Scientific Foundations

Recall Questions

1. Which of the following is a primary function of carbohydrates in the body?

   1. Provide a quick source of energy
   2. Form a barrier between two aqueous environments
   3. Form channels in the cell membrane
   4. Serve as genetic material

2. What is the primary structure of a protein?

   1. The overall three-dimensional shape of the protein
   2. The sequence of amino acids in a polypeptide chain
   3. The local folding into alpha-helices and beta-sheets
   4. The interactions between multiple polypeptide chains

3. Which level of protein structure is primarily determined by interactions between the side chains (R-groups) of the amino acids?

   1. Primary structure
   2. Secondary structure
   3. Tertiary structure
   4. Quaternary structure

4. What is the primary function of triglycerides in the body?

   1. Structural component of cell membranes
   2. Energy storage
   3. Act as enzyme
   4. Transport oxygen in the blood

5. Which of the following is a primary function of the poly-A tail in eukaryotic mRNAs?

   1. It signals for the mRNA to be translated.
   2. It aids in the stability of the mRNA.
   3. It initiates the splicing of introns
   4. It converts pre-mRNA into mature mRNA.

   Show Explanation

   The poly-A tail is added to the 3' end of the pre-mRNA following transcription and serves to stabilize the mRNA molecule, protecting it from degradation and assisting in its transport out of the nucleus.

6. How do antisense oligonucleotides (ASOs) correct splicing defects in spinal muscular atrophy (SMA)?

   1. They degrade the faulty SMN1 gene.
   2. They convert SMN1 to SMN2 gene.
   3. They inhibit the spliceosome activity.
   4. They recruit splicing factors to correct the splicing of SMN2.

   Show Explanation

   In the context of SMA, ASOs work by binding to RNA and modifying splicing such that the SMN2 gene can produce a functional SMN protein, thereby compensating for the lack of functional SMN1.

7. How do antisense oligonucleotides (ASOs) correct splicing defects in spinal muscular atrophy (SMA)?

   1. They degrade the faulty SMN1 gene.
   2. They convert SMN1 to SMN2 gene.
   3. They inhibit the spliceosome activity.
   4. They recruit splicing factors to correct the splicing of SMN2.

   Show Explanation

   In the context of SMA, ASOs work by binding to RNA and modifying splicing such that the SMN2 gene can produce a functional SMN protein, thereby compensating for the lack of functional SMN1.

8. What is the primary mechanism behind regulatory volume decrease (RVD) in cells?

   1. Increase in intracellular osmolytes
   2. Loss of ions
   3. Gain in intracellular osmolytes
   4. Cellular shrinkage due to water loss

   Show Explanation

   Regulatory volume decrease (RVD) occurs when cells lose ions in response to acute cell swelling, which helps in reducing the cell volume back to normal.

9. What is the importance of the peptide transferase reaction during translation?

   1. It initiates the replication of DNA.
   2. It catalyzes the formation of peptide bonds between amino acids.
   3. It transports mRNA to the ribosome
   4. It releases the formed protein from the ribosome.

   Show Explanation

   The peptide transferase reaction is crucial in translation as it forms peptide bonds between adjacent amino acids, a step that elongates the polypeptide chain. Options 1, 3, and 4 describe processes that are not related to the peptide transferase reaction.

10. What is the main difference in solute composition between plasma and interstitial fluid?

    1. Plasma has a higher concentration of proteins and fewer anions than interstitial fluid.
    2. Plasma has a lower concentration of proteins and fewer anions than interstitial fluid.
    3. Plasma and interstitial fluid have the same composition of solutes.
    4. Plasma has a higher concentration of anions and lower concentration of cations than interstitial fluid.

    Show Explanation

    Plasma contains a higher concentration of proteins, which occupy about 7% of the plasma volume. This higher protein concentration leads to a Gibbs-Donnan effect, causing fewer anions and more cations to reside in the interstitial fluid compared to the plasma.

11. What is the role of the Na-K pump (Na-K-ATPase) in maintaining intracellular and extracellular ion concentrations?

    1. It uses the gradient of Na+ to transport glucose into the cell.
    2. It pumps three K+ ions out of the cell and two Na+ ions into the cell.
    3. It hydrolyzes ATP to pump three Na+ ions out of the cell and two K+ ions into the cell.
    4. It allows the passive transport of Na+ and K+ ions across the cell membrane.

    Show Explanation

    The Na-K pump (Na-K-ATPase) is crucial for maintaining the correct concentrations of Na+ and K+ inside and outside the cell. It actively transports three Na+ ions out of the cell and two K+ ions into the cell against their concentration gradients, using the energy derived from ATP hydrolysis.

Application Questions

These questions are similar to the ones that will be on the self-assessment and qualifier

1. You measure the voltage across the membrane of a liposome (essentially a lipid bilayer that forms a large vesicle in solution). The liposome contains calcium channels that allow calcium to flow in either direction. Chloride cannot pass across the membrane. The concentration of calcium chloride inside the liposome is 100 mM while the concentration of calcium chloride outside the liposome is 10 mM. What membrane potential would you measure across the liposome membrane at 37° C?

