Cell and sub-cellular organelles

1.1Cells: the basic unit of life

One of the most important ideas in biology is the cell. It is the basic unit of structure and function of living organisms. All organisms are made of cells: some have a single cell, others have many.

• Single-celled (unicellular) organisms are Amoeba, Paramecium and Euglena.
• Multicellular organisms are more complex, and include plants and animals.

Cell

The structural and functional unit of living organisms. It is the smallest unit and the building block of life.

Cells exist in various shapes and sizes and perform a wide range of activities. Their shape and size are related to the function they perform.

The seven basic properties of life

The basic properties of life are movement, respiration, homeostasis, growth, reproduction, excretion and nutrition. A single cell does all of these basic things, which is why the cell is called the basic unit of life.

1.2Cell theoryOften examined

Robert Hooke was an English scientist. In 1665 he looked at thin pieces of cork under a simple microscope. He saw that cork was made of tiny empty spaces with walls around them. Under the microscope the cork looked like honeycomb. The honeycomb spaces reminded him of small rooms called 'cells' in a monastery, so he called the spaces in the cork 'cells'. Now we know that what Hooke really saw was the thick outer walls of what was once part of a cork tree.

Schleiden was a German botanist. He examined a large variety of plant cells and concluded that cells are the ultimate units forming the structures of all plant tissue.

At the same time Schwann, a German zoologist, studied many types of animal cells. He found that animal cells lack a cell wall and are covered by a membrane. He recognised that, apart from the cell wall which is unique to plants, the inside of plant and animal cells is identical. Schleiden and Schwann compared their findings and combined their views to formulate the cell theory. Later, Rudolf Virchow (pronounced Fir-koh) observed that new cells develop by the division of pre-existing cells.

The cell theory is a fundamental concept of biology. Its three tenets (principles) are:

1. The cell is the fundamental unit of structure and function in living things.
2. All organisms are composed of one or more cells.
3. Cells arise from pre-existing cells through cellular division.

The modern cell theory

The modern iteration of the cell theory adds three more concepts:

1. Energy moves through cells.
2. DNA is transferred from cell to cell, carrying genetic information.
3. All cells share the same primary chemical makeup.

1.2.1Validation of cell theory

To validate the cell theory means to show, by experiment and observation, that it is true. The following experimental evidences support it:

1. Cells removed from tissues can survive independently for short periods of time. This supports the first tenet: the cell is the unit of life.
2. Nothing smaller than a cell has been found that is able to live independently. So the cell is the smallest unit of life.
3. Experiments by Francesco Redi and Louis Pasteur have demonstrated that cells cannot grow in sealed and sterile conditions. New cells therefore do not appear from nothing: they come from pre-existing cells (the third tenet).

1.2.2Exceptions of cell theoryOften examined

A few living things do not fit one or more tenets of the cell theory. The book lists six exceptions:

1.3MicroscopyOften examined

The discovery and study of cells progressed with the invention of microscopes. Microscopy is the technique used to view objects that cannot be seen by the naked eye.

The light microscope

The microscopes you use in the laboratory are light microscopes. They use visible light to illuminate specimens in a two-lens system. The two lenses are the ocular lens in the eyepiece and the objective lens located in the revolving nosepiece. Because it uses two lenses, the light microscope is also called a compound microscope. Its components are shown in Figure 1.2.

Working principle

Magnification

Magnification

The capacity of an optical instrument to increase the size of an object over its original size.

Objects which cannot be seen by the naked eye can be observed by increasing the magnification. Different lenses have different magnification powers, written with the letter 'X', which means the number of times larger than the original size. A lens of $10\mathrm{X}$ magnification can increase the size of an object of $1\mu \mathrm{m}$ to $10\mu \mathrm{m}$.

The total magnification is found by multiplying the objective lens value by the ocular lens value.

The maximum magnification of a light microscope is $1500\mathrm{X}$, using a $100\mathrm{X}$ objective and a $15\mathrm{X}$ ocular lens. An electron microscope can magnify specimens between 1 and 50 million times, depending on which type is used.

Resolution

Resolution

A measure of the microscope's ability to distinguish between two points which are close together on an object. A microscope that can clearly distinguish the two points has a good, or high, resolution.

Difference between magnification and resolution

1.3.1Electron microscopyOften examined

Principle of electron microscopy

It uses a beam of accelerated electrons to visualise the specimen and has a high resolution.

Working principle of the electron microscope

Types of electron microscope

There are two major types of electron microscopes: the transmission electron microscope (TEM) and the scanning electron microscope (SEM). Sometimes TEM and SEM are combined in one instrument, the scanning transmission electron microscope (STEM).

Comparison between light microscope and electron microscope

1.4Ultrastructure of animal and plant cellsOften examined

Ultrastructure

The fine structure of the cell as seen with the electron microscope.

Figure 1.6 and Figure 1.7 show what an animal cell and a plant cell look like at this level of detail. Every label here is an organelle or structure that the rest of the unit describes one by one, so use these two figures as a map of the unit.

What differs between the two cells

1.5.1Cell wallOften examined

The plasma membrane is the outer living boundary of the cell. Many cells also have an extracellular component formed outside the membrane, which is called the cell wall.

Cell wall

A secreted, porous layer outside the plasma membrane of plant cells. It protects the cell, maintains its shape and prevents excessive uptake of water.

The cell wall is present in plant cells, prokaryotes, fungi and some protists, but animal cells do not have a cell wall. This is probably due to their locomotor mode of life. The chemical composition differs from group to group:

The book discusses only the plant cell wall. It is an extracellular structure. It protects the plant cell, maintains its shape and prevents excessive uptake of water. At the level of the whole plant, the strong cell walls of specialised cells hold the plant up against the force of gravity.

The cell wall is secreted by the cell. It is porous and allows free passage of water and dissolved material. The plant cell wall consists of three main layers: the primary cell wall, the middle lamella and the secondary cell wall.

