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Cell Biology - Subcellular organelles | 11th Biochemistry : Chapter 1 : Basic Concepts of Bio Chemistry and Cell Biology

Chapter: 11th Biochemistry : Chapter 1 : Basic Concepts of Bio Chemistry and Cell Biology

Subcellular organelles

An eukaryotic cell does not have a homogeneous internal environment.

Subcellular organelles


An eukaryotic cell does not have a homogeneous internal environment but is divided into two major compartments ,cytoplasm and nucleus and subsequently into individual compartments, each of which is surrounded by a membrane, addressed as organelles.


1. Cell Membrane


All plants, animal cells, prokaryotic cells, and fungal cells are bounded by a cell membrane, which is sometimes known as plasma membrane.


Chemical composition of Cell membrane: Cellular membranes including plasma membranes and internal membranes consist of mainly lipid, protein and water. Lipids constitute about 40 percent of the membrane composition. Lipids are complex mixtures of cholesterol and fatty acid esters, mainly in the form of glycerides and phospholipids. Glycerol is a three-carbon molecule that forms the backbone of membrane lipids. Within an individual glycerophospholipid, fatty acids are attached to the first and second carbons, and the phosphate group is attached to the third carbon of the glycerol backbone.


Lipid bilayer encircles a cell and is amphipathic with one end as a hydrophilic ‘head’ and the other end as a hydrophobic ‘tail’. Each ‘leaf ’ of the lipid bilayer has one side consisting of an array of the hydrophilic heads, while the other side consists of the hydrophobic tails. An aqueous environment causes the hydrophobic tails to aggregate, so that the hydrophobic sides of each leaf come together to form a non-ionic centre, like an oil drop in water. The hydrophilic end of the two leaves face into the ionic milieu on either side of the lipid bilayer. The lipid bilayer has the important property of fluidity which allows it to fuse with other membranes, generate new membranes by fission, and provide solvent for proteins that can reside within the layer and move around within it. It can permit water but will not permit ions, small charged molecules, and all large molecules.


The plasma membrane separates the contents of the cell from the external environment. In the unicellular organism, the ‘external environment’ is the exterior world; for a multicellular organism, it is both the exterior world outside the organism as well as the interior world created by other cells. For this process of division of a pre-existing cell, a cell must carry within it the information for reproducing all its components. The form of this information is a single type of genetic material, DNA, which codes for all the proteins of the cell.


Functions of cell membrane


·     It serves to keep all the component parts of the cell together in one place.


·     It regulates the continuous movement of substances into and out of the cell.


·     It can serve as a base of attachment for the cytoskeleton in some organisms and the cell wall in others. Thus, the cell membrane also serves to maintain its shape.


·     It can regulate the cell growth through the balance of endocytosis and exocytosis.


·     It can maintain the concentration of water, inorganic ions and organic molecules between the cell and the environment.


·     The plasma membrane also receives signals and coordinates molecular interactions at the surface such as cell to cell recognition, adhesion and communication.


2. Cell wall


The cell wall is a non-living rigid structure that forms an outer covering for the plasma membrane of fungi and plants. Cell wall not only gives shape to the cell and protects the cell from mechanical damage and infection, it also helps in cell-to-cell interaction and provides a barrier to undesirable macromolecules.


Bacterial cell wall:


Bacteria have a cell wall, which is a rigid, carbohydrate-containing structure that surrounds the bacterial cell. However, the genus Mycoplasma, do not have cell wall. The cell wall provides the bacteria with several benefits including protection of the bacterium from damage by encircling it with a tough, rigid structure. This structure is also porous. Small molecules are able to freely pass through the cell wall to the membrane, but large molecules are excluded. By performing this function, the cell wall acts as a coarse filter. The primary function of the cell wall, however, is to maintain the cell shape and prevent bursting due to osmotic pressure (called lysis).


Plant cell wall


Algae have cell wall, made of cellulose, galactans, mannans and minerals like calcium carbonate, while in other plants it consists of cellulose, hemicellulose, pectins and proteins. The cell wall of a young plant cell, the primary wall is capable of growth, which gradually diminishes as the cell matures and the secondary wall is formed on the inner (towards membrane) side of the cell. The middle lamella is a layer mainly of calcium pectate which holds or glues the different neighbouring cells together. The cell wall and middle lamellae may be traversed by plasmodesmata which connect the cytoplasm of neighbouring cells.


