1. MWENGE UNIVERSITY COLLEGE OF EDUCATION (MWUCE) CYTOLOGY AND CELL PHYSIOLOGY BIO 103
Unit Module Instructor: Martin Muthee
2014/ 2015

2. CYTOLOGY AND CELL PHYSIOLOGY What is cytology? - Cytology is the branch of biology that deals with the formation, structure, function, multiplication and life history of cells. Cells are complex systems of molecules capable of carrying out all the interactions of life including growth, reproduction, response to outside stimuli and movement. - A cell is an organized independent mass of protoplasm (nucleus and cytoplasm) which makes the basic primary structure of an organism. What is cell physiology? The term ―physiology‖ refers to all the normal functions that take place in a living organism. Physiology is therefore the study of how organisms and their parts work or function. There are many branches of physiology, e.g. cell physiology which is the scope of this course, plant physiology, invertebrate physiology, neurophysiology (working of nervous system) cardiac physiology (working of the heart) etc. Cell physiology: Is the biological study of the cell‘s mechanism and interaction in its environment. Cellular physiology include the study of the mechanism division and self-regulation, transport of nutrients, ions, and water into and out of the cell, as well as how cells communicate with each other through signaling pathways, or respond to external cues. It is the ―inner life of a cell‖. - Absorption of water by roots, production of food in the leaves, and growth of shoots towards light are examples of plant physiology - The heterotrophic metabolism of food derived from plants and animals and the use of movement to obtain nutrients are characteristics of animal physiology. Some of the cell physiological processes
 Movement of proteins - the movement of proteins about the cell for use in structure and enzymatic processes
 Active and passive transport - the processes facilitating the movement of molecules into and out of the cell
 Autophagy – the process whereby cells ―eat‖ their own internal components or microbial invaders
 Adhesion - the chemical processes whereby cells and other tissues are held together
 Cell division - a eukaryotic cell process resulting in formation of daughter cells. There are two major types; mitosis and meiosis.

3.  Cell movement – Chemotaxis (is chemically prompted taxis, in which somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment.), contraction, use of cilia and flagella.
 Cell signaling - regulation of cell behavior by signals from outside, such as the use of hormones and neurotransmitters.
 Metabolism- Glycolysis, respiration and photosynthesis- processes whereby energy is stored and/or liberated for use by cell.
CELL CONCEPT One of the most important concepts in biology is that a cell is the basic structural and functional unit of living organism. All organisms are composed of structural and functional units of life called ‗cells‘. The body of some organisms like bacteria, protozoan and some algae is made up of a single cell while the body of fungi, plants and animals are composed of many cells. Human body is built of about one trillion cells. Cells vary in size and structure as they are specialized to perform different functions. But the basic components of the cell are common to all cells. The cell theory In 1838 M.J. Schleiden a Belgian Botanist and T. Schwann a German Zoologist formulated the ―cell theory.‖ Also known as the cell doctrine. The cell theory states that:
 All organisms are composed of cells.
 Cell is the structural and functional unit of life, and
 Cells arise from pre-existing cells.
The cell theory, in its modern form, includes the following additional three principles:
 Cells contain hereditary information which is passed from cell to cell during cell division
 All cells are basically the same in chemical composition
 All energy flow (metabolism and biochemistry) of life occur within cells
THE CELL A cell may be defined as a unit of protoplasm bounded by a plasma membrane, cell membrane or plasmalemma. Protoplasm is the life giving substance and includes the cytoplasm and a nucleus. The cytoplasm has in it organelles such as ribosomes, mitochondria, golgi bodies plastids, lysosomes and endoplasmic reticulum. Plant cells have in their cytoplasm large vacuoles containing non-living inclusions like crystals, pigments etc. The bacteria have neither organelles nor a well formed nucleus. But every cell has three major components:

4.  Plasma membrane
 cytoplasm
 DNA (naked in bacteria and covered by a membrane in all other organisms)
Why Aren’t Cells Larger? Cells are, with a few notable exceptions small with length measured in micrometers (μm, where 1000 μm =1mm) read about the discovery of cell and the people involved in pg. 4. Most cells are not large for practical reasons. The most important of these is communication. The different regions of a cell need to communicate with one another in order for the cell as a whole to function effectively. Proteins and organelles are being synthesized, and materials are continually entering and leaving the cell. All of these processes involve the diffusion of substances at some point, and the larger a cell is, the longer it takes for substances to diffuse from the plasma membrane to the center of the cell. For this reason, an organism made up of many relatively small cells has an advantage over one composed of fewer, larger cells. The advantage of small cell size is readily visualized in terms of the surface area-to-volume ratio. As a cell‘s size increases, its volume increases much more rapidly than its surface area. For a spherical cell, the increase in surface area is equal to the square of the increase in diameter, while the increase in volume is equal to the cube of the increase in diameter. Thus, if two cells differ by a factor of 10 cm in diameter, the larger cell will have 102, or 100 times, the surface area, but 103, or 1000 times, the volume, of the smaller cell (figure 5.4).

5. Surface area-to-volume ratio: As a cell gets larger, its volume increases at a faster rate than its surface area. If the cell radius increases by10 times, the surface area increases by 100 times, but the volume increases by 1000 times. A cell’s surface area must be large enough to meet the needs of its volume. A cell‘s surface provides its only opportunity for interaction with the environment, as all substances enter and exit a cell via the plasma membrane. This membrane plays a key role in controlling cell function, and because small cells have more surface area per unit of volume than large ones, the control is more effective when cells are relatively small. Although most cells are small, some cells are nonetheless quite large and have apparently overcome the surface area-to- volume problem by one or more adaptive mechanisms. For example, some cells have more than one nucleus, allowing genetic information to be spread around a large cell. Also, some large cells actively move material around their cytoplasm so that diffusion is not a limiting factor. Lastly, some large cells, like your own neurons, are long and skinny so that any given point in the cytoplasm is close to the plasma membrane, and thus diffusion between the inside and outside of the cell can still be rapid. Slowing down metabolism: An e.g. in unfertilized chicken egg is another mechanism of overcoming this problem.

6. TWO BASIC TYPES OF CELLS Cytologists recognize two basic types of cells; prokaryotic (pro = early/primitive, karyon= nucleus) and eukaryotic (eu = true, karyon = nucleus) cells. Prokaryotic cells consist of a single closed compartment that is surrounded by the plasma membrane, lacks a true nucleus; their genetic material lies in a free region known as a nucleoid. They have a relatively simple internal organization. All prokaryotes have cells of this type. Bacteria, the most numerous prokaryotes, are single-celled organisms. Their differences have been tabulated below in on pg. 13. Organisms which do not possess a well formed nucleus and membrane-bound organelles are called prokaryote such as the bacteria. All others organisms possess a well defined nucleus, covered by a nuclear membrane and membrane-bound organelles. They are called eukaryotes. PROKARYOTIC CELLS (Bacteria Are Simple Cells) Prokaryotes, the bacteria, are the simplest organisms. Prokaryotic cells are small, consisting of cytoplasm surrounded by a plasma membrane and encased within a rigid cell wall, with no distinct interior compartments (figure below). A prokaryotic cell is like a one room cabin in which eating, sleeping, and watching TV all occur in the same room. Bacteria are very important in the economy of living organisms. They harvest light in photosynthesis, break down dead organisms and recycle their components, cause disease, and are involved in many important industrial processes.
 Strong cell wall
Most bacteria are encased by a strong cell wall composed of peptidoglycan,(also known as murein) which consists of a carbohydrate matrix (polymers of sugars) that is cross-linked by

7. short polypeptide units. No eukaryotes possess cell walls with this type of chemical composition. With a few exceptions like TB and leprosy-causing bacteria, all bacteria may be classified into two types based on differences in their cell walls detected by the Gram staining procedure. The name refers to the Danish microbiologist Hans Christian Gram, who developed the procedure to detect the presence of certain disease-causing bacteria. Gram-positive bacteria have a thick, single-layered cell wall that retains a violet dye from the Gram stain procedure, causing the stained cells to appear purple/violet under a microscope. More complex cell walls have evolved in other groups of bacteria. In them, the wall is multilayered and does not retain the purple dye after Gram staining; such bacteria exhibit the background red dye and are characterized as gram negative. The susceptibility of bacteria to antibiotics often depends on the structure of their cell walls. Penicillin and vancomycin, for example, interfere with the ability of bacteria to cross-link the peptide units that hold the carbohydrate chains of the wall together. Like removing all the nails from a wooden house, this destroys the integrity of the matrix, which can no longer prevent water from rushing in, swelling the cell to bursting. Cell walls protect the cell, maintain its shape, and prevent excessive uptake of water. Plants (cellulose), fungi (chitin), and most protists also have cell walls of a different chemical structure.
 Rotating Flagella
Some bacteria use a flagellum (plural, flagella) to move. Flagella are long, threadlike structures protruding from the surface of a cell that are used in locomotion and feeding. Bacterial flagella are protein fibers that extend out from a bacterial cell. There may be one or more per cell, or none, depending on the species. Bacteria can swim at speeds up to 20 cell diameters per second by rotating their flagella like screws (figure below). A ―motor‖ unique to bacteria that is embedded within their cell walls and membranes powers the rotation. Only a few eukaryotic cells have structures that truly rotate.