Primary cell wall

• It is a true wall and develops in newly growing cells, during cell division. Each cell produces a primary cell wall.
• It lies inner to the middle lamella.
• It is thin and slightly flexible.
• It is composed of cellulose microfibrils (bundles of cellulose chains) running through a matrix of other polysaccharides such as hemicelluloses and pectin.
• The microfibrils show a crisscross arrangement in layers one above the other. This gives the cell great strength.
• It is adapted to growth: the wall stretches plastically, that is, irreversibly.

Secondary cell wall

• It is formed between the primary cell wall and the plasma membrane, only in sclerenchyma cells. Cells with a secondary wall are generally dead and provide support for the plant.
• It develops only when the cell has reached maximum size, that is, has completed its growth, because it is very thick and rigid and so does not allow further growth.
• It consists of cellulose, hemicelluloses, lignin, inorganic salts and waxes. Its cellulose microfibrils also show a crisscross arrangement.
• Lignin cements and anchors the cellulose microfibrils together and is mainly responsible for rigidity.
• It provides definite shape and mechanical support to the cell.

Middle lamella

The middle lamella is present between the primary cell walls of adjacent cells and holds the cells together. It is composed of sticky, gel-like magnesium and calcium salts and pectin.

1.5.2Plasma membraneOften examined

The plasma membrane is also called the cell membrane. It is the boundary of the protoplasm and most organelles. It is found in all living prokaryotic and eukaryotic cells and controls the passage of materials into and out of the cell.

Composition of plasma membrane

Chemically the plasma membrane consists of proteins (60 to 80%), lipids (20 to 40%) and a small quantity of carbohydrates.

Structure of plasma membrane: the fluid mosaic model

The fluid mosaic model proposes that the membrane is a phospholipid bilayer in which protein molecules are either partially or wholly embedded. The proteins are scattered through the membrane in an irregular pattern, just like large icebergs floating in the sea. The pattern of distribution of proteins can vary from membrane to membrane and also on the two surfaces of a membrane. The membrane is about $7\mathrm{nm}$ thick.

• The lipid part consists of two layers (a bilayer) of phospholipids. They are arranged so that their hydrophobic ends face each other while their hydrophilic ends appear on the surface.
• The steroid cholesterol is wedged into the phospholipid bilayer at some intervals.
• The plasma membrane is asymmetrical: its two surfaces and halves are not identical.
• In general most membrane proteins drift sideways in the fluid bilayer. The proteins in a membrane determine most of its functions.
• Carbohydrates are attached to proteins (glycoproteins) or to lipids (glycolipids), generally on the outer side of the membrane.
• Filaments of the cytoskeleton are present on the inner surface of the membrane and support the plasma membrane.

Fluidity of the membrane

The lipid part of the plasma membrane controls its fluidity. When the concentration of unsaturated fatty acids in the phospholipids becomes greater, the bilayer becomes more fluid, which makes the cell membrane more flexible. Cholesterol helps to stabilise the lipid bilayer. It also restricts the entry and exit of polar molecules and ions.

Functions of plasma membrane proteins

A great variety of proteins is found in the plasma membrane. They may act as a transport channel or carrier, enzyme, receptor or antigen.

Roles of glycolipids and glycoproteins as cell surface markers

Mostly glycolipids and glycoproteins act as cell surface markers. They are involved in cell recognition and in sticking the correct cells together in tissues.

Regulation of the cell's interaction with its environment

The plasma membrane regulates the cell's interaction with its environment by controlling the transport of material across the cell. Transport across the plasma membrane takes place to maintain a suitable pH and ionic concentration within the cell for enzyme activity.

1.5.2Techniques used in studying the cell membrane

Biophysical imaging techniques have been developed to study biological structures such as the cell membrane. The book names three:

1.6Cell signalingOften examined

Cell signaling

The process by which cells communicate with other cells within their body or with the external environment; simply, the transfer of information from one cell to another.

Ligands and receptors

The signalling molecules are also known as ligands. They initiate signalling. Different types of molecules can serve as signalling molecules: proteins, lipids, amino acid metabolites, gases and many others.

The proteins that respond to ligands are called receptors. Signalling molecules and receptors exist in several varieties; however, a signalling molecule will bind to a specific receptor that typically binds only one type of signalling molecule.

Ligand

A signalling molecule that initiates signalling by binding to a receptor.

Receptor

A protein that responds to a ligand.

The three stages of cell signalling

1.6.1Pathway of a signal from outside to insideOften examined

Signal transduction pathway

The series of steps by which a signal on a cell's surface is converted into a specific cellular response.

The path depends on what kind of ligand carries the signal. The book describes two kinds: protein (and peptide) signals, and steroid signals.

Protein signaling

Protein and peptide hormones are water soluble, so they cannot pass through the plasma membrane. These hormones or environmental stimuli are the first messenger. They bind with their receptors on the plasma membrane of the target cell. This starts a series of events in the cell which generates a second messenger, for example cAMP (cyclic adenosine monophosphate). The second messenger then triggers various changes in the cell, including activation of enzymes and gene activation.

Steroid signaling

Small hydrophobic ligands can directly diffuse through the plasma membrane and interact with internal receptors. Important members of this class are the steroid hormones. Steroids are lipids that have a hydrocarbon skeleton with four fused rings. Steroid hormones are lipophilic (fat-loving), which means they can freely diffuse across the plasma membrane of a cell. Estrogen, progesterone and testosterone are examples of steroid hormones.

1.7Membrane transport mechanismOften examined

Cells need food materials, salts, water and oxygen. They also need to get rid of substances such as carbon dioxide. Membrane transport mechanisms control the movement of solutes such as ions and small molecules through a biological membrane.

Membrane transport depends upon the permeability, the solute concentration, and the size and charge of the solute. There are four types of transport mechanism in a cell: simple diffusion, facilitated diffusion, osmosis and active transport. Simple diffusion, facilitated diffusion and osmosis are passive transport mechanisms.

Concentration gradient

The difference in concentration between two regions.

Simple diffusionOften examined

Diffusion

The movement of molecules from a region of their higher concentration to a region of their lower concentration, down a concentration gradient.

In simple diffusion the molecules can travel directly through the membrane. Small molecules such as water, carbon dioxide and oxygen can pass through the cell membrane fairly easily. Diffusion therefore equalises the concentration of these molecules inside and outside the cell all the time.