The main functions of the cell wall are:


·     Cell wall provides structural and mechanical support.


·     Cell wall determines and maintains the shape of the plant cell and governs plant architecture


·     Cell wall resists internal turgor pressure of cell.


·     Cell wall regulates growth rate and diffusion of materials.


·     Cell wall functions as stores of carbohydrates.


·     Cell wall protects against pathogens, dehydration, and other environmental factors.


3. Nucleus


The largest organelle in the cell is nucleus which is enveloped by bound double layered nuclear membrane preserving the genetic material called chromatin. Nucleus occupies 1%-2% and 10% in yeast and animal cells respectively. The genetic material forms a mass called chromatin that is concentrated in one part of the nucleus. The outer and inner membranes are separated by lumen. The outer membrane of the nuclear envelope is continuous with the endoplasmice reticulum (ER) membrane, and the lumen of the nuclear envelope is continuous with the lumen of the ER. The inner nuclear membrane is usually supported by a network of filaments called the nuclear lamina, located in the nucleus and anchored to the inner membrane. The nucleus contains subcompartments with specialized functions and the major subcompartment in the nucleus is the nucleolus.


The pores of nuclear membranes are large enough to be completely permeable to smaller molecules, so there is no difference in the aqueous environment of the nucleus and the cytoplasm. The nucleus is considered to be the core of the cell which regulates all metabolic events.


Nuclear envelope: The nucleus is separated from the cytoplasm by a double membrane, the nuclear envelope and the two membranes separated from each other by a perinuclear space of varying width. There are little holes in the nuclear envelope called nuclear pores which help the substances to move into or out of the nucleus. DNA occupies most of the space inside a nucleus. DNA is the genetic material and provides the instructions essential for building proteins. Proteins are responsible for helping with most activities in a cell. Inside the nucleus is a round body called nucleolus, which is present in a eukaryotic cell. The nucleolus is devoid of an encircling membrane. The nucleolus produces the ribosomal subunits from proteins and ribosomal RNA, also known as rRNA. It then sends the subunits out to the rest of the cell where they combine into complete ribosomes. Ribosomes make proteins; therefore, the nucleolus plays a vital role in making proteins in the cell.


4. Mitochondria- the power houses of the cell


A cell has a compartment for energy production. It obtains energy from the food supplied by its environment. This energy then has to be converted into some form that can be distributed throughout the cell. The common solution is to store energy in the form of a common molecule that can be used whenever and wherever it is needed in the cell. The term ‘mitochondrion’ is derived from the Greek word ‘mitos’ which means ‘thread’ and ‘chondrion’ which means ‘granule’. Mitochondria is a membrane bound cellular structure and is found in most of the eukaryotic aerobic cells. Mitochondria may assume different shapes ranging from granular to filamentous depending upon the functional state of the cell. They are spherical in yeast cells, elliptical in kidney cells, elongated in liver cells and filamentous in fibroblasts. The size of the mitochondria ranges from 0.5 to 1.0 μm in diameter.

The mitochondria consist of a smooth outer membrane, which has a large number of special proteins known as the porins, separated by a space from an inner membrane. The inner membrane is thrown into folds or invagination called cristae which extend into matrix, the mitochondrial lumen. Both the membranes are separated by a clear inter membrane space. The cristae are irregularly shaped like villous and finger like projections. The membranes are made up of phospholipids and proteins.


Functions of Mitochondria


·     The mitochondria can help the living cell to convert energy supplied by the environment into ATP, the common molecule, required for chemical reactions. ATP can be generated in two pathways: in the cytosol, and in mitochondrion. First pathway exists in the cytosol of an eukaryotic cell (or within a bacterial cell) where glycolysis degrades glucose to lactate and releases two molecules of ATP.


·     Second pathway is the main source of energy production as ATP (called oxidative phosphorylation and involves the electron transport chain). Pyruvate generated from glycolysis enters the matrix (lumen) of the mitochondrion, where it is degraded and combined with coenzyme A to form acetyl CoA. The acetyl part of the acetyl CoA is then degraded to carbon dioxide by the citric acid cycle, releasing hydrogen atoms. The hydrogen atoms are used to reduce the carrier NAD+ to NADH, and then oxidation of NADH releases a proton and an electron.

