Cell: Structure and Functions

Cell Structure and Functions

1. The Cell Theory

Almost all the physical, physiological, metabolic and other activities of life (like glycolysis, TCA, photosynthesis, replication, transcription, translation, respiration, etc.) of a (cellular) living organisms (excluding viruses) occur inside the cells irrespective of the unicellularity or multicellularity of the organism. The cell structure and functions greatly varies among the three domains of life, but still they share a lot of similarities. For example, all the cells have a plasma membrane, have membranous scaffold for energy transduction processes, share glycolysis and many other metabolic pathways, and many more. 

Based on the presence or absence of a plasma or cell membrane, all the life forms can principally be classified into CELLULAR and ACELLULAR. The cellular life forms defined in the Three Domains of Life (Archea, Bacteria and Eukarya) are cellular because they’re constituted of one or more cells. The acellular or non-cellular life forms include viruses and viroids. These life forms lack a native cellular architecture on their own. 

A cell is the structural and functional unit of life. Since all the cellular life forms are constituted of one or more cells, the cells also act as the building block of life forms or organisms. All cells have a cell membrane or plasma membrane- the phospholipid bilayer that defines the intrinsic or integrated boundary of a cell. The genetic material, organelles and other sub-cellular components are housed inside this boundary defined by the plasma membrane. The term “cell” was coined by Robert Hooke in his 1665 book Micrographia for the honeycomb cavities or box-like structure in the cork tissue observed under microscope.    

The development of the Cell Theory a credited to Matthias Schleiden (a German physiologist) and Theodor Jakob Schwann (a German botanist) and Rudolph Virchow (a German physician). The first concept of the cell theory was proposed by Schwann in his book “Microscopic investigations on the similarity of structure and growth of animals and plants” in 1939. He had proposed three conclusions about the cell, first of the two are correct whereas the third claim “Cells form by free-cell formation, similar to the formation of crystals” was disproved and discarded by scientific studies in successive years. The third tenet is a contribution of Rudolph Virchow, who, in 1857, proposed “all cells arise from pre-existing cells”. In its final form, the classical cell theory states-    

         1. The cell is the unit of structure, physiology, and organization in living things.

2. The cell retains a dual existence as a distinct entity and a building block in the construction of organisms.

3. All cells arise only from pre-existing cells through cell division.

The first tenet “The cell is the unit of structure, physiology, and organization in living things” suggests that cell is the structural and functional unit of life. For example, if a multicellular animal need to exhibit motion, the activity occurs at cellular level (contraction and relaxation of myocytes), the orchestrated contraction and relaxation of all the participating myocytes is observed as an event of motion in the organism. The second tenet suggests that all organisms are made of one or more cells. In unicellular organisms like bacteria, a cell represents an organism. However, in case of multicellular organisms like animals and plants, a cell acts as the building block of that organism simultaneously with retaining its individuality (because it can reproduce and carry out its own metabolic activities like an individual cell).

2. Ultrastructure of the Eukaryotic cells

2.1. Plasma Membrane

S Jonathan Singer and Garth Nicolson proposed the ‘Fluid- Mosaic Model’ of plasma membrane in 1972. Plasma membrane defines the boundary of a cell and forms a semipermeable barrier between its internal environment (cytoplasm) and the extracellular space. It consists of two sheets of phospholipid molecules. The hydrophobic tail of the phospholipid molecules in one sheet faces the hydrophobic tails of the phospholipid molecules in another sheet forming a hydrophobic core. The polar (hydrophilic) head of the phospholipid molecules in each layer (sheet/ leaflet) faces opposite to the hydrophobic core. The polar heads in inner sheet of phospholipids face the cytoplasm whereas those of outer sheet faces the extracellular environment. The phospholipid molecules moves laterally, rotate, shake their hydrophobic tails, or bobble in each leaflet independently or even flip from one layer to another and are responsible for the fluidity of the plasma membrane. Unlike other modes of displacement in phospholipids, flipping is least frequent and mediated by flippase enzyme. The sterols (cholesterol) in plasma membrane randomly move through the hydrophobic core and flip between the bilayers and provide additional fluidity to the membrane. The presence of proteins on the outer surface of the leaflet gives a ‘mosaic’ appearance of the plasma membrane. fluid mosaic model of plasma membrane 

Numerous proteins are associated with plasma membrane and aid in various characteristic features like selective permeability, cell- cell adhesion, cell-cell interactions, receptors, antigens, etc. to the membrane. The proteins that can be separated from the membrane by treatment of mild salt solutions or treating with dilute acid or washing with water without disrupting the lipid bilayer are called extrinsic proteins. These proteins are associated with the membrane or another intrinsic protein with weak forces like ionic interaction, ion (Ca2+) bridges, hydrogen bonds or hydrophobic interactions, etc. Since the intrinsic proteins are generally present at the outer surface (periphery) of both leaflets of the plasma membrane, these are also called peripheral proteins. The proteins that cannot be removed from the membrane without disrupting the lipid bilayer are called intrinsic proteins. These proteins are usually embedded through the hydrophobic core of the lipid bilayer and are also called integral proteins. The intrinsic proteins which span the hydrophobic core and exposed to the outer periphery of both leaflets are called transmembrane proteins. All intrinsic proteins span the hydrophobic core but need not necessarily exposed to the outer periphery of both leaflets. Thus all transmembrane proteins are intrinsic proteins but not all intrinsic proteins are transmembrane proteins.

Plasma membrane is asymmetric because it exhibits difference in the relative abundance of phospholipids, proteins, etc. in the two leaflets of the bilayer. Outer (facing extracellular matrix) leaflet is rich in positively charged sphingomyelins and phosphatidylcholine. Cytoplasmic layer is rich in negatively charged phospholipids like phosphatidylserine, phosphatidylinositol, etc. The proteins are differentially integrated on the either face of the membrane (cytoplasmic face and external cell surface) and have numerous molecules specific-receptors. These proteins help the cell monitor the internal and external environments (for example, stimuli for energy molecules, light, pH, etc.) and regulate homeostasis, which is crucial for sustaining life. The asymmetric nature of membrane enables the cell to transfer solutes in a particular direction (for example, Na-K pump always pumps Na+ ion outside and imports K+ inside), establish proton gradient or electric potential difference across the membrane. This property is thus crucial for the unidirectional transport and to generate or receive stimuli.

The plasma membrane may increase or decrease its size through the formation of vesicles. For example, the cell size increase during interphase. The dynamic structure of membrane enables the cell to divide and reproduce forming smaller daughter cells without losing cellular integrity (the cell architecture). Endocytosis and exocytosis taking place in form of vesicles, requires integration of a new lipid bilayer sheet and loss of a bit portion of the membrane, respectively simultaneously with maintaining cellular integrity.

The fluidity of membrane is also crucial to sustain life. The organisms living in extreme conditions or facing a great fluctuation in the environmental condition always maintain the membrane in its structural and functional state. For example, in winters’ sub-freezing conditions (say, -20.00 C), the membrane of a plant cell also retains the fluid-nature instead of getting frozen or crystallized. Relatively larger abundance of cis-fatty acids, unsaturated fatty acid in the phospholipids and steroids makes the membrane more fluid because both the cis-form and unsaturation makes the chain irregular-shaped and hinders the close packing of hydrophobic core. So, such membrane retains its fluidity even at very low temperatures. The membrane of the thermophiles also maintains its optimum fluidity at elevated temperature by having relative abundance of saturated, long-chain fatty acids in trans-configuration. Such feature allows the hydrophobic tails interact more efficiently because of having a regular cylindrical shape. Thus, the dynamic nature of the lipid bilayer makes it perfect to maintain its optimum activity over a wide range of temperature and other environmental conditions.

Chemical Composition of the Plasma Membrane:

The chemical composition of cell membrane with respect to its functions are as follow-

Phospholipids: Phospholipids are the major constituent of cell membranes. They form the semipermeable lipid bilayer. Moreover, they determine the dynamic cell shape and size, involved in exocytosis and endocytosis processes as well as compartmentalization of various cellular organelles.