Each type of molecule moves down its own gradient, independently of other molecules. For example, oxygen diffuses from the lungs into the blood while at the same time carbon dioxide diffuses in the opposite direction.

Facilitated diffusionOften examined

Most water-soluble molecules cannot pass through the phospholipid bilayer. For the molecules to traverse (travel across or through) the membrane they should be small and non-polar. Other molecules can diffuse across only with the help of two types of transport proteins: channel proteins and carrier proteins.

Channel proteins

Channel proteins help in the entry and exit of substances in the cell. There are two types:

• Open channel proteins create a pore in the cell membrane and allow the charged molecules to pass through.
• Gated channel proteins are either closed or open and regulate the entry and exit of substances.

Carrier proteins

Carrier proteins are present on the cell membrane. They carry the molecules, change the shape of the molecules (as the book puts it) and release the molecules to the other side. Temperature and saturation affect the carrier proteins.

Facilitated diffusion

A type of diffusion in which the molecules move from the region of higher concentration to the region of lower concentration assisted by a carrier.

Comparison between simple diffusion and facilitated diffusion

OsmosisOften examined

A semipermeable membrane is an impervious sheet perforated with tiny pores. The pores allow solvent molecules, for example water, to pass through by diffusion but not larger solute molecules such as sugar and salt. Examples are the egg membrane, parchment paper and cellophane.

Osmosis

The process by which molecules pass from a solution of low concentration to a solution of high concentration through a semipermeable membrane.

Examples of osmosis are feeling thirsty after having salty food, dialysis of the kidney, and the swelling of resins and seeds when they are soaked in water.

Active transportOften examined

Active transport

A process that involves the movement of molecules from a region of lower concentration to a region of higher concentration, against a gradient or an obstacle, with the use of external energy.

The movement of molecules or ions across a membrane from a region of lower concentration to a region of higher concentration, against a concentration gradient, is called active transport. Movement is usually in one direction only. To achieve this movement it needs cellular energy. There are two types of active transport: primary active transport and secondary active transport.

Primary active transport

The energy is supplied in the form of ATP, an energy carrier made in respiration. Without respiration, active transport is not possible. The sodium-potassium pump is an example of this transport. Cell membranes have sodium pumps that actively pump sodium ions out of the cell. In animal cells the sodium pump is coupled with a potassium pump which actively moves potassium ions from outside to inside the cell. Its importance is revealed by the fact that more than a third of the ATP is used to pump sodium and potassium.

Secondary active transport

Secondary active transport uses electrochemical energy. It takes place across a biological membrane. A transporter protein couples the movement of an electrochemical ion (typically $\mathrm{Na}{}^{+}$ or $\mathrm{H}{}^{+}$) down its electrochemical gradient to the upward movement of another molecule or ion against a concentration or electrochemical gradient.

Active transport in plants

Active transport takes place in the root cells by absorbing water and minerals. Active transport always leads to accumulation of molecules and ions towards one side of the membrane. This mode of transportation in plants is carried out by membrane proteins and transports a substance from the lower concentration to the higher concentration.

Examples of active transport

1. Phagocytosis of bacteria by macrophages.
2. Movement of $\mathrm{Ca}{}^{2+}$ ions out of cardiac muscle cells.
3. Transportation of amino acids across the intestinal lining in the human gut.
4. Secretion of proteins like enzymes, peptide hormones and antibodies from different cells.
5. Functioning of the white blood cells in protecting our body by attacking disease-causing microbes and other foreign invaders.

Passive and active transport compared

1.8.1Cytoplasm

The living matter of a cell is called protoplasm. In eukaryotic cells it can be divided into two parts, the cytoplasm and the nucleus.

Cytoplasm

The region between the nuclear membrane and the plasma membrane. It is a common component of both prokaryotic and eukaryotic cells.

Cytosol

The matrix of the cytoplasm: the water-soluble liquid phase around the organelles. The term is now used to refer to the liquid phase of the cytoplasm in an intact cell.

What the cytoplasm is made of

The cytoplasm is about 90\% water and forms a solution that contains all the fundamental biochemicals of life.

• Some are ions and small molecules in true solution: salts, sugars, amino acids, fatty acids, nucleotides, vitamins and dissolved gases.
• Others are large molecules, such as proteins, which form colloidal solutions.
• The cytosol is a complex mixture of substances dissolved in water, although water forms the large majority of it.

Functions of the cytoplasm

The cytoplasm acts as a site of metabolism and a storehouse of the cell. The metabolic pathways generally occur in the cytosol, which includes protein synthesis and glycolysis.

1.8.2Cell organellesOften examined

In a eukaryotic cell the cytoplasm contains highly organised discrete structures which are specific for various cellular functions. They are called cell organelles. The cell organelles are generally enclosed by a membrane, except a few such as the ribosome.

The organelles in the cytoplasmic matrix of a cell are: endoplasmic reticulum, ribosomes, Golgi complex, lysosomes, peroxisomes, glyoxysomes, vacuoles, mitochondria and chloroplasts, and so on. The sections that follow take them one by one (with centrioles and the nucleus at the end).

Endoplasmic reticulumOften examined

The endoplasmic reticulum (ER) is an extensive network of membrane. The word endoplasmic means 'within the cytoplasm'. The ER consists of a network of membranous tubules and sacs called cisternae (from the Latin cisterna, a reservoir of liquid). The ER membrane separates the internal compartment of the ER, called the ER lumen (cavity), from the cytosol.

There are two types of ER, smooth ER and rough ER. They differ in their structure and functions. Most cells contain both types of ER. However, some cells (skeletal muscle cells) have more smooth ER; there it is called the sarcoplasmic reticulum.

Smooth ER

The smooth ER is continuous with the rough ER. Since ribosomes are not attached to it, it has a smooth appearance. It functions in diverse metabolic processes. Enzymes of the smooth ER are important in:

• The synthesis of lipids, including oil, cholesterol, phospholipids and steroids, for example sex hormones of vertebrates and various steroid hormones of the adrenal glands.
• Detoxification: other enzymes help detoxify drugs and poisons, especially in the liver cells.

