||Concepts of Biology
(BIOL115) - Dr. S.G. Saupe (firstname.lastname@example.org); Biology Department, College of St. Benedict/St. John's
University, Collegeville, MN 56321
Energy - Releasing Pathways
I. Biological Energetics: A Brief Primer
What is energy? A simple definition - energy is the ability
to do work (which is the same as moving matter). Organisms need to do a lot of
work (i.e., metabolism, membrane transport, movement). Measured in
units of kJ (kilojoule) or kcal (kilocalorie - this is the traditional
unit and less preferred than kJ since it is a unit of heat. It is used
since all work can essentially be converted to heat)
- Forms of energy.
There are three biologically-important forms of energy:
(1) Chemical energy - energy involved in chemical bonds; (2) Electrical
energy - energy associated with electron flow; (3) Radiant energy - energy
that travels in waves and discrete particles (photons). Each may exist in a
potential or kinetic state.
- States of energy.
Potential energy is energy in a stored or inactive form;
energy of position (e.g., dynamite, standing on a desk, pulling back
a bow); Kinetic energy is energy in action (e.g., burning wood,
falling off a cliff, releasing the arrow).
- First Law of Thermodynamics.
Energy can be converted from one form to another, but
never created or destroyed. Or, to state it another way, the total amount of
energy in the universe is constant. Thus, plants adhere to the First Law
when, during photosynthesis, they convert solar (radiant) energy into
chemical energy. Similarly, during respiration mitochondria convert glucose
(potential chemical energy) into ATP (another form of potential chemical
energy) and heat (radiant energy). This process requires a flow of electrons
through a series of electron carriers (electrical energy).
- Second Law of Thermodynamics.
No energy conversion is 100% efficient. Or stated another
way, all systems tend to run down (because of inefficient energy
conversions). Or, all systems tend to a state of minimum energy, which is
the most stable state, which is a state of disorganization - called entropy
(symbolized by the letter S). It's no surprise that our rooms and offices
tend to get messy - because it takes energy to maintain things in an
organized state. In fact, all housework can be considered a battle against
the Second Law. Remember the Morowitz article, "Women's Lib and
the energy crisis?"
- Do organisms violate the laws of thermodynamics, especially the Second
Law, considering that organisms are highly organized?
No way. Life follows the Rules! To maintain an
ordered state requires a constant input of energy. Just like keeping a room
tidy requires a constant energy input, life requires a constant energy
input. Life is an open system - meaning it exchanges energy with its
environment (constantly replenishing energy needs). Life could not persist
isolated in a closed system (one that doesn't exchange materials with the
environment). Death can be considered loosing the battle to entropy
and metabolism can be considered the process by which life battles the
Second Law - the collective chemical processes by which energy is acquired
and utilized. Remember the Morowitz article, "Six Million Dollar
II. Reducing Potential - ability of a substance to
participate in a redox reaction. Living organisms must carry out many redox
methane (most reduced form of
- Some definitions:
(1) Reduction - gain of electrons; (2) Oxidation - loss
of electrons; (3) A helpful mnemonic: "oil rig" - oxidation is
loss, reduction is gain; (4) Redox reaction - reaction in which one
component is oxidized and the other is reduced. Obviously, electrons must
come from somewhere and go somewhere.
- The reduction sequence of carbon
carbon dioxide (most oxidized form of carbon) →
carboxyl (organic acid)
Note: each step requires the addition (or removal) of two electrons and two
protons for reduction (oxidation). Two steps also require the addition of
How can you tell if something has been oxidized or reduced?
(1) look for a change in valence (i.e., Fe2+
Fe3+ is an oxidation because an electron was lost,
increasing the total positive charge on the molecule); (2) In many
biological redox reactions, oxidation is accompanied by a loss of protons
(hydrogen ions) and reduction is accompanied by a gain of protons. Thus, you
can count the number of hydrogen atoms on each side of the equation (the
more H, the more reduced), or count the number of oxygen atoms (the more O,
the more oxidized).
