Domain 3: Energy

3.1: All living systems require constant input of free energy.

(EK2.A.1)

1. Bioenergetic Theory
The First law of thermodynamics: Energy cannot be created or destroyed, only
transformed.

Consequences for living systems: Living systems need to continually acquire and
transform energy in order to do the work necessary to remain alive (metabolism).

Free energy: The energy available in a system to do work.

The Second law of thermodynamics: Every time energy is transformed, the entropy
(disorder) of the universe increases.

Consequences for living systems: In order to increase their internal order, or

maintain it, living systems must process more ordered forms of matter in to less
ordered forms of matter.

Living systems are open systems: Material and energy move in to living systems
from the environment. Following processing, living systems return matter and
energy back to the environment in less ordered forms.

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In order to increase control of energy processing, living systems produce free energy
in multiple-step pathways, mediated by enzyme catalysts (which lower the energy
required to cause a chemical reaction to occur).

Decreases in energy processing by living systems results in disease/death, and an

increase in the entropy of the living system.

2. MATH Skills: Gibbs Free Energy

Used to determine if a process can occur spontaneously or non-spontaneously.

If free energy is released during a process (exergonic) it will occur spontaneously

(no energy needed to sustain the reaction following activation.

If free energy is absorbed during a process (endergonic), it will occur non-

spontaneously (energy will be continually needed to sustain the reaction.

G= change in free energy (- = exergonic, + = endergonic)

H= change in enthalpy for the reaction (- = exothermic, + = endothermic)

T = kelvin temperature

S = change in entropy (+ = entropy increase, - = entropy decrease)

To solve problems, youll need to be given values.

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Exothermic reactions that increase entropy are always exergonic (Ex. Cellular
Respiration)

Endothermic reactions that decrease entropy are always endergonic (Ex.

Photosynthesis).

Other reactions will be spontaneous or not depending on the temperature at which

they occur.

Sample Problem:
Determine which of the following reactions will occur spontaneously at a
temperature of 298K, justify your answer mathematically:

Reaction 1:
A + B ! AB
Delta H: +245 KJ/mol
Delta S: -.02 KJ/K

Reaction 2:
BC ! B + C
Delta H: -334 KJ/mol
Delta S: +.12 KJ/K

Reaction 1 Delta G= + 245 (298*-.02) = + 250.96

Reaction 2 Delta G = -334 (298*.12) = - 369.76

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3. Metabolic Strategies
Uses of Biological free energy:
To accomplish cellular work (metabolism). Living systems use free energy to
repair themselves (maintain order), grow (increase their order), and reproduce
(transmit order through time).

Catabolism: Decomposition vs. Anabolism: Synthesis

Metabolic strategies:
The strategy an organism uses to acquire and process free energy will have
consequences for the life cycle of that organism.

Ex.: endothermy & ectothermy

Ectotherms: Organisms that conform their internal temperature to the temperature
of the environment. Requires that an organism only be metabolically active when
the external temperature allows, but benefits the organism by not requiring any
energy expenditure to maintain internal temperature. Examples: All organisms
except for birds and mammals.

Endotherms: Organisms that maintain a metabolically optimal internal temperature

regardless of the external temperature. Requires that an organism use free energy
to maintain internal temperature, but benefits the organism by allowing a high
metabolism, regardless of the external temperature. Examples: birds and
mammals.

Effects of Body size on metabolic rate:

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Larger organisms require less energy production per unit of mass than smaller
organisms. This is due mainly to the decreased surface area:volume ratio in larger
organisms, leading to decreased loss of heat energy to the environment.

Free energy considerations and reproduction:

Reproductive strategies are optimized for particular free energy considerations.

Example: seasonal reproduction- Organisms reproduce during particular times of

the year to make sure that they have enough free energy stored to allow for the
energy investment involved in reproduction, and to provide the offspring with
the free energy necessary to grow following birth.

Consequences of insufficient free energy production for individuals, populations,

ecosystems:
All levels of biological systems are affected by the amount of free energy available.
Individuals will suffer disease/death if they do not get sufficient free energy as
there is less energy to maintain internal order. Populations will decrease in
reproductive output, and decline in numbers as there is less energy being used to
maintain the number of individuals through reproduction. Ecosystems will
decrease in complexity and productivity, as there is less energy moving through
them.