Rough ER

The rough ER has ribosomes attached to its sides facing the cytoplasm, which gives it a rough appearance under the electron microscope. Many types of specialised cells secrete proteins produced by ribosomes attached to the rough ER.

In addition to making secretory proteins, the rough ER is a membrane factory for the cell: it grows in place by adding membrane proteins and phospholipids to its own membrane. The ER membrane expands and is transferred, in the form of transport vesicles, to other components of the endomembrane system.

RibosomesOften examined

Ribosomes are the particles made of ribosomal RNA (rRNA) and protein. These organelles carry out protein synthesis.

• Ribosomes were first observed using the electron microscope as dense granules.
• They are roughly spherical, granular, non-membranous bodies found in both eukaryotic and prokaryotic cells. They can be seen only under the electron microscope.
• Eukaryotic ribosomes are larger and are 80S ribosomes, while prokaryotic ribosomes are slightly smaller and are 70S ribosomes.
• They are made of almost equal amounts of RNA and protein, so they are ribonucleoprotein.
• Ribosomes are formed in the nucleolus. They are then transported to the cytoplasm through the nuclear pore.

Structure of the eukaryotic ribosome

The eukaryotic ribosome is composed of two subunits (particles) of different sizes. The larger one is the 60S particle and the smaller one is the 40S particle. The two subunits attach to form the 80S ribosome. The attachment is controlled by the concentration of magnesium ions, or by salt bonds between the phosphate group of RNA and the amino group of amino acids, or both. Both ribosomal subunits are generally attached together at the time of their function.

Polysomes

The ribosomes are involved in the events of protein synthesis. Sometimes, during protein synthesis, several ribosomes are attached to one mRNA molecule. Such a chain of many ribosomes is called a polysome or polyribosomes. In this way several copies of the same polypeptide can be produced in very little time.

Golgi complexOften examined

The Golgi complex is found in all eukaryotic cells. It was discovered by the Italian biologist Camillo Golgi in 1898. It is also called the Golgi apparatus and Golgi bodies.

Structure

The Golgi complex consists of a stack of flattened, membrane-bound sacs called cisternae, together with a system of associated vesicles called Golgi vesicles. It is a complex system of interconnected tubules formed around the central stack.

• At one end of the stack new cisternae are constantly being formed by the fusion of vesicles from the smooth ER. This outer end is the forming face (cis face), which is convex.
• The inner end is concave and is called the maturing face (trans face). Here the cisternae break up into vesicles again.

Functions

The most important function of the Golgi complex is the processing of cell secretions. Therefore these organelles are abundant in secretory cells. The cell secretions mainly consist of proteins. The Golgi complex collects these proteins from the RER through the SER, modifies them to perform specific functions and then exports these modified products in the form of vesicles.

• Certain organelles, such as lysosomes, peroxisomes and glyoxysomes, also originate from the Golgi complex.
• It is also involved in the formation of conjugated molecules such as glycoprotein and lipoprotein.
• In a plant cell during cell division, the Golgi complex gives rise to vesicles which contain cell wall synthesising materials. At cytokinesis these Golgi vesicles are arranged on the cell equator, fuse together and form a structure called the phragmoplast. Later the new cell wall is derived from this structure.

Vesicles

The word 'vesicle' derives from the Latin word vesicula, meaning 'small bladder'. Vesicles are small cell organelles present in cells. They are small, membrane-enclosed sacs: a small structure within a cell consisting of fluid enclosed by a lipid bilayer. The bilayer has hydrophilic heads and hydrophobic tails.

Origin

Many vesicles are made in the Golgi complex and the endoplasmic reticulum, or are made from parts of the cell membrane by endocytosis. Because vesicles are made of phospholipids, they can break off and fuse with other membranous material.

Examples of vesicles include secretory vesicles, transport vesicles, synaptic vesicles and lysosomes. Vesicles are found in bacteria, Archaea and plants as well as in animals.

Functions

• They transport substances to and from one cell to another and also from one part of a cell to another, for example a protein and other molecules. The first step of vesicular transport is the formation of a vesicle by budding from the membrane.
• They are involved in metabolism, buoyancy control and enzyme storage.
• They can also act as chemical reaction chambers.

LysosomesOften examined

Lyso means splitting and soma means body. Lysosomes are single-membrane, spherical vesicles. They contain digestive (hydrolytic) enzymes.

Formation

The lysosomal enzymes are made by the RER and then transported to the Golgi complex through the SER. After modification, these enzymes are released from the trans face of the Golgi complex in the form of vesicles. Such vesicles are called lysosomes. The newly formed lysosomes, before the start of their functions, are usually called primary lysosomes.

• In plants and fungi, certain vacuoles carry out enzymatic hydrolysis, a function shared by lysosomes in animal cells.
• Lysosomes contain about 40 different digestive enzymes. These enzymes can break down every major macromolecule of the cell.
• The contents of the lysosome are acidic.
• To perform its function the lysosome fuses with a membrane-bound vesicle that arises from any of these pathways: endocytosis, phagocytosis or autophagocytosis.

Functions

The key function of lysosomes is digestion and removal of waste.

Peroxisomes and glyoxysomes

Peroxisomes

The peroxisome is a small vesicle, a single-membrane-bound organelle. It is an oxidative organelle that is not part of the endomembrane system. Like the mitochondrion and chloroplast, it imports its proteins primarily from the cytosol. Peroxisomes can vary in shape and size, depending on the needs of the cell they serve. They will sometimes increase in number and size if, for example, they have a lot of alcohol to break down.

Peroxisomes and glyoxysomes are collectively called microbodies. These are similar to lysosomes in the sense that they are single membranous, vesicular structures. They contain enzymes (although different from those of lysosomes) and originate from the Golgi complex, but they are smaller than lysosomes.

Peroxisomes contain some oxidative enzymes such as peroxidases, catalases and glycolic acid oxidases. They are abundant in liver cells, where they are specifically involved in the formation and decomposition of hydrogen peroxide, so they are named peroxisomes. They are mainly concerned with the detoxification of alcohol.

