Download Bis2A 5.2 Mobile Energy Carriers

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Bis2A 5.2 Mobile Energy Carriers
The BIS2A Team
This work is produced by OpenStax-CNX and licensed under the
Creative Commons Attribution License 4.0†
Abstract
This module will discuss the general structure and function of NAD/NADH and the production and
use of ATP in cells.
Section Summary
Energy is moved around and transferred within the cell in a variety of ways. One critical mechanism that
Nature has evolved is the use of recyclable molecular energy carriers. While there are several major recyclable
energy carriers, they all share some common functional features:
Properties of Key Cellular Molecular Energy Carriers
•
We think of the energy carriers as existing in "pools" of available carriers.
One could, by analogy,
consider these mobile energy carriers analogous to the delivery vehicles of parcel carriers - the company
has a certain "pool" of available vehicles at any one time to pickup and make deliveries.
•
Each individual carrier in the pool can exist in one of multiple distinct states: it is either carrying a
"load" of energy, a fractional load, or is "empty". The molecule can interconvert between "loaded"
and empty and thus can be recycled. Again by analogy, the delivery vehicles can be either carrying
packages or be empty and switch between these states.
•
The balance or ratio in the pool between "loaded" and "unloaded" carriers is important for cellular
function, is regulated by the cell and can often tell us something about the state of a cell. Likewise, a
parcel carrier service keeps close tabs on how full or empty their delivery vehicles are - if they are too
full there may be insucient "empty" trucks to pick up new packages; if they are too empty, business
must not be going well or it is shut down; there is an appropriate balance for dierent situations.
In this course we will examine two major types of molecular recyclable energy carriers: (1) the adenine
nicotinamide adenine dinucleotide (NAD+ ), a close relative nicotinamide
adenine dinucleotide phosphate (NADP+ ), and avin adenine dinucleotide (FAD2+ ) and (2) nucleotide mono-, di- and triphosphates, with particular attention paid to adenosine triphosphate (ATP).
nucleotides, specically:
Each of these two types of molecules is involved in energy transfer that involve dierent classes of chemical
reactions. Adenine nucleotides are primarily associated with redox chemistry while the nucleotide triphosphates are associated with transfers of energy that are linked to the hydrolysis or condensation of inorganic
phosphates.
1 Redox Chemistry and Electron Carriers
The oxidation of, or removal of an electron from, a molecule (whether accompanied with the removal of an
accompanying proton or not) results in a change of free energy for that molecule - matter, internal energy,
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and entropy have all changed in the process. Likewise the reduction of (the gain of electron on) a molecule
also changes its free energy. The magnitude of change in free energy and its direction (positive or negative)
for a redox reaction dictates the spontaneity of the reaction and how much energy is transferred. In biological
systems, where a great deal of energy transfer happens via redox reactions, it is important to understand
how these reactions are mediated and begin to start considering ideas or hypotheses for why these reactions
are mediated in many cases by a small family of electron carriers.
note: Relate the burning of - full oxidation of the of the sugar in - a gummy bear
1 (If the embedded
link doesn't work try https://www.youtube.com/watch?v=xJf0o9TNNXI) with the last paragraph
above. What does that demonstration have to do with our upcoming discussion on redox carriers.
There is some mention above already - can you nd it?
note: The problem alluded to in the previous discussion question is a great place to start bringing
in the design challenge rubric. If you recall, the rst step of the rubric asks that you dene a problem or question. In this case let's imagine that there is a problem to dene for which the mobile
electron carriers below helped Nature solve.
*** Remember evolution DOES NOT forward engineer solutions to problems, but in retrospect we
can use our imagination and logic to infer that what we see preserved by natural selection provided
a selective advantage because the natural innovation "solved" a problem that limited success. ***
Design Challenge for Redox Carriers
•
•
What was a problem(s) that the evolution of mobile electron/redox carriers helped solve?
The next step of the design challenge asks you to identify criteria for successful solutions.
What are criteria for success in the problem you've identied?
