Unit 3: How Are Eukaryotic Cells Organized into molecules spontaneously align — with their heads

Smaller Parts? facing outward and their tails lining up in the

bilayer's interior. Thus, the hydrophilic heads of the
Scientists aren't just interested in the individual glycerophospholipids in a cell's plasma membrane
molecules found in cells or in cells' metabolic face both the water-based cytoplasm and the
functions and pathways; they also seek to learn exterior of the cell.
more about the ways in which larger groupings of Altogether, lipids account for about half the mass of
molecules serve cells. These groupings take on cell membranes. Cholesterol molecules, although
many forms and are responsible for a wide variety less abundant than glycerophospholipids, account
of functions. For instance, a cell's membranes make for about 20 percent of the lipids in animal cell
up its outer boundary and partition off its plasma membranes. However, cholesterol is not
organelles, and its cytoskeleton provides three- present in bacterial membranes or mitochondrial
dimensional support and the means for movement. membranes. Also, cholesterol helps regulate the
Other specialized structures, such as mitochondria, stiffness of membranes, while other less prominent
chloroplasts, and cell walls, have evolved to carry lipids play roles in cell signaling and cell
out vital functions, but they are found only in recognition.
specific categories of cells. Therefore, In addition to lipids, membranes are loaded with
understanding these structures not only provides proteins. In fact, proteins account for roughly half
insight into cellular function, but it also helps the mass of most cellular membranes. Many of
elucidate the differences between various types of these proteins are embedded into the membrane
organisms. and stick out on both sides; these are
called transmembrane proteins. The portions of
3.1 Specialized Membranes Organize the these proteins that are nested amid the
Eukaryotic Cell Cytoplasm into Compartments hydrocarbon tails have hydrophobic surface
characteristics, and the parts that stick out are
Cell membranes protect and organize cells. All cells hydrophilic.
have an outer plasma membrane that regulates not At physiological temperatures, cell membranes are
only what enters the cell, but also how much of any fluid; at cooler temperatures, they become gel-like.
given substance comes in. Unlike prokaryotes, Scientists who model membrane structure and
eukaryotic cells also possess internal membranes dynamics describe the membrane as a fluid mosaic
that encase their organelles and control the in which transmembrane proteins can move
exchange of essential cell components. Both types laterally in the lipid bilayer. Therefore, the
of membranes have a specialized structure that collection of lipids and proteins that make up a
facilitates their gatekeeping function. cellular membrane relies on natural biophysical
properties to form and function. In living cells,
What Are Cellular Membranes Made Of? however, many proteins are not free to move. They
With few exceptions, cellular membranes — are often anchored in place within the membrane
including plasma membranes and internal by tethers to proteins outside the cell, cytoskeletal
membranes — are made of glycerophospholipids, elements inside the cell, or both.
molecules composed of glycerol, a phosphate group,
and two fatty acid chains. Glycerol is a three-carbon What Do Membranes Do?
molecule that functions as the backbone of these Cell membranes serve as barriers and gatekeepers.
membrane lipids. Within an individual They are semi-permeable, which means that some
glycerophospholipid, fatty acids are attached to the molecules can diffuse across the lipid bilayer but
first and second carbons, and the phosphate group others cannot. Small hydrophobic molecules and
is attached to the third carbon of the glycerol gases like oxygen and carbon dioxide cross
backbone. Variable head groups are attached to the membranes rapidly. Small polar molecules, such as
phosphate. Space-filling models of these molecules water and ethanol, can also pass through
reveal their cylindrical shape, a geometry that membranes, but they do so more slowly. On the
allows glycerophospholipids to align side-by-side to other hand, cell membranes restrict diffusion of
form broad sheets. highly charged molecules, such as ions, and large
Glycerophospholipids are by far the most abundant molecules, such as sugars and amino acids. The
lipids in cell membranes. Like all lipids, they are passage of these molecules relies on specific
insoluble in water, but their unique geometry transport proteins embedded in the membrane.