In plant cells, peroxisomes are involved in photorespiration. A step of photorespiration takes place in peroxisomes in which glycolate is converted into glycine with the help of the enzyme glycolic acid oxidase.

Glyoxysomes

Specialised peroxisomes are called glyoxysomes. They are found only at the seedling stage in oil seed plants. These organelles have a number of enzymes specific for plant lipid metabolism that are not found in animal cells. The germinating seedlings convert stored fatty acids to carbohydrates. This is achieved through a metabolic pathway called the glyoxylate cycle, the enzymes of which are located in the glyoxysomes.

Vacuoles

Vacuoles are large vesicles that originate from the endoplasmic reticulum, the Golgi complex and the plasma membrane. Vacuoles perform a variety of functions in different kinds of cells.

Cell sap

The solution inside the central vacuole.

Tonoplast

The membrane separating the vacuole from the cytoplasm.

MitochondriaOften examined

Mitochondria (singular: mitochondrion) are present in all eukaryotic cells. Some cells have a single large mitochondrion, but more often a cell has hundreds or even thousands of mitochondria; the number correlates with the cell's level of metabolic activity. For example, cells that move or contract have proportionally more mitochondria per volume than less active cells. Mitochondria are capable of dividing themselves (self-replicating) in order to increase their number. They divide by fission.

Structure

Mitochondria are cylindrical or rod-shaped structures. They are enclosed by a double membrane, the outer membrane and the inner membrane.

• The outer membrane is smooth and somewhat like a sieve, due to the presence of porins. These are special proteins responsible for the transport of molecules across the membrane. Porins allow free passage of various molecules into the intermembrane space.
• The inner membrane is selectively permeable and folded inwards. The folds are called cristae, which serve to increase the surface area.
• The inner surface of the cristae has granular structures called F0-F1 particles. These particles are actually ATP synthase enzymes. In addition, several other complexes are found in the inner mitochondrial membrane, which serve as electron carriers in the electron transport chain.
• The inner membrane divides the mitochondrion into two internal compartments. The first is the intermembrane space, the narrow region between the inner and outer membranes. The second, the mitochondrial matrix, is enclosed by the inner membrane.
• The mitochondrial matrix is a jelly-like material that contains a small circular DNA, all kinds of RNA, ribosomes (70S) and enzymes. The presence of these components indicates that mitochondria have their own genetic system: the proteins which are required by mitochondria are synthesised by their own metabolic machinery.

Functions

Mitochondria are the sites of cellular respiration, the metabolic process that uses oxygen to generate ATP by extracting energy from sugars, fats and other organic compounds. Enzymes in the matrix catalyse some of the steps of cellular respiration, like the Krebs cycle. Other proteins that function in ATP generation through the electron transport chain are found in the inner membrane.

PlastidsOften examined

On the basis of the presence or absence and type of pigments, and the stage of development, plastids have been classified into proplastids, leucoplasts, chromoplasts and chloroplasts.

• Proplastids are young, immature and developing plastids. They are self-replicating organelles.
• Leucoplasts are colourless and are found in the parenchyma cells of root, stem and seeds.
• Chromoplasts synthesise different coloured pigments other than green.
• Chloroplasts are found in the green parts of plants and act as the site of photosynthesis.

Structure and functions of chloroplast

A chloroplast is a discoid structure which consists of three parts: the envelope, the stroma and the thylakoids.

• Each chloroplast is bounded by a smooth double membrane (the envelope). The outer membrane, like that of the mitochondrion, contains porins and is therefore freely permeable to small molecules. The inner membrane is semipermeable and rich in protein. Between the outer and inner membranes is the intermembrane space.
• The ground mass of the chloroplast is called the stroma. It is a colourless proteinaceous substance which, like the mitochondrial matrix, also contains a small circular DNA, all kinds of RNA, ribosomes (70S) and various enzymes.
• The stroma contains a system of chlorophyll-bearing double-membrane, flattened sac-like structures called thylakoids. There are two types of thylakoids, the smaller thylakoids and the larger thylakoids.

Functions

The chloroplast is the site of photosynthesis in a plant cell.

Centrioles

Centrioles are non-membranous cell organelles found mainly in animal cells. They are also found in fungus-like protists such as slime molds and water molds.

• Centrioles are rod-shaped structures and usually occur in pairs. The two lie at right angles to each other, near one pole of the nucleus.
• Each centriole is composed of nine triplets of microtubules circularly arranged around a central axis.

Functions

NucleusOften examined

The nucleus is the most prominent and most important part of a cell. In animal cells it is found in the centre (with the exception of muscle fibre cells), but in an adult plant cell it is slightly away from the centre due to the presence of a large central vacuole. A typical eukaryotic nucleus consists of the nuclear envelope, nucleoplasm, nucleoli and chromatin.

Nuclear envelope

The nuclear envelope (also called the nuclear membrane) is a double membrane covering which makes the boundary of the nucleus. The two membranes are composed of lipid bilayer and proteins and are separated by a fluid-filled perinuclear space. The outer membrane of the envelope is covered with ribosomes and is connected with the membranes of the ER.

There are numerous pores in the nuclear envelope called nuclear pores, which are composed of a specialised transport protein called nucleoporin. At the point of a nuclear pore both membranes are interconnected. These pores regulate the nucleo-cytoplasmic exchange of materials:

• RNA and ribosomal proteins move from the nucleus to the cytoplasm.
• Proteins (such as DNA polymerase), carbohydrates, signalling molecules and lipids move into the nucleus.
• Smaller molecules simply diffuse through the pores. Larger molecules may be recognised by specific signal sequences and then pass into or out of the nucleus with the help of nucleoporin.

Nucleoplasm

The nucleoplasm is the transparent semifluid ground substance formed by a mixture of proteins, enzymes (DNA and RNA polymerase), free nucleotides and some metal ions (Mg) for the synthesis of DNA and RNAs. It also contains histone and non-histone proteins, so the nucleoplasm is slightly different from the cytoplasm.

Nucleolus

The nucleolus is a non-membrane-bound structure in the nucleoplasm. A cell may have one or more nucleoli. The nucleolus appears during interphase and disappears during cell division. A nucleolus consists of a peripheral granular area (contains ribosomal subunits) and a central fibrillar area (contains rRNA and rDNA). Therefore the nucleolus is involved in the construction of ribosomes.

