Final Exam Biochem 811                                          
Dr. Nelson's Lectures   Dec. 13, 1996

There are eight questions, one on each lecture.  Each question is worth 3 points.

1) Describe the Q cycle.  Please include the following:
	Where do electrons enter?
	Where do electrons exit?
	What happens to the protons of reduced ubiquinone (CoQH2)?

Electrons enter at the P site, near the cytosolic side of the membrane.  Ubiquinone 
(CoQH2) binds to this site that already has a second oxidized ubiquinone (CoQ) tightly 
bound.  Protons are releasedto sites on the protein.  An electron from the new ubiquinone 
is donated to the tightly bound ubiquinone so they both become semiquinones (CoQH.).  
These simultaneously release their electrons, one goes to the Rieske iron sulfur center, then 
on to cytochrome c1, the other goes to the BL heme, then to the BH heme and finally it 
reduces a completely oxidized ubiqinone (CoQ) bound at the N site.  This forms a 
semiquinone (CoQH.) that stays bound until another cycle reduces it again to form CoQH2 
which is released.  The energy release from electron movement is used in pumping the 
protons across the membrane against the proton gradient.

2) The gamma subunit of the ATP synthase has an asymmetric structure.  Why is this 
important in the binding change mechanism of ATP synthesis?

The three conformations of the catalytic subunits are induced by rotation of the F1 ball 
about this asymmetric subunit.  If it was not asymmetric the mechanism would not 
function.

3) Describe the similarities between photosystem I and photosystem II.

Both have two subunits that carry all the electron transferring groups.  These include the 
special pair of chlorophylls (P680 in PSII and P700 in PSI).  Both systems transfer the 
electrons released by light to a second cholorphyll (pheophytin in PSII) then to a quinone.  
Both have a centrally located iron, though it is not an iron-sulfur center in PSII.  

4) The four reactions shown below are the first four steps in the fungal lysine biosynthetic 
pathway.  What other major pathway begins with these same four reactions, with a slightly 
shorter starting compound?

I was looking for the TCA cycle, but the last part of leucine biosynthesis is also acceptable.  
Two people answered the alpha ketoglutarate pathway of amino acid biosynthesis, or 
glutamate biosynthesis.  I will assume that they meant the synthesis of alpha ketoglutarate 
in the TCA cycle.

5) Plants and bacteria make all their amino acids, with about 84 enzymes involved in the 
process.  Mammals make about ten amino acids (depends on the species) and some of these 
are by salvage pathways that are not the normal plant or bacterial pathways.  These 
pathways are very short, using only 12 or 13 enzymes.  How can pharmaceutical or 
agrichemical companies take advantage of these missing pathways in mammals?

Drugs can be made targetting the missing pathway enzymes to be used as antibiotics or 
herbicides.  These drugs will be less likely to affect mammals since they don't have these 
enzymes.

6) Why are there many more metabolic diseases caused by defects in amino acid 
degradation than are caused by defects in amino acid biosynthesis?

The accumulation of amino acids can be harmful because they are often neurotransmitters.  
The breakdown products of amino acids can be toxic (phenylpyruvate inhibits pyruvate 
dehydrogenase).  Missing amino acids can be obtained in the diet and failure to make them 
is not that serious. 

7) Hsp70 proteins from gram negative bacteria and eukaryotes show a distinctive insertion 
of about 20-24 amino acids.  Archaea do not have this insert.  This and other observations 
like it have prompted Gupta and Golding to propose that eukaryotes arose by a fusion of 
Archaea and gram negative bacteria.  Give one alternative explanation for the presence of 
the insertion, assuming that eukaryotes evolved from an Archaeal ancestor.

The long form of the Hsp70 gene may have been donated to the eukaryotic host from the 
mitochondrial endosymbiont, a gram negative bacterium.  The gene could have been 
transferred after Archaea and bacteria split by a lateral gene transfer.

8) What is the homeobox?  What does it code for and why is it important?

The homeobox is a 180 base pair sequence that is conserved in homeobox genes.  It codes 
for a 60 amino acid domain that folds into an helix turn helix structure that binds DNA at 
specific sequences.  The homeodomain targets proteins to genes to regulate their 
expression.

9) This is an extra question for your entertainment.  It is worth 
zero points and does not have to be answered.  What famous 
person's head looks like this view of the F1 portion of the ATP 
synthase?  (Answers will be compiled and posted on the 
Biochem 811 page).

Ten people answered the question
Most popular answer     Einstein (3 votes)
Most original answer     Mitochondrial Eve
Other suggestions          Shirley Temple, George Washington, Gerry Garcia, Big Bird, 
Betty Boop, John Lennon
Faculty guesses       Whoopie Goldberg, Jimi Hendrix, Jim Morrison