Cells and Subcellular Organelles

Cells are the basic unit of life, making up every living organism. In unicellular organisms like amoebas and bacteria, a single cell carries out all the functions necessary for life. Multicellular organisms, such as plants and animals, are composed of numerous specialized cells that work together to sustain life.

All living organisms show the seven basic properties of life:

• Movement: Cells can move. For example, sperm cells move with their flagella, white blood cells travel through the bloodstream to fight infections, and inside cells organelles move to carry out vital functions.
• Nutrition: Cells obtain nutrients from their environment to produce energy, build cellular structures, and drive biochemical reactions.
• Respiration: Cells generate energy through respiration. This process breaks glucose to release ATP, the energy currency that powers cellular activities.
• Excretion: Cells remove waste products through diffusion and active transport, preventing toxic buildup.
• Homeostasis: Cells maintain a stable internal environment by regulating the movement of substances across their membranes.
• Growth: Cells grow by taking in nutrients and converting them into cellular components.
• Reproduction: Cells reproduce through mitosis and meiosis. Mitosis produces identical daughter cells for growth and repair, while meiosis creates gametes for sexual reproduction.

These properties actually define living organisms. Cells perform all the fundamental activities that characterize living organisms.

At the beginning of the 17th century, many scientists began the use of microscopes to study very small objects. The story of cell theory runs through these names:

• 1665 — Robert Hooke: The English scientist examined a thin slice of cork of an oak tree under a microscope. He observed that the cork was made of "many little boxes". He also examined pieces of stem and root of the oak tree and found them made of similar little boxes. He concluded that the parts of plants were made of compartments, which he named "cellulae".
• 1673 — Anton van Leeuwenhoek: The Dutch scientist made a better microscope and observed living cells in pond water. He called these cells "animalcules".
• 1809 — Jean Baptiste de-Lamarck: The French biologist also observed cells when he examined the parts of animals and plants under the microscope.
• 1831 — Robert Brown: The British botanist discovered the nucleus in the cell.
• 1838 — Matthias Schleiden: The German botanist observed many parts of plants under the microscope and concluded that all plants were composed of cells.
• 1839 — Theodor Schwann: The German zoologist concluded the same for animals.
• 1885 — Rudolf Virchow (1821–1902): The German physician observed that all cells come from other cells.
• 1862 — Louis Pasteur provided the experimental proof of this idea.

These observations were combined to form a basic theory about cells. It is called cell theory. It has three essential points:

1. All living organisms are composed of one or more cells.
2. Cells are the basic units of structure and function in an organism.
3. Cells come only from the division of pre-existing cells.

Validation of Cell Theory. Cell theory can be validated through several observations and experiments: (1) By using light microscopes and electron microscopes, scientists visualize cell structures and find tangible evidence that cells are indeed the structural units of all living organisms. (2) Through techniques like live-cell imaging and genetic studies, scientists can track how cells replicate and give rise to new cells, validating that all cells originate from pre-existing cells. (3) Techniques like DNA sequencing reveal that cells share common genetic material and metabolic pathways, reinforcing that the cell is the fundamental unit of life. (4) Experiments such as cell culture studies and tissue engineering validate cell theory by demonstrating cellular growth, differentiation, and reproduction.

Exceptions to Cell Theory. While cell theory is widely accepted, there are notable exceptions: (1) Viruses challenge cell theory because they are not made of cells and cannot carry out life processes independently. They require a host cell to replicate and are considered by many scientists to be at the border of living and non-living entities. Similarly, prions and viroids show properties of living organisms but are not composed of cells — they are made of only DNA, RNA or proteins. (2) Eukaryotic organelles mitochondria and chloroplasts have their own DNA and can replicate independently of the cell's nucleus. This suggests they may have originated from free-living prokaryotic cells. (3) Some organisms, such as certain fungi and algae, have structures where multiple nuclei coexist within a shared cytoplasmic mass, blurring the boundaries of individual cells as defined by traditional cell theory. (4) Muscle cells (myocytes) in vertebrates can fuse to form multinucleated fibres, challenging the concept of a single cell as the basic unit in complex tissues.

The discovery of cells and then the further studies of the internal structure of cells were dependent upon the use of microscopes. Microscopy is the technique of using microscopes to observe and study objects that are too small to be seen with the naked eye. Microscopes use lenses and light or electron beams to magnify and illuminate specimens.

Magnification and Resolution are two key characteristics of microscopes. Magnification refers to a microscope's ability to enlarge the image of an object. Different lenses within a microscope offer varying levels of magnification, denoted by the symbol X, indicating how many times larger the image appears compared to the actual size. For example, a 10X lens can enlarge a 1 µm object to 10 µm. Total magnification in a microscope is determined by multiplying the magnification of all lenses. Resolution refers to a microscope's ability to distinguish between two points that are close together on an object. The greater the resolution, the finer the detail that can be observed. The naked human eye has a resolution of about 0.1 mm. In contrast, a light microscope can resolve details down to approximately 250 nm (nanometres).

Light Microscopy. In a light microscope, light is used to make the image of an object. Light passes through the object and then through two glass lenses. One lens produces an enlarged image of the object and the second lens magnifies the image more. After passing through the object and lenses, the light forms an enlarged clear image of the object in the viewer's eye. The magnification of a light microscope is 1500X — it can magnify objects about 1500 times. Its resolving power is 0.2 micrometre (µm), and 1 µm = 1/1000 mm. In other words, the light microscope cannot distinguish objects smaller than 0.2 µm. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are coloured with special stains (coloured chemicals). Staining, however, usually kills the cells.

Electron Microscopy. In an electron microscope, a beam of electrons passes through the object. Magnetic lenses focus the electron beam on a screen or photographic film and make a much enlarged image. Its resolving power is much greater than a light microscope — it can clearly show objects as small as 0.2 nanometre (nm), and 1 nm = 1/1,000,000 mm. However, an electron microscope cannot be used for viewing living material because of the methods needed to prepare the specimens. Biologists use two types of electron microscopes. The Transmission Electron Microscope (TEM) is used to view the internal structure of a cell. TEM transmits a beam of electrons through a very thin specimen and can magnify objects up to 250,000 times. The Scanning Electron Microscope (SEM) is used to study the details of surfaces of cells or any other objects. The surfaces are coated with metal. When the electron beam hits the metal, it is reflected and makes an enlarged image. SEMs can magnify objects up to 100,000 times.

