UNIT 5 NOTES – ENERGY PROCESSES
METABOLISM
I.
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Metabolism, Energy and Matter
All living organisms must exchange energy with their environment. The energy can come from
light for photoautotrophs, photoheterotrophs or from chemical energy for chemoautotrophs
and chemoheterotrophs. The energy is used to fuel cellular processes.
Metabolism – all processes that are responsible for transforming energy and matter within an
organism. Two subtypes include:
o Anabolism – building up molecules by using energy and enzymes
o Catabolism – breaking down molecules by releasing energy and using enzymes
Metabolic pathways – sets of reactions in which the product of one reaction becomes the
reactant of the other. These pathways can be regulated together to form one certain product.
Energy is the capacity to do work and create heat (potential and kinetic energy)
First law of thermodynamics – Energy cannot be created or destroyed but can be converted to
different forms or transferred from one organism to the next.
Please review primary gross and net production, secondary production, production efficiency and
trophic efficiency.
Second law of thermodynamics – Every time energy is transformed from one form to an other,
some of it is lost as heat. Heat increases the kinetic energy of molecules and their random
motion, so the entropy (disorder) of the system also increases every time energy conversion or
transfer occurs.
Gibbs free energy – available energy for the system to use to perform work:
ΔG = Gfinal – Ginitial
When the reactants of a reaction with higher free energy are converted to the products with
lower free energy, the reaction is spontaneous, and the reaction is exergonic. The ΔG in this
case is negative. When the products have more free energy than the reactants, the reaction
does not occur spontaneously (non-spontaneous) and the reaction is endergonic. The value of
ΔG in this case is positive.
All reactions, including exergonic reactions need an initial investment of energy to activate the
reaction. This is called the activation energy.
Review enzymes and enzyme regulation
Coupled reactions team energy releasing reactions with energy-costing reactions. This way all
coupled reactions have a net release of ΔG as heat to fulfill the second law of thermodynamics.
An example of coupled reactions is the synthesis of DNA, where each nucleotide is added as a
GTP, ATP, TTP, CTP and two phosphates are broken down of these monomers to release enough
energy to form DNA. DNA synthesis is an anabolic endergonic process, while the hydrolysis of
the triphosphate monomers is a catabolic exergonic process.
II.
ATP Is The Main Energy Currency in Cells
 Most cellular work is directly fuelled by the hydrolysis of one simple molecule, called adenosine
triphosphate, ATP.
 The cell uses various molecules to store energy (such as starch, glycogen, proteins, simple lipids)
but for direct energy use the cell mostly uses ATP. (Incorrectly stated in the book)
 The structure of ATP is made up of:
o Adenine
o Ribose
o 3 phosphates
 ATP can break down into adenosine diphosphate (ADP) by hydrolysis in an exergonic reaction
and releases energy for cells to use. Also, the phosphate released can bind with other
molecules and energize them by changing their shape – Phosphorylation. The energy released
is sufficient enough to fuel other endergonic processes.
 ADP can also be refueled by using exergonic reactions that will phosphorylate it to form ATP
again. This way the cell regenerates ATP by using exergonic reactions such as cellular
respiration.
 Because ATP is universally used by all living organisms, it must have evolved early on and is an
indicator of the common origin of life.
 Other energy carrying molecules are also used by cells, such as GTP, NAD+, FAD, NADP+ and
others.
ENERGY TRANSFER
I.
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Energy In Living Systems
The chart below says it all:
General equations also show the interrelatedness of photosynthesis and cellular respiration.
II.
Overview of Cellular Respiration
 The main purpose of cellular respiration is to release energy from organic molecules by breaking
these down to simple carrier molecules than eventually to ATP.
 Cellular respiration can be aerobic – requires oxygen or anaerobic – does not require oxygen. In
the case of anaerobic pathway an alternative process called fermentation completes the
process.
 An aerobic or an anaerobic version of cellular respiration takes place in all living organisms.
Cellular respiration can break down glucose directly, but can also metabolize any other organic
molecule that is used as an energy source (anything except nucleic acids). Fat molecules
produce the most ATP /g of molecule, more than carbohydrates or proteins.
 Cellular respiration is the step by step oxidation of glucose. This process takes place in small
steps to minimize the loss of heat in the process and maximize the efficiency. The overall
equation that only shows the starting and end products is:
C6H12O6 + 6O2 --- 6CO2 + 6H2O + energy (in the form of ATP and heat)
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Because this process is exergonic, it releases heat, so ΔG is negative.