Biological redox reactions typically require electron donors and/or
These are usually: (1) NAD+ (2) NADP+
and (3) FAD. These are coenzymes (organic compounds, other than the
substrate, required by an enzyme for activity). The reaction sequence for
these coenzymes is given below:
NADH + H+
NAD+ + 2H+ + 2e-
NADP+ + 2H+ + 2e-
NADPH + H+
FAD + 2H+ + 2e-
III. Chemical Potential - energy available from bond cleavage.
The primary source is ATP (adenosine triphosphate), which is
the energy currency of life. If a cell or organism wants to get some
"work" done, it "pays" for the work with ATP. It is
estimated that we use and cycle approximately a body weight worth of ATP
ADP + Pi + energy
- Hydrolysis of ATP to ADP + Pi releases energy used by cells.
eqn: ATP + H2O →
ATP hydrolysis is exergonic (delta G = -7.3 kcal/mol).
ATP hydrolysis is coupled to endergonic reactions.
Remember the hill model - ATP is what pushes the rock up
ATP synthesis is termed a phosphorylation reaction (because a phosphate
group is added to ADP)
ATP formation - substrate level phosphorylation
Occurs during glycolysis or the Citric Acid cycle. In a
substrate level phosphorylation the phosphate used to phosphorylate ATP
comes from an organic compound and the process is NOT associated with redox
ATP formation - oxidative phosphorylation
Is the result of electron transport in the mitochondria
and chloroplasts. In contrast to substrate level phosphorylation, oxidative
phosphorylation uses inorganic phosphate and the process IS associated with
redox reactions via an electron transport chain (ETC).
IV. Equation Review.
Given that background, let�s review the equations for
photosynthesis and respiration that you�ve seen many times:
||CO2 + H2O + light
(CH20)n + O2
||(CH2O)n + O2
CO2 + H2O +
Now, let's look at some exciting details!
- Photosynthesis and respiration are redox reactions. For example, during
photosynthesis carbon dioxide is reduced to a carbohydrate (which is
abbreviated as (CH20)n ) and the water is oxidized
to yield oxygen. Thus, the purpose of water in photosynthesis is to supply
the electrons for the reduction of carbon dioxide to a carbohydrate. The
situation is reversed for respiration.
- Photosynthesis is an anabolic and endergonic reaction. Light energy is
required for the reduction of carbon dioxide.
- Respiration is a catabolic and exergonic reaction. There is a net energy
loss during the process. Some of the energy is used to make ATP.
- Hill Model Revisited - a diagram of the hill will be provided in class.
Some take-home-lessons from the hilltop:
- Anabolism is analogous to pushing the rock uphill, catabolism is
analogous to the rock rolling downhill;
- Photosynthesis (an anabolic process) is analogous to pushing the rock
uphill, respiration (a catabolic process) is analogous to the rock
- The energy required to push the rock (glucose) uphill comes from light
- The release of energy from glucose rolling downhill is coupled to ATP
production (ca. 40% of the energy is trapped in ATP but more than
half of the energy is lost as heat).
VI. Rolling metabolic rocks downhill - A look at Glucose Catabolism
- Glucose catabolism occurs in a series of small, sequential, highly
controlled and regulated steps (reactions).
- The processes involved are glycolysis, which is the first step of glucose
breakdown, and it is followed by either fermentation or cellular respiration
(depending on the availability of oxygen).
- Why so many steps? Back to our hill model for an answer. There are two
kinds of hills - those with a gradual, step-wise slope and those with a
steep precipice or overhang. In each case the rock will roll down the hill
and release the same total amount of energy, which is equal to the energy
difference between the top and bottom of the hill. However, the energy is
released so quickly when rolling off a steep cliff that it is difficult to
trap much in a usable form (ATP). However, if the energy release occurs in a
slow and orderly way, then it is possible to trap a greater percentage of
energy as ATP.
VII. Glycolysis - the first steps of glucose catabolism.
- Translation. Gr: glyco = sugar; Gr: lysis = split or cleave. Thus, the
literal translation of glycolysis is the splitting of glucose.
