Midterm answers, signal transduction, Fall 2000

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BL A512 -- Signal Transduction Fall -- 2000 -- Prof. Stark
Midterm Exam -- Tuesday, October 17 -- 98 points


1. Above is a diagram of a ligand gated G-protein signaling mechanism (Alberts et al., Fig 15-14B). For pedagogical reasons, it is greatly oversimplified. Suppose you are a college teacher presenting this material to undergraduates for the first time in anticipation of further developing the topic with more detailed diagrams. What are some of the first, most fundamental, things you would say about (a) the molecule to which the ligand binds and (b) the G-protein to prepare the students for that more detailed coverage? (3 points)

This G-protein-coupled receptor is a protein which crosses the membrane 7 times and is part of a superfamily; the visual pigment rhodopsin is the prototypical member of this family. (b) The G-protein is actually heterotrimeric, composed of alpha, beta and gamma subunits; alpha is activated when GTP replaces GDP, alpha activates the next molecule in the cascade and alpha ends its own activation with GTPase activity.

2. Above (Alberts et al., Fig. 15-1) is the figure used to introduce the "cell signaling" chapter. The top would easily apply to an example such as the beta adrenergic receptor. Describe the example given (so far this semester) of the mechanism for which the bottom diagram applies. Describe the molecular configurations of the signaling molecule and the receptor for that example. (5 points)

In the sevenless signalling pathway, boss (bride of sevenless) is the ligand. It is a 7 transmembrane protein on R8. Sev (sevenless) is dimerizes and each component crosses the membrane of the would-be R7 cell one time with a tyrosine kinase domain intracellularly

3. If this were a voltage-gated sodium channel, describe the molecular nature of the gating mechanism and what happens to this gating portion of the molecule prior to the open state. If this were a voltage gated channel (use Shaker as an example), describe the molecular nature of the inactivation mechanism (3 points) (from Fig. 11-22, Alberts et al.)

On the S4 transmembrane domain in each of the 4 components of the pseudotetramer, there are charged amino acids every 3 or 4 amino acids (and hence all lined up on one side of the otherwise hydrophobic alpha helix). This alpha helix rotates and moves to gate. There is a "stopper" (ball of amino acids) on the end of a "chain" (string of amino acids) on the N terminus that plugs the channel.

4. (a) What is this molecule? (Alberts et al., Fig. 15-6) (b) What is the precursor (in biological systems) of this molecule? (c) What enzyme splits this molecule off from its precursor? (d) What is this molecule converted to by the cyclooxygenase dependent pathway? (e) What drugs do people take to affect this step? (5 points)

(a) Arachidonic acid (C20:4 fatty acid) (b) a phospholipid (c) Phospholipase A2 (d) prostaglandin (e) COX (prostaglandin) inhibitors like aspirin, ibuprophen

5. What is the whole molecule (to the left) and the particular properties of that part of the molecule (to the right) to which the 4 cAMP molecules (circles) are shown to bind? What should be added to this diagram after the "+" sign? (Alberts et al., Fig. 15-24) (3 points)

Protein kinase A (PKA) (A-kinase); They are "regulatory" (inhibitory) subunits; the other 2 are the catalytic subunits

6. Here is a channel (Hamill and McBride 1995, Fig. 9) shown to interact with another membrane protein as well as some proteins housed intracellularly. What type of channel is this? What is dystrophin and how does it come to have that name? (3 points)

This is a mechanically gated channel. dystrophin is the protein affected in Duchenne (and Becker) muscular dystrophies, but it clearly has other functions (here related to its binding of actin)

7. Here is a picture of connexin-32 indicating mutations causing Charcot-Marie-Tooth disease. Draw a picture of how such proteins assemble in or near the membrane and describe what the function and name of such an assemblage of protein molecules is. (4 points) (Bergoffen et al., 1993)

Your picture would be one of a gap junction, with a patch on each cell of pores from one cell to another composed of hexamers of this protein in register from one membrane to the adjacent on

8. Here is gene product of the cystic fibrosis gene. What does it do to what ion? What is the NBF? (3 points) (Riordan et al., Fig. 7)

It is (half of a) chloride channel. nucleotide binding fold.

9. Shaker was cloned starting from the mutant. By contrast, the voltage gated sodium channel and the nicotinic receptor were cloned quite differently. How were these two cloned (starting how)? To which of these does shaker most closely compare (structure of the protein) and what is the major difference? (5 points) (Templ, Fig. 2)

sodium - Electrophorus, nicotinic - Torpedo (cloned based on abundance of gene product). shaker is a lot like the sodium channel except that it is 1/4 of the channel (a tetramer of shaker subunits makes up the channel) while all 4 subunits are in one big pseudotetramere of the sodium channel

10. Here (Jan and Jan Fig. 8) is a model we discussed, and it is replete with jargons, some of which you were exposed to repeatedly. Translate "GIRK." Give the pharmacological name of the Acetylcholine receptor shown. (4 points)

G for conductance, IR for inward rectifying, K for potassium; the muscarinic receptor is the major metabotropic acetylcholine receptor

11. What does this tell you about what kind of receptor in Paramecium? (3 points) (Eckert, 1972, Fig. 6, top right)

The line which closely fits the data as extracellular calcium ion concentration is changed suggests that the mechanoreceptive spike for anterior stimulation of Paramecium is well-described by the Nernst equation

12. What is trp? What is the InsP3 receptor? (2 points) (Fig. 2. B., Patterson)

trp is this calcium channel named after the transient receptor potential mutant affecting Drosophila phototransduction. The IP3 receptor is the closely linked calcium channel on intracellular stores gated by the intracellular ligand IP3

