Ch. 6 Tour of the Cell
Concept 6.1 Biologists use microscopes and the tools of biochemistry to study cells

In a light microscope (LM), visible light passes through the specimen and then through glass lenses.
○ The lenses refract light so that the image is magnified into the eye or a camera.

Microscopes vary in magnification, resolution, and contrast.
○ Magnification is the ratio of an object’s image to its real size.
○ Resolution is a measure of image clarity. It is the minimum distance two points can be separated and still be
distinguished as two separate points.
○ Contrast accentuates differences in parts of the sample. It can be improved by staining or labeling of cell
components so they stand out.

Although an LM can resolve individual cells, it cannot resolve much of the internal anatomy, especially the
organelles, membrane-enclosed structures within eukaryotic cells.
Concept 6.2 Eukaryotic cells have internal membranes that compartmentalize their functions
Prokaryotic and eukaryotic cells differ in size and complexity.

Organisms of the domains Bacteria and Archaea consist of prokaryotic cells. Protists, fungi, animals, and plants
consist of eukaryotic cells.
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All cells are surrounded by a selective barrier, the plasma membrane.
The semifluid substance within the membrane is the cytosol, in which subcellular components are suspended.

All cells contain chromosomes that carry genes in the form of DNA.

All cells have ribosomes, tiny complexes that make proteins based on instructions contained in genes.

A major difference between prokaryotic and eukaryotic cells is the location of the DNA.
○ In a eukaryotic cell, most of the DNA is in an organelle bounded by a double membrane, the nucleus.
○ In a prokaryotic cell, the DNA is concentrated in the nucleoid, without a membrane separating it from the rest
of the cell.

The interior of a prokaryotic cell and the region between the nucleus and the plasma membrane of a eukaryotic cell
is the cytoplasm.
Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles with specialized form and
function. These membrane-bound organelles are absent in prokaryotes.
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Eukaryotic cells are generally much larger than prokaryotic cells.
The plasma membrane functions as a selective barrier that allows the passage of oxygen, nutrients, and wastes for
the whole volume of the cell.
Concept 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes

The nucleus contains most of the genes in a eukaryotic cell.
○ Additional genes are located in mitochondria and chloroplasts.

The nucleus is separated from the cytoplasm by a double membrane called the nuclear envelope.

Within the nucleus, the DNA and associated proteins are organized into discrete units called chromosomes,
structures that carry the genetic information.
Ribosomes are protein factories.

Ribosomes, containing rRNA and protein, are the cellular components that carry out protein synthesis.
○ Cell types that synthesize large quantities of proteins (such as pancreas cells) have large numbers of ribosomes
and prominent nucleoli.

Free ribosomes are suspended in the cytosol and synthesize proteins that function within the cytosol.

Bound ribosomes are attached to the outside of the endoplasmic reticulum or nuclear envelope.
○ Bound ribosomes synthesize proteins that are inserted into membranes, packaged into organelles such as
ribosomes, or exported (secreted) from the cell.
○
Cells that specialize in protein secretion—for instance, the cells of the pancreas that secrete digestive
enzymes—frequently have a high proportion of bound ribosomes.
Concept 6.4 The endomembrane system regulates protein traffic and performs metabolic functions in the cell
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Membrane containing organelles = nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles,
vacuoles, and plasma membrane.
The tasks of the endomembrane system include synthesis of proteins and their transport into membranes and
organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons.
The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions.

The endoplasmic reticulum (ER) accounts for more than half the membranes in a eukaryotic cell..

There are two connected regions of ER that differ in structure and function.
○ Smooth ER looks smooth because it lacks ribosomes.
○ Rough ER looks rough because ribosomes are attached to the outside, including the outside of the nuclear
envelope.

Smooth ER is rich in enzymes and plays a role in a variety of metabolic processes, including synthesis of lipids,
metabolism of carbohydrates, detoxification of drugs and poisons, and storage of calcium ions.

Rough ER is also a membrane factory for the cell.
○ Membrane-bound proteins are synthesized directly into the ER membrane and anchored by their own
hydrophobic portions.
The Golgi apparatus is the shipping and receiving center for cell products.
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Many transport vesicles from the ER travel to the Golgi apparatus for modification of their contents.
The Golgi apparatus is a center of manufacturing, warehousing, sorting, and shipping.
○ Some products of the ER are modified and stored and then sent on.
Lysosomes are digestive compartments.

A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to digest macromolecules.
Vacuoles have diverse functions in cell maintenance.

Vacuoles are large vesicles derived from the EG and Golgi apparatus.
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These membrane-bound sacs have a variety of functions.
Contractile vacuoles, found in freshwater protists, pump excess water out of the cell to maintain the appropriate
concentration of ions and molecules inside the cell..
Concept 6.5 Mitochondria and chloroplasts change energy from one form to another

Mitochondria and chloroplasts are the organelles that convert energy to forms that cells can use for work.

Mitochondria are the sites of cellular respiration, using oxygen to generate ATP by extracting energy from sugars,
fats, and other fuels.

Chloroplasts, found in plants and algae, are the sites of photosynthesis.
○ Chloroplasts convert solar energy to chemical energy by absorbing sunshine and using it to synthesize new
organic compounds such as sugars from CO2 and H2O.
Mitochondria and chloroplasts have a similar evolutionary origin.

The endosymbiont theory states that an early ancestor of eukaryotic cells engulfed an oxygen-using
nonphotosynthetic prokaryotic cell.
○ The engulfed cell became an endosymbiont within its host cell.
○ Over the course of evolution, the host cell and its endosymbiont merged into a single organism, a eukaryotic cell
with a mitochondrion.
○ One of these cells engulfed a photosynthetic prokaryote and evolved into a eukaryotic cell containing
chloroplasts.
The peroxisome is an oxidative organelle.
Concept 6.6 The cytoskeleton is a network of fibers that organizes structures and activities in the cell
The cytoskeleton provides support, motility, and regulation.

The cytoskeleton is a network of fibers extending through the cytoplasm that provides mechanical support and
maintains the cell’s shape.
○ This function is especially important in animal cells, which lack walls.
Three main types of fibers make up the cytoskeleton: microtubules, microfilaments, and intermediate filaments.