The entire process of cellular respiration is broken down to small steps of redox reactions. In a
redox reaction, two steps occur at the same time. One of the reactants is reduced, meaning
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gains electrons (may be visible as a gain of hydrogen ions) while the other reactant is oxidized
because it loses electrons (may be visible as losing hydrogen ions). (“LEO the lion goes GER”)
In general, reduced forms of substances have more energy than the oxidized forms of the same
substances.
III.
Mobile Carriers
 As a series of redox reactions take place in cellular respiration, electrons are moved along and
their energy is gradually released. Because these electrons are not transferred directly from
glucose (oxidized) to oxygen (reduced), electron carriers are required to move the electrons
along.
 NAD+ is the most versatile carrier that picks up 2e- and 1H+ and carries them to the last step,
oxidative phosphorylation where it is going to be oxidized back to its empty form.
NAD+ + 2 e- + H+
NADH
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Another electron carrier is FAD, which is used only in the citric acid cycle and also carries
electrons to oxidative phosphorylation:
FAD + 2e_ + 2H+
IV.
Two Ways of Producing ATP:
 The main purpose of cellular respiration is to produce as much ATP as possible.
 ATP is always produced form ADP and P by phosphorylation. Phosphate binding to ADP can
occur in two ways:
o Substrate-level phosphorylation – Here phosphorylation occurs as the result of an
exergonic chemical reaction. The excess energy from the reaction fuels the binding of
phosphate to ADP by specific enzymes that perform that particular chemical reaction.
o Oxidative phosphorylation – uses an electrochemical gradient of hydrogen ions across a
membrane to fuel ATP production by one specific enzyme called ATP synthase.
Prezi link: http://prezi.com/m9s0caebmwdu/ap-bio-energy-3-chemoheterotrophic-nutrition/
THE STAGES AND STEPS OF AEROBIC CELLULAR RESPIRATION
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THE STAGES OF CELLULAR RESPIRATION: PREVIEW
There are three distinct stages of the cellular respiration:
oGlycolysis
oThe citric acid cycle (preceded by pyruvate oxidation)
oOxidative phosphorylation composed of electron transport + chemiosmosis
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II.
Glycolysis
Takes place in the cytoplasm.
In this process a glucose molecule is split to produce 2 pyruvate molecules.
The process consists of 10 steps which can be divided into two phases:
o Energy investment phase – during this phase the cell actually spends energy (uses ATP)
to phosphorylate and break the glucose.
o Energy payoff phase – ATP is produced by substrate-level phosphorylation and NADH is
also produced. The net energy yield from this process is 2 ATP + 2 NADH from every
glucose molecule.
This process does not require oxygen. Pyruvates that are produced in this process will either
continue into the mitochondria for aerobic cellular respiration or remain in the cytoplasm for
fermentation in anaerobic conditions.
Total products/glucose: 2 ATP, 2 NADPH, 2 pyruvate
Find out the fate of each molecule and also what is oxidized and what is reduced in this process.
http://www.youtube.com/watch?v=EfGlznwfu9U -- song
III.
The Citric Acid Cycle (Krebs Cycle)
 If molecular oxygen is present, the two pyruvate molecules enter the mitochondrion where the
enzymes of the citric acid cycle complete the oxidation process.
 However, pyruvate needs to be altered before it enters the citric acid cycle. This takes place
during pyruvate oxidation in the matrix of the mitochondrion.
 Conversion of pyruvate to acetyl CoA (pyruvate oxidation) consists of three reactions that are
catalyzed by multiple enzymes:
o The carboxyl group is removed from pyruvate and given off as CO2 gas
o The remaining 2 carbon compound is oxidized into an acetate
o A coenzyme A (a derivative of vitamin B) is attached to the acetate, making it very
reactive.
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In the citric acid cycle the acetyl group is gradually broken down to 2 more CO2 molecules, 1 ATP
molecule, 3 NADH molecules and another electron carrier FADH2 per turn (2 turns per glucose).
The NADH and FADH2 molecules move to the electron transport chain while the CO2 molecules
are released into the blood stream and eventually into the air during exhalation. The ATP
molecules can be used in endergonic processes.
IV.
