Study material

Unit-1
History of cell biology:

Although they are externally very different, internally, an elephant, a sunflower, and an amoeba
are all made of the same building blocks. From the single cells that make up the most basic
organisms to the trillions of cells that constitute the complex structure of the human body, each
and every living being on Earth is comprised of cells. This idea, part of the cell theory, is one of
the central tenants of biology. Cell theory also states that cells are the basic functional unit of
living organisms and that all cells come from other cells. Although this knowledge is
foundational today, scientists did not always know about cells.

The discovery of the cell would not have been possible if not for advancements to
the microscope. Interested in learning more about the microscopic world, scientist Robert Hooke
improved the design of the existing compound microscope in 1665. His microscope used three
lenses and a stage light, which illuminated and enlarged the specimens. These advancements
allowed Hooke to see something wondrous when he placed a piece of cork under the microscope.
Hooke detailed his observations of this tiny and previously unseen world in his
book, Micrographia. To him, the cork looked as if it was made of tiny pores, which he came to
call “cells” because they reminded him of the cells in a monastery.

In observing the cork’s cells, Hooke noted in Micrographia that, “I could exceedingly plainly
perceive it to be all perforated and porous, much like a Honey-comb, but that the pores of it were
not regular… these pores, or cells,…were indeed the first microscopical pores I ever saw, and
perhaps, that were ever seen, for I had not met with any Writer or Person, that had made any
mention of them before this…”

Not long after Hooke’s discovery, Dutch scientist Antonie van Leeuwenhoek detected other
hidden, minuscule organisms—bacteria and protozoa. It was unsurprising that van Leeuwenhoek
would make such a discovery. He was a master microscope maker and perfected the design of
the simple microscope (which only had a single lens), enabling it to magnify an object by around
two hundred to three hundred times its original size. What van Leeuwenhoek saw with these
microscopes was bacteria and protozoa, but he called these tiny creatures “animalcules.”

Van Leeuwenhoek became fascinated. He went on to be the first to observe and describe
spermatozoa in 1677. He even took a look at the plaque between his teeth under the microscope.
In a letter to the Royal Society, he wrote, "I then most always saw, with great wonder, that in the
said matter there were many very little living animalcules, very prettily a-moving.”

In the nineteenth century, biologists began taking a closer look at both animal and plant tissues,
perfecting cell theory. Scientists could readily tell that plants were completely made up of cells
due to their cell wall. However, this was not so obvious for animal cells, which lack a cell wall.
Many scientists believed that animals were made of “globules.”
German scientists Theodore Schwann and Mattias Schleiden studied cells of animals and plants
respectively. These scientists identified key differences between the two cell types and put forth
the idea that cells were the fundamental units of both plants and animals.

However, Schwann and Schleiden misunderstood how cells grow. Schleiden believed that cells
were “seeded” by the nucleus and grew from there. Similarly, Schwann claimed that animal cells
“crystalized” from the material between other cells. Eventually, other scientists began to uncover
the truth. Another piece of the cell theory puzzle was identified by Rudolf Virchow in 1855, who
stated that all cells are generated by existing cells.

At the turn of the century, attention began to shift toward cytogenetics, which aimed to link the
study of cells to the study of genetics. In the 1880s, Walter Sutton and Theodor Boveri were
responsible for identifying the chromosome as the hub for heredity—forever linking genetics and
cytology. Later discoveries further confirmed and solidified the role of the cell in heredity, such
as James Watson and Francis Crick’s studies on the structure of DNA.

The discovery of the cell continued to impact science one hundred years later, with the discovery
of stem cells, the undifferentiated cells that have yet to develop into more specialized cells.
Scientists began deriving embryonic stem cells from mice in the 1980s, and in 1998, James
Thomson isolated human embryonic stem cells and developed cell lines. His work was then
published in an article in the journal Science. It was later discovered that adult tissues, usually
skin, could be reprogrammed into stem cells and then form other cell types. These cells are
known as induced pluripotent stem cells. Stem cells are now used to treat many conditions such
as Alzheimer’s and heart disease.

The discovery of the cell has had a far greater impact on science than Hooke could have ever
dreamed in 1665. In addition to giving us a fundamental understanding of the building blocks of
all living organisms, the discovery of the cell has led to advances in medical technology and
treatment. Today, scientists are working on personalized medicine, which would allow us to
grow stem cells from our very own cells and then use them to understand disease processes. All
of this and more grew from a single observation of the cell in a cork.

Robert Hook refined the design of the compound microscope around 1665 and
published a book titled Micrographia which illustrated his findings using the instrument.

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Cell theory:

In biology, cell theory is the historic scientific theory, now universally accepted, that living organisms
are made up of cells, that they are the basic structural/organizational unit of all organisms, and that
all cells come from pre-existing cells.

Modern Cell theory:

The cell represents the elementary unit of construction and function in living organisms.
All cells come from the division of pre-existing cells.
Energy flow – metabolism and biochemistry – happens within cells.
Cells contain genetic information in the form of DNA passed on from cell to cell during
division.
In the organisms of similar species, all cells are fundamentally the same.
All living organisms consist of one or more cells.
Some cells – unicellular organisms – consist of only one cell.
Other living entities are multicellular, containing multiple cells.
The living organism's activities depend upon the combined actions of individual, independent
cells.
Compartmentalization of eukaryotic cells:

Cell compartmentalization refers to the way organelles in eukaryotic cells live and work in separate
areas within the cell in order to perform their specific functions more efficiently.

It was thought that compartmentalization is not found in prokaryotic cells., but the discovery
of carboxysomes and many other metabolosomes revealed that prokaryotic cells are capable of
making compartmentalized structures, albeit these are in most cases not surrounded by a lipid
bilayer, but of pure proteinaceous.

