Cell nucleus

Nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's
genetic material, organized as multiple long linear DNA molecules in complex with a large variety
of proteins, such as histones, to form chromosomes. The nucleus was the first organelle to be
discovered.

Structures- The nucleus is the largest cellular organelle in animals. In mammalian cells, the
average diameter of the nucleus is approximately 6 micrometers (µm), which occupies about 10%
of the total cell volume. The main structures making up the nucleus are the nuclear envelope, a
double membrane that encloses the entire organelle and separates its contents from the cellular
cytoplasm, and the nuclear lamina, a meshwork within the nucleus that adds mechanical support,
much like the cytoskeleton supports the cell as a whole.

Nuclear envelope- The nuclear envelope otherwise known as nuclear membrane consists of two
cellular membranes, an inner and an outer membrane, arranged parallel to one another and
separated by 10 to 50 nanometers (nm). The nuclear envelope completely encloses the nucleus and
separates the cell's genetic material from the surrounding cytoplasm, serving as a barrier to prevent
macromolecules from diffusing freely between the nucleoplasm and the cytoplasm. The outer
nuclear membrane is continuous with the membrane of the rough endoplasmic reticulum (RER),
and is similarly studded with ribosomes. The space between the membranes is called the
perinuclear space and is continuous with the RER lumen.

Nuclear Pore Complex- Nuclear pores, which provide aqueous channels through the envelope,
are composed of multiple proteins, collectively referred to as nucleoporins. The pores are about
125 million daltons in molecular weight and consist of around 50 (in yeast) to 100 proteins (in
vertebrates). The pores are 100 nm in total diameter; however, the gap through which molecules
freely diffuse is only about 9 nm wide, due to the presence of regulatory systems within the center
of the pore. This size allows the free passage of small water-soluble molecules while preventing
larger molecules, such as nucleic acids and larger proteins, from inappropriately entering or exiting
the nucleus. These large molecules must be actively transported into the nucleus instead. The
nucleus of a typical mammalian cell will have about 3000 to 4000 pores throughout its envelope,
each of which contains a donut-shaped, eightfold-symmetric ring-shaped structure at a position
where the inner and outer membranes fuse. Attached to the ring is a structure called the nuclear
basket that extends into the nucleoplasm, and a series of filamentous extensions that reach into the
cytoplasm.
Most proteins, ribosomal subunits, and some RNAs are transported through the pore complexes in
a process mediated by a family of transport factors known as karyopherins. Those karyopherins
that mediate movement into the nucleus are also called importins, while those that mediate
movement out of the nucleus are called exportins. Most karyopherins interact directly with their
cargo, although some use adaptor proteins. Steroid hormones such as cortisol and aldosterone, as
well as other small lipid-soluble molecules involved in intercellular signaling can diffuse through
the cell membrane and into the cytoplasm, where they bind nuclear receptor proteins that are
trafficked into the nucleus. There they serve as transcription factors when bound to their ligand; in
the absence of ligand many such receptors function as histone deacetylases that repress gene
expression. Any cargo with a nuclear localization signal (NLS) exposed will be destined for quick
and efficient transport through the pore. Several NLS sequences are known, generally containing
a conserved phospholipids sequence with basic residues such as PKKKRKV. Any material with
an NLS will be taken up by importins to the nucleus.

Export of proteins- Some molecules or macromolecular complexes need to be exported from the
nucleus to the cytoplasm, as do ribosome subunits and messenger RNAs. In the classical export
scheme, proteins with a nuclear export sequence (NES) can bind in the nucleus to form a
heterotrimeric complex with an exportin and RanGTP (for example the exportin CRM1). The
complex can then diffuse to the cytoplasm where GTP is hydrolysed and the NES-protein is
released. CRM1-RanGDP diffuses back to the nucleus where GDP is exchanged to GTP by
RanGEFs. This process is also energy dependent as it consumes one GTP.

Nuclear lamina- In animal cells, two networks of intermediate filaments provide the nucleus with
mechanical support: the nuclear lamina forms an organized meshwork on the internal face of the
envelope, while less organized support is provided on the cytosolic face of the envelope. The
nuclear lamina is mostly composed of lamin proteins. Like all proteins, lamins are synthesized in
the cytoplasm and later transported into the nucleus interior, where they are assembled before
being incorporated into the existing network of nuclear lamina.

Chromosomes- There are two types of chromatin. Euchromatin is the less compact DNA form,
and contains genes that are frequently expressed by the cell. The other type, heterochromatin, is
the more compact form, and contains DNA that are infrequently transcribed. During interphase the
chromatin organizes itself into discrete individual patches called chromosome territories. Active
genes, which are generally found in the euchromatic region of the chromosome, tend to be located
towards the chromosome's territory boundary.

