Biology Grade 11 · Unit 1 · Cell and Sub-Cellular Organelles

Biology Grade 11 · Unit 1 · Cell and Sub-Cellular Organelles · Athens Academy Islamabad

Let us begin gently. This whole chapter rests on one single idea: the cell is the smallest thing that can be called alive. Everything else in Unit 1 — microscopes, organelles, membranes, transport, signalling, stem cells, mitosis and meiosis — is simply a longer answer to the question, "What is inside a cell, and how does it work?"

Read this chapter the way you would walk into a house for the first time. First you look at the house from outside (the cell as a whole). Then you notice the walls and the door (cell wall and plasma membrane). Then you go room by room (the organelles). Then you watch how people come in and go out (transport, endocytosis, exocytosis). Finally, you see how a new house is built from the old one (cell division). Take it in that order and nothing will feel crowded.

How to use these notes

Every definition marked (examinable) has appeared in board papers in one form or another. Learn those word-perfect. Everything else you should be able to explain in your own words — that is what the paper actually rewards.

1Cells — The Basic Unit of Life

All organisms are made of cells. Some organisms are made of just one cell, and some are made of billions. Amoeba, Paramecium and Euglena are single-celled. More complex organisms, including all plants and animals, are multicellular.

Think of a brick. One brick is complete in itself — it has a shape, a size and a purpose. But you can also stack millions of bricks and get the Faisal Mosque. The cell is biology's brick: complete on its own, and also the building unit of everything larger.

Cell examinable

The cell is the structural and functional unit of living organisms. It is the basic structural unit of all unicellular and multicellular organisms — the smallest unit and building block of life.

Cells exist in many shapes and sizes, and they perform a wide range of activities. An important point the examiner likes: the shape and size of a cell are related to the function it performs. A nerve cell is long and thin because it must carry a message a long distance. A red blood cell is small and flexible because it must squeeze through narrow capillaries.

1.1 The seven properties of life

Why do we say a cell is alive and not just a small bag of chemicals? Because a single cell performs all seven basic properties of life by itself.

Property	What it means
Movement	Living things show movement, either externally or internally.
Respiration	Living things use substances from the environment to make energy.
Homeostasis	Living things maintain a stable internal environment.
Growth	Living things can move and change shape or size.
Reproduction	Living things produce offspring, either sexually or asexually.
Excretion	Living things remove waste products.
Nutrition	Living things exchange materials and gases with the environment.

Table 1.1 — The seven properties of life. A single cell performs every one of them.

Memory hook

"My Really Happy Grandmother Rarely Eats Nuts"

Movement · Respiration · Homeostasis · Growth · Reproduction · Excretion · Nutrition. Seven words, seven properties. Say it out loud three times now and you will still have it in the exam hall.

⚠ Exam trap

Students write "growth means getting bigger" and stop. The textbook wording is "living things can move and change shape or size" — use the book's phrasing, because that is what the marking key is matching against.

2Cell Theory

Cell theory did not arrive in one flash. Four scientists, spread across two hundred years, each added one piece. Learn the story and you will never confuse the names.

2.1 The scientists

Scientist	Year	Contribution
Robert Hooke English scientist	1665	Looked at thin pieces of cork under a simple microscope. He saw tiny empty spaces with walls around them — the cork looked like a honeycomb. The spaces reminded him of the small rooms called cells in a monastery, so he named them cells. What he actually saw were the thick outer walls of dead cork tree cells.
Schleiden German botanist	1938 *	Examined a large variety of cells and concluded that cells are the ultimate units forming the structures of all plant tissue.
Schwann German zoologist	—	Studied many types of animal cells. He found animal cells lack a cell wall and are covered by a membrane. He recognised that apart from the cell wall (unique to plants), the insides of plant and animal cells were identical. Schleiden and Schwann compared findings and together formulated the cell theory.
Rudolf Virchow	1885	Observed that new cells develop by the division of pre-existing cells.

Table 1.2 — The builders of cell theory. * The chapter prints Schleiden's year as 1938; this is a well-known printing slip for 1838. Write what your board textbook prints, but be aware of the discrepancy.

2.2 The three tenets

The three tenets of cell theory examinable

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 iteration adds three more

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

2.3 Validation of cell theory

Three experimental evidences validate the cell theory:

Cells removed from tissues can survive independently for short periods of time.
Nothing smaller than a cell has been found to be able to live independently.
Experiments by Francesco Redi and Louis Pasteur demonstrated that cells cannot grow in sealed and sterile conditions.

2.4 Exceptions to cell theory

This is a very frequent short-question. There are six, and each one breaks a different tenet.

Exception	Why it breaks the theory
Viruses	Considered acellular — they have no cell machinery. They are alive only while inside their host cell, and behave as dead when outside it.
Viroids and prions	Also behave like viruses, so they are exceptions too.
RBCs and sieve tube cells	They lack nuclei, so they cannot divide to form new cells.
Bacteria, cyanobacteria	Lack a well-organised nucleus. Nuclear membrane, nucleolus and nucleoplasm are absent. The DNA alone forms the chromosome and lies in direct contact with the cytoplasm. Basic proteins associated with nucleic acid are absent.
Coenocytic hyphae of Rhizopus; cells of the alga Vaucheria	They are multinucleate — many nuclei inside one continuous mass, so the "one nucleus per cell" picture fails.
Protozoans	They are acellular — their body is not divided into cells.

Table 1.3 — Six exceptions to cell theory.

Memory hook

"Very Very Rude Boys Can Play"

Viruses · Viroids & prions · RBCs and sieve tubes · Bacteria & cyanobacteria · Coenocytic hyphae · Protozoans.

⚠ Exam trap

Do not write "viruses are not living." The textbook is more careful: viruses are alive only inside the host cell and behave dead outside it. That precision earns the mark.

3Microscopy — Seeing the Invisible

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.

3.1 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 ocular lens in the eyepiece and the objective lens in the revolving nosepiece. Because it uses two lenses, the light microscope is also known as the compound microscope.

Working principle

The light source illuminates the object. The objective lens forms the first image — this image is real, inverted and magnified. That image then acts as the object for the eyepiece. The eyepiece produces the final image, which is virtual and magnified. So the final image is inverted with respect to the object.

Figure 1.1 — Working principle of the compound (light) microscope.

3.2 Magnification and resolution

These two words are constantly mixed up by students. Here is a homely way to keep them apart. Imagine a photograph on your phone. If you pinch and zoom, the picture gets bigger — that is magnification. But if it becomes blurry as it gets bigger, you cannot tell two things apart any more — that is poor resolution. Bigger is not the same as clearer.

Magnification examinable

Magnification is the capacity of an optical instrument to increase the size of an object beyond its original size. Different lenses have different magnification powers, represented by the letter X, meaning the number of times the original size. A lens of 10X magnification can increase the size of an object of 1 µm to 10 µm.

Resolution examinable

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

Total magnification

\text{Total magnification} = \text{objective lens value} \times \text{ocular lens value}

Maximum for a light microscope:

100X \times 15X = 1500X

Two numbers worth memorising exactly, because they get asked directly:

Quantity	Value from the textbook
Resolution of the naked eye	0.1 mm — and this cannot be increased by increasing magnification
Resolving power of a light microscope	250 nm
Resolving power of an electron microscope	0.2 nm
Maximum magnification, light microscope	1500X (100X objective × 15X ocular)
Magnification, electron microscope	1 to 50 million times, depending on type

Table 1.4 — Numbers you should be able to recall without hesitation.

