What is an organelle? Give four examples.

A discrete subunit of a cell that is adapted, by its structure, to carry out one or more specific functions. Examples include the nucleus, mitochondria, vesicles, ribosomes and the plasma membrane.

Why are the cell wall, cytoskeleton and cytoplasm not organelles?

The cell wall is outside the plasma membrane (extracellular). The cytoskeleton is a network extending through the whole cytoplasm, not a discrete unit. The cytoplasm is the whole region inside the membrane, with many functions rather than one specific one.

Why is tissue for cell fractionation kept in a cold, isotonic, buffered solution?

Cold slows enzymes that would digest the organelles; isotonic stops organelles gaining or losing water by osmosis and bursting or shrivelling; buffered keeps the pH constant so proteins are not denatured.

In differential centrifugation, in what order do the organelles sediment?

Largest and densest first, at the lowest speed. Nuclei (about 600–1,000 × g), then chloroplasts from plant tissue (about 1,000–4,000 × g), then mitochondria (about 10,000–20,000 × g), then fragments of ER and membrane, and finally ribosomes at the highest speeds (over 100,000 × g, in an ultracentrifuge).

What is the advantage of separating the nucleus from the cytoplasm?

Transcription happens in the nucleus and translation in the cytoplasm, so pre-mRNA can be modified (for example, introns removed) before it meets ribosomes. Only mature mRNA leaves through the pores.

Why can't prokaryotes modify mRNA before translating it?

They have no nucleus, so their DNA and ribosomes are in the same compartment. Ribosomes can start translating mRNA while it is still being transcribed.

Give three advantages of compartmentalization in the cytoplasm.

Enzymes and substrates are concentrated, so reactions are faster; incompatible processes are kept apart (e.g. lysosomal hydrolases away from the cell's macromolecules); each compartment can have its own optimal conditions, such as pH 4.5–5 in lysosomes.

How does a phagocyte digest a bacterium without digesting itself?

It engulfs the bacterium by endocytosis into a phagocytic vacuole. Lysosomes fuse with the vacuole, so their hydrolytic enzymes digest the bacterium inside it. The small products are then absorbed into the cytoplasm.

List four adaptations of the mitochondrion for ATP production.

A double membrane; a small intermembrane space, so a high proton concentration builds up quickly; cristae, giving a large surface area for electron transport chains and ATP synthase; a matrix in which the enzymes and substrates of the link reaction and Krebs cycle are concentrated.

List three adaptations of the chloroplast for photosynthesis.

A large surface area of thylakoid membranes (stacked in grana) carrying photosystems and ATP synthase; a small volume of fluid inside each thylakoid, so protons quickly reach a high concentration; Calvin cycle enzymes such as Rubisco and their substrates concentrated in the stroma.

Where do protons accumulate, and where is ATP made, in mitochondria and chloroplasts?

Mitochondria pump protons into the intermembrane space and make ATP in the matrix. Chloroplasts move protons into the thylakoid lumen and make ATP in the stroma.

What are the two functional benefits of the double membrane of the nucleus?

Pores can be formed by joining the outer and inner membranes; and the envelope can break up into vesicles during mitosis and meiosis, releasing the chromosomes, then be rebuilt around each daughter nucleus.

What moves through nuclear pores in each direction?

Out of the nucleus — mRNA and ribosome subunits. Into the nucleus — proteins made in the cytoplasm, such as histones and DNA and RNA polymerases, and nucleotides.

Contrast free ribosomes with ribosomes on the rough ER.

Both are identical 80S ribosomes. Free ribosomes make proteins for the cytosol and for import into the nucleus, mitochondria, chloroplasts and peroxisomes. Bound ribosomes, directed to the RER by a signal sequence, make proteins that enter the ER, for secretion, the plasma membrane, lysosomes, and the ER and Golgi.

Describe the structure of the Golgi apparatus and how it processes proteins.

A stack of separate, flattened, curved cisternae. Vesicles from the RER fuse with the convex cis face; enzymes modify the proteins (e.g. adding carbohydrate) as they pass towards the concave trans face, where vesicles bud off. Proinsulin is cut to insulin mainly later, in immature secretory vesicles that have left the trans face.

Give the route of a secreted protein from ribosome to outside the cell.

Ribosome on the rough ER → RER lumen → transport vesicle → cis face of the Golgi → cisternae → trans face → secretory vesicle → fusion with the plasma membrane (exocytosis).

How does clathrin help a vesicle to form?

Receptors in the membrane bind cargo; three-legged clathrin molecules assemble into a curved lattice on the cytoplasmic side, pulling the membrane into a coated pit; the pit pinches off as a coated vesicle, and the coat is then removed and the clathrin reused.