Many vital biochemical processes take place in or on membrane surfaces. Lipid metabolism, for
example, is catalyzed mostly by membrane-bound enzymes, and oxidative
phosphorylation and photosynthesis both require a membrane to couple the transport of H+ to the
synthesis of ATP. Intracellular membrane systems, however, do more for the cell than just
provide increased membrane area: they create enclosed compartments that are separate from
the cytosol, thus providing the cell with functionally specialized aqueous spaces. Because
the lipid bilayer of organelle membranes is impermeable to most hydrophilic molecules, the
membrane of each organelle must contain membrane transport proteins that are responsible for
the import and export of specific metabolites. Each organelle membrane must also have a
mechanism for importing, and incorporating into the organelle, the specific proteins that make
the organelle unique.
The nucleus contains the main genome and is the principal site of DNA and RNA synthesis. The
surrounding cytoplasm consists of the cytosol and the cytoplasmic organelles suspended in it.
The cytosol, constituting a little more than half the total volume of the cell, is the site
of protein synthesis and degradation. It also performs most of the cell's
intermediary metabolism—that is, the many reactions by which some small molecules are
degraded and others are synthesized to provide the building blocks for macromolecules.
About half the total area of membrane in a eucaryotic cell encloses the labyrinthine spaces of
the endoplasmic reticulum (ER). The ER has many ribosomes bound to its cytosolic surface;
these are engaged in the synthesis of both soluble and integral membrane proteins, most of which
are destined either for secretion to the cell exterior or for other organelles. We shall see that
whereas proteins are translocated into other organelles only after their synthesis is complete, they
are translocated into the ER as they are synthesized. This explains why the ER membrane is
unique in having ribosomes tethered to it. The ER also produces most of the lipid for the rest of
the cell and functions as a store for Ca2+ ions. The ER sends many of its proteins and lipids to the
Golgi apparatus. The Golgi apparatus consists of organized stacks of disclike compartments
called Golgi cisternae; it receives lipids and proteins from the ER and dispatches them to a
variety of destinations, usually covalently modifying them en route.
Mitochondria and (in plants) chloroplasts generate most of the ATP used by cells to drive
reactions that require an input of free energy; chloroplasts are a specialized version
of plastids, which can also have other functions in plant cells, such as the storage of food or
pigment molecules. Lysosomes contain digestive enzymes that degrade defunct intracellular
organelles, as well as macromolecules and particles taken in from outside the cell
by endocytosis. On their way to lysosomes, endocytosed material must first pass through a series
of organelles called endosomes. Peroxisomes are small vesicular compartments that contain
enzymes utilized in a variety of oxidative reactions.
In general, each membrane-enclosed organelle performs the same set of basic functions in all cell
types. But to serve the specialized functions of cells, these organelles will vary in abundance and
can have additional properties that differ from cell type to cell type.
On average, the membrane-enclosed compartments together occupy nearly half the volume of a
cell, and a large amount of intracellular membrane is required to make them all. In liver and
pancreatic cells, for example, the endoplasmic reticulum has a total membrane surface area that
is, respectively, 25 times and 12 times that of the plasma membrane . In terms of its area and
mass, the plasma membrane is only a minor membrane in most eucaryotic cells .
Membrane-enclosed organelles often have characteristic positions in the cytosol. In most cells,
for example, the Golgi apparatus is located close to the nucleus, whereas the network
of ER tubules extends from the nucleus throughout the entire cytosol. These characteristic
distributions depend on interactions of the organelles with the cytoskeleton. The localization of
both the ER and the Golgi apparatus, for instance, depends on an intact microtubule array; if the
microtubules are experimentally depolymerized with a drug, the Golgi apparatus fragments and
disperses throughout the cell, and the ER network collapses toward the cell center.
To understand the relationships between the compartments of the cell, it is helpful to consider
how they might have evolved. The precursors of the first eucaryotic cells are thought to have
been simple organisms that resembled bacteria, which generally have a plasma membrane but no
internal membranes. The plasma membrane in such cells therefore provides all membrane-
dependent functions, including the pumping of ions, ATP synthesis, protein secretion,
and lipid synthesis. Typical present-day eucaryotic cells are 10–30 times larger in linear
dimension and 1000–10,000 times greater in volume than a typical bacterium such as E. coli.
The profusion of internal membranes can be seen in part as an adaptation to this increase in size:
the eucaryotic cell has a much smaller ratio of surface area to volume, and its area of plasma
membrane is presumably too small to sustain the many vital functions for which membranes are
required. The extensive internal membrane systems of a eucaryotic cell alleviate this imbalance.
The evolution of internal membranes evidently accompanied the specialization
of membrane function. Consider, for example, the generation of thylakoid vesicles in
chloroplasts. These vesicles form during the development of chloroplasts from proplastids in the
green leaves of plants. Proplastids are small precursor organelles that are present in all immature
plant cells. They are surrounded by a double membrane and develop according to the needs of
the differentiated cells: they develop into chloroplasts in leaf cells, for example, and into
organelles that store starch, fat, or pigments in other cell types. In the process of differentiating
into chloroplasts, specialized membrane patches form and pinch off from the inner membrane of
the proplastid. The vesicles that pinch off form a new specialized compartment,
the thylakoid, that harbors all of the chloroplast's photosynthetic machinery.
Other compartments in eucaryotic cells may have originated in a conceptually similar way
.Pinching off of specialized intracellular membrane structures from the plasma membrane, for
example, would create organelles with an interior that is topologically equivalent to the exterior
of the cell. We shall see that this topological relationship holds for all of the organelles involved
in the secretory and endocytic pathways, including the ER, Golgi apparatus, endosomes, and
lysosomes. We can therefore think of all of these organelles as members of the same family. As
we discuss in detail in the next chapter, their interiors communicate extensively with one another
and with the outside of the cell via transport vesicles that bud off from one organelle and fuse
with another mitochondria and plastids differ from the other membrane-enclosed organelles in
containing their own genomes. The nature of these genomes, and the close resemblance of the
proteins in these organelles to those in some present-day bacteria, strongly suggest that
mitochondria and plastids evolved from bacteria that were engulfed by other cells with which
they initially lived in symbiosis . According to the hypothetical scheme, the inner membrane of
mitochondria and plastids corresponds to the original plasma membrane of the bacterium, while
the lumen of these organelles evolved from the bacterial cytosol. As might be expected from
such an endocytic origin, these two organelles are surrounded by a double membrane, and they
remain isolated from the extensive vesicular traffic that connects the interiors of most of the
other membrane-enclosed organelles to each other and to the outside of the cell.
The evolutionary scheme described above groups the intracellular compartments in eucaryotic
cells into four distinct families: (1) the nucleus and the cytosol, which communicate
through nuclear pore complexes and are thus topologically continuous (although functionally
distinct); (2) all organelles that function in the secretory and endocytic pathways—including
the ER, Golgi apparatus, endosomes, lysosomes, the numerous classes of transport intermediates
such as transport vesicles, and possibly peroxisomes; (3) the mitochondria; and (4) the plastids
(in plants only).

Proteins Can Move Between Compartments in Different Ways

All proteins begin being synthesized on ribosomes in the cytosol, except for the few that are
synthesized on the ribosomes of mitochondria and plastids. Their subsequent fate depends on
their amino acid sequence, which can contain sorting signals that direct their delivery to
locations outside the cytosol. Most proteins do not have a sorting signal and consequently remain
in the cytosol as permanent residents. Many others, however, have specific sorting signals that
direct their transport from the cytosol into the nucleus, the ER, mitochondria, plastids, or
peroxisomes; sorting signals can also direct the transport of proteins from the ER to other
destinations in the cell.
To understand the general principles by which sorting signals operate, it is important to
distinguish three fundamentally different ways by which proteins move from one compartment to
another. These three mechanisms are described below, and their sites of action in the cell are
outlined .

In gated transport, the protein traffic between the cytosol and nucleus occurs between
topologically equivalent spaces, which are in continuity through the nuclear pore
complexes. The nuclear pore complexes function as selective gates that actively transport
specific macromolecules and macromolecular assemblies, although they also allow
free diffusion of smaller molecules.

In transmembrane transport, membrane-bound protein translocators directly transport

specific proteins across a membrane from the cytosol into a space that is topologically
distinct. The transported protein molecule usually must unfold to snake through the
translocator. The initial transport of selected proteins from the cytosol into the ER
lumen or from the cytosol into mitochondria, for example, occurs in this way.
.
In vesicular transport, membrane-enclosed transport intermediates—which may be small,
spherical transport vesicles or larger, irregularly shaped organelle fragments—ferry
proteins from one compartment to another. The transport vesicles and fragments become
loaded with a cargo of molecules derived from the lumen of one compartment as they
pinch off from its membrane; they discharge their cargo into a second compartment by
fusing with that compartment .The transfer of soluble proteins from the ER to the Golgi
apparatus, for example, occurs in this way. Because the transported proteins do not cross
a membrane, vesicular transport can move proteins only between compartments that are
topologically equivalent.
Each of the three modes of protein transfer is usually guided by sorting signals in the transported
protein that are recognized by complementary receptor proteins. If a large protein is to be
 imported into the nucleus, for example, it must possess a sorting signal that is recognized by
receptor proteins that guide it through the nuclear pore complex. If a protein is to be transferred
directly across a membrane, it must possess a sorting signal that is recognized by the translocator

in the membrane to be crossed. Likewise, if a protein is to be loaded into a certain type

of vesicle or retained in certain organelles, its sorting signal must be recognized by a
complementary receptor in the appropriate membrane.