You know that there are two basic types of cells i.e., prokaryotic and eukaryotic. All bacteria are prokaryotes. Yeast and Euglena are examples of unicellular eukaryotes. Plants and animals are examples of multicellular eukaryotes. Eukaryotic cells are more complex than the prokaryotic cells. In the following paragraphs we will study the structures present in cells and their functions.

Cell Wall. The cell wall is a more or less solid layer surrounding a cell. It is found in bacteria, fungi, plants, and algae. When a cell wall is removed using cell wall degrading enzymes, the remaining components of the cell are called a protoplast. The primary wall is the actual cell wall of a cell. It is composed of polysaccharides i.e. cellulose, hemicellulose and pectin. The cellulose microfibrils are aligned at all angles and are held together by hydrogen bonds. Many proteins are also present in primary walls. The middle lamella is a gelatinous layer that separates and holds the primary walls of the neighbouring cells. It is laid first, formed from the cell plate during cytokinesis, and the primary cell wall is then expanded inside the middle lamella. It contains magnesium and calcium pectates (salts of pectic acid). In some plant cells, after maturation, a secondary wall is made between the protoplast and the primary wall. Secondary cell walls contain lignin, cellulose and hemicellulose. Due to the presence of lignin, the secondary wall is more rigid than the primary wall.

Plasmodesmata (singular: plasmodesma) are small channels that directly connect the cytoplasm of neighbouring plant cells to each other. Plasmodesmata penetrate both the primary and secondary cell walls. They allow certain molecules to pass directly from one cell to another. So, they are important in cellular communication. Plasmodesmata are formed during cell division when parts of the endoplasmic reticulum of the parent cell get trapped in the new cell wall. Plasmodesmata have caused debate among scientists regarding cell theory — some scientists suggest that the cells of higher plants are not really cells since they are not physically separated or independent from one another.

Cell walls have a number of functions: they provide rigidity to the cell for structural and mechanical support; maintain cell shape and the direction of cell growth and ultimately the architecture of the plant; the cell wall also prevents expansion when water enters the cell; cell walls protect against pathogens and the environment; and they are a store of carbohydrates for the plant.

The composition of the cell wall differs by group: the cell wall of algae contains cellulose and a variety of glycoproteins; the cell wall of fungi is composed of chitin, the same carbohydrate that gives strength to the exoskeletons of insects; the cell wall of prokaryotes (bacteria and cyanobacteria) is composed of peptidoglycan, a single large polymer of amino acids and sugar; the cell wall of archaebacteria is composed of different polysaccharides and proteins, with no peptidoglycan. The group of algae called diatoms synthesize their cell walls from silicic acid. The acid is polymerized inside cells, then the wall is extruded to protect the cell. The synthesis of silica cell walls requires less energy — that is why there are higher growth rates in diatoms.

Plasma Membrane. All prokaryotic and eukaryotic cells have a plasma membrane that encloses their contents and serves as a semi-porous barrier to the outside environment.

Structure of the plasma membrane. The fluid mosaic model is a widely accepted concept that describes the dynamic nature of the plasma membrane. It was proposed by two American biologists, S.J. Singer and Garth Nicolson, in 1972. According to the fluid mosaic model, the basic foundation of the plasma membrane is a lipid bilayer made of phospholipids. A collection of proteins float within the lipid bilayer.

The phospholipids have a phosphate group at one end of each molecule. Phospholipids are characteristically hydrophilic (water-loving) at their phosphate ends and hydrophobic (water-fearing) along their tail regions containing C–H chains. In the lipid bilayer of the plasma membrane, the hydrophobic lipid tails are oriented inwards and the hydrophilic phosphate groups are aligned outwards, either toward the cytoplasm of the cell or the extracellular environment. The interior of the lipid bilayer sheet is hydrophobic — it repels water-soluble molecules that attempt to pass through it. If a cell was fully encased in pure lipid bilayer, it would be completely impermeable to water-soluble molecules e.g., sugars and polar amino acids. That is why, in addition to phospholipid molecules, the membranes also contain proteins that provide passageways across the membrane.

In eukaryotes, plasma membranes have cholesterol molecules wedged into the phospholipid bilayer. They keep the fluidity of the membrane at low temperatures. Many proteins float within the phospholipid bilayer of the plasma membrane. Some other proteins simply adhere to the surfaces of the bilayer. The positioning of proteins is related to the organization of the cytoskeleton. Plasma membrane proteins function in several different ways: (1) Many proteins play a role in the selective transport of certain substances across the phospholipid bilayer, either acting as channels or active transport molecules. (2) Some proteins help in attachment of the plasma membrane to the cytoskeleton and external fibres. (3) Some proteins, on the exterior surface, attach with sugars and make identification marks. (4) Other proteins function as receptors, which bind messenger molecules (e.g., hormones) and transmit signals to the interior of the cell. (5) Some proteins also exhibit enzymatic activity, catalysing various reactions related to the plasma membrane.

The outside surface of the plasma membrane has chains of sugars bonded to proteins and lipids. A protein with attached sugar is called a glycoprotein, whereas a lipid with attached sugar is called a glycolipid. The glycoproteins and glycolipids vary from species to species, from individual to individual in the same species, and even from one cell type to another in the same individual. The glycolipids and glycoproteins (collectively called glycocalyx) function as cell identification marks that are recognized by other cells. The ability to distinguish among different cells is crucial to life — it allows cells in an embryo to sort themselves into tissues and organs, and it also helps cells of the immune system to recognize and reject foreign cells, e.g., infectious bacteria.

Functions of the plasma membrane. Plasma membranes serve as semi-porous barriers to the outside environment. The membrane acts as a boundary, holding the cell constituents together. The plasma membrane is permeable to specific molecules, however, and allows nutrients and other essential elements to enter the cell and waste materials to leave the cell. Small molecules, such as oxygen, carbon dioxide, and water, are able to pass freely across the membrane, but the passage of larger molecules, such as amino acids and sugars, is carefully regulated. Eukaryotic cells also have membranes around some of their interior organelles. Like the exterior plasma membrane, these membranes also regulate the flow of materials into and out of organelles.