- Net reaction - glucose (C6, a sugar with 6 carbon atoms) is cleaved to
yield two pyruvic acid molecules (C3).
- Glycolysis consists of about 10 different reactions.
- Each reaction is catalyzed by a different enzyme.
- Organic acids, like pyruvic acid, are usually ionized at cellular pH
values. We name the ionized form "ate". Thus, "pyruvic
acid" and pyruvate refer to the same compound but in a slightly
different form (ionized vs. not). Essentially these terms can be used
- Glycolysis occurs in the cytoplasm of virtually all cells. This suggests
that glycolysis is an evolutionary ancient pathway. In fact, glycolysis
likely evolved more than 3 billion years ago. Wow, it's even older than me!
- Oxygen is not required. Glycolysis functions with (aerobic conditions) or
without (anaerobic conditions) oxygen present.
- Two ATP are required to get the "rock" rolling (hmmm, sounds
like a beer brand). They "activate" the glucose making it
energetically favorable to react. Remember how people who
"misbehaved" were "drawn and quartered"? - this is the
- A total of four ATP are produced during the process at two different
reactions. Thus, there is a net yield of 2 ATP.
- ATP is produced during glycolysis by substrate level phosphorylation. For
example: ADP + phosphoenolpyruvate (PEP) �
ATP + pyruvate. (Note that the PEP is an organic phosphate).
- There is one redox reaction during glycolysis. The oxidation of glucose
begins during glycolysis. NAD+ accepts the electrons during the
oxidation, and as a result it gets reduced. A total of 2 NADH are produced.
Recall that NAD+ is a coenzyme (organic compound required by an
enzyme for activity) that is used in redox reactions. Enzymes that catalyze
redox reactions with the help of coenzymes such as NAD+ are
- Pyruvic acid is a branch point. It still has much energy and can be
further degraded. If oxygen is present (aerobic conditions) pyruvate is
metabolized via cellular respiration (i.e., citric acid cycle and ETC.
Without oxygen, anaerobic conditions, pyruvate is metabolized via
VIII. Fermentation - stepping in an anaerobic environment
- Occurs only in the absence of oxygen (anaerobic conditions)
- Occurs in the cytoplasm|
- Occurs in most organisms
- There are different types of fermentations depending upon the end
products. The two common ones are:
1. Alcohol fermentations - yeast, plants. Important in baking and
brewing industries. Don't over-water your plants because the soil pore spaces
fill with water, the roots become anaerobic, fermentation begins, and the
roots "pickle themselves".
2. Lactic acid fermentations - bacteria, humans. Commercially important
in cultured dairy industry (yogurt, cheese), silage, pickles. In humans,
excessive exercise results in periods of fermentation during which lactate
builds up and contributes to muscle fatigue and soreness. What if humans had
evolved alcohol fermentations instead of lactate ones? - every time you ran
around the block you'd get drunk!
The ultimate function of fermentation is to regenerate oxidized coenzymes,
Why is this necessary? - because glycolysis is the only
source of ATP under anaerobic conditions. Recall that during the redox
reaction in glycolysis, one of the key enzymes require OXIDIZED NAD+
as a coenzyme. After glycolysis works awhile, all of the coenzyme will be in
the reduced form (NADH) and the reaction will stop because the enzyme won't
have anywhere to dump off electrons. An analogy - imagine trying to bail out
a boat full of water with a glass. The glass is like a coenzyme. It can be
oxidized (empty) or full (reduced). You can continue to bail out the boat as
long as the glass is empty. When full, it can't accept any more water. Thus,
you're finished bailing, at least until you get another glass, or empty the
one you have.
Fermentation vs. anaerobic respiration.
There is a difference! In a fermentation, electrons
from coenzymes are donated back to part of the original substrate molecule.
In a respiration, the electrons are donated to a substance, other than part
of the original substrate. Thus, in an aerobic respiration, the electron
acceptor is oxygen. In an anaerobic respiration, the acceptor is something
else - like sulfur. This latter process occurs primarily in bacteria.
