Scientific Foundations

Recall Questions

1. 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

2. 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

3. 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.

4. 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.

5. Consider a cell with a membrane potential of -60 mV and an intracellular concentration of chloride concentration of 30 mM. If the cell is in normal interstitial fluid (110 mM chloride) and its chloride channels open, what would be the net direction of chloride movement?

   1. Out of the cell
   2. Into the cell
   3. Neither, chloride is at equilibrium

   Show Explanation

   To determine the net direction of chloride movement, we need to determine the equilibrium potential for chloride ion for the cell and compare that to the membrane potential. This is the equation to determine the equilibrium potential: $$ E_k = \frac{-RT}{zF} * \ln\frac{[Cl^{-}]_i}{[Cl^{-}]_o} $$ We can input the values for the constants and convert ln to log₁₀: $$ E_k = \frac{-60}{z} * \log_{10}\frac{[Cl^{-}]_i}{[Cl^{-}]_o} $$ Entering the concentrations for chloride in the cell and interstitial fluid and the valence for chloride (-1), we get an eqilibrium potential of -33 mV. $$ E_k = \frac{-60}{-1} * \log_{10}\frac{30}{110} $$ Because the membrane potential of the cell is more negative than the equilibrium potential, there will be net chloride movement out of the cell.

6. 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.

7. Classify the connective tissue at the top of the sample.

   

   1. Fibrocartilage
   2. Dense regular
   3. Hyaline cartilage
   4. Loose

   Show Explanation

   Note the glassy appearance of the tissue and the appearance of chondrocytes, making this hyaline cartilage.

8. What is primary function of the cells indicated by the arrow in bone?

   

   1. Synthsize bone
   2. Dissolve bone
   3. Synthesize cartilage
   4. Sense mechanical stress

   Show Explanation

   The cells are multinucleated and are resting on the surface of bone, which makes them osteoclasts.

9. Classify the epithelium in the image.

   

   1. Simple squamous
   2. Simple cuboidal
   3. Stratified squamous
   4. Stratified cuboidal

   Show Explanation

   Note the thin layer of cells at the top of the sample facing the external environment. The cells have flattened which makes the epithelium squamous. The epithelium also has only one layer of cells and is simple. There are a few cells beneth the squamous layer but these are part of a different tissue (note how sparse the cells are).

10. Classify the epithelium in the image.

    

    1. Simple stratified
    2. Simple cuboidal
    3. Stratified squamous
    4. Stratified cuboidal

    Show Explanation

    The epithelium is at the top of the sample and has multiple layers of cells, making it stratified. The most superficial layer (outer most) has flattened nuclei making this layer squamous.

11. 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.

Application Questions

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

1. 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.

2. A 45-year-old patient presents to the clinic with a recent history of frequent urination and increased thirst. Laboratory tests indicate elevated glucose levels in the urine, which suggests a reduced ability to transport glucose across the epithelium in the kidney. Which protein is most likely reduced in the kidney epithelial cells?

   1. SGLT2
   2. CFTR (chloride channel)
   3. Claudin 5
   4. Sodium-potassium-chloride channel

   Show Explanation

   SGLT2 channel co-transports sodium and glucose across the apical membrane from lumenal fluid (in this case urine). Fewer SGLT2 channels would reduce the efficiency of of glucose absorption by the epithelium, leading to elevated levels of glucose in the urine.

3. Pulsatile administration of parathyroid hormone (PTH) has been found to increase bone density by stimulating osteoblasts to synthesize bone but have minimal impact on osteoclast development. If you analyzed the genome around the COL1A1 gene in osteoblasts exposed to PTH what change would you observe compared to unstimulated osteoblasts?

   1. Acetylated histones
   2. Deacetylated histones
   3. Phosphorylated histones
   4. Glycosylated histones

   Show Explanation

   Activate transcription of genes is often associated with acetylation of the histones near the gene. Acetylation adds an acetyl group to a lysine on histones, removing the positive charge on the lysine. Without the positive charge, the histones associate less strongly to DNA (the positive charge interacted with the negative charge on the phosphate group in DNA), resulting in a more open chromatin structure that is amenable to transcription.

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. A patient reports muscle cramps, diffuse weakness, and tingling in their hands and feet for the past two weeks. Blood test results show hypomagnesium (low serum magnesium), while urinalysis reveals above normal levels of magnesium. Genome sequencing shows a mutation in claudin 19. Through which pathway does magnesium pass across the epithelium in the kidney?

   1. Magnesium channel
   2. Transcytosis
   3. Paracellular diffusion
   4. Magnesium pump

   Show Explanation

   The mutation in claudin 19 suggests magnesium passes across the epithelium paracellularly because claudin 19 is a key component of tight junctions which regulate paracellular transport.

8. 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.

9. A 24-year old presents with muscle weakness and a tingling sensation in their hands. The patient reports stumbling frequently and having trouble running. A nerve conduction test in forearm reveals a velocity of 62 m/s (normal 50 - 50 m/s) but the electrode over the muscle measures a below normal amplitude. The gene for which motor portein is most likely mutated in the patient?

   1. MYH2 (skeletal muscle myosin)
   2. MYH11 (smooth muscle myosin)
   3. DYNC1H1 (dynein)
   4. KIF1B (kinesin)

   Show Explanation

   The lack of amplitude in over the muscle indicates a reduction in the amount of acetylcholine released by the axons after a stimulus. Kinesin transports synaptic vesicles from the neuron cell body to the axon terminus. A mutation that inhibits the activity of kinesin would reduce the number of synaptic vesicles at the axon terminus and lower the amount acetylcholine released.