causes them to aggregate into bilayers without any Membrane transport proteins are specific and
energy input. This is because they are two-faced selective for the molecules they move, and they
molecules, with hydrophilic (water-loving) often use energy to catalyze passage. Also, these
phosphate heads and hydrophobic (water-fearing) proteins transport some nutrients against the
hydrocarbon tails of fatty acids. In water, these concentration gradient, which requires additional
energy. The ability to maintain concentration outside "out" and the inside "in," allowing only
gradients and sometimes move materials against certain molecules to cross and relaying messages
them is vital to cell health and maintenance. Thanks via a chain of molecular events
to membrane barriers and transport proteins, the
cell can accumulate nutrients in higher 3.2 Cytoskeletal Networks Provide Spatial
concentrations than exist in the environment and, Organization and Mechanical Support to
conversely, dispose of waste products. Eukaryotic Cells
Other transmembrane proteins have
communication-related jobs. These proteins bind The cytoskeleton is a structure that helps cells
signals, such as hormones or immune mediators, to maintain their shape and internal organization, and
their extracellular portions. Binding causes a it also provides mechanical support that enables
conformational change in the protein that transmits cells to carry out essential functions like division
a signal to intracellular messenger molecules. Like and movement. There is no single cytoskeletal
transport proteins, receptor proteins are specific component. Rather, several different components
and selective for the molecules they bind. work together to form the cytoskeleton.
Peripheral membrane proteins are associated with
the membrane but are not inserted into the bilayer. What Is the Cytoskeleton Made Of?
Rather, they are usually bound to other proteins in The cytoskeleton of eukaryotic cells is made of
the membrane. Some peripheral proteins form a filamentous proteins, and it provides mechanical
filamentous network just under the membrane that support to the cell and its cytoplasmic constituents.
provides attachment sites for transmembrane All cytoskeletons consist of three major classes of
proteins. Other peripheral proteins are secreted by elements that differ in size and in protein
the cell and form an extracellular matrix that composition. Microtubules are the largest type of
functions in cell recognition. filament, with a diameter of about 25 nanometers
(nm), and they are composed of a protein
How Diverse Are Cell Membranes? called tubulin. Actin filaments are the smallest type,
In contrast to prokaryotes, eukaryotic cells have not with a diameter of only about 6 nm, and they are
only a plasma membrane that encases the entire made of a protein called actin. Intermediate
cell, but also intracellular membranes that filaments, as their name suggests, are mid-sized,
surround various organelles. In such cells, the with a diameter of about 10 nm. Unlike actin
plasma membrane is part of an filaments and microtubules, intermediate filaments
extensive endomembrane system that includes the are constructed from a number of different subunit
endoplasmic reticulum (ER), the nuclear proteins.
membrane, the Golgi apparatus, and lysosomes.
Membrane components are exchanged throughout What Do Microtubules Do?
the endomembrane system in an organized fashion. Tubulin contains two polypeptide subunits, and
For instance, the membranes of the ER and the dimers of these subunits string together to make
Golgi apparatus have different compositions, and long strands called protofilaments. Thirteen
the proteins that are found in these membranes protofilaments then come together to form the
contain sorting signals, which are like molecular zip hollow, straw-shaped filaments of microtubules.
codes that specify their final destination. Microtubules are ever-changing, with reactions
Mitochondria and chloroplasts are also surrounded constantly adding and subtracting tubulin dimers at
by membranes, but they have unusual membrane both ends of the filament. The rates of change at
structures — specifically, each of these organelles either end are not balanced — one end grows more
has two surrounding membranes instead of just rapidly and is called the plus end, whereas the
one. The outer membrane of mitochondria and other end is known as the minus end. In cells, the
chloroplasts has pores that allow small molecules minus ends of microtubules are anchored in
to pass easily. The inner membrane is loaded with structures called microtubule organizing
the proteins that make up the electron transport centers (MTOCs). The primary MTOC in a cell is
chain and help generate energy for the cell. The called the centrosome, and it is usually located
double membrane enclosures of mitochondria and adjacent to the nucleus.
chloroplasts are similar to certain modern-day Microtubules tend to grow out from the centrosome
prokaryotes and are thought to reflect these to the plasma membrane. In non-dividing cells,
organelles' evolutionary origins. microtubule networks radiate out from the
centrosome to provide the basic organization of the
Conclusion cytoplasm, including the positioning of organelles.
Membranes are made of lipids and proteins, and
they serve a variety of barrier functions for cells
and intracellular organelles. Membranes keep the
What Do Actin Filaments Do? contractile capacity of actin filament networks.
