Payne, BSCI330 Exam #1

2/17/12Print Your Name:

Your Laboratory Section: DAY

TIME

Directions :1. Print Your Name and Section on every page of this exam NOW.

2. Use a PEN to complete this exam or you will not be eligible for a regrade.

3. Check to see that you have 3 sheets. If you dont, raise your hand.

4. You must confine your answers to the spaces provided.

5. Read the questions! - Be as specific and as concise as you can. Use the minimal number of words necesnsary to completely answer the question. Use diagrams and graphs if needed, but remember to label them!

6. You must hand in your exam by 9:50 AM.

Good Luck.

Scoring:

Possible Pts.

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Signed1) Which THREE statements below are true of all cells?

( CIRCLE THE SQUARES TO THE LEFT OF THE TRUE STATEMENTS; 10pts) All cells have endoplasmic reticulum FALSE (Bacteria do not) All cells require at least a thousand genes to function FALSE (parasitic bacteria do not) All cells derive their energy from organic molecules (TRUE, even Lithotrophs and phototrophs store energy in bonds within organic molecules and so they, too also derive their energy from those molecules. GTAs accepted either a TRUE or FALSE ofr this answer) All cells use proteins as catalysts TRUE All cells are enclosed by a plasma membrane TRUE2) Genes that duplicated as a result of speciation are called _______orthologs___________ of each other. [N>B. The GTAs felt that the term duplicated (rather than diverged might have confused some students and so may have accepted some other answers for full or partial credit (2pts)3) Name TWO characteristics that allow an organism to be used as a model organism. (4pts)

From the lecture notes:

The genome has been sequenced Site-directed and tissue-specific mutagenesis is possible Expression of Multiple genes can be tracked across many cells simultaneously The developmental sequence is known4) Why cannot you tell whether a protein has a round or an elongated shape using light microscopy? (2pts)

Resolution is too poor5) What property of a specimen (e.g. absorption of light etc.) does phase contrast microscopy detect? (2pts)Refractive index6) Why does CONFOCAL fluorescence microscopy show you details of fluorescence from a specimen that is obscured in images from conventional fluorescence microscopy? (4pts)

Because it eliminates fluorescence coming from outside the focal point of the microscope lens7) What microscopy method might you try to use in order to measure the force needed to detach a single myosin motor protein from an actin protein filament that it is attached to? (2pts)

Atomic Force Microscopy

8) Why is GFP-tagging of a protein, and NOT the use of fluorescent antibodies, the most common method for examining the localization of proteins in living cells? (6pts)Because antibody labeling usually requires that the tissue is fixed and cut into sections9) Molecule A is formed from molecule B in a cell through an enzyme-catalyzed reaction in a cells cytoplasm. You observe that the concentration of A and B in the cell do not change with time. The concentration of A in the cells cytoplasm is 1mM and that of B is also 1mM. The standard free energy change for the reversible reaction by which B is formed (A B) is -5kcal/mole.

Answer the following questions about this situation, assume T = 293 degrees Kelvin and R = 2 cal/mole/degree Kelvin.a) Is the reaction between A and B at equilibrium? Explain your reasoning, referring to specific thermodynamic equations (4pts)

G = RTln([products]pre//([reactants]pre + G0 = RTln(1mM/1mM) 5 = -5kcal/mole

G is not zero and so reaction is not at equilibriumb) If the reaction is not at equilibrium, what might be a reason for why the concentrations of the reactants are not changing with time? (5pts)

Could be in a steady state in which products are continuously removed and reactants added10) A cell in a petri dish releases a signaling molecule that reaches a high concentration in the medium surrounding the cell and then spreads to neighboring cells. Explain in terms of thermodynamic equations that include free energy, why the spread of the molecule to neighboring cells is spontaneous and does not require an external source of energy, such as that derived from the making or breaking of chemical bonds (e.g. ATP)? (6 pts)GS and S is positive because the cloud of signaling molecules becomes more disordered as it spreads, so G is negative for the spreading process and does not require energy11) What are the major products of the two kinds of fermentation pathways performed by cells? (8 pts)

Pathway 1) lactosePathway 2) ethanol + carbon dioxideWhy is fermentation necessary under anaerobic conditions?To regenerate NAD+ from NADH. The NAD+ is needed to continue ATP production via glycolysis.12) In addition to phosphorylation of a protein, which attaches a phosphate to a protein, two OTHER biochemical processes can also covalently attach small molecules to some proteins. Name the class of small molecules that are attached to the protein in each case and whether the new modified domain of the protein is more or less hydrophobic than it was before the attachment (e.g. phosphate ions, LESS hydrophobic) (8pts)

Process 1. ______sugar molecules (less hydrophobic)_____________Process 2. _________lipids (more hydrophobic)

What stabilizes quaternary structures? (4 pts)

Weak bonds and, sometimes, disulfide bridges13) Briefly discuss this sentence. Proteins fold into stable structures because catalysts called chaperonins use energy from ATP to package them into their correct shape. Is this statement generally correct? give your reasoning (6 pts)

No - in general proteins fold into their lowest energy state spontaneously. Chaperonins can speed folding for some special proteins, just as enzymes speed chemical reactions, but they cannot force the proteins into anything other than their lowest energy state. Even if they did so, the protein would eventually refold into its lowest energy state anyway. 14) Why are proline residues not usually found in alpha helical sections of proteins (2 pts)?

They introduce a kink into the backbone15) Why must X-ray crystal structures be viewed initially as only one possible model of the natural structure of a protein and not the final, definitive structure (4pts)? Because the structure of the protein in a crystal may not be its native (natural) structure in its cellular environment16) Why might replacement of non-polar valine residues with charged aspartate residues in the alpha helical domains of bacteriorhodopsin reduce its structural stability? (5pts)Because the helices are transmembrane and so the negative charges introduced into the helices by the aspartate residue would not favorably interact with the hydrophobic core of the membrane (as valine does)17) Imagine that, with some magical microscope, you could actually view the structure of a protein in a living cell. Would you be able to watch its structure unfold in real time as it flips between conformational states? If not, why not? (4pts)

Even large conformational changes are complete within milliseconds (see lecture notes) and so are too fast to be seen in real time. Youd just see a blurred average structure. 18) What is the difference in protein structure between a heteromer and a homomer? (2 pts)Homomer identical subunits. Heteromer different subunits19) A protein reversibly binds a small ligand molecule. Draw a graph that describes how many protein molecules have ligand bound to them as ligand concentration increases. Draw on this graph a second line to indicate how the graph line would change if a mutation to the protein increased kOFF for the reaction between the protein and its ligand. (8pts)

Would the affinity of the mutant protein for its ligand be INCREASED OR DECREASED? (Circle ONE; 2pts) DECREASED

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