Techniques to study the structure of the plasma membrane: (1) Transmission Electron Microscopy can reveal detailed structures of the lipid bilayer and associated proteins. (2) Scanning Electron Microscopy is useful for examining the surface topology of cells and membranes. (3) Confocal Microscopy uses laser scanning and fluorescence to create sharp, detailed images of the cell membrane. (4) Total Internal Reflection Fluorescence Microscopy is used for high-resolution images of the membrane and its interactions with the cytoskeleton and other cellular components. (5) Atomic Force Microscopy provides topographical images of the cell membrane at high resolution. (6) X-ray Crystallography is used to determine the atomic structure of membrane proteins. (7) Lipidomics involves the comprehensive analysis of lipids in the cell membrane using techniques like mass spectrometry. (8) Fluorescence Recovery After Photobleaching (FRAP) is used to study the mobility and dynamics of membrane proteins and lipids — it involves bleaching a fluorescently labelled region of the membrane with a laser and observing the recovery as unbleached molecules move into the area.

Cytoplasm and Organelles. You know that a cell consists of three major components i.e., plasma membrane, cytoplasm and nucleus. The cytoplasm is a semi-viscous and semi-transparent substance. In eukaryotic cells, it is present between the plasma membrane and the nuclear envelope. In prokaryotic cells, it covers all the space beneath the plasma membrane. It consists of an aqueous ground substance, known as cytosol, which contains a variety of organelles and other inclusions. Cytosol contains water in which many organic (proteins, carbohydrates, lipids) and inorganic salts are completely or partially dissolved. The cytoplasm of the cell provides space for the proper functioning of the organelles and also acts as the site for various biochemical (metabolic) reactions, for example Glycolysis (breakdown of glucose during aerobic respiration). The cytoplasm contains discrete structures which are specific for various cellular functions and are called cell organelles. The organelles are generally enclosed by a membrane except a few such as the ribosome.

1 — Nucleus. A prominent nucleus is present in all eukaryotic cells (at the centre in animal cells while pushed to the side in plant cells). The spherical nucleus typically occupies about 10 percent of a eukaryotic cell's volume. It serves as the information processing and administrative centre of the cell. It performs two major functions: it stores the cell's hereditary material (DNA) and coordinates the cell's activities e.g., growth, protein synthesis and cell division. The semifluid matrix found inside the nucleus is called nucleoplasm. Within the nucleoplasm, most of the nuclear material consists of chromatin that organizes to form chromosomes during cell division. The nucleus also contains one or more nucleoli, which synthesize ribosomes. Building blocks of DNA and RNA and ATPs are allowed to enter into the nucleus. Ribosomal subunits which are built in nucleoli are examples of materials that are allowed to leave the nucleus and enter the cytoplasm.

The Nuclear Envelope and Nuclear Pores. The nuclear envelope is a double-layered membrane that encloses the contents of the nucleus during most of the cell's lifecycle. The space between the double layers is called the perinuclear space and is connected with the rough endoplasmic reticulum. During cell division, the nuclear envelope disintegrates, but reforms in the daughter cells. On the inner side of the nuclear envelope, there is a protein lining, called the nuclear lamina, which binds to chromatin to give it structural support. The nuclear envelope has tiny holes known as nuclear pores. These pores regulate the passage of molecules between the nucleus and cytoplasm. Nuclear pores are permeable to small molecules. Some larger proteins, e.g., histones, are also allowed to enter into the nucleus. A nuclear pore is made of an elaborate structure called the nuclear pore complex, composed of several subunits: the annular subunit (surrounding the inside of the pore), the column subunit (making the wall of the complex), the ring subunit (attached to the outer side of the column subunit), and the lumenal subunit (anchoring the pore complex into the nuclear envelope). Tiny fibrils usually extend from the complex and make a basket-like structure on the nuclear side of the complex.

Nucleolus. The nucleolus is a prominent darkly stained structure in the nucleoplasm. There may be one or two nucleoli in a nucleus. Nucleoli manufacture the subunits that combine to form ribosomes. Nucleoli are formed at certain sites in a chromosome called Nucleolus Organizer Regions (NORs). The DNA found at NORs encodes the ribosomal RNA (rRNA). The nucleolus consists of granular and fibrillar components, and DNA. The granules consist of ribosomal subunits that have already been formed. The fibrils are composed of the raw materials of ribosome subunits i.e., rRNA molecules and associated proteins. In cells that produce large amounts of protein, and thus require significant numbers of ribosomes, the size of the nucleolus is considerable. At the onset of mitosis, the single nucleolus present in a cell disappears, and after division a new nucleolus is formed from the NORs.

Chromatin and Chromosomes. The nucleus contains string-like fibres, collectively called chromatin. It is composed of DNA and proteins. The structure of chromatin reveals that it is made of a series of bead-like structures, called nucleosomes. In a nucleosome, a DNA strand wraps around groups of small proteins called histones. During interphase (when the cell is carrying out its normal functions), the chromatin is dispersed throughout the nucleus in the form of a tangle of fibres. When the cell begins to divide, all chromatin strands are compressed into specialized structures, the chromosomes. A chromosome is made of arms, called chromatids, and a central point, called the centromere. Inside the nucleus of every human cell, there is a 6 feet long DNA, subdivided into 46 individual molecules (each 1.5 inches long), one for each chromosome. There are two types of chromatin: Euchromatin is the genetically active chromatin involved in transcribing RNA to produce proteins, while heterochromatin is genetically inactive. The number of chromosomes within the nuclei of an organism's cells is species-specific. Human diploid cells (those that are not gametes) have 46 chromosomes. The chromosome number may be as low as 2, as in some ants and roundworms, or more than a thousand, as in the Indian fern (Ophioglossum reticulatum), which has 1,260 chromosomes. This means that the number of chromosomes in a species does not correlate to the complexity of the organism.