4. MATH Skills: Coefficient Q10

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t2 = higher temperature
t1 = lower temperature
k2= metabolic rate at higher temperature
k1= metabolic rate at lower temperature
Q10 = the factor by which the reaction rate increases when the temperature is raised
by ten degrees.

Q10 tells us how a particular process will be affected by a 10 degree change in

temperature.
Most biological processes have a Q10 value between 2 and 3

Sample Problem:
Data taken to determine the effect of temperature on the rate of respiration in a
goldfish is given in the table below. Calculate the Q10 value for this data.

Temperature (C) Heartbeats per minute

20 18

25 32

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Solution: Q10 = (32/18)(10/5) = ~1.78 2 = ~3.178

3.2: Interactions between molecules affect their structure and

function. (EK4.B.1)

1. Enzyme structure and function

The relationship between structure and function:
Because the structure of a molecule allows it to accomplish its functions, changes to
the structure of a molecule will also affect its function.

These changes can have a negative or positive effect on the function of a molecule.

Molecules can interact with other molecules or their environment in order to change
their structures.

Enzymes:
Enzymes are reaction catalysts in biological systems.

Most enzymes are proteins, though RNA (ribozymes) also have some catalytic
functions.

Catalyst: any substance that increases the rate of a chemical reaction by lowering
the activation energy of that reaction while not participating in the reaction.

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 Enzymes work by physically positioning reactants (substrate) in orientations that
increase the likelihood of chemical bonds being broken or formed. Enzymes are
highly specific for the substrates that they interact with.

Typically, the name of an enzyme tells you about its substrate in the first part of its
name, and ends in ase. Ex. Protease, lipase, polymerase.

The induced fit model of enzyme function:

In order to catalyze a reaction, substrate molecules will physically bind to an area of
the enzyme called the active site. The binding of the substrate to the active site
will cause the conformation of the enzyme to change slightly, catalyzing the
reaction.

co-factors/co-enzymes:
In order to function, many enzymes require organic (co-enzymes: vitamins) or
inorganic (co-factors: minerals) groups of atoms to be complexed with the
enzyme. Ex. Many enzymes involved in interacting with DNA require zinc 2+
ions as co-factors.

2. Regulation of Enzyme Activity

Other molecules can affect enzyme structure and function:
Competitive interactions:
Refer to any substance that occupies the active site of an enzyme that is not the
substrate of that enzyme. These interactions will inhibit enzyme function.

Non-Competitive (allosteric) Interactions:

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Refer to any substance that binds to an area of an enzyme that is not the active site
and by doing so affects the function of the enzyme (usually by changing the shape
of the active site).

In this way, the end product of a metabolic pathway can influence the continuation of
that pathway by interacting with an enzyme that catalyzes an earlier step in the
pathway (feedback inhibition)

Environmental conditions affect enzyme structure and function:

The local environment of the enzyme can affect the shape of the enzyme, which will
affect the function of the enzyme. Major environmental factors include
temperature, pH, and salt concentration.

Other environmental variables can affect the function of the enzyme by increasing or
limiting enzyme-substrate binding. Major factors that do this include enzyme
concentration, and substrate concentration.

Enzyme action can be measured in many different ways:

Typical methods include:
Appearance of a product.
Disappearance of a substrate.
Indirect analogs: color change, change in temperature, etc.

3.3: Organisms capture and store free energy for use in

biological processes. (EK2.A.2)

1. Energy Processing
Autotrophic nutrition:
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Autotrophs (self-feeders) are able to use energy from the environment to convert
inorganic molecules in to organic compounds where free energy is stored. They
are the producers in all food chains on Earth.

Photosynthetic organisms: Use visible light energy to convert water and carbon
dioxide in to oxygen gas (waste product) and organic compounds (sugar precursor
molecules). Examples: all plants, and phytoplankton (the major producers on the
planet).

Chemosynthetic organisms: Use high energy inorganic compounds to convert

carbon dioxide and water in to organic compounds. The specific high energy
compounds depend on the organism. Example: hydrothermal vent producers:
Use H2S as their high energy compound, which is released from the vents.

