At 05:33 PM 11/1/99 -0800, you wrote:
>Dr. Stith, I have a couple questions on both exam one and exam two. I have just now gotten to correcting my exams, sorry for putting it off for so long. On all of my questions will you please address where my thinking is off or address my comments where appropriate.
>#1:Question #35 on the first exam. My understanding of what an imino group is, is a nitrogen bonded to three things and I thought these were used to stablize tertiary structure.
answer: The hydrogen of the imino group is involved in hydrogen bonding in an alpha helix (secondary structure). We showed and noted in lecture a picture of an alpha helix (secondary structure) that had hydrogen bonding (this is figure 3-6; note how the imino group is involved; its hydrogen forms the hydrogen bond with an oxygen from a carbonyl group). We also discussed in lecture various functional groups (you are right, the imino group has three things bound to the nitrogen, in a polypeptide, N would have a hydrogen and two carbons bound; note that amino group is where four things are bound to the nitrogen and the nitrogen has a positive charge).

>#2:Question #41 on the first exam. My answer to the question was: >"Reactions are coupled by using a common intermediate which makes the delta G prime of the overall reaction positive thereby making the non-spontaneous reaction spontaneous."
answer:The delta G prime for the overall reaction should be "negative"...

You added linking ATP hydrolysis after coupled.
answer: you did not state that ATP hydrolysis is the chemical reaction that is typically used to change a non-spontaneous reaction to a spontaneous reaction....so the two points off is appropriate.

>And I missed two points on this question. I have two questions about this, one, to the best of my knowledge not all reactions are linked to ATP hydrolysis so it seems limiting to put this in the answer.
answer: We made the accurate generalization that ATP hydrolysis is the chemical reaction that drives chemical reactions and this should be part of your answer...

The second question is that in the answer that you give in your key you referred to a "nonspecific reaction" and I don't know what this is. Are you meaning a nonspontaneous reaction or is this something else? answer: you got it; the key should read "nonspontaneous reaction"...this did not affect grading.

>#3:Question #38 on exam two. I thought that membranes kept enzymes apart that are in the same pathway so that the reaction can be better controlled.
answer: no

> Does this ever occur or are the enzymes of a particular pathway always kept together?
answer: to the latter statement, yes (see examples given in class; e.g., organelles are thought to exist to keep certain enzymes together because the enzymes all act in the same metabolic path).

>#4:Question #40 on Exam two. The question says these make up the membrane and have a sphingosine backbone. I chose glycolipid and ceramide and not sphingomyelin because I thought that sphingomyelin is not in the membrane but makes up the myelin sheath around neurons. Can you explain this please.
answer: Sphingomyelin is in membranes (see lecture notes, text); the myelin sheath is a series of closely spaced membranes. You could also have noted that they must be located in the same place since sphingosine is converted to ceramide, and ceramide is converted into sphingomyelin. You were close..

Good luck!
> I realize that I have asked several questions that may take some time to answer so please take your time and get back to me when you can. Thanks a

> ANOTHER SET OF QUESTIONS:
At 09:24 PM 11/6/99 -0700, you wrote:> >Dr. Stith, > >I've been working on the homework questions and have come across some >confusion.> >RE: Question #47 . . .I know that the three molecules which make up the >extracellular matrix are collagen, proteoglycans, and adhesive >glycoproteins. What I don't understand are their relationships to one >another as outlined in the "corrected figure 7.29" in the course packet.
ANSWER: I AM NOT SURE WHAT YOU MEAN BY "RELATIONSHIPS;" BUT NOTE THAT COLLAGEN AND PROTEOGLYCANS ARE CONNECTED TO THE ADHESIVE GLYCOPROTEINS. THE ADHESIVE GLYCOPROTEIN IS CONNECTED TO THE MEMBRANE PROTEIN.

