Assignment #2 BIO504f14 metabolic integration and overviews Due November 19th 2014 Prelude: For each question, produce an answer as requested, paying attention to significant figures and units requested. These questions all involve some pathway overviews. For each produce an “overview sketch” giving key intermediates ONLY and “energetically relevant compounds” (ATP, NADH, FADH) and processes (H+ flow, FoF1) in schematic only. As you will see below, generally there are several questions per sketch; or you could potentially (and perhaps better) produce one sketch for all or several sections. It is up to you. Be creative and professional, as well as clear and explanatory. You must justify your answer with brief calculations and reference to the above sketches. Simple unjustified answers, correct or not, will not receive full credit. The point of this exercise is to examine HOW these solutions are arrived at, so that you can better understand what is happening inside oyu and inside any organism - and so you are better prepared for exams. Produce a single PDF file and submit on BB as usual, as well as well as in hard copy, except non-local -02 section who are exempt from hard copy requirements copy. Local -02 students should submit hard copies. Be sure each numerical answer is easy to find. To facilitate numerical grading you must ALSO enter your numerical values into a separate assignment that will be put up as the due date nears. The questions: On midterm 2, you were asked to examine the conversion of glucose to fat. Do that here again, more precisely (i.e. with exact values for FW, G, R etc.). You should look at the solution, but then produce your own sketches and calculations. 1. 1.00 g glucose is converted to palmitic acid. How much glucose is obtained? 2. How much does this process cost or produce? Give this in three ways: i. in terms of ATP and reducing equivalents (NADH and FADH; i.e. do NOT convert these to ATP), ii. Convert the reducing equivalents to ATP using the known vertebrate ETC - FoF1 stoichiometry, and then give an answer in J under standard state conditions. For part ii, we get the energy involved in this process, using the known Go’ for ATP. However, in the body [ATP], [ADP] and [Pi ] are NOT at standard conditions, so the actual free energy G of ATP is significantly higher than Go’. Utilize the values [ATP]=2.00 mM, [ADP]=0.200 mM, [Pi]=1.00 mM, and then calculate: iii. What is the actual free energy G for the hydrolysis of ATP under these physiologically relevant conditions? iv. use this value to calculate the actual energy yield in J under these conditions Now examine the reverse process, conversion of 1.00 g palmitic acid to glucose. 3. What kinds of organisms can do this, and what kinds cannot? 4. How much glucose is obtained? 5. How much does this process cost or produce, once again expressing in both: i. ATP and reducing eq ...

1. Assignment #2 BIO504f14
metabolic integration and overviews
Due
November 19th 2014
Prelude:
For each question, produce an answer as requested, paying
attention to significant figures and units
requested.
These questions all involve some pathway overviews. For each
produce an “overview sketch” giving key
intermediates ONLY and “energetically relevant compounds”
(ATP, NADH, FADH) and processes (H+ flow,
FoF1) in schematic only. As you will see below, generally there
are several questions per sketch; or you
could potentially (and perhaps better) produce one sketch for all
or several sections. It is up to you. Be
creative and professional, as well as clear and explanatory.
You must justify your answer with brief calculations and
reference to the above sketches. Simple
unjustified answers, correct or not, will not receive full credit.
The point of this exercise is to examine

2. HOW these solutions are arrived at, so that you can better
understand what is happening inside oyu and
inside any organism - and so you are better prepared for exams.
Produce a single PDF file and submit on BB as usual, as well as
well as in hard copy, except non-local -02
section who are exempt from hard copy requirements copy.
Local -02 students should submit hard copies.
Be sure each numerical answer is easy to find. To facilitate
numerical grading you must ALSO enter your
numerical values into a separate assignment that will be put up
as the due date nears.
The questions:
On midterm 2, you were asked to examine the conversion of
glucose to fat. Do that here again, more
should look at the solution, but then produce
your own sketches and calculations.
1. 1.00 g glucose is converted to palmitic acid. How much
glucose is obtained?
2. How much does this process cost or produce? Give this in
three ways:
i. in terms of ATP and reducing equivalents (NADH and FADH;
i.e. do NOT convert these to

3. ATP),
ii. Convert the reducing equivalents to ATP using the known
vertebrate ETC - FoF1
stoichiometry, and then give an answer in J under standard state
conditions.
For part ii, we get the energy involved in this process, using the
However, in the body
[ATP], [ADP] and [Pi ] are NOT at standard conditions, so the
[ADP]=0.200 mM, [Pi]=1.00 mM, and then calculate:
iii. What is the ac
under these physiologically
relevant conditions?
iv. use this value to calculate the actual energy yield in J under
these conditions
Now examine the reverse process, conversion of 1.00 g palmitic
acid to glucose.
3. What kinds of organisms can do this, and what kinds cannot?
4. How much glucose is obtained?