⚠ Exam trap

"Magnification and resolution are the same thing" — no. Magnification is making small objects appear larger using an optical instrument. Resolution is the ability to distinguish two objects from each other. Increasing magnification without resolution just gives you a bigger blur.

3.3 The electron microscope

Principle of electron microscopy examinable

It uses a beam of accelerated electrons to visualise specimens, and has a high resolution.

Working principle

The beam of electrons produced from the electron gun is focused on the specimen through two sets of condenser lenses. An accelerating potential is applied between filament and anode to move the electrons downwards. The specimen is kept as a thin section of 20–100 nm on a specimen holder. The beam goes through the specimen; the denser regions scatter more electrons on the screen than the lighter regions. The scattered beam passes through the objective lens to create a magnified image, which is further magnified by the ocular lens.

Two major types

TEM — transmission electron microscope. Uses transmitted electrons to form an image.
SEM — scanning electron microscope. Produces an image by detecting secondary or backscattered electrons.
Sometimes both are combined in one instrument, the STEM (scanning transmission electron microscope).

3.4 Light microscope versus electron microscope

Light microscope	Electron microscope
Uses light (approx. 400–700 nm) as illuminating source	Uses electron beams (approx. 1 nm) as illuminating source
Magnification 1500X	1 to 50 million times, depending on type
Both live and dead specimens can be seen	Only dead and dried specimens can be seen
Image formation depends on light absorption from different zones of the specimen	Image formation depends on electron scattering
Low resolution (250 nm)	High resolution (0.2 nm)
Useful magnification 500X to 1500X	Direct magnification as high as 16 000X; photographic magnification as high as 1 000 000X
Image is usually coloured	Image is black and white
Vacuum is not required	Vacuum is essential for its operation

Table 1.5 — Comparison between light and electron microscope. This table is worth full marks on its own — learn all eight rows.

The one advantage of a light microscope

An MCQ from the textbook exercise asks the major advantage of a light microscope over an electron microscope. The answer is observation of living matter. The electron microscope beats it on resolution and magnification — but it can only show you something already dead and dried.

4Ultrastructure of Animal and Plant Cells

Ultrastructure examinable

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

Before we go organelle by organelle, look at the two cells side by side. Nearly everything is shared. The differences are few — and those few differences are exactly what the examiner asks about.

Figure 1.2 — Ultrastructure compared. Original diagram, drawn to show the four structural differences the board asks about.

Structure	Animal cell	Plant cell
Cell wall	Absent	Present, made of cellulose
Chloroplast / plastids	Absent	Present in green parts
Vacuole	Small food vacuoles	Large central vacuole in mature cells
Centrioles	Present	Absent
Position of nucleus	Central (except muscle fibre cells)	Pushed slightly away from centre by the large central vacuole

Table 1.6 — Structural differences between animal and plant cells.

Science note — the Svedberg unit (S)

The Svedberg unit (symbol S) is a measure of the sedimentation rate of a particle when centrifuged. It indicates the size of the molecule — larger molecules have a larger sedimentation coefficient. It depends on the particle's volume, shape and molecular mass: a heavier particle with a more compact shape has a greater Svedberg value than a lighter particle with a less compact shape. Named after the Swedish chemist Theodor Svedberg (1884–1971), who won the 1926 Nobel Prize in Chemistry for his work on colloids and the invention of the ultracentrifuge.

⚠ Exam trap — S values do not add up

A eukaryotic ribosome is 80S, made of a 60S and a 40S subunit. But $60 + 40 = 100$ , not 80. This is not a printing error. S measures sedimentation rate, not mass, so the values are not additive. Same for prokaryotes: 50S + 30S makes 70S.

5Cell Wall and Plasma Membrane

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

5.1 The cell wall

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 — an animal that must move cannot afford a rigid box around every cell.

Organism group	Cell wall is made of
Plants	Cellulose
Prokaryotes	Peptidoglycan
Fungi	Chitin

Table 1.7 — Chemical composition of the cell wall differs between groups.

Memory hook

"Plants Play Cello, Bacteria Play Piano, Fungi Play Chimes"

Cellulose (plants) · Peptidoglycan (prokaryotes) · Chitin (fungi).

Functions of the plant cell wall

Protects the plant cell.
Maintains its shape.
Prevents excessive uptake of water.
At whole-plant level, 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 — so the answer to the textbook's critical-thinking question is that the plant cell wall is fully permeable, not semipermeable. The membrane underneath is the selective one.

The three layers

Figure 1.3 — Layers of the plant cell wall. The middle lamella is shared and glues the two neighbouring cells together.

Layer	Where it is	Made of	Key points
Primary cell wall	Inner to the middle lamella; develops in a newly growing cell during cell division	Cellulose microfibrils (bundles of cellulose chains) running through a matrix of hemicelluloses and pectin	Thin and slightly flexible. Microfibrils show a crisscross arrangement in layers, giving great strength. Adapted to growth — stretches plastically, i.e. irreversibly. Every cell produces one.
Secondary cell wall	Between the primary cell wall and the plasma membrane; only in sclerenchyma cells	Cellulose, hemicelluloses, lignin, inorganic salts and waxes	Develops only after the cell reaches maximum size, because it is thick and rigid and does not allow further growth. Cells with it are generally dead and provide support. Lignin cements and anchors the microfibrils and is mainly responsible for rigidity. Provides definite shape and mechanical support.
Middle lamella	Between the primary cell walls of two adjacent cells	Sticky, gel-like magnesium and calcium salts and pectin	Holds neighbouring cells together — the glue of plant tissue.

Table 1.8 — The three layers of the plant cell wall. This is a standard extensive-answer question.

Science titbit — pectin

Pectin is a polymer of around 200 galacturonic acid molecules. The majority of its carboxyl groups are methylated. It is less hydrophilic than pectic acid but soluble in hot water. Pectic acids are strongly hydrophilic and form insoluble gels with $Ca^{2+}$ and $Mg^{2+}$ . Both are major components of the middle lamella but are also found in primary walls. This is exactly why jam sets — the pectin from the fruit forms a gel.

5.2 The plasma membrane

Plasma membrane examinable

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

Chemical composition

Component	Proportion
Proteins	60–80%
Lipids	20–40%
Carbohydrates	Small quantity

Table 1.9 — Chemical composition of the plasma membrane.

The fluid mosaic model

The model proposes that the membrane is a phospholipid bilayer in which protein molecules are either partially or wholly embedded. The proteins are scattered throughout the membrane in an irregular pattern — the textbook's own image is just like large icebergs floating in the sea. Hold on to that picture: the sea is fluid and moving (the lipid bilayer), the icebergs drift about in it (the proteins). Together, a moving pattern — a fluid mosaic.

The pattern of distribution of proteins can vary from membrane to membrane, and also on the two surfaces of the same membrane. The membrane is about 7 nm thick.

Figure 1.4 — The fluid mosaic model. Proteins float in the phospholipid bilayer like icebergs in the sea.

How the bilayer is arranged

The lipid part consists of two layers (a bilayer) of phospholipids, arranged so that their hydrophobic ends face each other while the hydrophilic ends appear on the surfaces. Steroids — cholesterol — are wedged into the bilayer at intervals. The plasma membrane is asymmetrical: its two surfaces and halves are not identical.