Heterotrophic nutrition:
Heterotrophs release free energy from organic compounds (from the food chain,
either autotrophs or other heterotrophs), and convert those organic compounds
in to inorganic compounds.

Anaerobic heterotrophs: Do not require oxygen in order to release free energy.

Examples: many bacteria, yeast (facultative anaerobes: can do it if they have to).

Aerobic heterotrophs: Use oxygen to release free energy. Release ~20X more free
energy from food molecules than anaerobes do. Examples: all multicellular fungi
and animals.

Electron shuttles:
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 Biological energy production utilizes reduction/oxidation reactions. Electrons are
taken from some molecules (oxidation) and transferred to other molecules
(oxidation). This does not happen directly. The transfer of electrons occurs via
electron shuttle molecules, which can hold electrons when they are taken from
molecules and release them to other molecules when needed. This transfer of
electrons also bring protons along for the ride in Biological systems. Examples:
NAD+/NADH, FAD/FADH2, NADP+/NADPH

ATP in Metabolism:
ATP is a short-term free energy storage molecule used in all biological systems.
When a cell releases free energy from a food molecule (or incorporates it from
sunlight), that free energy is used to turn a molecule of ADP (2 phosphates) in to a
molecule of ATP (3 phosphates). The bond between the 2nd and 3rd phosphate is
very unstable and easily broken. When it is broken, the free energy that is
released is used by biological systems to power cellular work.

2. Photoautotrophic nutrition- light reactions

Photosynthesis is a two-part process:
The light reactions
Carbon Fixation

Mechanisms of photosynthesis- light reactions

Light is energy: photons of specific wavelengths are used in the light reactions.

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The light reactions occur in specialized collections of proteins and chlorophyll called
photosystems. These photosystems are embedded in the thylakoid membranes of
chloroplasts.

During the light reactions, light energy is used to remove electrons from chlorophyll,
and use those electrons to produce ATP and NADPH.

When excited by photons, chlorophyll sends an electron in to the excited state.

This excited electron then enters an electron transport chain of proteins.

Water supplies photosystem II with replacement electrons, and converts the water
in to protons and molecular oxygen.

Non-cyclic electron flow produces NADPH:

The ETC connects two different photosystems (PS II and PSI). Electrons produced
at PSII move to PSI. Electrons produced at PSI either cycle back in to the ETC,
and back to PSI, or they are used by an enzyme to produce NADPH from NAD+

Chemiosmosis produces ATP:

As Electrons move through the ETC, the free energy that is released is used by the
proteins in the chain to actively transport protons from the stroma into the
thylakoid space. The high concentration of protons in the thylakoid space
provides the free energy needed to produce ATP. The only way protons can
diffuse back in to the stroma is through the motor protein ATP synthase.

3. Photoautotrophic nutrition 2- Carbon fixation

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Mechanisms of photosynthesis- Carbon fixation
Carbon fixation happens in the stroma of the chloroplasts, controlled by a
collection of enzymes that modulate the Calvin cycle.

During carbon fixation, the ATP and NADPH produced during the light reactions
will be used to drive the incorporation of carbon dioxide in to an organic sugar
building block called G3P.

Rubisco is the enzyme that incorporates CO2 in to the beginning of the Calvin
cycle.

During the Calvin cycle, the energy in ATP and the electrons in NADPH are used
to reduce 3 5-Carbon molecules of RuBP (plus 3 CO2 from rubisco) in to 6 3-
Carbon molecules of G3P. One of these is the product of the cycle. The
remaining 5 G3P molecules are then converted back in to 3 5-Carbon RuBP
molecules to continue the cycle.

G3P can be combined to make sugars, and then used in respiration to produce
ATP to power cellular work or serve as raw materials (along with other nutrients)
to make lipids, amino acids, or nucleotides.

4. Chemoheterotrophic nutrition- anaerobic cellular respiration

Mechanisms of Respiration- glycolysis/fermentation
Glycolysis occurs in the cytoplasm, controlled by a collection of enzymes.