Protein: Proteins are the second most abundant constituent of the membrane giving the ‘mosaic’ appearance in Singer-Nicolson “Fluid- mosaic model”. Several integral and peripheral proteins are anchored to the plasma membrane. The transmembrane proteins may serve as transport proteins, channels, antiporter, symporter, form various types of cell-cell junctions and may transduce extracellular signals (stimuli) into the cell and vice-versa by acting as receptors. The peripheral proteins mediate signal-transduction between extracellular and intracellular environment as well as help in both physical and chemical interactions among cells. They also constitute the energy transduction machinery in mitochondria, chloroplast and bacteria. 

Carbohydrates: The proteins to which one or more carbohydrate moieties are attached are called glycoproteins. The carbohydrate moieties constitute a very less fraction of the mass of the glycoproteins. These are generally present at the cell surfaces and may act as antigens (Antigen AB on mammalian RBCs, O-antigen on gram-negative bacteria, etc.) or mark the cell as target for viral adsorption or binding of other cells/ cellular components, etc. The proteins with carbohydrate moieties (glycosylated proteins) constituting their major fraction of total mass are called proteoglycans. Proteoglycans usually have sulfate or uronic acid groups and provide structural support to the cell. Several components of the extracellular matrix of connective tissues like chondroitin sulfate, mucoproteins, etc. are proteoglycans.

Steroids: Presence of steroids in lipid bilayers increases the ‘fluidity’ of membrane and prevents it from freezing at low temperatures.  

Functions of Plasma Membrane

Provides dynamic cell shape: Being fluidic in nature, the plasma membrane provides a dynamic cell shape to the cell. It can also form and release vesicles and coalesce vesicles, increase or decrease the cell size as signaled, etc.

Shelters various proteins: Several integral and peripheral proteins are anchored to the plasma membrane. The proteins to which one or more carbohydrate moieties are attached are called glycoproteins. The carbohydrate moieties constitute a very less fraction of the mass of the glycoproteins. These are generally present at the cell surfaces and may act as antigens (Antigen AB on mammalian RBCs, O-antigen on gram-negative bacteria, etc.) or mark the cell as target for viral adsorption or binding of other cells/ cellular components, etc. The proteins with carbohydrate moieties (glycosylated proteins) constituting their major fraction of total mass are called proteoglycans. Proteoglycans usually have sulfate or uronic acid groups and provide structural support to the cell. Several components of the extracellular matrix of connective tissues like chondroitin sulfate, mucoproteins, etc. are proteoglycans. Different types of cell express different membrane proteins depending on physiological conditions, and abiotic and biotic factors. 

Semipermeable Barrier: The plasma membrane facilitates the movement of only selected molecules across it, the characteristic being known as semipermeable because it is permeable to some molecules while impermeable to others. Only small, nonpolar, uncharged molecules like O2, CO2, and N2 can freely diffuse across the plasma membrane. It is also freely permeable to mmall lipid molecules like sterols and small chain fatty acids. Other molecules like H2O, Urea (small, uncharged, polar), Glucose (Large, polar, uncharged), and ions (H+, Na+, K+, Ca2+, etc.) can diffuse across the plasma membrane but NOT freely. The rate of diffusion of the molecules across the plasma membrane depends on their size, polarity, charge, concentration, etc. Generally large (/ small), polar, charge molecules/ ions do not diffuse across the plasma membrane at significant rates and are transported across the plasma membrane through transmembrane proteins. The example includes aquaporin (transports H2O), Na+-K+ pump (transport 3 Na+ outside and 2 K+ ions inside the cell) and proton pumps (transports H+ ions) etc.

Interactions with Other Cells or Extracellular Molecules: The glycoproteins in the plasma membrane of a cell mediate its interaction with neighbor cells like those in tissues.The transmembrane proteins may interact with the extracellular molecules (ex- hormones, metabolites, etc.) and transmit the signal to the intracellular environment/ cytoplasm and the cell responds accordingly. The glycoprotein antigens of a cell help it interact with other cells, extracellular components, viruses, bacteria, etc. Proteoglycans are essential for the arrangement of cells into connective tissues in higher animals. 

Cellular Compartmentalization: The cell’s boundary is defined by plasma membrane. Various organelles like nucleus, endoplasmic reticulum, Golgi bodies, mitochondria, chloroplast, etc.are metabolic compartments and their boundaries are also defined by plasma membrane. Each organelle performs specified functions and their functions in the cell are coordinated. While the cell as well as its membrane-bound organelles are surrounded by the plasma membrane, the term “cell membrane” is restricted to the “plasma membrane that surrounds the cell”.  

Energy Transduction/Scaffold of metabolic pathways: Several proteins associated with plasma membrane help the cell transduce energy. Plasma membrane may form scaffolds (a framework or platform) to mediate various metabolic processes. For example, the electron transport chain in mitochondria and chloroplasts are embedded in the respective membranes where they are meant to carry out cellular respiration and photosynthesis, respectively. In prokaryotes where membrane-bound organelles are absent, similar energy transduction process machinery is directly embedded in their cell membrane. The proteins associated with the membrane of chloroplast help the cell harvest solar/ light energy in form of chemical energy (generally carbohydrates and/ or ATPs). Mitochondria convert the chemical energy into ATPs, another form of chemical energy readily usable by the cells.

The Endomembrane System: During evolution of the eukaryotic cell, the plasma membrane invaginated into the cytoplasm, surrounded the cellular genetic material inside it and formed the nucleus.The nucleus is surrounded by two plasma membranes. The outer membrane is relatively more permeable than the inner one and is continuous with endoplasmic reticulum (ER). The vesicles released from ER further coalesce together to form Golgi bodies (GB). Because of sharing a common origin and being integrated to each other, nucleus, ER and GB, lysosomes and endosomes are collectively called the endomembrane system.  

2.2. Nucleus

Nucleus is a double membrane (two plasma membranes) bound organelle housing the genetic material of a eukaryotic cell.  The nuclear envelop consists of two concentric plasma membranes with the intermembrane space of 10-50 nm. It is studded with hundreds/ thousands of nuclear pores or nuclear pore complexes with regulate the exchange of selected molecules between the nucleoplasm and cytoplasm. The nuclear pore complex (NPC) is doughnut shaped and are constituted of nucleoporins family of proteins. The nucleoporins are present in multiple of 8 (i.e. 8, 16, 32, etc.) in a NPC, and thus the NPCs show octagonal symmetry. In animal cells just beneath the inner nuclear membrane lies the nuclear lamina. The nuclear lamina is bound to the integral proteins of the inner nuclear membrane and serve as a site for chromatin attachment simultaneously with proving a structural support to the nuclear envelop. Lamin proteins, the constituent of nuclear lamina, play important roles in appearance and disappearance of the nuclear membrane during cell division.   

Eukaryotic Nucleus

Nuclear Bodies: The membrane-less morphologically and metabolically distinct portions within the eukaryotic nuclei (animals, plants, fungi)are called nuclear bodies. Example: Nucleoli, Cajal bodies, Gemini of coiled bodies (GEMs),

Nucleoli: The regions of nucleus consisting of rDNA clusters are called nucleoli. The nucleus may contain one or more nucleoli. In an interphase nucleus the portion of nucleolus consisting of nascent ribosomal subunits at different stages of assembly is called granular center because itappears granular under electron microscope. The granular center has a fibrillar center embedded in it which is majorly consisted of rDNA. The fibrillar center is surrounded by dense fibrillar components that consists of rRNA transcripts and associated proteins.

Cajal bodies/ Coiled Bodies (CB): First describes by Ramon Y Cajal, 1903, as randomly coiled threads (chromatin). CB, 1-10 in number per nucleus, are sites of transcription assembly. CBs are marked by P80-coilin protein and are bound to the nucleoli by coilin proteins. These nuclear bodies are involved in biogenesis, maturation and recycling of small RNAs like nuclear ribonucleoproteins (snRNPs), small nuclear RNPs (snoRNPs) and RNA polymerases. These are also involved in the biogenesis of telomerase and its recruitment to telomere.