8.  Simple Interior Organization
If you were to look at an electron micrograph of a bacterial cell, you would be struck by the cell‘s simple organization. There are few, if any, internal compartments, and while they contain simple structures like ribosomes, most have no membrane-bounded organelles, the kinds so characteristic of eukaryotic cells. Nor do bacteria have a true nucleus. The entire cytoplasm of a bacterial cell is one unit with no internal support structure. Consequently the strength of the cell comes primarily from its rigid wall. The plasma membrane of a bacterial cell carries out some of the functions organelles perform in eukaryotic cells. When a bacterial cell divides, for example, the bacterial chromosome, a simple circle of DNA, replicates before the cell divides. The two DNA molecules that result from the replication attach to the plasma membrane at different points, ensuring that each daughter cell will contain one of the identical units of DNA. Moreover, some photosynthetic bacteria, such as cyanobacteria and Prochloron have an extensively folded plasma membrane, with the folds extending into the cell‘s interior. These membrane folds contain the bacterial pigments connected with photosynthesis. Because a bacterial cell contains no membrane-bounded organelles, the DNA, enzymes, and other cytoplasmic constituents have access to all parts of the cell. Reactions are not compartmentalized as they are in eukaryotic cells, and the whole bacterium operates as a single unit. EUKARYOTIC CELLS (have complex interiors) Eukaryotic cells are far more complex than prokaryotic cells. Eukaryotic cells contain membrane-bounded organelles that carry out specialized functions. The hallmark of the eukaryotic cell is compartmentalization. The interiors of eukaryotic cells contain numerous organelles, membrane-bounded structures that close off compartments within which multiple biochemical processes can proceed simultaneously and independently.
Plant cells often have a large membrane-bounded sac called a central vacuole, which stores proteins, pigments, and waste materials. Both plant and animal cells contain vesicles, smaller

9. sacs that store and transport a variety of materials. Inside the nucleus, the DNA is wound tightly around proteins and packaged into compact units called chromosomes. All eukaryotic cells are supported by an internal protein scaffold, the cytoskeleton. While the cells of animals and some protists lack cell walls, the cells of fungi, plants, and many protists have strong cell walls composed of cellulose or chitin fibers embedded in a matrix of other polysaccharides and proteins. This composition is very different from the peptidoglycan that makes up bacterial cell walls. The differences between prokaryotic and eukaryotic cell
CHARACTERISTIC
PROKARYOTIC CELL
EUKARYOTIC CELL
Nucleus
Distinct with well formed nuclear membrane
Absent , it is in the form of a nuclear zone called a nucleoid nuclear membrane absent
DNA
Circular DNA in cytoplasm (nucleoid)
Linear DNA bounded by a nuclear envelop
Ribosomes
80s
70s
Organelles
 Few organelles in cytoplasm
 No membrane-bound organelles such chloroplast and mitochondria.
 Many organelles in cytoplasm
 Membrane-bound organelles present
Flagella
Lack 9-2 fibrillar structure if present.
Has 9-2 fibrillar structure if present
Cytoplasmic streaming
Does not occur
May occur
Cell wall
Made of peptidoglycan
When present made up of other component but not peptidoglycan
Cell division
Occurs by binary fission
Occurs by mitosis or meiosis
Cytoplasmic streaming (Protoplasmic streaming)
Absent
May occur
Cytoskeleton
Absent
Present

10. Nucleolus
Absent
Present
Photosynthetic apparatus
May contain chlorophyll but not in chloroplast
Chlorophyll when present contained in chloroplast
Organisms
Bacteria, blue-green algae, cyanobacteria.
Protists, fungi, plants and animals
Svedberg unit: When the cell is fractionated or broken down into its components by rotating in an ultracentrifuge at different speeds the ribosomes of eukaryotic and prokaryotic sediment (settle down) at different speeds. The coefficient of sedimentation is represented in Svedberg unit and depicted as S. Let’s now examine the structure and function of the internal components of eukaryotic cells in more detail. CELL MEMBRANE. Each cell has a limiting boundary, the cell membrane, plasma membrane or plasmalemma. It is a living membrane, outermost in animal cells but next to cell wall in plant cells. It is flexible and can fold in (as in food vacuoles of Amoeba) or fold out (as in the formation of pseudopodia of Amoeba). The plasma membrane is made of proteins and lipids and several models were proposed regarding the arrangement of proteins and lipids. The lipid layer that forms the foundation of a cell membrane is composed of molecules called phospholipids. (Next chapter).

11. THE NUCLEUS: (Information center for the cell) Nucleus is the largest and most easily seen organelle within a eukaryotic cell that is not dividing. First described by the English botanist Robert Brown in 1831, nuclei are roughly spherical in shape and, in animal cells; they are typically located in the central region of the cell. In some cells, a network of fine cytoplasm filaments seems to cradle the nucleus in this position. The nucleus is the repository of the genetic information that directs all of the activities of a living cell. Most eukaryotic cells possess a single nucleus (uninucleate), although the cells of fungi and some other groups may have several to many nuclei (multinucleate) Mammalian erythrocytes (red blood cells) lose their nuclei when they mature. Many nuclei exhibit a dark staining zone called the nucleolus, which is a region where intensive synthesis of ribosomal RNA is taking place. A nucleus contain the following; chromosomes, nucleoli, nucleoplasm, (The fluid found inside the nucleus of eukaryotic cells made up of water and other dissolved substances) and nuclear membrane. Functions:
 Maintains the cell in a working order.
 Co-ordinates the activities of organelles.
 Takes care of repair work. Participates directly in cell division to produce genetically identical daughter cells, this division is called mitosis.
 Participates in production of gametes through another type of cell division called meiosis.
The Nuclear Envelope: Getting In and Out The surface of the nucleus is bounded by two phospholipid bilayer membranes, which together make up the nuclear envelope. The outer membrane of the nuclear envelope is continuous with the cytoplasm‘s interior membrane system, called the endoplasmic reticulum. Scattered over the surface of the nuclear envelope, like craters on the moon, are shallow depressions called nuclear pores. These pores form 50 to 80 nanometers apart at locations where the two membrane layers of the nuclear envelope pinch together. Rather than being empty, nuclear pores are filled with proteins that act as molecular channels, permitting certain molecules to pass into and out of the nucleus. Passage is restricted primarily to two kinds of molecules: (1) proteins moving into the nucleus to be incorporated into nuclear structures or to catalyze nuclear activities; and (2) RNA and protein-RNA complexes formed in the nucleus and exported to the cytoplasm.

12. THE ENDOPLASMIC RETICULUM: (Compartmentalizing the cell) The interior of a eukaryotic cell is packed with membranes. So thin that they are invisible under the low resolving power of light microscopes, this endomembrane system fills the cell, dividing it into compartments, channeling the passage of molecules through the interior of the cell, and providing surfaces for the synthesis of lipids and some proteins. The presence of these membranes in eukaryotic cells constitutes one of the most fundamental distinctions between eukaryotes and prokaryotes. The largest of the internal membranes is called the endoplasmic reticulum (ER). The term endoplasmic means ―within the cytoplasm,‖ and the term reticulum is Latin for ―a little net.‖ Like the plasma membrane, the ER is composed of a lipid bilayer embedded with proteins. It weaves in sheets through the interior of the cell, creating a series of channels between its folds. Of the many compartments in eukaryotic cells, the two largest are the inner region of the ER, called the cisternal space, and the region exterior to it, the cytosol. Rough ER: Manufacturing Proteins for Export The ER surface regions that are devoted to protein synthesis are heavily studded with ribosomes, large molecular aggregates of protein and ribonucleic acid (RNA) that translate RNA copies of genes into protein (we will examine ribosomes in detail later in this chapter). Through the electron microscope, these ribosome-rich regions of the ER appear pebbly, like the surface of sandpaper, and they are therefore called rough ER. The proteins synthesized on the surface of the rough ER are destined to be exported from the cell. Proteins to be exported contain special amino acid sequences called signal sequences. As a new protein is made by a free ribosome (one not attached to a membrane), the signal sequence of the growing polypeptide attaches to a recognition factor that carries the ribosome and its partially completed protein to a ―docking site‖ on the surface of the ER. As the protein is assembled it passes through the ER membrane into the interior ER compartment, the cisternal space, from which it is transported by vesicles to the Golgi apparatus. The protein then travels within vesicles to the inner surface of the plasma membrane, where it is released to the outside of the cell. Smooth ER: Organizing Internal Activities
Regions of the ER with relatively few bound ribosomes are referred to as smooth ER. The membranes of the smooth ER contain many embedded enzymes, most of them active only when associated with a membrane. Enzymes anchored within the ER, for example, catalyze the synthesis of a variety of carbohydrates and lipids. In cells that carry out extensive lipid synthesis, such as those in the testes, intestine, and brain, smooth ER is particularly abundant. In the liver, the enzymes of the smooth ER are involved in the detoxification of drugs including