Microtubules are the thickest of the three types of fibers; microfilaments (or actin filaments) are the thinnest; and
intermediate filaments are fibers with diameters in a middle range.
Concept 6.7 Extracellular components and connections between cells help coordinate cellular activities
Plant cells are encased by cell walls.

In plants, the cell wall protects the cell, maintains its shape, prevents excessive uptake of water, and supports the
plant against the force of gravity.
The extracellular matrix of animal cells provides support, adhesion, movement, and regulation.

Though lacking cell walls, animal cells do have an elaborate extracellular matrix (ECM).

The primary constituents of the ECM are glycoproteins, especially collagen fibers, embedded in a network of
glycoprotein proteoglycans.
Intercellular junctions help integrate cells into higher levels of structure and function.

Neighboring cells in tissues, organs, and organ systems often adhere, interact, and communicate through direct
physical contact.
Ch. 7 Membrane structure and function
Concept 7.1 Cellular membranes are fluid mosaics of lipids and proteins

The main macromolecules in membranes are lipids and proteins, but carbohydrates are also important.

The most abundant lipids are phospholipids.

Phospholipids and most other membrane constituents are amphipathic molecules, which have both hydrophobic
and hydrophilic regions.
Membrane models have evolved to fit new data.

The arrangement of phospholipids and proteins in biological membranes is described by the fluid mosaic model.
○ In this model, the membrane is a fluid structure with a “mosaic” of various proteins embedded in or attached to
a double layer (bilayer) of phospholipids.
Membranes are fluid.

Membrane molecules are held in place by relatively weak hydrophobic interactions.

Most of the lipids and some proteins drift laterally in the plane of the membrane but rarely flip-flop from one
phospholipid layer to the other.

Some large membrane proteins drift within the phospholipid bilayer, although they move more slowly than the
phospholipids.

Membrane fluidity is influenced by temperature.
○ As temperatures cool, membranes switch from a fluid state to a solid state as the phospholipids pack more
closely.

Membrane fluidity is also influenced by the components of the membrane.
○ Membranes rich in unsaturated fatty acids are more fluid that those dominated by saturated fatty acids because
kinks in the unsaturated fatty acid tails at the locations of the double bonds prevent tight packing.

The steroid cholesterol is wedged between phospholipid molecules in the plasma membrane of animal cells.
○ At warm temperatures (such as 37°C), cholesterol restrains the movement of phospholipids and reduces fluidity.
○ At cool temperatures, cholesterol maintains fluidity by preventing tight packing.
○
Thus, cholesterol acts as a “fluidity buffer” for the membrane, resisting changes in membrane fluidity as
temperature changes.

Variations in the lipid composition of cell membranes of many species are evolutionary adaptations to maintain
membrane fluidity under specific environmental conditions.
○ The membranes of fishes that live in extreme cold have a high proportion of unsaturated hydrocarbon tails,
enabling them to stay fluid.
○ The membranes of bacteria and archaea living in thermal hot springs and geysers include unusual lipids that
prevent excessive fluidity at such high temperatures.

Many organisms that experience variable temperatures have evolved the ability to change the lipid composition of
cell membranes.
○ For example, cold-adapted organisms such as winter wheat increase the percentage of unsaturated
phospholipids in their membranes in the autumn to prevent the membranes from solidifying during winter.
Membranes are mosaics of structure and function.

A membrane is a collage of different proteins embedded in the fluid matrix of the lipid bilayer.

Proteins determine most of the membrane’s specific functions.

There are two major populations of membrane proteins: integral and peripheral.

Integral proteins penetrate the hydrophobic interior of the lipid bilayer, usually completely spanning the membrane
as transmembrane proteins.
○ Other integral proteins extend partway into the hydrophobic interior.
○ The hydrophobic regions are embedded in the membrane’s interior
○ The hydrophilic regions of integral proteins are in contact with the aqueous environment.
○ Some integral proteins have a hydrophilic channel through their center that allows passage of hydrophilic
substances.

Peripheral proteins are not embedded in the lipid bilayer at all.
○ Instead, peripheral proteins are loosely bound to the surface of the membrane, often to integral proteins.

The proteins of the plasma membrane have six major functions:
1. Transport of specific solutes into or out of cells
2. Enzymatic activity, sometimes catalyzing one of a number of steps of a metabolic pathway
3. Signal transduction, relaying hormonal messages to the cell
4. Cell-cell recognition, allowing other proteins to attach two adjacent cells together
5. Intercellular joining of adjacent cells with gap or tight junctions
6. Attachment to the cytoskeleton and extracellular matrix, maintaining cell shape and stabilizing the location of
certain membrane proteins
Membrane carbohydrates are important for cell-cell recognition.

Cell-cell recognition, the ability of a cell to distinguish one type of neighboring cell from another, is crucial to the
functioning of an organism.
○ Cell-cell recognition is important in the sorting and organizing of cells into tissues and organs during
development.
○ Recognition is also the basis for the rejection of foreign cells by the immune system.
○ Cells recognize other cells by binding to surface molecules, often containing carbohydrates, on the extracellular
surface of the plasma membrane.
Concept 7.2 Membrane structure results in selective permeability

Substances do not move across the barrier indiscriminately; membranes are selectively permeable.
○ The cell is able to take up many varieties of small molecules and ions and exclude others.
○ Substances that move through the membrane do so at different rates.

Movement of a molecule through a membrane depends on the interaction of the molecule with the hydrophobic
interior of the membrane.
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○
○
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Nonpolar molecules, such as hydrocarbons, CO2, and O2, are hydrophobic and can dissolve in the lipid bilayer
and cross easily, without the assistance of membrane proteins.
The hydrophobic interior of the membrane impedes the direct passage of ions and polar molecules, which are
hydrophilic.
Polar molecules, such as glucose and other sugars, and even water, an extremely small polar molecule, cross the
lipid bilayer slowly.
An ion, whether a charged atom or a molecule, and its surrounding shell of water also have difficulty penetrating
the hydrophobic interior of the membrane.

Proteins assist and regulate the transport of ions and polar molecules.