IX. Aerobic or Cellular Respiration - stepping in air.
- This is not the same thing as breathing.
- Occurs only in the presence of oxygen.
- Occurs In the mitochondrion.
(Note, the entire cell of an aerobic bacteria can act like a
mitochondrion to produce ATP aerobically). Remember the structure of a
mitochondrion? (a) double membrane, inner and outer; (b) matrix - central or
inner compartment; (c) inter-membrane space. Simply put, there is a liquid
matrix where "biochemical reactions" occur, an inner membrane where
electron transfer reactions occur and an area where low pH won�t do any harm
- Pyruvate Oxidation.
Pyruvate from glycolysis is shuttled into the
mitochondrion. As it enters, both of the pyruvate are oxidized (another
redox reaction involving NAD+) and a carbon dioxide is lost from
each. Note, that two carbons (one from each of the pyruvate molecules that
originated from glucose) have been lost. The leftover two carbon piece is hooked
onto a carrier (Acetyl coenzyme A).
- Welcome to the Citric Acid Cycle or Kreb�s cycle or Tricarboxylic Acid
- It is named in honor of Sir Hans Krebs, who owned a bicycle shop in
Kent, England. Just kidding - he was a British biochemist who worked out the
details of many
of the reactions. It is also called "Citric Acid Cycle" because
citric acid is one of the important intermediate molecules or called the "Tricarboxylic
Acid Cycle" (TCA) because citric acid has three carboxyl groups.
Take your pick of names.
- Occurs in the matrix of the mitochondrion (thus the reactants are water
- There are several different reactions in the Citric Acid cycle, each
catalyzed by a different enzyme.
- There is one substrate level phosphorylation reaction that produces ATP.
[Actually, the first product of the cycle is GTP (which is a nucleotide
phosphate carrier like ATP). The GTP then donates a phosphate to ADP to make
- Carbon dioxide is released during two reactions (alpha-ketoglutarate
dehydrogenase and isocitrate dehydrogenase) (or three total reactions if you
include the reaction during which pyruvate was shuttled into the
mitochondrion). Thus, during the Citric Acid cycle, the breakdown of glucose
into carbon dioxide is completed.
- There are four redox reactions, three of which yield reduced NADH and
one FADH2. Thus, the oxidation of glucose is completed in the
Kreb's cycle. If you count the redox reaction that occurred when shuttling
pyruvate into the mitochondrion there is a total of 5 redox reactions in the
X. Regenerating Coenzymes in aerobic conditions
Recall that one problem of glycolysis was
regenerating oxidized coenzymes. Under anaerobic conditions, this problem was
solved by a variety of fermentation reactions or anaerobic respiration. Well,
the solution is much more elegant in cells in an aerobic environment. Not only
are oxidized coenzymes recovered, but the process is coupled to the production
of ATP. Thus, the evolution of an oxygenated atmosphere allowed cells the added
bonus of producing additional cellular energy while regenerating oxidized
coenzymes. The electron transport chain (ETC) provided the means for this
XI. Mitochondrial Electron Transport Chain
- Occurs in the inner membrane (cristae)
Thus, the components are more or less lipid-soluble and
are embedded in the membrane
- Occurs only under aerobic conditions
- The mitochondrial ETC consists of a series of electron carriers that
alternately accept and pass along an electron - like a hot potato or to use our glass
analog - like a glass that
is alternately filled (given an electron) and emptied (pass it off to the next
carrier). In the process the carriers become reduced (glass full) and then oxidized
again (glass empty).
� III �
- There are four major groups, called complexes, of electron carriers in the
membrane. This is the reason why the text shows several blobs in the membrane.
Each complex has a unique set of carriers. In addition, there are molecules that
shuttle electrons from one complex to another.