13. amphetamines, morphine, codeine, and phenobarbital. Some vesicles form at the plasma membrane by budding inward, a process called endocytosis. Some then move into the cytoplasm and fuse with the smooth endoplasmic reticulum. Others form secondary lysosomes or other interior vesicles.
THE GOLGI APPARATUS: (Delivery System of the Cell) At various locations within the endomembrane system, flattened stacks of membranes called Golgi bodies occur, often interconnected with one another. These structures are named for Camillo Golgi, the nineteenth-century Italian physician who first called attention to them. The numbers of Golgi bodies a cell contains ranges from 1 or a few in protists, to 20 or more in animal cells and several hundred in plant cells. They are especially abundant in glandular cells, which manufacture and secrete substances. Collectively the Golgi bodies are referred to as the Golgi apparatus. The Golgi apparatus functions in the collection, packaging, and distribution of molecules synthesized at one place in the cell and utilized at another location in the cell. A Golgi body has a front and a back, with distinctly different membrane compositions at the opposite ends. The front, or receiving end, is called the cis face, and is usually located near ER. Materials move to the cis face in transport vesicles that bud off of the ER. These vesicles fuse with the cis face, emptying their contents into the interior, or lumen, of the Golgi apparatus. These ER-synthesized molecules then pass through the channels of the Golgi apparatus until they reach the back, or discharging end, called the trans face, where they are discharged in secretory vesicles (figure 5.16).
Proteins and lipids manufactured on the rough and smooth ER membranes are transported into the Golgi apparatus and modified as they pass through it. The most common alteration is the addition or modification of short sugar chains, forming a glycoprotein when sugars are

14. complexed to a protein and a glycolipid when sugars are bound to a lipid. In many instances, enzymes in the Golgi apparatus modify existing glycoproteins and glycolipids made in the ER by cleaving a sugar from their sugar chain or modifying one or more of the sugars. The newly formed or altered glycoproteins and glycolipids collect at the ends of the Golgi bodies, in flattened stacked membrane folds called cisternae (Latin, ―collecting vessels‖). Periodically, the membranes of the cisternae push together, pinching off small, membrane bounded secretory vesicles containing the glycoprotein and glycolipid molecules. These vesicles then move to other locations in the cell, distributing the newly synthesized molecules to their appropriate destinations. Liposomes are synthetically manufactured vesicles that contain any variety of desirable substances (such as drugs), and can be injected into the body. Because the membrane of liposomes is similar to plasma and organellar membranes, these liposomes serve as an effective and natural delivery system to cells and may prove to be of great therapeutic value. MICROBODIES: (Tiny but important) Eukaryotic cells contain a variety of enzyme-bearing, membrane-enclosed vesicles called Microbodies. Microbodies are found in the cells of plants, animals, fungi, and protists. The distribution of enzymes into microbodies is one of the principal ways in which eukaryotic cells organize their metabolism. Three main types of Microbodies are:
a) Lysosomes (lysis = breaking down; soma = body)
These are membrane-bounded digestive vesicles are also components of the endomembrane system that arise from the Golgi apparatus. They perform intracellular digestion. They contain high levels of degrading enzymes (sometimes 40 in number), which catalyze the rapid breakdown of proteins, nucleic acids, lipids, and carbohydrates. Some examples of enzymes present in the lysosomes include nucleases, proteases, lipases and carbohydrases. Throughout the lives of eukaryotic cells, lysosomal enzymes break down old organelles, recycling their component molecules and making room for newly formed organelles. For example, mitochondria are replaced in some tissues every 10 days. The digestive enzymes in lysosomes function best in an acidic environment. Lysosomes actively engaged in digestion keep their battery of hydrolytic enzymes (enzymes that catalyze the hydrolysis of molecules) fully active by pumping protons into their interiors and thereby maintaining a low internal pH. Lysosomes that are not functioning actively do not maintain an acidic internal pH and are called primary lysosomes. When a primary lysosome fuses with a food vesicle or other organelle, its pH falls and its arsenal of hydrolytic enzymes is activated; it is then called a secondary lysosome.

15. In addition to breaking down organelles and other structures within cells, lysosomes also eliminate other cells that the cell has engulfed in a process called phagocytosis (see. also Pinocytosis), a specific type of endocytosis (see chapter 6). When a white blood cell, for example, phagocytizes a passing pathogen, lysosomes fuse with the resulting ―food vesicle,‖ releasing their enzymes into the vesicle and degrading the material within. Lysosomes are called ―suicidal bags‖ as enzymes contained in them can digest the cell‘s own material when damaged or dead. Lysosomes are common in the cells of Animals, Protoctista and even Fungi, but rare in plants
NB: While lysosomes bud from the endomembrane system, other microbodies grow by incorporating lipids and protein, then dividing. Importance of intracellular digestion by the lysosomes: (i) Help in nutrition of the cell by digesting food, as they are rich in various enzymes which enable them to digest almost all major chemical constituents of the living cell. (ii) Help in defense by digesting germs, as in white blood cells. (iii) Help in cleaning up the cell by digesting damaged material of the cell. (iv) Provide energy during cell starvation by digestion of the cells own parts (autophagic, auto : self; phagos: eat up). (v) Help sperm cells in entering the egg by breaking through (digesting) the egg membrane. (vi) In plant cells, mature xylem cells lose all cellular contents by lysosome activity.

16. (vii) When cells are old, diseased or injured, lysosomes attack their cell organelles and digest them. In other words lysosomes are autophagic, i.e. self devouring.
b) Peroxisomes.
Found both in plant and animal cells. Found in the green leaves of higher plants. They participate in oxidation of substrates. One of the byproducts of the digestion is hydrogen peroxide (H2O2). Peroxisomes have developed to a point where they are able to contain that hydrogen peroxide and break it down into water (H2O) and oxygen (O2). The water is harmless to the cell and the oxygen can be used in the next digestive reaction. They are very well known for digesting fatty acids.
 They often contain a central core of crystalline material called nucleoid composed of urate oxidase crystals.
 These bodies are mostly spherical or ovoid and about the size of mitochondria and lysosomes.
 They are usually closely associated with E.R.
 They are involved in with photorespiration in plant cells.
 They bring about fat metabolism in cells.
c) Glyoxysomes
These microbodies are present in plant cells (particularly in the fat storage tissues of germinating seeds) and are morphologically similar to peroxisomes. Found in the cell of yeast and certain fungi and oil rich seeds in plants. Functionally they contain enzyme of fatty acid metabolism involved in the conversion of lipids to carbohydrates during germination. RIBOSOMES: (Sites of protein synthesis) Although the DNA in a cell‘s nucleus encodes the amino acid sequence of each protein in the cell, the proteins are not assembled there. A simple experiment demonstrates this: if a brief pulse of radioactive amino acid is administered to a cell, the radioactivity shows up associated with newly made protein, not in the nucleus, but in the cytoplasm. When investigators first carried out these experiments, they found that protein synthesis was associated with large RNA protein complexes they called ribosomes.
Ribosomes are made up of several molecules of a special form of RNA called ribosomal RNA, or rRNA, bound within a complex of several dozen different proteins. Ribosomes are among the most complex molecular assemblies found in cells. Each ribosome is composed of two subunits. The subunits join to form a functional ribosome only when they attach to another kind of RNA, called messenger RNA (mRNA) in the cytoplasm. To make proteins, the ribosome attaches to

17. the mRNA, which is a transcribed copy of a portion of DNA, and uses the information to direct the synthesis of a protein. Ribosomes are the site of protein synthesis in a cell. They are the most common organelles in almost all cells. Some are free in the cytoplasm (Prokaryotes); others line the membranes of rough endoplasmic reticulum (rough ER). They exist in two sizes: 70s are found in all Prokaryotes, chloroplasts and mitochondria, suggesting that they have evolved from ancestral Prokaryotic organisms. They are free-floating. 80s found in all eukaryotic cells – some free in the cytoplasm others attached to the rough ER (they are rather larger). So bacterial ribosomes are smaller than eukaryotic ribosomes. Also, a bacterial cell typically has only a few thousand ribosomes, while a metabolically active eukaryotic cell, such as a human liver cell, contains several million. Proteins that function in the cytoplasm are made by free ribosomes suspended there, while proteins bound within membranes or destined for export from the cell are assembled by ribosomes bound to rough ER. NB: Unlike most other organelles, ribosomes are not surrounded by a membrane and because of this some biologists prefer not to call them organelles.

