Questions about Cell Biology Exam Questions from CELL BIO STUDENTS:
>""Dr. Stith,
>I have a question regarding the last exam. There is a question that I got
wrong, but I don't understand why.
Question 14. T F Since carboxypeptidase A has a Zinc atom, it uses an
electrophilic substitution reaction.
I marked True. I know the primary substitution is nucleophilic, but was also
under the impression that an electrophilic reaction takes place because of the
following from the course packet: "The zinc acts as an electrophile (like
negative charge) but it is not the attacking group."
Did I misinterpret this wording?
Thanks for reviewing my question.""
Dr. Stith's response: The attacking group for carboxypeptidase A is glutamic
acid. It has a negative charge; thus, the substrate has to have a (partial)
positive charge (the carbon atom of the peptide bond). So, if the enzyme is
negative and it loves a positive substrate- the reaction is nucleophilic (philic="loves"
and "nucleo"= like a nucleus, has a positive charge). Zinc is not the attacking
group.
So what does zinc do? It forms a weak ionic bond with the partially negative
oxygen atom of the bond to be broken (the peptide bond). It does not attack the
peptide bond and break it but merely pulls on it and stretches the peptide bond
(this weakens the peptide bond to be broken- or lowers the Ea; this is the idea
of induced fit model for enzymes). This ionic bond is formed because zinc is an
electrophile (it is positive and likes negative charges). Negative ions are
nucleophiles. A different enzyme could use zinc as the attacking group to break
a bond (because the positive charges of functional groups of amino acids are not
strong enough), in this case, the reaction would be an electrophilic
substitution. However, carboxypeptidase A does not use zinc as the attacking
group to break the peptide bond.
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30. T F Moving a sodium atom from an area of negativity, to an area of positive charge would require electrical, not chemical, work. In opposition, movement of the sodium in the opposite direction could do work.
STUDENT QUESTION:
For question #30 - I put false as the answer however I am confused as to why it is true. I was thinking that if sodium is going from a negative area to a positive area this is going up its concentration gradient so it requires energy or chemical work by ATP. And then if sodium moves from and area of positivity to an area of negativity this does not include chemical work but it does have to potential to set up an electrical gradient that could do work. Am I thinking about this right?
BELOW, I WILL TRY TO REVIEW ALL PERTINENT FACTS (SOME OF WHICH YOU PROBABLY KNOW). I AM USING CAPS TO DIFFERENTIATE BETWEEN YOUR QUESTION AND MY ANSWER.
CHEMICAL (ALSO CALLED CONCENTRATION BUT NOT REALLY CORRECT TERM; SEE ELECTROCHEMICAL GRADIENT WHERE CHEMICAL GRADIENT IS REFERRED TO) GRADIENTS REFER ONLY TO GRADIENTS WHERE YOU GO FROM HIGH TO LOW (OR LOW TO HIGH) CONCENTRATION OF AN ION LIKE SODIUM, OR AN UNCHARGED MOLECULE LIKE GLUCOSE. SO YOU WOULD HAVE TO DO CHEMICAL WORK TO MOVE SOMETHING FROM LOW TO HIGH CONCENTRATION, BUT WORK CAN BE DONE WHEN SOMETHING MOVES FROM HIGH TO LOW CONCENTRATION.
NOTE THAT THE QUESTION DOES NOT GIVE YOU ANY INFORMATION ABOUT THE CHEMICAL GRADIENT FOR SODIUM SO YOU HAVE TO IGNORE CHEMICAL WORK. IN FACT, THE QUESTION NOTES THAT YOU ARE NOT REFERRING TO CHEMICAL WORK.
SO, CONTRAST THIS CHEMICAL WORK TO ELECTRICAL WORK. WHEN A POSITIVE ION LIKE SODIUM MOVES FROM AN AREA WITH A NET NEGATIVE CHARGE (LIKE THE CYTOPLASM) TO AN AREA WITH A NET POSITIVE CHARGE (OUTSIDE THE CELL), THEN THIS MOVEMENT REQUIRES ELECTRICAL WORK (THE MOVEMENT IS NOT SPONTANEOUS, MUST BE DRIVEN WITH ENERGY).
HOWEVER, WHEN POSITIVE SODIUM MOVES FROM AN AREA OF EXCESS POSITIVE CHARGES (NET POSITIVE CHARGE), TO AN AREA WITH NET NEGATIVE CHARGE, THEN THE MOVEMENT CAN ACTUALLY PERFORM WORK (AND THE MOVEMENT IS SPONTANEOUS).
SO ALL STATEMENTS IN THE QUESTION ARE TRUE.
31. T F Moving sodium from a region where sodium concentration is 20 mM to a region with 100 mM sodium, would require only chemical work (there is no potential difference between the two regions).
STUDENT QUESTION: For question #31 - I put false as well because I was thinking that to go from 20mM to a region with 100mM is against the concentration gradient thus yes it requires chemical work but also if the concentration of Na in the cell 20mM and the concentration of Na outside of the cell is 100mM this does set up a potential difference between the two regions. Inside the cell would be negative and the outside would be positive. So wouldn't the answer be false?
NO, AS NOTED IN THE QUESTION, THERE IS NO POTENTIAL DIFFERENCE BETWEEN THE TWO "REGIONS." I USED THE TERM REGIONS, SO THERE IS NO CELL INVOLVED.
IF A CELL WAS INVOLVED, THE POTENTIAL DIFFERENCE ACROSS A CELL MEMBRANE IS DUE TO THE EFFLUX OF POTASSIUM; SODIUM IS RELATIVELY IMPERMEANT AND SO WOULD NOT GENERATE A MEMBRANE POTENTIAL (THE RELATIVE PERMEABILTY CHANGES OF COURSE DURING AN ACTION POTENTIAL).