The protein actin is abundant in all eukaryotic cells. Actin filaments are extremely dynamic and can
It was first discovered in skeletal muscle, where rapidly form and disassemble. In fact, this dynamic
actin filaments slide along filaments of another action underlies the crawling behavior of cells such
protein called myos into make the cells contract. (In as amoebae. At the leading edge of a moving cell,
non-muscle cells, actin filaments are less organized actin filaments are rapidly polymerizing; at its rear
and myosin is much less prominent.) Actin edge, they are quickly depolymerizing. A large
filaments are made up of identical actin proteins number of other proteins participate in actin
arranged in a long spiral chain. Like microtubules, assembly and disassembly as well.
actin filaments have plus and minus ends, with
more ATP-powered growth occurring at a Conclusion
filament's plus end. The cytoskeleton of a cell is made up of
In many types of cells, networks of actin filaments microtubules, actin filaments, and intermediate
are found beneath the cell cortex, which is the filaments. These structures give the cell its shape
meshwork of membrane-associated proteins that and help organize the cell's parts. In addition, they
supports and strengthens the plasma membrane. provide a basis for movement and cell division.
Such networks allow cells to hold — and move —
specialized shapes, such as the brush border of 3.3 The Endoplasmic Reticulum, Golgi
microvilli. Actin filaments are also involved in Apparatus, and Lysosomes Are Part of an
cytokinesis and cell movement. Extensive Endomembrane System in Eukaryotic
Cells
What Do Intermediate Filaments Do?
Intermediate filaments come in several types, but Cells have extensive sets of intracellular
they are generally strong and ropelike. Their membranes, which together compose
functions are primarily mechanical and, as a class, the endomembrane system. The endomembrane
intermediate filaments are less dynamic than actin system was first discovered in the late 1800s when
filaments or microtubules. Intermediate filaments scientist Camillo Golgi noticed that a certain stain
commonly work in tandem with microtubules, selectively marked only some internal cellular
providing strength and support for the fragile membranes. Golgi thought that these intracellular
tubulin structures. membranes were interconnected, but advances in
All cells have intermediate filaments, but the microscopy and biochemical studies of the various
protein subunits of these structures vary. Some membrane-encased organelles later made it clear
cells have multiple types of intermediate filaments, the organelles in the endomembrane system are
and some intermediate filaments are associated separate compartments with specific functions.
with specific cell types. For example, These structures do exchange membrane material,
neurofilaments are found specifically in neurons however, via a special type of transport.
(most prominently in the long axons of these cells), Today, scientists know that the endomembrane
desmin filaments are found specifically in muscle system includes the endoplasmic
cells, and keratins are found specifically in reticulum (ER), Golgi apparatus,
epithelial cells. Other intermediate filaments are and lysosomes. Vesicles also allow the exchange of
distributed more widely. For example, vimentin membrane components with a cell's plasma
filaments are found in a broad range of cell types membrane.
and frequently colocalize with microtubules.
Similarly, lamins are found in all cell types, where How Are Cell Membranes Synthesized?
they form a meshwork that reinforces the inside of Membranes and their constituent proteins are
the nuclear membrane. Note that intermediate assembled in the ER. This organelle contains the
filaments are not polar in the way that actin or enzymes involved in lipid synthesis, and as lipids
tubulin are. are manufactured in the ER, they are inserted into
the organelle's own membranes. This happens in
How Do Cells Move? part because the lipids are too hydrophobic to
Cytoskeletal filaments provide the basis for cell dissolve into the cytoplasm.
movement. For instance, cilia and Similarly, transmembrane proteins have enough
(eukaryotic) flagella move as a result of hydrophobic surfaces that they are also inserted
microtubules sliding along each other. In fact, cross into the ER membrane while they are still being
sections of these tail-like cellular extensions show synthesized. Here, future membrane proteins make
organized arrays of microtubules. their way to the ER membrane with the help of a
Other cell movements, such as the pinching off of signal sequence in the newly translated protein.