2 — Endoplasmic Reticulum (ER). It is a network of flattened sacs and branching tubules that extends throughout the cytoplasm in plant and animal cells. These sacs and tubules are called cisternae (singular: cisterna). Due to their physical membranous connection, the lumen of the endoplasmic reticulum and the space between the layers of the nuclear envelope comprise a single compartment. This close association enables the ER and the nucleus to share information in a very efficient manner. All cisternae are interconnected so that the ER has only one large and highly convoluted lumen, called the cisternal space. It takes up more than 10 percent of the total volume of a cell. The cisternae are also connected to the double-layered nuclear envelope. So, the ER provides a pipeline between the nucleus and cytoplasm. The ER manufactures, processes, and transports a wide variety of biochemical compounds for use inside and outside of the cell. There are two kinds of endoplasmic reticulum: rough and smooth. The surface of rough endoplasmic reticulum (RER) is covered with ribosomes, giving it a bumpy appearance when viewed through the microscope. This type of endoplasmic reticulum is involved mainly in the production and processing of proteins. During processing of proteins, RER adds other chemicals (e.g., sugars) to proteins. Then RER transports the processed proteins to areas of the cell where they are needed, or sends them to the Golgi apparatus for further processing and modification. The surface of smooth endoplasmic reticulum (SER) lacks ribosomes, so it appears more even under the microscope. In most cells, it is much less extensive than the rough endoplasmic reticulum. Smooth endoplasmic reticulum is chiefly involved in the production of lipids, building blocks for carbohydrate metabolism, and the detoxification of drugs and poisons. Smooth endoplasmic reticulum also plays a role in various cellular activities by storing calcium and doing calcium metabolism. In muscle cells, smooth endoplasmic reticulum releases calcium to trigger muscle contractions. SER is much more extensive in the cells which do a lot of lipid and carbohydrate metabolism (brain and muscle) or detoxification (liver).

3 — Ribosomes. All living cells contain ribosomes that are tiny granular structures composed of approximately 60 percent ribosomal RNA (rRNA) and 40 percent protein. Ribosomes are not bound by a membrane and are much smaller than other organelles. In eukaryotic cells, ribosomes are mainly found attached to the rough endoplasmic reticulum and some are scattered freely. In prokaryotic cells, all ribosomes are freely scattered in the cytoplasm. Ribosomes serve as the protein production machinery for the cell. They are most abundant in cells that are active in protein synthesis, such as pancreas and brain cells. A typical cell contains several thousand ribosomes but some cell types may have a few million ribosomes. Eukaryote ribosomes are produced and assembled in the nucleolus. Ribosomal proteins enter the nucleolus and combine with rRNA strands to create the two ribosomal subunits (one small and one large). The ribosome subunits leave the nucleus through the nuclear pores. In the cytoplasm, both subunits combine for the purpose of protein synthesis. When protein synthesis is not being done, the two subunits get separated. In addition to the most familiar cellular locations of ribosomes, they can also be found inside mitochondria and the chloroplasts of plants. These ribosomes notably differ in size and makeup from the ribosomes found in cytoplasm, and are more like those present in prokaryotes. Protein synthesis requires the assistance of two other kinds of RNA molecules in addition to rRNA: Messenger RNA (mRNA) provides the instructions, which it has taken from the DNA, and Transfer RNA (tRNA) brings amino acids to the ribosome. Once the chain of amino acids has been synthesized, the ribosome releases it. The proteins synthesized by free ribosomes are for the cell's own internal use, while the proteins produced by the ribosomes bound to RER are transported outside of the cell. The subunits of a ribosome are described by their Svedberg (S) values, which are based upon their rate of sedimentation in a centrifuge. The complete ribosome in a eukaryotic cell has a Svedberg value of 80S — the smaller subunit has a value of 40S while the larger subunit has 60S. Prokaryotic cells, on the other hand, contain 70S ribosomes, each of which consists of a 30S and a 50S subunit. The Svedberg values are not additive — the values of the two subunits of a ribosome do not add up to the Svedberg value of the complete ribosome, because the rate of sedimentation of a molecule depends upon its size and shape, rather than simply its molecular weight.

4 — Mitochondria (singular: mitochondrion) are rod-shaped organelles that are considered the power generators of the cell. A mitochondrion is bounded by two membranes. There is a narrow intermembrane space between the two membranes. Beneath the inner membrane, there is a larger internal matrix. The outer membrane is smooth and acts like a sieve, filtering out molecules that are too big. The inner membrane is highly convoluted and forms many infoldings called cristae which increase the surface area. The inner surface of the cristae has knob-like extensions into the matrix, known as F-1 particles — these particles are actually the enzymes called ATP-synthase. Other complexes are also found in the inner mitochondrial membrane, which serve as electron carriers in the electron transport chain. Mitochondria are different from most other organelles: a mitochondrion has its own circular DNA (similar to the DNA of prokaryotes), all kinds of RNA and 70S ribosomes, and a mitochondrion can replicate independently of the cell. Scientists hypothesize about the origin of mitochondria: millions of years ago small, free-living prokaryotes were engulfed, but not consumed, by larger prokaryotes. The two organisms developed a symbiotic relationship over time, the larger organism providing the smaller with ample nutrients and the smaller organism providing ATP molecules to the larger one. Mitochondria are the sites of cellular respiration. They generate adenosine triphosphate (ATP) from oxygen and nutrients. ATP is the chemical energy "currency" of the cell that powers the cell's metabolic activities. Enzymes in the matrix catalyse some of the steps of cellular respiration like the Krebs cycle. Other proteins that function in the electron transport chain are bound on the inner membrane. The number of mitochondria present in a cell depends upon the metabolic requirements of that cell, and may range from one to thousands. Mitochondria are found in nearly all eukaryotes, including plants, animals, fungi, and protists, and are large enough to be observed with a light microscope.