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During glycolysis, 2 ATP are used to convert one 6-Carbon glucose in to 2 3-carbon
pyruvate molecules. This process also produces 4 ATP molecules (2 net), and 2
molecules of NADH.

Following glycolysis, cells either commit to aerobic cellular respiration, or use a

fermentation pathway to oxidize the NADH produced in glycolysis back to NAD+
in order to continue glycolysis.

Fermentation will oxidize NADH by reducing pyruvate in to another organic

molecule (which depends upon the organism undergoing fermentation). Ex:
yeast cells- convert pyruvate in to 1 carbon dioxide molecule and 1 2-Carbon
ethanol molecule. Human muscle cells convert pyruvate in to lactic acid.

All fermentation end products are more toxic than pyruvate, but the conversion is
necessary in order to supply glycolysis with continual NAD+

5. Chemoheterotrophic nutrition: Aerobic cellular respiration

Mechanisms of Respiration- Aerobic Cellular Respiration
In eukaryotes, ACR occurs in the mitochondrion. Pyruvate must be transported
in to the matrix of the mitochondria. It is also converted in to a 2-Carbon acetyl
group, which is combined with a molecule of co-enzyme A. Acetyl Co-A is the
input for the Citric Acid Cycle. This conversion produces another molecule of
NADH

The Citric Acid Cycle:

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 The citric acid cycle occurs in the mitochondrial matrix, controlled by a
collection of enzymes.

During the citric acid cycle, the remaining carbons from glucose (on the acetyl group)
are converted in to carbon dioxide (oxidation). This process produces 3 NADH
and 1 FADH2, along with 1 ATP per acetyl group.

Chemiosmosis produces ATP:

Following the citric acid cycle, the NADH and FADH2 that have been produced
during all prior parts of cellular respiration are oxidized at electron transport
chains embedded in the mitochondrial inner membrane.

As Electrons move through the ETC, the free energy that is released is used by the
proteins in the chain to actively transport protons from the matrix into the
intermembrane space. The high concentration of protons in the intermembrane
space provides the free energy needed to produce ATP. The only way protons can
diffuse back in to the matrix is through the motor protein ATP synthase.

Approximately 3 ATP are produced per NADH oxidized. Approximately 2 ATP

are produced per FADH2 oxidized. These numbers vary depending on the
particular cellular system.

At the end of the ETC, the electrons combine with oxygen and protons to produce
water.

All macromolecules are able to enter cellular respiration pathways, either by being
converted in to glucose, or by being converted in to pathway intermediaries.
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3.4: Cooperative interactions within organisms promote
efficiency in the use of energy and matter. (EK4.B.2)

1. Organizational efficiency in energy processing.

Compartmentalization allows for increased efficiency.

Cellular compartmentalization:
By having different metabolic processes occurring in different cellular
compartments, the conditions that those processes occur under can be varied
without interfering with other processes.

Compartmentalization also allows cells to establish specific locations for specific

processes.

Example: Mitochondrial/Chloroplast compartmentalization allows for the varied

pH/proton sequestration that chemiosmosis will generate.

Example: all of the proteins for required metabolic processes are isolated and
grouped in to different cellular compartments. This allows for more efficient
progression through a metabolic sequence, and also increases the likelihood that
any feedback inhibition will be efficient.

Ex. Gram-negative bacteria have adapted their cell membranes to

compartmentalize processes needed to carry out aerobic cellular respiration and
photosynthesis

Multicellular compartmentalization:

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 Different systems in a multicellular organism serve different, cooperative purposes
for matter and energy processing:
Digestive system: Conversion/absorption of complex food molecules in to
metabolic inputs (starch in to glucose)
Respiratory system: exchange of metabolic gases (oxygen and carbon dioxide)
Circulatory system: Delivery of nutrients and removal of waste products from
all cells.
Excretory system: Removal of waste molecules (water and nitrogenous wastes).

All of these systems have different roles in contributing to an overall metabolic

goal.

Microbial cooperation:
Microbial communities diversify in their functions to cooperatively accomplish
metabolic tasks.

Ex: Animal rumen communities. Ruminants are herbivorous mammals (eg cows)
who are able to digest cellulose due to the cooperative actions of microbial
communities in their expanded upper digestive tract (the rumen)

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