the cell membrane in the final step of cell division The signal sequence stops translation and directs
(also known as cytokinesis) are produced by the the ribosomes — which are carrying the unfinished
proteins — to dock with ER proteins before sacs from the ER — called the trans-Golgi. At each
finishing their work. Translation then recommences workstation along the assembly line, Golgi enzymes
after the signal sequence docks with the ER, and it catalyze distinct reactions. Later, as vesicles of
takes place within the ER membrane. Thus, by the membrane lipids and proteins bud off from the
time the protein achieves its final form, it is already trans-Golgi, they are directed to their appropriate
inserted into a membrane. destinations — either lysosomes, storage vesicles,
The proteins that will be secreted by a cell are also or the plasma membrane.
directed to the ER during translation, where they
end up in the lumen, the internal cavity, where they What Do Lysosomes Do?
are then packaged for vesicular release from the Lysosomes break down macromolecules into their
cell. The hormones insulin and erythropoietin constituent parts, which are then recycled. These
(EPO) are both examples of vesicular proteins. membrane-bound organelles contain a variety of
enzymes called hydrolases that can digest proteins,
How Are Organelle Membranes Maintained? nucleic acids, lipids, and complex sugars. The lumen
The ER, Golgi apparatus, and lysosomes are all of a lysosome is more acidic than the cytoplasm.
members of a network of membranes, but they are This environment activates the hydrolases and
not continuous with one another. Therefore, the confines their destructive work to the lysosome. In
membrane lipids and proteins that are synthesized plants and fungi, lysosomes are called
in the ER must be transported through the network acidic vacuoles.
to their final destination in membrane- Lysosomes are formed by the fusion of vesicles that
bound vesicles. Cargo-bearing vesicles pinch off of have budded off from the trans-Golgi. The sorting
one set of membranes and travel along microtubule system recognizes address sequences in the
tracks to the next set of membranes, where they hydrolytic enzymes and directs them to growing
fuse with these structures. Trafficking occurs in lysosomes. In addition, vesicles that bud off from
both directions; the forward direction takes the plasma membrane via endocytosis are also sent
vesicles from the site of synthesis to the Golgi to lysosomes, where their contents — fluid and
apparatus and next to a cell's lysosomes or plasma molecules from the extracellular environment —
membrane. Vesicles that have released their cargo are processed. The process of endocytosis is an
return via the reverse direction. The proteins that example of reverse vesicle trafficking, and it plays
are synthesized in the ER have, as part of their an important role in nutrition and immunity as well
amino acid sequence, a signal that directs them as membrane recycling. Lysosomes break down and
where to go, much like an address directs a letter to thus disarm many kinds of foreign and potentially
its destination. pathogenic materials that get into the cell through
Soluble proteins are carried in the lumens of such extracellular sampling.
vesicles. Any proteins that are destined for a
lysosome are delivered to the lysosome interior Conclusion
when the vesicle that carries them fuses with the The endomembrane system of eukaryotic cells
lysosomal membrane and joins its contents. In consists of the ER, the Golgi apparatus, and
contrast, the proteins that will be secreted by a cell, lysosomes. Membrane components, including
such as insulin and EPO, are held in storage proteins and lipids, are exchanged among these
vesicles. When signaled by the cell, these vesicles organelles and the plasma membrane via vesicular
fuse with the plasma membrane and release their transport with the help of molecular tags that direct
contents into the extracellular space. specific components to their proper destinations.

What Does the Golgi Apparatus Do? 3.4 Mitochondria Are Independently Replicating
The Golgi apparatus functions as a molecular Organelles That Supply Much of the Energy of
assembly line in which membrane proteins undergo the Cell
extensive post-translational modification. Many
Golgi reactions involve the addition of sugar Mitochondria are unusual organelles. They act as
residues to membrane proteins and secreted the power plants of the cell, are surrounded by two
proteins. The carbohydrates that the Golgi attaches membranes, and have their own genome. They also
to membrane proteins are often quite complex, and divide independently of the cell in which they
their synthesis requires multiple steps. reside, meaning mitochondrial replication is not
In electron micrographs, the Golgi apparatus looks coupled to cell division. Some of these features
like a set of flattened sacs. Vesicles that bud off are holdovers from the ancient ancestors of
from the ER fuse with the closest Golgi membranes, mitochondria, which were likely free-living
called the cis-Golgi. Molecules then travel through prokaryotes.