Signal Sequences and Signal Patches Direct Proteins to the Correct

Cellular Address
There are at least two types of sorting signals in proteins. One type resides in a continuous
stretch of amino acid sequence, typically 15–60 residues long. Some of these signal
sequences are removed from the finished protein by specialized signal peptidases once the
sorting process has been completed. The other type consists of a specific three-dimensional
arrangement of atoms on the protein's surface that forms when the protein folds up. The amino
acid residues that comprise this signal patch can be distant from one another in the linear amino
acid sequence, and they generally persist in the finished protein .Signal sequences are used to
direct proteins from the cytosol into the ER, mitochondria, chloroplasts, and peroxisomes, and
they are also used to transport proteins from the nucleus to the cytosol and from the Golgi
apparatus to the ER. The sorting signals that direct proteins into the nucleus from the cytosol can
be either short signal sequences or longer sequences that are likely to fold into signal patches.
Signal patches also direct newly synthesized degradative enzymes into lysosomes.
Each signal sequence specifies a particular destination in the cell. Proteins destined for initial
transfer to the ER usually have a signal sequence at their N terminus, which characteristically
includes a sequence composed of about 5–10 hydrophobic amino acids. Many of these proteins
will in turn pass from the ER to the Golgi apparatus, but those with a specific sequence of four
amino acids at their C terminus are recognized as ER residents and are returned to the ER.
Proteins destined for mitochondria have signal sequences of yet another type, in which positively
charged amino acids alternate with hydrophobic ones. Finally, many proteins destined for
peroxisomes have a signal peptide of three characteristic amino acids at their C terminus.
Some specific signal sequences. The importance of each of these signal sequences
for protein targeting has been shown by experiments in which the peptide is transferred from one
protein to another by genetic engineering techniques. Placing the N-terminal ER signal
sequence at the beginning of a cytosolic protein, for example, redirects the protein to the ER.
Signal sequences are therefore both necessary and sufficient for protein targeting. Even though
their amino acid sequences can vary greatly, the signal sequences of all proteins having the same
destination are functionally interchangeable, and physical properties, such as hydrophobicity,
often seem to be more important in the signal-recognition process than the exact amino acid
sequence.
Signal patches are far more difficult to analyze than signal sequences, so less is known about
their structure. Because they often result from a complex three-dimensional protein-folding
pattern, they cannot be easily transferred experimentally from one protein to another.
Both types of sorting signals are recognized by complementary sorting receptors that guide
proteins to their appropriate destination, where the receptors unload their cargo. The receptors
function catalytically: after completing one round of targeting, they return to their point of origin
to be reused. Most sorting receptors recognize classes of proteins rather than just an
individual protein species. They therefore can be viewed as public transportation systems
dedicated to delivering groups of components to their correct location in the cell.

Most Membrane-enclosed Organelles Cannot Be Constructed From

Scratch: They Require Information in the Organelle Itself
When a cell reproduces by division, it has to duplicate its membrane-enclosed organelles. In
general, cells do this by enlarging the existing organelles by incorporating new molecules into
them; the enlarged organelles then divide and are distributed to the two daughter cells. Thus,
each daughter cell inherits from its mother a complete set of specialized cell membranes. This
inheritance is essential because a cell could not make such membranes from scratch. If
the ER were completely removed from a cell, for example, how could the cell reconstruct it? As
we shall discuss later, the membrane proteins that define the ER and perform many of its
functions are themselves products of the ER. A new ER could not be made without an existing
ER or, at the very least, a membrane that specifically contains the protein translocators required
to import selected proteins into the ER from the cytosol (including the ER-specific translocators
themselves). The same is true for mitochondria, plastids, and peroxisomes.
Thus, it seems that the information required to construct a membrane-enclosed organelle does
not reside exclusively in the DNA that specifies the organelle's proteins. Epigenetic information
in the form of at least one distinct protein that preexists in the organelle membrane is also
required, and this information is passed from parent cell to progeny cell in the form of the
organelle itself. Presumably, such information is essential for the propagation of the cell's
compartmental organization, just as the information in DNA is essential for the propagation of
the cell's nucleotide and amino acid sequences. However, the ER sheds a constant stream
of membrane vesicles that incorporate only specific proteins and therefore have a different
composition from the ER itself. Similarly, the plasma membrane constantly produces specialized
endocytic vesicles. Thus, some membrane-enclosed compartments can form from other
organelles and do not have to be inherited at cell division.

Importance of compartmentalization
All reactions occurring in cells take place in certain space – compartment, which is separated from
other compartments by means of semipermeable membranes. They help to separate even
chemically quite heterogeneous environments and so to optimise the course of chemical reactions.

Enzymes catalysing individual reactions often have different temperature and pH optimums and if
there was only one cellular compartment a portion of enzymes would probably not function or
them-catalysed reactions would not be sufficiently efficient. By dividing the cellular
space, optimal conditions for individual enzymatically catalysed reactions are created.
At the same time, cell also protects itself against the activity of lytic enzymes. For example, sealing
the cellular digestion in lysosomes prevents an unwanted auto-digestion of other organelles within
cell. Common processes that accompany the disruption of some of the compartments (like spilling
the content of lysosomes or mitochondria) are necrosis or activation of apoptosis (the process of
programmed cell death).

Compartmentalization affects the regulation of metabolic pathways as well, making them more
accurate and targeted and less interfering with each other. It is sometimes possible to regulate the
course of the reaction at the point of entry of particular substrate into the compartment (transport
across the membrane, often mediated by transport mechanisms).

Despite its advantages, compartmentalization at the same time puts greater demand on the energy
consumption. It arises from a frequent need to use ATP-dependent transporters, transporting
substances across membranes against the concentration gradient and thus creating different
environments in different compartments.

_
Biological membranes
One of the necessary conditions for the emergence of live was the separation of cellular environment
from the outside (external) environment. Resulting from this, there was a need for selective transport
mechanisms between both spaces and later a need for intercellular communication.

Cytoplasmic membrane creates the border with the extracellular compartment and membranes of a
similar composition separate other compartments inside the cell.

Architecture
The width of a cell membrane is approximately 6-10 nm. The core of its architecture is made of
phospholipid bilayer with embedded proteins and cholesterol molecules. The latter two can bind
various saccharides and so form glycolipids and glycoproteins. This basic structure is, in the case of
membranes of different organelles, modified to a certain degree, thus affecting the physico-chemical
properties of the membrane (especially its permeability), which are in close connection to the
function and course of the biochemical processes in the organelle.

A good example is the myelin sheath of a neuron, which has a ratio of proteins to lipids 19 % to 81 %
and thus has excellent insulating properties. On the other hand, the inner mitochondrial membrane
has the ration reversed in a favor of proteins (76 % to 24 %) and that is the reason for its relative
impermeability (even for substances that pass through standard membranes).
Molecules of phospholipids consist of two physically distinct parts:

1) Polar (hydrophilic) part:

The polar part is made up of a phosphate group with other optionally attached groups – this part
of the molecule faces the aqueous medium (or other polar solvent).

2) Non-polar (hydrophobic) part

The non-polar part consists of fatty acid chains turned against each other and thus forming
the hydrophobic core of the membrane. The hydrophobic interactions of lipid molecules are
responsible for their tendency to aggregate and form membranes.

Phospholipid molecule, containing polar as well as non-polar part, belongs to the group
of amphipathic molecules.

Historical correlation:
The currently accepted model of the structure of biological membranes was created in year 1972 by
S.J. Singer and G.L. Nicols. According to this, so-called fluid-mosaic model, we can consider the
biological membrane as a 2-dimensional liquid in which lipid and protein molecules diffuse more or
less easily.

The diffusion rate of phospholipids is much faster than that of other membrane components. Places
of membrane with higher content of proteins and cholesterol therefore have lower lateral diffusion
rate and stabilise membrane (this applies especially to cholesterol). On the other hand, parts of
membrane containing mostly lipids have the ability to flip to the opposite side (through so-
called flip-flop mechanism).

The fluidity of membrane depends mostly on:

1) The temperature: the higher the temperature the more mobile the membrane is (sol phase), at
lower temperatures it is stiffer (gel phase).

2) The proportion of unsaturated FA: the higher the content of unsaturated FA, the more mobile
the phase is.

Proteins form a basic component of cellular membranes. According to

their localisation within the membrane, they can be divided into peripheral and integral:
1) Peripheral proteins
Peripheral proteins do not penetrate to the hydrophobic core of the membrane; they only bind to
its surface area (on extra- or intracellular side) and thereby can be separated from the membrane
without damaging it. The main binding interactions include electrostatic forces and hydrogen bonds.

2) Integral proteins
Integral proteins permeate the membrane, either through its full thickness
(transmembrane proteins) or only up to a certain depth. Separation of these proteins is associated
with the disruption of membrane integrity.

Membrane proteins perform various functions, for example receptor, enzymatic or transport.

