1. Fill in the blanks in the following seven statements using the list of words to the right.

One point per blank.

A. Biological membranes consist of a bilayer

having two in which Monolayers

are embedded. Cytoplasm

Fluidity

B. Most integral membrane proteins have at least one Inner monolayer

transmembrane domain. Outer monolayer

Plasma membrane

C. Integral membrane proteins may also be held to the membrane Endoplasmic reticulum

by . Membrane proteins

Extrinsic (peripheral)

D. is a planar lipid, chemically similar to Integral

steroids, that affects the of the plasma Phospholipid

membrane in a complex manner. Sphingomyelin

Alpha-helical

E. Glycolipids (have sugar molecules in the polar head group) are Cholesterol

located preferentially in the of Bonds to lipids

the . Cytosolic

Lumenal

F. Loosely attached, membrane proteins can often

be removed from the membrane by alterations of the salt concentrations.

G. The enzymes which carry out the synthesis of membrane bilayer lipids are integral membrane proteins of the membrane. The active sites of these enzymes are located in the domain of the protein.

2. Eukaryotic transcription regulatory proteins bind to DNA primarily in the major groove. Which of the following is not related to major groove binding?

1. Regulatory proteins are more readily bound at the major groove because it is wider than the minor groove.

2. The chemical groups on nucleotides to which the proteins bind are more accessible in the major groove than in the minor.

3. One mode of interaction between protein and DNA is by way of covalent bonds.

4. The strength of binding depends on numerous, weak interactions.

3. There is a DNA-binding regulatory protein ‘X’ that enhances the transcription of gene ‘A’. Another protein, ‘Z’, inhibits the expression of the same gene. A clever molecular biologist cloned the genes for both ‘X’ and ‘Z’ and, by recombinant DNA technology, replaced the DNA-binding domain of protein ‘Z’ with the DNA-binding domain of ‘X’, and expressed the new construct in animal cells that were already expressing gene ‘A’. What is the likely effect on ‘A’ expression in these cells going to be?

1. Expression of gene ‘A’ will be upregulated.

2. ‘A’ will be downregulated.

3. ‘A’ continues to be expressed as it was before the recombinant gene was expressed. The new, chimeric (half ‘X’, half ‘Z’) regulator protein has no effect.

4. The cell will get cancer and die.

4. The active conformations of many transcription regulatory proteins are often homodimers (2 identical proteins) or heterodimers (2 different proteins). What is the advantage to the cell of active heterodimers?

1. Heterodimers allow a wider range of regulatory activities for a particular number of regulatory protein genes.

2. Hetrodimerization allows the regulator to insinuate farther into the grooves of the DNA.

3. Helix-turn-helix motifs, among others, are active only when heterodimerized.

4. Homodimers are positive regulators while heterodimers are negative. This gives cells a simple ‘on-off’ switch mechanism.

5. In the regulation of the bacterial genes responsible for tryptophan synthesis, the function of the amino acid tryptophan is:

1. To bind to the operator portion of the promoter and regulate transcription.

2. To bind to RNA polymerase and regulate its activity.

3. To bind to an inducer protein which then facilitates the binding of the polymerase to the promoter.

4. To bind to a repressor protein which then binds to the operator.

6. There is a particular eukaryotic transcription regulatory protein that binds to a DNA sequence 640 base pairs ‘upstream’ of the TATA box for a particular gene. This protein exerts its activity within the cell by binding to the general transcription factor IIE. When the regulatory protein and TF-IIE were purified and mixed, it was seen that they do not bind to each other, even at high concentrations. How can this apparent paradox be explained?

1. In the cell, the regulatory protein must bind to another protein before it can bind to IIE.

2. The regulatory protein must bind to DNA before its conformation is correct for binding to IIE.

3. IIE must bind to the complex of multiple general transcription factors at the promoter before this regulatory protein can bind to it.

4. All of the above

5. None of the above

7. Which of the following alterations to lipid bilayers would be expected to have little or no effect on the bilayer’s viscosity (fluidity)?

1. Increased concentration of cholesterol in the bilayer.

2. Increasing the temperature.

3. Decreasing the number of C=C bonds in fatty acids.

4. Increasing the average length of the fatty acids.

5. Replacement of half the phosphatidyl choline (PC) by sphingomyelin (SM).

8. Lipids in bilayers move in many modes but one movement they make only very rarely is to ‘flip-flop’ from one monolayer to the other. The likeliest reason for this is:

1. The polar head groups of adjacent lipids are attracted to each other so strongly that they cannot be easily separated.

2. The fatty acid ‘tails’ of adjacent lipids are so strongly attracted to each other that they cannot be easily separated.

3. The water molecules associated with the polar head groups make the lipid too bulky to be moved through the relatively small open spaces in the interior of the bilayer.

4. The energy barrier to moving a polar head group through the hydrophobic core of a bilayer is too great to be overcome by thermal motion.