Nucleolus- The nucleolus is a discrete densely stained structure found in the nucleus. It is not
surrounded by a membrane, and is sometimes called a suborganelle. It forms around tandem
repeats of rDNA, DNA coding for ribosomal RNA (rRNA). These regions are called nucleolar
organizer regions (NOR). The main roles of the nucleolus are to synthesize rRNA and assemble
ribosomes. The first step in ribosomal assembly is transcription of the rDNA, by a protein called
RNA polymerase I, forming a large prerRNA precursor. This is cleaved into the subunits 5.8S,
18S, and 28S rRNA. The transcription, post-transcriptional processing, and assembly of rRNA
occurs in the nucleolus, aided by small nucleolar RNA (snoRNA) molecules, some of which are
derived from spliced introns from messenger RNAs encoding genes related to ribosomal function.
The assembled ribosomal subunits are the largest structures passed through the nuclear pores.
 Chromatin Structure and Chromosome Organisation

Introduction

Chromatin refers to a complex of DNA and proteins in which the formation of chromosomes takes
place. This formation of chromosomes happens within the nucleus of eukaryotic cells. There is
no appearance of nuclear DNA in free linear strands. The nuclear DNA is highly condensed, and
its wrapping takes place around nuclear proteins to make it fit inside the nucleus. There are
two types of chromatin– euchromatin and heterochromatin. Heterochromatin is an area of highly
coiled DNA and stains darkly whereas euchromatin is an area of less coiling and stains lightly. As
a result of this chromosomes show transverse bands of lightly and darkly stained regions. The
appearance of this complex is like beads on a string; when observed under a microscope. Experts
call these beads nucleosomes. Keep on reading to learn about the basic structure, functions and
types of this complex.

Chromatin Structure
Chromatin is a complex of macromolecules that comprises three main parts- protein, DNA, and
RNA. One can find this complex inside the nucleus of eukaryotic cells. Two types of chromatin
exist in nature in two forms. These two forms are- heterochromatin (which is the condensed form)
and euchromatin (which is the extended form).

Histones are the primary protein components of this complex. These primary protein components
organise the DNA into “bead-like” structures. Experts call these structures nucleosomes. Histones
provide a base on which the wrapping around of the DNA can take place.

A nucleosome involves 147 DNA base pairs that are wrapped around an octamer. An octamer is
simply a set of 8 histones. Further folding of nucleosomes can result in the production of this
complex’s fibre.

The coiling and condensation of these fibres happen to produce chromosomes. Some cell processes
are made possible by this complex to occur. Such cell processes are as follows:

 DNA replication
 Transcription
 DNA repair
 Genetic recombination
 Cell division
 Relationship between epigenetics & chromatin:

Epigenetics refers to the study of changes in patterns of gene expression patterns. The reason for
such changes is the mechanisms in the underlying DNA sequence. Daughter cells inherit
epigenetic modifications during the process of cell division.

Chromatin structure alterations govern the changes in gene expression, whose association is with
epigenetics. This shows the relationship between epigenetics & chromatin structure.

Chromatin Functions
Below are the various functions of chromatin in a cell:

 DNA Packaging:

Perhaps the critical function of chromatin in a cell is the compactification of long DNA strands. In
the nucleus, DNA length is far more significant in comparison to the size of the compartment in
which it is stored. There is a need to condense the DNA to fit it into this compartment.

Experts use the packing ratio to describe the degree of condensation of DNA. The DNA packaging
does not take place directly in the complex structure. This is necessary to achieve the overall
packing ratio. So, instead of direct placement, there exist several levels of packing.

The winding of DNA takes place around the nucleosome to achieve the first level of packing. This
structure is basic in both types of chromatin. The second level of packing involves the wrapping
of beads that can be found in a 30 nm fibre. In the final packaging, the organisation of the fiber
takes place in domains, scaffolds, and loops.

Transcription regulation:
Transcription is a three-step process which is as follows:

 Reading of the DNA stored genetic information occurs by proteins

 Transcribing takes place into RNA
 Finally, the translation of the RNA takes place into functional proteins. It will not happen if the
complex restricts access to the read proteins

In euchromatin, the extended type, the transcription process is conducted. In contrast, in

heterochromatin, the condensed type, the tight packing prevents the DNA reading by proteins.
Chromatin and DNA Repair:
The packaging of DNA into the complex poses a barrier to every process related to DNA. This
complex readily changes its structure because of the high dynamic arrangement of proteins and
DNA. Relaxation happens at a rapid rate at the DNA damage site. This leads to the repairing of
proteins, which binds to DNA to repair it.

Chromatin Types
Two types of chromatin are found in nature. These two types are heterochromatin and euchromatin.
These two types of chromatin are responsible for giving light and dark bands to chromosomes.