   1. 60 mV
   2. 30 mV
   3. -30 mV
   4. -60 mV

   Show Explanation

   Because the liposome contains a calcium channel, calcium will flow down its concentration gradient until the membrane potential reaches a point at which it counterbalances the calcium concentration gradient. To calculate that membrane potential, we use the Nerst equation.

   $$ V_m = \frac{-60 mV}{z_{Ca}} * log_{10}\frac{[Ca^{2+}]_i}{[Ca^{2+}]_o} $$ $$ V_m = \frac{-60 mV}{2} * log_{10}\frac{100 mM}{10 mM} $$ $$ V_m = -30 mV $$

2. You see a female patient who complains of episodes of nausea, lightheadedness and dizziness. You would like to prescribe an anti-histamine to alleviate some of the patient's symptoms but need to estimate the volume of the patient's extracellular fluid to determine an appropriate dosage. The patient weighs 56 kg. What is the volume of the patient's extracellular fluid?

   1. 11.2 L
   2. 13.4 L
   3. 16.8 L
   4. 20.2 L

   Show Explanation

   To determine extracellular fluid, first calculate total body water = 0.5 * body weight = 28 L. Extracellular fluid = 0.4 * TBW = 11.2 L.

3. You are working in a clinical that treats patients who suffer from lysosomal storage disease. You find a group of patients whose lysosome accumulate cellular material but appear to have all the requisite digestive enzymes. You measure the pH of the lysosomes in the patients' cells at 6.5. Normally, lysosomal pH should be between 5 and 5.5. The hydrogen ion pump in the patients' lysosome appears to work as efficiently as the pump in lysosomes from unaffected patients. Surprisingly, you discover a hydrogen ion channel in the lysosomal membrane in your patients' cells. Assuming the pH in the cytosol is 7.4, what membrane potential would you measure across the lysosome membrane?

   1. 108 mV
   2. 54 mV
   3. -54 mV
   4. -108 mV

   Show Explanation

   The presence of a channel in the lysosomal membrane would allow hydrogen ions to flow down their electrochemical gradient until the membrane potential across the lysosome membrane equaled the equilibrium potential for hydrogen ions. To determine the equilibrium potential, you first need to calculate the hydrogen ion concentration in the lysosome and cytosol.

   Recall from the course primer: pH = -log[H⁺] and [H⁺] = 10^-pH. So, lysosome [H⁺] = 10^-6.5 = 3.2 x 10^-7 M and cytosol [H⁺] = 10^-7.4 = 4.0 x 10^-8 M. From the Nernst equation: $$ V_m = \frac{-60 mV}{Z} * log_{10}\frac{[H^{+}]_i}{[H^{+}]_o} $$ $$ V_m = \frac{-60 mV}{Z} * log_{10}\frac{3.2 x 10^{-7} M}{4.0 x 10^{-8} M} $$ $$ V_m = -54 mV $$

4. A patient presents with headache, fatigue, and muscle cramps. The patient reports having diarrhea for over a day. A physical exam reveals the patient has dry skin and lips. The patient's urine is dark. You diagnose the patient as being dehydrated and start oral rehydration therapy. The oral hydration fluid contains sodium to increase plasma sodium levels which helps the patient retain water. What else is added to oral rehydration therapy to increase uptake of sodium?

   1. Fatty acid
   2. Glucose
   3. Potassium
   4. Calcium

   Show Explanation

   One way to think about the problem is how can you get sodium to enter the cells lining the GI tract. We know there is a strong electrochemical gradient that favors sodium entering the cell, but without a channel there is no route for sodium to pass across the cell membrane. There are several sodium channels in the genome but in the GI tract the main route for sodium entry is through the co-transporters (with glucose or amino acids) because the cells use the strong sodium electrochemical gradient to move glucose and amino acids against their chemical gradients. These co-transporters only open if both components are present (i.e. sodium and glucose). So we can “trick” the cells to take up sodium through the SGLT channel by including glucose in the rehydration mix. Once in the cell, sodium can be moved into the interstitial fluid by the sodium-potassium pump.

5. You are on your clerkship rotation in internal medicine, and you receive the blood test results for one of your assigned patients. The results show normal levels of protein and potassium but a serum sodium concentration of 130 mmol/liter. The attending physician asks you to calculate the sodium concentration in the patient's interstitial fluid. Which value is most accurate?

   1. 115 mmol/liter
   2. 127 mmol/liter
   3. 133 mmol/liter
   4. 147 mmol/liter

   Show Explanation

   The correct answer is 133 mmol/liter. Recall that the serum protein affects the calculation of interstitial sodium in two ways. First, you must account for the volume of serum that is occupied by protein which under normal conditions is 7%. This increase the effective concentration of serum sodium in the patient by 130/.93 = 140 mmol/liter. Second, because serum protein is negatively charged, cations tend to be retained in serum, lowering the interstitial cation concentration by about 5%. 140 mmol/liter x 0.95 = 133 mmol/liter.