5 — Chloroplasts. One of the most important characteristics of plants is their ability to conduct photosynthesis i.e., to make their own food by converting light energy into chemical energy. This process occurs in almost all plant species and is carried out in specialized organelles known as chloroplasts. All of the green structures in plants, including stems and unripened fruit, contain chloroplasts, but the majority of photosynthetic activity in most plants occurs in the leaves. On the average, the chloroplast density on the surface of a leaf is about one-half million per square millimetre. Chloroplasts contain the pigments chlorophyll "a" and chlorophyll "b", which are able to absorb the light energy needed for photosynthesis to occur. The ellipsoid-shaped chloroplast is enclosed by two membranes and the area between the two membranes is called the intermembrane space. A semi-fluid called stroma is present inside the inner membrane. It contains dissolved enzymes and comprises most of the chloroplast's volume. The outer membrane is much more permeable than the inner layer. The inner membranes lie in close association with one another and fuse along their peripheries. In this way, two adjacent membranes form a disk-shaped compartment called a thylakoid. Many thylakoids form stacks called grana (singular: granum). The lamellae are the non-green compartments that connect two grana. Each granum may contain a few to several thylakoids, and a chloroplast may contain a hundred or more grana. Like the mitochondrion, the chloroplast is different from most other organelles because it has its own DNA and reproduces independently of the cell in which it is found. Light is absorbed by chlorophyll molecules embedded in the thylakoid disks. When these chlorophyll molecules absorb light, they emit electrons and thus ATPs are formed. Using these ATPs, in the stroma, low-energy carbon dioxide is transformed into a high-energy compound like glucose. Cells of plants and many protists have three types of plastids i.e., chloroplasts, chromoplasts and leucoplasts. The colourless leucoplasts are involved in storage, and yellow-to-red coloured chromoplasts give colours to plant parts. Mitochondria are similar to chloroplasts: both organelles convert energy for the cell. Mitochondria perform aerobic respiration, generating chemical energy in the form of ATP by metabolizing sugars, fats and other chemical fuels with the assistance of oxygen. Chloroplasts perform photosynthesis, converting energy from the sun into the biosynthesis of organic nutrients using carbon dioxide and water. Like mitochondria, chloroplasts also contain their own DNA and are able to grow and reproduce independently of the cell.

6 — Golgi Apparatus. The Golgi apparatus consists of five to eight cup-shaped, membrane-covered sacs called cisternae, that are stacked over each other. It is found in the cells of plant, animal and unicellular eukaryotes. In some unicellular flagellates, the Golgi apparatus may consist of 60 cisternae. Similarly, the number of Golgi apparatuses in a cell varies according to its function. Animal cells generally contain between ten and twenty Golgi stacks in their Golgi apparatus. This complex is usually located close to the nucleus. Golgi apparatus was discovered by Camillo Golgi: he was investigating the nervous system by using a new staining technique (known as Golgi staining), observed a structure inside cells and named it as reticular apparatus, and publicly announced his discovery in 1898. The structure was named after him as the Golgi apparatus. Many scientists did not believe that what Golgi observed was a real organelle and instead argued that the apparent body was a visual distortion caused by staining. The invention of the electron microscope in the twentieth century finally confirmed that the Golgi apparatus is a cellular organelle. Each Golgi stack has two distinct faces: the 'cis' face is found near the endoplasmic reticulum, while the 'trans' face is positioned near the plasma membrane. The Golgi apparatus is the distribution and shipping department for the cell's chemical products. It modifies proteins and lipids that have been built in the endoplasmic reticulum and prepares them for export outside the cell or for transport to other locations in the cell. Small vesicles that contain proteins, carbohydrates, phospholipids and other molecules bud off from the ER. These vesicles move through the cytoplasm until they reach the 'cis' face of the Golgi apparatus. The vesicles fuse with the Golgi apparatus and release their molecules into it. Here, the compounds are further processed. Enzymes present in the Golgi lumen convert them into glycoproteins and glycolipids. The product is extruded from the 'trans' face of the Golgi apparatus in a vesicle and directed to its final destination inside or outside the cell. The exported products are known as secretions. Other products are returned to the endoplasmic reticulum or may undergo maturation to become lysosomes. In addition, the Golgi apparatus in plant cells produces pectin and other polysaccharides specifically needed for plant structure and metabolism.

7 — Lysosomes. Lysosomes are spherical organelles bounded by a single membrane. They serve as digestive compartments of the cell. Lysosomes are found in most eukaryotic cells. In animals, they are most numerous in disease-fighting cells, such as white blood cells — because white blood cells must digest materials like bacteria, viruses, and other foreign intruders. Lysosomes were discovered by a Belgian scientist, Christian René de Duve, who also discovered peroxisomes. He was investigating carbohydrate metabolism in liver cells and observed that when cells are damaged in the centrifuge, they release acid phosphatase. He suggested that this digestive enzyme was encased in some membrane bounded organelle within the cell, which he named as lysosome. Lysosomes are also involved in breaking down cellular materials that have exceeded their lifetime or are no longer useful — in this regard, the lysosomes perform autophagy. They break down cellular waste products, fats, carbohydrates, proteins, and other macromolecules into simple compounds, which are then transferred back into the cytoplasm for making new materials. Lysosomes have about 40 different hydrolytic enzymes, all of which are manufactured in the endoplasmic reticulum and modified in the Golgi apparatus. The membrane covering of the lysosomes protects the rest of the cell from the harsh digestive enzymes contained in the lysosomes, which would otherwise cause significant damage. The cell is safe from the enzymes of lysosomes: these enzymes require an acidic environment (of pH of about 4.8). The lysosomal matrix is acidic but the cytosol is a neutral environment, so even if a lysosome is ruptured, its digestive enzymes become inactive and the cell remains uninjured. In lysosomal storage diseases the patient lacks one of the hydrolytic enzymes of lysosomes. The abnormal lysosome fills with indigestible substances, which interfere with cellular functions. For example, in Pompe's disease the lysosome lacks a glycogen-digesting enzyme, so harmful amounts of glycogen accumulate in liver cells. In Tay-Sachs disease an essential lipid-digesting enzyme is missing; accumulation of these lipids in the nerve cells of the brain damages the nervous system, causes mental retardation, and death in early childhood. Lysosomes also function in the elimination of whole cells: selective cell death is a mechanism used by multicellular organisms in their development. For example, when a tadpole develops into a frog, the cells of the tail are destroyed by the enzymes of lysosomes. Many cells in your brain die during development — this directed suicide is accomplished by the rupture of the lysosomes within the cells that are being eliminated.