- 2. Among the carriers in the complexes (don't memorize these): Complex I -
flavoproteins (FMN) and Fe-S proteins; Complex II - more flavoproteins, Fe-S
proteins; Complex III - an assortment of proteins including cytochromes (c1 and
b); Complex IV - cytochrome a,a3.
- The sequence of electron flow occurs from complex I to complex IV as
Since the complexes are physically separate in the membrane, carriers must
shuttle electrons from one complex to another. Ubiquinone (coenzyme Q, or
simply, Q) shuttles electrons from complex I to complex III (and also between II
and III). Cytochrome c shuttles electrons from complex III to complex IV. Thus:
→ cyt c
- NADH from the Kreb's cycle donates its electrons at the end of the chain
(to complex I). After donating its electrons, NADH gets oxidized to NAD+.
Thus, we can modify the reaction chain:
NADH → I →
Q → III → cyt
c → IV
- The final acceptor of the electrons in the ETC is oxygen. Oxygen becomes
reduced to water. Thus:
NADH → I →
Q → III → cyt
c → O2
- FADH2 and exogenous NADH (produced outside of the mitochondria,
i.e., during glycolysis) donate electrons to Complex II and then on to
oxygen. Thus, the electrons bypass Complex I. We can write this as:
FADH2/NADHex → II →
Q → III → cyt
c → IV → O2
D. The passage of electrons along the ETC is associated with the production
XII. Chemiosmotic Production of ATP
- The mechanism of ATP production is the same as for chloroplasts - via
- A review of chemiosmosis: (a) at intervals along the ETC, protons
(hydrogen ions) are moved from the matrix (or stroma) side of the membrane to
the space between the inner and outer membranes; (b) the membrane is impermeable
to protons which results in; (c) a pH and electrochemical (more positive charges
in the intermembrane space than the matrix) gradient is established across the
membrane. The pH of the matrix (or stoma) is alkaline (about pH 8) relative to
the space (pH 5); (d) this gradient provides the driving force for ATP
production; (e) ATP is made at an ATPase - which are stalked
"lollipops", protein channels that span the membrane. Protons flow
(like a waterwheel) through these.
- There are three sites where protons are moved across the mitochondrial
membrane "roughly" associated with complexes I, III and IV.
- Each site is "roughly" associated with synthesis of 1 ATP. Thus
the ATP yields: 3 ATP/NADH (endogenous - those produced inside the mitochondrion
such as during the Kreb�s cycle); 2 ATP/NADH (exogenous - those produced in
the cytoplasm such as during glycolysis); 2 ATP/FADH2.
- The total yield of ATP from oxidizing glucose is about 36 ATP/glucose.
Let's add 'em up - 4 ATP (2 NADH from glycolysis which each yield 2 ATP) plus 24
ATP (NADH is produced in four steps in the mitochondria times 2 for each pyruvic
acid times 3 ATP) plus 4 ATP (2 FADH2 times 2 ATP) plus 2 ATP from
glycolysis plus 2 ATP from Kreb's cycle = 36 ATP.
- Note there are 18x more ATP produced under aerobic conditions (36) than
under anaerobic conditions (2). Which do you choose?
XIII. Function of Aerobic Respiration/Glucose Catabolism
- Energy production (36 ATP/glucose)
- Produce intermediates for many other metabolic reactions. Thus, various
molecules can be siphoned off and used for other purposes.
- Heat production. Glucose catabolism yields a TOTAL of 38 ATP. 38 ATP x 7.3
kcal/mol ATP = 262 kcal. Glucose has 686 kcal. Thus the efficiency of glucose
metabolism is 262/686 x 100 = 38%. Or in other words, about 62% of the energy is
lost as heat. This keeps us, shrews, and elephants warm. It also explains why
compost piles generate lots of heat (microbial decomposition) and why there are
sometimes spontaneous silo fires (improperly dried/prepared silage). But don't
worry - there is no such thing as spontaneous human combustion.
Many of the enzymes of glycolysis and respiration are
allosteric enzymes. This allows for tight control of metabolism.
Last updated: August 20, 2004 Visitors to this site:
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