6. Receptors that are bound to cargo are often internalized through clathrin-mediated endocytosis. The endocytic vesicles develop into endosomes and the pH of the lumen decreases to around 6.0. The lower pH is often sufficient to dissociate the receptor from its cargo. What change to the amino acids in the receptor likely lead to dissociation from its cargo?

   1. Become more positively charged
   2. Become more negatively charged
   3. Become more hydrophobic
   4. Become more hydrophilic

   Show Explanation

   As pH decreases and the concentration of hydrogen ion increases, charged amino acids are more likely to be found in their protonated form. This makes the overall protein more positively charged. This change in charge can weaken the association of the receptor for its cargo.

7. The sodium-amino acid co-transporter depends primarily on which of the following for its activity.

   1. Sodium-potassium-chloride co-transporter
   2. Sodium-hydrogen antiporter
   3. Sodium-potassium pump
   4. Sodium-calcium exchanger

   Show Explanation

   The sodium-potassium pump uses ATP hydrolysis to move sodium ions out of the cell. This maintains a gradient of sodium across the cell membrane that favors the movement of sodium into the cell. The sodium-amino acid co-transporter exploits this gradient to move amino acids into the cell.

8. Osteogenesis imperfecta (brittle bone disease) is caused by mutations in the genes that encode proteins for type I collagen (COL1A1 and COL1A2) that compromise the structural integrity of bone. Which type of mutation in one allele of a type I collagen gene would cause the greatest reduction in the mechanical strength of bone.

   1. Mutation in promoter region that reduces binding of TFIID
   2. Nonsense mutation in the first codon
   3. Missense mutation converts glycine to alanine
   4. Missense mutation converts glycine to aspartate

   Show Explanation

   A mutation in the promoter or the first codon might reduce the amount of type I collagen but cells could still make type I collagen from the wild-type allele. A mutation that changed glycine to a different amino would result in about half of collagen containing a different amino acid from glycine at one position. Recall that the alpha-helical region of collagen usually contains a glycine every third amino acid which allows the collagens to pack close together in trimers as glycine has the smallest side chain. Introducing an amino acid with a larger side chain would reduce the packing of the trimers. Because aspartate has a larger side group than alanine, it disrupts the trimer packing to a greater extent and results in weaker collagen.

9. Cells can obtain cholesterol through endocytosis of low-density lipoprotein (LDL) from the extracellular fluid. Cells express a receptor for LDL (LDL-receptor). You are treating patients who have a mutation in the LDL receptor and whose cells have reduced ability to take up LDL. This leads to hypercholesterolemia, which is a risk factor for coronary artery disease. To better understand why the mutations affect uptake of LDL, you examine expression and location of the LDL receptor. In one mutation, you detect LDL-receptor mRNA in the cytosol and some LDL-receptor in the ER but do not detect LDL-receptor at the cell membrane or in the Golgi. How does the mutation affect LDL-receptor?

   1. Causes localization to lysosomes
   2. Causes localization to secretory vesicles
   3. Increases rate of endocytosis
   4. Inhibits folding

   Show Explanation

   Proteins that enter the secretory pathway must fold properly in the ER in order to leave the ER a travel through the rest of the secretory pathway. Because some protein is detected in the ER but no where else in the secretory pathway, the most likely explanation is that the protein is synthesized but never leaves the ER. This is most likely due to the mutation inhibiting folding of the protein. The other three options are less likely because they require LDL-receptor to first traffic through the Golgi but LDL-receptor was not detected in the Golgi.

10. Ouabain is a drug that inhibits the activity of the sodium-potassium pump. What would be the most significant change in a cell treated with ouabain?

    1. Cell swelling
    2. Cell shrinkage
    3. Increase in membrane potential
    4. Decrease in membrane potential

    Show Explanation

    One of the functions of the sodium-potassium pump is to maintain proper cell volume. Cells must ensure that solute concentrations inside the cell are similar to the fluid outside the cell. Cells have a high concentration of macromolecules in their cytosol. The fluid surrounding cells lacks most of these macromolecules and consequently, another solute(s) must exist at higher concentration outside the cell compared to inside. The sodium-potassium pump moves three sodium ions outside the cell for every two potassium ions in takes in. The net movement of solute outside the cell helps balance the higher concentration of macromolecules inside the cell. Inhibiting the sodium-potassium pump, would lead to higher concentration of solute inside cells which would draw water into the cell and cause the cell to swell.

    Although the sodium-potassium pump is electrogenic (it moves three positive ions out for every two positive ions in brings in), it is not the primary determinant of membrane potential. Membrane potential is primarily determined by the concentration difference (equilibrium potential) of ions across the membrane and the permeability of the membrane to those ions. Because membranes are most permeable to potassium, the potassium equilibrium potential is the main determinant of membrane potential.