8 — Peroxisomes. Peroxisomes are single membrane bounded organelles in all eukaryotic cells. These were discovered by Christian de Duve, who also discovered lysosomes. Peroxisomes contain a variety of enzymes. Many of these enzymes are oxidative — they carry out oxidation i.e. the removal of electrons and hydrogens. These enzymes primarily function to rid the cell of toxic substances. Some peroxisomes, such as those in liver cells, detoxify alcohol and other harmful compounds by carrying out their oxidation. Some peroxisomes contain catalase enzymes, which break down hydrogen peroxide (a common by-product of cellular metabolism) into water and oxygen: 2H₂O₂ → 2H₂O + O₂. Defects in peroxisomes cause a number of metabolic disorders. The most serious of these disorders is Zellweger syndrome, which is characterized by absence or reduced number of peroxisomes in the cells. It is a congenital disorder (present at birth) and has no cure or effective treatment and usually causes death within the first year of life.

9 — Glyoxysomes. Glyoxysomes are similar to peroxisomes but are found only in plant cells. These organelles contain enzymes that convert lipids into carbohydrates. They are most abundant in the cells of lipid-rich seeds (e.g. castor beans and soyabeans). During germination, these organelles convert stored lipids into carbohydrates that provide energy for seed germination.

10 — Vacuoles. These are membrane-bounded sacs. Vacuoles function in several ways. For example, in mature plant cells, a single large vacuole provides structural support, as well as serves functions in storage, waste disposal, protection, and growth. Vacuoles in animal cells, however, are much smaller, and are more commonly used to temporarily store materials or to transport substances. Vacuoles are fluid filled single-membrane bounded organelles. Cells have many small vacuoles in their cytoplasm. However, when a plant cell matures its small vacuoles fuse to form a single large vacuole. Many plant cells have a large, single central vacuole. This large vacuole slowly develops by fusion of smaller vacuoles. It takes up most of the space in the cell (80 percent or more). The vacuole in plant cells is enclosed by a membrane called the tonoplast. The material inside the vacuole is called cell sap, which differs markedly from the surrounding cytoplasm. The central vacuole in plant cells plays an important structural role for the plant. This role of the vacuole is related to its ability to control turgor pressure. Turgor pressure makes the rigidity of the cell. Under optimum conditions, a plant receives adequate amounts of water and the central vacuoles of its cells swell as the liquid collects within them. It creates a high turgor pressure, which helps maintain the structural integrity of the plant, along with the support from the cell wall. Vacuoles also often store the pigments that give certain flowers their colours, which aid them in the attraction of bees and other pollinators. Vacuoles also release molecules that are poisonous to various insects and animals, thus discouraging them from consuming the plant. Several materials commonly stored in plant vacuoles have been found to be useful for humans, such as opium, rubber, and garlic flavouring.

11 — Centrioles. In the cells of animals and most protists, centrioles are organelles associated with the assembly and organization of the fibres of the cytoskeleton i.e., microtubules (including spindle fibres). Centrioles are hollow and cylindrical organelles. A centriole is made of nine triplets of microtubules. In eukaryotic cells centrioles occur in pairs. The two centrioles are located at right angles to one another near the nuclear envelope. In ciliated or flagellated cells centrioles are involved in the formation of cilia and flagella. Each cilium and flagellum is anchored by a centriole, known as the basal body. The cells of plants and fungi lack centrioles and basal bodies, and their microtubules and spindle fibres are organized from structures of the cytoplasm.

12 — Cytoskeleton. It is a network of protein fibres present in the cytoplasm. It includes the following types of fibres: (1) Microfilaments: These are present in all eukaryotic cells. Microfilaments are solid rods made of a globular protein, called actin. Microfilaments disassemble and re-assemble and help the cells to change shape and move. Microfilaments also enable a dividing cell to pinch off into two cells. In association with myosin, microfilaments help in cellular contraction. (2) Microtubules: These straight, hollow cylinders are composed of subunits. Each subunit is made of two different tubulin proteins known as alpha-tubulin and beta-tubulin. Microtubules give structure and shape to a cell. They also serve as highways for the transport of organelles. Moreover, microtubules are the major components of cilia and flagella, and participate in the formation of spindle fibres during cell division. (3) Intermediate filaments: These are found only in some higher animal groups. They are made of different proteins but the most common type of protein subunit is vimentin. Some cells may have intermediate filaments made of other proteins. For example, skin cells contain a protein called keratin. Intermediate filaments maintain cell shape and rigidity, and serve to anchor several organelles, including the nucleus.

13 — Cilia and Flagella. A cilium (plural: cilia) and a flagellum (plural: flagella) are the locomotor appendages that protrude from certain cells. They are thin, tail-like projections extending from the cell body. Cilia are short in length and are usually numerous in number, while flagella are longer but less numerous in number. Cilia are rare in plants. Many protozoans (ciliates) possess cilia. Larger eukaryotes such as mammals have cilia on some cells' surfaces. For example, in humans, cilia are found in the lining of the trachea where they sweep mucus and dirt out of the breathing tubes. The core of eukaryotic cilia and flagella is called the axoneme. It contains two central microtubules that are surrounded by an outer ring of nine doublet microtubules. Dynein molecules are located around the circumference of the axoneme. These dynein molecules bridge the gaps between adjacent microtubule doublets. Biologists refer to this organization as a "9 + 2" structure. A plasma membrane surrounds the entire axoneme. At the base of the cilium its organising centre, called the basal body, is present. The basal body has the same basic structure of the outer ring of the axoneme, but each of the nine sets of outer filaments is composed of three microtubules, rather than a doublet of microtubules. The basal body is actually the centriole. Prokaryotic flagella have a completely different structure built from the protein flagellin.

Bacteria and archaea are made of prokaryotic cells whereas all other forms are composed of eukaryotic cells. Both prokaryotic and eukaryotic cells have DNA as their genetic material; both have plasma membranes as their coverings; and both have ribosomes for protein synthesis.