>Q47 asks if these three molecules are connected to a membrane receptor. >Am I correct in assuming that only the adhesive glycoprotein is attached >to a membrane receptor? And is this membrane receptor the membrane >protein "integrin"?
ANSWER: YES, YES

> >Q47 also asks if the membrane receptor is connected to any intracellular >molecules. If integrin is indeed the membrane receptor in question, then >my answer is yes, it is connected to "talin", but not the microfilaments >below (?).
YES (THE MEMBRANE PROTEIN INTEGRIN IS INDIRECTLY CONNECTED TO THE MICROFILAMENTS). NOTE THAT OTHER PROTEINS BESIDES TALIN CAN BIND INTEGRIN (YOU MAY SEE THEM SHOWN IN DIFFERENT TEXTS)....BUT WE DID NOT DISCUSS THEM. >

>If you have the time, could you drop me a quick line to let me know if I'm >on track?
> GOOD LUCK! KEEP ASKING QUESTIONS....
ANOTHER MESSAGE: At 01:53 AM 11/10/99 MST, you wrote: >1. In class on Monday, you mentioned "steps" in development of membrane >potential. I know of only diffusion of K+ down chemical gradient in >combination with Na-K pump. What steps are you looking for to develop the >potential?
The steps that we went over in lecture is that there has to be a NaK pump to set up the chemical or concentration gradient for K. Then, since K is themost permeant ion, K moves due to this gradient. The positive K moves out of the cell due to the chemical gradient. a positive ion moving out means that the cytoplasm takes on a slightly negative charge.

>2. For action potential, do we need to know more than the fact that P of Na >becomes greater than P of K and therefore diffuses into the cell during the >action potential? That is all I found in my notes from class.
This is the basic idea we did not go into detail with the action potential (we noted that you could use the Nernst equation to estimate the membrane potential).

>3. Regarding the shipping pathways from Golgi out of cells: >a) Do only secreted vesicles and lysosomes leaving the cell exit the golgi?
The term is secretory vesicle. I do not understand your question. Both the sec. vesicle and lysosome are made at the Golgi, typically, only the secretory vesicle merges with the plasma membrane.

>b) What does mannose-6-phosphate label? Lysosomes/secretory vesicles/both? >Anything leaving the cell? I understand how and why it lables, just not >what it lables.
Mannose-6-phosphate is only found on acid hydrolases.

>c) Three "piles" that the golgi sorts to are lysosomes, s.v., and plasma >membrane bound protiens. Is this statement correct?
The Golgi sorts proteins that end up in the lysosomes from those proteins that end up in the secretory vesicle (the proteins in the sec. ves. are those proteins to be secreted or are membrane proteins).

> >Thanks for your help.
another email:
""Hi! I have a question regarding the Nernst Equation. First, could you tell me if I am following the correct logic. When calculating the direction and magnitude of pure, simple diffusion, we calculate the theoretical membrane potential, Ek, and then subtract this from the true membrane potential, usually -0.06 volts. The value we receive is the electromotive force, the direction and magnitude of pure simple diffusion. However, if this is all correct, I do not understand the determination of the direction after this point. For a positive ion, if the EMF is positive, then the ion moves out of the cell? ""
Yes; for example, if you calculate an EMF of +20 mV, the number 20 gives you the magnitude and the fact that it is plus means that a positive ion like K+ will be pushed out of the cell by the electrochemical gradient.

""This is what I wrote down in class, but doing the problems in the homework and the book, it seems that the contrary is true."" See me about specific problems.

""If you would please explain the determination of the direction of pure, simple diffusion, I would be very grateful!!""
Pure simple diffusion is movement due to the electrochemical gradient (interfusion) and any convection (remember, most cells have no convective water movement across their plasma membrane so we ignore convection). So, we can use delta G inward (is it a negative number? if so, then pure simple diffusion is going to push the ion into the cell) or the Nernst equation to determine the direction of pure simple diffusion. For the Nernst equation, if you calculate a positive number for the EMF for an ion, then the force of pure simple diffusion is going to push the ion outside the cell.
Dr. Stith > >