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Cytology - Any cell consists of two main compartments:

Cytoplasm and the Nucleus.

- The cytoplasm; composed of matrix (cytosol) in which various organic and non-organic substances are dissolved. - Cytoplasm includes organelles and inclusions. - Organelles are metabolically active structures carrying out specific functions, and are classified into membranous and non-membranous organelles. -Membranous organelles such as; Cell membrane, RER, SER, Golgi, Lysosomes, Endosomes, Mitochondria… -Non-membranous organelles such as, Ribosomes, Centrioles, Microtubules, Glycogen inclusions…

Diagrammatic illustration of a cell and its structure

Cell membrane


Maintain the structural integrity of the cell.


Control movement of substances in and out the cell.


Regulate cell – cell interaction.


Act as interface between the cytoplasm and the external environment.


Cell membrane is not visible by the light microscope, seen only by E/M. It can be recognized via receptors, antigens…



It is 7.5nm thick, and appears as a trilaminar structure of two thin, dense lines, and a light line in between.


The entire structure is called a unit membrane.


The inner cytoplasmic dense line is its inner leaflet, and its outer dense line is the outer leaflet.


- Each leaflet is composed of a single layer of phospholipids and associated proteins.


Each phospholipid molecule is composed of a polar hydrophilic head (at the surface) and two long non-polar hydrophobic fatty acyl tail (toward the center).


The polar head is composed of glycerol, to which other molecules are attached.


The protein components of the cell membrane either span the entire lipid bilayer (integral proteins) or attached to the cytoplasmic aspect of the lipid bilayer (peripheral proteins).


The integral or trans-membrane proteins form channels proteins (ion channels) and carrier proteins that facilitate passage of specific ions and molecules across the cell membrane.

Diagrammatic illustration showing the structure of the membrane unit

Membrane transport protein - The hydrophobic components of the plasma membrane limit or prevent movement of polar molecules across it. - The presence and activity of trans membrane proteins will facilitate the transfer of these hydrophilic molecules across this barrier. - The transmembrane proteins form:

a- Channel proteins

b- Carrier proteins 2

Diagrammatic illustration showing movement of molecules through cell membrane

Function of cell membrane


It maintains and preserves the integrity of the cell.


It permits the movement of substances in and out the cell by:

Passive diffusion of simple substances as water and some ions.

Facilitated diffusion: some substances as glucose and amino acids can pass through it with the help of carrier, but not need energy.

Active transport: some substances can pass through it against diffusion gradient, and required energy.

Selective transport: depends on the presence of receptors on the surface of cell membrane to select and determine the substances to enter the cell.








Regulate the cell to cell interaction by special type of cell junctions.

Endocytosis The process by which a cell ingests macromolecule, particulate matter, and other substances from the extra-cellular space is referred as: ENDOCYTOSIS. 

Then, endocytosed material is engulfed in a vesicle.

If the vesicle is large (>250 nm in diameter): the method is called phagocytosis (cell eating), and a vesicle is called a phagosome.

If the vesicle is small (<150 nm in diameter): the method is called pinocytosis (cell drinking), and a vesicle is called a pinocytotic vesicle. 3

Phagocytosis; the process of engulfing large particles, or even cells by phagocytic cells such as monocytes, neutrophils, macrophages.

Membrane trafficking; the cycle of membrane shuffling during exocytosis and endocytosis (membrane recycling).

Diagrammatic illustration showing pinocytosis, endocytosis and exocytosis

Receptors mediated endocytosis


Many cells specialize in pinocytosis of specific macro- or micro-molecules. The most efficient form of capturing these substances depends on the presence of receptors proteins (cargo protein) in the cell membrane.


Cargo proteins are trans-membrane proteins associated with a particular macromolecules (ligand) extracellulary, and with a clathrin coat intracellular.

Mitochondria 

They are flexible, rod-shape organelles; with diameter of 0.5 girth and ~7.0μ length.

Their number are variable in human cells; e.g. they are abundant in hepatocytes (~2000) and muscles.

Mitochondria are self replicating and possess their own DNA, and perform oxidative phosphorylation and lipid synthesis.


Each mitochondrion possesses an smooth outer membrane and folded inner membrane (Cristae) with a narrow space (10 – 20nm) between them is called intermembrane space.

-The space enclosing cristae is called inter-crystals space or matrix space.

Cristae increase the surface area of the inner membrane for ATP synthase and the respiratory chain; and also their number are related directly to the energy requirement of the cell.

The outer mitochondrial membrane possesses a large number of porins (Multipass trans-membrane proteins).

Porins form large aqueous channels through which water soluble molecules can pass.

The outer membrane is relatively permeable to small molecules, so the contents of the inter-membrane space resemble the cytosol.

