Final Flashcards
Lysosomes contain pump proteins that when activated transport protons against proton concentration gradients. Alpha-Galactosidase A is a soluble enzyme found in the interior of the lysosome. The enzyme catalyzes the hydrolysis of melibiose (which is a disaccharide) into galactose and glucose. Where does the synthesis of the two proteins occur? Justify your answer.
Both proteins are synthesized in the RER. The RER is responsible for synthesizing proteins used outside the cell, transmembrane proteins, and also the: RER, golgi, SER and lysosomes. The pump protein (transmembrane protein) and the enzyme that breaks down sugar (soluble protein) are made in the RER.
Integrins mediate the adhesion of cells to their substratum (or to other cells) and the transmission of signals between the external environment and the cell interior. Signaling can occur in an inside-out direction, or in the opposite direction.
a. What is the difference between inside-out and outside-in signaling?
b. what is the role of integrin in each process?
c. Example of either signaling.
a. In inside-out, the signal is initiatied in cytoplasmic region causing activation of the integrin protein that relays the message to extracellular matrix.
For outside-in, the binding of the extracellular domain of integrin to ligand can induce a conformational change at the opposite end. Changes here can alter the way the integrin interacts with many different cytoplasmic proteins, modifying activity.
b. integrin is the mediator in these processes
c. Outside-in signaling: can induce conformational change in talin on the inside of the membrane, initiating a cascade of events leading to the polymerization of actin filaments of the cytoskeleton.
The drawing below shows a transmembrane protein. The protein has a group of aspartate and glutamate residues at the C terminal end of the alpha helix, and a group of lysine and arginine in the N terminal end of the alpha helix.
a. Draw the correct orintation.
b. Explain how the orientation of the protein is determined. In your answer, be sure to explain, how does the chemical characteristics of the translocon help to orient the protein and how the protein is finally translocated into the rough ER membrane.
The correct orientation of N to C needs to be labeled with the protein going through the translocon. The explanation in part b needs to include something about opposite charges attracting or how the charges of the translocon orients the protein. A complete answer will have something about how the hydrophobic residues are translocated either in writing or shown via the drawing.
Insulin is a peptide hormone that contains 51 amino acids. The islets of Langerhans in the pancreas are responsible for the production and secretion of insulin. Describe the steps that occur between the time a ribosome attaches to an insulin mRNA and the time the protein leaves the RER
Insulin mRNA binds to the ribosome and then a signal sequence of hydrophobic residues is translated and attracts the Signal Recognition Particle (SRP). The SRP brings the ribosome/mRNA complex to the RER membrane and docks the complex at a translocon. Inside the RER, chaperone proteins help fold the protein and the protein is packaged in vesicles to be sent off to the golgi.
- Distinguish the structural differences and similarities between a hemidesmosome, desmosome, and an adherens junction. Also explain the function of each of these structures
ALL: involved in cell adhesion, structural integrity and signaling/communication
Both: contain a dense plaque on inner surface of PM with keratin filaments to connect to others. Composed of intermediate filaments
hemidesmosomes: site of interaction between a cell and the underlying basal lamina. Resemble half a desmosome.
desmosomes: site of interaction between two cells. used for mechanical stress
Adherens junction: composed of actin filaments. involved in cell to cell interactions
Describe how membrane asymmetry is maintained as the membrane moves from the ER to the plasma membrane. Include in your answer how proteins orient correctly in the correct orientation as it moves through the membrane and how the lipids and the proteins of the membranes are established and maintained.
For proteins membrane asymmetry is initiated in the ER (from where all membranes originate.) The correct position of the integrate proteins is set up when the protein is co-translated-translocated in the translocon and this orientation is maintained through the movement of the protein in the endomembrane system because the chemical characteristics of the lumen of the rough RE, vesicles lumen of the Golgi and the extracellular space is the same.
It was noted that two different autoimmune diseases can cause severe blistering of the skin. However, one of the two diseases produce antibodies against a component of hemidesmosomes, while the other produces antibodies against a component of desmosomes. Why do you think these two conditions have such similar symptoms?
Both types of adhesive junctions are important in maintaining the integrity of an epithelium. Hemidesmosomes are important in holding the layer to the underlying substrate and desmosomes in holding the cells to one another. Autoimmune disease in in the desmosome or the hemidesmosomes will compromise the integrity of these two structures which lead to the detachment of the cell to the substratum or cell where the hemidesmosome and desmosome must be attached causing epithelial tissue to easily blistering of the tissue with moderated mechanical stress.