Most membrane proteins drift sideways in the fluid bilayer. The proteins within a membrane determine most of its functions. Carbohydrates are attached either to proteins (glycoproteins) or to lipids (glycolipids), generally on the outer side. Filaments of the cytoskeleton are present on the inner surface, supporting the membrane.

What controls membrane fluidity

The lipid part controls the fluidity of the membrane.
When the concentration of unsaturated fatty acids in the phospholipids becomes greater, the bilayer becomes more fluid, making the 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

Type of protein	Function
Transport channel	Has a channel through which a substance simply moves across the membrane
Carrier	Combines with a substance and helps it move across the membrane
Enzyme	Some plasma membrane proteins have enzymatic functions
Receptor	Receives signals from other cells. For example, hormones circulate in the blood but bind to specific target cells with specific receptors
Antigen	Enables cells to recognise other cells

Table 1.10 — The five roles of plasma membrane proteins.

Memory hook

"CCERA" — Channel, Carrier, Enzyme, Receptor, Antigen.

Glycolipids and glycoproteins as cell surface markers

Mostly glycolipids and glycoproteins act as cell surface markers. They are involved in cell-to-cell recognition and in sticking the correct cells together in tissues. Think of them as the name badge on a uniform — that is how one cell knows another belongs to the same body.

Regulating the cell's interaction with its environment

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

Techniques used to study the cell membrane

Atomic force microscopy — a biophysical imaging technique.
Super-resolution fluorescent microscopy.
Scanning electron microscopy (SEM) — one of the fundamental techniques for membrane characterisation. It gives morphology and topography data of prepared membranes, and can be used to determine pore size in a porous membrane.

6Cell Signalling

Cell signalling examinable

The process by which cells communicate with other cells within their body or with the external environment is called cell signalling. Put simply — the transfer of information from one cell to another.

Here is a familiar picture. A WAPDA control room sends an instruction down a line to a grid station. The line carries the message, the station receives it, and only then does the light in your house switch on. Reception, transduction, response. Cells work exactly this way.

6.1 Ligands and receptors

The signalling molecules are also known as ligands. They initiate signalling. They can be proteins, lipids, amino acid metabolites, gases and many others.
The proteins that respond to ligands are called receptors.
A signalling molecule will bind to a specific receptor that typically binds only one type of signalling molecule — like one key for one lock.

6.2 The three stages of signalling

Stage	What happens
1. Reception	The target cell's detection of a signal molecule coming from outside the cell. A chemical signal is detected when it binds to a receptor protein located at the cell's surface or inside the cell.
2. Transduction	The conversion of a signal from outside the cell into a form that can bring about a specific cellular response. The binding of the signal molecule changes the receptor protein in some way, initiating transduction.
3. Response	The transduced signal triggers a specific cellular response — such as catalysis by an enzyme, rearrangement of the cytoskeleton, or activation of a specific gene in the nucleus.

Table 1.11 — Reception → Transduction → Response. The whole series of steps is called a signal transduction pathway.

6.3 The two pathways

Everything here turns on one question: can the signal molecule get through the membrane or not? Proteins cannot. Steroids can. That single fact produces two completely different pathways.

Figure 1.5 — Protein signalling versus steroid signalling. The difference begins with solubility.

Protein signalling

Protein and peptide hormones are water soluble, so they cannot pass through the plasma membrane. These hormones — or an environmental stimulus — are the first messenger. They bind with their receptors on the plasma membrane of the target cell, starting a series of events inside 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 signalling

Small hydrophobic ligands can directly diffuse through the plasma membrane and interact with internal receptors. The 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), so they freely diffuse across the plasma membrane. They bind to receptors in either the cytoplasm or the nucleus of the target cell, forming an active receptor–hormone complex. This activated complex moves into the nucleus and binds directly to DNA, acting as a transcription factor for gene expression. Examples: estrogen, progesterone and testosterone.

Protein signal	Steroid signal
Water soluble — cannot cross the membrane	Lipophilic — freely diffuses across the membrane
Receptor is on the plasma membrane surface	Receptor is inside — cytoplasm or nucleus
Needs a second messenger such as cAMP	No second messenger needed
Response: enzyme activation, gene activation	Complex binds DNA directly as a transcription factor

Table 1.12 — Protein signal against steroid signal, side by side.

Memory hook

"Water waits outside, fat walks in."

Water-soluble protein hormones wait at the door and send a messenger (cAMP) inside. Fat-soluble steroid hormones walk straight in and go to the nucleus themselves.

Worked scenario 1 — Identifying a signalling pathway

Given

A hormone binds to a receptor on the outer surface of a liver cell. Shortly afterwards, the level of cAMP inside the cell rises sharply.

Required

Identify the type of hormone and explain why it behaves this way.

Approach

Use the receptor's location and the presence of a second messenger to decide which of the two pathways is operating.

Steps

1. The receptor is on the outer surface. Only a molecule that cannot cross the membrane needs a surface receptor.
2. Protein and peptide hormones are water soluble and cannot pass through the plasma membrane.
3. cAMP is a second messenger. A second messenger is only generated when the first messenger stays outside.
4. A steroid hormone would have diffused in and gone straight to an internal receptor — no second messenger would be needed.

Result

Both clues — surface receptor and cAMP — point to the same pathway.

∴ Answer

It is a protein (or peptide) hormone acting through the protein signalling pathway. Because it is water soluble it cannot cross the membrane, so it acts as the first messenger at a surface receptor and generates cAMP as the second messenger, which then activates enzymes and genes inside the cell.

⚠ Exam trap

Students write that the second messenger "carries the hormone inside". It does not. The hormone never enters the cell. It changes the receptor, and the changed receptor causes a different molecule — cAMP — to be made inside. The message crosses; the molecule does not.

7Membrane Transport Mechanisms

Cells need food materials, salts, water and oxygen. They also need to get rid of substances such as carbon dioxide.

Membrane transport examinable

A set of transport mechanisms that control the movement of solutes such as ions and small molecules through a biological membrane. It depends upon the permeability, the solute concentration, and the size and charge of the solute.

There are four types of transport mechanism: simple diffusion, facilitated diffusion, osmosis and active transport. The first three are passive. Only active transport uses energy.

Figure 1.6 — The four membrane transport mechanisms. Notice which arrows run downhill and which runs uphill.

7.1 Simple diffusion

Diffusion examinable

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

Molecules travel directly through the membrane in simple diffusion. Small molecules such as water, carbon dioxide and oxygen pass through the cell membrane fairly easily, so diffusion equalises their concentration inside and outside the cell all the time.

An important detail: 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. Think of two crowds passing through the same gate in opposite directions — neither one cares about the other.

Everyday anchor

Someone lights agarbatti in the far corner of a room and within a minute you can smell it at the door. Nobody carried it to you. The scent molecules simply moved from where they were crowded to where they were not. That is simple diffusion, and it cost nothing.

7.2 Facilitated diffusion

Most water-soluble molecules cannot pass through the phospholipid bilayer. To traverse the membrane directly, a molecule needs to be small and non-polar. Other molecules can only diffuse across with the help of two types of transport protein.