Gemini of Coiled Bodies (GEMs): GEMs are morphologically similar to Cajal bodies and may assist CB in biogenesis of snRNPs. These are characterized by the presence of survival of motor neuron (SMN) proteins.

Promyelocytic Leukemia (PML) Bodies/ Nuclear Domain 10 (ND10): PML are morphologically and functionally distinct nuclear bodies. Generally, 0.5μm in diameter, these nuclear bodies may regulate transcription, carry out DNA repair and have roles in defending the genome against viral infections. The outer layer of PML bodies contain PML proteins but the interior lacks them.

Nuclear Speckles/ Interchromatin granule clusters: These are irregular shaped nuclear bodies involved in storage and recycling of pre-mRNA splicing factors present in the Interchromatin regions of the nucleoplasm of mammalian cells.

DNA, Chromatin and Chromosomes

Deoxyribonucleic acid (DNA) serves as genetic material in all cellular organisms. DNA in eukaryotes is associated with several proteins (ex- histones). Ribonucleic acid (RNA) which may help in condensation and decondensation, stability, gene expressions (transcription, translation), recombination, transposition and other processes in response to cellular and extracellular signals. A DNA associated with protein complexes is called chromatin. The condensed form of chromatin (as observed during mitosis) is called chromosome.

The primary constriction on a chromosome to which sister chromatids are attached during mitosis, most conspicuous at metaphase, is called a centromere. Centromere is also associated with the kinetochore protein complex, one on each sister chromatid, to which microtubules (spindle fibers) bind and assists the segregation of chromosomes during mitosis and meiosis. The smaller arm of chromosome (assuming centromere anywhere along the length of chromosome) is designated ‘p’ and the larger arm is designated ‘q’. A chromosome is said to be metacentric if the centromere is at the middle of the length of the chromosome. In a sub-metacentric chromosome, the centromere is a bit away from the center of the chromosome. The centromere of an acrocentric chromosome is situated near one end of the chromosome. The telocentric chromosome has its centromere located at its end.

The non-coding region of DNA consists of tandem repeats and interspersed sequences. Tandem repeats consists of same DNA sequence repeated thousands or millions times in tandem (one after another) and form discrete blocks on the chromosome. The tandem repeats may constitute more than half of the genome in many eukaryotes. These may be rich in AT or GC sequences and have roles in centromere organization and satellite formation. The discrete regions of chromosome containing the tandem repeats are called satellites. Satellite DNA bands have different base composition and density when compared to the main band DNA. The constriction on chromosome other than centromere are referred as secondary constrictions. The DNA next to secondary constrictions (towards the terminal of chromosome) is also called satellite as it consists of tandem repeats. The interspersed sequences are specific DNA sequences dispersed in the genome but do not form tandem repeats.

2.4. Endoplasmic Reticulum

Endoplasmic reticulum (ER) consists of a network of the lipid bilayer into the cytoplasm as a continuous extension of the outer nuclear membrane. The flattened sac-like membranous structures of the ER are called cisternae. The cisternae are held together to the adjacent cisternae with cytoskeletons. The lumen of cisterna of ER is called luminal or cisternal space. The part of cytoplasm in between adjacent cisternae is called cytosolic space.

The ER with numerous ribosomes on its cytosolic surface is called rough endoplasmic reticulum (RER) because of its such appearance under electron microscope. RER is continuous with outer nuclear membrane and consists of cisternae studded with ribosomes at their cytosolic surface. RER is the site of biosynthesis of proteins as well as their modifications (excision of amino acids from peptide chain, selective cleavage of the peptide chain, N-linked glycosylation, etc.) or other biomolecules (phospholipids, oligosaccharides) which are destined to be secreted outside the cell or to be transported to other organelles. RER are particularly abundant in cells involved in active secretions like hepatocytes, plasma B cells, etc.

The ER without ribosomes on its surface is called smooth endoplasmic reticulum (SER) because of its smooth appearance under electron microscope. The membranes of SER are highly curved and tubular and interconnected to each other forming an extensive mesh work in the cytoplasm. SER is principally involved in the biosynthesis of lipids (steroid hormones) and detoxification of harmful molecules. Oxygenases (a group of oxygen-transferring enzymes, ex- cytochrome p450) present in SER lumen act on the hydrophobic molecules to increase their hydrophilicity and reduce/ minimize their toxicity.  Once converted to a hydrophilic form, the toxic molecules can be excreted outside the body.

2.5. Golgi complex

Golgi complex was discovered by Camillo Golgi in 1898. It consists of curved concentric cisternae stacked together to form a convex face at its end near to ER. This convex face is called cis Golgi or forming face. The cis face nearest to ER, called cis Golgi Network (CGN), consists of interconnected tubules. The vesicles with proteins packed in them fuse with the CGN and are sorted for their trafficking to various destination. The end of GC opposite to the cis face is called trans Golgi. The trans face farthest from the cis end consists of interconnected tubules and vesicles and referred to as trans Golgi Network (TGN). The stack of cisternae in between the cis and trans Golgi is called medial Golgi. The proteins imported to the CGN through vesicles from ER are modified, repacked in the vesicles and finally pinch off from TGN. These vesicle may fuse to the cell membrane if the protein packed in it is meant to be transported to the plasma membrane or outside the cell. Instead, the vesicle may fuse to an organelle if the protein packed in it is destined to be delivered to that specific organelle.

O-linked glycosylation of proteins occurs in GC. The synthesis of complex polysaccharides like hemicellulose and pectin in plants and glycosaminoglycan (GAGs) chains of proteoglycans in animal connective tissues are synthesized in GC.

2.6. Lysosomes

Lysosomes are membrane bound organelles containing several hydrolytic enzymes capable of digesting almost all types of biomolecules in the cell. Since these hydrolytic enzymes (nucleases, proteases, lipases, glycosidase, etc.) have their optimal activity at pH 4.6 (acidic condition) these are also called acidic hydrolases. The highly acidic environment of the organelle is maintained by V-type H+-ATPase (a proton pump) integrated in its membrane. The integral proteins of its membrane are highly glycosylated at the interior face (facing the lysosomal matrix) and prevent the membrane being acted upon by the enzymes housed in it.

Lysosomes are abundantly present in cells involved in active phagocytosis (macrophages, most of unicellular eukaryotes, etc.). The organelle plays important roles in recycling the worn out biomolecules in the cell (ex- enzymes, proteins, phospholipids, etc.) as well as cellular compartments (parts of plasma membrane in form of vesicles) or even other organelles. The organelle is also responsible for lysing the whole cell under strictly regulated pathways induced by stresses (nutrient deficiency, viral infection, etc.) or other signaling pathways. Hence, it’s also called the ‘suicide bag’ of the cell. The deficiency of one or more lysosomal enzymes may lead to impaired recycling of various biomolecules as well as their accumulation (toxic in higher concentrations) in the cell/organs and lead to disease conditions collectively known as lysosomal storage disease. Lysosomal enzymes deficiency disease include Gaucher’s disease (deficient enzyme (de)- Glucocerebrosidase), Tay-Sachs disease (de- Hexosaminidase A), Sandhoff’s disease (de- Hexosaminidase A & B), Fabry’s disease (de- α-Galactosidase A) etc.

2.7. Mitochondria

Mitochondrion, also called ‘the power house of the cell’, is a double membrane bound organelle involved in generating ATPs through aerobic respiration. In multicellular organisms undergoing sexual reproduction, mitochondria are maternally inherited.

The outer membrane is relatively more permeable than the inner one. The space between outer and inner mitochondrial membrane is called intermembrane space. The inner membrane forms inward invaginations called cristae. Formation of cristae increases the active surface area of the inner membrane several times. The content enclosed within the inner mitochondrial membrane is called mitochondrial matrix. The mitochondrial matrix consists of a vast array of enzymes and proteins and many other molecules involved in tricarboxylic acid cycle (TCA), electron transport chain (ETC), Fatty acid metabolisms, etc. Integrated into the inner membrane are complexes of ETC, succinate dehydrogenase, F0-F1 ATP synthase, H+– pumps, uncouplers (move H+ from inter membrane space to matrix), etc. During evolution, aerobic bacteria was engulfed by another cell and both cells coexisted symbiotically. Thus, mitochondrion of the eukaryotic cell originated from prokaryotic cells. It has its own single circular chromosome devoid of histones, 70s type ribosomes and divides by binary fission like other prokaryotes. 