Cholesterol makes up approximately ¼ of all membrane lipids. Its molecule, similarly to the
molecule of phospholipids, has amphipathic character (due to the presence of OH- group attached
to the 3rd carbon atom). The main function of cholesterol is to stabilise the membrane
and lower its fluidity.
Properties
Permeability, expressing the rate of passive diffusion of molecules through the membrane, follows
the Fick’s law of diffusion and depends on:

1) The size and the polarity of diffusing molecules

2) The concentration gradient

3) The thickness of a membrane

4) The surface area of a membrane

1) The size and polarity of diffusing molecules

In general, small and non-polar molecules pass through the membrane quite easily while larger
and polar ones usually need transporters or channels.

2) The concentration gradient

The higher the concentration of a substance on one side of the membrane,
the higher its tendency to pass to the other side. This rule applies to other gradients as well –
electrochemical (given by the difference of charges on both sides) or osmotic (given by the
difference of osmotically active particles on both sides of the membrane).
3) The thickness of a membrane
Substances pass more slowly through a membrane that is thicker.

4) The surface area of a membrane

Larger quantity of substance diffuses through the membrane per unit of time if the membrane has
larger surface area.

Other properties of membranes are:

the degree of thermal and electrical insulation, electric charge (the total charge of a cell
membrane is negative – primarily due to the presence of negative sialic acids residues attached to
the glycoproteins and glycolipids) and the ability of selective transport.

Selective transport
Selective transport can be divided to:

1) Passive

2) Active

3) Transport of macromolecules

This diagram shows an example of transport processes through the blood-brain barrier (barrier
between the blood and nervous tissue):

1) Passive transport
Passive transport takes place without energy consumption, as it is based on the physical principle
of diffusion (driven by the concentration gradient of a substance on both sides of the
membrane). Without the existence of such gradient, the passive transport halts. There are two
basic types of passive transport:

a) Simple diffusion

b) Facilitated diffusion

a) Simple diffusion
Simple diffusion is a transfer of substances through a membrane without the help of transport
proteins. Substances must pass through the hydrophobic core of the membrane, which explains why
is this type of transport mechanism typical for:
1. Small non-polar molecule: like gases (CO2, O2,)
2. Small polar molecule: water, urea

3. Larger non-polar molecules: FA, cholesterol or fat-soluble vitamins

Hydrophilic and larger molecules (mostly with M r over 200) pass through the membrane by simple
diffusion only very slowly or not at all. Transport of ions, whose molecules are relatively small, is
difficult due to the presence of a large hydration shell consisting of water molecules.
b) Facilitated diffusion
Facilitated diffusion is a type of passive transport assisted by transport proteins that non-covalently
bind the molecule and transport it to the other side of the membrane. It is faster than the simple
diffusion and can be accompanied by a transport of other substance in the opposite
direction (so-called antiport, for example ATP with ADP or Cl –with HCO3–). Another possibility is the
transport with the help of channel protein that penetrates the whole width of the membrane. The
transfer of a molecule is associated with the change of the channel’s conformation. Some channels
are controlled through the changes in membrane electric potential (voltage-gated channels).
There is a difference between the kinetics of the simple and facilitated diffusion. In the case of simple
diffusion, increasing the concentration of transferred substance leads to the linear increase in the
rate of diffusion. Transport proteins involved in the facilitated diffusion, on the other hand,
have limited capacity (given by their total number in the membrane) and when the concentration
reaches high values, the rate of the diffusion slows down until it reaches its maximum speed (where
the transport capacity is fully saturated).

Among the most important examples of facilitated diffusion are glucose GLUT transporters.
Intracellular transformation of glucose to glucose-6-phosphate and its subsequent usage ensures
the existence of continuous concentration gradient. Overall, there exist seven types of GLUT
transporters of which the most important are:

1. GLUT 1 and 3, serving to maintain the basal glucose uptake by tissues, whose metabolism is
dependent on glucose (brain, erythrocytes, kidneys or placenta).

2. GLUT 2, localised on the membrane of pancreatic β-cells and hepatocytes. It also enables the
transfer of glucose form absorptive epithelia (e.g. the epithelia of proximal convoluted tubule of
kidney, intestinal epithelia or enterocytes) to the blood.

3. GLUT 4 is the glucose transporter of so-called insulin-dependent tissues (skeletal muscle,

myocardium and adipose tissue). Its presence on the membrane of these tissues is subject to the
effect of insulin. This mainly occurs after the meal when are the above-mentioned tissues
responsible of up to 80% of glucose metabolism. Between the meals, on the contrary, they do not
absorb glucose and save it for the tissues that are dependent upon it.

2) Active transport
Active transport can take place against the concentration and electrochemical gradient as well. It
is possible because the transport is coupled with the ATP hydrolysis (ATP → ADP a Pi) and the
energy released is used in the process of transport. We recognize two basic types of this transport:

a) Primary

b) Secondary

a) Primary active transport

Energy of ATP is used directly in the process of transportation of a particular substance. Examples
are Na+/K+-ATPase, H+/K+-ATPase or Ca2+-ATPase.
Na+/K+-ATPase is a tetramer made up of two alpha and two beta subunits. Alpha subunits are
transmembrane, their intracellular domains have a binding site for Na+ and extracellular domains
for K+. Beta subunits are glycolysed (as opposed to alpha) and do not penetrate through the whole
membrane. Their oligosaccharide chains are facing the extracellular space. There exist two distinct
conformational states of the enzyme, depending on whether it is phosphorylated or not. Na +/K+-
ATPase serves as an antiport and in return for the energy released from the ATP it transports 3
Na+ cations out of the cell in exchange for 2 K+ cations. The result is an uneven distribution of
ions on the membrane that forms the basis for the resting membrane potential. Na+/K+-ATPase is
ubiquitous – it probably present in all human cells.
Animation shows function of this transporter (located in the center) during the action potential:

H+/K+-ATPase is an antiport operating similar to Na+/K+-ATPase. It can be found in

the parietal cells of the stomach (where it produces the gastric juices) and in the cells of
the proximal convoluted tubule of kidney. It transports one H+ out of the cell in exchange for one
K+ ion.

Ca2+-ATPase, a calcium pump, is mostly localized in muscle and nerve cells. It actively pumps
calcium ions out of the cytoplasm, either into the sarcoplasmic reticulum or extracellularly, thus
lowering the Ca2+ concentration back to the previous level (for example before the contraction of a
muscle cell).
b) Secondary active transport (or cotransport)
In this case of active transport, the energy released from ATP is not directly used to transport the
particular molecule (like glucose). Instead, it is used to transport other substances (e.g. sodium
cation), which causes the formation of the concentration or
chemical gradient across the membrane. It is this gradient that drives the transport of the (relevant)
substance with the help of other transporters (e.g. SGLT – Sodium Glucose Transporter).

A transporter carrying out the secondary active transport (SGLT) thus displaces at
least two particles – firstly the one, that is supposed to be transported (glucose) and secondly the
one, that drives (through the existence of its gradient across the membrane) the transport (Na+). To
maintain this gradient, a second transporter is necessary (e.g. Na+/K+-ATPase), which can be located
in other portion of the membrane. It is this second transporter that consumes the energy (ATP) –
that is why this kind of transport mechanism belongs to the group of active transport. In
parentheses, we’ve provided an example of secondary active transport of glucose
through SGLT transporter, which uses the gradient of Na created by Na /K -ATPase. According to
+ + +

the direction of the transport we recognise symport (both particles are transported in the same
direction, from or into the cell) and antiport (particles are transported in the opposite direction – one
is carried into the cell and the other out of it). SGLT provides the symport of glucose and Na+.

Tertiary active transport works on the similar principle.

3) Transport of macromolecules across the membrane

According to the direction:

a) Exocytosis is a process by which macromolecules leave the cell. Cytoplasmic membrane fuses
with the membrane of the transport vesicle and the macromolecule is either released in the
extracellular space or remains a part of the cell membrane.

b) Endocytosis is the process of uptake of macromolecules into the cells. Cytoplasmic membrane
invaginates inwards and creates a transport vesicle. According to the nature of the transported
particles, the process is carried out differently:

1. Pinocytosis: the transport of macromolecules in solution. The process can be selective (only
occurring through specific membrane receptors) or non-selective (the place of invagination is
random).