18. MITOCHONDRIA: (The cell’s chemical furnaces) Mitochondria (singular, mitochondrion) are typically tubular or sausage-shaped organelles about the size of bacteria and found in all types of eukaryotic cells. Mitochondria are bounded by two membranes: a smooth outer membrane and an inner one folded into numerous contiguous (adjacent) layers called cristae (singular, crista). The cristae partition the mitochondrion into two compartments: a matrix, lying inside the inner membrane; and an outer compartment, or intermembrane space, lying between the two mitochondrial membranes. On the surface of the inner membrane, and also embedded within it, are proteins that carry out oxidative metabolism, the oxygen-requiring process by which energy in macromolecules is stored in ATP. Mitochondria are often referred to as the powerhouses of the cell, for it is within them that energy is released from organic molecules by the process of respiration (to be discussed later). They have their own DNA; this DNA contains several genes that produce proteins essential to the mitochondrion‘s role in oxidative metabolism. All of these genes are copied into RNA and used to make proteins within the mitochondrion. In this process, the mitochondria employ small RNA molecules and ribosomal components that the mitochondrial DNA also encodes. However, most of the genes that produce the enzymes used in oxidative metabolism are located in the nucleus. A eukaryotic cell does not produce brand new mitochondria each time the cell divides. Instead, the mitochondria themselves divide in two, doubling in number, and these are partitioned between the new cells. Most of the components required for mitochondrial division are encoded by genes in the nucleus and translated into proteins by cytoplasmic ribosomes. Mitochondrial replication is, therefore, impossible without nuclear participation, and mitochondria thus cannot be grown in a cell-free culture. Mitochondria are more numerous in cells that have a high energy requirement - our muscle cells contain a large number of mitochondria, as do liver, heart and sperm cells. They are surrounded by two membranes; hence the theory that they were once free-living organisms that have become mutualistic and then a part of almost every eukaryotic cell with the exception of RBC and xylem vessels. (Endosymbiotic hypothesis).

19. PLASTIDS A characteristic feature of plant cells and some algae is the presence of plastids that make or store food. Plastids are not present in animal cells. They occur in a variety of size, shape and colour. Based on this fact, there are three types of plastids.
i. Chloroplast – green
ii. Chromoplast – blue, red, red, yellow etc.
iii. Leucoplast - white or colourless
i) CHLOROPLASTS: Where Photosynthesis Takes Place
Plants and other eukaryotic organisms that carry out photosynthesis typically contain from one to several hundred chloroplasts. Chloroplasts bestow an obvious advantage on the organisms that possess them: they can manufacture their own food. Chloroplasts contain the photosynthetic pigment chlorophyll that gives most plants their green color. The chloroplast body is enclosed, like the mitochondrion, within two membranes that resemble those of mitochondria. However, chloroplasts are larger and more complex than mitochondria. In addition to the outer and inner membranes, which lie in close association with each other, chloroplasts have a closed compartment of stacked membranes called grana (singular, granum), which lie internal to the inner membrane. A chloroplast may contain a hundred or more grana, and each granum may contain from a few to several dozen disk-shaped structures called thylakoids. On the surface of the thylakoids are the light-capturing photosynthetic pigments. Surrounding the thylakoid is a fluid matrix called the stroma.

20. Like mitochondria, chloroplasts contain DNA, but many of the genes that specify chloroplast components are also located in the nucleus. Some of the elements used in the photosynthetic process, including the specific protein components necessary to accomplish the reaction, are synthesized entirely within the chloroplast.
NB: Mitochondria and chloroplast are among the most interesting cell organelles because they contain DNA (the genetic material) and ribosome (for protein synthesis) unlike all other organelles. Since chloroplasts and mitochondria contain their own DNA the hereditary molecule and also their own ribosomes, they are termed semi-autonomous organelles only because they are incapable of independent existence though they have ribosomes and DNA.
ii) Chromoplasts:
These are a second type of plastids found in some cells of more complex. Although chromoplasts are similar to chloroplasts in size, they vary considerably in shape, often being angular. They are usually yellow, orange or red in colour due to the presence of carotenoid pigments, which they synthesis and accumulate. They are most abundant in yellow, orange or some red parts of plants such as ripe tomatoes, carrots or red pepper.
iii) Leucoplasts:
Leucoplasts are a third type of plastids common to cells of higher plants. They are essentially colorless and include amyloplasts which synthesize and store starch and elaioplasts which synthesize oils. If exposed to light some leucoplasts will develop into chloroplasts and vice versa. NB: All plastids come from the division of existing plastids.

21. CENTRIOLES: (Microtubule Assembly Centers) Centrioles are barrel-shaped organelles found in the cells of animals and most protists. They occur in pairs, usually located at right angles to each other near the nuclear membranes; the region surrounding the pair in almost all animal cells is referred to as a centrosome. Although the matter is in some dispute, at least some centrioles seem to contain DNA, which apparently is involved in producing their structural proteins. Centrioles help to assemble microtubules, long, hollow cylinders of the protein tubulin. Microtubules influence cell shape, move the chromosomes in cell division, and provide the functional internal structure of flagella and cilia, as we will discuss later. Centrioles may be contained in areas called microtubule-organizing centers (MTOCs). The cells of plants and fungi lack centrioles, and cell biologists are still in the process of characterizing their MTOCs. A centriole has 9 sets of peripheral tubules but none in the centre. Each set has three tubules arranged at definite angles (Fig. below). It has its own DNA and RNA and therefore it is self duplicating.
Read about:
 Basal bodies.
 Cilia and flagella (structure and differences)

22. CYTOPLASM: An aqueous substance containing a variety of cell organelles and other structures such as insoluble wastes and storage products. The soluble part of cytoplasm forms the ‗background material‘ or ‗ground substances‘ between the cell organelles. It contains about 90% water and forms a solution which contains all the fundamental biochemical of life. Some of these are ions and small molecules in true solution; others are large molecules such as proteins which form colloidal solutions. VACUOLE Vacuole is a fluid filled sac bounded by as single membrane. Animal cells contain relatively small vacuoles, such as phagocytic vacuoles, food vacuoles, autophagic vacuoles and contractile vacuoles. Typically plant cells have one or two large vacuoles filled with fluid known as cell sap and surrounded by a membrane called tonoplast. The cell sap is a watery fluid containing water, sugar, organic acid, mineral salts, pigments and toxic substances. Functions:
1. Water generally enters the concentrated cell sap by osmosis. Osmotic uptake of water is important in cell expansion during cell growth as well as in the normal water relations of plants.
2. The vacuole sometimes contain pigments in solution e.g. anthocynins which are red, blue and purple and other related compounds which are yellow and ivory.
3. Plant vacuole sometimes contains hydrolytic enzymes and act as lysosomes. After cell death, the tonoplast loses its partial permeability and the enzymes escapes causing autolysis.
4. Vacuoles contain waste products and certain secondary products of plant metabolism such as calcium oxalate, alkaloid, and tannin which offers protection from consumption by herbivores.
5. Vacuole acts as a food storage organelle. It stores sucrose and mineral salts which can be utilized by the cytoplasm when necessary.