Structure of Mitochondria

2.8. Plastids

Origin, Structure and Interconversion of Plastids: Plastids are three membrane-system organelles of eukaryotic photoautotrophs with their own genome and acting as the site of photosynthesis and/or storage of starch, oils, and other metabolites. A plastid has two concentric plasma membrane (sometimes referred as the envelop) and a third membrane-system enclosed in the double-layered envelop. The third membrane system may be in form of simple discs as in case of storage plastids or developed in form of three dimensional, interconnected discs as in case of the photosynthesizing plastids (chloroplast).  

Plastids have a single circular DNA devoid of histones as their genetic material, have 70s ribosomes and reproduce by simple binary fission- the characteristics that present their origin from prokaryotic cells (cyanobacteria) in the course of their evolution.  

All plastids origin from the precursor or progenitor plastid known as proplastid. Some plastids may also convert into each other depending on the availability of light, growth phase of the plant part and other physiological conditions. For example, the new leaves and stem of many plants are generally non-green (brown, pink, red, etc.) because of the chromoplasts in them. In these photosynthesizing parts, chromoplasts gradually turn into chloroplast with exposure to light during maturation, thus causing their color to change to green. As you might have observed, many fruit and vegetables (like apple, guava, oranges, papaya, tomato, chillies, etc.) appearing green gradually exhibit non-green colors (red, orange, yellow, etc.) because of conversion of chloroplasts (green) into chromoplast (non-green colored) during their ripening.  

Reproduction and Inheritance of Plastids: Both the proplastids of a meristematic cell and a mature plastid in well-differentiated plant cell divide and reproduce by binary fission method. During reproduction in Angiosperm plants, the proplastid is transferred to the successive progeny from the female gametophyte or egg cell; that is, the proplastid is maternally inherited in these plants. The gymnosperm plants generally exhibit paternal (transferred to the progeny from male gametophyte or sperm cells) from sperm inheritance of the plastids. Some plants may exhibit a combination of both the maternal and paternal inheritance simultaneously. However, note that it is the proplastid, but not the plastid itself, being transferred from the parent(s) to the offspring.     

Stromule: A plant cell may have one to several plastids, and the number may change depending on the cell type, stage of development, physiological conditions and other stimuli. A stroma-filled tubular extension of the plastid’s double-membraned envelope, called stromule, makes a tubular connection between two plastids in a cell. It also forms tubular connections between a plastid and other organelles like mitochondria, nucleus, etc. The stroma of the stromule lacks DNA and ribosomes. By forming a continuous tubular connection between a plastid and other plastid(s) and other double-membraned organelles, it principally facilitates the movement of stromal metabolites, proteins, enzymes, etc. among them. It may also help positioning the plastid and interconnected organelles within the cell to optimize photosynthesis and other metabolic activities. The number and length of the stromules in a cell may increase or decrease depending on the physiological needs and stimuli in the cell.

Types of Plastids: Based on the arrangement of the stromal membranous structure and types of pigments, the plastids are classified into chloroplast, chromoplast and leucoplast. As mentioned above, all types of plastids may arise from the proplastid, as well as my interconvert into each other depending on the physiological conditions, light availability, hormones and other stimuli.

Types of Plastids in Plants

Chloroplast is characterized by the arrangement of stromal membrane into thylakoid, and chlorophyll pigment. These arrangements further facilitate the assembly of the photosynthesis apparatus. So, these are the single types of plastids capable of carrying out photosynthesis. During early stage of development, proplastid gives rise to pre-granal plastid, characterized by presence of protochlorophyllide in it. In presence of light, the pre-granal structures in stroma successively develop into thylakoid and grana, and the precursor pigment protochlorophyllide is converted into chlorophyll. Gradually, the chlorophyll molecules associate with specific proteins and pigments to form the photosystems and light harvesting complexes. Once the assembly of the complete photosynthesis machinery, the mature chloroplast acts as the site of photosynthesis.

When a pre-granal plastid doesn’t get sufficient light during its development stage, it’s converted into Etioplast. A mature chloroplast also transforms into Etioplast if the plant is kept is dark for prolonged period. Etioplast lacks the three-dimensional granal and thylakoid architecture. Instead, it is characterized by the presence of prolamellar bodies (PLM). The prolamellar bodies are the single-membrane bound tubular structure suspended as crystalline lattice in the stroma. It is often associated with protochlorophyllide and the light-dependent enzyme protochlorophyllide oxidoreductase. Normal light conditions trigger the conversion of PLM into thylakoid and grana, and formation of chlorophyll pigment. Subsequently, the colorless Etioplast is converted into matured chloroplast under normal light conditions. 

Gerontoplast: As a chloroplast senesces in an aging leaf, the thylakoid system and associated photosynthesis machinery gradually disintegrate for the recycling of the stromal proteins. Protein, which constitute around 75% of a photosynthesizing cell, are recycles to other cells in form of protein exclusion bodies (PEB). There is formation of many large plastoglobuli from the disintegrating granal system. During leaf senescence, around 75% of the chlorophylls and 50% carotenoids degrade. There is also accumulation of some anthocyanins. The overall result is the appearance of brown-yellow color of the aging leaf.       

Chromoplast: Chromoplasts are characterized by the presence of plastoglobuli and carotenoids in the plastoglobule’s core. The plastoglobule is a micelle-like structure fused to the outer leaflet of the thylakoid membrane. The Presence of carotenoids (carotenes and xanthophylls) imparts red, orange and yellow color to the plants parts they’re located in.

Chromoplasts may directly differentiate from the proplastid in petals of many flowers like buttercups and marigold. During ripening of many fruit and vegetables, chloroplasts in the green-colored plant parts like fruit’s peel convert into chloroplast; thus, turning their color from green to red, orange or yellow. Chromoplasts also differentiate from leucoplasts. For example, the leucoplasts in colorless pulp of fruit like mango, melon, etc. differentiate into chromoplast during their maturation; thus, causing their pulp turn yellow, orange or red. Chromoplast may also differentiate into chloroplast in the newly formed leaflets and stem of some plants during maturation.

Leucoplasts: Leucoplast is a general term referring to the group of colorless plastids. They develop from proplastid in the non-photosynthesizing parts like roots, tubers and endosperms, etc. primarily involved in storage of various biomolecules like starch, oils, proteins, etc. Its stroma contains few tubular membranous structures but there is absence of thylakoid-associate membrane system.

Remember that the “color” alone shall not be considered sufficient to classify a plastid. For example, etioplasts, pre-granal plastids and the proplastid are also colorless plastids but they are not classified as leucoplasts because of the well-defined architecture and composition of the internal membrane system in their stroma.

More specifically, the term “leucoplast” refers to the non-pigmented plastids involved in the synthesis and storage of monoterpenes while lacking the thylakoid-associated membrane system in the stroma. It occurs in the oil-secreting cavities of the peel of citrus fruit, nectaries of flowers and the secretory gland cells of leaves and stems. It may differentiate into amyloplast and elaioplast.

Amyloplast is the unpigmented plastic characterized by its ability to synthesize and store large quantity of starch. Its name is derived from “amylose”- one of the two polysaccharides constituting starch. The seed endosperm of cereals like rice and wheat, and potato tubers are primarily constituted of amyloplasts. It is also present in some cotyledons. Statoliths are the modified amyloplasts that imparts gravitropism to the host cells- statocytes or columella cells of the root caps.