Chromatin and chromosomes

Chromatin is a network of thin thread-like structures made up of DNA and proteins. During cell division the chromatin fibres begin to condense and coil up into separate structures called chromosomes, which are thick enough to be seen under a light microscope.

A typical chromosome consists of two strands called chromatids, attached to each other at a point known as the centromere. A centromere is a constriction functionally related to the movement of chromosomes during cell division. Each centromere has a complex of kinetochore proteins present on opposite sides of the constriction.

1.9Prokaryotic and eukaryotic cellsOften examined

Two kinds of structurally different cells have evolved over time. Prokaryotic cells include archaea, bacteria and cyanobacteria, whereas all other forms of life are composed of eukaryotic cells.

1.10Stem cells

Stem cells are cells with the potential to develop into many different types of cells in the body. Under the right conditions in the body or in a laboratory, stem cells divide to form more cells called daughter cells.

These daughter cells become either new stem cells or specialised cells (differentiation) with a more specific function, such as blood cells, nerve cells, liver cells, heart muscle cells or bone cells. No other cell in the body has the natural ability to generate new cell types.

Advantages of using stem cells

• New cells are provided by the stem cells as we grow.
• They replace the specialised cells that are damaged or lost.
• They can divide again and again to produce new cells. As the stem cells divide they can change into the other types of cell that make up the body.

The benefits of stem cell therapy are in the treatment of spinal cord injuries, type 1 diabetes, Parkinson's disease, Alzheimer's disease, heart disease, stroke, burns, cancer and osteoarthritis.

Types of stem cellsOften examined

There are several different types of stem cells, each with its own unique properties and applications in medical research and practice. The book discusses three main types.

1. Adult stem cells. These cells supply new cells as an organism grows and replace cells that get damaged. Adult stem cells are multipotent, which means they can only change into some specific cells in the body, not any cell.
2. Embryonic stem cells (ESCs). These cells provide new cells for a growing embryo. They are called pluripotent, which means they can naturally produce every type of cell in the body.
3. Induced pluripotent stem cells (iPSCs). The stem cells that scientists make in the laboratory are called induced pluripotent stem cells. They can develop into any cell type.

Potency: the full classification

Researchers categorise stem cells according to their potential to differentiate into other types of cells (their potency). The full classification includes the five types below.

Induced pluripotent stem cells

Advantages of induced pluripotent stem cells

• Ability to give rise to almost any cell type desired.
• Avoidance of the ethical concerns associated with human embryonic stem cells (ESCs).
• Induced pluripotent stem cells generated from the patient themselves could be used to grow new organs that would have a lower risk of being rejected.

Disadvantages of induced pluripotent stem cells

For human iPSC production, viruses were initially used as delivery vectors for the genes required for cell reprogramming.

The main issue is the use of retroviruses to generate iPSCs, as they are associated with cancer. More specifically, retroviruses can insert their DNA anywhere in the genome and subsequently trigger cancer-causing gene expression. In addition, the risk of overgrowth of the transplanted cells, or in other words cancer, continues to be a major hurdle.

1.11Endocytosis and exocytosisOften examined

The active, bulk transport of products across the cell membrane is called endocytosis and exocytosis. They are two processes that allow large molecules, bacteria and waste materials that cannot diffuse through the lipid bilayer to cross the cell membrane.

Endocytosis

Endocytosis is the process by which substances are engulfed within the cell membrane, which then forms a vesicle containing the ingested material. The two main subtypes of endocytosis are phagocytosis and pinocytosis.

Phagocytosis

Phagocytosis is the process through which phagocytes ingest or consume other cells or particles. A phagocyte may be Amoeba or a white blood cell. Some species, for example sponges and Amoeba, have a way of feeding called phagocytosis. Extensions of the cytoplasm, termed pseudopodia ('false feet'), sense, surround and enclose the target, creating a vacuole or phagosome on the inside of the cell membrane. In higher animals phagocytosis is primarily a defensive mechanism against infection and antigens.

Pinocytosis

Cell drinking is also known as pinocytosis. It is widespread in plant and animal cells. Through this process cells take in nutrients such as ions, enzymes and hormones. The cell membrane invaginates before budding off to form a vesicle called a pinosome.

Receptor-mediated endocytosis

Receptor-mediated endocytosis is a kind of pinocytosis. Macromolecules bind to receptors on the surface of the plasma membrane during this process. The example given is cholesterol absorption. Receptors cluster in regions termed coated pits, as they are coated with proteins. This causes the coated pit to invaginate and become a coated vesicle, bringing the desired ligand into the cell.

Exocytosis

Exocytosis is the process by which the transfer of material takes place from inside of the cell to the outside of the cell. It is an active transport. Vesicles are packaged within the cell and transported to the cell membrane, where their phospholipid bilayers fuse. This allows the contents to be released outside the cell. Exocytosis is used in many areas of the body, including neurotransmitter release at synapses and release of secretions in the sweat glands.

1.12Cell division

The continuity of life is based on the reproduction of cells, that is cell division. The dividing cell is called the parent cell and the two new cells formed are called daughter cells. The two main types of cell division are mitosis and meiosis. The somatic cells divide by mitosis and the germ line cells divide by meiosis.

Cell cycle

The cell cycle is a series of stages a cell passes through to divide and produce new cells. The process of cell division can be divided into two main phases, mitosis and cytokinesis. Mitosis is the process of division of the nucleus. Cytokinesis is the process of division of the cytoplasm.

Phases of the cell cycle

Mitosis is only a part of the cell cycle. The mitotic (M) phase includes both mitosis and cytokinesis. The M phase is the shortest part of the cell cycle. Mitotic cell division alternates with a much longer stage called interphase. This phase can be divided into three sub-phases: the **G_1 phase (first gap), the S phase (synthesis) and the G_2 phase** (second gap).