23. THE CYTOSKELETON: (Interior framework of the cell) Cytoskeleton is a system of protein fibers (very thin strands, like threads) in the cytoplasm of a eukaryotic cell that contributes to the structure and organization of a eukaryotic cell and gives it the capacity for direct movement. Thus the cytoplasm of all eukaryotic cells is crisscrossed by a network of protein fibers that supports the shape of the cell and anchors organelles to fixed locations. Cytoskeleton which is involved with in movement within a cell and in a cell‘s architecture, is an intricate network constructed mainly of three kinds of cytoskeletal fibers, each formed from a different kind of subunit namely; actin filaments, microtubules and intermediate filaments. How are protein filaments/fibers formed? Molecules of a single type of protein can interact to form geometrically regular assemblies. If a protein has a binding site that is complementary to a region of its own surface, it will assemble spontaneously to form a large structure. More often, an extended polymer of subunits will results, and provided that each subunit is bound to its neighbor in an identical way, the subunits in the polymer will be arranged in a helix that can be extended indefinitely. An actin filament for example is a supermolecular helix formed from units of the globular protein actin (fibrous?). Similarly, globular proteins can assemble into sheets, tubes, spheres or coils. Fibrous proteins form coiled coils by pairing of two alpha helical subunits that have a repeating nonpolar side chains.
1. Actin filaments
Actin filaments are long fibers about 7 nanometers in diameter. Each filament is composed of two protein chains loosely twined together like two strands of pearls. Each ―pearl,‖ or subunit, on the chains is the globular protein actin. Actin molecules spontaneously form these filaments, even in a test tube; a cell regulates the rate of their formation through other proteins that act as switches, turning on polymerization when appropriate. Actin filaments are responsible for

24. cellular movements such as contraction, crawling, ―pinching‖ during division, and formation of cellular extensions.
2. Microtubules.
Microtubules are hollow tubes about 25 nanometers in diameter, each composed of a ring of 13 protein protofilaments. Globular proteins consisting of dimers of alpha and beta tubulin subunits polymerize to form the 13 protofilaments. The protofilaments are arrayed side by side around a central core, giving the microtubule its characteristic tube shape. In many cells, microtubules form from MTOC (microtubule-organizing centers) nucleation centers near the center of the cell and radiate toward the periphery. They are in a constant state of flux, continually polymerizing and depolymerizing (the average half life of a microtubule ranges from 10 minutes in a nondividing animal cell to as short as 20 seconds in a dividing animal cell), unless stabilized by the binding of guanosine triphosphate (GTP) to the ends, which inhibits depolymerization. The ends of the microtubule are designated as ―+‖ (away from the nucleation center) or ―−‖ (toward the nucleation center).

25. Along with allowing for cellular movement, microtubules are responsible for moving materials and organelles within the cell itself. Special motor proteins, (to be discussed later), move cellular organelles around the cell on microtubular ―tracks.‖
Microtubules participate in a wide variety of cell activities. Most involve motion. The motion is provided by special motor proteins that use the energy of ATP to move along the microtubule (microtubular ―tracks‖).
Microtubule motors
There are two major groups of microtubule motors:
 Kinesins Move toward the + end of the microtubules (i.e. towards the cell periphery)
 Dyneins Move toward the - end (i.e. towards the cell center.)
3. Intermediate filaments.
Intermediate filaments have a diameter of about 10 nm, which is intermediate between the diameters of the two other principal elements of the cytoskeleton, actin filaments (about 7 nm) and microtubules (about 25 nm). - Which is why they are called intermediate filaments. They are the most durable element of the cytoskeleton in animal cells found in a system of tough, fibrous protein molecules twined together in an overlapping arrangement. Unlike microtubules and actin filaments, intermediate filaments are polymers of fibrous protein. In contrast to actin filaments and microtubules, the intermediate filaments are not directly involved in cell movements. Instead, they appear to play basically a structural role by providing mechanical strength to cells and tissues. Once formed, intermediate filaments are stable and usually do not break down. Intermediate filaments constitute a heterogeneous group of cytoskeletal fibers. Whereas actin filaments and microtubules are polymers of single types of proteins (actin and tubulin, respectively), intermediate filaments are composed of a variety of proteins that are expressed in different types of cells. More than 50 different intermediate filament proteins have been identified and classified into six groups based on similarities between their amino acid sequences.

26. The most common type, composed of protein subunits called vimentin, provides structural stability for many kinds of cells. Keratin, another class of intermediate filament, is found in epithelial cells (cells that line organs and body cavities) and associated structures such as hair and fingernails. The intermediate filaments of nerve cells are called neurofilaments. The cytoskeleton provides an interior framework that supports the shape of the cell, stretching the plasma membrane much as the poles of a circus tent. Changing the relative length of cytoskeleton filaments allows cells to rapidly alter their shape, extending projections out or folding inward. Within the cell, the framework of filaments provides a molecular highway along which molecules can be transported.
FIGURE Molecules that make up the cytoskeleton. (a) Actin filaments. Actin filaments are made of two strands of the fibrous protein actin twisted together and usually occur in bundles. Actin filaments are ubiquitous, although they are concentrated below the plasma membrane in bundles known as stress fibers, which may have a contractile function. (b) Microtubules. Microtubules are composed of 13 stacks of tubulin protein subunits arranged side by side to form a tube. Microtubules are comparatively stiff cytoskeletal elements that serve to organize metabolism and intracellular transport in the nondividing cell. (c) Intermediate filaments. Intermediate filaments are composed of overlapping staggered tetramers of protein. This molecular arrangement allows for a ropelike structure that imparts tremendous mechanical strength to the cell

27. CELL SURFACE SPECIALIZATION: MATRIX BETWEEN ANIMAL CELLS, CELL TO CELL JUNCTION Communication between cells: Communication between cells is common in nature. Cell signaling occurs in all multicellular organisms, providing an indispensable mechanism for cells to influence one another. The cells of multicellular organisms use a variety of molecules as signals, including not only peptides, but also large proteins, individual amino acids, nucleotides, steroids and other lipids. Some of these molecules are attached to the surface of the signaling cell; others are secreted through the plasma membrane or released by exocytosis. Any given cell of a multicellular organism is exposed to a constant stream of signals. At any time, hundreds of different chemical signals may be in the environment surrounding the cell. However, each cell responds only to certain signals and ignores the rest (figure below), like a person following the conversation of one or two individuals in a noisy, crowded room. How does a cell ―choose‖ which signals to respond to? Located on or within the cell are receptor proteins, each with a three-dimensional shape that fits the shape of a specific signal molecule. When a signal molecule approaches a receptor protein of the right shape, the two can bind. This binding induces a change in the receptor protein‘s shape, ultimately producing a response in the cell. Hence, a given cell responds to the signal molecules that fit the particular set of receptor proteins it

28. Cell Signaling: Four kinds of cell signaling. Cells communicate in several ways. (a) Two cells in direct contact with each other may send signals across gap junctions. (b) In paracrine signaling, secretions from one cell have an effect only on cells in the immediate area. (c) In endocrine signaling, hormones are released into the circulatory system, which carries them to the target cells. (d) Chemical synaptic signaling involves transmission of signal molecules, called neurotransmitters, from a neuron over a small synaptic gap to the target cell.
The area of cell surface receptors and signaling is a wide one which will not be dealt with in this course; instead our focus will be on the junction between cells. Multicellular organisms have many advantages over single celled organisms, but certainly one of the major advantages is that in a co-operative “family” of cells, each is free to specialize in ways that would be impossible if each cell had to live alone. It is customary for groups of specialized cells to be organized into tissues, which can, in turn, be further organized in to organs and organ systems. This kind of association and co-operativity requires that similar cells be held together in close and direct physical contact with one another. Neighbors must not only work together, they must be joined together.

29. There are two major ways in which cells in tissues can be held together; an extracellular matrix of macromolecules can form a lattice-work that can then be used by the associated cells to move, change position and a framework in which cells can interact with one another, and cell junctions can create firm, direct, specialized points of fusion between two cells in direct physical contact. Junctions between Cells: A cell junction is a structure that exists within the tissue of many multicellular organisms, including humans. Cell junctions consist of protein complexes that provide contact between neighboring cells or between a cell and the extracellular matrix. The space between cells created by cell junctions is known as the paracellular space and serves an important role in numerous forms of cell-cell communication and transport. Cell junctions are especially abundant in epithelial tissues, like skin. Junctions between cells most occur on or very near the cell's plasma membrane, but can also involve the tiny space between cells and sometimes the layer of cytoplasm that lies just below the plasma membrane. There are many way of classifying junctions, we can for example categorize cell depending on the function they serve. i.e.; communicating junctions; these types of junctions usually help small molecules pass from one cell to the next; Impermeable junctions; these junctions hold cells in contact with their neighbors, but prevent them from sharing their contents and adhering junctions; a simple, mechanical fastening between two cells. Four kinds of junctions occur in vertebrates:
1. Tight junctions
Tight junctions, or zonula occludens/ occluding junctions, are structures joining the membranes of two cells to form a barrier that is nearly impermeable to fluid. Tight junctions are composed of a branching network of sealing strands, with each strand formed from a row of transmembrane proteins embedded in the plasma membranes of adjacent cells, linking the cells by way of extracellular domains. Although tight junctions are comprised of many proteins, the major components are the claudins and the occludins. These associate with intracellular proteins that anchor the sealing strands to the actin cytoskeleton. Tight junctions connect the plasma membranes of adjacent cells in a sheet, preventing small molecules from leaking between the cells and through the sheet (figure below). This allows the sheet of cells to act as a wall within the organ, keeping molecules on one side or the other. Tight junctions are common in epithelial tissues, e.g. the epithelial cells that line the small intestine in humans are arranged into a sheet of cells that separate the contents of the guts and the inner cavity of the organ that eventually empties into blood vessels. Epithelia are sheets of cells that provide the interface between masses of cells and a cavity or space (a lumen). The portion of the cell exposed to the lumen is called its apical surface. The rest of the cell (i.e., its sides and base) make up the basolateral surface.