Oxidative Phosphorylation
 At this point there is still a large amount of energy stored in the 8 NADH and 2 FADH2 molecules
that move to the inner membrane of the mitochondrion from glycolysis, pyruvate oxidation and
citric acid cycle. The electrons and H+ ions are released and two processes take place:
A. Electron Transport:
 Electron transport is performed on a collection of molecules that are located on the inner
membrane of the mitochondrion. The large surface that is provided by the cristae of the
mitochondrion makes thousands of these processes possible all at once. There are four groups
of proteins in the electron transport chain, they are numbered from I through IV. As the
electrons move in the electron transport chain, they gradually lose some of their free energy.
This energy is used to fuel the active transport of H+ across the mitochondrial inner membrane
from the matrix into the intermembrane space. This process sets up an electrochemical
gradient of H+ ions between the two sides of the inner membrane. This potential energy will be
used to fuel the second part of oxidative phosphorylation.
B. Chemiosmosis
 Chemiosmosis – energy stored in the form of hydrogen ion gradient across a membrane is used
to drive cellular work such as the synthesis of ATP.
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This process also takes place on the inner membrane of the mitochondrion, where many copies
of another protein complex are located. This complex is called ATP synthase – an enzyme that
makes ATP from ADP and inorganic phosphate. This enzyme works like an ion pump but pushes
the H+ ions in reverse (from the higher to the lower concentration area) and uses the potential
energy of the concentration gradient to fuel ATP synthesis.
ATP synthase is a complex protein that has several subunits. As an H+ ion flows through a
narrow space in the enzyme, it rotates a part of the enzyme and every three electrons will this
way form an ATP molecule.
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To complete oxidative phosphorylation, H+ ions from the ATP synthase and the electrons from
the 4th transport protein have to be neutralized so they don’t harm the mitochondria. They bind
with O2 that we exhale (this is the only reason why we need to exhale oxygen) and form water
as the final product of cellular respiration.
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Oxidative phosphorylation produces 32-34 ATP molecules/glucose.
Watch: http://vcell.ndsu.nodak.edu/animations/atpgradient/movie.htm
And http://vcell.ndsu.nodak.edu/animations/etc/movie.htm
http://www.youtube.com/watch?v=VCpNk92uswY
V. Fermentation
 All known forms of cellular respiration begin with glycolysis. Glycolysis alone does not require
oxygen.
 Every living cell performs this process so it is a very ancient process that appeared early on
during the history of life when there was little free oxygen in the atmosphere. Early on this was
the only process to generate ATP for living organisms.
 Some organisms that are anaerobic still perform only this process and use different electron
donors and acceptors for oxidation and reduction reactions.
 While in cellular respiration O2 is the final electron acceptor, anaerobic respiration uses various
other electron acceptors.
 The main purpose of fermentation is to recycle the reduced forms of electron carriers (NADH)
back to oxidized forms (NAD+) so glycolysis can continue.
 This process does not yield additional ATP after glycolysis.
 There are numerous fermentation pathways. The two most commonly used ones by humans is
lactic acid fermentation and alcoholic fermentation.
 Lactic acid fermentation can take place in our muscle fibers for a short period of time during
intense exercise and also used by the dairy industry to produce yoghurt, cheese etc.
pyruvate + NADH --- Lactic acid + NAD+
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Alcoholic fermentation is used by yeast and various bacteria, but exploited by humans to make
bread and alcoholic drinks like beer and wine.
pyruvate + NADH -- Ethyl alcohol + CO2 + NAD+
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Lactic acid, according to current research can be recycled back into the mitochondria, if oxygen
becomes available in the muscle fibers and can be broken down further by aerobic cellular
respiration.
Under laboratory conditions, the rate of fermentation can be measured by measuring the
change in pH because of the acid production during fermentation. As the process goes on, the
pH decreases gradually. The rate of fermentation can also be measured by measuring the
production of some of the products such as CO2 or ethanol (in alcoholic fermentation).
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THE STAGES AND STEPS OF PHOTOSYNTHESIS
I. Overview
 Importance: Autotroph organisms perform this process by capturing the energy of sunlight and
converting this energy into organic matter. This organic matter will serve as a source of energy
and matter for the entire ecosystem. The source of carbon for making organic matter comes
from CO2.
6 CO2 + 6 H2O + energy (light)
C6H12O6 + 6 O2
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Heterotrophs cannot synthesize their organic matter so they have to obtain this matter by
consuming autotrophs or other heterotrophs.