Cell membranes are permeable to specific ions and a variety of polar molecules, which can avoid contact with the
lipid bilayer by passing through transport proteins that span the membrane.
Some transport proteins called channel proteins have a hydrophilic channel that certain molecules or ions can use as
a tunnel through the membrane.
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The passage of water through the membrane can be greatly facilitated by channel proteins known as aquaporins.

Some transport proteins called carrier proteins bind to molecules and change shape to shuttle them across the
membrane.
Concept 7.3 Passive transport is diffusion of a substance across a membrane with no energy investment

Molecules have thermal energy or heat, due to their constant motion.
○ One result of thermal motion is diffusion, the movement of molecules of any substance to spread out in the
available space.

In the absence of other forces, a substance diffuses from where it is more concentrated to where it is less
concentrated, down its concentration gradient.
No work must be done to move substances down the concentration gradient; diffusion is a spontaneous process,
needing no input of energy.
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The diffusion of a substance across a biological membrane is passive transport because it requires no energy from
the cell to make it happen.
○ The concentration gradient itself represents potential energy and drives diffusion.
Osmosis is the passive transport of water.

The diffusion of water across a selectively permeable membrane is called osmosis.

Both solute concentration and membrane permeability affect tonicity, the ability of a surrounding solution to cause
a cell to gain or lose water.

If a cell without a cell wall, such as an animal cell, is immersed in an environment that is isotonic to the cell, there is
no net movement of water across the plasma membrane.

If the cell is immersed in a solution that is hypertonic to the cell (containing nonpenetrating solutes), the cell loses
water to its environment, shrivels, and probably dies. .
If the cell is immersed in a solution that is hypotonic to the cell, water enters the cell faster than it leaves, and the
cell swells and lyses (bursts) like an overfilled water balloon.

Specific proteins facilitate the passive transport of water and selected solutes.

Many polar molecules and ions that are normally impeded by the lipid bilayer of the membrane diffuse passively
with the help of transport proteins that span the membrane.

The passive movement of molecules down their concentration gradient with the help of transport proteins is called
facilitated diffusion.
○ Most transport proteins are very specific: They transport some substances but not others.

Two types of transport proteins facilitate the movement of molecules or ions across membranes: channel proteins
and carrier proteins.

Channel proteins provide hydrophilic corridors for the passage of specific molecules or ions.

Many ion channels function as gated channels.
○

These channels open or close depending on the presence or absence of an electrical, chemical, or physical
stimulus.
Some transport proteins do not provide channels but appear to actually translocate the solute-binding site and the
solute across the membrane as the transport protein changes shape.
○ These shape changes may be triggered by the binding and release of the transported molecule.
Concept 7.4 Active transport uses energy to move solutes against their gradients

Some transport proteins can move solutes across membranes against their concentration gradient, from the side
where they are less concentrated to the side where they are more concentrated.

This active transport requires the cell to expend metabolic energy and enables a cell to maintain internal
concentrations of small molecules that would otherwise diffuse across the membrane.

ATP supplies the energy for most active transport by transferring its terminal phosphate group directly to the
transport protein.
○ This process may induce a conformational change in the transport protein, translocating the bound solute across
the membrane.
○ The sodium-potassium pump works this way in exchanging sodium ions (Na+) for potassium ions (K+) across the
plasma membrane of animal cells.
Some ion pumps generate voltage across membranes.

All cells maintain a voltage across their plasma membranes.


Voltage is electrical potential energy resulting from the separation of opposite charges.
The cytoplasm of a cell is negative in charge relative to the extracellular fluid because of an unequal distribution of
cations and anions on the two sides of the membrane.
The voltage across a membrane is called a membrane potential and ranges from −50 to −200 millivolts (mV). The
inside of the cell is negative compared to the outside.
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The membrane potential acts like a battery. Because the inside of the cell is negative compared with the outside, the
membrane potential favors the passive transport of cations into the cell and anions out of the cell.

Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a
membrane.
○ One is a chemical force based on an ion’s concentration gradient.
○ The other is an electrical force based on the effect of the membrane potential on the ion’s movement.

An ion does not simply diffuse down its concentration gradient but diffuses down its electrochemical gradient.
○ For example, there is a higher concentration of Na+ outside a resting nerve cell than inside.
○ When the neuron is stimulated, gated channels open and Na+ diffuses into the cell down the electrochemical
gradient.
○ The diffusion of Na+ is driven by the concentration gradient and by the attraction of cations to the negative side
(inside) of the membrane.
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Special transport proteins, called electrogenic pumps, generate the voltage gradient across a membrane.
The sodium-potassium pump, the major electrogenic pump in animals, restores the electrochemical gradient not
only by the active transport of Na+ and K+, setting up a concentration gradient, but also because it pumps two K+
inside for every three Na+ that it moves out, setting up a voltage across the membrane.

In plants, bacteria, and fungi, a proton pump is the major electrogenic pump, actively transporting protons out of
the cell and transferring positive charge from the cytoplasm to the extracellular solution.
By generating voltage across membranes, electrogenic pumps help store energy that can be tapped for cellular
work.

In cotransport, a membrane protein couples the transport of two solutes.

A single ATP-powered pump that transports a specific solute can indirectly drive the active transport of several other
solutes in a mechanism called cotransport.

As the solute that has been actively transported diffuses back passively through a transport protein, its movement
can be coupled with the active transport of another substance against its concentration (or electrochemical)
gradient.
○ Plants commonly use the gradient of H+ generated by proton pumps to drive the active transport of amino acids,
sugars, and other nutrients into the cell.
○ One specific transport protein couples the diffusion of H+ out of the cell and the transport of sucrose into the
cell.
Concept 7.5 Bulk transport across the plasma membrane occurs by exocytosis and endocytosis

Particles and large molecules, such as polysaccharides and proteins, cross the membrane via packaging in vesicles.

Like active transport, these processes require energy.

In exocytosis, a transport vesicle budded from the Golgi apparatus is moved by the cytoskeleton to the plasma
membrane.
○ When the two membranes come in contact, the bilayers fuse and spill the contents to the outside.

During endocytosis, a cell brings in biological molecules and particulate matter by forming new vesicles from the
plasma membrane.
○
 In endocytosis, a small area of the plasma membrane sinks inward to form a pocket.
As the pocket deepens, it pinches in to form a vesicle containing the material that had been outside the cell.
Ch. 8 Metabolism
Concept 8.1 An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics.