30. Tight junctions seal adjacent epithelial cells in a narrow band just beneath their apical surface.
Functions:
Tight Junctions (TJ)/occluding junctions. In simple epithelial and endothelial cells they were shown to fulfil different functions, the most prominent being the paracellular “barrier function‖ and the ―fence function‖, which separates the apical membrane domain from the basolateral part. Additionally, tight junctions perform other vital functions including providing structural support. In addition, tight junctions act as both functional and protective barriers. As an example of a functional barrier, tight junctions maintain the polarity of cells by preventing the lateral diffusion of membrane proteins between the apical and basal surfaces, preserving the specialized functions of each. As an example of a protective barrier, tight junctions prevent the passage of

31. molecules through the space between cells. Instead, materials must enter cells first in order to pass through the tissue, providing control over the passage of substances. In this way, tight junctions play a critical role in maintaining the blood-brain barrier (BBB).
2. Adherens junctions
An adherens junction (or zonula adherens, intermediate junction) is defined as a cell junction whose cytoplasmic face is linked to the actin cytoskeleton. They are protein complexes that occur at cell–cell junctions in epithelial and endothelial tissues. They are intercellular structures that couple intercellular adhesion to the cytoskeleton thereby creating a transcellular network that coordinate the behavior of a population of cells. Adherens junctions are built primarily from cadherins, whose extracellular segments bind to each other and whose intracellular segments bind to catenins. Catenins are connected to actin filaments.

32. They regulate cytoskeletal dynamics and cell polarity. As such, they regulate a diverse range of other cellular processes next to adhesion, such as cell shape, division, growth, apoptosis and barrier function. Adherens junctions provide additional mechanical structural support between adjacent cells. For example, they hold cardiac muscle cells tightly together as the heart expands and contracts.
3. Gap junctions
A gap junction (also called communicating junctions) is a specialized cell junction that directly connects the cytoplasm of two cells. In this way, gap junctions allow various molecules and ions to pass freely between cells. A single gap junction channel is composed of two opposing connexons, also known as hemichannels, joined across the intercellular space. In vertebrates, most gap junction hemichannels are composed of a complex of six connexin proteins, each characterized by four transmembrane domains. Six connexin sub-units assemble to create one connexon, or hemichannel. Hemichannels of uniform connexin composition are called homomeric, while those with differing connexins are heteromeric. Furthermore, gap junction channels formed from two identical hemichannels are called homotypic, while those with differing hemichannels are heterotypic. Channel composition, both at the level of the individual connexin proteins and the hemichannel, influences the function of the gap junction.

33. Functions: Gap junctions serve a number of critical cellular functions. Most notably, gap junctions provide cytoplasmic channels from one cell to an adjacent cell and thus allow for direct electrical communication between cells. However, gap junctions also permit forms of chemical communication between cells through the diffusion of small-sized material. Although different connexin subunits can impart different pore sizes to a gap junction channel, large biomolecules,

34. such as nucleic acid and proteins, are too large to pass through gap junctions and are precluded from cytoplasmic transfer between cells.
Gap junctions are expressed in virtually all tissues of the body, but the role of gap junctions is most obvious for cell types that benefit from direct electrical communication, such as neurons and cardiac muscle. Gap junctions in cardiac muscle allow the cells of the heart to contract in tandem, and the smooth muscle cells responsible for the peristaltic movements of the intestine for example
Also the normal development of ovarian follicles also depends on gap-junction-mediated communication—in this case, between the oocyte and the surrounding granulosa cells. A mutation in the gene that encodes the connexin that normally couples these two cell types causes infertility.
4. Desmosomes
Desmosomes are localized patches that hold two cells tightly together. Desmosomes are attached to intermediate filaments of keratin in the cytoplasm. They are characterized by a localized patch that holds two cells tightly together. They are common in numerous epithelia including the skin and are also found in muscle tissue where they bind muscle cells to one another. They are present in tissues subject to shear or lateral stress and help tissues resist shearing forces.
The cell adhesion proteins of the desmosome - desmoglein and desmocollin - are members of the cadherin family of cell adhesion molecules. They are transmembrane proteins that bridge the space between adjacent epithelial cells by way of homophilic binding of their extracellular domains to other desmosomal cadherins on the adjacent cell.

35. .
Summary of junctions in animals:

36. Read on:
1. Hemidesmosome
2. In many plant tissues, it turns out that the plasma membrane of each cell is continuous with that of the adjacent cells. The membranes contact each other through openings in the cell wall called Plasmodesmata.

37. CELL CYCLE AND CELL DIVISION BACKGROUND: Are you aware that all organisms, even the largest, start their life from a single cell? You may wonder how a single cell then goes on to form such large organisms. Growth and reproduction are characteristics of cells, indeed of all living organisms. All cells reproduce by dividing into two, with each parental cell giving rise to two daughter cells each time they divide. These newly formed daughter cells can themselves grow and divide; giving rise to a new cell population that is formed by the growth and division of a single parental cell and its progeny. In other words, such cycles of growth and division allow a single cell to form a structure consisting of millions of cells (Refer to cell theory). One of the most important characteristics of living things therefore is the ability to replicate and pass on genetic information to the next generation. Cell division in individual bacteria and Achaea usually occurs by binary fission. Mitochondria and chloroplasts also replicate by binary fission, which is evidence of the evolutionary relationship between these organelles and prokaryotes. Cell division in eukaryotes is more complex. It requires the cell to manage a complicated process of duplicating the nucleus, other organelles and multiple chromosomes.

38. CELL CYCLE Why do cells divide? There are many reasons for this. Cells absorb and release nutrients through their membrane. The larger the cell, the harder it is to get rid of all the waste that is produced. So, if there are many small cells (more surface area) rather than one large cell, the waste can be disposed of more readily (Refer to: Why Aren’t Cells Larger?). The other 3 reasons are critical to the survival of all organisms: Growth, repair and reproduction.
 Growth: This is a result of mitosis. The more cells in an organism, the larger that organism is. Humans start off as one single cell, and by the time they are adults, they have over 10 trillion cells! This increase in the number of cells also allows for some of those cells to be specialized for various functions. This is important to the survival of many organisms.
 Repair: This too is a result of mitosis. If tissue is damaged, repair is extremely important. With some organism, they are even able to regenerate lost limbs (such as arms or tails). For us, this is important because it can repair skin, blood vessels and bones, for example. This also replaces cells that have died. You have a ―new‖ skin every 28 days! That means that the old cells died and the new ones took their place.
 Reproduction: This is a result of mitosis or meiosis, depending on the type of reproduction. There are two types of reproduction. The first type is asexual reproduction, and this is when there is only one parent. This results from normal cell division i.e. mitosis. This occurs in bacteria, protests, fungi, some plants and some animals. The offspring are genetically identical to that of the parent. The other type of reproduction is sexual reproduction. This is when the offspring have a combination of both parents DNA and is a result of meiosis.
Cell division is a very important process in all living organisms. During the division of a cell, DNA replication and cell growth also take place. All these processes, i.e., cell division, DNA replication, and cell growth, hence, have to take place in a coordinated way to ensure correct division and formation of progeny cells containing intact genomes. The sequence of events by which a cell duplicates its genome, synthesizes the other constituents of the cell and eventually divides into two daughter cells is termed as cell cycle. Although cell growth (in terms of cytoplasmic increase) is a continuous process, DNA synthesis occurs only during one specific stage in the cell cycle. The replicated chromosomes (DNA) are then distributed to daughter nuclei by a complex series of events during cell division. These events are themselves under genetic control. The increased size and more complex organization of eukaryotic genomes over those of bacteria required radical changes in the process by which the two replicas of the genome are partitioned into the daughter cells during cell division. This process called the cell cycle is divided into three parts: interphase, mitosis and cytokinesis. The first part is further divided into three phases thus cell cycle can be viewed as consisting of consisting of five phases:

39. Duration of the Cell Cycle: The time it takes to complete a cell cycle varies greatly among organisms. Cells in growing embryos can complete their cell cycle in less than 20 minutes; the shortest known animal nuclear division cycles occur in fruit fly embryos (8 minutes). Cells such as these simply divide their nuclei as quickly as they can replicate their DNA, without cell growth. Half of the cycle is taken up by S, half by M, and essentially none by G1 or G2. Because mature cells require time to grow, most of their cycles are much longer than those of embryonic tissue. Typically, a dividing mammalian cell completes its cell cycle in about 24 hours, but some cells, like certain cells in the human liver, have cell cycles lasting more than a year. During the cycle, growth occurs throughout the G1 and G2 phases (referred to as ―gap‖ phases, as they separate S from M), as well as during the S phase. The M phase takes only about an hour, a small fraction of the entire cycle.