Chemoautotrophs -- organisms that can synthesize their own organic matter by using chemical
energy sources (such as H2S, Fe2+) not sunlight
Oxygen release during photosynthesis changed the composition of the early atmosphere and
caused the evolution and adaptive radiation of aerobic organisms -- punctuated equilibrium.
This release of oxygen also caused the evolution of aerobic cellular respiration.
II. The Location of Photosynthesis
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Photosynthesis mostly takes place in the leaves of plants in the mesophyll tissue layer.
Please review from honors:
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Within the cells of the mesophyll tissue, photosynthesis takes place in the chloroplast.
Review chloroplast structure and function
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Light harvesting pigments, located in the thylakoid membrane of the chloroplast gather the
energy of sunlight. These molecules are able to take in the energy of sunlight by temporarily
exciting an electron to a higher energy level when light is absorbed.
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The most important pigment is called chlorophyll that is able to absorb light mostly in the red
and blue range of the visible light. There are other pigments, called accessory pigments that can
also absorb light but in different wavelength than chlorophyll.
The light that is not absorbed by the pigments is reflected back and is visible for other organisms
such as humans with color vision.
The two main processes of photosynthesis are:
o The light-dependent process
o The Calvin Cycle
All processes are also oxidation and reduction reactions.
Spectrophotometers are used to measure a pigment's absorption spectrum:
These machines measure the absorption spectrum of any material. A photodetector measures
the transmitted or absorbed light of a sample and calculates the % of light that is absorbed by
this material on any particular wavelength.
The action spectrum measures the efficiency of photosynthesis across the visible light spectrum
by measuring the oxygen released or CO2 used on a given wavelength of light.
A famous experiment that measures the action spectrum of photosynthesis was done by
Engelmann in the late 1800's. In this experiment, Engelmann used a filament of a
photosynthetic alga that was lit by a lamp with the help of a prism. He grew oxygen-seeking
bacteria to grow around the alga. When the light was not switched on, the bacteria were evenly
distributed around the alga. However, when the light was switched on, the bacteria grew better
around the blue and red light because the oxygen production (and with that photosynthesis)
was most active under those wavelength of light.
III. The Light-Dependent Process
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Plants take in the energy of visible light that is part of the electromagnetic spectrum that
reaches the surface of the earth. This form of the electromagnetic radiation is the most
common that is emitted from the sun.
Light travels in waves but also has particle characteristics. These particles are called photons.
The energy of these photons is used to excite the electrons in the pigment molecules in the
chloroplast.
Each pigment is tightly bound on the thylakoid membrane to various proteins. The proteins and
various pigments together form photosystems. These are responsible for collecting the energy
of sunlight and releasing electrons to continue the light dependent process.
We are going to take notes on the steps of the light dependent process together in class. We are
drawing and describing the steps on the following image:
Watch: http://vcell.ndsu.nodak.edu/animations/photosynthesis/movie.htm and
http://vcell.ndsu.nodak.edu/animations/photosystemII/movie.htm
IV. The Cyclic Electron Flow
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Under certain conditions only photosystem I is used in the light reaction but not photosystem II.
In this case the electrons cycle back from the electron acceptor of PS I to the electron transport
chain and from that to PS I again
This process does not produce NADPH and does not release oxygen and used only to generate
ATP.
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This cyclic process is useful, if there is plenty of NADPH available but there is a need for ATP in
the Calvin cycle. The Calvin cycle in general needs more ATP than NADPH so the difference is
made up by using the cyclic electron flow.
NADPH seems to be the regulator that determines which process takes place – regulation in the
cell
V.
The Calvin Cycle
 This process uses NADPH and ATP from the light-dependent process and also takes in CO2 from
the atmosphere through the stomata to form organic matter (G3P).
 This is a cyclic process in which each step is catalyzed by a different enzyme.
 Because it takes 3 turns of the cycle to produce 1 G3P, we are going to follow 3 turns at a time.
 The steps of this process are followed below:
o Carbon Fixation: Rubisco enzyme (the most common enzyme on the planet) binds 3CO2
to 3 C5 molecules called RuBP and indirectly forms 6 C3 molecules.
o Reduction Phase: 6 ATP and 6 NADPH from the light reaction are taken in by molecules
of the cycle and after three turns one G3P is released from the cycle. The rest of the
G3P molecules remain in the cycle and continue to the next phase.
o Regeneration of RuBP: This phase uses additional 3 ATP molecules to regenerate 3 RuBP
molecules.