Electrophoresis and Protein Separation (5C)
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MCAT Chemical and Physical Foundations of Biological Systems › Electrophoresis and Protein Separation (5C)
A lab tested the effect of voltage on band resolution in SDS-PAGE (10% gel) for two proteins: A (50 kDa) and B (55 kDa). Samples were denatured with SDS and run in identical buffer at either 80 V for 60 min or 200 V for 24 min (same approximate run length). Band separation (distance between band centers) and band broadening were measured.
Results:
- 80 V: separation 0.35 cm; average band width 0.18 cm
- 200 V: separation 0.30 cm; average band width 0.34 cm
Based on the data, which factor most likely reduced separation efficiency at 200 V?
Higher voltage decreased the electric field strength, lowering protein velocity and increasing overlap.
Increased Joule heating at higher voltage increased diffusion and band broadening.
At higher voltage, SDS no longer binds uniformly, making smaller proteins less negatively charged than larger proteins.
Higher voltage increased protein molecular mass by promoting aggregation, reducing migration differences.
Explanation
This question tests understanding of how voltage affects band resolution in SDS-PAGE through Joule heating effects. In gel electrophoresis, applying voltage generates heat (Joule heating) proportional to the square of the voltage, and excessive heating can reduce separation quality by increasing molecular diffusion and band broadening. The data shows that at 200V, despite similar total migration distance, band separation decreased (0.35 to 0.30 cm) while band width nearly doubled (0.18 to 0.34 cm), indicating significant band broadening that reduced resolution between the two proteins. Increased Joule heating at higher voltage causes uneven temperature distribution in the gel, leading to increased diffusion of protein bands and loss of sharpness, which explains the observed reduction in separation efficiency. Choice B incorrectly states higher voltage decreases electric field strength, when voltage directly increases field strength; the issue is the thermal effects, not field strength. For optimal SDS-PAGE resolution, balance voltage to achieve reasonable run times while minimizing Joule heating - lower voltage with longer run times often provides sharper bands than high voltage with shorter times.
A researcher ran native PAGE at pH 6.5 to separate two proteins of different size and pI under a constant 140 V for 22 min. Wells were near the cathode (−). Protein M: 30 kDa, pI 6.0. Protein N: 90 kDa, pI 8.5. Migration distances toward the anode were M = 1.9 cm and N = 0.0 cm.
Which conclusion about the proteins’ net charges at pH 6.5 is most supported?
Protein N is net neutral at pH 6.5 because proteins with higher pI values always have zero net charge.
Protein N is net negative at pH 6.5 but remains at the well because it is larger than Protein M.
Protein M is net positive at pH 6.5 because proteins below their pI migrate toward the anode.
Protein M is net negative at pH 6.5, while Protein N is net positive or near neutral at pH 6.5.
Explanation
This question tests understanding of how protein net charge at a specific pH determines migration in native PAGE. In native electrophoresis, proteins migrate based on their net charge relative to the running pH - proteins with pI below the running pH are negatively charged and migrate toward the anode, while proteins with pI above the running pH are positively charged and typically show little to no anode migration. At pH 6.5, Protein M (pI 6.0) has pH > pI by 0.5 units, making it slightly negatively charged and explaining its migration of 1.9 cm toward the anode. Protein N (pI 8.5) has pH < pI by 2.0 units, making it positively charged at pH 6.5, which explains why it remained at the well (0.0 cm migration) - positively charged proteins don't migrate toward the positive anode. The correct answer accurately identifies that M is net negative while N is net positive or near neutral at the running pH. Choice A incorrectly suggests size prevents migration when the actual cause is positive charge, as native gels separate by charge-to-mass ratio, not size alone. To predict migration in native PAGE, always compare running pH to pI: if pH > pI, expect negative charge and anode migration; if pH < pI, expect positive charge and minimal/no anode migration.
A physiology study used native gel electrophoresis (pH 8.3 buffer) to compare a patient’s serum proteins before and after acute dehydration. The gel was run at 100 V for 30 min with wells near the cathode (−). Albumin (pI 4.7) and a basic peptide hormone carrier protein (pI 9.6) were monitored by immunostaining. Densitometry indicated both proteins were present at similar concentrations in both samples, but their migration distances differed.