Transport protein	How it works
Channel proteins	Help in the entry and exit of substances. Two kinds: open channel proteins create a pore in the membrane and allow charged molecules to pass through; gated channel proteins are either closed or open and so regulate entry and exit.
Carrier proteins	Present on the cell membrane. They carry the molecules, change the shape of the molecules, and release them on the other side. Temperature and saturation affect carrier proteins.

Table 1.13 — The two transport proteins of facilitated diffusion.

Facilitated diffusion examinable

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

7.3 Simple versus facilitated diffusion

Simple diffusion	Facilitated diffusion
A type of passive transport	A type of passive transport
Substances move from higher to lower concentration	Substances move from higher to lower concentration
Does not directly require chemical energy such as ATP or GTP	Does not directly require chemical energy such as ATP or GTP
Transport proteins not required	Transport proteins required
Rate is generally slower but more straightforward, as it does not rely on the binding capacity of membrane proteins	Rate is generally faster, but affected by temperature and by the types of membrane protein involved, and may be affected by membrane protein inhibitors
Small non-polar molecules (e.g. oxygen, carbon dioxide) diffuse easily across the plasma membrane	Polar molecules (e.g. glucose, amino acids), larger ions (e.g. sodium ions, chloride ions) and large non-polar molecules (e.g. retinol) use it

Table 1.14 — Comparison between simple and facilitated diffusion. Note the first three rows are identical — that is the point.

⚠ Exam trap

Do not write that facilitated diffusion "needs energy" just because it uses a protein. It needs a protein, not ATP. It is still passive transport, and the molecule still moves downhill.

7.4 Osmosis

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

Osmosis examinable

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 from the textbook

Feeling thirsty after having salty food.
Dialysis of the kidney.
Swelling of resins and seeds when they are soaked in water.

Two related terms worth knowing

Osmotic pressure is the minimum pressure applied to a solution to stop the flow of solvent molecules through a semipermeable membrane. Water potential is a measure of the tendency of water to move from one place to another.

⚠ Exam trap — the wording that traps everyone

The osmosis definition says molecules pass "from low concentration to high concentration". Students panic and think osmosis is active. It is not. The definition is talking about solute concentration. In terms of water, the water is still moving from where water is abundant to where water is scarce — downhill for water. Osmosis is passive.

7.5 Active transport

Active transport examinable

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, with the use of external energy. Movement is usually in one direction only.

Compare it to lifting a bucket of water from the ground floor to the roof. Water will run down a pipe by itself; to send it up, you must pay — with a pump and electricity. Active transport is the cell's pump, and ATP is its electricity bill.

Type	Energy source and mechanism
Primary active transport	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 the example. Cell membranes have sodium pumps that actively pump 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. Its importance is shown by the fact that more than a third of the cell's ATP is used to pump sodium and potassium.
Secondary active transport	Uses electrochemical energy and takes place across a biological membrane. A transporter protein couples the movement of an electrochemical ion (typically $Na^+$ or $H^+$ ) down its electrochemical gradient to the upward movement of another molecule or ion against a concentration or electrochemical gradient.

Type

Energy source and mechanism

Primary active transport

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 the example. Cell membranes have sodium pumps that actively pump 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. Its importance is shown by the fact that more than a third of the cell's ATP is used to pump sodium and potassium.

Secondary active transport

Uses electrochemical energy and takes place across a biological membrane. A transporter protein couples the movement of an electrochemical ion (typically

Na^+

H^+

) down its electrochemical gradient to the upward movement of another molecule or ion against a concentration or electrochemical gradient.

Table 1.15 — Primary and secondary active transport.

Figure 1.7 — The sodium–potassium pump, the textbook example of primary active transport.

Active transport in plants

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

Examples of active transport

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

Worked scenario 2 — Naming the transport mechanism

Given

A root cell of a wheat plant is absorbing mineral ions from the soil. The concentration of these ions is already higher inside the root cell than in the surrounding soil water. When the soil becomes waterlogged and oxygen supply is cut off, the absorption stops.

Required

Name the transport mechanism and justify the answer using the evidence given.

Approach

Check the direction of movement against the gradient, then check whether the process depends on energy.

Steps

1. Ions are moving from lower concentration (soil) to higher concentration (inside the cell) — that is against the concentration gradient.
2. All passive mechanisms — simple diffusion, facilitated diffusion, osmosis — only move substances down a gradient. All three are eliminated.
3. Absorption stops when oxygen is cut off. No oxygen means no aerobic respiration; no respiration means no ATP.
4. The textbook states plainly that in primary active transport, without respiration, active transport is not possible.

Result

Uphill movement plus dependence on respiration equals only one possible mechanism.

∴ Answer

Primary active transport. The ions move against the concentration gradient, which requires external energy supplied as ATP from respiration. When waterlogging removes oxygen, respiration halts, ATP is no longer produced, and the pumping stops — which is exactly what is observed.

8Cytoplasm and the Organelles

The living matter of a cell is called protoplasm. In eukaryotic cells it divides into two parts: the cytoplasm and the nucleus.

8.1 Cytoplasm and cytosol

Cytoplasm examinable

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

It is about 90% water and forms a solution containing 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.

Cytosol is the matrix of the cytoplasm. It surrounds the cell organelles in eukaryotes, and is the water-soluble component of the cytoplasm — a liquid matrix around the organelles, a complex mixture of substances dissolved in water. The term now refers to the liquid phase of the cytoplasm in an intact cell. In prokaryotes, most of the chemical reactions of metabolism take place in the cytosol.

The cytoplasm acts as a site of metabolism and storehouse of the cell. Metabolic pathways such as protein synthesis and glycolysis generally occur in the cytosol.

Cell organelles examinable

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

8.2 Endoplasmic reticulum

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 — the ER lumen — from the cytosol.

There are two types, and most cells contain both. Some cells, such as skeletal muscle cells, have more smooth ER, where it is called sarcoplasmic reticulum.

	Smooth ER	Rough ER
Appearance	Continuous with the rough ER. Ribosomes are not attached, so it has a smooth appearance.	Has ribosomes attached to the side facing the cytoplasm, so it looks rough under the electron microscope.
Functions	Functions in diverse metabolic processes. Its enzymes are important to the synthesis of lipids including oil, cholesterol, phospholipids and steroids — for example the sex hormones of vertebrates and the steroid hormones of the adrenal glands. Other enzymes help to detoxify drugs and poisons, especially in liver cells.	Many specialised cells secrete proteins produced by the ribosomes attached to it. Secretory proteins depart wrapped in membranes or vesicles that bud from a specialised region called the transitional 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, then transfers membrane as transport vesicles to other components of the endomembrane system.

Table 1.16 — Smooth ER and rough ER compared.

Memory hook

"Rough makes Ribosome-proteins; Smooth makes Steroids."

Both begin with the same letter as their job. R for rough, R for ribosome and protein secretion. S for smooth, S for steroid and lipid synthesis.

8.3 Ribosomes

Ribosomes examinable

Particles made of ribosomal RNA and protein. These organelles carry out protein synthesis.

First observed using the electron microscope as dense granules.
Roughly spherical, granular, non-membranous bodies found in both eukaryotic and prokaryotic cells.
Eukaryotic ribosomes are larger — 80S. Prokaryotic ribosomes are slightly smaller — 70S.
They can be seen only under the electron microscope.
Made of almost equal amounts of RNA and protein, so they are ribonucleoprotein.
Formed in the nucleolus, then transported to the cytoplasm through the nuclear pore.