Other proteins located on the outer membrane are responsible for the formation of mitochondrial lipids.

- The inner mitochondrial membrane is richly endowed with phospholipids that makes it permeable to ions, electrons and protons.

In certain regions, the outer and the inner membranes contact each other; the contact site (composed of carrier protein) acts as channels for proteins and small molecules to enter or leave the matrix space.


The inner and outer membranes possess receptor molecules that recognize the transported macromolecules and the cytosolic carrier molecules and chaperones responsible for their delivery.

The inner membrane display a large number of protein complexes such as ATP synthase and Respiratory chains, so mitochondria can be regarded as the power house of the cell .










dehydrogenase, Cytochrome b-c1 and Cytochrome oxidase complexes. 

These enzyme complexes form electron transport chains that are responsible for passage of electrons along this chain and act as proton pumps that transport H+ from the matrix into the inter-membrane space that provide energy for ATP-generating action of ATP synthase.

The matrix space contains also mitochondrial ribosomes, mRNA, tRNA, and dense spherical matrix granules.

Moreover, matrix contains the double-stranded circular DNA (cDNA) and enzymes necessary for expression of the mitochondrial genome.

Protein Synthetic and Packaging Machinery of the Cell The protein synthetic machinery of the cell composed of:

Ribosomes, and polyribosomes

Endoplasmic reticulum

Golgi apparatus



They are small (12nm wide and 25nm long), non-membranous particles composed of protein and ribosomal RNA.


Each ribosome is composed of large subunit and small subunit.


They are assembled in the nucleolus and released in the cytoplasm as separate entities.


The small subunit has a site for binding mRNA, a P-site to bind to peptidyl tRNA, and an A-site for binding aminoacyl tRNAs.


The small and large subunits are present in the cytoplasm individually, and do not form ribosomes until protein synthesis begins. 6

Ribosomes; free and attached to rER

Endoplasmic Reticulum (ER)


It is the largest membranous system in the cell.


It is a system of interconnection tubules and vesicles whose lumen is referred as cistern.


ER has 2 types; smooth and rough ER.

- Their Functions are: Manufacture of all membranes of the cell.  Protein synthesis and modification.  Lipid and steroid synthesis.  Detoxification of certain toxic compounds.

Smooth Endoplasmic Reticulum (SER)


SER is a system of anastmosing tubules and flattened membrane-bound vesicles. The lumen of SER is assumed to be continuous with that of RER. They are abundant in cells that active in synthesis of steroids, cholesterol, triglycerides, and also in cells that are functioning in detoxification.


Their surface is not attached to ribosomes, and so, it is called smooth.


Illustration of Rough and Smooth Endoplasmic Reticulum

Rough Endoplasmic Reticulum (RER)


Their membranes possess integral proteins that function in recognizing and binding ribosomes to their surfaces and maintain their flattened shape.


RER participates in the synthesis of all proteins that are packaged and delivered to the plasma membrane.


RER performs post-translational modification of these proteins.


RER also manufactures lipid and integral proteins of the cell membrane.

The cisternae of RER are continuous with the peri-nuclear cisterna (the space between the inner and the outer nuclear membrane).

Golgi complex


Proteins manufactured in the RER go to Goli apparatus for post-translational modification and packaging.


Golgi is composed of one or more series of flattened, slightly curved membranebound cisternae.


Each Golgi stack has three levels of cisternae:- the cis-face, the medial-face, and the trans-face, and then smooth or coated vesicles.


The cis-face is convex in shape and present closes to the RER. The newly formed proteins from RER inter first to the cis-face. The trans-face is concave in shape and is located at the distal part of the Golgi apparatus, where the modified proteins are ready to be packaged and transport. 8

There are another two compartments, one associated with the cis-face and the other with trans-face: 

The endoplasmic reticulum/Golgi intermediate compartment (ERGIC), which is known as tubulo-vesicular complex: located between RER and cis-face Golgi.

The trans-Golgi network (TGN): located at the distal side of Golgi apparatus.

Illustration of Golgi complex



Lysosomes are small rounded or polymorphic in shape, with a diameter of 0.3 – 0.8μ.


Lysosomes have an acidic pH, and contain hydrolytic enzymes (~ 40 different types of acid hydrolases).


Lysosomal membranes contain proton pumps that transport H+ ions into the lysosomes to maintain its luminal pH at 5.0.


Lysosomes help in digesting macromolecules, phagocytosed micro-organisms, cellular debris, cells, and senescent organelles such as mitochondria & RER.


Lysosomes receive their hydrolytic enzymes and membranes from the Trans-Golgi Network that arrive in different clathrin coated vesicles.