Observed migration distance toward the anode (cm):
- Albumin: 4.5 (baseline), 4.5 (dehydration)
- Carrier protein: 0.2 (baseline), 0.2 (dehydration)
Which conclusion is most consistent with these electrophoresis results?
Dehydration increased serum ionic strength, reversing the electric field direction and preventing albumin migration.
Albumin became net positive during dehydration, but its increased mass offset the charge change, keeping distance constant.
Both proteins maintained similar net charges at pH 8.3 across conditions, so their mobilities were unchanged.
The carrier protein must be smaller than albumin, because smaller proteins always migrate less in native gels.
Explanation
This question tests understanding of how protein charge and migration in native gel electrophoresis remain consistent when intrinsic protein properties are unchanged. In native electrophoresis at pH 8.3, proteins migrate based on their net charge - albumin (pI 4.7) is well below the running pH, giving it a strong negative charge and causing significant migration toward the anode (4.5 cm), while the carrier protein (pI 9.6) is above the running pH, making it positively charged with minimal anode migration (0.2 cm). The key observation is that both proteins maintained identical migration distances before and after dehydration, indicating their net charges at pH 8.3 remained unchanged - this is expected because protein pI values and the buffer pH are intrinsic properties unaffected by serum concentration changes. Both proteins maintained similar net charges across conditions because dehydration doesn't alter protein structure or pI values when the buffer system maintains constant pH. Choice A incorrectly suggests ionic strength changes would reverse the electric field, which is impossible as field direction is determined by electrode polarity, not solution conditions. The principle for verification: if migration distance remains constant under identical electrophoresis conditions, the protein's net charge hasn't changed, regardless of sample concentration or other non-denaturing treatments.
A researcher optimized separation of three similarly sized enzymes using native PAGE (8% gel) in pH 8.0 buffer. Wells were near the cathode (−). The enzymes had the same mass (50 kDa) but different pI values: E1 pI 5.0, E2 pI 7.8, E3 pI 9.5. The gel was run for 18 min at different voltages.
Migration distance toward the anode (cm):
- 75 V: E1 1.8, E2 0.3, E3 0.0
- 150 V: E1 3.6, E2 0.6, E3 0.0
Based on the data, which factor most influences separation efficiency between E1 and E2 under these conditions?
Net charge at the running pH, because E1 is farther from its pI than E2 and migrates more.
Direction of the electric field, because reversing the leads would increase the distance between E1 and E2.
Molecular size, because proteins of identical mass separate primarily by sieving through the gel.
Voltage, because increasing voltage changes the proteins’ pI values and increases their charge difference.
Explanation
This question tests understanding of factors affecting protein separation in native PAGE, specifically the role of net charge versus other parameters. In native electrophoresis, proteins separate based on their charge-to-mass ratio and size, with net charge being the primary factor when proteins have similar sizes. At pH 8.0, E1 (pI 5.0) is 3.0 pH units above its pI, giving it a large negative charge, while E2 (pI 7.8) is only 0.2 pH units above its pI, resulting in a very small negative charge - this large difference in net charge explains why E1 migrates much farther (3.6 cm at 150V) than E2 (0.6 cm). The separation efficiency between E1 and E2 is determined by their different net charges at the running pH, not by voltage (which affects migration speed but not relative separation), molecular size (they're identical), or field direction. Choice A incorrectly suggests voltage changes pI values, when pI is an intrinsic protein property independent of applied voltage. To optimize protein separation in native PAGE, choose a pH that maximizes the difference in net charge between proteins by considering their pI values - proteins far from their pI at the running pH will have larger net charges and migrate more.
A clinical lab analyzed a plasma protein mixture by native agarose gel electrophoresis to assess inflammatory status. The gel was run in 25 mM Tris-glycine buffer at pH 8.6 with the wells placed near the cathode (−) and the anode (+) at the far end. A constant 120 V was applied for 25 min. Four purified proteins (each 1 mg/mL) were run in adjacent lanes: albumin (66 kDa, pI 4.7), transferrin (80 kDa, pI 5.9), IgG (150 kDa, pI 7.4), and lysozyme (14 kDa, pI 11.0). Migration distances from the wells were recorded.