2. Phagocytosis: ingestion of large particles. The cell initially surrounds the particle with protrusions
of the cytoplasmic membrane (pseudopodia) and then encloses it to the vesicle.

_
Intracellular transport
Transport inside the cell usually occurs through:

1) Diffusion: particles dissolved in aqueous medium of cytosol

2) Transport in secretory vesicles: proteins are most commonly formed at rough endoplasmic
reticulum, followed by their transport to Golgi apparatus. Secretory vesicles or lysosomes break free
from GA and are further transported within the cell. This kind of transport is carried out by motor
proteins (dyneins and kinesins) that use the ATP in order to move across the surface of microtubules
(dynein moves towards their – end and kinesin towards their + end) carrying the vesicle attached to
their second end.

_
Compartmentalization of metabolic pathways
Cytosol (cytoplasm without organelles):
1) Metabolism of saccharides: glycolysis, part of gluconeogenesis, glycogenolysis and synthesis of
glycogen, pentose cycle

2) Metabolism of fatty acids: FA synthesis

3) Metabolism of amino acids: synthesis of nonessential AA, some of the transamination reactions

4) Other pathways: parts of heme and urea synthesis pathways, metabolism of purines and
pyrimidines

Mitochondria:
1) Metabolism of saccharides: PDH, part of gluconeogenesis (conversion of pyruvate to OAA)

2) Metabolism of fatty acids: beta-oxidation of FA (Linen’s spiral), synthesis (hepatocytes only) and
degradation (extrahepatic tissues) of ketone bodies

3) Metabolism of amino acids: oxidative deamination, some of the transamination reactions

4) Other pathways: Krebs cycle, respiratory chain and oxidative phosphorylation, parts of heme and
urea synthesis pathways

gER:
1) Proteosynthesis (translation of mRNA)
2) Posttranslational modifications (oxidations, cleavage, methylations, phosphorylations,
glycosylations)

hER:
1) TAG and phospholipid synthesis

2) FA elongation (to a maximal length of 24 carbon atoms – in nerve tissue) and desaturation
(maximally at 9th carbon atom – counted from carboxyl group)
3) Parts of steroid synthesis pathway

4) Biotransformation of xenobiotics

5) Conversion of glucose-6-phosphate to glucose (only in tissues with glucose-6-phosphatase)

GA:
1) Posttranslational modifications (glycosylations, …)

2) Proteins sorting and formation of secretory vesicles

Lysosomes:
1) Hydrolysis of proteins, saccharides, lipids and nucleic acids

Peroxisomes:
1) Degradation of long-chain FA (> 20 carbon atoms)

Cell fractionation is the process used to separate cellular components while preserving individual
functions of each component. This is a method that was originally used to demonstrate
the cellular location of various biochemical processes.

Step One: Breaking Your Cells

To get to the content inside of something, you have to open it. Cells are no different. Detergents allow the
cell membrane to be opened so that the contents inside the cell can be obtained. Detergents disrupt
cellular membranes because they can interact with both membranes and parts of the cell that are soluble
in water. Since detergents can interact with both lipid (membrane) and soluble (cytoplasmic) parts of the
cell, they allow cellular components to be mixed or homogenized.
When the cellular components are mixed, a cell homogenate, or cell lysate, is formed. In fact, the reason
detergents and soaps wash away oil and grease is because they allow things that don't normally mix with
water to be dissolved in water and washed away. Lysing, or opening the cells, in detergent is usually
combined with a physical method that breaks the cell further, such as machines that are similar to
blenders, glass beads, or breaking the cell using sound energy. Using physical methods in combination
with detergents ensures that all of the cells in the sample get broken, and you can isolate as much of your
cellular fraction as possible.

Step Two: Separation

Cell homogenates are separated into fractions by spinning them super-fast in a process called
centrifugation. If you have ever ridden an anti-gravity carnival ride, then you understand how
centrifugation works. These rides eventually reach enough speed that you are pushed against the walls
and do not need a seat belt to stay up. Similarly, centrifugation produces forces that are thousands of
times higher than gravity, and cellular components are pushed toward the bottom of the container they are
in.
Centrifugation applies enough force to cell homogenates to allow different cellular fractions to separate
based on properties such as mass, density, and shape, as shown here in the figure here. Centrifugation
causes components that are too heavy to resist the force of gravity to move to the bottom of the tube, as
seen in this figure.

The smaller components stay homogenized in the liquid (labeled the supernatant in the image) and
the larger components will move to the bottom. Repeating the centrifugation with increasing force
allows smaller cellular components to be separated as seen in this figure.

Step Three: Collection

The way cell fractions are collected will depend on the liquid in which the cell fractions are centrifuged.
Cell fractions are usually centrifuged in a medium, or liquid, that provides osmotic support such as
sucrose or Percoll. The liquids aid in the separation of cellular components based on density and size. If
only one concentration of sucrose or Percoll is used, it is called differential centrifugation because the
different fractions will be collected by centrifuging the sample several times, as shown in this figure.

FLUID MOSAIC MODEL:

The fluid mosaic model explains various observations regarding the structure of functional cell membranes.
According to this biological model, there is a lipid bilayer (two molecules thick layer consisting primarily of
amphipathic phospholipids) in which protein molecules are embedded. The lipid bilayer
gives fluidity and elasticity to the membrane. Small amounts of carbohydrates are also found in the cell
membrane. The biological model, which was devised by SJ Singer and G. L. Nicolson in 1972, describes the
cell membrane as a two-dimensional liquid that restricts the lateral diffusion of membrane components. Such
domains are defined by the existence of regions within the membrane with special lipid and protein cocoon
that promote the formation of lipid rafts or protein and glycoprotein complexes. Another way to define
membrane domains is the association of the lipid membrane with the cytoskeleton filaments and
the extracellular matrix through membrane proteins The current model describes important features relevant to
many cellular processes, including: cell-cell signaling, apoptosis, cell division, membrane budding, and cell
fusion. The fluid mosaic model is the most acceptable model of the plasma membrane. Its main function is to
separate the contents of the cell from the outside.