The sum total of an organism’s chemical reactions is called metabolism.
The chemistry of life is organized into metabolic pathways.

A metabolic pathway begins with a specific molecule, which is then altered in a series of defined steps to form a
specific product.

A specific enzyme catalyzes each step of the pathway.

Catabolic pathways release energy by breaking down complex molecules to simpler compounds.
○ A major pathway of catabolism is cellular respiration, in which the sugar glucose is broken down in the presence
of oxygen to carbon dioxide and water.
○ The energy released by catabolic pathways becomes available to do the work of the cell

Anabolic pathways, also called biosynthetic pathways, consume energy to build complicated molecules from
simpler compounds.
○ The synthesis of amino acids from simpler molecules and the synthesis of a protein from amino acids are both
examples of anabolism.

Energy released from the “downhill” reactions of catabolic pathways can be stored and then used to drive the
“uphill” reactions of anabolic pathways.
Organisms transform energy.
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
Energy is the capacity to cause change.
Energy exists in various forms, and cells transform energy from one type to another.

Kinetic energy is the energy associated with the relative motion of objects.
○ Heat or thermal energy is kinetic energy associated with the random movement of atoms or molecules.

Potential energy is the energy that matter possesses because of its location or structure.
○ Water behind a dam possesses energy because of its altitude above sea level.
○ Chemical energy is a term used by biologists to refer to the potential energy available for release in a chemical
reaction.
○ During a catabolic reaction, some bonds are broken and others are formed, releasing energy and producing
lower-energy breakdown products.

Energy can be converted from one form to another.
The energy transformations of life are subject to two laws of thermodynamics.

Thermodynamics is the study of energy transformations that occur in a collection of matter.

In this field, the term system refers to the matter under study, and the surroundings include the rest of the
universe—everything outside the system.

An isolated system, approximated by liquid in a thermos, is unable to exchange either energy or matter with its
surroundings.

In an open system, energy and matter can be transferred between the system and its surroundings.

Organisms are open systems: They absorb energy—light or chemical energy in the form of organic molecules—and
release heat and metabolic waste products, such as urea or CO2, to their surroundings.

Two laws of thermodynamics govern energy transformations in organisms and all other collections of matter.

The first law of thermodynamics states that the energy of the universe is constant: Energy can be transferred and
transformed, but it cannot be created or destroyed.
○
○
The first law is also known as the principle of conservation of energy.
Plants do not produce energy; they transform light energy to chemical energy.

During every transfer or transformation of energy, some energy is converted to heat, which is the energy associated
with the random movement of atoms and molecules.

Energy transfers and transformations make the universe more disordered due to the loss of usable energy.

Entropy is a measure of disorder or randomness: The more random a collection of matter, the greater its entropy.

The second law of thermodynamics states: Every energy transfer or transformation increases the entropy of the
universe.
Although order can increase locally, there is an unstoppable trend toward randomization of the universe.
Much of the increased entropy of the universe takes the form of increasing heat, which is the energy of random
molecular motion.
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

For a process to occur on its own, without outside help in the form of energy input, it must increase the entropy of
the universe.

Spontaneous processes can occur without an input of energy, although they need not occur quickly.

A spontaneous process is one that is energetically favorable. A process that cannot occur on its own is said to be
nonspontaneous: it will happen only if energy is added to the system.

Here is another way to state the second law of thermodynamics: For a process to occur spontaneously, it must
increase the entropy of the universe.

Living systems increase the entropy of their surroundings, even though they create ordered structures from less
ordered starting materials.
○ For example, amino acids are ordered into polypeptide chains.
However, an organism also takes in organized forms of matter and energy from its surroundings and replaces them
with less ordered forms.
○ For example, an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide
and water.

Concept 8.2 The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously.

How can we determine which reactions occur spontaneously and which ones require an input of energy?

The concept of free energy (symbolized by the letter G) is useful for measuring the spontaneity of a system.

Free energy is the portion of a system’s energy that can perform work when temperature and pressure are uniform
throughout the system, as in a living cell.

The change in free energy, ∆G, can be calculated for any specific chemical reaction by applying the following
equation:
∆G = ∆H – T∆S

In this equation, ∆H symbolizes the change in the system’s enthalpy (in biological systems, equivalent to total
energy); ∆S is the change in the system’s entropy; and T is the absolute temperature

For a process to occur spontaneously, the system must give up enthalpy (H must decrease), give up order (T∆S must
increase), or both.
∆G must have a negative value (∆G < 0) in order for a process to be spontaneous.


Knowing the value of G gives biologists the power to predict which kinds of change can happen without help.
○ Such spontaneous changes can be harnessed to perform work.
○ This information is important in the study of metabolism, where a major goal is to determine which reactions
can supply energy to do work in the living cell.

In any spontaneous process, the free energy of a system decreases (∆G is negative).

Because it has less free energy, the system in its final state is less likely to change and is therefore more stable than
it was previously.

A system at equilibrium is at maximum stability.
○ At equilibrium, G = 0, and the system can do no work.
Chemical reactions can be classified as either exergonic or endergonic.

An exergonic reaction proceeds with a net release of free energy; G is negative.

An endergonic reaction is one that absorbs free energy from its surroundings.
○ Endergonic reactions store energy in molecules; G is positive.

Reactions in an isolated system eventually reach equilibrium and can do no work.
○ A cell that has reached metabolic equilibrium has a G = 0 and is dead!
Concept 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic reactions.

A cell does three main kinds of work:
7. Chemical work, pushing endergonic reactions such as the synthesis of polymers from monomers;
8. Transport work, pumping substances across membranes against the direction of spontaneous movement;
9. Mechanical work, such as the beating of cilia, contraction of muscle cells, and movement of chromosomes
during cellular reproduction;

Cells manage their energy resources to do this work by energy coupling, using an exergonic process to drive an
endergonic one.

ATP is responsible for mediating most energy coupling in cells, and
ATP mediates most energy coupling in cells.