Elaioplast is the non-pigmented plastid involved in the synthesis and storage of lipids (oils, terpenes, fatty acids). These are abundantly present in the tapetal cells of the developing anther. During maturation, the lysis of tapetal cells release lipids at the outer surface exine of the pollens, making them waterproof. The pericarp (peel) of citrus fruit also contains numerous elaioplasts. The terpenes in the essential oil are generally responsibly for the characteristic aroma and taste of the many fruit.

Proteinoplast, also known as aleuroplast or aleuronaplast, are the non-pigmented plastids. They are often present in plant produces rich in proteins including the seeds of pulses, peanuts.   

2.8.1. Chloroplasts

Chloroplasts are the most conspicuous plastids in the eukaryotic photoautotrophs. In higher plants, it is present in mesophyll cells of leaf, usually 20-40 in each cell. It is usually lens shaped, 2-4 µm wide and 5-10 µm long.  These organelles have chlorophyll (chlorophyll ‘a’ and ‘b’) molecules as well as carotenoids (yellow, orange or red colored). Since the amount of chlorophyll molecules in chloroplast is far greater than carotenoids, chloroplasts appear green, and so are the plant organs containing them.

It is a three-membrane system organelle involved in photosynthesis in autotrophic eukaryotes. The outermost outer membrane and inner membrane lying beneath it forms the double membrane. The inner membrane further invaginates/ convolutes into the stroma forming thylakoid- the third membrane system. The outer membrane has porin proteins which non-specifically transfer water and metabolites up to 10kDa size across the intermembrane space. The inner membrane is relatively more selectively permeable (like the generalized plasma membrane) than outer membrane. The chloroplast of photoautotrophic eukaryotes also evolved from prokaryotes (cyanobacteria- a photoautotrophic prokaryote). The organelle has its own circular chromosomes devoid of histones, 70s ribosomes and divide by binary fission like prokaryotes. 

Chloroplast Structure

The space enclosed by the inner membrane is called stroma. The inner membrane of chloroplast invaginate into stroma forming a branched internal membrane system. Each disc-shaped invagination of the inner membrane into the stroma of a chloroplast is called a thylakoid. In other words, thylakoid is a single membrane bound, disk-shaped membranous system suspended in stroma. The space enclosed by the thylakoid membrane is called a thylakoid lumen. The thylakoid membrane has relatively low content of phospholipids and higher content of galactose-containing glycolipids (ex- monogalactosyl diacylglycerol). The resultant higher fluidity is crucial to efficient lateral diffusion of various proteins (ex- electron carrier) along thylakoid membrane during photosynthesis. The photosystems (PS I and PS II having chlorophyll molecules), CF0-F1 ATP synthase, and many other proteins complexes participating in light reaction of photosynthesis are integral proteins of the thylakoid membrane. During photosynthesis the H+ ions are transported from stroma to thylakoid lumen as high energy electrons (ejected from PS I/ PS II) return to their lower energy level through various intermediate electron carriers. Thus, solar energy is first stored in the potential energy of the electrochemical gradient of H+ ions in thylakoid lumen. When H+ ions are transported back into the stroma through CF0-F1 ATP synthase, ATP is produced in the stroma.

In chloroplast, a thylakoid can exist either in the stacked or un-stacked form. The stacked form, a stack of two or more thylakoids, is called a granum; and each thylakoid in a granum (stacked-form) is called granum thylakoid. The non-stacked thylakoid is simply called a “thylakoid” or more specifically, stroma thylakoid or thylakoid lamella or frets. A tubular extension of the stroma thylakoid, called thylakoid lamella connects two grana, and also facilitates transfer of matter between them. The lumen of all grana in a chloroplast are interconnected through thylakoid lamellae, thus, the internal membrane system has a common and continuous lumen.

Photosystem I (PS I) is generally abundant in stromal thylakoid whereas photosystem II (PS II) is abundant in the grana thylakoid. This relative abundance of PS I and PS II in different regions of thylakoid membrane is called lateral heterogeneity. ATP synthase is exclusively present in stromal thylakoid. Cytochrome b6f complex is generally evenly distributed.

2.9. Cytoskeletons


Microfilaments, also called actin filaments or F actin, are composed of actin proteins. The globular actin (G actin) with two binding sites (positioned ≈1600 to each other) for two other G actin and another binding site for ATP acts as the monomer for actin filaments. A G actin first binds to ATP and binds to another G actin at the growing end. The ATP is hydrolyzed into ADP by the ATPase activity of G-actin and forms actin- ADP complex which becomes a part of the actin filament, 8 nm in diameter. Since each binding site in the monomer is positioned at 1600, their polymerized actin filaments appear helical.

The end of actin filament with relatively higher affinity for actin-ATP is called plus/ barbed end and the filament elongates at this end. The other end of actin filament, called the pointed/ minus end, has lower affinity for actin-ATP and the filament length regresses at this end. At 0.35 μM actin-ATP concentration in the cell the rate of addition of monomers at the plus end is equal to the rate of removal of monomers from the minus end, thus the length of actin filaments dynamically remains constant. At conditions above 0.35 μM actin-ATP of the cell, the actin filament grows more rapidly at the plus/ barbed end than regression at the minus end. Because of the dynamic nature of association involving the polymerization of actin-ATP monomers at plus end and simultaneous removal of monomers from the minus end, though at slower rates, the formation of actin filaments is also referred to ‘tread milling’ of actin filaments. 

Intermediate Filaments

Intermediate filaments are solid, ropelike cytoskeleton with a diameter of 10-12 nm and found only in animal cells. These proteins form a network in the cell in all directions and bind to other cytoskeletons (microtubules, microfilaments or intermediate filaments) through a bridging protein called plectin.  Due to their considerable strength and flexibility these proteins provide mechanical support and help the cells (ex- those lining GIT lumen, muscle cells, neurons, etc.) to retain their shapes and positions after a mechanical stress. The intermediate filament consists of a polypeptide with a relatively constant central α- helix and highly variable N-terminal and C-terminal domains. Two such polypeptides wind around parallelly (both polypeptides have N-terminal at same end) each other in a coiled- coil manner and form a dimer. Two such dimers associate with each other antiparallelly forming a tetramer. Eight such tetramers associate with each other side by side to form a solid cylinder (diameter- 10-12 nm, length- 60 nm) acting as the unit of assembly into higher orders. Several units join end to end to form highly elongated intermediate filaments. Intermediate filaments are dynamic structures undergoing continuous assemble and disassembly through the addition or removal of assembly units from the middle NOT from ends as it happens in microtubules. These cytoskeletons are chemically more stable than microtubules and microfilaments. These are composed of a diverse array of proteins encoded by around 70 genes. Depending on their amino acid composition, intermediate filaments are classified into five groups (I- V). The types of intermediate filaments, their constituting proteins and occurrence are summarized as below:

TypeConstituting ProteinsOccurrence
IAcidic KeratinEpithelia
IIBasic KeratinEpithelia
  IIIVimentin Desmin Peripherin Glial fibrillar acidic proteins (GFAP)Mesenchymal cells, fibroblasts, WBCs, smooth muscles Muscles Peripheral neurons Glial cells
IVNeurofilament proteins (NL-L, NL-M, NL-H) α-internexinNeurons Neurons
VLamin proteins (Lamin A, B, C)Nuclear lamina
VINestinNeuroepithelia, Stem cells of CNS

Intermediate Filament Structure


Microtubules are composed of tubulin proteins. Two structurally similar globular proteins, α-tubulin and β-tubulin interact noncovalently forming a dimer. Several such tubulin dimers join together through noncovalent interactions to form a longitudinal row called a protofilament. 13 protofilaments of same polarity (all have α-tubulin at one end and β-tubulin and another end of the protofilament) align parallel to each other longitudinally and form a complete hollow tubular structure called microfilament. Thus, microfilament also have polarity i.e. all the constituent protofilament end with α-tubulin (called ‘minus end’) at one end and β-tubulin (called ‘plus end’) at the opposite end of the tubule. The microfilament has inner diameter of 21 nm, outer diameter of 25 nm and the thickness of 4 nm. 