·     Mitochondria  help  the  cells  to maintain proper concentration of calcium ions within the compartments of the cell.


·     Mitochondria also help in erythropoiesis and biosynthesis of hormones like testosterone and estrogen.


·     The mitochondria of liver cells have enzymes that detoxify ammonia.


·     The mitochondria also play an important role in the process of apoptosis or programmed cell death. Abnormal death of cells due to the dysfunction of mitochondria can affect the function of an organ.

·     The mitochondria are  involved in  other  cellular  activities  like signalling, cellular differentiation and cell senescence.  They  also regulate the control of cell cycle and cell growth.

·     Unlike the outer membrane, the inner membrane is strictly permeable, it is permeable only to oxygen, ATP and it also helps in regulating transfer of metabolites across the membrane.


·     The matrix of the mitochondria is a complex mixture of proteins and enzymes. These enzymes are important for the synthesis of ATP molecules, mitochondrial ribosomes, tRNAs and mitochondrial DNA.


·     Mitochondria also affect human health. Mitochondrial disorders and cardiac dysfunction also play an important role in the aging process.


5. Endoplasmic reticulum (ER):

Eukaryotic cells contain several interrelated membrane-bound compartments, collectively termed as ‘endomembrane system’ or ER.It is a continuous membrane, which is present in both plant cells, animal cells and absent in prokaryotic cells.There is a series of convoluted membrane sheets which are contiguous with the outer membrane of the nuclear envelope. This series of membrane delimited compartments in a typical eukaryotic cell are related and interact with one another by fission and fusion of their membranes. The space, which is present in the endoplasmic reticulum, is called as the lumen.


There are three morphological patterns in ER.

a.  Granular or Rough endoplasmic reticulum


b.  Smooth endoplasmic Reticulum


c.   Lamellar and Vesicular endoplasmic reticulum


The rough endoplasmic reticulum contains ribosome attached to the cytoplasmic side of the membrane and it forms a lace like system. The smooth Endoplasmic reticulum lacks the attached ribosome and it forms tubular structures.


The major functions of Endoplasmic reticulum are:


• They play a vital role in the formation of the skeletal framework

• They provide the increased surface area for cellular reactions

• They help in the formation of nuclear membrane during cell division

• They play a vital role in the synthesis of proteins, lipids, glycogen and other steroids like cholesterol, progesterone, testosterone, etc.

They are responsible for the secretion, synthesis, modification and transportation of proteins and other carbohydrates to another organelle, which includes lysosomes, Golgi apparatus, plasma membrane, etc.


6. Golgi Apparatus

Camillo Golgi (1898) had made the first report on the densely stained reticular structures near the nucleus. Hence these were later named Golgi bodies, attributed to him. They consist of many flat, disc-shaped sacs or cisternae of 0.5μm to 1.0μm diameter. These are stacked parallel to each other. Varied numbers of cisternae are present in a Golgi complex. The Golgi cisternae are concentrically arranged near the nucleus with distinct convex cis or the forming face and concave trans or the maturing face.


The cis and the trans faces of the organelle are entirely different, but interconnected. The golgi apparatus principally performs the function of packaging materials, to be delivered either to the intra-cellular targets or secreted outside the cell. Materials to be packaged in the form of vesicles from the ER fuse with the cis face of the golgi apparatus and move towards the maturing face. This explains, why the golgi apparatus remains in close association with the endoplasmic reticulum. A number of proteins synthesized by ribosomes on the endoplasmic reticulum are modified in the cisternae of the golgi apparatus before they are released from its trans face. Golgi apparatus is the important site of formation of glycoproteins and glycolipids.


Functions of Golgi apparatus


a.  Golgi apparatus helps in protein sorting from one compartment to another by the secretory pathway.


b.  Covalent modifications of proteins involving the addition of small sugar molecules occur in the ER and Golgi apparatus.