The vesicles loss their clathrin coat shortly after formation, and fused with late endosomes.

Substances subjected for degradation within lysosomes pass through 3 ways:

Phagosomes either join lysosomes or late indosomes. The hydrolytic enzymes digest most the contents of phagosomes except lipid which resist complete digestion and changed into residual body. 9


Pinocytotic vesicles.


Autophagosomes: Organelles that no longer required by the cell become surrounded by elements of SER, and then enclosed in vesicles called autophagosomes.



Endosomes are divided into early and late compartments: Early endosomes are situated near the periphery of the cell near the Golgi apparatus. Late endosomes are situated deeper in the cytoplasm.




Peroxisomes (microbodies) are self replicating organelles (can divide or undergo fission) that contain more than 40 oxidative enzymes (urate oxidase; catalase; Damino acid oxidase).


They are small (0.2 – 1.0 μ) spherical or ovoid membranous organelles that present in almost all animal cells and function in catabolism long chain fatty acids (Beta oxidation) forming acyle coenzyme A (CoA) and H2O2.



Proteasomes are small organelles composed of protein complex that are responsible for proteolysis of mal-formed and ubiquitin tagged protein.


The process of cytosolic proteolysis is controlled by the cell, and it requires that the protein be recognized as a potential candidate for degradation.

Cell Inclusions - Thy are non-living components of the cell that do not possess metabolic activity and are not bounded by membranes. - The most common inclusions are:

Stored food: o Glycogen: abundant in liver and muscle cells o Lipid droplets; stored mainly in adipocytes, and present also in other cells.

Pigments: could be endogenous or exogenous. o Exogenous pigments as carotene, carbon, and dust. o Endogenous pigments such as; Hemoglobin, Melanin, lipofuscin or lipochrom.

Crystals: are not commonly seen. Present in Sertoli cells as (Crystals of CharcotBottcher) and in interstitial cells as (Crystals of Reinke). -

Cytoskeleton -They are meshwork of protein filaments responsible for maintenance of cellular morphology, and participate in cellular motion, - The cytoskeleton has three major components;

1- Thin filaments

2- Intermediate filaments

3- Microtubules 11

1- Thin filaments (Actin)


The actin filaments are composed of 2 chains of G-actin (globular actin) subunits coiled around each other to form F-actin (filamentous proteins).


There are 3 types of actin filaments: α-actin of muscle cells reacting with myocin. β-actin in non-muscle cells. Ƴ-actin in non-muscle cells.

- In non-muscle cells actin filaments form 3 types of bundles of variable length and function: 

Contractile bundles

Gel-like networks

Parallel bundles

2- Intermediate filaments 

The intermediate filaments and their associated proteins perform the following:

Provide structure support of the cell

Establish a 3-dimensional structural framework for the cell.

Anchor the nucleus in place- Provide connection between the cell membrane and the cytoskeleton.

Maintenance of the nuclear envelop and its subsequent changes that takes place in mitosis

3- Microtubules


Microtubules are long, strait, rigid, hollow-like cylindrical structures act as intracellular pathways.


The centrosome is considered to be the micro-tubule-organizing center (MTOC) of the cell from which most of the cell's microtubules emanate.


Their main functions of microtubules are:  Provide rigidity and maintain cell shape  Regulate intracellular movement of vesicles and organelles.  Established intracellular compartments  Provide the capability of ciliary motion - Microtubule-associated proteins: Motor proteins that assist in translocation of organelles and vesicles inside the cell, such as Dynein and Kinesin. 12

Centriols and the Micro-tubule organizing Center (MTOC)

Centromere and Centrioles -Centromere is present in all dividing cells near the nucleus, and is composed of 2 perpendicular centriols. The centriols duplicated during cell division. - Centriol is cylindrical in shape. - Each centriol composed of nine sets of triplet microtubules.

Arrangement of Microtubules in Centriol E/M picture showing the centriols


Cilia and Flagella







processes extend from the free surface of ciliated cells.


Flagellated cells (sperm) has only one flagellum.


Both cilium and flagellum composed of the same core organization (axoneme).


The axoneme is formed of nine pairs (doublets)







At the base of cilia or flagella there is a basal body, which is similar to centriol in structure.

Diagrammatic illustration of the cilia and the basal body

Cell activities 

Cell division.



Cell death: o Apoptosis (programmed cell death)

Apoptosis is an expression of

programmed cell death, where the cell takes an active, controlling part in its demise. o Necrosis: The alternative form of cell death (necrosis) is where the cell is overwhelmed by outside influences and comes apart in a disorganized & inflammatory way.




All human cells contain nucleus except the mature red blood corpuscles. Normally each cell contains a single nucleus, but sometimes contains two as liver cells or more (multinucleated) as skeletal muscle cells, and osteoclasts.


