20.2 to estimate a KM value for the enzyme in the presence of these metabolites. Classify the metabolites listed in Table 20.2 as inhibitors or activators. Fill in your answers in the table provided. Explain how you decided whether these metabolites are inhibitors or activators, based on the graph.

b. How would you classify NADH, ADP and ATP? (These data are not presented in the graph). Are they inhibitors or activators? Add this information to Table 20.2.

c. Explain the physiological significance of your answers to questions 4a and 4b. NAD+ -dependent Glyceraldehyde-3-phosphate + Dehyd

5. In the absence of NADP+, the binding of NAD+ to the T. tenax GAPDH showed no cooperative binding (closed circles, Figure 2 above). In the presence of NADP however, the binding of NAD+ to the T. tenax GAPDH was found to have a Hill coefficient of 2 (open circles, Figure 2 above).

a) What is the significance of the change in the value of the Hill coefficient?

b) Is this consistent with the shape of the curve and the information given in the background concerning the enzyme's quaternary structure?

6. What is the ATP yield for one mole of glucose oxidized by the pathway that uses the non-phosphorylating GAPDH enzyme?

Adam and Eve are stranded on a desert island. There are only two goods on the island: Apples (A) and Bananas (B). The utility functions of Adam and Eve are U^Adam(DA, DB) = (DA)^1/2 (DB)^1/2 and U^Eve(DA, DB) = (DA)^1/2 (DB)^1/2 respectively (they have the same preferences). Total endowments on the island are 20 Apples and 60 Bananas. Adam owns all the bananas and Eve all the apples.

(a) Draw the Edgeworth box for this exchange economy, including Adam and Eve’s indifference curves and endowments.

(b) Write the equation of the contract curve of this economy.

(c) Will Adam consume any apple in a competitive equilibrium?

(d) Now assume U^Adam(DA, DB) = U^Eve(DA, DB) = DA + DB. What is the new contract “curve”? (Hint: note the quotation marks and recall the condition that must be satisfied for the contract curve, i.e. MRS for the consumers must be equal.)