 Heterochromatin:

Heterochromatin is characterised by very tight packing and condensing. When heterochromatin

forms, histones are modified as well as the recruitment and spreading of silencing complexes
happens. The result of all this is bringing about changes to its structure. These changes impact
gene transcription and other DNA processes.

Heterochromatin is inhibitory to gene expression because of its repressive structure. It can fold
into structures that are of higher order. The formation of heterochromatin causes an increase in the
DNA negative supercoiling.

 Euchromatin:

Euchromatin involves a loosely wrapped complex, thereby making DNA more accessible. Histone
modifications allow the complex to be more open; as we have read previously, modifications lead
to the closing off of heterochromatin to DNA replication enzymes. Such modifications, in
euchromatin, are reversed.

Euchromatin is more open compared to heterochromatin when it comes to recruiting gene

regulatory proteins as well as RNA polymerase complexes. This allows the initiation of the
transcription. There is a direct relationship between the amount of euchromatin in a cell’s nucleus
and the level of the cell’s operational productivity.

Conclusion
Chromatin is a complex of proteins and DNA in which the formation of chromosomes
happens. This happens within the eukaryotic cell’s nucleus. The nuclear DNA is highly condensed
to make it fit inside the nucleus. This complex looks like beads on a string under a microscope. Its
basic structure is essentially a macromolecules complex consisting of protein, DNA, and RNA.
There exists a relationship between epigenetics & chromatin structure. This complex has three
functions- DNA Packaging, transcription regulation, and chromatin and DNA Repair. There are
two types of chromatin in existence which are euchromatin and heterochromatin.

Chloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct
photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and
reduce NADP to NADPH through a complex set of processes called photosynthesis. The word
chloroplast is derived from the Greek words chloros, which means green, and plast, which means
form or entity. Chloroplasts are members of a class of organelles known as plastids. Chloroplasts
are one of the many different types of organelles in the plant cell. In general, they are considered
to have originated from cyanobacteria through endosymbiosis. This was first suggested by
Mereschkowsky in 1905 after an observation by Schimper in 1883 that chloroplasts closely
resemble cyanobacteria. The chloroplast is surrounded by a double-layered composite membrane
with an intermembrane space; further, it has reticulations, or many infoldings, filling the inner
spaces. The chloroplast has its own DNA, which codes for redox proteins involved in electron
transport in photosynthesis; this is termed the plastome. Plastids may contain 60-100 genes
whereas cyanobacteria often contain more than 1500 genes. Many of the missing genes are
encoded in the nuclear genome of the host.

Structure and Function- Chloroplasts are observable as flat discs usually 2 to 10 micrometers in
diameter and 1 micrometer thick. In land plants, they are, in general, 5 µm in diameter and 2.3 µm
thick. They are 200-400 nm (nano-meters). The chloroplast is contained by an envelope that
consists of an inner and an outer phospholipid membrane. Between these two layers is the
intermembrane space. A typical parenchyma cell contains about 10 to 100 chloroplasts.
The material within the chloroplast is called the stroma, corresponding to the cytosol of the original
bacterium, and contains one or more molecules of small circular DNA. It also contains ribosomes;
however most of its proteins are encoded by genes contained in the host cell nucleus, with the
protein products transported to the chloroplast. Within the stroma are stacks of thylakoids, the sub-
organelles, which are the site of photosynthesis. The thylakoids are arranged in stacks called grana
(singular: granum). A thylakoid has a flattened disk shape. Inside it is an empty area called the
thylakoid space or lumen. Photosynthesis takes place on the thylakoid membrane; as in
mitochondrial oxidative phosphorylation, it involves the coupling of cross-membrane fluxes with
biosynthesis via the dissipation of a proton electrochemical gradient. Embedded in the thylakoid
membrane are antenna complexes, each of which consists of the light-absorbing pigments,
including chlorophyll and carotenoids, as well as proteins that bind the pigments. This complex
both increases the surface area for light capture, and allows capture of photons with a wider range
of wavelengths. The energy of the incident photons is absorbed by the pigments and funneled to
the reaction center of this complex through resonance energy transfer. Two chlorophyll molecules
are then ionized, producing an excited electron, which then passes onto the photochemical reaction
center.
 Mitochondrion
A mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These
organelles range from 0.5 to 10 micrometers (µm) in diameter. Mitochondria are sometimes
described as "cellular power plants" because they generate most of the cell's supply of adenosine
triphosphate (ATP), used as a source of chemical energy.

Structure - A mitochondrion contains outer and inner membranes composed of phospholipid

bilayers and proteins. The two membranes, however, have different properties. Because of this
double-membraned organization, there are five distinct compartments within the mitochondrion.
There is the outer mitochondrial membrane, the intermembrane space (the space between the outer
and inner membranes), the inner mitochondrial membrane, the crista space (formed by infoldings
of the inner membrane), and the matrix (space within the inner membrane).