•
Step 3 in the design challenge ask you to identify possible solutions.
Well here Nature has
identied some for us - we consider three in the reading below. It looks like Nature is happy
to have multiple solutions to the problem.
•
The penultimate step of the design challenge rubric asks you to evaluate the proposed solutions
against the criteria for success.
This should make you think/discuss about why there are
multiple dierent electron carriers?
Are there dierent criteria for success?
Are they each
solving slightly dierent problems? What do you think? Be on the lookout as we go through
metabolism for clues.
1.1 NAD+ /H and FADH/H2
In living systems, a small class of compounds function as electron shuttles: They bind and carry electrons
between compounds in dierent metabolic pathways.
The principal electron carriers we will consider are
derived from the B vitamin group and are derivatives of nucleotides. These compounds can be both reduced
(that is, they accept electrons) or oxidized (they lose electrons) depending on the reduction potential of a
potential electron donor or acceptor that they might transfer electrons to and from. Nicotinamide adenine
dinucleotide (NAD+) (the structure is shown below) is derived from vitamin B3, niacin.
+
NAD
is the
oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two electrons
and a proton (which together are the equivalent of a hydrogen atom with an extra electron-review module
5.1, Redox Tower).
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NAD
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can accept electrons from an organic molecule according to the general equation:
+
NAD
RH
Reducing
+
Oxidizing
agent
agent
→
NADH
Reduced
+
R
(1)
Oxidized
A bit of vocabulary: When electrons are added to a compound, the compound is said to have been
A compound that reduces another (donates electrons) is called a
+
RH is a reducing agent, and NAD
becomes
+
NAD
oxidized.
reducing agent.
reduced.
In the above equation,
is reduced to NADH. When electrons are removed from a compound, it
A compound that oxidizes another is called an
oxidizing agent.
In the above equation,
is an oxidizing agent, and RH is oxidized to R.
You need to get this down!
We will (a) test specically on your ability to do so - as "easy" questions
and (b) we will use the terms with the expectation that you know what they mean and can relate them to
biochemical reactions correctly (in class and on tests).
+
+ contains an extra phosphate group and plays an important role in
anabolic reactions such and photosynthesis. Flavin adenine dinucleotide (FAD+ ) is derived from vitamin
B2 , also called riboavin. Its reduced form is FADH2 .
A second variation of NAD , NADP
Figure 1: The oxidized form of the electron carrier (NAD+ ) is shown on the left and the reduced form
(NADH) is shown on the right. The nitrogenous base in NADH has one more hydrogen ion and two
more electrons than in NAD+ .
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+ is used by the cell to pull electrons o of compounds and to "carry" them to other locations within
+
the cell, thus they are called electron carriers. NAD /H compounds are used in many of the metabolic
+ is used as a reactant in
processes we will discuss in this class. For example, in its oxidized form NAD
NAD
glycolysis and the TCA cycle whereas in its reduced form (NADH) it is a reactant in fermentation and the
electron transport chain (ETC). Each of these processes will be discussed in later modules.
Energy Story for a Redox Reaction
+
***As a rule of thumb, when we see NAD /H as a reactant or product we know we are looking at a redox
reaction.*** When NADH is a product and NAD
+
is a reactant we know that NAD
+
has become reduced
(forming NADH) therefore the other reactant must have been the electron donor and become oxidized. The
+
vice versa is also true. If NADH has become NAD , then the other reactant must have gained the electron
from NADH and become reduced.
Figure 2: This reaction shows the conversion of pyruvate to lactic acid coupled with the conversion of
NADH to NAD
Source:https://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/sequential_reactions
In the gure above we see the reaction of pyruvate becoming lactic acid, coupled with the conversion of
+
NADH into NAD . This reaction is catalyzed by LDH. Using our 'rule of thumb' above, we categorize this
reaction as a redox reaction. NADH is the reduced form of the electron carrier and NADH is converted into
+
NAD . This half of the reaction results in an oxidation of the electron carrier.