During the sub-phases the cell grows by producing proteins and cytoplasmic organelles. Chromosomes are duplicated only during the S phase. Thus a cell grows (G_1), continues to grow as it copies its chromosomes (S), grows more as it completes preparation for cell division (G_2), and divides. The daughter cells may then repeat the cycle.

MitosisOften examined

The word mitosis comes from the Greek word 'mitos', which means thread, and refers to the threadlike appearance of chromosomes during this period. Mitosis can be defined as "the division of the cell in such a manner that the chromosomes are duplicated and distributed equally to the daughter cells".

Mitosis is a continuous process that is arbitrarily divided into five phases for the convenience of description: prophase, prometaphase, metaphase, anaphase and telophase.

Interphase

A nuclear envelope surrounds the nucleus. The nucleus contains one or more nucleoli. By the replication of a single centrosome two centrosomes are formed. Each centrosome has two centrioles. The chromosomes that duplicated during S phase are not visible under a light microscope as they have not yet condensed.

Prophase

The chromatin fibres become more tightly coiled. They condense into discrete chromosomes, which are observable with a light microscope. Each duplicated chromosome appears as two identical sister chromatids joined together. The nucleoli disappear. The mitotic spindle begins to form. It is composed of centrosomes and the microtubules that extend from them. The radial arrays of shorter microtubules that extend from the centrosomes are called asters (stars). The centrosomes move away from each other. This is due to the lengthening of the microtubules between them.

Prometaphase

During the formation of the spindle, the nuclear membrane breaks. The microtubules of the spindle can now invade the nuclear area and interact with the chromosomes, which have become even more condensed. Microtubules extend from each centrosome towards the middle of the cell. Each of the two chromatids of a chromosome now has a kinetochore. Some of the microtubules attach to the kinetochore, becoming 'kinetochore microtubules'. Non-kinetochore microtubules interact with those from the opposite pole of the spindle.

Metaphase

It is the longest stage of mitosis, lasting about twenty minutes. The centrosomes are now at opposite ends of the cell. The chromosomes arrange on the metaphase plate, an imaginary plane that is equidistant between the two poles of the spindle. The centromeres of the chromosomes lie on the metaphase plate. For each chromosome, the kinetochores of the sister chromatids are attached to kinetochore microtubules coming from opposite poles. The entire apparatus is called the spindle because of its shape.

Anaphase

It is the shortest stage of mitosis, lasting only a few minutes. It begins when the two sister chromatids of each pair suddenly part. Each chromatid thus becomes a full-fledged chromosome. The two liberated chromosomes begin moving towards opposite ends of the cell, as their kinetochore microtubules shorten. Because these microtubules are attached at the centromere region, the chromosomes move centromere first. The cell elongates as the non-kinetochore microtubules lengthen. By the end of anaphase, the two ends of the cell have an equivalent and complete collection of chromosomes.

Telophase

The two daughter nuclei begin to form in the cell. Nuclear envelopes arise from the fragments of the parent cell's nuclear envelope and other portions of the endomembrane system. The chromosomes become less condensed. Mitosis, the division of one nucleus into two genetically identical nuclei, is now complete.

Cytokinesis

The division of the cytoplasm is usually well underway by the late telophase, so the two daughter cells appear shortly after the end of mitosis. Commonly the nuclear division is followed by separation of the cytoplasm into two parts. This separation is accomplished by pinching of the cell membrane. The pinching near the middle of an animal cell forms a cleavage furrow. The process of cytoplasmic division is called cytokinesis (Greek cyto, cell; kinesis, movement). Cell organelles are distributed to the two daughter cells.

MeiosisOften examined

The process where a single cell divides twice to produce four cells containing half the original amount of genetic information is called meiosis. Sperms and eggs are produced by meiosis in animals. Spores are produced by meiosis in plants.

The stages of meiosis

Meiosis is a continuous process. It can be described most easily by dividing it into two arbitrary stages: meiosis I and meiosis II.

The first meiotic division

It consists of interphase I, prophase I, metaphase I, anaphase I and telophase I.

Interphase I

The DNA in the cell is copied, and as a result two identical full sets of chromosomes are formed. There are two centrosomes outside the nucleus, each containing a pair of centrioles. During interphase, microtubules extend from these centrosomes.

Prophase I

It is the lengthy stage of meiosis. Each chromosome has two chromatids. Chromosomes look like interweaving threads. Due to condensation of chromatin material, chromosomes become apparent and distinct, and the nucleus increases in size. Initially the thin chromosomes become shorter and thicker. The chromosome number of the cell is seen. Homologous chromosomes start getting closer to each other. In the cell there are two of each type of chromosome. Identical chromosomes are called homologous chromosomes. The homologous chromosomes begin to pair length-wise with their homologue. The process of pairing is called synapsis. The synapsis may start from any point, with the corresponding complementary DNA strand of the other.

Each pair of synapsed chromosomes consists of four chromatids and two centromeres and is called a tetrad or bivalent. The chromatids of the homologues may cross each other, and the point of crossing is an X-shaped figure under the light microscope. It is called a chiasma (plural: chiasmata). A chromosome segment is exchanged between the two homologous chromosomes at the chiasma, and this is called crossing over.

The paired homologous chromosomes begin to separate by repelling. The tetrads are more evenly distributed in the nucleus. The nucleoli disappear. The nuclear membrane is still present. The diad (the two chromatids attached to a single centromere is called a diad) behaves as a single unit because they are held together by a common centromere throughout meiosis.

Metaphase I

The nuclear membrane disintegrates. The microtubules form the spindle. The chromosomes line up in a double row, that is, pairs on the equator. Microtubules bind only to one kinetochore of each centromere. The centromere of one homologue becomes attached to microtubules extending to one pole, whereas the centromere of the other homologue becomes attached to microtubules extending to the other pole.

Anaphase I

The attachment of chromosomes to the spindle is complete. The microtubules that are attached to the homologous chromosomes begin to slide over one another, and as a result the spindle poles move apart. The spindle fibres become shorter as they are dragged to the poles. They are broken by the action of enzymes. With the shortening of the spindle fibres, the chromosomes that are attached to the spindle are also pulled towards each pole. When the shortening of the spindle fibres is completed, each pole has a single set of chromosomes, consisting of one member of each homologous pair.

