Energy in the Cell
• Energy is in two basic forms:
• 1. potential energy, which is energy
stored up, ready to use, like a coiled
spring, the capacity to do work. 2.
kinetic energy, which is energy of
motion, actually doing work.
• Food molecules contain potential
energy in their chemical bonds.
• ―calories‖ are a measure of energy.
Some foods contain more energy per
gram than others, because their
chemical bonds store more energy.
For instance, carbohydrates and
proteins store 4 calories per gram,
while fats store 9 calories per gram.
• Cells convert the chemical bond
energy in food molecules to chemical
bond energy stored in ATP molecules.
• ATP energy is used to run metabolism
and all other bodily processes.
• First Law: the total mount of energy in
the Universe is constant. Energy is
neither created not destroyed, it just
• When energy is expended, part of it
goes to do useful work, and the rest
ends up as heat. None of it is lost, but
it changes forms.
• Second Law: disorder (entropy)
increases. Energy goes from useful
forms to useless heat.
• Every energy transformation step is
inefficient (as a consequence of the
Second Law), meaning that some of
the energy is converted to waste heat
at every step, and the amount of
useful work decreases with every step.
• Life is very orderly compared to non-
living things. Living things are able to
locally reverse the overall direction of
entropy by using a lot of energy.
• The energy of living cells comes from
the Sun, and it ends up as waste heat.
• In living cells, energy for
immediate use is stored as
molecules of ATP, adenosine
triphosphate. When the
energy is used, one of the
phosphates attached to ATP is
released, giving ADP,
• The 3 phosphates each have a
negative charge, and so they
repel each other. When the
bond holding them together is
broken, the phosphates fly
apart, like a spring being
released. The cell can use this
energy in many different ways.
• A metabolic reaction is the
conversion of one chemical
compound into another one inside
a living cell.
• For every metabolic reaction, you
start with reactants and convert
them to products. An enzyme
does the conversion. Each
reaction uses a different enzyme.
• The basic rule: reactions run
downhill: more energetic reactants
are converted to less energetic
• If a reaction needs to run uphill,
creating products that contain
more energy than the reactants,
energy in the form of ATP must be
• Reactants are also called
• Enzymes are proteins that cause
specific chemical reactions to occur.
• Enzymes act as catalysts: they help
the reaction occur, but they aren’t
used up in the reaction.
• All reactions require an input of energy
to get them started: the activation
energy. Think of touching a match to
a piece of paper to start a fire: the
match is supplying the activation
• Enzymes work by lowering the
activation energy for a reaction. The
reaction occurs thousands or millions
of times faster than without the
enzyme. The little bit of activation
energy needed is supplied by the
collision of the molecules involved.
• Enzymes are very specific for their
substrates: they work on only a very
limited number of similar molecules.
• Each enzyme has an active site, a special region
that holds the substrates together and causes
them to react
• The active site promotes the reaction by orienting
the substrates properly, straining their bonds so
they break more easily, and by providing acidic or
basic amino acids to help the reaction along.
• Enzymes often use small accessory molecules
called coenzymes to help carry out the reaction.
Most vitamins are coenzymes. .
• Enzymes often have small molecules that act as
inhibitors or activators of their activity. These
molecules alter the active site so the enzyme
reacts differently to the substrate.
• Enzyme activity is strongly influenced by
temperature. They have an optimum
temperature: to hot or too cold slows them down.
Most of the enzymes in humans have an optimum
temperature near body temperature.
• pH and salt level also influence enzyme activity,
with optimum values for each.
Generating ATP from Food
• ATP (adenosine triphosphate) is made
from ADP (adenosine diphosphate)
plus a phosphate ion (symbolized by
Pi). Making ATP requires energy,
which comes form the potential energy
stored in food molecules.
• More specifically, electrons from
glucose or other food molecules are
passed through a series of steps,
releasing part of their energy in each
step, and ultimately ending up
attached to oxygen. The energy from
the electrons going down the energy
hill is used to create ATP from ADP
• Similarly, high energy electrons are
carried by the molecule NADH. When
NADH uses its high energy electrons,
it is converted to NAD+. Electrons in
the cell are often accompanied by an
• Energy from chemical bonds is transferred in the form of electrons. Oxidation means removing
electrons. Its opposite is reduction, which is gaining electrons. LEO = Lose Electrons Oxidation;
GER = Gain Electrons Reduction.