Subunits

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

Polysome (polyribosome) examinable

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

Short question you will meet

"What holds the ribosomes together in a polysome?" The answer is the single mRNA molecule that all of them are attached to and reading at once.

8.4 Golgi complex

Found in all eukaryotic cells. Discovered by the Italian biologist Camillo Golgi in 1898. Also called the Golgi apparatus or Golgi bodies.

Structure

It 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, new cisternae are constantly formed by the fusion of vesicles from the smooth ER. This outer or forming face (cis face) is convex.
The inner end is concave and is called the maturing face (trans face), where the cisternae break up into vesicles again.

Figure 1.8 — The Golgi complex. Think of a post office: parcels come in one door, get labelled and sorted, and leave by another.

Functions

The most important function is the processing of cell secretions, which is why these organelles are abundant in secretory cells. Cell secretions consist mainly of proteins. The Golgi complex collects these proteins from the RER through the SER, modifies them to perform specific functions, then exports them in the form of vesicles.
Certain organelles — lysosomes, peroxisomes and glyoxysomes — also originate from the Golgi complex.
Involved in the formation of conjugated molecules such as glycoproteins and lipoproteins.
In plant cells during cell division, the Golgi complex gives rise to vesicles containing cell-wall-synthesising materials. At cytokinesis these vesicles arrange on the cell equator, fuse together and form a structure called the phragmoplast, from which the new cell wall is later derived.

A route you will be asked to trace

When a glycoprotein is being synthesised for secretion, the route it takes is RER → SER → Golgi complex. Made on the rough ER, passed through the smooth ER, finished and packaged by the Golgi.

8.5 Vesicles

The word vesicle derives from the Latin vesicula, meaning "small bladder". Vesicles are small, membrane-enclosed sacs — a small structure within a cell consisting of fluid enclosed by a lipid bilayer. A vesicle consists of a hydrophilic head and a hydrophobic tail.

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

Functions of vesicles

Transport substances from one cell to another, and from one part of a cell to another — for example proteins and other molecules. The first step in vesicular transport is the formation of a vesicle by budding from the membrane.
Involved in metabolism, buoyancy control and enzyme storage.
Can act as chemical reaction chambers.

8.6 Lysosomes

Lyso means splitting and soma means body. These are single-membranous, spherical vesicles containing digestive or hydrolytic enzymes. Notice the -ase suffix that marks nearly every enzyme name you will meet from here on — hydrolase, peroxidase, catalase, ATP synthase. Whenever you see -ase at the end of a word in biology, read it as "this is an enzyme".

How lysosomes are formed

The lysosomal enzymes are made by the RER, transported to the Golgi complex through the SER, and after modification are released from the trans face of the Golgi complex in the form of vesicles. Such vesicles are lysosomes. Newly formed lysosomes, before they begin their functions, are called primary lysosomes.

Lysosomes contain about 40 different digestive enzymes which 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 arising from endocytosis, phagocytosis or autophagocytosis.

In plants and fungi, certain vacuoles carry out enzymatic hydrolysis — a function shared by lysosomes in animal cells.

The three key processes

Process	What happens
Endocytosis	Foreign particles are pulled into the cell. The cell membrane falls in on itself (invagination), creating a vacuole or pouch around the external contents and bringing them into the cell. Then the lysosome fuses with it and digests the contents.
Autophagy	The process by which unwanted structures within the cell are engulfed and digested within the lysosomes. This is the cell's self-eating process, in which a lysosome begins to digest the cell's own organelles. Such lysosomes are also called autophagosomes. It occurs during starvation to obtain energy, or routinely to control the number of specific organelles.
Autolysis	Especially during the developmental phase, when a particular cell is required to be disintegrated, a type of programmed cell death is committed. Lysosomes burst and their enzymes are quickly dispersed throughout the cytoplasm, disintegrating the cell into fragments which are phagocytosed by other cells. Because of this, lysosomes are called suicidal bags.

Table 1.17 — Endocytosis, autophagy and autolysis.

The textbook's own example of autophagy

If someone starts heavy muscular exercise, the number of mitochondria begins to increase in his muscle cells. If he stops exercising, the number of mitochondria decreases again — by autophagy. The body does not maintain machinery it no longer uses.

Worked scenario 3 — The tadpole's tail

Given

A tadpole's tail is gradually broken down during metamorphosis into an adult frog.

Required

Name the organelle that increases in number in the cells of the tail at this time, and explain the process.

Approach

Identify what kind of activity "gradual breakdown of the animal's own tissue" is, then match it to the organelle responsible.

Steps

1. The tail is part of the tadpole's own body, so this is not digestion of foreign material — it is the destruction of the animal's own cells.
2. The organelle containing about 40 hydrolytic enzymes capable of breaking down every major macromolecule is the lysosome.
3. The textbook states that during the developmental phase, when a cell is required to be disintegrated, lysosomes burst and disperse their enzymes — this is autolysis, programmed cell death.
4. The fragments are then phagocytosed by other cells, so nothing is wasted; the material is recycled into the growing frog.

Result

Tail cells are removed deliberately and their contents reused.

∴ Answer

Lysosomes increase in number. They carry out autolysis — programmed cell death — bursting and releasing hydrolytic enzymes that disintegrate the tail cells. This is precisely why lysosomes are called suicidal bags.

⚠ Exam trap — three similar words

Autophagy is the cell eating its own organelles and surviving. Autolysis is the cell destroying itself completely. Phagocytosis is the cell eating something from outside. Mixing these up costs marks in almost every session.

8.7 Peroxisomes and glyoxysomes

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

Peroxisomes

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

Peroxisomes contain oxidative enzymes such as peroxidases, catalases and glycolic acid oxidases. They are abundant in liver cells, where they are involved in the formation and decomposition of hydrogen peroxide — which is how they got their name.

The detoxification of alcohol — the two-step story

Step 1. Alcohol is oxidised into hydrogen peroxide ( $H_2O_2$ ) with the help of the peroxidase enzyme.
Step 2. Hydrogen peroxide is itself a toxic molecule, so it is immediately broken down into water and oxygen by another enzyme called catalase.

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. Germinating seedlings convert stored fatty acids to carbohydrates, achieved through a metabolic pathway called the glyoxylate cycle, whose enzymes are located in the glyoxysomes.

Why this makes sense

An oil seed — think of a sunflower or mustard seed — stores its food as fat, not sugar. But a growing seedling needs sugar. The glyoxysome is the little workshop that converts one into the other. Once the seedling can photosynthesise, it does not need the workshop any more — which is exactly why glyoxysomes are found only at the seedling stage.

8.8 Vacuoles

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

Cell type	Vacuole and its role
Animal cells	Food vacuoles are formed by phagocytosis.
Freshwater protists	Many have contractile vacuoles that pump excess water out of the cell, maintaining a suitable concentration of ions and molecules inside.
Young plant cells	Many small vacuoles hold reserves of important organic compounds. They may also help protect the plant against herbivores by storing compounds that are poisonous or unpleasant to animals.
Mature plant cells	Generally contain a large central vacuole formed by the joining of smaller vacuoles.

Table 1.18 — Vacuoles across different cell types.