Prokaryotic cells are much simpler than eukaryotic ones. Most prokaryotic cells range from 2 to 8 µm in length i.e., about one-tenth of the size of a typical eukaryotic cell. A prokaryotic cell lacks a nucleus. The much less extensive DNA of a prokaryotic cell is present in the more-or-less central region known as the nucleoid (nucleus-like). A prokaryotic cell also lacks other membrane-bounded organelles like endoplasmic reticulum, mitochondria, chloroplasts, Golgi apparatus, lysosomes, peroxisomes etc. The entire cytoplasm of a prokaryotic cell is one unit with no internal support structures. Ribosomes are present in a prokaryotic cell but these are smaller in size than those of eukaryotic cells. The Svedberg values (sedimentation rates) of the smaller and larger subunits of ribosomes of prokaryotic cells are 30S and 50S respectively. The sedimentation rate of a complete ribosome is 70S. Surrounding the plasma membrane of most prokaryotic cells is a cell wall but it does not contain cellulose. It is composed of peptidoglycan, a single large polymer of amino acids and sugar. In bacteria the cell wall may also be surrounded by a capsule and may also have extensions for attachment known as pili (singular: pilus). Prokaryotic flagella are made of repeating units of the protein flagellin and they do not contain microtubule triplets. Mitosis and meiosis are missing in a prokaryotic cell and it divides by direct division (binary fission).

Cell signalling is the ability of cells to respond to stimuli from their environment producing cellular responses. It involves the transmission of signals between cells through a series of molecular events, often leading to a cellular response.

Steps of Cell Signalling. 1 — Signal Reception: Cell signalling begins when a signal molecule (ligand) binds to a receptor on the membrane of a target cell. These receptors are typically proteins embedded in the cell membrane but can also be located inside the cell. Each receptor is specific to a particular ligand. 2 — Signal Transduction: Once the receptor binds to the ligand, it undergoes a conformational change that activates an intracellular signalling pathway. This often involves a series of interactions and modifications, creating a signalling cascade that amplifies the signal. Small molecules like cAMP (cyclic AMP), calcium ions, and inositol triphosphate (IP3) can act as second messengers, transmitting the signal from the receptor to target molecules inside the cell. 3 — Cellular Response: The signal transduction pathway often leads to changes in gene expression, turning specific genes on or off. This can result in various cellular responses, such as cell growth, division, differentiation, or apoptosis (programmed cell death). Signalling can also lead to changes in cellular metabolism, enzyme activity, or the opening and closing of ion channels.

Pathways of Cell Signals from Outside to Inside. Cell signalling pathways involve the transmission of signals from the cell's exterior to its interior, resulting in a specific cellular response. There are two main types of signalling pathways.

Protein/Peptide Signalling. Protein or peptide signalling molecules are water-soluble. So, they cannot pass through the plasma membrane. When such a ligand approaches the cell surface, it binds to its specific receptor on the plasma membrane. This binding causes a conformational change in the receptor protein and activates it. The activated receptor triggers a series of reactions within the cell. These reactions generate a second messenger like cyclic AMP (cAMP) which starts changes e.g., changes in gene expression. The pathway can lead to changes in metabolism, cell growth, division, or apoptosis.

Steroid Signalling. Steroid hormones, being lipophilic, can diffuse through the plasma membrane of the target cell. Once inside, they bind to specific intracellular receptors located in the cytoplasm or nucleus. This binding results in the formation of an active receptor-hormone complex which moves into the nucleus if it was not already there. Inside the nucleus, the receptor-hormone complex binds to specific DNA sequences in target genes. This binding regulates the transcription of these genes, leading to increased or decreased production of specific proteins.

You know that the movement of substances in and out of cells is crucial for cellular functions. These movements are done for nutrient uptake, waste elimination, gas exchange, and signal transduction. Cells rely on the plasma membrane for regulating the movement of substances in and out of the cell. Membrane transport mechanisms are essential processes that enable the cell to maintain homeostasis, acquire nutrients, remove waste products, and communicate with its environment. While exchanging matter with the cells' environment, plasma membranes maintain equilibrium inside the cell as well as outside. These mechanisms include two mechanisms i.e., passive transport (which requires no energy input) and active transport (which utilizes energy).

Passive Transport. The movement of molecules across the plasma membrane without any expenditure of energy is called passive transport. The following are the types of passive transport.

Diffusion. Diffusion is the net movement of a substance (liquid or gas) from an area of higher concentration to one of lower concentration i.e., along the concentration gradient. Because a cell does not expend energy when molecules diffuse across its membrane, the diffusion of molecules is a type of passive transport.

Facilitated Diffusion. Some molecules are taken into or out of the cells with the help of transport-proteins present in the plasma membranes. When a transport protein helps a substance to move down its concentration gradient (from higher to lower concentration), the process is called facilitated diffusion. It is also a type of passive transport because no energy is used in facilitated diffusion. The rate of facilitated diffusion depends on how many transport-protein molecules are available in the membrane. The main types of transport proteins involved in facilitated diffusion are: 1. Channel Proteins: These proteins form hydrophilic channels across the membrane that allow specific molecules or ions to pass through. They can be gated or non-gated. Gated channels open or close in response to specific stimuli (such as voltage changes, ligand binding, or mechanical stress). Examples include ion channels (allow the passage of specific ions e.g., Na⁺, K⁺, Ca²⁺, Cl⁻) and aquaporins (facilitate the rapid transport of water molecules). 2. Carrier Proteins (Transporters): These proteins bind to the specific molecule they transport, undergo a conformational change, and move the molecule across the membrane. They are highly specific for the molecule they transport. They can become saturated, meaning there is a maximum rate of transport when all carrier proteins are occupied. Examples include glucose transporters (facilitate the transport of glucose) and amino acid transporters (transport specific amino acids into or out of the cell).