The minus end of microtubule remains embedded in the microtubule organizing centers (MTOC, ex- pericentriolar material, PCM of centrosomes in animal cells) and the plus end interacts with cellular components like organelles and chromosomes and assign their specific position in cell. 

Microtubule Structure

2.10. Centriole and Centrosome

Centrioles are cylindrical structures (diameter= 200nm, length≈ 400nm) composed of microtubules. In a centrosome, the centrioles are almost always in pair and lie perpendicular to each other. In most animal cells, each centriole consists of 9 triplets of microtubules which are connected to the central proteinaceous axis, called hub, by radial spokes. Each triplet of tubules has three microtubules, named A, B, C, from centre to outward. A microtubule is complete (i.e. has 13 tubulin protofilaments), B overlaps A and C overlaps B; and hence B & C are incomplete microtubules. In the embryos of Drosophila melanogaster and crab, centrioles consist of nine doublets of microtubules. The centrioles of sperm cells of Caenorhabditis elegans consists of 9 singlet of microtubules. Another family of protein, γ- tubulin is present in the centrosome. Though γ- tubulin is not a part of the microtubule, it helps in the nucleation of microtubules. The dense, amorphous matrix surrounding the centrioles is called pericentriolar material (PCM). The organization of PCM is controlled by centrioles. The centrioles and PCM are collectively called centrosome. In animal cells the centrosomes (especially PCM) are involved in formation and organization of microtubules and thus also act as microtubules organizing center (MTOC). The centrioles also form the basal body of cilia and flagella.

2.11. Cilia and Flagella

These are hair-like cellular projections of eukaryotic cells, which provide them motility. Structurally cilia and flagella are more or less the same. Though both are roughly equal in diameter (0.25μm= 250 nm), cilia (length- 10 μm) are generally smaller than flagella (length – 40 μm). Generally, most eukaryotes cells have a single or a pair of flagella. The number of cilia on a eukaryotic cell is very large. The pattern of motility produced differentiates these organelles. The motility provided to a cell by cilia is similar to use oars for propelling boats. In the effective (power) stroke, the cilium remains rigid while it pushes through the surrounding medium, and bends at it base. In the recovery stroke, the bend passes to the tip. The direction of movement produced by the cilia is perpendicular to the cilia.  Flagella provide motility to the host cell by beating in various patterns. The flagella beating generates waves that usually passes from the base to the apex and displaces the cell in a direction parallel to the flagellar axis. The beating of flagella can be asymmetric (ex- some unicellular algae) or symmetric (ex- animal sperm cells).The core of these structures (cilia & flagella), called axoneme, has 9+2 arrangement of microtubules running along their length. The axoneme has 9 doublets of microtubules at its periphery and 2 singlet microtubules at its center. Each of the peripheral doublet consists of one complete microtubule (13 protofilaments) called the A tubule and one incomplete (10-11 protofilaments) microtubule called the B tubule. An interdoublet bridge composed of nexin (an elastic protein) connects the doublets to each other. The A tubules has a pair of dynein (called ciliary or axonemal dynein) molecules attached to them. One dynein molecule (two headed) projects towards the center and is called the inner dynein arm whereas the other dynein (three headed) molecule projects outward the periphery and is called outer dynein arm. Dynein is a motor protein with ATPase activity, which hydrolyze ATPs and provide energy for the mechanical movements in cilia and flagella. The microtubule pair at the center is surrounded by central sheath. The radial spokes connect the central sheath to the A tubule.

Axoneme- Cilia- Flagella

The axoneme is attached to the basal body anchored in the plasma membrane of the cell. The basal body consists of nine triplets of microtubules similar to centrioles. The axoneme is covered by extension of plasma membrane around it. The plus end of the microtubules is present at the tip of cilia/ flagella and their minus ends are embedded in the basal body.

2.12. Ribosomes

Ribosomes are ribonucleoproteins (composed of rRNA and proteins) acting as the site of protein synthesis. These are non-membranous organelles. In cytoplasm, the ribosomes exist as free subunits- large (roughly hemispherical in shape) and small (roughly flat & elongated) subunits. The large and small subunits assemble as a complete functional structure on mRNA during translation. Several ribosomes bound to the mRNA during translation are called polyribosomes. A cell has millions of ribosomes in its cytoplasm. Ribosomes consists of roughly 50% rRNA and rest of proteins. Because a cell usually contains millions of ribosomes in it, rRNA is the most abundant (consists of around 80% of the total RNA) and stable form of RNA in the cell. The large subunits of a functional ribosomes catalyze the formation of peptide bond between two amino acids, thus also act as peptidyl transferase enzyme. Since the catalytic activity of the ribosomes is due to presence of rRNA (23S rRNA of prokaryotic 50S subunit, 28S rRNA of eukaryotic 60S subunit) in it, ribosomes are also an example of ribozyme.

Eukaryotic Ribosomes (80s)Prokaryotic Ribosomes (80s)
Larger Subunit60S rRNA- 5S, 5.8S, 28S            Proteins-  4950S rRNA- 5S, 23S                    Proteins- 31
Smaller subunit40S rRNA- 18S                          Proteins- 3330S rRNA- 16S                           Proteins- 21
DimensionRoughly globular with diameter ≈ 2.8 nmRoughly globular with diameter ≈ 2.5 nm
OccurrenceCytoplasm of the eukaryotic cellsProkaryotes

The size of ribosomes (small RNAs, also) are most frequently expressed in Svedberg unit. It is the rate of sedimentation of particles during centrifugation and expressed in terms of sedimentation coefficient (sedimentation velocity/ centrifugal force) of 1013 seconds.

The ribosomes present in the mitochondria (animals & plants) and chloroplast (plants) of eukaryotes are also called organellar ribosomes. Organellar ribosomes are always smaller than cytoplasmic ribosomes. Mitochondria and chloroplast became a part of the eukaryotic cell through endosymbiosis of aerobic and photosynthetic bacteria, respectively, with eukaryotic cells. Though being of prokaryotic origin, the organellar ribosomes are quite different from prokaryotic as well as eukaryotic ribosomes. Generally, the chloroplast ribosomes are 67-68S. However, the mitochondrial ribosomes may vary from 55S (mammalian ribosomes) to 77S (yeast).

Ribosome structure

2.13. Peroxisomes

 Peroxisomes are single membrane bound organelles characterized by generation and neutralization of hydrogen peroxide in them. The oxidase enzyme (a flavoprotein) produce hydrogen peroxide by transferring electrons from a substrate to oxygen. Catalase, an intrinsic component of this organelle, neutralizes H2O2 by converting it into water. In animal cells, these are involved in detoxification. In plants these organelles play crucial roles in glycolate pathway (photorespiration). Peroxisomes divide to produce new peroxisomes.

2.14. Glyoxysomes

Glyoxysomes arespecialized peroxisomes carrying out bet-oxidation of fatty acids during germination of oil-rich seeds. The fatty acid first enters beta-oxidation pathway and then converted into succinate through glyoxylate cycle. Succinate is transported to cytoplasms and converted into carbohydrates, where it is used by growing parts of the seed. H2O2 produced during b-oxidation is converted into water by the catalases present in it.

3. Ultrastructure of Prokaryotic cell:

Prokaryotes include eubacteria and archaebacteria and have a single circular ds DNA as their genetic material. The chromosome is associated with polyamines and other DNA-binding proteins (NOT histones) and appears as a condensed region in the cytoplasm, called the nucleoid or nuclear body. These cells lack double membrane bound organelle like nucleus, mitochondria, chloroplast, endoplasmic reticulum, Golgi complex, etc. Ribosomes is 70S type. The inward invagination of plasma membrane pf Gram-positive bacteria visible under electron microscope were called mesosomes. Mesosomes are artifacts produced due to chemical fixation of the bacterial cells. The eubacterial cell wall is composed of peptidoglycan. It is a polymer of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) linked together by β (1-4) glycosidic bond. Two peptidoglycan chains are cross-linked by a tetrapeptide in between adjacent NAM residues. This tetrapeptide consists of L-alanine, D-alanine, D-glutamate and L-lysine (or a structurally related molecule Diaminopimelic acid, DAP). The glycosidic bond of peptidoglycan is susceptible to the enzyme Lysozyme present in the saliva, tears and other body fluids. Thus, lysosomes can kill bacteria.