The fluid mosaic model incorporates the dynamic nature of bilayer membrane organization that
occurs due to the constant rotational and lateral motion of the integral lipid and protein
molecules.
Cell membranes are dynamic, fluid structures, and most of their molecules are able to move
about in the plane of the membrane. This lipid bilayer provides the basic fluid structure of
the membrane and serves as a relatively impermeable barrier to the passage of most water-
soluble molecules.
All biological membranes have a common general structure: each is a very thin film
of lipid and protein molecules, held together mainly by noncovalent interactions. Cell
membranes are dynamic, fluid structures, and most of their molecules are able to move about in
the plane of the membrane. The lipid molecules are arranged as a continuous double layer about
5 nm thick. This lipid bilayer provides the basic fluid structure of the membrane and serves as a
relatively impermeable barrier to the passage of most water-soluble molecules. Protein molecules
that span the lipid bilayer mediate nearly all of the other functions of the membrane, transporting
specific molecules across it, for example, or catalyzing membrane-associated reactions, such as
ATP synthesis. In the plasma membrane, some proteins serve as structural links that connect
the cytoskeleton through the lipid bilayer to either the extracellular matrix or an adjacent cell,
while others serve as receptors to detect and transduce chemical signals in the cell's environment.
As would be expected, it takes many different membrane proteins to enable a cell to function and
interact with its environment. In fact, it is estimated that about 30% of the proteins that are
encoded in an animal cell's genome are membrane proteins.
Proteins of plasma membrane:
While membrane lipids form the basic structure of the lipid bilayer, the active functions of the
membrane are dependent on the proteins. Cell adhesion, energy transduction, signaling, cell
recognition and transport are just some of the important biological processes carried out by membrane
proteins.
Proteins can associate with the membrane in one of three ways. Intrinsic or integral membrane
proteins embed in the hydrophobic region of the lipid bilayer. Experimentally, these proteins can only
be isolated by physically disrupting the membrane with detergent or other non-polar solvent.
Mono Save topic proteins insert in one leaflet but do not span the membrane. Transmembrane
proteins are the classic examples of intrinsic membrane proteins. These span the membrane, typically
in an α-helix conformation and can span the membrane multiple times. Some intergral membrane
proteins use β-barrels to cross the membrane. These structures are typically large and form water filled
channels. Extrinsic or peripheral membrane proteins associate loosely with the hydrophilic surfaces of
the lipid bilayer or intrinsic membrane proteins. They form weak hydrophobic, electrostatic or non-
covalent bonds, but do not embed with the hydrophobic core of the membrane. These proteins can be
dissociated from the membrane without disrupting it through application of polar reagents or high pH
solutions. Extrinsic membrane proteins may interact with the inner or outer leaflet.
Physical and chemical properties of Plasma membrane
 Ion channels are specialized proteins in the plasma membrane that provide a passageway
through which charged ions can cross the plasma membrane down their electrochemical
gradient. The resulting ionic current, generated by the movement of
charged ions through membrane channels, can be measured by patch-clamp methods.
Ion channel receptors are usually multimeric proteins located in the plasma membrane. Each of
these proteins arranges itself so that it forms a passageway or pore extending from one side of
the membrane to the other. These passageways, or ion channels, have the ability to open and
close in response to chemical or mechanical signals. When an ion channel is open, ions move
into or out of the cell in single-file fashion. Individual ion channels are specific to particular ions,
meaning that they usually allow only a single type of ion to pass through them. Both the amino
acids that line a channel and the physical width of the channel determine which ions are able to
wiggle through from the cell exterior to its interior, and vice versa. The opening of an ion
channel is a fleeting event. Within a few milliseconds of opening, most ion channels close and
enter a resting state, where they are unresponsive to signals for a short period of time.
The opening of ion channels alters the charge distribution across the plasma membrane. Recall
that the ionic composition of the cytoplasm is quite different from that of the extracellular
environment. For instance, the concentration of sodium ions in the cytoplasm is far lower than
that in the cell's exterior environment. Conversely, potassium ions exist at higher concentrations
within a cell than outside it. Such differences create a so-called electrochemical gradient, which
is a combination of a chemical gradient and a charge gradient. The opening of ion channels
permits the ions on either side of the plasma membrane to flow down this dual gradient. The
exact direction of flow varies by ion type, and it depends on both the concentration difference
and the voltage difference for each variety of ion. This ion flow results in the production of an
electrical signal. The actual number of ions required to change the voltage across the membrane
is quite small. During the short times that an ion channel is open, the concentration of a
particular ion in the cytoplasm as a whole does not change significantly, only the concentration
in the immediate vicinity of the channel. In excitable cells, the electrical signal initiated by ion
channel receptor activity travels rapidly over the surface of the cell due to the opening of other
ion channels that are sensitive to the voltage change caused by the initial channel opening.

Membrane transport is essential for cellular life. As cells proceed through their life cycle, a vast
amount of exchange is necessary to maintain function. Transport may involve the incorporation
of biological molecules and the discharge of waste products that are necessary for normal
function.

Membrane transport refers to the movement of particles (solute) across or through a membranous
barrier. These membranous barriers, in the case of the cell for example, consist of a phospholipid
bilayer. The phospholipids orient themselves in such a way so that the hydrophilic (polar) heads
are nearest the extracellular and intracellular mediums, and the hydrophobic (non-polar) tails
align between the two hydrophilic head groups.

Membrane transport is dependent upon the permeability of the membrane, transmembrane solute
concentration, and the size and charge of the solute. Solute particles can traverse the membrane
via three mechanisms: passive, facilitated, and active transport. Some of these transport
mechanisms require the input of energy and use of a transmembrane protein, whereas other
mechanisms do not incorporate secondary molecules.
Cell junctions (or intercellular bridges) are a class of cellular structures consisting
of multiprotein complexes that provide contact or adhesion between neighboring cells or
between a cell and the extracellular matrix in animals. They also maintain the paracellular barrier
of epithelia and control paracellular transport. Cell junctions are especially abundant in epithelial
tissues. Combined with cell adhesion molecules and extracellular matrix, cell junctions help
hold animal cells together.
Cell junctions are also especially important in enabling communication between neighboring
cells via specialized protein complexes called communicating (gap) junctions. Cell junctions are
also important in reducing stress placed upon cells.

In vertebrates, there are three major types of cell junction:

Adherens junctions, desmosomes and hemidesmosomes (anchoring junctions)

Gap junctions (communicating junction)
Tight junctions (occluding junctions)
Invertebrates have several other types of specific junctions, for example septate junctions or
the C. elegans apical junction.
In multicellular plants, the structural functions of cell junctions are instead provided for by cell
walls. The analogues of communicative cell junctions in plants are called plasmodesmata.
Anchoring junctions
Cells within tissues and organs must be anchored to one another and attached to components of
the extracellular matrix. Cells have developed several types of junctional complexes to serve
these functions, and in each case, anchoring proteins extend through the plasma membrane to
link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells as well as to
proteins in the extracellular matrix .
Communicating (gap) junctions:
Communicating junctions, or gap junctions allow for direct chemical communication between
adjacent cellular cytoplasm through diffusion without contact with the extracellular fluid. This is
possible due to six connexin proteins interacting to form a cylinder with a pore in the centre
called a connexon. The connexon complexes stretches across the cell membrane and when two
adjacent cell connexons interact, they form a complete gap junction channel. Connexon pores
vary in size, polarity and therefore can be specific depending on the connexin proteins that
constitute each individual connexon. Whilst variation in gap junction channels do occur, their
structure remains relatively standard, and this interaction ensures efficient communication
without the escape of molecules or ions to the extracellular fluid.
Gap junctions play vital roles in the human body, including their role in the uniform contractile
of the heart muscle. They are also relevant in signal transfers in the brain, and their absence
shows a decreased cell density in the brain. Retinal and skin cells are also dependent on gap
junctions in cell differentiation and proliferation.
Tight junctions:
Found in vertebrate epithelia, tight junctions act as barriers that regulate the movement of water
and solutes between epithelial layers. Tight junctions are classified as a paracellular barrier
which is defined as not having directional discrimination; however, movement of the solute is
largely dependent upon size and charge. There is evidence to suggest that the structures in which
solutes pass through are somewhat like pores.
Physiological pH plays a part in the selectivity of solutes passing through tight junctions with
most tight junctions being slightly selective for cations. Tight junctions present in different types
of epithelia are selective for solutes of differing size, charge, and polarity.
Proteins:
There have been approximately 40 proteins identified to be involved in tight junctions. These
proteins can be classified into four major categories; scaffolding proteins, signalling
proteins, regulation proteins, and transmembrane proteins.
Roles:
Scaffolding proteins – organise the transmembrane proteins, couple transmembrane proteins to
other cytoplasmic proteins as well as to actin filaments.

Signaling proteins – involved in junctions assembly, barrier regulation, and gene

transcription.
Regulation proteins – regulate membrane vesicle targeting.
Transmembrane proteins – including junctional adhesion molecule, occludin, and claudin.
It is believed that claudin is the protein molecule responsible for the selective permeability
between epithelial layers.
A three-dimensional image is still yet to be achieved and as such specific information about the
function of tight junctions is yet to be determined.
Tricellular junctions
Tricellular junctions seal epithelia at the corners of three cells. Due to the geometry of three-cell
vertices, the sealing of the cells at these sites requires a specific junctional organization, different
from those in bicellular junctions. In vertebrates, components tricellular junctions are tricellulin
and lipolysis-stimulated lipoprotein receptors. In invertebrates, the components are gliotactin and
anakonda.
Tricellular junctions are also implicated in the regulation of cytoskeletal organization and cell
divisions. In particular they ensure that cells divide according to the Hertwig rule. In some
Drosophila epithelia, during cell divisions tricellular junctions establish physical contact
with spindle apparatus through astral microtubules. Tricellular junctions exert a pulling force on
the spindle apparatus and serve as a geometrical clues to determine orientation of cell
divisions.[12]