Based on the data, which conclusion about protein net charge at pH 8.6 is most supported by the electrophoresis results?
Data (distance toward anode, cm): albumin 4.8; transferrin 3.6; IgG 1.1; lysozyme 0.0.
Transferrin is net positive at pH 8.6 because proteins with higher pI values migrate farther toward the anode.
IgG is net positive at pH 8.6 because it migrates only a short distance toward the anode.
Albumin is net negative at pH 8.6, consistent with its strong migration toward the anode.
Lysozyme is net negative at pH 8.6 because it is the smallest protein and should migrate farthest toward the anode.
Explanation
This question tests understanding of protein net charge and migration in native gel electrophoresis at a specific pH. In electrophoresis, proteins migrate based on their net charge - negatively charged proteins move toward the positive anode, while positively charged proteins move toward the negative cathode. At pH 8.6, proteins with pI values below 8.6 will be negatively charged (pH > pI), while those with pI values above 8.6 will be positively charged (pH < pI). The data shows albumin (pI 4.7) migrated 4.8 cm toward the anode, confirming it is negatively charged at pH 8.6, which is consistent with its pI being well below the running pH. Choice A incorrectly relates size to charge, as lysozyme's lack of migration (0.0 cm) indicates it's positively charged (pI 11.0 > pH 8.6), not negative. To verify protein charge in electrophoresis, always compare the running pH to the protein's pI: if pH > pI, the protein is negative; if pH < pI, the protein is positive.
A lab separated a physiological mixture of muscle proteins by native electrophoresis at pH 8.8, applying 130 V for 30 min. Wells were near the cathode (−). Two bands were excised and identified by mass spectrometry: Band 1 contained protein R (20 kDa, pI 4.9) and Band 2 contained protein S (20 kDa, pI 9.1). The recorded migration distances toward the anode were R = 5.0 cm and S = 0.1 cm.
Which statement is most consistent with electrophoresis principles under these conditions?
Protein R migrated farther because native electrophoresis separates only by size, and pI does not affect migration.
Protein S migrated less because at pH 8.8 it is near its pI and has reduced net charge.
Protein S migrated less because smaller proteins experience less electric force and therefore move more slowly.
Protein R migrated farther because at pH 8.8 it is net positive and is attracted to the anode.
Explanation
This question tests understanding of how protein pI values determine net charge and migration in native electrophoresis at a specific pH. In native gel electrophoresis, proteins migrate based on their net charge, which depends on the relationship between the running pH and the protein's pI - proteins far from their pI have larger net charges and migrate more. At pH 8.8, Protein R (pI 4.9) is 3.9 pH units above its pI, giving it a large negative charge and explaining its substantial migration toward the anode (5.0 cm). Protein S (pI 9.1) is only 0.3 pH units below its pI at pH 8.8, making it nearly neutral with minimal net charge, which explains its negligible migration (0.1 cm) - proteins near their pI have very small net charges regardless of their size. The correct answer properly identifies that S migrated less because it's near its pI and has reduced net charge at the running pH. Choice C incorrectly attributes the difference to size effects on electric force, when both proteins are the same size (20 kDa) and the difference is purely due to charge. For native electrophoresis, the key principle is that migration distance correlates with net charge magnitude - proteins near their pI (within ~0.5 pH units) show minimal migration regardless of size.
A clinical lab analyzed a plasma protein mixture (albumin plus three globulins) using native agarose gel electrophoresis in 50 mM Tris buffer at pH 8.6. Samples were loaded near the cathode and run at 120 V for 25 min. Migration distance toward the anode was recorded.
Data (migration toward anode):
Albumin: 42 mm
Protein X: 28 mm
Protein Y: 12 mm
Protein Z: 3 mm
Which conclusion about protein charge at pH 8.6 is most supported by these electrophoresis results?
Protein Y is net positive at pH 8.6 because it migrated toward the anode.
Albumin has the greatest net negative charge at pH 8.6.
Protein Z has the greatest net negative charge at pH 8.6.
All proteins have identical net charge because the voltage was constant.