the Golgi apparatus via vesicle transport until they
reach the end of the assembly line at the farthest
What Is the Origin of Mitochondria? evolution. Mitochondrial genes that have been
Mitochondria are thought to have originated from conserved across evolution include rRNA genes,
an ancient symbiosis that resulted when a tRNA genes, and a small number of genes that
nucleated cell engulfed an aerobic prokaryote. The encode proteins involved in electron transport and
engulfed cell came to rely on the protective ATP synthesis. The mitochondrial genome retains
environment of the host cell, and, conversely, the similarity to its prokaryotic ancestor, as does some
host cell came to rely on the engulfed prokaryote of the machinery mitochondria use to synthesize
for energy production. Over time, the descendants proteins. In fact, mitochondrial rRNAs more closely
of the engulfed prokaryote developed into resemble bacterial rRNAs than the eukaryotic
mitochondria, and the work of these organelles — rRNAs found in cell cytoplasm. In addition, some of
using oxygen to create energy — became critical to the codons that mitochondria use to specify amino
eukaryotic evolution. acids differ from the standard eukaryotic codons.
Modern mitochondria have striking similarities to Still, the vast majority of mitochondrial proteins are
some modern prokaryotes, even though they have synthesized from nuclear genes and transported
diverged significantly since the ancient symbiotic into the mitochondria. These include the enzymes
event. For example, the inner mitochondrial required for the citric acid cycle, the proteins
membrane contains electron transport proteins like involved in DNA replication and transcription, and
the plasma membrane of prokaryotes, and ribosomal proteins. The protein complexes of the
mitochondria also have their own prokaryote-like respiratory chain are a mixture of proteins encoded
circular genome. One difference is that these by mitochondrial genes and proteins encoded by
organelles are thought to have lost most of the nuclear genes. Proteins in both the outer and inner
genes once carried by their prokaryotic ancestor. mitochondrial membranes help transport newly
Although present-day mitochondria do synthesize a synthesized, unfolded proteins from the cytoplasm
few of their own proteins, the vast majority of the into the matrix, where folding ensues.
proteins they require are now encoded in the
nuclear genome. How Many Mitochondria Do Cells Have?
Mitochondria cannot be made "from scratch"
What Is the Purpose of a Mitochondrial because they need both mitochondrial and nuclear
Membranes? gene products. These organelles replicate by
As previously mentioned, mitochondria contain two dividing in two, using a process similar to the
major membranes. The outer mitochondrial simple, asexual form of cell division employed by
membrane fully surrounds the inner membrane, bacteria. Video microscopy shows that
with a small intermembrane space in between. The mitochondria are incredibly dynamic. They are
outer membrane has many protein-based pores constantly dividing, fusing, and changing shape.
that are big enough to allow the passage of ions and Indeed, a single mitochondrion may contain
molecules as large as a small protein. In contrast, multiple copies of its genome at any given time.
the inner membrane has much more restricted Logically, mitochondria multiply when a the energy
permeability, much like the plasma membrane of a needs of a cell increase. Therefore, power-hungry
cell. The inner membrane is also loaded with cells have more mitochondria than cells with lower
proteins involved in electron transport and ATP energy needs. For example, repeatedly stimulating
synthesis. This membrane surrounds a muscle cell will spur the production of more
the mitochondrial matrix, where the citric acid mitochondria in that cell, to keep up with energy
cycle produces the electrons that travel from one demand.
protein complex to the next in the inner membrane.
At the end of this electron transport chain, the final Conclusion
electron acceptor is oxygen, and this ultimately Mitochondria, the so-called "powerhouses" of cells,
forms water (H20). At the same time, the electron are unusual organelles in that they are surrounded
transport chain produces ATP. (This is why the the by a double membrane and retain their own small
process is called oxidative phosphorylation.) genome. They also divide independently of the cell
During electron transport, the participating protein cycle by simple fission. Mitochondrial division is
complexes push protons from the matrix out to the stimulated by energy demand, so cells with an
intermembrane space. This creates a concentration increased need for energy contain greater numbers
gradient of protons that another protein complex, of these organelles than cells with lower energy
calledATP synthase, uses to power synthesis of the needs.
energy carrier molecule ATP.

Is the Mitochondrial Genome Still Functional?