Cell junction molecules

The molecules responsible for creating cell junctions include various cell adhesion molecules.
There are four main types: selectins, cadherins, integrins, and the immunoglobulin superfamily.
Selectins are cell adhesion molecules that play an important role in the initiation of inflammatory
processes. The functional capacity of selectin is limited to leukocyte collaborations with vascular
endothelium. There are three types of selectins found in humans; L-selectin, P-selectin and E-
selectin. L-selectin deals with lymphocytes, monocytes and neutrophils, P-selectin deals with
platelets and endothelium and E-selectin deals only with endothelium. They have extracellular
regions made up of an amino-terminal lectin domain, attached to a carbohydrate ligand, growth
factor-like domain, and short repeat units (numbered circles) that match the complementary
binding protein domains.
Cadherins are calcium-dependent adhesion molecules. Cadherins are extremely important in the
process of morphogenesis – fetal development. Together with an alpha-beta catenin complex, the
cadherin can bind to the microfilaments of the cytoskeleton of the cell. This allows for
homophilic cell–cell adhesion. The β-catenin–α-catenin linked complex at the adherens junctions
allows for the formation of a dynamic link to the actin cytoskeleton.
Integrins act as adhesion receptors, transporting signals across the plasma membrane in multiple
directions. These molecules are an invaluable part of cellular communication, as a single ligand
can be used for many integrins. Unfortunately these molecules still have a long way to go in the
ways of research.
Immunoglobulin superfamily are a group of calcium independent proteins capable of homophilic
and heterophilic adhesion. Homophilic adhesion involves the immunoglobulin-like domains on
the cell surface binding to the immunoglobulin-like domains on an opposing cell’s surface while
heterophilic adhesion refers to the binding of the immunoglobulin-like domains to integrins and
carbohydrates instead.
Cytoskeleton:
The eukaryotic cytoskeleton is a network of three long filament systems, made from the repetitive
assembly and disassembly of dynamic protein components. The primary filament systems comprising
the cytoskeleton are microtubules, actin filaments, and intermediate filaments. It creates an internal
architecture (see figure below) to give a cell its shape through elaborate linkage(s) to itself, the plasma
membrane, and internal organelles.

The cytoskeleton structure is modified by adhesion to neighboring cells or to the extracellular

matrix (ECM). The strength and the type of these adhesions are pivotal for regulating the
assembly/disassembly of the cytoskeleton components. This dynamic property enables cellular
movement, which is governed by forces (both internal and external). This information is sensed by
mechanosensors and disseminated via the cytoskeleton leading to chemical signalling and response.

Although subunits of all three filament systems are present throughout the cell, differences in the
subunit structures and the attractive forces between them impart each system with variable stabilities
and distinct mechanical properties. These characteristics explain their distribution in particular
structures and/or regions of the cell. Numerous cytoskeletal-associated proteins also help to regulate
the spatial and temporal distribution of the cytoskeleton. The organization and assembly of one
filament system is influenced by the others in a coordinated fashion for most cellular functions.
Accessory proteins organize filaments into higher-order structures:

Crosslinking of the filaments by specific motors or multivalent binding proteins (accessory proteins)
increases stability and forms higher-order structures. Such organization facilitates generation of long-
term contractile forces and occasionally support compressive forces while being dynamic. These
structures are connected across cells through junctions and hence facilitate mechanotransduction and
cumulative response at a tissue- or organ-level (see the lower panel in the figure below and
“Mediators of mechanotransduction” for details on junctions).

Accessory proteins are a critical part of the signaling network that integrates extra- and intracellular
signals (e.g. force, ions etc.) with the cytoskeleton assembly module(s). These can be specific for
certain types of filaments. E.g., fimbrin binds only actin filaments, while others like plectin are non-
specific.

Accessory factors can also help regulate the stability, mechanical properties, and force production for
the individual filaments within the larger structure. For example, fascin crosslinks actin filaments into
rigid bundles that have mechanical strength for generating protrusive force, while filamin cross links
the actin filaments into gel-like networks that are flexible and produce less force. Examples of higher-
order cytoskeleton structures:

Contractile bundles found in muscle cells: Composed of actin filaments and a number of accessory
proteins – tropomyosin stabilizes actin filaments and regulates the association of myosin to control the
timing of contraction.

The microtubule organizing center (MTOC) creates global organization of the microtubule network
to establish the polarity and positioning of the cell organelles.

Nuclear lamina: Composed of intermediate filaments and the mitotic spindle (made of microtubules).
Laminas are tensed mechanistically with the continuous network of chromosomes and nuclear matrix.

The intermediate filaments also form flexible cables from the cell surface to the center to form a
‘cage’ around the nucleus. These structures equipped with accessory proteins have extra resilience and
toughness relative to individual filaments. E.g., filaggrin tightly bundles keratin filaments in the upper
layer(s) of skin cells providing resistance to physical stress and water loss. Bacteria harbor similar
proteins and filaments, however, the filament-associated proteins vary greatly between species and it
is not currently known how they evolved from prokaryotes to eukaryotes.

PROTOPLASM:

Mitochondria-

Mitochondria are membrane-bound cell organelles (mitochondrion, singular) that generate

most of the chemical energy needed to power the cell's biochemical reactions. Chemical energy
produced by the mitochondria is stored in a small molecule called adenosine triphosphate
(ATP).The classic role of mitochondria is oxidative phosphorylation, which generates ATP by
utilizing the energy released during the oxidation of the food we eat. ATP is used in turn as the
primary energy source for most biochemical and physiological processes, such as growth,
movement and homeostasis.

Most of the proteins and other molecules that make up mitochondria originate in the
cell nucleus. However, 37 genes are contained in the human mitochondrial genome, 13 of which
produce various components of the ETC. Mitochondrial DNA (mtDNA) is highly susceptible
to mutations, largely because it does not possess the robust DNA repair mechanisms common to
nuclear DNA. In addition, the mitochondrion is a major site for the production of reactive
oxygen species (ROS; or free radicals) due to the high propensity for aberrant release of free
electrons. While several different antioxidant proteins within the mitochondria scavenge and
neutralize these molecules, some ROS may inflict damage to mtDNA. In addition, certain
chemicals and infectious agents, as well as alcohol abuse, can damage mtDNA. In the latter
instance, excessive ethanol intake saturates detoxification enzymes, causing highly reactive
electrons to leak from the inner membrane into the cytoplasm or into the mitochondrial matrix,
where they combine with other molecules to form numerous radicals.

In many organisms, the mitochondrial genome is inherited maternally. This is because the
mother’s egg cell donates the majority of cytoplasm to the embryo, and mitochondria inherited
from the father’s sperm are usually destroyed. There are numerous inherited and acquired
mitochondrial diseases. Inherited diseases may arise from mutations transmitted in maternal or
paternal nuclear DNA or in maternal mtDNA. Both inherited and acquired mitochondrial
dysfunction is implicated in several diseases, including Alzheimer disease and Parkinson disease.
The accumulation of mtDNA mutations throughout an organism’s life span are suspected to play
an important role in aging, as well as in the development of certain cancers and other diseases.
Because mitochondria also are a central component of apoptosis (programmed cell death), which
is routinely used to rid the body of cells that are no longer useful or functioning properly,
mitochondrial dysfunction that inhibits cell death can contribute to the development of cancer.

Chloroplast:

Chloroplasts are organelles found in plant cells and eukaryotic algae that conduct
photosynthesis. Chloroplasts absorb sunlight and use it in conjunction with water and carbon
dioxide gas to produce food for the plant.

Chloroplasts are roughly 1–2 μm (1 μm = 0.001 mm) thick and 5–7 μm in diameter. They are
enclosed in a chloroplast envelope, which consists of a double membrane with outer and inner
layers, between which is a gap called the intermembrane space. A third, internal membrane,
extensively folded and characterized by the presence of closed disks (or thylakoids), is known as
the thylakoid membrane. In most higher plants, the thylakoids are arranged in tight stacks called
grana (singular granum). Grana are connected by stromal lamellae, extensions that run from one
granum, through the stroma, into a neighbouring granum. The thylakoid membrane envelops a
central aqueous region known as the thylakoid lumen. The space between the inner membrane
and the thylakoid membrane is filled with stroma, a matrix containing
dissolved enzymes, starch granules, and copies of the chloroplast genome.