• Some common forms of oxidation: burning and rusting.
• Cells oxidize glucose to form carbon dioxide and water. The cell removes electrons from glucose
(in a series of steps), which converts it to carbon dioxide. The energy stored in the electrons is
used to make ATP. Finally, the electrons are given to oxygen molecules, converting them to
• By passing the electrons through a series of steps before their final destination in water, the cell
can harvest the energy efficiently. In contrast, burning releases the energy all at once, so it can’t
be captured easily.
• The electrons are often accompanied by a hydrogen (H), and they are usually carried in the cell by
the molecule NADH (or its close relative NADPH).
Aerobic and Anaerobic Respiration
• Respiration is generating energy by breaking down food molecules,
converting the energy in their chemical bonds to ATP energy.
• Before oxygen was present in the atmosphere, all cells used
anaerobic respiration, which means generating energy in the
absence of oxygen.
• Many bacteria only have anaerobic respiration. Some are even
poisoned by the presence of oxygen: the bacteria that cause
gangrene, for example.
• Most eukaryotes use aerobic respiration, generating energy with the
use of oxygen , in addition to anaerobic respiration. We use
anaerobic respiration to start the process, but finish it with aerobic.
Aerobic respiration is much more efficient than anaerobic.
• The anaerobic pathway is called glycolysis, which means ―breaking
down glucose‖. It occurs in the cytoplasm.
• The aerobic pathway occurs in the mitochondria.
Summary of Respiration
• 1. glycolysis (anaerobic) breaks glucose (a 6 carbon
chain) into 2 molecules of pyruvate (3 carbons each).
This require 2 ATPs as input, and yields 4 ATPs.
Glycolysis thus nets 2 ATPs for each glucose.
– intermediate step between glycolysis and the Krebs cycle:
conversion of pyruvate to acetyl CoA.
• 2. Krebs cycle: acetyl CoA converted to carbon dioxide
• 3. electron transport: high energy electrons converted to
• Aerobic respiration yields 34 more ATPs per glucose,
giving a total of 36 ATPs generated from each glucose.
All but 2 of them come from aerobic respiration.
• Occurs in the cytoplasm, not in
• Does not use oxygen.
• Almost all living things use this pathway.
• Basic process: add phosphates (from ATP)
to each end of the glucose, then split it in
half, using that chemical bond energy to
generate 4 ATPs. Final 3-carbon products
• Also releases 2 electrons, which are
carried by NADH. These electrons can be
converted to energy if oxygen is present,
but they cause problems if not.
• What to do with excess electrons? Need to
regenerate NAD+ so it can take up more
electrons, so give the electrons back to
pyruvate in some way:
– In yeast, the pyruvate gets converted to
ethanol when the electrons are added back.
– In humans and many bacteria, pyruvate
gets converted to lactate (lactic acid).
Causes muscle pain during intense exercise
when not enough oxygen gets to the muscle
• Requires oxygen, occurs in the
• Conversion of pyruvate (from
glycolysis) to carbon dioxide, with
generation of high energy
electrons and ATP.
• Preliminary steps before starting
the Krebs cycle: 3 carbon
pyruvate to 2 carbon acetyl CoA;
third carbon lost as carbon
dioxide. Generates high energy
electrons carried by NADH.
• Krebs cycle: add 2 carbon acetyl
CoA to 4 carbon sugar, remove
the 2 extra carbons one at a time
as carbon dioxide, generate
several high energy electrons on
NADH plus some ATP.
• The final stage in aerobic respiration
• Krebs cycle generates many high energy
electrons (carried by NADH). Also some
from glycolysis. These need to be
converted to ATP so the cell can use them.
• Electron transport pumps electrons from the
inner compartment to the outer compartment
of the mitochondria.
• Electrons are passed from NADH through 3
proteins which use the electron energy to
pump H+ ions through the membrane. Each
protein pump drains energy from the
electrons, so by the end of the process, the
electrons are low energy.