9. Which of the following is not a characteristic associated with transmembrane integral membrane proteins?

1. Exposure of the C=O and N-H groups on the outside of the transmembrane domain.

2. An alpha-helical segment long enough, about 20-25 amino acids, to span the lipid bilayer.

3. A sequence of hydrophobic amino acids.

4. Association of some amino acid residues (R-groups) with the fatty acid tails of lipids.

5. None of the above.

10. The uptake of the amino acid leucine into animal cells was examined by adding large concentrations of leucine to the aqueous environment around the cells This aqueous environment contained 140mM NaCl, 5mM KCl, and 1mM CaCl₂. Leucine entered the cells rapidly. When the KCl or CaCl₂ was removed from the environment, uptake of leucine was unaffected, but when the NaCl was removed, leucine uptake stopped. How is leucine entering these cells?

1. Active transport.

2. A sodium and leucine symporter.

3. A potassium and leucine antiporter.

4. A leucine uniporter.

5. Simple diffusion through the plasma membrane.

11. Many different plasma membrane ion channels are voltage gated. What this means is:

1. The ion channel offers a pathway (the channel) for ions to move across the plasma membrane, thus there is a change of voltage in the cell.

2. If the distribution of positive and negative ions across the PM changes, the ion gradients will be changed as will the rate of movement of ions through the channels.

3. When the membrane potential changes, ions move by simple diffusion into the cell.

4. When the distribution of positive and negative ions across the PM changes, electrostatic interactions within channel proteins change, causing their tertiary structure to change.

12. In most animal and plant cells, the greatest amount of membrane is contained in the:

1. Plasma membrane.

2. Golgi apparatus.

3. Endoplasmic reticulum.

4. Lysosomes.

13. Proteins found in cell nuclei are synthesized in the cytosol and later move into the nucleus. Which of the following statements correctly describes entry of a protein into the nucleus?

1. After binding to the nuclear pore, the protein must be unfolded by chaperones before it can move into the nucleus.

2. After the protein binds to the pore, the pore structure changes, allowing the protein to move into the nucleus.

3. Nuclear proteins are synthesied by ribosomes bound to the outer nuclear envelope membrane and are translocated through the nuclear pore during their synthesis.

4. The signal for transport of a protein into the nucleus is composed of an oligosaccharide attached to the protein.

14. Signal recognition particle (SRP) is a multi-domain, multi-subunit complex of protein and RNA that plays a vital role in synthesis of some proteins. One of its activities is the inhibition of translation of signal-sequence containing proteins. If this particular activity were removed from the SRP, what effect would it have on a cell?

1. Translocation of proteins into the ER would cease or nearly cease.

2. Translocation of proteins into the ER would be accelerated.

3. Ribosome-mRNA complexes would dissociate.

4. All protein synthesis would stop.

5. Synthesis of only transmembrane integral membrane proteins would cease.

15. For 5 points, explain why you chose the answer to the previous question.

16. The primary structure of an integral membrane protein caan be drawn as shown below, where N and C are the amino- and carboxy-terminals, respectively, and the dark-shaded boxes represent hydrophobic segments 23 amino acids long. The + and - signs indicate charges of amino acid R-groups near the ends of one of the hydrophobic segments. The other segment does not have such charges.

What is the correct orientation of this IMP in the RER membrane?

1. 2.

3. 4.

17. Which of the following may aid in the translocation of proteins across the rough endoplasmic reticulum membrane?

1. N-linked glycosylation.

2. Chaperones.

3. Folding up of the protein.

4. All of the above.

5. None of the above.

18. Many proteins are called ‘RER-resident’ because the vast majority of them are found located in the RER. The mechanism cells employ to guarantee their presence in the RER is:

1. RER-resident proteins have a signal peptide that causes their return to the RER should they leave it.

2. RER-resident proteins have affinity for each other and form large aggregates that cannot be moved to any other organelle.

3. RER-residents are embedded tightly in the ER membrane.

4. If they leave the RER, the proteins are destroyed.

19. Which of the following is a correct statement about the Golgi apparatus.

1. Vesicles that arise from endocytosis (the uptake of material from the outside environment) travel to and fuse with the Golgi, facilitating the destruction of the vesicle contents.

2. N-linked glycosylation of newly-made proteins occurs in the Golgi.

3. The Golgi membrane is continuous with the nuclear envelope membrane.

. 4. Each compartment of the Golgi apparatus carries out a particular set of enzyme reactions that facilitate the step-wise processing and modification of newly synthesized proteins.

20. (12 points) The diagram shows a passive facilitated diffusion carrier that mediates the transfer of a solute down its concentration gradient across the membrane. How would you need to change the diagram to convert the carrier protein into a pump that transports the solute up its electrochemical gradient by hydrolyzing ATP? Explain the need for each of the steps in your new diagram.

21. (8 points )The Na⁺ -glucose symporter is a carrier protein that allows Na⁺ and glucose to enter cells. Na⁺ channels can operate in the same cells. When the Na⁺-glucose symporter and Na⁺ channel operate at the same time in the same cell, the rate of Na⁺ entry through individual channels is thousands of times faster than the rate through individual symporters. Why do the ions enter cells so much faster through the one than the other?

22. (12 points)There are integral membrane proteins of the trans-Golgi network (or reticulum) that bind specifically to phosphorylated mannose. Discuss the functions of these IMPs and describe the pathway they take and interactions they undergo while carrying out these functions.