The solution inside the central vacuole is called cell sap. It is the plant cell's main reservoir of inorganic ions, including potassium and chloride. The central vacuole plays a major role in mechanical support by maintaining turgor, and acts as a storehouse of the cell. The membrane separating the vacuole from the cytoplasm is called the tonoplast.

⚠ Exam trap

The membrane around the vacuole has its own name — tonoplast — and the fluid inside has its own name — cell sap. One-mark questions ask for exactly these words. Do not answer "vacuole membrane" and "vacuole fluid".

8.9 Mitochondria

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. The number correlates with the cell's level of metabolic activity — cells that move or contract have proportionally more mitochondria per volume than less active cells. Mitochondria are self-replicating: they can divide themselves to increase their number, and they divide by fission.

Figure 1.9 — The mitochondrion. Cristae exist for one reason: more surface means more ATP.

Structure

Mitochondria are cylindrical or rod-shaped and enclosed by a double membrane.
The outer membrane is smooth and somewhat like a sieve due to the presence of porins — 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, which are actually ATP synthase enzymes. Other complexes in the inner membrane serve as electron carriers in the electron transport chain.

Two internal compartments

Intermembrane space — the narrow region between the inner and outer membranes.
Mitochondrial matrix — enclosed by the inner membrane. A jelly-like material containing 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 required by mitochondria are synthesised by their own metabolic machinery.

Function

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 steps of cellular respiration such as the Krebs cycle. Proteins that function in ATP generation through the electron transport chain are found in the inner membrane.

Extra reading — the endosymbiont idea

Mitochondria and chloroplasts display similarities with bacteria: both are self-replicating, both have their own genetic system and metabolic machinery — small circular DNA, all kinds of RNA, and 70S ribosomes. Both can survive outside the cell in artificial medium if carefully fractionated. Based on these observations, evolutionists believe they were once independent organisms engulfed by the early ancestor of eukaryotic cells, eventually becoming an endosymbiont — a cell living within another cell. Lysosomes regulate the number of mitochondria; excess mitochondria are digested by lysosomes. And because mitochondria are contained within ova but not within the heads of sperm cells, all the mitochondria in a fertilised egg are derived from the mother.

8.10 Plastids

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

Proplastids are young, immature and developing plastids. They are self-replicating organelles. There are three types of mature plastids:

Plastid	Description
Leucoplasts	Colourless; found in parenchyma cells of root, stem and seeds.
Chromoplasts	Synthesise different coloured pigments other than green.
Chloroplasts	Found in green parts of plants; act as the site of photosynthesis.

Table 1.19 — The three types of plastid.

Structure of the chloroplast

The chloroplast is a discoid structure consisting of three parts: envelope, stroma and thylakoids.

Envelope — each chloroplast is bounded by a smooth double membrane. The outer membrane, like that of mitochondria, contains porins and is therefore freely permeable to small molecules. The inner membrane is semipermeable and rich in protein. Between them lies the intermembrane space.
Stroma — the ground mass of the chloroplast; a colourless proteinaceous substance which, like the mitochondrial matrix, contains a small circular DNA, all kinds of RNA, ribosomes (70S) and various enzymes.
Thylakoids — the stroma contains a system of chlorophyll-bearing, double-membrane, flattened sac-like structures. There are two types.

Thylakoid type	Details
Smaller thylakoids	Disc-like sacs piled over one another like a stack of coins. Each stack is called a granum (plural: grana). Each granum consists of 25–50 thylakoids, and there are about 40–60 grana in each chloroplast. Photosynthetic pigments are found in the membranes of the smaller thylakoids.
Larger thylakoids	Connect the grana with each other; also called intergrana. These membranes are colourless as they do not have pigments.

Table 1.20 — The two types of thylakoid.

Function of the chloroplast

Light-dependent reaction — sunlight is captured and transformed into ATP. Takes place in the grana region.
Light-independent reaction (dark reaction) — $CO_2$ is reduced to make carbohydrates. The enzymes for this activity are found in the stroma.

Memory hook

"Light hits the Grana; Dark works in the Stroma."

Light needs pigment, and pigment sits in the grana. The dark reaction needs only enzymes, and enzymes float in the stroma.

8.11 Centrioles

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

Rod-shaped structures, usually occurring in pairs, at right angles to each other near one pole of the nucleus.
Each centriole is composed of nine triplets of microtubules arranged circularly around a central axis.
Just before cell division, the pair of centrioles duplicates into two pairs, which migrate to the opposite sides of the nucleus.
Both centriole pairs give rise to microtubules (spindle fibres) during cell division. The whole structure of spindle fibres is known as the mitotic apparatus, which helps in the distribution of chromosomes between the daughter cells.
Centrioles also give rise to the basal bodies of cilia and flagella.

8.12 The cytoskeleton

The term cytoskeleton is generally applied to three different kinds of fibrous structures distributed from the nucleus to the plasma membrane throughout the cytoplasm of a eukaryotic cell. These fibres are microfilaments, microtubules and intermediate filaments.

8.13 The nucleus

The nucleus is the most prominent and the most important part of a cell. In animal cells it is found in the centre — with the exception of muscle fibre cells. In an adult plant cell it is slightly away from the centre due to the presence of the large central vacuole.

A typical eukaryotic nucleus consists of the nuclear envelope, nucleoplasm, nucleoli and chromatin.

Nuclear envelope

Also called the nuclear membrane; a double membrane covering that forms the boundary of the nucleus.
Both membranes are separated by a fluid-filled perinuclear space, and are composed of lipid bilayer and proteins.
The outer membrane is covered with ribosomes and is connected with the membranes of the ER.
There are numerous nuclear pores, composed of a specialised transport protein called nucleoporin. At the point of a pore, both membranes are interconnected.
These pores regulate the nucleo-cytoplasmic exchange of materials — RNA and ribosomal proteins moving out to the cytoplasm, and proteins (such as DNA polymerase), carbohydrates, signalling and moving lipids into the nucleus. Smaller molecules simply diffuse through the pores; larger molecules are recognised by specific signal sequences and diffused with the help of nucleoporin.

Nucleoplasm

The transparent semifluid ground substance, formed of 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

A non-membrane-bound structure in the nucleoplasm. A cell may have one or more nucleoli.
It appears during interphase and disappears during cell division.
It 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. This is also why the nucleolus contains the highest concentration of RNA of any cell structure.

Chromatin and chromosomes

Chromatin is a network of thin, thread-like structures made up of DNA and proteins. During cell division, chromatin fibres 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. The centromere is a constriction functionally related to the movement of chromosomes during cell division. Each centromere has a complex kinetochore protein present on opposite sides of the constriction.

⚠ Exam trap

Chromatin and chromosome are the same material in two different states, not two different things. Chromatin is the uncoiled, working form during interphase. Chromosome is the condensed, coiled, transport-ready form during cell division. Write it as a change of state and the mark is yours.

8.14 Organelle quick-reference

Membrane status	Organelles
Double membrane	Nucleus, mitochondrion, chloroplast (and plastids generally)
Single membrane	Endoplasmic reticulum, Golgi complex, lysosome, peroxisome, glyoxysome, vacuole, vesicles
No membrane	Ribosome, nucleolus, centriole, cytoskeleton fibres

Table 1.21 — A frequent short question: which organelles are single-, double-, or non-membranous.