7. Ribosomes:


Ribosomes are the granular structures first observed under the electron microscope as dense particles by George Palade (1953). In the word ribosome, the pharse ‘ribo’ is derived from ribonucleic acid and ‘somes’ from the Greek word ‘soma’ which means ‘body’. Ribosomes are tiny particles about 200 Å. They are composed of ribonucleic acid (RNA) and proteins. Ribosomes are not considered as organelles because of the lack of a membrane around them. However, when they are producing certain proteins they can become bound to the endoplasmic reticulum membrane. Free floating ribosomes are also present. Ribosomes are composed of both RNA and proteins. About 37 - 62% of ribosomes are made up of RNA and the rest is proteins. There are two types of ribosomes based on their sedimentation properties. Prokaryotes possess 70 S ribosomes and Eukaryotes possess 80 S ribosomes. The subunits of ribosomes are named owning to their sedimentation rate measured as special Svedberg Unit (‘S’). The ribosomes share a core structure which is similar to all ribosomes despite differences in their size. The ribosomes are made up of two subunits - a small and a large subunit. The small subunit reads the mRNA while the large subunit joins the amino acids to form a chain of polypeptides.


Functions of ribosomes:


·     The bound and the free ribosomes are similar in structure and are involved in protein synthesis.


·     The location of the ribosomes in a cell is a determining factor of the type of protein produced. If the ribosomes are free floating throughout the cell, the proteins that are used within the cell are produced. When ribosomes are attached to endoplasmic reticulum (referred as rough endoplasmic reticulum or rough ER), the proteins that are used inside the cell or outside the cell are produced.


·     The catalytic activity of the ribosome is carried out by the RNA.

8. Lysosomes


These are membrane bound vesicular structures formed by the process of packaging in the golgi apparatus. The isolated lysosomal vesicles have been found to be very rich in hydrolytic enzymes, called hydrolases such as lipases, proteases, carbohydrases, which are optimally active at the acidic pH. These enzymes are capable of digesting carbohydrates, proteins, lipids and nucleic acids.


9. Peroxisome:


Peroxisomes are microbodies that are abundantly present in mammalian liver and kidney, and also in plant cells. It depends on the type of eukaryotic cell. The matrix of Peroxisomes is rich in enzymes but a few enzymes are located in the membrane. The common enzymes present in the matrix of peroxisomes are catalases and peroxidases which metabolize a number of substrates. Enzymes present in the membrane of peroxisomes are cytochrome b5 and NADH cytochrome b5 reductase.


Functions of peroxisomes


·     A major function of the peroxisome, in yeast and plant cells are to breakdown the  fatty acid molecules, in a process called beta-oxidation. Peroxisomes are involved in lipid biosynthesis


·     Peroxisomes contain enzymes required for the synthesis of plasmalogens


·     Peroxisomes in seeds are responsible for the conversion of stored fatty acids to carbohydrates, which is critical in providing energy and raw materials for growth of the germinating plant.


10. Cytoplasm:


The ground substance that fills the interior of the cell is called cytosol or cytoplasm. It is a jelly-like substance and it is made up of eighty percent water and is usually clear. It appears as a transparent and colourless fluid. The cytoplasm serves as a molecular soup. It is in the cytoplasm where all the cellular organelles are suspended and are bound together by a lipid bilayer membrane. The cytoskeleton present in the cytoplasm gives the cell its shape. Cytoplasm also constitutes numerous salts and is a very good conductor of electricity.


Various metabolic activities occur in the cytoplasm. Metabolic pathways like glycolysis and cellular processes like cell division take place in the cytoplasm.


·     Cytoplasm shows differential staining properties, the areas stained with the basic dyes are the basophilic areas of the cytoplasm and are termed as ergatoplasm for this material.


·     It is a heterogenous mixture of opaque granules and organic compounds which gives it its colloidal nature.


·     The cytoplasm conatains dissolved nutrients and it aids to dissolve waste products.


·     It helps movement of the cellular materials around the cell through a process called cytoplasmic streaming.


·     The peripheral zone of cytoplasm is jelly-like and is known as the plasmogel. The surrounding area of the nuclear zone is thin and liquefied in nature and is known as the plasmosol.


·     The physical nature of cytoplasm is colloidal. It has a high percentage of water and particles of various shapes and sizes are suspended in it.


·     It also contains proteins, of which 20-25 percent are soluble proteins including enzymes.


·     Also, certain amount of carbohydrates, RNAs, inorganic salts and lipid substances are found.


·     The plasmogel part of the cytoplasm is capable of absorbing water and removing it, according to the cell's need.


·     The stomatal guard cells present in the leaves exhibit this property.


·     An organized system of fibres can be observed by specific staining techniques.


