Answer Key
Metabolism and Biochemistry
1. Name three proteins that require ATP in order to function properly and their
roles in the cell. You may need to search through your text to find examples.
There are many, many answers. A few examples:
The sodium/potassium pump that makes it possible for neurons to send signals
to other cells (and is vital in other cells as well).
The myosin ATPase that allows our muscles to contract.
Aminoacyl-tRNA-synthetase, which sticks amino acids to tRNA and makes
translation possible, requires ATP to do so.
2. a) What is the difference between the change in free energy associated with a
reaction and the heat release (enthalpy change) associated with a reaction?
Free energy takes into account change in entropy; in a sense, it tells us how
much "useful" energy is taken in or released by a reaction. We can harness free
energy released from one reaction to drive another, less spontaneous, reaction.
Enthalpy just tells us how much energy overall was released to the environment
as heat, or taken in (exothermic vs. endothermic).
b) Which of those values directly tells us whether or not a reaction is
spontaneous?
Spontaneous reactions have a negative free energy change (release). While
exothermic reactions with a negative enthalpy change TEND to be spontaneous,
this is not true at all temperatures!
3. a) Give an example of a reaction that is spontaneous, yet would proceed slowly
at room temperature if there were no catalysts present.
The breakdown of sugar into water and carbon dioxide is spontaneous.
However, it does not happen at an appreciable rate if you just dump sugar into
water.
b) What do we call proteins that cells use as catalysts to speed up chemical
reactions?
Enzymes.
4. a) Are all of the steps of glycolysis spontaneous? If not, name one nonspontaneous step.
Not all steps of glycolysis are spontaneous. Several steps require an investment
of free energy. All steps listed with a positive delta-G on this diagram are non-
Answer Key
Metabolism and Biochemistry
spontaneous (endergonic):
http://web.campbell.edu/faculty/nemecz/323_lect/glycolysis/energy.html
b) Is the entire process of glycolysis spontaneous as a whole? Why or why not?
Glycolysis IS spontaneous. If you add the appropriate enzymes, glycolysis will
release free energy and proceed on its own. Even without the enzymes,
glycolysis is still technically spontaneous, if impractically slow at room
temperature.
5. a) How much free energy is released (per molecule or per mole, your choice),
when converting ATP into ADP and phosphate? You may need to look online to
find this.
A quick Internet search will show that ATP hydrolysis releases 30.5 kJ/mole of
free energy under standard chemistry lab conditions.
(Note: In real cells at physiological concentrations, the release of energy is
significantly higher. If you used a higher value, such as 48 kJ/mol, just bear in
mind that this is not "standard" free energy release, but also takes into account
concentration differences and other factors in the cell, such as magnesium ions.)
b) Assuming that our metabolism can produce 38 moles or molecules of ATP
(some books say 36) out of every mole/molecule of glucose, estimate how much
energy we harvest from each mole/molecule of glucose. (Use your result from
part a).
Multiply your answer to part a by 38 or 36, and you'll have this.
c) How much free energy is released, in theory, when you light glucose on fire,
converting it into carbon dioxide and water? (You will need to look up the delta G
for glucose combustion online. Do NOT use the enthalpy change!)
The standard free energy release for glucose combustion is -2900 kJ/mole.
Again, this may not apply to physiological conditions.
d) What percentage of the available free energy of combustion in sugar (answer to
c) is actually used to make ATP (answer to b)? Given that the rest of this energy is
lost as waste heat (or used to heat the body), this will tell you the efficiency of
energy conversion in our cells!
Divide your answer to part b by your answer to part c, then multiply by 100%.
If you had 30.5 kJ/mole for ATP hydrolysis, your answer here should be about
40%. Some biochemists would call this an underestimate, though.
6. Draw a simplified diagram illustrating the steps of the citric acid cycle. Instead
of drawing the molecules in detail, however, draw them as carbon chains,
Answer Key
Metabolism and Biochemistry
ignoring any attached atoms. This will give you a better idea of how carbon enters
and leaves the citric acid cycle. This diagram of glycolysis is a useful model to
follow when deciding how to depict the reactions, but of course you will be
showing different reactions occurring in a cycle:
http://adapaproject.org/images/biobook_images/Glycolysis_overview.gif
Your diagram might look a little like this:
http://hyperphysics.phy-astr.gsu.edu/hbase/biology/imgbio/tcam.gif
7: How does fermentation differ from aerobic respiration? What is one advantage
of fermentation? What is one disadvantage of fermentation? Name two different
waste products that can be produced by fermentation.
Fermentation allows organisms to recycle NADH to NAD+ directly, without
transferring electrons to the electron transport chain. Its main disadvantage is
that it produces far less ATP than aerobic respiration. Its main advantage is
that it does not require oxygen. Two common waste products of fermentation
are ethanol and lactic acid.
8: Choose one of the enzymes involved in glycolysis and explain the logic behind
their naming. Here is an example to get you started:
"Phosphofructokinase is a kinase enzyme - one that adds/removes phosphate
groups from a molecule. It adds a phosphate group to fructose-6-phosphate to
turn it into fructose-1,6-bisphosphate. The fructo- in its name refers to its target
being fructose. The phospho- in its name means that the fructose that it targets
already has one phosphate added."
Here are a few more examples:
"Hexokinase is a kinase, an enzyme that adds/removes phosphate groups, that
targets the sixth (hence hexo-) carbon of glucose, turning it into glucose-6phosphate."
"Phosphoglucose isomerase takes glucose that has had phosphate added to it as
a substrate. It then rearranges it into fructose without adding/removing any
atoms. We call that kind of rearrangement isomerization, so this enzyme is an
isomerase."
"Glyceraldehyde phosphate dehydrogenase takes glyceraldehyde phosphate as
a substrate, and then removes a hydrogen atom (dehydrogenates) it, converting
NAD+ into NADH, adding a phosphate group, and rearranging it to 1,3bisphosphoglycerate. It is NOT a kinase, since it does not use ATP to
add/remove any phosphate groups."
Answer Key
Metabolism and Biochemistry
"Pyruvate kinase produces pyruvate from phosphoenolpyruvate. It is a kinase
because it removes a phosphate from PEP and converts ADP into ATP in the
process."
9: a) "Uncoupling proteins" can be embedded in the inner mitochondrial
membrane, allowing protons (H+) to cross the membrane without driving the
ATPase enzyme. What effect would this have on the ability of the mitochondrion
to maintain a proton gradient? What effect would this have on ATP production?
This would dissipate the proton gradient by allowing protons to flow freely.
Since they couldn't build up on one side of the membrane, they could not drive
the mitochondrial ATPase and allow us to make ATP. ATP production would be
decreased.
b) Energy cannot be created or destroyed, so any energy harvested via the
electron transport chain must go somewhere. What happens to energy harvested
from glucose when uncoupling proteins are present? How might this be useful to
some organisms?
This energy would be released as heat rather than usable chemical energy.
Some organisms could use this to increase their body temperatures during cold
periods or hibernation. The name of the first uncoupling protein found,
thermogenin, reflects this function.