Contains DNA	The three, and only three
Nucleus	Chromatin and chromosomes — the main genetic store
Mitochondrion	Small circular DNA in the matrix
Chloroplast	Small circular DNA in the stroma

Table 1.22 — The DNA-containing organelles. An MCQ asks which organelle always contains DNA — among centriole, Golgi complex, lysosome and mitochondria, the answer is mitochondria.

9Prokaryotic and Eukaryotic Cells

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

Figure 1.10 — Prokaryotic and eukaryotic cell compared. The defining difference is the nucleus.

Prokaryotic cells	Eukaryotic cells
Nucleus and other membrane-bound organelles are absent	Nucleus and other membrane-bound organelles are present
Always unicellular	Unicellular and also multicellular organisms
DNA is stored in the cytoplasm	DNA is stored within the nucleus
Have one primary circular chromosome and various plasmids	DNA is stored in double-stranded chromosomes
Ribosomes are 70S, with 30S and 50S subunits	Ribosomes are 80S, with 40S and 60S subunits
Locomotive structures composed of repeated flagellin, a hook and a motor complex	Locomotive structures composed of dynein and plasma membrane
Divide by binary fission	Divide by mitosis and meiosis

Table 1.23 — Differences between prokaryotic and eukaryotic cells. Learn all seven rows; this is a guaranteed question.

What is present in a prokaryotic cell?

A recurring MCQ. The answer is cytoplasm, DNA and ribosomes — the three things every cell must have. What is missing is the nuclear envelope, mitochondria, chloroplast, ER, Golgi complex and lysosomes.

10Stem Cells

Stem cell examinable

A cell with the unique ability to develop into specialised cell types 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 — a process called 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.

They are called stem cells because, like the stem of a plant, everything else branches out of them. From one stem come leaves, flowers and fruit — all different, all from the same origin.

10.1 Advantages of using stem cells

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

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

10.2 The three main types

Type	Description
Adult stem cells	Supply new cells as an organism grows and replace cells that get damaged. They are multipotent — they can only change into some specific cells in the body, not any cell.
Embryonic stem cells (ESCs)	Provide new cells for a growing embryo. They are pluripotent — they can naturally produce every type of cell in the body.
Induced pluripotent stem cells (iPSCs)	Stem cells that scientists make in the laboratory. They can develop into any cell type.

Table 1.24 — The three main types of stem cell.

10.3 Classification by potency

Researchers also categorise stem cells according to their potential to differentiate into other types of cell. Read this list from most powerful to least — it forms a neat ladder.

Figure 1.11 — The potency ladder. Notice the width narrows as the ability narrows.

Memory hook

"Total, Plenty, Many, Few, One"

Totipotent = total · Pluripotent = plenty · Multipotent = many (one family) · Oligopotent = a few · Unipotent = one. The Latin prefix always tells you the answer.

⚠ Exam trap

A unipotent cell can only make one kind of cell — but it is still a stem cell, because it can renew itself. Self-renewal, not versatility, is what makes something a stem cell. Also note: an MCQ asks which stem cells are known as true stem cells — the answer is totipotent.

10.4 Induced pluripotent stem cells (iPSCs)

How they are generated

Signals in the body tell a cell what type of specialised cell it should be, by switching some genes on and some genes off. To generate iPSCs, scientists re-introduce the signals that normally tell stem cells to stay as stem cells in the early embryo. These switch off any genes that tell the cell to be specialised, and switch on genes that tell the cell to be a stem cell.

Advantages of iPSCs	Disadvantages of iPSCs
Ability to give rise to almost any cell type desired	For human iPSC production, viruses were initially used as delivery vectors for the genes required for cell reprogramming
Avoidance of the ethical concerns associated with human embryonic stem cells	The main issue is the use of retroviruses, which are associated with cancer — they can insert their DNA anywhere in the genome and subsequently trigger cancer-causing gene expression
Generated from the patient themselves, so they could be used to grow new organs with a lower risk of being rejected	The risk of overgrowth of the transplanted cells — in other words, cancer — continues to be a major hurdle

Table 1.25 — Evaluating iPSCs. Note the ✗ and ✓ symbols read correctly even in a black-and-white printout.

Science titbit

iPSCs were first described by Shinya Yamanaka and his colleagues at Kyoto University in 2006. They were jointly awarded the 2012 Nobel Prize in Physiology or Medicine for their work.

11Endocytosis and Exocytosis

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

Figure 1.12 — Endocytosis and exocytosis. Same machinery, opposite direction.

11.1 Endocytosis

Endocytosis examinable

The process by which substances are engulfed within the cell membrane, which then forms a vesicle containing the ingested material.

The two main subtypes are phagocytosis and pinocytosis.

Phagocytosis

The process through which phagocytes or liver cells ingest or consume other cells or particles. A phagocyte may be an Amoeba or a white blood cell. Some species — sponges, Amoeba — feed this way. Extensions of the cytoplasm called 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

Also known as cell drinking. 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

This is a kind of pinocytosis. Macromolecules bind to receptors on the surface of the plasma membrane. 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. The textbook's example is cholesterol absorption.

Memory hook

"Phago = food. Pino = ping (a drink)."

Phagocytosis is cell eating — solid particles. Pinocytosis is cell drinking — fluids and dissolved nutrients.

11.2 Exocytosis

Exocytosis examinable

The process by which the transfer of material takes place from inside 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 the release of secretions in the sweat glands.

12Cell Division

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

12.1 The cell cycle

Cell cycle examinable

A series of stages a cell passes through in order to divide and produce new cells.

The process of cell division can be divided into two main phases: mitosis, the division of the nucleus, and cytokinesis, the division of the cytoplasm.

Mitosis is only a part of the cell cycle. The mitotic (M) phase includes both mitosis and cytokinesis, and the M phase is the shortest part of the cell cycle. Mitotic cell division alternates with a much longer stage called interphase.

Figure 1.13 — The cell cycle. Chromosomes are duplicated only during S phase.

⚠ Exam trap

An MCQ asks which of the following does not occur in mitosis. The answer is replication of DNA — because DNA replication happens in the S phase of interphase, before mitosis begins. Condensation of chromosomes, separation of sister chromatids and spindle formation all do occur in mitosis.

12.2 Mitosis

The word mitosis comes from the Greek mitos, meaning thread, referring to the threadlike appearance of chromosomes during this period.

Mitosis examinable

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, arbitrarily divided into five phases for convenience of description: prophase, prometaphase, metaphase, anaphase and telophase.

Memory hook

"Please Pray More After Twilight"

Prophase · Prometaphase · Metaphase · Anaphase · Telophase — with Interphase before it all begins.

Stage	What happens
Interphase	A nuclear envelope surrounds the nucleus, which contains one or more nucleoli. By replication of a single centrosome, two centrosomes are formed, each with two centrioles. The chromosomes duplicated during S phase are not yet visible under a light microscope, as they have not condensed.
Prophase	Chromatin fibres become more tightly coiled and condense into discrete chromosomes 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, composed of centrosomes and the microtubules extending from them. The radial arrays of shorter microtubules extending from the centrosomes are called asters (stars). The centrosomes move away from each other due to the lengthening of the microtubules between them.
Prometaphase	During spindle formation, the nuclear membrane breaks. Spindle microtubules 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 now has a kinetochore. Some microtubules attach to the kinetochore, becoming kinetochore microtubules; non-kinetochore microtubules interact with those from the opposite pole.
Metaphase	The longest stage of mitosis, lasting about twenty minutes. The centrosomes are now at opposite ends of the cell. Chromosomes arrange on the metaphase plate — an imaginary plane equidistant between the two poles. The centromeres 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	The shortest stage, lasting only a few minutes. It begins when the two sister chromatids of each pair suddenly part; each chromatid becomes a full-fledged chromosome. The liberated chromosomes move towards opposite ends of the cell as their kinetochore microtubules shorten. Because these microtubules attach at the centromere region, the chromosomes move centromere first. The cell elongates as the non-kinetochore microtubules lengthen. By the end, the two ends of the cell have equivalent and complete collections of chromosomes.
Telophase	Two daughter nuclei begin to form. 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.

