UTA Cell Physiology (BIOL 3301) Exam 1 with Dr. Pellegrino

1. The primary structure of a protein is determined by:

b) The sequence of covalently linked amino acids via peptide bonds.

2. Which of the following statements about lipid structure is FALSE?

b) Cholesterol is a sterol that increases membrane fluidity by preventing tight packing of phospholipids.

3. During transcription, RNA polymerase synthesizes an RNA strand complementary to the DNA template strand.

If the template strand sequence is 3’-ATG CGA-5’, what is the sequence of the RNA transcript?

a) 5’-UAC GCU-3’

4. What is the primary role of chaperone proteins in protein folding?

c) To provide an environment that facilitates proper folding and prevents aggregation.

5. A competitive inhibitor of an enzyme affects reaction kinetics by:

b) Increasing the Km (Michaelis constant) without affecting Vmax.

6. Which of the following molecules would MOST easily diffuse directly across a pure phospholipid bilayer without the aid of a transporter?

c) O₂ (a small nonpolar gas)

7. The "fluid mosaic model" of the membrane primarily describes:

b) The ability of lipids and proteins to diffuse laterally within the plane of the bilayer.

8. In eukaryotic gene expression, what is the function of the promoter?

b) It is the site where transcription factors and RNA polymerase bind to initiate transcription.

9. Alternative splicing allows for:

b) The generation of multiple different protein isoforms from a single gene.

10. The difference between an integral membrane protein and a peripheral membrane protein is that:

b) Integral proteins span or are embedded in the lipid bilayer via hydrophobic interactions, while peripheral proteins are loosely associated with the surface.

11. Which property of phospholipids is MOST critical for the formation of a stable lipid bilayer in an aqueous environment?

b) Their amphipathic nature, leading to self-assembly.

12. A mutation changes a codon in an mRNA from 5’-UCA-3’ (serine) to 5’-UAA-3’. What is the most likely consequence?

b) Premature termination of translation.

13. The ubiquitin-proteasome system is primarily responsible for:

b) Tagging and degrading specific, unneeded, or misfolded proteins.

14. Which type of noncovalent interaction is primarily responsible for the stability of an alpha-helix in a protein's secondary structure?

c) Hydrogen bonds between the carbonyl oxygen of one residue and the amide hydrogen of another.

15. In a condensation reaction linking two monosaccharides to form a disaccharide:

b) A glycosidic bond is formed and a water molecule is released.

1. The primary reason ATP is considered the "energy currency of the cell" is because:

b) Hydrolysis of its phosphoanhydride bonds is highly exergonic and can be coupled to endergonic cellular processes.

2. In glycolysis, phosphofructokinase-1 (PFK-1) is a major regulatory enzyme. Which of the following best describes its allosteric regulation?

c) High ATP acts as an allosteric inhibitor, and AMP can relieve this inhibition.

3. Compared to oxidative phosphorylation, substrate-level phosphorylation (as seen in glycolysis and the citric acid cycle) is characterized by:

a) Direct transfer of a phosphate group from a high-energy substrate to ADP, independent of an electron transport chain.

4. What is the primary fate of the acetyl-CoA molecules produced from pyruvate decarboxylation in the mitochondrial matrix?

b) They enter the citric acid cycle to be oxidized to CO₂, producing NADH and FADH₂.

5. The chemiosmotic theory explains ATP synthesis in oxidative phosphorylation. The critical intermediate is:

c) An electrochemical proton gradient (Δp) established across the inner mitochondrial membrane.

6. During beta-oxidation of fatty acids, what critical step must occur before the fatty acetyl-CoA can enter the mitochondrial matrix?

b) It must be conjugated to carnitine via carnitine acyltransferase I.

7. The electrons carried by NADH (produced in glycolysis) face a specific challenge. How are they typically shuttled into the mitochondrial matrix for the electron transport chain?

b) Special shuttle systems (e.g., malate-aspartate) transfer the reducing equivalents, as the inner membrane is impermeable to NADH.

8. The final electron acceptor in the mitochondrial electron transport chain is:

c) Molecular oxygen (O₂)

9. If the proton gradient across the inner mitochondrial membrane is dissipated (e.g., by an uncoupler), what is the most direct consequence for ATP synthase?

a) It will hydrolyze ATP to pump protons back into the intermembrane space.

10. According to standard calculations, approximately how many molecules of ATP are produced from the oxidation of one molecule of glucose under aerobic conditions?

c) 30-32 ATP

11. What is the primary reason triglycerides are considered more efficient long-term energy storage molecules than glycogen?

c) Triglycerides yield more than twice the ATP per gram upon complete oxidation.

12. During oxidative phosphorylation, complexes I, III, and IV of the electron transport chain all act as:

b) Proton pumps, using energy from electron transfer to move H⁺ into the intermembrane space.

13. A key difference between the products of the citric acid cycle and glycolysis is that the citric acid cycle:

a) Produces ATP via substrate-level phosphorylation and generates large quantities of reduced electron carriers (NADH, FADH₂).

14. The molecule that serves as the critical link between carbohydrate, fat, and protein metabolism by entering the citric acid cycle is:

c) Acetyl-CoA

15. During prolonged starvation, the body's metabolism shifts. What is a major adaptation to provide fuel for the brain?

b) The liver produces ketone bodies from fatty acid derivatives.

1. The primary advantage of compartmentalization in eukaryotic cells is:

b) It allows for the creation of distinct microenvironments optimized for specific functions.