A. Outer membrane
The outer mitochondrial membrane, which encloses the entire organelle, has a protein-to-
phospholipid ratio similar to that of the eukaryotic plasma membrane. It contains large
numbers of integral proteins called porins. These porins form channels that allow
molecules 5000 Daltons or less in molecular weight to freely diffuse from one side of the
membrane to the other. Larger proteins can enter the mitochondrion if a signalling
sequence at their N-terminus binds to a large multi-subunit protein called translocase of the
outer membrane, which then actively moves them across the membrane. The mitochondrial
 outer membrane can associate with the endoplasmic reticulum (ER) membrane, in a
structure called MAM (mitochondria-associated ER membrane). This is important in ER-
mitochondria calcium signalling and involved in the transfer of lipids between the ER and
mitochondria.

B. Intermembrane space
The intermembrane space is the space between the outer membrane and the inner
membrane. Because the outer membrane is freely permeable to small molecules, the
concentrations of small molecules such as ions and sugars in the intermembrane space are
the same as the cytosol. However, large proteins must have a specific signalling sequence
to be transported across the outer membrane, the protein composition of this space is
different from the protein composition of the cytosol.
C. Inner membrane
It contains more than 151 different polypeptides and has a very high protein-to-
phospholipid ratio (more than 3:1 by weight, which is about 1 protein for 15
phospholipids). The inner membrane is home to around 1/5 of the total protein in a
mitochondrion. In addition, the inner membrane is rich in an unusual phospholipid,
cardiolipin. Cardiolipin contains four fatty acids rather than two and may help to make the
inner membrane impermeable. Unlike the outer membrane, the inner membrane does not
contain porins and is highly impermeable to all molecules. Almost all ions and molecules
require special membrane transporters to enter or exit the matrix. Proteins are carried into
the matrix via the translocase of the inner membrane (TIM) complex or via Oxa1. In
addition, there is a membrane potential across the inner membrane formed by the action of
the enzymes of the electron transport chain. The inner mitochondrial membrane contains
proteins with five types of functions:
1. Those that perform the redox reactions of oxidative phosphorylation
2. ATP synthase, which generates ATP in the matrix
3. Specific transport proteins that regulate metabolite passage into and out of the matrix
4. Protein import machinery.
5. Mitochondria fusion and fission protein

Cristae: The inner mitochondrial membrane is compartmentalized into numerous cristae,

which expand the surface area of the inner mitochondrial membrane, enhancing its ability
to produce ATP. For typical liver mitochondria, the area of the inner membrane is about
five times greater than the outer membrane. This ratio is variable and mitochondria from
cells that have a greater demand for ATP, such as muscle cells, contain even more cristae.
These folds are studded with small round bodies known as F1 particles or oxysomes. These
are not simple random folds but rather invaginations of the inner membrane, which can
affect overall chemiosmotic function.
D. The Matrix
The matrix is the space enclosed by the inner membrane. It contains about 2/3 of the total
protein in a mitochondrion. The matrix is important in the production of ATP with the aid
of the ATP synthase contained in the inner membrane. The matrix contains a highly-
concentrated mixture of hundreds of enzymes, special mitochondrial ribosomes, tRNA,
and several copies of the mitochondrial DNA genome. Of the enzymes, the major functions
include oxidation of pyruvate and fatty acids, and the citric acid cycle. A human
mitochondrial DNA sequence revealed 16,569 base pairs encoding 37 total genes: 22
tRNA, 2 rRNA, and 13 peptide genes. The 13 mitochondrial peptides in humans are
integrated into the inner mitochondrial membrane, along with proteins encoded by genes
that reside in the host cell's nucleus.

Genome- The human mitochondrial genome is a circular DNA molecule of about 16

kilobases. It encodes 37 genes: 13 for subunits of respiratory complexes I, III, IV and V,
22 for mitochondrial tRNA (for the 20 standard amino acids, plus an extra gene for leucine
and serine), and 2 for rRNA. One mitochondrion can contain two to ten copies of its DNA.
As in prokaryotes, there is a very high proportion of coding DNA and an absence of repeats.
Mitochondrial genes are transcribed as multigenic transcripts, which are cleaved and
polyadenylated to yield mature mRNAs. However, introns have been observed in some
eukaryotic mitochondrial DNA, such as that of yeast and protists, including Dictyostelium
discoideum. Many slight variants have been discovered since, including various alternative
mitochondrial codes. Further, the AUA, AUC, and AUU codons are all allowable start
codons.