List the structural characteristics and at least one function of collagen, proteoglycan, fibronectin, and laminin
Collagen: three a helix wound around each other to form rod-like triple helix bound by H+ bonds. These align in rows that stagger to form fibers held by covalent bonds
function: mechanical properties of the fiber, withstanding mechanical stress
Proteoglycans: core protein w/ lots of glycosaminoglycan chains consisting of repeating disaccharide. Then assemble by linking proteins to hyaluronic acid
function: negative charges to attract H2O to regulate extracellular matrix viscocity
Fibronectin: two similar polypeptides joined by disulfide bonds in c-terminal. Each is composed of a linear series of distinct fibronectin domains containing RGB sites to bind collagen or peptidoglycan
function: cell migration and embryonic development
Laminin: consist of three diff polypeptide chains linked via disulfide bonds and organized into cross-like structure
function: involved in migration
The pH of the fluid inside the intestinal lumen is extremely low and if it leaks through the intracellular space of the tissue it could destroy the cement created by the adherent junction, which establishes the apical and basal domain of the cells. What structure do epithelial cells use to prevent the destruction of the adherent desmosomes?
desmosomes tight junction must be found in the apical domain of the cell, the barrier of these structure will avoid the leakage in between these cells avoiding contact with the adjacent or desmosome junctions
Scurvy is a disease that results from a deficiency of vitamin C (ascorbic acid) and is characterized by inflamed gums and tooth loss, poor wound healing, brittle bones, and the weakening of the lining of blood vessels, causing internal bleeding. It has been found that patients with scurvy have problems in their collagen fiber of the ECM. Describe the structural organization of the collagen fibers and explain how the absence of ascorbic acid affects collagen at the molecular level.
A collagen molecule is composed of three alpha helixes that are wound around each other to form a rod-like molecule triple helix. The alpha helix of the collagen molecule contains many proline and leucine residues that are hydroxylated. The hydroxylation of these residues is used to hold together the three alpha helixes with hydrogen bonds which stabilized the triple helix. Vitamin C (ascorbic acid) is a coenzyme of the enzyme that adds the hydroxyl group to proline and lysine. Therefore, if vitamin C is not present the triple helix of collagen won’t be stable and it will cause the weakness of this extracellular protein.
Describe two mechanisms in which energy is utilized to move ions and molecules against their concentration gradient.
1- Active transport- In this mechanism molecules of ATP serve as the source as energy to move molecules using a pump.
2- In the case of co-transport the potential energy of the sodium ions is used as they move from high concentration to lower concentration to transport molecules against their concentration gradient.
You are exploring a rather inhospitable planet, which has seas that are somewhat hydrophobic in nature. Surprisingly, there are living organisms in the seas whose cytoplasm is hydrophobic to a similar degree. These organisms have membranes made primarily of phospholipids arranged in a bilayer.
a. What is the most probable orientation of these phospholipids?
b. In these extraterrestrial cells, how would you expect this new condition to affect a transmembrane protein in regards to its extra cellular domain, cytoplasmic domain, and inner membrane?
A-The polar heads of the phospholipids face toward the middle of the bilayer with the hydrophobic fatty acid tails facing outward.
B-The transmembrane domain of the protein will be hydrophobic and the extracellular and cytoplasmic domain will be hydrophobic
2- How might a stealth liposome be prepared so that it could potentially be used in the treatment of a tumor whose cells have a protein called tumor cell antigen (TCA) in their membranes? This protein (TCA) is not found at all in normal cells.
a. Describe how you will design your liposome so it could deliver a toxic drug that will kill the tumor cells without affecting healthy cells. In your design, explain how you will specifically target the tumor cell (be specific) (5 points)
b. How will you protect the stealth liposome from destruction by immune cells. Mention the name of the molecule. (5 points)
c. Explain where the drug will be found in the stealth liposome if the drug is hydrophilic vs hydrophobic. (5 points)
Solution:
1- TCA protein is unique to these tumor cells an antibody against that proteins should be made.
2- Inserted the antibody in the membrane of the liposome.
3- In the toxic drug is hydrophilic then it must be deposited in the aqueous part of the liposome.
4- If the drug is hydrophobic it must be inserted in the inside if the inner membrane.
5- To avoid that the degradation of the liposome by the immune system a coat of polythene glycol will be added over the membrane.
3- You determine the transition temperatures for two membranes. The first has a transition temperature of 28°C, the second has a transition temperature of 15°C.
a. What can you conclude about the compositions of these two membranes? (5 points)
b. Explain two mechanisms of membrane remodeling (that does not involve new synthesis of lipids if the temperature decreases from 28°C to 15°C. In your answer mention the enzymes involved in this process. (5 points)
A- At 28oC will have more saturated fatty acids than the 15 oC (alternative correct answer they could answer the following At 28oC will have more longer fatty acids than the 15 oC.)
B- -Desaturases will add double covalent bonds to the fatty acids.
-phospholipases will cut the fatty acids tails and acyl-transferaces will re-shuffle them.
4- Parietal cells are responsible for increasing the acidity in the stomach during food digestion using a H+/K+ ATPase pump.
a. Explain the process by which this pump is activated (5 points)
b. How the pump functions and
c. How the initial activation of the pump could be inhibited. (5 points)
A- The pump is activated when histidine bind its receptor causing the vesicles that contains the pumps. Fuse with the cell membrane of the parietal cell inserting the pump in the cell membrane. Once in the membrane the pump start working.