ATP (adenosine triphosphate) has three phosphate groups.

adenosine diphosphate, or ADP has 2 phosphate groups:
ATP + H2O  ADP + Pi

In the cell, the energy from the hydrolysis of ATP is directly coupled to endergonic processes by the transfer of the
phosphate group to another molecule.

Mechanical, transport, and chemical work in the cell are nearly always powered by the hydrolysis of ATP.
ATP is a renewable resource.


Although organisms use ATP continuously, ATP is a renewable resource that can be regenerated by the addition of a
phosphate group to ADP.
The free energy to phosphorylate ADP comes from exergonic (catabolic) reactions in the cell.

The ATP cycle, the shuttling of inorganic phosphate and energy, couples the cell’s energy-yielding (exergonic)
processes to the energy-consuming (endergonic) ones.

Regeneration of ATP is an endergonic process, requiring an investment of energy:

Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the endergonic regeneration
of ATP.
Concept 8.4 Enzymes speed up metabolic reactions by lowering energy barriers.

An enzyme is a macromolecule that acts as a catalyst, a chemical agent that speeds up the rate of a reaction without
being consumed by the reaction.

The initial investment of energy for starting a reaction is the free energy of activation, or activation energy (EA).

Activation energy is the amount of energy necessary to push the reactants over an energy barrier so that the
“downhill” part of the reaction can begin.

Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from the
surroundings.
○ The absorption of thermal energy accelerates the reactant molecules, which then collide more often with more
force.
○ It also agitates the atoms within the molecules, making the breakage of bonds more likely.
○ When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable
condition called the transition state.

At the summit, when the energy equivalent to EA has been absorbed, the reactants are in the transition state. They
are activated and their bonds can be broken.

The bond-forming phase of the reaction corresponds to the downhill part of the curve, which shows the loss of free
energy by the molecules.

As the molecules settle into new, stable bonding arrangements, energy is released to the surroundings.
○ The overall decrease in free energy means that EA is repaid with interest.
Enzymes are substrate specific.

The reactant that an enzyme acts on is the substrate.

The enzyme binds to a substrate, or substrates, forming an enzyme-substrate complex.

While the enzyme and substrate are bound, the catalytic action of the enzyme converts the substrate to the product
or products.

The reaction catalyzed by each enzyme is very specific.

What accounts for this molecular recognition? The specificity of an enzyme results from its three-dimensional
shape, which is a consequence of its amino acid sequence.

Only a restricted region of the enzyme binds to the substrate.
○ The active site of an enzyme is typically a pocket or groove on the surface of the protein where catalysis occurs.

The specificity of an enzyme is due to the fit between the active site and the substrate.
A cell’s physical and chemical environment affects enzyme activity.

The activity of an enzyme is affected by general environmental conditions, such as temperature and pH.

Each enzyme works best at certain optimal conditions, which favor the most active conformation for the enzyme
molecule.
Binding by inhibitors prevents enzymes from catalyzing reactions.

Certain chemicals selectively inhibit the action of specific enzymes.

Some reversible inhibitors resemble the substrate and compete for binding to the active site. These molecules are
called competitive inhibitors.

Noncompetitive inhibitors impede enzymatic reactions by binding to another part of the molecule.
Ch. 9 Cellular respiration and fermentation
Concept 9.1 Catabolic pathways yield energy by oxidizing organic fuels

Catabolic metabolic pathways release energy stored in complex organic molecules.
o Electron transfer plays a major role in these pathways.

Organic compounds possess potential energy as a result of the arrangement of electrons in the bonds between their
atoms.

Enzymes catalyze the systematic degradation of organic molecules that are rich in energy to simpler waste products
that have less energy.

Some of the released energy is used to do work; the rest is dissipated as heat.

One type of catabolic process, fermentation, leads to the partial degradation of sugars without the use of oxygen.

A more efficient and widespread catabolic process, aerobic respiration, consumes oxygen as a reactant to complete
the breakdown of a variety of organic molecules.
o Most eukaryotic and many prokaryotic organisms can carry out aerobic respiration.
o
Some prokaryotes use compounds other than oxygen as reactants in a similar process called anaerobic
respiration.

The overall catabolic process is: organic compounds + O2  CO2 + H2O + energy (ATP + heat).
C6H12O6 + 6O2  6CO2 + 6H2O + energy (ATP + heat)

Some of this energy is used to produce ATP, which can perform cellular work.
Redox reactions release energy when electrons move closer to electronegative atoms.

Catabolic pathways transfer the electrons stored in food molecules, releasing energy that is used to synthesize ATP.

Reactions that result in the transfer of one or more electrons (e−) from one reactant to another are oxidationreduction reactions, or redox reactions.
o The loss of electrons from a substance is called oxidation.
o The addition of electrons to another substance is called reduction.
○ Adding electrons is called reduction because negatively charged electrons added to an atom reduce the amount
of positive charge of that atom.

The formation of table salt from sodium and chloride, Na + Cl  Na+ + Cl−, is a redox reaction.
○ Sodium is oxidized, and chlorine is reduced (its charge drops from 0 to −1).

More generally: Xe− + Y  X + Ye−.
○ X, the electron donor, is the reducing agent and reduces Y by donating an electron to it.
○ Y, the electron recipient, is the oxidizing agent and oxidizes X by removing its electron.
Organic fuel molecules are oxidized during cellular respiration.

Respiration, the oxidation of glucose and other molecules in food, is a redox process.
○ In a series of reactions, glucose is oxidized and oxygen is reduced.
○ The electrons lose potential energy along the way, and energy is released.

Organic molecules that contain an abundance of hydrogen are excellent fuels.
○ The bonds of these molecules are a source of “hilltop” electrons, whose energy may be released as the electrons
“fall” down an energy gradient when they are transferred to oxygen.
○ As hydrogen is transferred from glucose to oxygen, the energy state of the electron changes.
○ In respiration, the oxidation of glucose transfers electrons to a lower energy state, releasing energy that
becomes available for ATP synthesis.

The main energy-yielding foods, carbohydrates and fats, are reservoirs of electrons associated with hydrogen.
The “fall” of electrons during respiration is stepwise, via NAD+ and an electron transport chain.