11. Plastids


Plastids are found in all plant cells and in euglenoides. These are easily observed under the microscope as they are large. They bear some specific pigments, thus imparting specific colours to the plants. Based on the type of pigments

plastids can be classified into different types:


Protoplastids, Amyloplastids, Leucoplastids, Etioplasts, Chloro-amyloplasts and Chromoplasts.


•  Protoplasts contain brown carotenoids, chlorophyll a and chlorophyll c pigments


•  Amyloplasts synthesizes starch and stores them as granules in the stroma. Some types of plastids contain enzymes for the synthesis of certain small compounds.


•  The leucoplasts are the colourless plastids of varied shapes and sizes.


•  Rhodoplasts contain chlorophyll a and chlorophyll d along with phycobilin and phycoerythrin pigments.


•  Chloroplasts-occur in green plants are characterised by the presence of Chlorophyll a and Chlorophyll b.


•  Chromoplasts synthesize and store pigments called carotenoids, which are red, orange, or yellow molecules that give some flowers and fruits their colour.


12. Chloroplasts


Chloroplasts are members of a group of plant organelles collectively known as plastids. These are associated with photosynthesis. Majority of the chloroplasts of the green plants are found in the mesophyll cells of the leaves. These are lens-shaped, oval, spherical, discoid or even ribbon-like organelles having variable length (5-10 jm) and width (2-4 μm). Their number varies from 1 per cell of the Chlamydomonas, a green alga to 20-40 per cell in the mesophyll. Of the two, the inner chloroplast membrane is relatively less permeable. The space limited by the inner membrane of the chloroplast is called the stroma. A number of organised flattened membranous sacs called the thylakoids, are present in the stroma. Thylakoids are arranged in stacks like the piles of coins called grana (singular: granum) or the intergranal thylakoids. In addition, there are flat membranous tubules called the stroma lamellae connecting the thylakoids of the different grana. The membrane of the thylakoids enclose a space called a lumen. The stroma of the chloroplast contains enzymes required for the synthesis of carbohydrates and proteins. It also contains small, double-stranded circular DNA molecules and ribosomes. Chlorophyll pigments are present in the thylakoids.


The thylakoids in chloroplasts contain chlorophyll and carotenoid pigments which are responsible for trapping light energy essential for photosynthesis. Chloroplasts develop in the parts of a plant, such as leaves, in which light gathering and photosynthesis will occur. Plants that are grown in the dark do not develop chloroplasts but instead develop a different type of plastid in their leaves. Chloroplasts develop into chromoplasts when tomatoes ripen from green to red and when green leaves of deciduous trees turn redorange or yellow.


Functions of chloroplast


·     Chloroplasts function as the food producers of the cell and every green plant in the planet is working to convert the solar energy into sugars.


·     They are responsible for breaking down the nutrients and sugars that the cell receives and convert that into energy.


·     It enables a plant to make ATP from a system in which the electrons are provided by chlorophyll that have been activated by light.


13. Vacuole:


The vacuole is the membrane-bound space found in the cytoplasm. Plant cells possess a well-developed vacuolar system, which becomes more prominent in maturing cells. It is also present in the cells of animals, fungi and bacteria but they are smaller in size. In plant cells the vacuoles can occupy up to 90 percent of the volume of the cell. Vacuoles contain water, sap, excretory product and other materials not useful for the cell. The vacuole is bound by a single membrane called tonoplast. In plants, the tonoplast facilitates the transport of a number of ions and other materials against concentration gradients into the vacuole, hence, their concentration is significantly higher in the vacuole than in the cytoplasm. In Amoeba, the contractile vacuole is important for excretion. In many cells, as in protists, food vacuoles are formed by engulfing the food particles.


In plant cells, the vacuoles accumulate a high concentration of sugars and other soluble compounds. Water enters the vacuole to dilute these sugars, generating hydrostatic pressure that is counterbalanced by the rigid wall. In this way the cells of the plant become stiff or turgid, in the same way that when an inner tube is inflated inside a bicycle tyre the combination becomes stiff. Vacuoles are generally pigmented. The beautiful colors of petals and fruits are due to presence of compounds such as the purple anthocyanins in the vacuole.


Functions of vacuole:


·     Vacuoles aid in storing salts, nutrients, pigments, minerals, proteins, facilitating the growth of the plant and playing a vital structural role for the plant.


·     It serves in other functions such as protection, storage organelles for metabolites, growth and disposal of toxic excretory substances.


14. Distinguishing features of Plant and Animal Cells

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