The Photosynthetic Machinery

The thylakoid membrane houses chlorophylls and different protein complexes, including
photosystem I, photosystem II, and ATP (adenosine triphosphate) synthase, which are
specialized for light-dependent photosynthesis. When sunlight strikes the thylakoids, the light
energy excites chlorophyll pigments, causing them to give up electrons. The electrons then enter
the electron transport chain, a series of reactions that ultimately drives the phosphorylation of
adenosine diphosphate (ADP) to the energy-rich storage compound ATP. Electron transport also
results in the production of the reducing agent nicotinamide adenine dinucleotide phosphate
(NADPH). ATP and NADPH are used in the light-independent reactions (dark reactions) of
photosynthesis, in which carbon dioxide and water are assimilated into organic compounds. The
light-independent reactions of photosynthesis are carried out in the chloroplast stroma, which
contains the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco). Rubisco
catalyzes the first step of carbon fixation in the Calvin cycle (also called Calvin-Benson cycle),
the primary pathway of carbon transport in plants. Among so-called C4 plants, the initial carbon
fixation step and the Calvin cycle are separated spatially—carbon fixation occurs via
phosphoenolpyruvate (PEP) carboxylation in chloroplasts located in the mesophyll, while
malate, the four-carbon product of that process, is transported to chloroplasts in bundle-sheath
cells, where the Calvin cycle is carried out. C4 photosynthesis attempts to minimize the loss of
carbon dioxide to photorespiration. In plants that use crassulacean acid metabolism (CAM), PEP
carboxylation and the Calvin cycle are separated temporally in chloroplasts, the former taking
place at night and the latter during the day. The CAM pathway allows plants to carry out
photosynthesis with minimal water loss.

Endoplasmic Reticulum:
Endoplasmic reticulum (ER), in biology, a continuous membrane system that forms a series of
flattened sacs within the cytoplasm of eukaryotic cells and serves multiple functions, being
important particularly in the synthesis, folding, modification, and transport of proteins.
The entire structure can account for a large proportion of the endomembrane system of the
cell. For instance, in cells such as liver hepatocytes that are specialized for protein secretion and
detoxification, the ER can account for more than 50% of the total lipid bilayer of the
cell. Similarly, the ER membrane system is particularly prominent in pancreatic beta cells that
secrete insulin, or within activated B-lymphocytes that produce antibodies.
Functions of ER:
Functions of smooth ER include lipid metabolism (both catabolism and anabolism; they
synthesize a variety of phospholipids, cholesterol, and steroids).
Glycogenolysis (degradation of glycogen; glycogen being polymerized in the cytosol).
Drug detoxification (by the help of the cytochrome P-450).
The endoplasmic reticulum provides an ultrastructural skeletal framework to the cell and
gives mechanical support to the colloidal cytoplasmic matrix.
The exchange of molecules by the process of osmosis, diffusion and active transport
occurs through the membranes of the endoplasmic reticulum.
The endoplasmic reticulum is the main component of the endomembrane system, also
called the cytoplasmic vacuolar system or cytocavity network.
The endoplasmic membranes contain many enzymes that perform various synthetic and
metabolic activities. Further, the endoplasmic reticulum provides an increased surface for
various enzymatic reactions.
The endoplasmic reticulum acts as an intracellular circulatory or transporting system.
As a growing secretory polypeptide emerges from the ribosome, it passes through the
RER membrane and gets accumulated in the lumen of RER. Here, the polypeptide chains
undergo tailoring, maturation, and molecular folding to form functional secondary or
tertiary protein molecules.
RER pinches off certain tiny protein-filled vesicles which ultimately get fused to cis
Golgi.
The ER membranes are found to conduct intra-cellular impulses. For example, the
sarcoplasmic reticulum transmits impulses from the surface membrane into the deep
region of the muscle fibers.
The ER membranes form the new nuclear envelope after each nuclear division.
The SER contains several key enzymes that catalyze the synthesis of cholesterol which is
also a precursor substance for the biosynthesis of two types of compounds— the steroid
hormones and bile acids.
RER also synthesize membrane proteins and glycoproteins which are cotranslationally
inserted into the rough ER membranes. Thus, the endoplasmic reticulum is the site of the
biogenesis of cellular membranes.

Golgi Complex:
A stack of small flat sacs formed by membranes inside the cell's cytoplasm (gel-like fluid).
The Golgi complex prepares proteins and lipid (fat) molecules for use in other places inside and
outside the cell. The Golgi complex is a cell organelle. Also called Golgi apparatus and Golgi
body.
In general, the Golgi apparatus is made up of approximately four to eight cisternae, although in
some single-celled organisms it may consist of as many as 60 cisternae. The cisternae are held
together by matrix proteins, and the whole of the Golgi apparatus is supported by
cytoplasmic microtubules. The apparatus has three primary compartments, known generally as
“cis” (cisternae nearest the endoplasmic reticulum), “medial” (central layers of cisternae), and
“trans” (cisternae farthest from the endoplasmic reticulum). Two networks, the cis Golgi network
and the trans Golgi network, which are made up of the outermost cisternae at the cis and trans
faces, are responsible for the essential task of sorting proteins and lipids that are received (at the
cis face) or released (at the trans face) by the organelle.

The proteins and lipids received at the cis face arrive in clusters of fused vesicles. These fused
vesicles migrate along microtubules through a special trafficking compartment, called the
vesicular-tubular cluster, that lies between the endoplasmic reticulum and the Golgi apparatus.
When a vesicle cluster fuses with the cis membrane, the contents are delivered into the lumen of
the cis face cisterna. As proteins and lipids progress from the cis face to the trans face, they are
modified into functional molecules and are marked for delivery to specific intracellular or
extracellular locations. Some modifications involve cleavage of oligosaccharide side chains
followed by attachment of different sugar moieties in place of the side chain. Other
modifications may involve the addition of fatty acids or phosphate groups (phosphorylation) or
the removal of monosaccharides. The different enzyme-driven modification reactions are
specific to the compartments of the Golgi apparatus. For example, the removal of mannose
moieties occurs primarily in the cis and medial cisternae, whereas the addition
of galactose or sulfate occurs primarily in the trans cisternae. In the final stage of transport
through the Golgi apparatus, modified proteins and lipids are sorted in the trans Golgi network
and are packaged into vesicles at the trans face. These vesicles then deliver the molecules to their
target destinations, such as lysosomes or the cell membrane. Some molecules, including certain
soluble proteins and secretory proteins, are carried in vesicles to the cell membrane
for exocytosis (release into the extracellular environment). The exocytosis of secretory proteins
may be regulated, whereby a ligand must bind to a receptor to trigger vesicle fusion
and protein secretion.

The way in which proteins and lipids move from the cis face to the trans face is a matter of
debate, and today there exist multiple models, with quite different perceptions of the Golgi
apparatus, competing to explain this movement. The vesicular transport model, for example,
stems from initial studies that identified vesicles in association with the Golgi apparatus. This
model is based on the idea that vesicles bud off and fuse to cisternae membranes, thus moving
molecules from one cisterna to the next; budding vesicles can also be used to transport molecules
back to the endoplasmic reticulum. A vital element of this model is that the cisternae themselves
are stationary. In contrast, the cisternal maturation model depicts the Golgi apparatus as a far
more dynamic organelle than does the vesicular transport model. The cisternal maturation model
indicates that cis cisternae move forward and mature into trans cisternae, with new cis cisternae
forming from the fusion of vesicles at the cis face. In this model, vesicles are formed but are used
only to transport molecules back to the endoplasmic reticulum. Other examples of models to
explain protein and lipid movement through the Golgi apparatus include the rapid partitioning
model, in which the Golgi apparatus is viewed as being divided into separately functioning
compartments (e.g., processing versus exporting regions), and the stable compartments as
cisternal progenitors model, in which compartments within the Golgi apparatus are considered to
be defined by Rab proteins.
Soluble and secretory proteins leaving the Golgi apparatus undergo exocytosis. The secretion of soluble
proteins occurs constitutively. In contrast, the exocytosis of secretory proteins is a highly regulated
process, in which a ligand must bind to a receptor to trigger vesicle fusion and protein secretion.

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