B- The pump moves H+ ions outside of the cell and bring in K+ ion inside the cell.
C- Drugs that bind the histidine receptor will inhibit the initial activation.
5- Look at the hydropathy plot of the protein connexin in the figure below and determine.
a. How many transmembrane domains are indicated for the protein connexin in the plot? (2.5 points)
b. How the values plotted in this graph. were calculated (2.5 points)
c. If any transmembrane domains contain charged amino acids, where do you expect to find them within the membrane. (Be specific). (2.5 points)
A- Three transmebrane domains (If a student said 2 I will give it the points because when I reduced the size of the figure it made difficult to clearly distinguish the one of the peak) If a student said 4 that will be incorrect.
B- By making an average of the of the hydrophobicity of group of three amino acids.
C- At the very end of the alpha helix.
Note: Use Figure A, Table B, Figure C, and Table D to answer these questions.
a. Explain what changes in the membrane must take place in a lymphocyte that has aged to the point in which it does not function properly and must be targeted for degradation (5 points)
b. Your answer should include: the lipid translocating enzyme that must be activated to accomplish this change. (5 points)
A- Phosphatidylserine must be flip from the inside to the outside.
B- Scrablasses will move them.
7- Which of the four 20 amino acid sequences listed below in the single-letter amino acid code is the most likely candidate to form a transmembrane region (alpha helix) of a transmembrane protein. Explain your answer.
A. ITEIYFGRMAGVIGTDLLIS
B. ITLIYFGNMSSVTQTILLIS
C. LLKKFFRDMAAVHETILEES
D. LLLIFFGVMALVIVVILLIA
D is the correct answer because all the amino acids are hydrophobic with only
Aquaporins are channel proteins that facilitate the movement of water molecules across the plasma membrane. It is important that for this protein to be effective, it must be extremely selective for water. Explain what would be the physiological consequence to the cell and proteins if residues 203 AND 68 are mutated on aquaporin.
if the amino acid is mutated for a another positively charge amino acid it will not cause changes in the function of this channel proteins
9- KcsA is a prokaryotic potassium channel. If a mutation is introduced in the sequence of the portion of DNA that encodes the region for the selectivity filter.
A) Predict what will be the consequence on the function of this channel if this mutation causes a decrease in the width of the selective filter from 0.134 to 0.096 nM.
B) Explain your answer.
NOTE. The width of both ions are K+ 0.133nM and NA+ 0.095nM.
Reducing the width of the channel will allow now NA+ to interact with the 4 oxygens of the channel which will allow them to cross the membrane.
9- Explain how cells deal with small tonicity (osmolarity) changes in their environment. (5 points)
By Allowing ions toc cross the membrane to counteract these changes in osmolarity.
10- Assume that you are measuring the diffusion rate of a group of membrane proteins by exposing the cell to a cancer drug to determine whether the cell will experience a dramatic change in the movement of proteins after treatment with the drug.
a. What technique you will use (1 point)
b. Explain what steps need to be done to perform this study (4 points)
A- The technique is FRAP.
B- 1) Proteins are labeled with florescence dye. 2) photobleach spots with laser beam 3) measure the rate of recovery in the region that was photobleached.
11- Describe the characteristics of lipid rafts, how they have been observed, and why some researchers are concerned that they don’t exist in cells in vivo.
It is a region with specific composition of proteins and lipids that is more gelated and highly ordered than surrounded regions.
The vast majority of these regions have been produced and study in in-vitro after unnatural processes have been used to create the region while attempts to study in living cells are usually unsuccessful.
12- You are studying a protein that you believe works as a secondary active transport in cells lining the small intestine. Previous data suggests that the protein assists glucose in entering these cells against its concentration gradient using sodium ions as a source of energy.
A- Design an experiment to isolate this protein. What type of detergent you will use and explain why. (5 Points)
B- Describe how you will create a liposome, so you can test this protein. (5 points)
C- Explain how you will obtain the lipids that you need to create the liposome. Explain, why this is important. (5 points)
D- How would you maintain the flow of Na+ ions going through the cell. Explain why this step is important. (5 points)
E- Glucose is moving against its concentration gradient, explain where the energy for this movement will come from. (5 points)
1- The cell is expose to an non-ionic detergent do avoid the denaturalization of the protein.
2- The complexed of proteins and detergents are used to purify the protein of interest
3- The micelles of detergent and membrane lipids are saved because the specific lipid composition could be required for the proper function of the protein.
4- Micelles of detergent/lipid are added to the purified protein of interest and the detergent is remove. At this point the function protein could be tested.
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D- A high concentration of NA+ is created in the environment
E- Secondary active transport requires ions to move in favor of concentration gradient to provide the energy that will allow glucose to move against its concentration gradient