2. An ER signal sequence is best described as:

c) A short stretch of hydrophobic amino acids at the N-terminus or internally within a polypeptide.

3. The Signal Recognition Particle (SRP) plays a critical role in co-translational translocation by:

b) Binding to the ER signal sequence on the ribosome and pausing translation until it docks with the SRP receptor on the ER membrane.

4. What is the fundamental difference between the destination of a soluble protein with an ER signal sequence and a transmembrane protein with a start-transfer and stop-transfer sequence?

a) Soluble proteins are fully translocated into the ER lumen; transmembrane proteins are arrested and integrated into the lipid bilayer.

5. The stop-transfer sequence in a single-pass transmembrane protein functions to:

b) Signal the translocon to release the protein laterally into the ER membrane, halting further translocation.

6. How does the orientation of a single-pass transmembrane protein type I (N-terminus in the ER lumen, C-terminus in the cytosol) become established during translocation?

c) The start-transfer sequence is cleaved, and translocation continues until a hydrophobic stop-transfer sequence enters the translocon.

7. For a protein with multiple transmembrane domains, the translocation process involves:

b) Repeated cycles of SRP binding, translocon engagement, and ribosome detachment/re-attachment for each pair of start-stop transfer sequences.

8. The Rough ER is structurally and functionally distinct from the Smooth ER. Its primary role is:

c) Synthesis of secretory proteins and membrane proteins via ribosome-studded membranes.

9. In the context of protein sorting, "co-translational translocation" specifically refers to:

c) The coupling of protein translation on the ribosome with its simultaneous import into the ER.

10. What is the fate of the ER signal sequence for a soluble luminal protein after it has served its purpose?

c) It is cleaved off by signal peptidase in the ER membrane and degraded.

11. Which of the following proteins would MOST LIKELY be synthesized on free ribosomes in the cytosol?

c) The enzyme catalase, destined for the peroxisome (which uses a post-translational import system).

12. The functional role of the translocon (Sec61 complex) is to:

b) Provide a protein-conducting aqueous channel through the ER membrane.

13. A mutation that deletes the hydrophobic core of an ER signal sequence from a secretory protein would most likely result in:

c) The protein remaining in the cytosol, as it cannot engage the SRP/translocon machinery.

14. The endoplasmic reticulum (ER) is considered the entry point for the secretory pathway because:

c) Proteins destined for secretion or for membranes of the endomembrane system must first be targeted to and processed by the ER.

15. Which statement best distinguishes the roles of Rough ER (RER) and Smooth ER (SER)?

a) RER is involved in protein synthesis and initial modification; SER is involved in lipid synthesis, detoxification, and calcium storage.

1. Which statement best describes the functional relationship between the lumen of a transport vesicle and the compartments of the endomembrane system?

c) The vesicle lumen is topologically equivalent to the extracellular space and the lumen of organelles like the ER and Golgi.

2. The primary function of coat proteins (like clathrin, COPII, and COPI) on transport vesicles is to:

c) Shape the donor membrane into a vesicle and selectively concentrate cargo molecules.

3. COPII-coated vesicles are primarily responsible for transport:

d) From the ER to the Golgi apparatus (anterograde transport).

4. How does the GTPase Sar1 initiate the formation of a COPII vesicle?

b) A GEF in the ER membrane exchanges Sar1's GDP for GTP, causing a conformational change that exposes an amphipathic helix for membrane insertion.

5. The GTPase Dynamin plays a critical role in vesicle formation by:

b) Forming a helical polymer around the neck of a budding vesicle and using GTP hydrolysis to pinch it off from the donor membrane.

6. The specificity of vesicle docking—ensuring a vesicle fuses only with its correct target membrane—is primarily determined by:

b) Complementary pairs of Rab GTPases (on the vesicle and target) and their effectors, which mediate tethering.

7. Membrane fusion between a transport vesicle and its target requires SNARE proteins. The correct statement about SNAREs is:

c) They form a stable trans-SNARE complex (a 4-helical bundle) that overcomes energy barriers and brings the lipid bilayers into close contact.

8. The KDEL receptor is crucial for which specific transport pathway?

b) Retrieval of escaped soluble ER resident proteins (with a KDEL signal) from the Golgi back to the ER.

9. How are lysosomal hydrolases (e.g., acid hydrolases) specifically recognized and packaged into vesicles at the trans-Golgi Network (TGN)?

b) They are tagged with mannose-6-phosphate (M6P), which is bound by M6P receptors in the TGN.

10. What is the key role of the pH gradient in the M6P receptor cycle?

a) The receptor binds M6P in the neutral pH of the TGN and releases it in the acidic pH of the endosome, allowing receptor recycling.

11. The retrograde transport pathway from the Golgi back to the ER, which returns escaped resident proteins and recycling components, primarily utilizes which type of coated vesicle?

c) COPI

12. What is the primary function of glycosylation as proteins pass through the ER and Golgi?

c) To aid in protein folding, stability, and to act as a sorting signal for destination.

13. Vesicle movement from the ER to the Golgi often involves an intermediate structure called a vesicular-tubular cluster (VTC). What is a key feature of transport from VTCs to the Golgi?

b) It is mediated by motor proteins moving the clusters along microtubules.

14. The protein Retromer is specifically associated with which recycling pathway?

a) Recycling of M6P receptors from endosomes back to the TGN.

15. What is the fundamental role of GTPases (like Sar1, ARF, and Rabs) in vesicular trafficking?

b) They act as molecular switches, using GTP binding and hydrolysis to control the timing, location, and specificity of vesicle formation, docking, and fusion.