• The final protein pump adds the electrons
(plus hydrogens) to oxygen, producing
• The H+ level builds up between the
membranes. It flows back into the inside
through a special protein channel called
ATP synthase, which uses the energy of
their flow to combine ADP and Pi into ATP.
This is the main way energy is generated in
• Cyanide blocks electron transport chain—no
more ATP is made
• Brown fat runs electron transport chain
without generating ATP, just to produce
Energy from Other Foods
• Glucose is the primary food molecule
• Carbohydrates are broken down into glucose in
the stomach. It enters the blood through the small
• Cells absorb glucose and trap it inside by adding a
phosphate to it.
• It is then either used directly or converted into
starch, to be used later.
• Fats are the primary energy storage molecules,
containing more than twice as much energy per
gram as carbohydrates or proteins. The fatty acids
are converted to acetyl CoA (preliminary steps of
aerobic metabolism). From there they enter the
Krebs cycle. The glycerol molecules go into
• The liver converts excess starch into fat.
• Proteins are mostly broken down into amino acids
which become parts of new proteins.
• When proteins are used for energy, their carbon
backbones enter glycolysis or Krebs cycle at
various points. The amino group becomes
ammonia, which is poisonous. Ammonia gets
converted to urea, which is a lot less toxic, and
then gets excreted in urine.
• Photosynthesis means taking energy from
sunlight and converting it to a form usable
by living cells.
• Green plants do photosynthesis; so do
many bacteria and protists (which are single
• Two parts to photosynthesis:
• 1. the light-dependent reactions, in which
sunlight is used to extract high energy
electrons from water. These high energy
electrons are then used to make ATP.
Oxygen from the water is released into the
• 2. the light-independent reactions (or dark
reactions, or Calvin cycle), in which that
ATP energy is used to convert carbon
dioxide into glucose.
• In plants, all of these reactions occur in the
chloroplast, an organelle that contains its
own DNA and is thought to be derived from
an ancient symbiosis between a free-living
photosynthetic bacterium and a primitive
eukaryote (just like the mitochondria).
• All the food we animals eat comes from
Light and Pigments
• Visible light is a form of
electromagnetic radiation, along with
X-rays, ultraviolet, infrared,
microwaves, radio waves, etc. The
only difference between these forms of
radiation is the wavelength.
• Visible light is all frequencies between
400 and 700 nanometers, with blue
light at the 400 end and red at the 700
• White light is a mixture of all these
wavelengths; colors appear when only
some wavelengths are present.
• Chlorophyll is green because it
absorbs the red and blue wavelengths,
reflecting only the green wavelengths.
• Other plant pigments absorb different
wavelengths, so they have different
• Absorbing light puts chlorophyll into a
high energy state. This energy is then
harvested by a series of metabolic
• The chlorophyll molecules are
arranged in groups of 200-300, called
photosystems. Each photosystem
acts like an antenna—any of the
molecules can capture a photon of
sunlight, but then that energy is
transferred to a central ―reaction
center‖ molecule, which passes the
energy (excited electrons) out of the
• In green plants, there are 2 separate
ways of extracting electrons. The
more heavily used pathway needs 2
photons to boost electrons up to a high
enough energy to be bound to the
plant cell’s energy carrying molecule,
NADPH. The electrons on NADPH are
then passed to the light-independent
reactions to generate glucose.
• The electrons are initially extracted
from water, carried along with the
hydrogens. The waste product is
oxygen, which goes into the
atmosphere. This is the source of all
the oxygen in the atmosphere.
• The energy from sunlight is captured
in the form of excited electrons, which
are bound to the electron-carrying
• To form glucose, carbon dioxide
(which has 1 carbon atom) is attached
to a 5-carbon sugar, then processed
through a series of intermediates
called the ―Calvin cycle‖.
• The Calvin cycle goes around 6 times
to create the 6-carbon glucose from
carbon dioxide. Each turn regenerates
all the necessary intermediates. The
cycle uses electrons from NADPH, and
also energy from ATP.
• After glucose is synthesized, it is
converted to starch for storage, and
then the starch is converted to sucrose
(a disaccharide) for transport to other
parts of the plant.