Telophase I and cytokinesis

The chromosomes complete their movement to the opposite poles of the cell. At each pole of the cell a full set of chromosomes gather together. A membrane forms around each set of chromosomes to create two new nuclei. The single cell, through the process of cytokinesis, forms two separate daughter cells, which are haploid.

The second meiotic division

Meiosis II is simply a mitotic division. It occurs to separate the sister chromatids as in mitosis.

• Interphase II. DNA does not duplicate in interphase II. It is a very brief phase. Each of the two cells resulting from meiosis I progresses into meiosis II very quickly.
• Prophase II. The complicated nuclear events of prophase do not take place.
• Metaphase II and anaphase II. The chromosomes line up in the same fashion as they did in metaphase I. Here again a random distribution of chromosomes takes place. The centromere divides, and as a result the two chromatids are separated. As each chromatid is now a separate structure, they are called chromosomes. Chromosomes are distributed in equal number to each pole.
• Telophase II. The nuclei are reconstructed in the typical manner. Each nucleus now contains a haploid set of chromosomes, because DNA has duplicated only once during the cell division.

Formula sheet

Key terms

Cell

The basic structural and functional unit of life.

Cell theory

All living things are made of cells, the cell is the basic unit of life, and new cells arise only from pre-existing cells.

Resolution

The ability of a microscope to show two close points as separate; it sets the limit of useful magnification.

Plasma membrane

The thin flexible boundary of the cell, a phospholipid bilayer with proteins, that controls what enters and leaves.

Cell wall

The rigid outer layer outside the plasma membrane of plant cells and prokaryotes that gives shape and protection.

Ligand

A signalling molecule that binds to a receptor.

Receptor

A protein that binds a specific ligand and so starts a response in the cell.

Diffusion

The net movement of particles from a region of higher concentration to a region of lower concentration, needing no energy.

Facilitated diffusion

Passive movement of substances across a membrane with the help of carrier or channel proteins.

Osmosis

The movement of water across a selectively permeable membrane from a region of higher water potential to lower water potential.

Active transport

Movement of substances across a membrane against a concentration gradient using energy (ATP).

Cytoplasm

Everything inside the plasma membrane except the nucleus: cytosol plus organelles.

Organelle

A specialised structure inside a cell that carries out a particular function.

Endoplasmic reticulum

A network of membrane-bound channels and sacs (cisternae) in the cytoplasm; rough with ribosomes, smooth without.

Ribosome

A small particle of RNA and protein where proteins are made.

Golgi complex

A stack of flattened membrane sacs (cisternae) that modifies, sorts and packages proteins and lipids.

Vesicle

A small membrane-bound sac that carries materials within or out of the cell.

Lysosome

A single-membrane vesicle containing digestive enzymes, formed from the Golgi complex.

Peroxisome

A single-membrane oxidative organelle with enzymes such as catalase that detoxifies alcohol and breaks down hydrogen peroxide.

Glyoxysome

A specialised peroxisome in germinating oil seeds that converts stored fats to carbohydrates.

Vacuole

A large membrane-bound vesicle; in mature plant cells a large central vacuole holding cell sap.

Tonoplast

The membrane surrounding the vacuole.

Mitochondrion

A double-membrane organelle with folded cristae where aerobic respiration makes ATP.

Plastid

A plant organelle such as a chloroplast, chromoplast, leucoplast or proplastid.

Chloroplast

A double-membrane plastid with grana of thylakoids where photosynthesis takes place.

Centriole

A cylinder of nine triplets of microtubules found in pairs in the centrosome.

Nucleus

The organelle surrounded by a double nuclear envelope that contains the chromatin and nucleolus.

Nucleolus

A dense region inside the nucleus where ribosomal RNA is made.

Chromatin

The thread-like material of DNA and protein in the nucleus that condenses into chromosomes.

Centromere

The constriction of a chromosome that holds the sister chromatids together and is related to chromosome movement.

Kinetochore

A protein complex on each side of the centromere to which spindle microtubules attach.

Prokaryotic cell

A cell with no nucleus or membrane-bound organelles, such as bacteria, archaea and cyanobacteria.

Eukaryotic cell

A cell with a membrane-bound nucleus and organelles.

Stem cell

A cell with the unique ability to develop into specialised cell types and to renew itself.

Differentiation

The change of a daughter cell into a specialised cell with a specific function.

Totipotent

Able to become all possible cell types, such as the first cells of a dividing zygote.

Pluripotent

Able to become almost any cell, such as cells of the early embryo.

Multipotent

Able to become a closely related family of cells, such as adult haematopoietic stem cells.

Oligopotent

Able to become a few different cell types.

Unipotent

Able to produce only cells of its own kind, but still able to renew itself.

Induced pluripotent stem cell (iPSC)

A stem cell made in the laboratory by reprogramming a specialised cell; it can develop into any cell type.

Endocytosis

Active bulk transport in which substances are engulfed by the cell membrane to form a vesicle.

Phagocytosis

Endocytosis of cells or large particles, using pseudopodia to form a vacuole (phagosome).

Pinocytosis

Cell drinking: the membrane invaginates to take in fluid and dissolved substances as a pinosome.

Exocytosis

Active bulk transport in which vesicles fuse with the cell membrane and release their contents outside.

Cell cycle

The series of stages a cell passes through to divide and produce new cells.

Interphase

The long stage between divisions, made of G1, S and G2 phases.

Mitosis

Division of the nucleus so that the chromosomes are duplicated and distributed equally to two daughter cells.

Cytokinesis

Division of the cytoplasm after nuclear division.

Sister chromatids

The two identical halves of a duplicated chromosome joined at the centromere.

Metaphase plate

The imaginary plane midway between the spindle poles where chromosomes line up.

Meiosis

Division in which one cell divides twice to produce four haploid cells.

Synapsis

The length-wise pairing of homologous chromosomes in prophase I.

Chiasma

The X-shaped point where chromatids of homologous chromosomes cross.

Crossing over

Exchange of chromosome segments between homologous chromosomes at the chiasma.

Haploid

Having a single set of chromosomes, as in the cells formed by meiosis.