40. Most of the variation in the length of the cell cycle from one organism or tissue to the next
occurs in the G1 phase. Some cells in the adult animals do not appear to exhibit division (e.g.,
heart cells) and many other cells divide only occasionally, as needed to replace cells that have
been lost because of injury or cell death. These cells that do not divide further exit G1 phase to
enter an inactive stage called G0 phase (Quiescent stage); of the cell cycle. Cells in this stage
remain metabolically active but no longer proliferate unless called on to do so depending on the
requirement of the organism. They may remain in this phase for days to years before resuming
cell division. At any given time, most of the cells in an animal‘s body are in G0 phase (Cell cycle
arrest). Some, such as muscle and nerve cells, remain there permanently; others, such as liver
cells, can resume G1 phase in response to factors released during injury.

41. a) Interphase: (Preparing for Mitosis)
The interphase, though called the ‗resting phase’, is a period of great cellular activity. It is the time during which the cell is preparing for division by undergoing both cell growth and DNA replication in an orderly manner. The interphase which is very important for the successful completion of mitosis is divided into three further phases: G1, S, and G2. G1 phase (first gap): This phase corresponds to the interval between mitosis and initiation of DNA replication. During G1 phase the cell is metabolically active and continuously growing but does not replicate its DNA. The cell grows in volume as it produces tRNA, mRNA, ribosomes, enzymes, and other cell component. This is therefore a period where the cell grows and develops. Since some cells divide more actively than others, the time spent in the G1 phase will greatly vary from cell to cell. There is no division that takes place in this phase; just growth and development. Metabolic changes prepare the cell for division. At a certain point - the restriction point, the cell is committed to division and moves into the S phase. S phase (synthesis): The S phase, short for synthesis phase, is a period in the cell cycle during interphase, between G1 phase and the G2 phase. In this phase DNA synthesis or replication occurs. During this time the amount of DNA per cell doubles. If the initial amount of DNA is denoted as 2C then it increases to 4C. However, there is no increase in the chromosome number; if the cell had diploid or 2n number of chromosomes at G1, even after S phase the number of chromosomes remains the same, i.e., 2n. Each chromosome replicates to produce two sister chromatids, which remain attached to each other at the centromere. The centromere is a point of constriction on the chromosome, containing a specific DNA sequence to which is bound a disk of protein called a kinetochore. This disk functions as an attachment site for fibers that assist in cell division. Each chromosome‘s centromere is located at a characteristic site. This replication is important, because it allows there to be two full sets of DNA in each of the new cells, at the end of the division.
G2 phase (second gap): During this phase, metabolic changes assemble the cytoplasmic materials necessary for mitosis and cytokinesis. Organelles and other material required for cell

42. division are replicated or formed. For example, the centrioles in animal cells replicate themselves, to form 2 pairs. During the G2 phase, proteins are synthesized in preparation for mitosis while cell growth continues. An example is the proteins that will be used in the formation of microtubules. b) M Phase (Mitosis phase) This is the most dramatic period of the cell cycle, involving a major reorganization of virtually all components of the cell. Since the number of chromosomes in the parent and progeny cells is the same, it is also called as equational division. Mitosis is a form of eukaryotic cell division that produces two daughter cells with the same genetic component as the parent cell. Chromosomes replicated during the S phase are divided in such a way as to ensure that each daughter cell receives a copy of every chromosome. The M Phase represents the phase when the actual cell division or mitosis occurs. It is significant to note that in the 24 hour average duration of cell cycle of a human cell, cell division proper lasts for only about an hour. The interphase lasts more than 95% of the duration of cell cycle. The M phase is broken down into 4 sub-phases: Prophase, Metaphase, Anaphase, and Telophase. Though for convenience mitosis has been divided into four stages of nuclear division, it is very essential to understand that cell division is a progressive process and very clear-cut lines cannot be drawn between various stages Prophase: Prophase which is the first stage of mitosis follows the S and G2 phases of interphase. In the S and G2 phases the new DNA molecules formed are not distinct but interwined. During prophase, the nuclear envelope of the cell begins to break down. The centrioles, which are only present in animal cells, separate and each moves to an opposite end of the cell. As they move apart, a network of protein fibers that are made up of microtubules is left in their wake. These protein fibers are known as spindle fibers. As the centrioles take their places at opposite sides of the cell, they send out more spindle fibers. These spindle fibers seek out the sister chromatids that are present in the cell. Spindle fibers from one side of the cell attach to one of the sister chromatids. The spindle fibers from the other side of the cell attach to the other sister chromatids in the chromosome. They attach at a point called the kinetochore, which is a disk or protein that is on each side of the centromere. The spindle fibers will move the chromosomes until they are lined up at the spindle equator. At the end of this phase, the chromosomal material has condensed to form compact mitotic chromosomes. Chromosomes are seen to be composed of two chromatids attached together at the centromere.

43. Metaphase: (inclu’ Prometaphase) The complete disintegration of the nuclear envelope marks the start of the second phase of mitosis; Metaphase. By this stage, condensation of chromosomes is completed and they can be observed clearly under the microscope. This then, is the stage at which morphology of chromosomes is most easily studied. At this stage, metaphase chromosome is made up of two sister chromatids, which are held together by the centromere. Small disc-shaped structures at the surface of the centromeres are called kinetochores. These structures serve as the sites of attachment of spindle fibres to the chromosomes that are moved into position at the centre of the cell. Hence, the metaphase is characterized by all the chromosomes coming to lie at the equator with one chromatid of each chromosome connected by its kinetochore to spindle fibres from one pole and its sister chromatid connected by its kinetochore to spindle fibres from the opposite pole The plane of alignment of the chromosomes at metaphase is referred to as the metaphase plate. The key features of metaphase are:
 Spindle fibres attach to kinetochores of chromosomes.
 Chromosomes are moved to spindle equator and get aligned along metaphase plate through spindle fibres to both poles.

44. Anaphase: Of all the stages of mitosis, anaphase is the shortest and the most beautiful to watch. It starts when the centromeres divide. Each centromere splits in two, freeing the two sister chromatids from each other. The centromeres of all the chromosomes separate simultaneously, but the mechanism that achieves this synchrony is not known. The sister chromatids of each chromosome are pulled apart and moves away from the equatorial plate, to the opposite ends of the cell, pulled by spindle fibres attached to the kinetochore regions. These separated sister chromatids are known from this point forward as daughter chromosomes. This process is critical, because it ensures that the soon to be daughter cells will each have full, identical sets of chromosomes, also being identical to the parent cell. (NB: It is the alignment and separation in metaphase and anaphase that is important in ensuring that each daughter cell receives a copy of every chromosome.) As each chromosome moves away from the equatorial plate, the centromere of each chromosome is towards the pole and hence at the leading edge, with the arms of the chromosome trailing behind. Thus, anaphase stage is characterized by the following key events:
 Centromeres split and chromatids separate.
 Chromatids move to opposite poles.
Telophase: This is the final stage of mitosis, and a reversal of many of the processes observed during prophase. The nuclear membrane reforms around each set of sister chromatids, which can now be called chromosomes because each has its own centromere. The chromosomes soon begin to uncoil into the more extended form that permits gene expression. One of the early group of genes expressed are the rRNA genes, resulting in the reappearance of the nucleolus. This is the stage which shows the following key events:
 Chromosomes cluster at opposite spindle poles and their identity is lost as discrete elements.
 Nuclear envelope assembles around the chromosome clusters.
 Nucleolus, golgi complex and ER reform.