Cellular respiration does not oxidize glucose in a single step that transfers all the hydrogen in the fuel to oxygen at
one time.
○ Rather, glucose and other fuels are broken down in a series of steps, each catalyzed by a specific enzyme.

At key steps, electrons are stripped from the glucose.

In many oxidation reactions, the electron is transferred with a proton, as a hydrogen atom.

The hydrogen atoms are not transferred directly to oxygen but are passed first to a coenzyme called NAD+
(nicotinamide adenine dinucleotide).
○ NAD+ is well suited as an electron carrier because it can cycle easily between oxidized (NAD+) and reduced
(NADH) states.
○ As an electron acceptor, NAD+ functions as an oxidizing agent during respiration.

How does NAD+ trap electrons from glucose?
○ enzymes strip two hydrogen atoms from the substrate (glucose), thus oxidizing it.
○ The enzyme passes two electrons and one proton to NAD+.
○ The other proton is released as H+ to the surrounding solution.

By receiving two electrons and only one proton, NAD+ has its charge neutralized when it is reduced to NADH.
○ NAD+ functions as the oxidizing agent in many of the redox steps during the breakdown of glucose.

The electrons carried by NADH lose very little of their potential energy in this process.

Each NADH molecule formed during respiration represents stored energy. This energy is tapped to synthesize ATP as
electrons “fall” down an energy gradient from NADH to oxygen.

How are electrons extracted from glucose and stored in NADH finally transferred to oxygen?

Unlike the explosive release of heat energy that occurs when H2 and O2 are combined (with a spark for activation
energy), cellular respiration uses an electron transport chain to break the fall of electrons to O2 into several energyreleasing steps.

Electron transfer from NADH to oxygen is an exergonic reaction

Electrons are passed to increasingly electronegative molecules in the chain until they reduce oxygen, the most
electronegative receptor.

Each “downhill” carrier is more electronegative than, and thus capable of oxidizing, its “uphill” neighbor, with
oxygen at the bottom of the chain.

The electrons removed from glucose by NAD+ fall down an energy gradient in the electron transport chain to a far
more stable location in the electronegative oxygen atom.

In summary, during cellular respiration, most electrons travel the following “downhill” route: glucose  NADH 
electron transport chain  oxygen.
The stages of cellular respiration: a preview.

Respiration occurs in three metabolic stages: glycolysis, the citric acid cycle, and the electron transport chain and
oxidative phosphorylation.
○ Biochemists usually reserve the term cellular respiration for stages 2 and 3.
○ Glycolysis is included here because most respiring cells deriving energy from glucose use glycolysis to produce
starting material for the citric acid cycle.

Glycolysis occurs in the cytosol. It begins catabolism by breaking glucose into two molecules of pyruvate.

In eukaryotes, pyruvate enters the mitochondrion and is oxidized to a compound called acetyl CoA, which enters the
citric acid cycle.

Several steps in glycolysis and the citric acid cycle are redox reactions in which enzymes transfer electrons from
substrates to NAD+, forming NADH.

In the third stage of respiration, the electron transport chain accepts electrons from the breakdown products of the
first two stages (most often via NADH).

In the electron transport chain, the electrons move from molecule to molecule until they combine with molecular
oxygen and hydrogen ions to form water.
○ As the electrons are passed along the chain, the energy released at each step in the chain is stored in a form the
mitochondrion (or prokaryotic cell) can use to make ATP.
○ This mode of ATP synthesis is called oxidative phosphorylation because it is powered by the redox reactions of
the electron transport chain.

In eukaryotic cells, the inner membrane of the mitochondrion is the site of electron transport and chemiosmosis, the
processes that together constitute oxidative phosphorylation.

Oxidative phosphorylation produces almost 90% of the ATP generated by respiration.

Some ATP is also formed directly during glycolysis and the citric acid cycle by substrate-level phosphorylation, in
which an enzyme transfers a phosphate group from an organic substrate molecule to ADP, forming ATP.

For each molecule of glucose degraded to carbon dioxide and water by respiration, the cell makes up to 32 ATP,

Respiration uses the small steps in the respiratory pathway to break the large denomination of energy contained in
glucose into the small change of ATP.
○ The quantity of energy in ATP is more appropriate for the energy level of work required in the cell.
Concept 9.2 Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

These steps can be divided into two phases.
1. In the energy investment phase, the cell spends ATP.
2. In the energy payoff phase, this investment is repaid with interest. ATP is produced by substrate-level
phosphorylation, and NAD+ is reduced to NADH by electrons released by the oxidation of glucose.

The net yield from glycolysis is 2 ATP and 2 NADH per glucose.
○ No carbon is released as CO2 during glycolysis.

Glycolysis can occur whether or not O2 is present.
○ If O2 is present, the chemical energy stored in pyruvate and NADH can be extracted by pyruvate oxidation, the
citric acid cycle, and oxidative phosphorylation.
Concept 9.3 After pyruvate is oxidized, the citric acid cycle completes the energy-yielding oxidation of organic
molecules

If molecular oxygen is present in eukaryotic cells, pyruvate enters the mitochondrion, where enzymes of the citric
acid cycle complete the oxidation of the organic fuel to carbon dioxide.
Concept 9.4 During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis
The inner mitochondrial membrane couples electron transport to ATP synthesis.

The electron transport chain is a collection of molecules embedded in the cristae, the folded inner membrane of the
mitochondrion.

During electron transport along the chain, electron carriers alternate between reduced and oxidized states as they
accept and donate electrons.
○ Each component of the chain becomes reduced when it accepts electrons from its “uphill” neighbor, which is
less electronegative.
○ It then returns to its oxidized form as it passes electrons to its more electronegative “downhill” neighbor.
Chemiosmosis couples electron transport and energy release to ATP synthesis.

A protein complex in the cristae, ATP synthase, actually makes ATP from ADP and inorganic phosphate.

ATP synthase works like an ion pump running in reverse.
○ Ion pumps usually use ATP as an energy source to transport ions against their gradients.

ATP synthase is a multisubunit complex with four main parts, each made up of multiple polypeptides.
○ Protons move one by one into binding sites on one of the parts (the rotor), causing it to spin in a way that
catalyzes ATP production from ADP and inorganic phosphate.

Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a
membrane to drive cellular work.
Here is an accounting of ATP production by cellular respiration.

During cellular respiration, most energy flows as follows: glucose  NADH  electron transport chain  protonmotive force  ATP.
Concept 9.5 Fermentation and anaerobic respiration enable cells to produce ATP without the use of oxygen

Fermentation provides a mechanism by which some cells can oxidize organic fuel and generate ATP without the use
of oxygen or any electron transport chain (that is, without cellular respiration).
o Glycolysis oxidizes glucose to two pyruvate molecules, with NAD+ as the oxidizing agent.
o Glycolysis is exergonic and produces 2 ATP (net) by substrate-level phosphorylation.

If oxygen is present, additional ATP can be generated when NADH delivers its electrons to the electron transport
chain.
o However, glycolysis generates 2 ATP whether oxygen is present (aerobic) or not (anaerobic).
Fermentation and cellular respiration are compared.

Fermentation, anaerobic respiration, and aerobic respiration are three alternative cellular pathways for producing
ATP from sugars.
o All three use glycolysis to oxidize sugars to pyruvate with a net production of 2 ATP by substrate-level
phosphorylation.
o In all three, NAD+ is the oxidizing agent that accepts electrons from food during glycolysis.

A key difference is the mechanisms for oxidizing NADH to NAD+, which is required to sustain glycolysis.
o In fermentation, the final electron acceptor is an organic molecule such as pyruvate (lactic acid fermentation) or
acetaldehyde (alcohol fermentation).
o In cellular respiration, electrons carried by NADH are transferred to an electron transport chain and move
stepwise down a series of redox reactions to a final electron acceptor.

In aerobic respiration, the final electron acceptor is oxygen; in anaerobic respiration, the final acceptor is another
molecule that is less electronegative than oxygen.

Transfer of electrons from NADH to the electron transport chain not only regenerates the NAD+ required for
glycolysis but also pays an ATP bonus when the stepwise electron transport from this NADH to oxygen drives
oxidative phosphorylation.

More ATP is produced by the oxidation of pyruvate in the mitochondrion, which is unique to respiration.
o Without an electron transport chain, the energy still stored in pyruvate is unavailable to most cells.
o Thus, cellular respiration harvests much more energy from each sugar molecule than fermentation can.

Aerobic respiration yields up to 16 times as much ATP per glucose molecule as does fermentation—up to 32
molecules of ATP for respiration, compared with 2 molecules of ATP produced by substrate-level phosphorylation in
fermentation.
Ch. 10 Photosynthesis
Concept 10.1 Photosynthesis converts light energy to the chemical energy of food

Photosynthetic enzymes and other molecules are grouped together in a biological membrane, allowing the
necessary series of chemical reactions to be carried out efficiently.

The process of photosynthesis likely originated in a group of bacteria with infolded regions of the plasma membrane
containing clusters of such molecules.
○ In existing photosynthetic bacteria, infolded photosynthetic membranes function similarly to the internal
membranes of the chloroplast.
○ The endosymbiont theory suggests that original chloroplast was a photosynthetic prokaryote that lived inside a
eukaryotic cell.
Chloroplasts are the sites of photosynthesis in plants.

All green parts of a plant have chloroplasts, but leaves are the major sites of photosynthesis for most plants.
○ There are about half a million chloroplasts per square millimeter of leaf surface.

Chloroplasts are found mainly in cells of mesophyll, the tissue in the interior of the leaf.

O2 exits and CO2 enters the leaf through microscopic pores called stomata in the leaf.

Veins deliver water from the roots and carry off sugar from mesophyll cells to roots and other nonphotosynthetic
areas of the plant.

A typical mesophyll cell has 30–40 chloroplasts, each measuring about 2–4 µm by 4–7 µm.

Each chloroplast has two membranes around a dense fluid called the stroma.

Suspended within the stroma is an internal membrane system of sacs, the thylakoids.
○ The interior of the thylakoids forms another compartment, the thylakoid space.
○ Thylakoids may be stacked in columns called grana.

Chlorophyll, the green pigment in the chloroplasts, is located in the thylakoid membranes.

Chlorophyll plays an important role in the absorption of light energy during photosynthesis.

The photosynthetic membranes of prokaryotes arise from infolded regions of the plasma membranes, also called
thylakoid membranes.
Powered by light, photosynthesis produces organic compounds and O2 from CO2 and H2O.

6CO2 + 6H2O + light energy  C6H12O6 + 6O2

Written this way, the overall chemical change during photosynthesis is the reverse of cellular respiration.
Photosynthesis is a redox reaction.

Both photosynthesis and aerobic respiration involve redox reactions.

During cellular respiration, energy is released from sugar when electrons associated with hydrogen are transported
by carriers to oxygen, forming water as a by-product.
The electrons lose potential energy as they “fall” down the electron transport chain toward electronegative oxygen,
and the mitochondrion harnesses that energy to synthesize ATP.


Photosynthesis reverses the direction of electron flow.

Water is split and electrons are transferred with H+ from water to CO2, reducing it to sugar.

Because the electrons increase in potential energy as they move from water to sugar, the process requires energy.
The energy boost is provided by light.
A preview of the two stages of photosynthesis.

Photosynthesis is two processes, each with multiple steps: light reactions and the Calvin cycle.
○ The light reactions (photo) convert solar energy to chemical energy.
○ The Calvin cycle (synthesis) uses energy from the light reactions to incorporate CO2 from the atmosphere into
sugar.

In the light reactions, water is split, providing a source of electrons and protons (H+ ions) and giving off O2 as a byproduct.

Light absorbed by chlorophyll drives the transfer of electrons and hydrogen ions from water to NADP+ (nicotinamide
adenine dinucleotide phosphate), forming NADPH.

The light reactions also generate ATP using chemiosmosis, in a process called photophosphorylation.

Thus, light energy is initially converted to chemical energy in the form of two compounds: NADPH, a source of
electrons as reducing power that can be passed along to an electron acceptor, and ATP, the energy currency of cells.

The light reactions produce no sugar; that happens in the second stage of photosynthesis, the Calvin cycle.


The cycle begins with the incorporation of CO2 into organic molecules, a process known as carbon fixation.
The fixed carbon is reduced with electrons provided by NADPH.