4. 5. How much does this process cost or produce, once again
expressing in both:
i. ATP and reducing equivalents
ii. J (under physiological
2.iv)
The primary purpose of moving glucose to fat is to store excess
food for later. (We also need some fatty
acids for structural purposed for our membranes). We may
examine the efficiency of this process. First,
how much energy is obtained without storage, using glucose
directly:
6. How much energy is obtained from the complete metabolism
of 1.00 g glucose to CO2 via
glycolysis – TCA – ETC – FoF1 ? Go all the way to ATP here,
and express this in J under physiological
conditions as in parts 2.iv or 5.ii above.
You may note that this value, and other values later in the
assignment, are slightly
different than various values you may have been told in the past
or may see in
various places. There are two major reasons for this:
processes (i.e.

5. ‘shuttles’) that are need to move the various metabolites in and
out of the
cell and the mitochondria. I will entertain the possibility of
bonus points for
anyone wishing to look these up and incorporate them into your
calculations.
misunderstood until
recently. The determination that there are 8 c subunits was only
done in
2010 (Watt et al., 2010) and many textbooks still utilize an
erroneous value
of 9 or 10.
Watt, I.N., Montgomery, M.G., Runswick, M.J., Leslie, A.G.W.,
and Walker, J.E. (2010). Bioenergetic cost
of making an adenosine triphosphate molecule in animal
mitochondria. Proc. Natl. Acad. Sci. 107,
16823–16827.
Now consider the conversion of this same 1.00 g glucose to
palmitic acid, then its metabolism to CO2 i.e.
the same process as above, only with a ‘detour ‘ to fat:

6. glycolysis – fatty acid biosynthesis – fatty acid
-oxidation - TCA – ETC – FoF1 ?
7. How much energy is obtained in this case (J; physiological)?
8. What is the energy efficiency of fat storage in this case?
Now compare this to the use of this process for C storage.
Imaging 1.00 g glucose, being converted to
palmitic acid, and then moved back to glucose (for those
organism that can do this).
9. How much glucose is obtained (g)? (this is not quite the same
question as #4 – but not far off)
10. What is the C efficiency (i.e. moles of C returned/moles of
C initial)?
11. How much energy is used/produced in this process in terms
of
i. ATP and reducing equivalents.
ii. J (converting reducing equivalents to ATP, and then under
physiological conditions)
That initial 1.00 g glucose represents some amount of energy
(you did this already in #6). When it is
moved to fat and back, we lose not only C, but we also lose
whatever energy equivalent that amount of
glucose that was not returned represented. This is combined
with whatever energetic consequences this

7. conversion has (you did this already in #11.ii) to produce an
overall energy balance for this process.
12. What is the net cost/benefit of this process energetically,
taking into account both the loss of C
and its energy equivalent; as well as the energy consequences of
the process.
13. Produce a graphical representation of the conservation of
both energy and C for this process of
fat as a storage compound. You have considerable latitude here,
but do something simple,
professional, as well as clear and explanatory.
Photosynthesis
14. How many photons does it take to produce 1.00 g of glucose
(assuming no photorespiration)?
15. What fraction of these photons must be absorbed by PSI,
and what fraction by PSII?
16. What is the energy value of these photons?
17. Compare this to the energy content of that glucose (i.e. #6
above) to get a figure for the “Energy
Efficiency of life on Earth”
Photorespiration is a so-called “wasteful” process in which O2
reacts with ribulose-bis-phosphate to
ultimately un-fix CO2. It has some cost in terms of ATP and

8. NADPH. We also need to consider the cost of
re-fixing that lost CO2 (via the regular Calvin cycle) to
completely “get back even” and so measure the true
cost of this photorespiration.
18. If photorespiration occurs at the rate of 10% of CO2
fixation (i.e. RUBISCO reacts with one O2 for
every 10 CO2 molecules) how many photons are absorbed in
total to make 1.00 g glucose? (You
need to figure out how many photons are needed to produce the
ATP and NADPH needed to do
both photorespiration recovery and the CO2 fixation)
19. How does this affect the efficiency of life now? (i.e. revise
#17)
20. Is the PSI/ PSII ratio changed?
The C4 pathways (there are several – pick one) are ways to
ameliorate this problem by pumping CO2 (but
not O2) to a location or time inaccessible to O2, and so largely
eliminate photorespiration. However, this
costs extra ATP and/or NADPH.
21. How much photorespiration must occur to make the extra
cost of C4 metabolism worthwhile?

9. Note that this does not take into account the cost of building the
infrastructure necessary to conduct C4
metabolism (distinct new tissue types, regulatory apparatus, and
transport systems).