45. c) Cytokinesis. This is the final cellular division to form two new cells. Mitosis accomplishes not only the segregation of duplicated chromosomes into daughter nuclei (karyokinesis), but the cell itself is divided into two daughter cells by a separate process called cytokinesis at the end of which cell division is complete. In an animal cell, this is achieved by the appearance of a cleavage furrow in the plasma membrane. The furrow gradually deepens and ultimately joins in the centre dividing the cell cytoplasm into two. Plant cells however, are enclosed by a relatively inextensible cell wall; therefore they undergo cytokinesis by a different mechanism. Cytokinesis in plant cells, which have cell walls, is markedly different. There is no cleavage furrow. Instead, during telophase, vesicles derived from the Golgi apparatus move along microtubules to the middle of the cell, where they coalesce, producing a cell plate that represents the middle lamella between the walls of two adjacent cells. Cell wall materials carried in the vesicles collect in the cell plate as it grows. The cell plate enlarges until its surrounding membrane fuses with the plasma membrane along the perimeter of the cell. Two daughter cells result, each with its own plasma membrane. Meanwhile, a new cell wall arising from the contents of the cell plate has formed between the daughter cells. At the time of cytoplasmic division, organelles like mitochondria and plastids get distributed between the two daughter cells. In some organisms karyokinesis is not followed by cytokinesis as a result of which multinucleate condition arises leading to the formation of syncytium (e.g., diagrammatic liquid endosperm in coconut).

46. Significance of Mitosis: Mitosis or the equational division is usually restricted to the diploid cells only. However, in some lower plants and in some social insects haploid cells also divide by mitosis. It is very essential to understand the significance of this division in the life of an organism. Mitosis results in the production of diploid daughter cells with identical genetic complement usually. The growth of multicellular organisms is due to mitosis. Cell growth results in disturbing the ratio between the nucleus and the cytoplasm. It therefore becomes essential for the cell to divide to restore the nucleo-cytoplasmic ratio. A very significant contribution of mitosis is cell repair. The cells of the upper layer of the epidermis, cells of the lining of the gut, and blood cells are being constantly replaced. Mitotic divisions in the meristematic tissues – the apical and the lateral cambium, result in a continuous growth of plants throughout their life.

47. Meiosis (The Germ Cell Cycle/ reduction division) The production of offspring by sexual reproduction includes the fusion of two gametes, each with a complete haploid set of chromosomes. Gametes are formed from specialized diploid cells. This specialized kind of cell division reduces the chromosome number by half results in the production of haploid daughter cells (hence the name reduction division). This kind of division is called meiosis or germ cell cycle. Meiosis ensures the production of haploid phase in the life cycle of sexually reproducing organisms whereas fertilization restores the diploid phase.

48. We come across meiosis during gametogenesis in plants and animals. This leads to the formation of haploid gametes. The key features of meiosis are as follows:
 Meiosis involves two sequential cycles of nuclear and cell division called meiosis I and meiosis II but only a single cycle of DNA replication. The two are preceded by an interphase phase which is much the same as interphase for somatic cells. Germ cells are growing; chromosomes are replicating.
 Meiosis I is initiated after the parental chromosomes have replicated to produce identical sister chromatids at the S phase.
 Meiosis involves pairing of homologous chromosomes and recombination between them.
 Four haploid cells are formed at the end of meiosis II.
Meiotic events can be grouped under the following phases:
Meiosis I:
Prophase I: Prophase of the first meiotic division is typically longer and more complex when compared to prophase of mitosis. It has been further subdivided into the following five phases

49. based on chromosomal behaviour i.e., Leptotene, Zygotene, Pachytene, Diplotene and Diakinesis.
 Leptotene: chromosomes start to condense and become gradually visible under the light microscope. The compaction of chromosomes continues throughout leptotene.
 Zygotene: Chromosomes start pairing together, such a paired chromosomes are called homologous chromosomes and become closely associated (synapsis) to form pairs of chromosomes (bivalents) consisting of four chromatids (tetrads).
 Pachytene: This stage is characterized by the appearance of recombination nodules the site at which crossing over between non-sister chromatids of the homologous chromosomes occurs. Crossing over is the exchange of genetic material between two homologous chromosomes. Crossing over leads to recombination of genetic material on the two chromosomes. Recombination between homologous chromosomes is completed by the end of pachytene, leaving the chromosomes linked at the sites of crossing over.
 Diplotene: Homologous chromosomes start to separate but remain attached by chiasmata (the sites of crossovers). In oocytes of some vertebrates, diplotene can last for months or years.
 Diakinesis: Homologous chromosomes continue to separate, and chiasmata move to the ends of the chromosomes. During this phase the chromosomes are fully condensed and the meiotic spindle is assembled to prepare the homologous chromosomes for separation. By the end of diakinesis, the nucleolus disappears and the nuclear envelope also breaks down. Diakinesis represents transition to metaphase
Metaphase I: The bivalent chromosomes align on the equatorial plate. The spindle apparatus forms from opposite ends of the cell. The spindle apparatus then sends out spindle fibers to attach to the chromosomes. However, since the homologous chromosomes are lined up side by side for crossing over, they are tightly held together. Therefore, the spindle fibers are only able to make contact with the kinetochore on the sister chromatid that is facing outward in each chromosome pair. Which chromosome is oriented toward which end of the cell is a matter of chance; each pair is independent of one another.

50. Anaphase I: The attachment of the spindle fibers is complete. The homologous chromosomes are pulled apart and move towards opposite ends of the cell. The homologous chromosomes separate, while sister chromatids remain associated at their centromeres. All possible combinations of genetic material are created from the independent assortment. At this point, the sister chromatids are still attached to each other.
Telophase I: The chromosomes are now at opposite ends of the cell and begin to form two distinct chromosome clusters. At this point, nuclear division begins, and the parent cell is divided in half, forming 2 daughter cells. The nuclear membrane and nucleolus reappear, cytokinesis follows and this is called as diad of cells. Each daughter cell will have half of the original chromosomes. Each chromosome consists of 2 sister chromatids. The daughter cells now move in to the third and final phase of meiosis: meiosis II. At the end of meiosis I there are two haploid cells. Although in many cases the chromosomes do undergo some dispersion, they do not reach the extremely extended state of the interphase nucleus. The stage between the two meiotic divisions is called interkinesis and is generally short lived. Interkinesis is followed by prophase II, a much simpler prophase than prophase I.

51. Meiosis II
Meiosis II is the second division of meiosis. It occurs in both of the newly formed daughter cells
simultaneously. In contrast to meiosis I, meiosis II resembles a normal mitosis in that the sister
chromatids are separated. It consists of 4 sub-phases: Prophase II, Metaphase II, Anaphase II,
Telophase II.
Prophase II: During prophase II, the nuclear membrane disappears by the end of prophase II.
The chromosomes begin to recondense and become compact and spindle fibers begin to form
once again. These spindle fibers seek out the sister chromatids that are present in the cell.

52. Metaphase II: At this stage the chromosomes align at the equator and the microtubules from
opposite poles of the spindle get attached to the kinetochores of sister chromatids.
Anaphase II: During anaphase II, the centromere splits, freeing the sister chromatids from each
other. At this point, spindle fibers begin to shorten, pulling the newly-separated sister chromatids
towards opposite ends of the cell. Unlike the sister chromatids in mitosis, the sister chromatids in
meiosis are not genetically identical due to crossing over.
Telophase II: During Telophase II, cell division begins again in each of the two daughter cells,
creating 4 daughter cells. Each of these 4 daughter cells contains 23 chromosomes, making them
haploid, and none of the 4 is exactly alike (due to crossing over and independent assortment).

53. Significance of meiosis: Meiosis is the mechanism by which conservation of specific chromosome number of each species is achieved across generations in sexually reproducing organisms, even though the process, per se, paradoxically, results in reduction of chromosome number by half. It also increases the genetic variability in the population of organisms from one generation to the next as a result of crossing over. Variations are very important for the process of evolution. Meiosis generates genetic diversity through:
 The exchange of genetic material between homologous chromosomes during Meiosis I
 The random alignment of maternal and paternal chromosomes in Meiosis I
 The random alignment of the sister chromatids at Meiosis II
NB A checkpoint in the cell cycle is a control point where stop and go-ahead signals can regulate the cycle. (The signals are transmitted within the cell by the kinds of signal transduction pathways. Rhythmic fluctuations in the abundance and activity of cell cycle control molecules pace the sequential events of the cell cycle. These regulatory molecules are mainly proteins of two types: protein kinases and cyclins.