Pyruvate is converted into lactic acid in this reaction. Both of these sugars are negatively charged so it would
be dicult to see which compound is more reduced using the charges of the compounds. However, we know
that pyruvate has become reduced to form lactic acid because this conversion is coupled to the oxidation of
+ But how can we tell that lactic acid is more reduced than pyruvate?
NADH into NAD .
The
answer is to look at the carbon-hydrogen bonds in both compounds. As electrons are transferred, they are
often accompanied by a hydrogen atom. There are a total of 3 C-H bonds in pyruvate and there are a total
of 4 C-H bonds in lactic acid. When we compare these two compounds in the before and after state, we see
that lactic acid has one more C-H bond, therefore, lactic acid is more reduced than pyruvate. This holds
true for multiple compounds. For example, using gure 3 below, you should be able to rank the compounds
from most to least reduced using the C-H bonds as your guide.
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Figure 3: Above are a series of compounds than can be ranked or reorganized from most to least
reduced. Compare the number of C-H bonds in each compound. Carbon dioxide has no C-H bonds and
is the most oxidized form of carbon we will discuss in this class.
Answer: Most reduced is methane (compound 3), then methanol (4), formaldehyde (1), carboxylic acid
(2), and nally carbon dioxide (5).
Figure 4: This reaction shows the conversion of G3P, Pi, NAD+ into NADH and 1,3-BPG. This reaction
is catalyzed by Glyceraldehyde -3-phosphate dehydrogenase.
Energy story:
Lets make an energy story for the reaction above.
First, lets characterize the reactants and products. The reactants are Glyceraldehyde-3-phosphate (a carbon
+
compound), Pi (inorganic phosphate) and NAD . These three reactants enter into a chemical reaction to
produce two products, NADH and 1,3-Bisphosphoglycerate. If you look closely you can see that the 1,3-BPG
contains two phosphates. This is important when we are double checking that no mass has been lost. There
are two phosphates in the reactants so there need to be two phosphates in the products (conservation of
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mass!). You can double check that all the other atoms are also accounted for. The enzyme that catalyzes
this reaction is called Glyceraldehyde -3-phosphate dehydrogenase. The standard free energy change of this
reaction is
∼6.3kJ/mol so under standard conditions we can say that the free energy of the products is higher
than that of the reactants and that this reaction is not spontaneous under standard conditions.
What can we say about this reaction in gure 2?
This is a redox reaction. We know that because we have produced a reduced electron carrier (NADH) as a
+
product and NAD
is a reactant. Where did the electron come from to make NADH? The electron must
have come from the other reactant (the carbon compound).
note:
We will spend some time examining the reaction in Figure 2 in more detail as we move
through the lectures and text. The rst thing to discuss here is that the gure above is a highly
simplied or condensed version of the steps that take place - one could in fact break that reaction
above into TWO conceptual reactions. Can you imagine what those two "subreactions" might be?
Discuss amongst yourselves.
note: The text above notes that the standard change in free energy for this complex reaction is
∼+6.3kJ/mol.
Under standard conditions this reaction is NOT spontaneous. However, this is one
of the key reactions in the oxidation of glucose. It needs to GO in the cell. The questions are: why
is it important to note things like "standard change of free energy" or "under standard conditions"
when reporting that
∆G
◦
?
What could possibly be going on in the cell to make what is under
standard conditions an endergonic reaction "go"?
Exercise 1
(Solution on p. 12.)
A reducing chemical reaction ________.
a. reduces the compound to a simpler form
b. adds an electron to the substrate
c. removes a hydrogen atom from the substrate
d. is a catabolic reaction
2 ATP
Another chemical compound we need to become familiar with is adenosine triphospate (
ATP).