Depending on the composition of their cell wall, the eubacteria are classified into Gram-positive, Gram-negative and acid- fast bacteria. Hans Christian Gram developed the technique of cellular staining. The bacteria retaining the primary stain (violet colored by crystal violet) after decolorization were termed Gram-positive and those stained by the counter stain (purple colored by safranin) after decolorizing were termed Gram-negative bacteria. Presence of mycolic acid in the cell wall of acid-fast bacteria resists decolorization of cell wall by acids. When gram-stained these bacteria give abnormal gram-positive appearance.

3.1. Cell Wall of Gram-positive Bacteria

 The cell wall of Gram-positive bacterial consists of a rigid, multilayered, thick (20-80 nm) peptidoglycan layer attached to the plasma membrane. The peptidoglycan layer also has teichoic acids embedded in it. Teichoic acids are roughly 30 subunits long polymer (polysaccharides) of glycerol phosphate or ribitol phosphate linked together by phosphodiester bond. The teichoic acids, which are integrated into the plasma membrane and span the peptidoglycan layer, are called lipoteichoic acids. The teichoic acid molecules integrated to NAM of the peptidoglycan layer and spanning its thickness are called wall teichoic acids. Teichoic acids provide antigenicity to the host bacteria. Teichoic acids may also bind cations (Ca2+, Mg2+) and transport them into the cell.

Gram positive & negative Cell walls

3.2. Cell Wall of Gram-negative Bacteria

 The outer wall of Gram-negative bacteria is similar to plasma membrane except that it also consists of some specialized polysaccharides and proteins. Lipopolysaccharide (LPS) is the most important polysaccharide and consists of Lipid A (embedded in the outer membrane), core polysaccharide (attached to Lipid A) and O-polysaccharide (attached to core polysaccharide). The Lipid A component of LPS is also referred to as endotoxin because it triggers fever, gas, diarrhea, and vomiting in human and other animals infected by pathogen Gram-negative bacteria (E.coli, Salmonella, Shigella, etc.). Specific and non-specific porin proteins forms a channel across the outer membrane and allow diffusion of only small molecules between the periplasm and outer environment. Outer membrane is integrated into the peptidoglycan by lipoproteins. Lipoproteins, also present throughout the outer membrane, are the most abundant proteins and are also called Braun’s lipoprotein/ murein lipoprotein. The space between the cell membrane and outer membrane is called periplasm. It has a thin layer, usually one or few layer thick, of peptidoglycan. Periplasm consists of high amount of proteins (hydrolytic enzymes, chemoreceptors, etc.) dissolved in its aqueous suspension. Under electron microscope, the outer membrane and the plasma membrane appear to be fused at few points called zone of adhesions or Bayer’s junctions.  

3.3. Cell Wall of Acid-fast Bacteria

Cell wall acid fast bacteria (ex- Mycobacterium, Nocardia) has little content of peptidoglycan and high content of lipids/ waxes. Most significantly of these lipids is a very-long chain fatty acid, named mycolic acid (cord factor), which is responsible for their pathogenicity. High content of complex lipids in their walls makes them highly resistant to dyes/ chemical and decolorization during Gram staining.

The cell wall of Archaebacteria is composed of pseudomurein or pseudopeptidoglycan. It is a polymer of N-acetylglucosamine (NAG) and N-acetyltalosaminuronic acid (NAT) linked together by β (1-3) glycosidic bond. Two peptidoglycan chains are cross-linked by a tetrapeptide of L-alanine, D-alanine, D-glutamate and L-lysine (or a structurally related molecule Diaminopimelic acid, DAP) like that in bacterial cell wall. The β (1-3) glycosidic bond of Pseudomurein is insensitive to lysozymes.

3.4. Glycocalyx

Many of the bacterial cells have a viscous, gelatinous coat outside the cell wall and is composed of polysaccharides (in Streptococcus pneumoniae), or polypeptide (Bacillus anthracis) or both depending upon the species. These components are synthesized inside the cell and deposited outside the cell wall. Glycocalyx in the cells may provide adherence, pathogenicity and even a mechanism to escape the immune responses. Capsule is the glycocalyx organized tightly around the cell wall, excludes small particles (ex- Indian ink) and is easily observable under light microscope. It may be covalently linked to peptidoglycan of the bacterial cell wall and hence difficult to separate from the cell. Slime Layer is present as a loose meshwork around the cell wall, poorly excludes Indian ink and not easily observed under light microscope. It can easily be lost from the cell.

3.5. S-Layer

In addition to plasma membrane, some, methanogens(Methanocaldococcus jannaschi) has an outermost layer of interlocking glycoproteins but no cell wall. Its presence makes the cell withstand osmotic pressure. Many bacteria as well as archaea have S-layer addition to the cell wall. In all conditions, the S-layer is always the outermost layer of the prokaryotic cells. It may also act as a selective sieve for the cell.

3.6. Pilus

[Plural- Pili] – Pili are hair-like cell appendages present on the surface of many bacterial cells. It is composed of ‘pilin’- a fibrous protein, with diameter of 6-7 nanometer. It mediates the conjugation between two bacteria and may also act as receptors for the attachment of bacteriophage to the host cell. The number of pili on a cell may be one to few. Example- Conjugation pili (Fertility factor) encoded by F plasmid involved in bacterial conjugation. Some bacteria (ex– Myxococcus xanthus) have type IV pili which provide twitching/ gliding motility to them. These are generally present only at the pole of the rod-shaped bacteria that possess them.

3.7. Fimbriae

Also called ‘Attachment pili’ and composed of the ‘curlin’ proteins with a diameter of 3-10 nm, relatively shorter than pili. It’s antigenic in nature and helps the bacteria (E. coli, Salmonella, Bordetella pertussis, Neisseria gonorrhea, Staphylococcus, Streptococcus, etc.) to attach to an animal cell and cause diseases. It also helps the bacteria to attach to a non-living substratum (ex- teeth, rocks, etc.) or to each other forming biofilm/ pellicle on the surface of a liquid substratum.

3.8. Flagella

Filaments are 5-10 µm long hollow, helical cylinders with outer diameter of 15-20 nm. Each filament generally consist of 11 protofilaments of flagellin proteins (monomers) in most eubacteria species. Cocci rarely have flagella. Bacillary (rods) cells often have flagella. Non-flagellated cells are called atrichous. When grown on a culture medium, the flagellated bacteria often show a spreading growth of colonies on agar plates resembling a watery film, thus, flagellar antigen are also called H- antigen (from German word ‘Hauch’– ‘breeze’/ watery film of a solid surface). The non-flagellated bacteria do not show spreading colonies on agar plates and their antigen are called somatic antigen or O-antigen (ohne Hauch- no breeze).

The basal body consists of C ring (at Cytoplasmic face of plasma membrane and extends into cytoplasm), MS ring (M ring embedded in the plasma membrane towards peptidoglycan end, a thin S-ring is stacked on the M-ring), P-ring (embedded in Peptidoglycan), L ring (Embedded in LPS) and the central rod. A complex of Mot proteins is integrated in the plasma membrane and surrounds the C ring. Mot proteins translocate approx. 1000 H+ from cytoplasm to outside the plasma membrane causing the filament to rotate a complete turn. The Fli proteins, associated with C ring, act as motor switch and reverses the direction of flagella rotation in response to the intracellular signals.

Flagella- Gram negative Bacteria

Spirochetes are Gram-negative bacteria characterized by the presence of axial filaments (endoflagella). It consists of a protoplasmic cylinder (similar to basal body) and the filament (axial filament). The protoplasmic cylinder is integrated into the plasma membrane, extends into the cytoplasm at one end and to the cell wall in opposite end. The filament emerges from the hook outwardly and is twisted around the longitudinal axis of the cell but lies within the outer sheath. The coordinated movement of axial filaments causes spirochetes to rotate in the surrounding and thus move. The number of axial filaments per cell is generally two in most but may be numerous in others. Composition and functioning of axial filament is similar to that of bacterial flagella.  Example: Treponema palladium palladium (causes syphilis), Borrelia burgdorferi, B. garinii, B. afzelii (causes Lyme disease).

