The instructions for doing all the PS1 assignments are available on...

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The instructions for doing all the PS1 assignments are available on the information tab of course BB. Briefly you do the PS1 individually. You are required to attempt every problem. You must turn your attempted PS1 into your group by the date on the syllabus through the group DB. Then each group should examine everyone’s first attempts and determine the correct solution to each problem. You discuss the problems and the different solutions on the group DB during the time-frame listed on the syllabus. The group turns in 1 PS1 for the group by the date listed on the syllabus.

1. Water would have a much higher heat capacity when compared to its closest neighbors (assuming they were in liquid form): NH3, H2S and HF. Why is this so? The heat capacity of liquid water is 75.291 J*K-1*mol-1; that of liquid ammonia is 46.0 J*K-1*mol-1 (measured at 273.15 K).
a. Calculate the change in temperature that both of these liquids would undergo when 10 J of heat is added.
b. Why is the high heat capacity of water important to living organisms?
2. Write a 1-3 paragraph essay that addresses the following questions:
a. What is misleading about the term hydrophobic bond?
b. What drives the hydrophobic effect?
c. How is it less correct to think about the attraction of hydrophobic groups than to consider the change in the water structure?
d. Describe how the entropy and enthalpy of water change when a small amount of nonpolar solute is added to water.

Fructose-1,6bis phosphate + H2O → Fructose-6-phosphate + PO4-3

3. The reaction above occurs as part of the gluconeogenesis pathway and has a standard free energy change (∆G°’) of -16.7kJ/mol. The reverse reaction does not occur in cells.
a. Explain why this makes sense in 1-2 sentences.
b. Assume the concentration of Fructose-1,6bis phosphate is 0.031mM and the concentration of Fructose-6-phosphate   is 0.014mM calculate the concentration of PO4-3 that would be required to drive the reaction in the reverse direction. You may assume the concentration of water does not impact the reaction.

4. Using 3D CHEMDRAW
a. Draw the amino acid R and display it in the following 3 modes: sticks, ball-and-stick, and space filling. Generate a high quality PNG using the “Save as  PNG” function in the file menu and import these into your word document by “insert picture” from file.
b. Draw a ball and stick model of the tripeptide KDA. Rotate the model such that you can identify all three side chains. Generate a high quality PNG using the “Save as  PNG” function in the file menu and import these into your word document by “insert picture” from file.
c. Draw a stick representation of the membrane fatty acid oleic acid. Generate a high quality PNG using the “Save as  PNG” function in the file menu and import these into your word document by “insert picture” from file.
5. Using CHEMDRAW Professional
a. Draw out a reaction glucose plus inorganic phosphate going to glucose-6-P. Look up the standard free energy change for this reaction in your textbook. Based on this information redraw the reaction in the correct direction with the correct type of arrow.
b. Draw the reaction from question 3 and show the electron movement (Chapter 14 section “How to Read and Write Mechanisms” will be of help. Note in Biochem you can assume a general Base (B:) or general acid (BH) in any mechanism as enzyme routinely preform these chemical functions.)
6. Look up the structure of hexokinase. First go to PDB and search hexokinase or just the four letter code 1HKB. Download the file 1HKB from the PDB and open it with PyMOL.
a. Display the protein as a cartoon, and change the image to have different colors for each protein chain. This will show the protein domains. Describe in 1-2 sentences how you change the colors. How many domains are in the structure?

b. Under the DISPLAY menu, change the background to white. Using the PyMOL video tutorial as a guide, create a quality image of the protein that shows any ligands or cofactors bound the protein. Describe in words how you found your ligands or cofactors.
c. Provide an image of the structure you generated in (b). This should not be a screenshot; generate a high quality PNG using the “Save as  PNG” function in the file menu.
d. Display the protein as each of the four main types of display under the S (or SHOW) command tool.

Write a short paragraph describing what you can discover about the protein using each display. Be sure to list each display type, describe what you can see using this display, and explain why and when this display is most useful. Points to consider: What level of structure is apparent from the display? Is there a benefit of using this display over another? What would you be able to tell about the protein if you were looking at sticks vs. cartoon, for example? What is the advantage of sticks over lines? Is there a time you might use both?

e. HIDE everything, and then using the SHOW function, display the protein as SURFACE. Hide that, and then show as MESH. Describe the purpose of visualizing the protein in this manner. What is the difference between visualizing as mesh vs. surface?

Now, let’s use what we know about commands to view some details about the amino acid composition of the protein.

f. With the protein displayed as cartoon, color the protein all one color. Write a command to make a new selection all charged residues in the protein and write that command here.

g. Determine a good way to display the charged residues such that they contrast the protein, and so you can easily see them among the uncharged amino acids in the protein. Provide a PNG image of the representation you’ve generated.

h. Change the coloring back to one color, and write a command to make a new selection of just the hydrophobic residues. Write that command down here.

i. See if you can pick out the hydrophobic core of one subunit. Create a PNG to show how the hydrophobic core is surrounded by non-hydrophobic residues.

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These solutions may offer step-by-step problem-solving explanations or good writing examples that include modern styles of formatting and construction of bibliographies out of text citations and references. Students may use these solutions for personal skill-building and practice. Unethical use is strictly forbidden.

The hydrophobic term is misleading and more correct is a hydrophobic interaction or effect. It is merely the noncovalent interaction, and it’s an effect and nothing like bonds usually observed in bond formation.
Generally nonpolar hydrocarbons are lipophilic and tend to form the aggregates in an aqueous medium, because of intermolecular interaction are known as hydrophobic interaction or effect. The main driving force for hydrophobic effect or interaction is repulsion between water and hydrocarbon. This self-assembly separates hydrocarbons from water by the hydrophobic effect.
This effect is most likely occurs in biology such as cell membrane, an association of small molecules, vesicle formation, protein folding, the interaction of the protein with small molecules, etc.
The repulsion through water and attraction of hydrophobic groups are the correct factors for hydrophobic effect rather than thinking of the change in water structure. It’s because water structure is arranged by a network of hydrogen bonds which is difficult to break but somehow interfere in the highly ordered structure.
When a small amount of nonpolar solute is added to water at vicinity it cause the disturbances in hydrogen bonds of water results in H-bonded water network rearranges toward the formation of a local cage like (clathrate) structure surrounding each solute molecule. There is a net change in enthalpy (ΔH) by a small gain of enthalpy. There is a decrease in entropy of water during solubilization of non-polar solute which causes the energetically unfavorable orientation of water.

Due to ΔG is positive, the nonpolar solute remains insoluble...

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