The main
cellular role of ATP is as a "short term" energy transfer device for the cell. The hydrolysis reactions that
liberate one or more of ATP's phosphates are exergonic and many, many cellular proteins have evolved to
interact with ATP in ways that help to facilitate the transfer of energy from hydrolysis to myriad other
cellular functions. In this way, ATP is often called the energy currency of the cell - it has reasonably xed
values of energy to transfer to or from itself and can exchange that energy between many potential donors
and acceptors. We will see many examples of ATP "at work" in the cell - be on the lookout for them and
as you see them try to think of them as functional examples of Nature's uses for ATP that you could be
expected to see in another reaction or context.
2.1 ATP Structure and Function
At the heart of ATP is the nucleotide adenosine monophosphate (AMP). Like the other nucleotides AMP is
composed of a nitrogenous base (an adenine molecule) bonded to a ribose molecule and a single phosphate
group (Figure 5). The addition of a second phosphate group to this core molecule results in the formation of
adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).
To further review the structure of ATP please see module 2.1 and 3.3.
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Figure 5: ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis
to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).
The
phosphorylation
or condensation of phosphate groups onto AMP is an endergonic process.
contrast, the hydrolysis of one or two phosphate groups from ATP, a process called
By
dephosphorylation, is
exergonic. Why? Let's recall that the terms endergonic and exergonic refer to the sign on the dierence in
free energy of a reaction between the products and reactants,
∆G.
In this case we are explicitly assigning
direction to the reaction, either in the direction of phosphorylation or dephosphorylation of the nucleotide. In
the phosphorylation reaction the reactants are the nucleotide and an inorganic phosphate while the products
are a phosphorylated nucleotide and WATER. In the dephosphorylation/hydrolysis reaction, the reactants
are the phosphorylated nucleotide and WATER while the products are inorganic phosphate and the nucleotide minus one phosphate.
Since Gibbs free energy is a state function, it doesn't matter how the reaction happens, you just consider the beginning and ending states. So, let's for example examine the hydrolysis of ATP. The reactants
ATP and water are characterized by their atomic makeup and the kinds of bonds between the constituent
atoms and some free energy can be associated with each of the bonds and their possible congurations likewise for the products.
If we examine the reaction from the standpoint of the products and reactants
and ask "how can we recombine atoms and bonds in the reactants to get the products?", we nd that a
phosphoanhydride bond between an oxygen and a phosphorus must be broken in the ATP, a bond between
an oxygen and hydrogen broken in the water, a bond made between the OH (that came from the splitting
of water) and the phosphorus (from the freed PO
3 -2 ), and a bond must be formed between the H (derived
from the splitting of water), and the terminal oxygen on the phosphorylated nucleotide. It is the sum of
energies associated with all of those bond rearrangements (including those directly associated with water)
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that make this reaction exergonic. A similar analysis could be made with the reverse reaction.
note:
Use the gure of ATP above and your knowledge of what a water molecule looks like to
draw a gure of the reaction steps described above: breaking of phosphoanhydride bond, breaking
of water, and formation of new bonds to form ADP and inorganic phosphate. Track the atoms in
dierent colors if that helps.
Is there something special about the specic bonds involved in these molecules? Much is made in various
texts about the types of bonds between the phosphates of ATP. Certainly, the properties of the bonds in
ATP help dene the molecule's free energy and reactivity. However, while it is appropriate to apply concepts
like charge density and availability of resonance structures to this discussion, trotting these terms out as
an "explanation" without a thorough understanding of how these factors inuence the free energy of the
reactants is a special kind of hand-waving that we prefer not to engage in. Most BIS2A students have not
had any college chemistry and those that have are not likely to have discussed those terms in any meaningful
way.
So, trying to explain the process using the ideas above would do nothing but give a false sense of
understanding, tend to assign some mystical quality to ATP and is "special" bonds that doesn't exist, and
distract from the real point, that the hydrolysis reaction is exergonic because of the properties of ATP
but ALSO because of the chemical properties of water and those of the reaction products. For this class,
it is sucient to know that dedicated physical chemists are still studying the process of ATP hydrolysis
in solution and in the context of proteins and that they are still trying to account for the key enthalpic
and entropic components of the component free energies.