Nucleus could be spherical, oval, flattened, or lobulated. Also, nucleus could be central, basal or peripheral.

Structure of the nucleus - Nucleus composed of: - Nuclear membrane (Envelop)

- Chromatin

- Nucleolus

- Nucleoplasm

Nucleus structure: showing the nuclear envelop, nuclear pore complex, and chromatin

1- Nuclear Envelop - Nuclear envelop is composed of two parallel unit membranes; the outer and the inner membranes separated from each other by a 10-30 nm space called perinuclear cisterna. - The two membranes fuse with each other at certain regions known as nuclear pores that permit communication between cytoplasm and nucleus. - The nuclear pores are surrounded by a non- membranous structure called pore complex.


Diagrammatic illustration of the nuclear pore complex, showing the nucleoplasmic and cytoplasmic ring subunits (Basket)

Diagrammatic illustration of the nuclear pore complex

2- Chromatin - Chromatin is a complex basophilic structure formed of DNA associated with histone and non-histone proteins. - Depending on its transcriptional activity chromatin can be divided into:- Euchromatin; uncoiled or not condensed, stained lightly basophilic, gene rich, and early transcript. - Heterochromatin; highly coiled or condensed, stained deeply basophilic, gene poor, and late transcript. 16

 Nucleosomes. Isolated chromatin appears as thin strands studded with bead-like particles at regular intervals. Each strand is a double-helical molecule of DNA, and the particles are the repeating structural subunits of chromatin termed nucleosomes. Each nucleosome is composed of 166 base pairs of the DNA strand coiled around a core of 8 histones (2 copies each of H2A, H2B, H3, and H4). The portion of the strand between 2 nucleosomes contains an additional 48 base pairs and is called the linker region. Another histone (usually H1) is bound to the outside of the nucleosome and to the linker. The beaded strand coils into a superhelix with 6 nucleosomes per turn (selenoid) to form the condensed form of chromatin, ie, heterochromatin.   Chromatin pattern. a rim of heterochromatin is often found on the inner surface of the nuclear envelope in association with the fibrous lamina. This envelope associated heterochromatin allows resolution of the nuclear boundary with the light micro- scope.   Chromosomes, the most highly condensed form of chromatin, are visible during mitosis. To form chromosomes, selenoids fold further and wind on a central non-histone protein scaffold. The human cells contain 46 chromosomes, 44 (the somatic chromosomes), the other pair (sex chromosomes) consists of dissimilar chromosomes (XY) in males and similar ones (XX) in females. In females, only one X chromosome is active; the inactive X chromosome is often visible as a clump of heterochromatin termed sex chromatin, or the Barr body. In most cells, the Barr body is attached to the inner surface of the nuclear envelope. In a neutrophilic leukocyte, it may appear as a drumstick-shaped appendage of the lobulated nucleus.


ď&#x201A;ˇ Karyotyping, A cell's karyotype is a picture of its chromesomes arranged by chromosome type. Preparing such a picture is called karyotyping. Cells in culture are stimulated to enter mitosis with phytohemagglutinin (a mitogen). The dividing cells are treated with colchicine to arrest them in metaphase, when the chromosomes are highly coiled and visible. Lysis of the cells with a hypotonic solution causes the chromosomes to spread out on the slide with little or no overlapping. The chromosome spread is photographed, and pictures of the chromosomes are cut out, paired, and assembled into a specific sequence. Karyotyping allows cataloging of chromosomes for detection of structural abnormalities and deleted or excess chromosomes.

3- Nucleolus


Nucleolus is a non-membranous deeply stained structure located in the nucleus.


It present during interphase and disappear during cell division.


It contains ribosomal RNA, some proteins and small amount of DNA.


Structure of the nucleolus: formed of four areas


 Pale staining Fibrillar center containing inactive DNA, and nucleolar organizing regions (tips of acrocentric chromosomes).  Pars Fibrosa containing nucleoluar RNAs  Pars Granulosa in which mature ribosomal subunits are assembled  Nucleolar Matrix: a network of fibers active in nuclear organization.

EM picture of the nucleolus showing the Fibrillar material (F) and the granular material (G)

4- Nucleoplasm: composed of the following


Interchromatin Granules: They are located in clusters scattered throughout the nucleus among the chromatin material.


Perichromatin Granules: They are located at the margin of the heterochromatin, and are composed of: - Heterogeneous nuclear ribo-nucleo-proteins - Small nuclear ribo-protein particles


Nuclear Matrix: Contain DNA, RNA, Proteins, and nuclear phosphate.


2, 3 cytology  
2, 3 cytology