13. Here (Alberts et al., Fig. 11-34) is an activated neuromuscular junction. (a) What gates the channel marked "3" on the muscle cell membrane away from the neuromuscular junction. (b) Given the information that "4" is the transverse tubule, what is that channel? (c) Given the information that "5" is the calcium channel from the muscle's internal reservoir, what is the name of this reservoir? (3 points)

(a) a voltage gated sodium channel (b) calcium channel blocked by dyhydropyridine (c) sarcoplasmic reticulum

14. This (Wittinghofer, Fig. 2) is a schematic of the interaction of a receptor with another protein complex. (a,b) If it were a rod, what would the receptor and protein complex be called respectively? © If this were inhibitory, where would ADP ribosylation by pertussis toxin take place? (d) Why are 2, 3, and C cross-hatched? (4 points)

(a) rhodopsin, (b) transducin (c) Cys at C terminal of alpha of Gi (d) these are the receptor domains for G-protein activation

15. Calcium is coming in through a channel to what natural ligand? What keeps NOS near the NMDA-R? After NO leaves the cell, what is the main enzyme it affects? (3 points) (Snyder, 1992)

The NMDA receptor is for glutamate. A PDZ domain protein holds things together. It activates GC.

16. This snippit from the vertebrate phototransduction cascade (Poulans) shows GCAP. Where did the calcium come from? What process does calcium mediate in vertebrate phototransduction? In Drosophila phototransduction, what are the two sources of calcium? In Paramecium, what different calcium binding protein was found to be mutated in pantophobiac mutants? (5 points)

Calcium ions come in through the same cation channel that sodium ions come in through, that cGMP gated channel. It is involved in adaptation. In Drosophila, calcium ions come in through trp channels and a submicrovillar reticulum.Calmodulin

17. Here is a diagram of arrestin binding to rhodopsin subsequent to its activation by light (Jindrova, Fig. 2). (a) What had to happen to (b) what kinds of amino acids on (c) what part of the molecule on (d) what side of the membrane before arrestin binds? (e) What enzyme did this to rhodopsin? What enzyme would have done the same thing to the beta adrenergic receptor? (6 points)

Serines and threonines get phosphorylated near the C terminal inside the cell. Rhodopsin kinase. Beta adrenergic receptor kinase (BARK)

18. Here is the molecule that transducin activates in the rod. What is it? After transducin activates it, how is it different from this picture? In the rd (rodless) mouse, what is wrong with what part of this molecule? When it is normal, activated and functioning, it converts what to what? (6 points) (Farber, Fig. 1)

A phosphodiesterase for cGMP. the gamma subunits, which had been inhibitory, are removed. There is a point mutation in the beta subunit (also a retroviral insert in an intron). PDE (alpha-beta subunits) convert cGMP to 5'GMP

19. Here is "red vs. green" in the human opsin cloning paper (Nathans et al., 1986, Fig. 11 D). What are the black dots and how would their number compare for green vs. blue and green vs. rod rhodopsin? What is missing in these old figures of G-protein-coupled receptors in terms of membrane embedding? Luminal and cytoplasmic faces are shown. Where is the N terminal?(4 points)

Black dots are different amino acids. There would be more for any other comparison (since red and green are most closely related). Two cysteines near the C terminus are palmitylated, and those fatty acids are embedded in the membrane. Inside lumen is like outside cell, so inside lumen.

20. Here is a diagram of the olfactory transduction cascade, replete with jargon (Molday, 1996). What is CaM and what does it look like molecularly? What is CNGC and what does it look like molecularly? Fot the human, how many different R's are there, and how are these coded in genes and chromosomes? (6 points)

calmodulin is one protein, about 150 amino acids long, z-shaped, with 2 calcium binding sites on each end (top and bottom of z). Cyclic nucleotide gated channel looks a little like shaker (6 transmembrane domains, a pore liner) but with a cyclic nucleotide binding site.lots of receptors, each with a separate gene, and some chromosomal clustering of the genes

21. This snippit (from Kinnamon and Margolskee Fig. 2) shows a cAMP mechanism for sweet taste. How does this differ from how the cyclic nucleotides affect channels in rods. (4 points)

here, cAMP works through PKA, while in rods, cGMP is the ligand that gates the channel

22. Here is a diagram pertaining to ras (Alberts et al., Fig. 15.53). How does this GTP binding protein differ in its dealings with GTP/GDP from those of the alpha subunit of the heterotrimeric G-protein? (4 points)

Here, a GAP (GTPase activating protein is needed, while in the heterotrimeric situation, alpha has ist own GTPase ability. Here, a separate GNRP (guanine nucleotide releasing protein), namely SOS, is needed, where as in the heterotrimeric G-protein, that function arises through the interaction with the G-protein coupled receptor

23. Here is a simplified diagram of a hormone mechanism (Mangelsdorf et al., Fig. 2). If this were a steroid hormone, what are the major domains of its receptor? If this were a retinoid mechanism, about how big is the HRE and what is its configuration? (5 points)

There would be DNA binding, transcriptional activating and steroid hormone / inhibitor protein binding domains for the steroid receptor. For retinoids, something like a dimer of AGGTCA with a spacing of 1 to 5 nucleotides between

24. Describe the function of this metabotropic glutamate receptor in the taste receptor. (3 points) (Kinnamon and Margolskee, Fig. 2)

glutamate functions for taste stimuli such as monosodium glutamate as a probable 5th taste called umami


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