Difference between Flagella of Archaebacteria and Eubacteria

Outer Diameter15-20 nm10-14 nm
Flagellin in each flagellaOne type (Homopolymer)Several types (Heteropolymer)
Energy for flagella motilityH+ pumpsATPs expenditure

3.9. Bacteria Lacking Cell wall

Mycoplasma: Mycoplasma are smallest prokaryotes (0.1 µm in diameter), lack a cell wall, and require cholesterol for growth. These are generally parasitic/ saprophytic in nature. Like other bacteria these also have 70S ribosomes and divide by binary fission. P1 antigen is the primary virulence factor of mycoplasma. The erythrocytes and cells lining the GIT of animal express receptors for P1 antigen on their plasma membrane. Example: Mycoplsama pneumoniae, M. genitalum.

Cell wall-Deficient (CWD) / L- Form/ L-Phase Variant Bacteria: These are strains of bacteria lacking a cell wall. These cells can be derived from normal (wall-forming) bacteria by mutations and/or occurrence of changes that triggers loss of the cell wall. Though the normal bacteria have no cholesterol in their plasma membrane, these L-forms may contain 25-30% cholesterol/ sterol of total mass of their plasma membrane like eukaryotes. Example- Streptobacillus moniliformis and Proteus mirabilis form L-forms.

3.10. Endospores

Endospores are highly desiccated, light refractive and metabolically dormant forms which are resistant to heat, chemical, radiations (UV) and lytic enzymes. These are produced (Sporulation) inside the bacterial cell under environmental stress like heat, nutrients deficiency, etc. Upon getting favorable conditions, these endospores germinate to give rise to the new bacterial cell. Many of theGram-positive bacteria including Bacillus (B. thuringiensis, B. anthrasis, etc.) and Clostridium (C. tetani) and others produce endospores. Spore formation is most frequently observed in many Gram-positive bacteria and very few Gram-negative bacteria.

During sporulation, the duplicated genetic material, ribosomes and other essential components along with little amount of cytoplasm is separated from rest of the mother cell by septation. The central portion consisting of the one copy of genetic material, ribosomes and cytoplasm around it is called the core or spore core. The core wall is formed around the core. The core wall consists of plasma membrane immediately surrounding the core and a wall over the plasma membrane. Outside the core wall lies the cortex- the loosely cross-linked peptidoglycan layer. A multilayered spore coat consisting of spore-specific proteins surrounds the cortex. Outer to spore coat is exosporium- the outermost, thin proteinaceous covering of the endospore.

Endospore structure

The spore core has high concentration of dipicolinic acid (absent in vegetative cells). Dipicolinic acid is often complexed with Ca2+ ions. The Ca2+– dipicolinic acid complexes, called calcium dipicolinate, binds to the DNA bases and protect its structure against dehydration. Simultaneously calcium dipicolinate also binds free water molecules in the endospores and result further dehydration. Thus, calcium dipicolinate is the major component responsible for thermal resistance of the endospores. The small acid soluble proteins (SASPs, absent in vegetative cells) present in the core prevents the endospore from UV radiation, and assists in heat resistance. 

3.11. Inclusion Bodies

Polyhydroxybutyrate (PHB): In response to limited nitrogen and phosphorous and abundant carbon source many eubacteria and archaebacteria form discrete granules of PHB in their cytoplasm. One or more granules may be present in one cell. Several thousands of 3-Hydroxybutyrate subunits are polymerized to form one PHB granule. A thin protein layer (not true membrane) surrounds the PHB granules. PHB granules are maintained at dynamic equilibrium in the cell. The carbon present abundantly in the surrounding may be stored in form of PHB granules in the cytoplasm. PHB granules are depolymerized to release carbon when carbon source in surrounding is depleted. The term polyhydroxyalkanoate (C3-C18) is generally used if the carbon source of this group is other than hydroxybutyrate.

PHB is produced at industrial scale by using microbes for the formation of biodegradable containers (water bottles, food trays).

Polyphosphate Granules: Under certain physiological conditions (ex- phosphorous starvation followed by abundance of phosphorous in medium) some bacteria may form membrane-less polyphosphate granules in their cytoplasm. Polyphosphate may serve as reservoir of inorganic phosphate (PO43-) maintained at dynamic equilibrium, Ca2+/ Mg 2+ chelators or may even show buffering activity in the cells. Polyphosphate granules are also called volutin granules. When stained with methylene blue, these granules appear red. So, the phosphate granules are also called metachromatic granules (as shows metachromatic effect).

Glycogen/ Polyglucose: In response to limited nitrogen/ phosphorous/ sulfur and abundant carbon source many eubacteria and archaebacteria form glycogen/ polyglucose deposits in their cytoplasm. Polyglucose serves as energy reservoirs. 

Magnetosomes: Some bacteria may deposit ferromagnetic crystals of magnetite (Fe3O4) or gregrite (Fe3S4) in their cytoplasm.The magnetosomes help the bacteria orient themselves along the magnetic field of the Earth. It may also help the anaerobes bacteria to move towards toward the bottom of aquatic systems and reach a depth of O2 concentration optimum for them.

Carboxysomes: Many cyanobacteria and few non-oxygenic photosynthetic bacteria consists of the enzyme RuBisCO (ribulose, 1, 5-bisphosphate carboxylase/ oxygenase) enclosed in a 3.5 nm thick shell (not true membrane). These inclusions are called carboxysomes. RuBisCO molecules is present in chains or circles in carbosysomes.

Gas Vesicles: These are bipyramidal (cylindrical with both ends conical) in shape. The gas vesicles are freely permeable and store gases (O2, N2, H2, CH4, CO2, etc.) but impermeable to water vapor. Gas vesicles are composed of small hydrophobic proteins (GvpA, GvpC). The outer surface of gas vesicles is hydrophilic in nature and interacts with cytoplasm whereas the internal surface is hydrophobic. These inclusions are frequently observed in cyanobacteria and others and may help them maintain buoyancy.

Sulfur Globules: sulfur globules are present in many non-oxygenic photoautotrophs (ex- Thiobacterium, Thiospira, Leucothrix, etc.) and serve as sulfur reservoirs. It consists of polythionates in chain; however, elemental sulfur (S0) in chains of 7-9 atoms may also be present in its interior. Sulfur globules have hydration shell around them and lack a true membrane.

3.12. Difference between Gram-positive, Gram-negative and Acid-fast bacteria







Multilayered, thick

One or few layers, thin

Relatively thin

Teichoic acid

Generally present



Outer membrane





Small amount

Lipopolysaccharide (LPS)

Mycolic acid, glycolipids, wax

Antigenic property due to

Teichoic acid


Mycolic acid (cord factor)

Periplasmic space


Present, fluid-filled


Lysozyme sensitivity




Structure after lysozyme treatment



Difficult to digest

Dyes/ antibiotic sensitivity




3.13. Differences between Eukaryotes, Eubacteria and Archaebacteria





Genetic material

One or more linear chromosomes

Single circular chromosome

Single circular chromosome

Histones associated with DNA




Genetic material found in




Cholesterol in membrane




Mode of reproduction

Asexual (mitosis/ fission, etc.); Sexual

Asexual (binary fission)

Asexual (binary fission)

Membrane bound organelles




Extrachromosomal DNA

Mitochondria/ chloroplasts; plasmids in few




9+2 arrangement of microtubules, if any.

Homopolymer of Flagellin

Heteropolymer of Flagellins













Location of respiratory enzymes


Plasma membrane

Plasma membrane


80S in cytoplasm, 70S in mitochondria/ chloroplast



Cell Wall

Animal (absent), plants (cellulose), fungi (chitin), Diatoms (silica), etc.



BioChem Calculations
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