Function- The most prominent roles of mitochondria are to produce ATP (i.e.,
phosphorylation of ADP) through respiration, and to regulate cellular metabolism. The
central set of reactions involved in ATP production is collectively known as the citric acid
cycle, or the Krebs Cycle. However, the mitochondrion has many other functions in
addition to the production of ATP.
 Endoplasmic reticulum
The endoplasmic reticulum (ER) is an eukaryotic organelle that forms an interconnected network
of tubules, vesicles, and cisternae within cells. Rough endoplasmic reticulums synthesize proteins,
while smooth endoplasmic reticulums synthesize lipids and steroids, metabolize carbohydrates and
steroids, and regulate calcium concentration, drug detoxification, and attachment of receptors on
cell membrane proteins. Sarcoplasmic reticulums solely regulate calcium levels.
Structure-

The general structure of the endoplasmic reticulum is an extensive membrane network of cisternae
(sac-like structures) held together by the cytoskeleton. The phospholipid membrane encloses a
space, the cisternal space (or lumen), from the cytosol, which is continuous with the perinuclear
space. The two varieties are called rough endoplasmic reticulum and smooth endoplasmic
reticulum.

The quantity of RER and SER in a cell can quickly interchange from one type to the other,
depending on changing metabolic needs: one type will undergo numerous changes including new
proteins embedded in the membranes to transform.

Rough endoplasmic reticulum-

The surface of the rough endoplasmic reticulum (RER) is studded with protein-manufacturing
ribosomes giving it a "rough" appearance (hence its name). However, the ribosomes bound to the
RER at any one time are not a stable part of this organelle's structure as ribosomes are constantly
being bound and released from the membrane. A ribosome only binds to the ER once it begins to
synthesize a protein destined for the secretory pathway. A signal sequence of 5-15 hydrophobic
amino acids preceded by a positively charged amino acid allows the recognition particle to bind to
the ribosome, causing the ribosome to bind to the RER and pass the new protein through the ER
membrane. The pre-piece is then cleaved off within the lumen of the ER and the ribosome is
released back into the cytosol.

The membrane of the RER is continuous with the outer layer of the nuclear envelope. Although
there is no continuous membrane between the RER and the Golgi apparatus, membrane-bound
vesicles shuttle proteins between these two compartments. Vesicles are surrounded by coating
proteins called COPI and COPII. COPII targets vesicles to the Golgi and COPI marks them to be
brought back to the RER. The RER works in concert with the Golgi complex to target new proteins
to their proper destinations. A second method of transport out of the ER’s areas is called membrane
contact sites, where the membranes of the ER and other organelles are held closely together,
allowing the transfer of lipids and other small molecules.

Smooth endoplasmic reticulum-

The smooth endoplasmic reticulum (SER) has functions in several metabolic processes, including
synthesis of lipids and steroids, metabolism of carbohydrates, regulation of calcium concentration,
drug detoxification, attachment of receptors on cell membrane proteins, and steroid metabolism. It
is connected to the nuclear envelope. Smooth endoplasmic reticulum is found in a variety of cell
types (both animal and plant) and it serves different functions in each. The Smooth ER also contains
the enzyme glucose-6-phosphatase which converts glucose-6-phosphate to glucose, a step in
gluconeogenesis. The SER consists of tubules and vesicles that branch forming a network. In some
cells there are dilated areas like the sacs of RER. The network of SER allows increased surface area
for the action or storage of key enzymes and the products of these enzymes.

Transport of proteins
Secretory proteins, mostly glycoproteins, are moved across the endoplasmic reticulum membrane.
Proteins that are transported by the endoplasmic reticulum and from there throughout the cell are
marked with an address tag called a signal sequence. The endoplasmic reticulum is also part of a
protein sorting pathway. The majority of endoplasmic reticulum resident proteins are retained in
the endoplasmic reticulum through a retention motif. This motif is composed of four amino acids
at the end of the protein sequence. The most common retention sequence is KDEL (lys-asp-glu-
leu). However, variation on KDEL does occur and other sequences can also give rise to
endoplasmic reticulum retention. It is not known if such variation can lead to sub-endoplasmic
reticulum localizations.

Other functions
• Insertion of proteins into the endoplasmic reticulum membrane: Integral membrane
proteins are inserted into the endoplasmic reticulum membrane as they are being
synthesized (co-translational translocation). Insertion into the endoplasmic reticulum
membrane requires the correct topogenic signal sequences in the protein.
• Glycosylation: Glycosylation involves the attachment of oligosaccharides.
• Disulfide bond formation and rearrangement: Disulfide bonds stabilize the tertiary
and quaternary structure of many proteins.

• Drug Metabolism: The smooth ER is the site at which some drugs are modified by
microsomal enzymes which include the cytochrome P450 enzymes.
 Lysosome
Lysosomes are cellular organelles which contain acid hydrolase enzymes to break up waste
materials and cellular debris. Lysosomes digest excess or worn-out organelles, food particles, and
engulfed viruses or bacteria. The membrane around a lysosome allows the digestive enzymes to
work at the 4.5 pH they require. Lysosomes fuse with vacuoles and dispense their enzymes into
the vacuoles, digesting their contents. They are frequently nicknamed "suicide-bags" or "suicide-
sacs" by cell biologists due to their role in autolysis. Lysosomes were discovered by the Belgian
cytologist Christian de Duve in 1949.