Explanation
This question tests understanding of protein charge and migration in native agarose gel electrophoresis. In electrophoresis, proteins migrate based on their net charge - negatively charged proteins move toward the positive anode, with more negative proteins migrating farther. At pH 8.6, which is above most protein pI values, proteins typically carry net negative charges. Since albumin migrated the farthest (42 mm) toward the anode, it must have the greatest net negative charge among the tested proteins. The migration pattern (albumin > Protein X > Protein Y > Protein Z) indicates decreasing net negative charge in that order. Choice C is incorrect because proteins migrating toward the anode are negatively charged, not positive.
Two purified enzymes (P1 and P2) were compared by native PAGE (no SDS) at constant size marker calibration. Runs were performed at 150 V for 20 min in buffers of different pH. The gel was oriented with cathode at the top and anode at the bottom.
Migration distance toward anode (mm):
- pH 6.0: P1 = 6, P2 = 24
- pH 8.5: P1 = 20, P2 = 8
Which conclusion about relative isoelectric points ($pI$) is most supported by the data?
Both proteins have the same $pI$ because they swap migration distances.
P1 has a higher $pI$ than P2.
P2 has a higher $pI$ than P1.
Neither protein has a $pI$ because only nucleic acids have $pI$ values.
Explanation
This question tests understanding of how protein migration changes with pH relative to pI in native PAGE. In electrophoresis, proteins are positively charged below their pI and negatively charged above their pI. At pH 6.0, P2 migrates farther toward the anode (24 mm vs 6 mm), indicating it has more negative charge. At pH 8.5, P1 migrates farther (20 mm vs 8 mm), showing P1 is more negative at higher pH. This reversal indicates P2's pI lies between pH 6.0 and 8.5, while P1's pI is below pH 6.0. Since P2 transitions from more negative to less negative as pH increases from 6.0 to 8.5, P2 must have the higher pI. A useful check is that proteins become less negative as pH approaches their pI from above.
A membrane protein complex was analyzed by native PAGE at pH 7.4 (no SDS). Two conditions were tested: 100 V and 200 V, each for 15 min, same gel and buffer. Migration distances toward the anode were measured.
Condition (V) vs migration (mm):
- 100 V: Protein M = 9, Protein N = 18
- 200 V: Protein M = 17, Protein N = 34
Based on the data, which factor most directly explains the change in migration distance when voltage is increased?
Higher voltage decreases gel pore size, increasing separation.
Higher voltage increases the electric field, increasing electrophoretic force on charged proteins.
Higher voltage reverses the direction of migration toward the cathode.
Higher voltage decreases protein charge by shifting amino acid $pK_a$ values.
Explanation
This question tests understanding of how voltage affects protein migration in electrophoresis. Electrophoresis separates proteins by applying an electric field that exerts force on charged molecules. Doubling the voltage from 100V to 200V doubles the electric field strength, which doubles the electrophoretic force on each charged protein. The data shows both proteins approximately doubled their migration distances (M: 9→17 mm, N: 18→34 mm), confirming that migration distance is proportional to applied voltage. Choice B is incorrect because voltage doesn't change protein charge - the charge depends on amino acid composition and pH. The key principle is that electrophoretic velocity equals (charge × field strength) / friction, so doubling field strength doubles velocity.
A lab compared two proteins of similar mass (~50 kDa) by native PAGE at pH 7.0. The gel was run at 140 V for 18 min. Protein Q migrated 26 mm toward the anode, while Protein R migrated 5 mm toward the anode.
Which statement is most consistent with electrophoresis principles under these conditions?
Protein R must be positively charged because it migrated toward the anode.
Protein Q likely has a larger hydrodynamic radius, causing faster migration.
Protein R likely has a more negative net charge than Protein Q at pH 7.0.
Protein Q likely has a more negative net charge than Protein R at pH 7.0.
Explanation
This question tests understanding of how net charge affects migration in native PAGE. In native electrophoresis at pH 7.0, proteins migrate toward the anode based on their net negative charge - more negative proteins migrate farther. Since Protein Q migrated 26 mm while Protein R only migrated 5 mm (both toward the anode), Protein Q must have a more negative net charge at pH 7.0. The similar masses (~50 kDa) rule out size as the primary factor differentiating their migration. Choice A reverses the charge relationship, while Choice D incorrectly states that anode-migrating proteins are positive (they're actually negative). A key check is that in native PAGE, migration distance directly correlates with net charge magnitude when sizes are similar.