Osmosis. The process by which water molecules diffuse across a cell membrane from an area of higher concentration to an area of lower concentration is called osmosis. Because water is moving from a higher to lower concentration, osmosis does not require cells to expend energy. Therefore, osmosis is the passive transport of water. The direction of osmosis depends on the concentration of solutes on the two sides of the membrane. Water always moves from a hypotonic solution (with lower solute concentration) to a hypertonic solution (with higher solute concentration). The term tonicity refers to the relative concentration of solutes in the solutions. Hypertonic solutions are those in which more solute is present. Hypotonic solutions are those with less solute. Isotonic solutions have equal concentrations of solutes. Osmosis occurs through a selectively permeable membrane, which allows water to pass while restricting many solutes. Osmosis is crucial for maintaining cell turgor, which is vital for plant cells, and for balancing the internal water content in cells. The direction and rate of osmosis are influenced by the osmotic gradient and the permeability of the membrane to water. Specialized proteins called aquaporins facilitate the rapid transport of water molecules across the cell membrane, ensuring efficient regulation of cellular hydration and volume.

Reverse osmosis is a widely used technology for purifying water by removing contaminants and impurities. Unlike natural osmosis, which moves water from a lower to a higher solute concentration, reverse osmosis applies external pressure to push water through a semi-permeable membrane from a higher to a lower solute concentration. This process effectively filters out dissolved salts and other impurities, providing clean and safe drinking water. Reverse osmosis is commonly used in water treatment plants, desalination facilities, and even in household water purification systems.

Active Transport. The movement of substances across the plasma membrane from lower concentration to higher concentration with the expenditure of energy is known as active transport. The following types of active transport occur through the plasma membrane.

Active transport through carrier proteins. In this process, carrier (transport) proteins in the plasma membrane use energy to move the molecules against the concentration gradient. For example, the membranes of nerve cells have carrier proteins in the form of the "sodium-potassium pump". In a resting (not conducting nerve impulse) nerve cell, this pump spends energy (ATP) to maintain higher concentrations of K⁺ and lower concentrations of Na⁺ inside the cell. For this purpose, the pump actively moves Na⁺ to the outside of the cell and K⁺ to the inside of the cell.

Endocytosis. In endocytosis, bulky materials are moved into the cell across the plasma membrane. During endocytosis a portion of the plasma membrane invaginates (depressed inward). The material from outside is taken inside the invagination, and its ends seal. Thus, a small vesicle is formed. It detaches from the plasma membrane and moves into the cytoplasm. The two common forms of endocytosis are phagocytosis and pinocytosis. In phagocytosis the cell takes in solid material while in pinocytosis the cell takes in liquids in the form of droplets. Receptor-mediated endocytosis: Specific receptor proteins of the plasma membrane pick up material from outside and pinch inside to form a vesicle. For example, the cells of the liver have receptor proteins for cholesterol. Cholesterol circulates in our blood in the form of low-density-lipoproteins (LDLs). The receptor proteins of the plasma membrane of liver cells recognize and take up LDLs from the blood by receptor-mediated endocytosis.

Exocytosis. It is the process through which bulky material is exported out of the cell. In exocytosis, the bulky material is packed inside a membrane and a vesicle is formed. The vesicle moves to the plasma membrane and fuses with it to release its contents into the extracellular environment.

Stem cells are unique cells with the remarkable ability to develop into many different cell types in the body. When a stem cell divides, each new cell has the potential either to remain a stem cell or to become a specialized cell, such as a muscle cell, a red blood cell, or a brain cell.

Major categories of stem cells on the basis of the number of types of cells which they can make: 1. Totipotent: These stem cells can differentiate into all possible cell types. For example, the zygote and the cells produced by the first few divisions in the zygote. 2. Pluripotent: These cells can turn into almost any cell. For example, cells from the early embryo. 3. Multipotent: These cells can differentiate into a closely related family of cells. For example, the hematopoietic stem cells can become red and white blood cells or platelets. 4. Oligopotent: These can differentiate into a few different cell types. For example, adult lymphoid or myeloid stem cells. 5. Unipotent: These only produce cells of one kind, which is their own type. However, they are still stem cells because they can renew themselves. For example, adult muscle stem cells.

Use of Stem Cells. 1. Regenerative Medicine: Stem cells have the potential to repair or replace damaged tissues and organs. Therefore, they are used for treating conditions such as spinal cord injuries, type 1 diabetes, Parkinson's disease, and heart disease. 2. Drug Testing and Development: By differentiating stem cells into specific cell types, researchers can create models of human diseases, allowing for more accurate testing of drug effects and reducing the reliance on animal models. 3. Personalized Medicine: Stem cells can be derived from a patient's own cells, reducing the risk of immune rejection when used in treatments. This personalized approach can lead to more effective and safer therapies.

Categories of Stem Cells on the basis of their origin: 1 — Embryonic Stem Cells (ESCs): ESCs are derived from the inner cell mass of blastocysts (early-stage embryos). These stem cells are pluripotent, meaning they can differentiate into nearly all cell types in the body. They have high differentiation potential, making them extremely versatile for research and therapy. Ethical concerns of using ESCs include the use of human embryos, risk of teratoma formation, and potential immune rejection. 2 — Adult Stem Cells (ASCs): These stem cells are found in various tissues throughout the body, such as bone marrow, fat, and blood. They are multipotent, meaning they can differentiate into a limited range of cell types related to their tissue of origin. Using them involves less ethical controversy, lower risk of immune rejection when derived from the patient's own tissues. However, they have limited differentiation potential and are harder to isolate and culture. 3 — Induced Pluripotent Stem Cells (iPSCs): They are generated in the lab by reprogramming adult somatic cells to a pluripotent state using specific transcription factors. They are pluripotent, similar to embryonic stem cells.

Advantages of using iPSCs: They do not have the ethical controversies linked to embryonic stem cells, as they do not require the destruction of embryos. They can be generated from a patient's own cells, minimizing the risk of immune rejection. They offer potential for regenerating damaged tissues and organs (e.g., new heart cells for patients with heart disease or new neurons for patients with neurodegenerative conditions).

Disadvantages of using iPSCs: The reprogramming process can introduce genetic changes that may affect iPSCs. They could form tumours (teratomas) when transplanted into patients. Directing iPSCs to differentiate into specific, fully functional cell types remains a complex task. It is still difficult to ensure that these cells function properly.