At pH 4.8, the interior of the lysosomes is acidic compared to the slightly alkaline cytosol (pH
7.2). The lysosome maintains this pH differential by pumping protons (H+ ions) from the cytosol
across the membrane via proton pumps and chloride ion channels. The lysosomal membrane
protects the cytosol, and therefore the rest of the cell, from the degradative enzymes within the
lysosome. The cell is additionally protected from any lysosomal acid hydrolases that leak into the
cytosol as these enzymes are pH-sensitive and function less well in the alkaline environment of
the cytosol.

Enzymes
Some important enzymes found within lysosomes include:
• Lipase, which digests lipids
• Amylase, which digests amylose, starch, and maltodextrins
• Proteases, which digest proteins
• Nucleases, which digest nucleic acids
• Phosphoric acid monoesters.

Lysosomal enzymes are synthesized in the cytosol and the endoplasmic reticulum, where they
receive a mannose-6-phosphate tag that targets them for the lysosome. Aberrant lysosomal
targeting causes inclusion-cell disease, whereby enzymes do not properly reach the lysosome,
resulting in the accumulation of waste within these organelles.

Functions
Lysosomes are the cell's waste disposal system. They are used for the digestion of macromolecules
from phagocytosis (ingestion of other dying cells or larger extracellular material, like foreign
invading microbes), endocytosis, and autophagy. Autophagy may also lead to autophagic cell
death, a form of programmed self-destruction, or autolysis, of the cell, which means that the cell
is digesting itself.
Other functions include digesting foreign bacteria that invade a cell and helping repair damage to
the plasma membrane by serving as a membrane patch, sealing the wound. In the past, lysosomes
were thought to kill cells that were no longer wanted, such as those in the tails of tadpoles or in
the web from the fingers of a 3- to 6-month-old fetus. While lysosomes digest some materials in
this process, it is accomplished through programmed cell death, called apoptosis.
 Golgi complex
Camillo Golgi in 1898 discovered the Golgi apparatus in the nerve cells of barn owls and cats by
metallic impregnation method. After it's discoverer's name, the Golgi apparatus has been variously
named as Golgisome, Golgi material, Golgi membranes, Golgi body, etc.

Structure of Golgi Bodies

Golgi bodies vary in size and form in different types of cells, but they have similar organization in
all kinds of cells. For example, it is well-developed in secretory and nerve cells but is rather small
in muscle cells. Golgi bodies are compiled as a central stack (pile) of flattened sacs or cisternae
and many peripheral tubules and vesicles.

1. Cisternae- The cisternae vary in number from 3 to 7 in most animal cells and from 10 to
24 in plant cells. They are usually equally spaced in piles so that they are nearly parallel to
one another, having 200-300Å wide inter-cisternal spaces containing a layer of parallel
fibres called inter-cisternal elements. These support the cisternae and maintain regular
spacing between them. The cisternae may be flat but are often curved, having a distinct
polarity with a convex face towards the cell membrane and a concave face towards the
nucleus. They are free of ribosomes and have swollen ends. They look like the smooth
endoplasmic reticulum and are continuous with it at certain places. This suggests that the
Golgi apparatus is derived from the smooth endoplasmic reticulum. A cisterna is about 0.5-
1 µm in diameter and its cavity is about 100Å wide. It is fenestrated at the margin as here
it passes into tubules. All the cisternae have a continuous lumen filled with a fluid.
2. Tubules- Short tubules arise from the periphery of the cisternae. Some of these enlarge at
their ends to form vesicles.
3. Vesicles- The vesicles lie near the ends and concave surface of the Golgi complex. They
are pinched off from the tubules of the cisternae. They are of three types: transitional,
smooth or secretary and coated vesicles.
The Golgi complex has 3 functional regions: the cis region that lies nearest the ER, the medial
region in the middle, and the Trans region with the trans-Golgi reticulum nearest to the plasma
membrane. These regions have different enzymes which introduce different modifications to
secretaries and membrane proteins passing through them. The principal modification is
glycosylation, i.e., the addition of sugars to proteins, forming glycoproteins. Glycosylation starts
in the ER and is completed in the Golgi complex. Modification of proteins in the Golgi apparatus
also involves the addition of lipids, forming lipoproteins (liposylation), and even the addition of
other groups
Functions of Golgi Bodies:-
Golgi apparatus is metabolically very active. Many functions have been assigned to it:

1. Formation of secretary vesicles- The Golgi complex processes and packages proteins and
lipids coming from the ER for transport to other parts of the cell or out of the cell.
Packaging involves wrapping the materials in a membrane, forming secretory vesicles. The
materials so packed include zymogen in pancreatic cells, mucus in goblet cells, lactoprotein
in mammary gland cells, pigment granules in pigment cells, collagen in connective tissue
cells, hormones in endocrine cells, etc.
2. Synthesis of carbohydrates- The Golgi apparatus synthesizes certain muco-
polysaccharides from simple sugars
3. Formation of Glycoproteins- the Golgi apparatus links the sugars with proteins coming
from rough ER to form glycoproteins.
4. Formation of Lipoproteins- Lipids and proteins coming from the ER are complexed into
lipoproteins in the Golgi apparatus.
5. Addition to Cell Membrane- the Golgi apparatus provides membrane material for the
plasma membrane when the later must enlarge for the formation of pinocytotic and
phagocytotic vesicles and the formation of cleavage furrow during the division of animal
cells. As the secretary vesicles discharge their contents by exocytosis, their membranes are
incorporated into the cell membrane. This enlarges the cell membrane. Since endocytosis
removes segments of the cell membrane, the latter's enlargement by exocytosis is
temporary, rather compensatory. The transfer of membrane from the ER via transition
 vesicles, Golgi complex and secretory vesicles to the plasma membrane is called membrane
flow.
6. Membrane Transformation- The Golgi apparatus changes one type of membrane into
another type. Membranes are gradually modified from the ER type to one with
characteristics of the plasma membrane as they shift through the Golgi complex.
7. Formation of cell wall- In some algae, cellulose plates for the cell wall are synthesized in
the Golgi complex. In higher plants, the Golgi complex (a) synthesizes pectin and some
carbohydrates necessary for the formation of cell walls and (b) produces some secretions
such as mucilage, gums, etc.
8. Formation of lysosomes- The Golgi complex gives rise to primary lysosomes by budding.
The lysosomes may also arise from ER.
9. Acrosome Formation- The Golgi complex gives rise to the acrosome in a sperm.
10. Formation of Yolk and Cortical Granules- the Golgi complex produces yolk and cortical
granules in the eggs. The formation of yolk is called vitellogenesis.
11. Storage of Secretions- the Golgi complex stores cell secretions such as proteins and lipids.
12. Absorption of Materials- Golgi apparatus absorbs materials from the environment. For
example, cells of the intestinal lining use the Golgi apparatus to absorb lipids from the
intestine.
13. Location of Enzymes- A variety of enzymes is localized in the Golgi complex to help in
the cell's biochemical reactions.

Importance of Golgi Bodies:-

The Golgi apparatus is often referred to as the "traffic police" of the cell because its enzymes sort
out and modify the cell's secretary proteins passing through its lumen and membrane proteins in
its membranes and directs them to their proper destination.
 Cytoskeletons and their Molecular Structures
There are three types of cytoskeleton, each of which plays unique roles within cells. These are
actin filaments, microtubules and intermediate filaments. All have thin, fibrous structures and are
polymers of basic unit proteins. They have unique characteristics and perform various functions
according to their nature. The cytoskeleton has both structural roles and functional roles. The
former refers to the roles played by filaments in cells to maintain the cell shape and the
arrangement of organelles. The latter refers to the functional roles played through the interaction
with other proteins, such as muscle contraction, cell locomotion, cell division and intracellular
transport.

Actin Filaments
The basic unit of actin filaments is a protein called G-actin, whose structure is very similar in many
organisms including amoeba, plants and humans. G-actin polymerizes to form actin filaments with
a diameter of around 7 nm. Since the G-actin molecule has a plus end and minus end, the
polymerized filament also has a plus end and minus end.

Actin filaments are found in all types of cells and are particularly abundant in the contractile
apparatus of muscle cells. The main constituents of such apparatus are myosin and actin filaments.
Additionally, in normal animal cells other than muscle cells, actin filaments are abundant
immediately below the plasma membrane and in cell processes. The actin filaments located below
the plasma membrane stabilize it and tether membrane proteins by forming a network structure.
The actin filaments in cell processes are involved in the formation of the pseudopodia (processes)
of moving cells and processes known as microvilli often found in usual cells.
G-actin has a binding site for ATP or ADP, and ATP bound G-actin molecules (ATP-G-actin)
polymerize stably. However, after polymerization, when bound ATP is hydrolyzed into ADP, the
polymer becomes unstable and is easily depolymerized. After de-polymerization, when ADP is
replaced with ATP, G-actin molecules again become able to bind to actin filaments. In this way,
G-actin is recycled. In cells, compared with an in vitro environment, polymerization and de-
polymerization of actin filaments take place faster and more accurately. This is due to the action
of many types of regulatory protein that bind to actin filaments to regulate their polymerization.
These proteins are called actin-binding proteins.
ATP-G-actin binds to the plus end of actin filaments. Hydrolysis of the ATP facilitates the de-
polymerization, removing G-actin molecules from its minus end. If the ADP of the dissociated G-
actin is replaced with ATP, the G-actin is able to polymerize again.