Table 1.26 — The stages of mitosis.

Cytokinesis

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

⚠ Exam trap — longest and shortest

Metaphase is the longest stage of mitosis (about twenty minutes). Anaphase is the shortest (a few minutes). And the M phase is the shortest part of the whole cell cycle. These three facts get asked directly — do not confuse them.

Significance of mitosis

Important for the growth and multiplication of cells.
Ensures the two daughter cells inherit the same number of chromosomes, and hence the same characteristics as the parent cell.
Maintains the continuity of metabolism by transmitting to the daughter cells exactly the same information as is coded in the DNA of the parent cell.
Plays a significant role in wound healing, regeneration of damaged parts, and replacement of cells lost during normal wear and tear.
May give rise to tumour or cancerous growth if the process goes out of control.

12.3 Meiosis

Meiosis examinable

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

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

The first meiotic division

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

Stage	What happens
Interphase I	The DNA in the cell is copied, so two identical full sets of chromosomes are formed. There are two centrosomes outside the nucleus, each containing a pair of centrioles. Microtubules extend from these centrosomes.
Prophase I	The lengthiest process 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. Thin chromosomes become shorter and thicker. Homologous chromosomes start getting closer to each other and begin to pair lengthwise — this pairing is called synapsis. 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; the point of crossing appears as an X shape under the light microscope and is called a chiasma (plural: chiasmata). A chromosome segment is exchanged between the two homologous chromosomes at the chiasma — this is crossing over. The paired homologues then begin to separate by repelling; the tetrads become more evenly distributed. The nucleoli disappear, but the nuclear membrane is still present. The diad — two chromatids attached to a single centromere — behaves as a single unit throughout meiosis, held together by a common centromere.
Metaphase I	The nuclear membrane disintegrates. Microtubules form the spindle. Chromosomes line up in a double row — in pairs — on the equator. Microtubules bind to only one kinetochore of each centromere: the centromere of one homologue attaches to microtubules extending to one pole, while the centromere of the other homologue attaches to microtubules extending to the other pole.
Anaphase I	Attachment of chromosomes to the spindle is complete. The microtubules attached to homologous chromosomes slide over one another, so the spindle poles move apart. The spindle fibres shorten as they are dragged to the poles, and are broken by the action of enzymes. With this shortening, the attached chromosomes are pulled towards each pole. When shortening is complete, each pole has a single set of chromosomes, consisting of one member of each homologous pair.
Telophase I and cytokinesis	Chromosomes complete their movement to opposite poles. At each pole a full set gathers together. A membrane forms around each set to create two new nuclei. Through cytokinesis, the single cell forms two separate daughter cells, which are haploid.

Table 1.27 — The first meiotic division.

Figure 1.14 — Crossing over. Notice the colours swap over — that swap is why no two siblings are identical.

The second meiotic division

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

Stage	What happens
Interphase II	DNA does not duplicate. 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 I do not take place.
Metaphase II and Anaphase II	Chromosomes line up in the same fashion as in metaphase I. Again a random distribution of chromosomes takes place. The centromere divides, so 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.

Table 1.28 — The second meiotic division.

⚠ Exam trap — why the number halves

Students say "meiosis halves the chromosome number because there are two divisions." Be precise: DNA duplicates only once (in interphase I), but the cell divides twice. One duplication and two divisions is what produces four haploid cells. Write that sentence and you have earned the mark.

Significance of meiosis

The number of chromosomes becomes half in the gametes, so the chromosome number remains constant from generation to generation.
Provides a mechanism for the transmission of genetic material from one generation to the next.
Provides genetic variability.
Offers a chance for the production of the best adapted individual and a better chance of survival in a changed environment.
Provides raw material for evolution.

12.4 Mitosis versus meiosis

	Mitosis	Meiosis
Cells involved	Somatic cells	Germ line cells
Number of divisions	One	Two — meiosis I and meiosis II
Daughter cells	Two	Four
Chromosome number	Same as parent — daughter cells inherit the same number	Half the original amount of genetic information — haploid
Genetic outcome	Two genetically identical nuclei	Genetic variability through crossing over and random distribution
Crossing over	Does not occur	Occurs at the chiasma during prophase I
Purpose	Growth, multiplication, wound healing, regeneration, replacement	Production of sperms and eggs in animals, spores in plants; raw material for evolution

Table 1.29 — Mitosis and meiosis, side by side. Built from the textbook's own statements about each process.

Worked scenario 4 — Deducing the type of division

Given

A biologist observes a dividing cell under a light microscope. She sees chromosomes lined up on the equator in a double row, in pairs. Earlier, she had recorded X-shaped structures where chromatids appeared to cross.

Required

Identify the type and stage of division, and predict the chromosome number of the resulting cells relative to the parent.

Approach

Use the arrangement at the equator and the presence of chiasmata to distinguish mitosis from meiosis, then apply what each division does to chromosome number.

Steps

1. In metaphase of mitosis, chromosomes arrange in a single row on the metaphase plate.
2. The observation is a double row, in pairs — the textbook describes this exact arrangement for metaphase I of meiosis.
3. The X-shaped crossing structures are chiasmata, which form only during prophase I of meiosis. Crossing over does not occur in mitosis.
4. Both observations point to the first meiotic division.
5. Telophase I produces two haploid daughter cells; meiosis II then produces four cells in total, each haploid, because DNA duplicated only once.

Result

Paired arrangement plus chiasmata identifies meiosis I unambiguously.

∴ Answer

The cell is in metaphase I of meiosis. The process will ultimately yield four haploid daughter cells, each with half the chromosome number of the parent cell, and each genetically different due to crossing over at the chiasmata.

Final word from Athens Academy

This is a long chapter, and if it felt heavy the first time through, that is completely normal. Every student who has ever sat this paper felt the same on the first reading. The chapter is long because it is foundational — almost every unit that follows will lean on something you learned here.

So do not try to swallow it whole. Take one section a day. Read the prose, then cover the page and say the definition out loud. Draw the mitochondrion on a rough sheet without looking — badly is fine, the labels are what matter. Then move on. In twelve days you will have the whole chapter, and it will feel like yours rather than like something borrowed from a book.

And remember why any of this matters. Right now, as you read this line, roughly two million of your red blood cells are being replaced. Lysosomes are cleaning up. Mitochondria are making the ATP that lets your eyes track this sentence. You are not studying something distant — you are studying yourself.

You can do this. Go one section at a time, and keep going.

Athens Academy Islamabad · Biology · Grade 11 · Unit 1 · Cell and Sub-Cellular Organelles · FBISE · Exam 2027

🌱 Chapter 1 · Cells and Sub-Cellular Organelles