Mitochondrial genomes are very small and show a
great deal of variation as a result of divergent
3.5 Plant Cells Have Chloroplasts and Other tensile strength and protection against mechanical
Structures Not Present in Animal Cells and osmotic stress. It also allows cells to
develop turgor pressure, which is the pressure of
Plant cells have several structures not found in the cell contents against the cell wall. Plant cells
other eukaryotes. In particular, organelles have high concentrations of molecules dissolved in
called chloroplasts allow plants to capture the their cytoplasm, which causes water to come into
energy of the Sun in energy-rich molecules; cell the cell under normal conditions and makes the
walls allow plants to have rigid structures as varied cell's central vacuoles well and press against the
as wood trunks and supple leaves; and vacuoles cell wall. With a healthy supply of water, turgor
allow plant cells to change size. pressure keeps a plant from wilting. In drought, a
plant may wilt, but its cell walls help maintain the
What Is the Origin of Chloroplasts? structural integrity of its stems, leaves, and other
Like mitochondria, chloroplasts likely originated structures, despite a shrinking, less turgid vacuole.
from an ancient symbiosis, in this case when a Plant cell walls are primarily made of cellulose,
nucleated cell engulfed a photosynthetic which is the most abundant macromolecule on
prokaryote. Indeed, chloroplasts resemble modern Earth. Cellulose fibers are long, linear polymers of
cyanobacteria, which remain similar to the hundreds of glucose molecules. These fibers
cyanobacteria of 3 million years ago. However, the aggregate into bundles of about 40, which are
evolution of photosynthesis goes back even further, called microfibrils. Microfibrils are embedded in a
to the earliest cells that evolved the ability to hydrated network of other polysaccharides. The cell
capture light energy and use it to produce energy- wall is assembled in place. Precursor components
rich molecules. When these organisms developed are synthesized inside the cell and then assembled
the ability to split water molecules and use the by enzymes associated with the cell membrane.
electrons from these molecules, photosynthetic
cells started generating oxygen — an event that had What Are Vacuoles?
dramatic consequences for the evolution of all Plant cells additionally possess large, fluid-filled
living things on Earth. vesicles called vacuoles within their cytoplasm.
Today, chloroplasts retain small, circular genomes Vacuoles typically compose about 30 percent of a
that resemble those of cyanobacteria, although they cell's volume, but they can fill as much as 90
are much smaller. (Mitochondrial genomes are even percent of the intracellular space. Plant cells use
smaller than the genomes of chloroplasts.) Coding vacuoles to adjust their size and turgor pressure.
sequences for the majority of chloroplast proteins Vacuoles usually account for changes in cell size
have been lost, so these proteins are now encoded when the cytoplasmic volume stays constant.
by the nuclear genome, synthesized in the Some vacuoles have specialized functions, and plant
cytoplasm, and transported from the cytoplasm cells can have more than one type of vacuole.
into the chloroplast. Vacuoles are related to lysosomes and share some
functions with these structures; for instance, both
What Is the Function of Chloroplast contain degradative enzymes for breaking down
Membranes? macromolecules. Vacuoles can also serve as storage
Like mitochondria, chloroplasts are surrounded by compartments for nutrients and metabolites. For
two membranes. The outer membrane is permeable instance, proteins are stored in the vacuoles of
to small organic molecules, whereas the inner seeds, and rubber and opium are metabolites that
membrane is less permeable and studded with are stored in plant vacuoles.
transport proteins. The innermost matrix of
chloroplasts, called the stroma, contains metabolic Conclusion
enzymes and multiple copies of the chloroplast Plant cells have certain distinguishing features,
genome. including chloroplasts, cell walls, and intracellular
Chloroplasts also have a third internal membrane vacuoles. Photosynthesis takes place in
called the thylakoid membrane, which is chloroplasts; cell walls allow plants to have strong,
extensively folded and appears as stacks of upright structures; and vacuoles help regulate how
flattened disks in electron micrographs. The cells handle water and storage of other molecules.
thylakoids contain the light-harvesting complex,
including pigments such as chlorophyll, as well as
the electron transport chains used in
photosynthesis.
Besides the presence of chloroplasts, another major
difference between plant and animal cells is the
presence of a cell wall. The cell wall surrounds the
plasma membrane of plant cells and provides