Microtubules
The basic unit of microtubules is dimer of α- and β-tubulin. Microtubules - long, thin fibrous
structures - are polymers of these dimers

A microtubule is a tubular filament of approximately 25 nm in diameter, with each turn of the helix
containing 13 dimers. A microtubule has polarity; one end of the filament with β-tubulin is the
plus end, and the opposite end is the minus end. Microtubules in cells frequently repeat
polymerization and de-polymerization in the similar way as actin filaments. Dimers whose β-
tubulin is bound with GTP are more stably polymerize than those bound with GDP. Polymerization
is more likely to occur at the plus end of microtubules. After polymerization, hydrolysis of GTP
bound to βtubulin into GDP destabilizes the dimer, depolymerizing the tubulins from the minus
end.
The basic unit of microtubules is dimer consisting of α- and β-tubulins. Microtubules have a long
tubular structure, with each turn of the helix containing 13 dimers. They have plus and minus ends,
and polymerization occurs at the plus end.

An organelle that serves as the polymerization origin of microtubules exists in cells. This structure
is called the centrosome, localized near the nucleus. Special protein complexes that serve as the
starting point in the polymerization of microtubules are found in the centrosome. In most cells,
microtubules radiate from the centrosome. Therefore, their growth ends (i.e., those opposite from
the centrosome) are the plus ends. One of the important roles of microtubules is to segregate
chromosomes during cell division. Centrioles are replicated into two during the DNA replication
phase of the cell cycle, and form two centrosomes (spindle poles) prior to the mitotic phase. In the
mitotic phase, microtubules extending from two spindle poles form mitotic spindles that bind to
sister chromatids. The microtubules segregate chromosomes by pulling apart pairs of sister
chromatid to spindle poles.
Intermediate Filaments
The name intermediate comes from the diameter (10 nm) of these filaments. Like actin filaments
and microtubules, intermediate filaments are polymers of elementary unit protein

However, their polymerization mechanism differs. Polymerization does not require nucleotides
such as ATP and GTP. Other differences include a lack of polarity- the plus and minus ends - in
filaments. Intermediate filaments in cells form complex networks with actin filaments and
microtubules. They are abundant in cells to which physical tension is applied (e.g., epidermal cells
and muscle cells) and neurons. Generally, intermediate filaments exist stably (degradation and
reconstruction are infrequent), but when significant changes (such as cell division) occur, their
degradation and reconstruction become very active
The polymerization steps of intermediate filaments are shown here. As the first step, two basic
units (i.e., monomers) associate in the same direction to form a dimer. Two dimers running in the
reverse direction are line up to form a tetramer, with the two strands lightly offset in their opposite
directions. Tetramers are arranged side by side to form a proto-filament. Eight proto-filaments are
bundled to form an intermediate filament with a diameter of approximately 10 nm.

Motor Proteins:
Material transport takes place actively in cells. As an example, proteins synthesized in ribosomes
must be transported to their destinations. Additionally, organelles such as endoplasmic reticulum,
mitochondria and chloroplasts frequently move within cells. Specialized carriers in the cytoplasm
are involved in such protein transport and organelle movement. These carriers are called motor
proteins, and three groups are known: kinesins and dyneins (two groups of proteins that move
along microtubules) and myosins (a group of proteins that move along actin filaments).

 Kinesins
A typical kinesin is a complex of two large proteins (heavy chains) and two small proteins (light
chains). Heavy chains consist of head and tail structures. The head domains play a central role in
movement. Kinesin heads interact with microtubules and move toward the plus end. During
movement, the tail binds and carries cargo (e.g., endoplasmic reticulum and mitochondria). Like
walking on two legs, kinesins proceed by alternately moving their two heads forward. This head
(ATPase) movement is caused by conformational change through ATP hydrolysis.
  Dyneins
Dyneins are also complexes consisting of multiple proteins but have more complicated and larger
molecular structures than those of kinesins (Fig. 6-8A). They consist of a part that is involved in
migration and a part for binding cargo. Like kinesins, they move using structural changes caused
by ATP hydrolysis. Dyneins walk on two legs along microtubules in the same way as kinesins but
move toward the minus end. Dyneins play another important role involving the movement of cilia
and flagella. Cilia are well known for the movement of paramecia, and flagella are the structures
used in the locomotion of some protozoa, bacteria and animal sperm

 Myosins
There are many types of myosins. All have heads that bind and hydrolyze ATP, but their tails vary
among different types. The diversity of their tails reflects the diversity of functions of myosin
molecules. Some myosin types function as motor proteins that move along actin filaments; Type I
and Type V myosins are well-known examples. Their tails differ greatly in structure from those of
Type II myosins located in the contractile apparatus of muscle cells.