ATP from the light reactions also powers parts of the Calvin cycle.

Thus, it is the Calvin cycle that makes sugar, but only with the help of ATP and NADPH from the light reactions.

The metabolic steps of the Calvin cycle are sometimes referred to as light-independent reactions because none of
the steps requires light directly. DARK Cycle
○ Nevertheless, the Calvin cycle in most plants occurs during daylight because that is when the light reactions can
provide the NADPH and ATP the Calvin cycle requires.

In essence, the chloroplast uses light energy to make sugar by coordinating the two stages of photosy nthesis.

Whereas the light reactions occur at the thylakoids, the Calvin cycle occurs in the stroma.
○ In the thylakoids, molecules of NADP+ and ADP pick up electrons and phosphate, respectively, and NADPH and
ATP are then released to the stroma, where they play crucial roles in the Calvin cycle.
Concept 10.2 The light reactions convert solar energy to the chemical energy of ATP and NADPH

Light is a form of electromagnetic energy or radiation.

Like other forms of electromagnetic energy, light travels in rhythmic waves.

The distance between crests of electromagnetic waves is called the wavelength.

The entire range of electromagnetic radiation is the electromagnetic spectrum.

The most important segment of the electromagnetic spectrum for life is a narrow band between 380 and 750 nm,
the band of visible light detected as colors by the human eye.

Although light travels as a wave, many of its properties are those of a discrete particle, a photon.

Photons are not tangible objects, but do have fixed quantities of energy.
○ The amount of energy packaged in a photon is inversely related to its wavelength: Photons with shorter
wavelengths pack more energy.

Although the sun radiates a full electromagnetic spectrum, the atmosphere selectively screens out most
wavelengths, permitting only visible light to pass in significant quantities.
○ Visible light is the radiation that drives photosynthesis.
Photosynthetic pigments are light receptors.

When light meets matter, it may be reflected, transmitted, or absorbed.

Substances that absorb visible light are known as pigments.
○ Different pigments absorb photons of different wavelengths, and the wavelengths that are absorbed disappear.
○ A leaf looks green because chlorophyll, the dominant pigment, absorbs red and violet-blue light while
transmitting and reflecting green light.

A spectrophotometer measures the ability of a pigment to absorb various wavelengths of light.
○ A spectrophotometer beams narrow wavelengths of light through a solution containing the pigment and then
measures the fraction of light transmitted at each wavelength.
○ An absorption spectrum plots a pigment’s light absorption versus wavelength.

The light reactions can perform work with wavelengths of light that are absorbed.

Several pigments in the thylakoid differ in their absorption spectra.
○ Chlorophyll a, which participates directly in the light reactions, absorbs best in the red and violet-blue
wavelengths and absorbs least in the green.
○ Accessory pigments include chlorophyll b and a group of molecules called carotenoids.

An overall action spectrum for photosynthesis profiles the relative effectiveness of different wavelengths of
radiation in driving the process.
○ An action spectrum measures changes in some measure of photosynthetic activity (for example, O2 release) as
the wavelength is varied.

The action spectrum of photosynthesis was first demonstrated in 1883 in a clever experiment performed by Thomas
Engelmann.
○ Different segments of a filamentous alga were exposed to different wavelengths of light.
○ Areas receiving wavelengths favorable to photosynthesis produced excess O2.
○ Engelmann used the abundance of aerobic bacteria that clustered along the alga at different segments as a
measure of O2 production.
○ His results are a striking match to the modern action spectrum.

Only chlorophyll a participates directly in the light reactions, but accessory photosynthetic pigments absorb light and
transfer energy to chlorophyll a.
○ Chlorophyll b, with a slightly different structure than chlorophyll a, has a slightly different absorption spectrum
and funnels the energy from these wavelengths to chlorophyll a.
○
○
Carotenoids can funnel the energy from other wavelengths to chlorophyll a and also participate in
photoprotection against excessive light.
These compounds absorb and dissipate excessive light energy that would otherwise damage chlorophyll or
interact with oxygen to form reactive oxidative molecules that could damage the cell.
When chlorophyll and other pigments absorb light, an electron is boosted to an excited state.

When a molecule absorbs a photon, one of the molecule’s electrons is elevated to an orbital with more potential
energy.

The electron moves from its ground state to an excited state.

The only photons that a molecule can absorb are those whose energy matches exactly the energy difference
between the ground state and the excited state of this electron.
Because this energy difference varies among atoms and molecules, a particular compound absorbs only photons
corresponding to specific wavelengths.
○ This is the reason each pigment has a unique absorption spectrum.


Excited electrons are unstable. Generally, they drop to their ground state in a billionth of a second, releasing heat
energy.

In isolation, some pigments emit light after absorbing photons, in a process called fluorescence.

In the thylakoid membrane, chlorophyll is organized along with proteins and smaller organic molecules into
photosystems.

A photosystem is composed of a reaction-center complex surrounded by several light-harvesting complexes.
○ The reaction-center complex is an organized association of proteins holding a special pair of chlorophyll a
molecules.

Each light-harvesting complex consists of pigment molecules (which may include chlorophyll a, chlorophyll b, and
carotenoids) bound to proteins.

Together, the light-harvesting complexes act as an antenna for the reaction-center complex.

When a pigment molecule absorbs a photon, the energy is transferred from pigment molecule to pigment molecule
until it is funneled into the reaction-center complex.

At the reaction center is a primary electron acceptor, which accepts an excited electron from the reaction center
chlorophyll a.

The solar-powered transfer of an electron from a special chlorophyll a molecule to the primary electron acceptor is
the first step of the light reactions.

As soon as the chlorophyll electron is excited to a higher energy level, the primary electron acceptor captures it in a
redox reaction.

Isolated chlorophyll fluoresces because there is no electron acceptor, so electrons of photoexcited chlorophyll drop
right back to the ground state.
○ In a chloroplast, the potential energy represented by the excited electron is not dissipated as light and heat.

Each photosystem—a reaction-center complex surrounded by light-harvesting complexes—functions in the
chloroplast as a unit, converting light energy to chemical energy.
There are two types of photosystems in the thylakoid membrane.