We'll just need to accept a certain degree of
mechanistic chemical ignorance and be content with a description of gross thermodynamic properties. The
latter is perfectly sucient to have deep discussions about the relevant biology.
"High Energy" Bonds
What about the term "high energy bonds" that we so often hear associated with ATP? If there is nothing
"special" about the bonds in ATP why do we always hear the term "high energy bonds" associated with the
molecule? The answer is deceptively simple. In biology the term "high energy bond" is used to describe an
exergonic reaction involving the hydrolysis of the bond in question that results in a "large" negative change
in free energy. Remember that this change in free energy does not only have to do with the bond in question
but rather the sum of all bond rearrangements in the reaction. What constitutes a large change? This it
seems is a rather arbitrary assignment that is usually associated with an amount of energy that is associated
with the types of anabolic reactions we typically observe in biology. If there is something special about the
bonds in ATP it is not uniquely tied to the free energy of hydrolysis as there are plenty of other bonds whose
hydrolysis result in greater negative dierences in free energy.
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Figure 6: The free energy of hydrolysis of dierent types of bonds can be compared to that of the
hydrolysis of ATP.
Source: http://biowiki.ucdavis.edu/Biochemistry/Oxidation_and_Phosphorylation/ATP_and_Oxidative_Phosphorylation/Pr
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Figure 7: Table of common cellular phosphorylated molecules and there respective free energies of
hydrolysis.
Video on electron and electron/proton carriers
For a 7 minute YouTube video on the role of carriers in respiration clicke here
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.
2.2 The cycling of ATP pools
Estimates for the number of ATP molecules in a typical human cell range from
ATP/cell) in a white blood cell to
9
-15
5x10 (∼9x10
∼3x107 (∼5x10-17
moles
moles ATP/cell) in an active cancer cell. While these
numbers might seem large, and already amazing, consider that it is estimated that this pool of ATP turns
over (becomes ADP and then back to ATP) 1.5x per minute. Extending this analysis yields the estimate
that this daily turnover amounts to roughly the equivalent of one body weight of ATP getting turned over
per day. That is, if no turnover/recycling of ATP happened, it would take 1 body weights worth of ATP for
the human body to function - hence our previous characterization of ATP as a "short term" energy transfer
device for the cell.
While the pool of ATP/ADP may be recycled, some of the energy that is transferred in the many
conversions between ATP, ADP and other biomolecules is also transferred to the environment.
In order
to maintain cellular energy pools energy must transfer in from the environment as well. Where does this
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energy come from? The answer depends a lot on where energy is available and what mechanisms Nature
has evolved to transfer energy from the environment to molecular carriers like ATP. In nearly all cases,
however, the mechanism of transfer has evolved to include some form of red/ox chemistry. In this and the
following sections that follow we are concerned with learning some critical examples of energy transfer from
the environment, key types of chemistry and biological reactions involved in this process, and some key
biological reactions and cellular components associated with energy ow between dierent parts of the living
system. We focus rst on reactions involved in the (re)generation of ATP in the cell (not those involved in
the creation of the nucleotide per se but rather those associated with the transfer of phosphates onto AMP
and ADP).
Video Link
For a more detailed explanation of ATP and how this molecule stores energy take a look at this video (10
minutes) by clicking here
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. (Caveat - not yet BIS2A instructor validated)
2.3 How do cells generate ATP?
A variety of mechanisms have ermerged over the 3.25 billion years of evolution to create ATP from ADP and
AMP. The majority of these mechanism are modications on two themes: direct synthesis of ATP or indirect
synthesis of ATP with two basic mechanisms known respectively as:
(SLP) and oxidative phosphorylation.
in detail in the next few modules.
Substrate Level Phosphorylation
These topics are substantive enough that they will be discussed
Suce it to say both mechanisms rely on biochemical reactions that
transfer energy from some energy source to ADP or AMP, to synthesize ATP.
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Solutions to Exercises in this Module
to Exercise (p. 6)
B
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