B2.2 Organelles and compartmentalization

What counts as an organelle

SL & HLSyllabus understandings: B2.2.1

An organelle is a discrete subunit of a cell (a separate, distinct structure) that is adapted, by its structure, to carry out one or more specific functions. Many organelles are bounded by membranes, but a membrane is not required: ribosomes have none.

	Structure	Why
Organelle	Nucleus	Discrete, enclosed by the nuclear envelope; holds the chromosomes and is where transcription happens
Organelle	Mitochondria, chloroplasts, ER, Golgi apparatus, lysosomes, vacuoles	Discrete compartments, each bounded by membrane and with its own functions
Organelle	Vesicles	Small, separate sacs of membrane that carry materials
Organelle	Ribosomes	Discrete particles of RNA and protein, adapted for translation
Organelle	Plasma membrane	A discrete structure with specific functions, such as controlling what enters and leaves
Not an organelle	Cell wall	Lies outside the plasma membrane, so it is extracellular
Not an organelle	Cytoskeleton	A network running through the whole cytoplasm, not a discrete unit
Not an organelle	Cytoplasm	The whole region inside the plasma membrane, with many functions rather than one specific one; organelles are found within it

How organelles were studied: cell fractionation

To find out what each organelle does, biologists needed to collect large numbers of one type, separate from the rest. This became possible with cell fractionation.

Tissue is cut up in a solution that is cold (slowing enzymes that would digest the organelles), isotonic (so organelles do not gain or lose water by osmosis and burst or shrivel) and buffered (keeping the pH constant so proteins are not denatured).
The tissue is homogenized (broken up in a blender or homogenizer), which bursts the cells and releases their organelles. The homogenate is filtered to remove debris.
Differential centrifugation: the homogenate is spun, and the sediment (pellet) collected; the liquid above it (supernatant) is spun again, faster and for longer, and so on.

Typical spin	Main contents of the pellet
≈ 600–1,000 × g for 10 min	Nuclei
≈ 1,000–4,000 × g for 10 min	Chloroplasts (from plant tissue)
≈ 10,000–20,000 × g for 20 min	Mitochondria
≈ 80,000 × g for 60 min	Small fragments of ER and plasma membrane
≈ 150,000 × g for 3 h	Ribosomes

The highest speeds need an ultracentrifuge, a machine first developed in the 1920s that spins samples fast enough to produce forces many thousands of times gravity.

Separating the nucleus from the cytoplasm

SL & HLSyllabus understandings: B2.2.2

Organelles and their compartments in 3D

Outer membrane of the nuclear envelope
Inner membrane of the nuclear envelope (no ribosomes)
Space between the two membranes (perinuclear space)
Nuclear pore: the two membranes are joined around it
Rough ER: flattened sacs (cisternae) of membrane
Ribosomes on the cytoplasmic face of the RER and outer membrane
The outer membrane is continuous with the RER membrane
Nucleolus: no membrane; ribosome subunits are made here
Heterochromatin: densely packed chromatin, mostly near the envelope
Euchromatin: loosely packed chromatin in the nucleoplasm
Cytoplasm: where translation takes place

Text description of this visual

Four cut-away models, each sliced open by a flat plane so you look into the back half. Proportions are schematic: the spaces between membranes, the pores, proteins and ribosomes are drawn far larger than they really are so that they can be seen. The nucleus is surrounded by a double membrane, the nuclear envelope, with a narrow space between its two membranes. At each nuclear pore the outer and inner membranes join, and a ring-shaped pore complex of proteins sits in the opening. On one side the outer membrane runs straight into sheets of rough ER, so the space between the nuclear membranes is continuous with the ER lumen; ribosomes stud the outer membrane and the ER but not the inner membrane. Inside are threads and dense patches of chromatin and a nucleolus. A strand of mRNA leaves through a pore and is translated by ribosomes in the cytoplasm. The mitochondrion has a smooth outer membrane and an inner membrane folded into cristae, a very narrow intermembrane space crowded with protons, ATP synthase and electron transport proteins in the inner membrane, and a matrix with enzymes, 70S ribosomes and loops of DNA. The chloroplast has a double-membrane envelope around the stroma, stacks of thylakoids (grana) joined by single lamellae, each thylakoid enclosing a small lumen, photosystems and ATP synthase in the thylakoid membranes, starch grains, 70S ribosomes and DNA. The fourth model follows a protein from bound ribosomes on the rough ER, through a transport vesicle and the Golgi apparatus, to exocytosis at the plasma membrane, beside a free ribosome whose protein stays in the cytosol.

Nucleus and rough ER

Nuclear envelope (two membranes): A double membrane around the nucleus that separates the chromosomes and nucleoplasm from the cytoplasm. Transcription happens inside it; translation happens outside it, in the cytoplasm.
Outer membrane: The outer nuclear membrane runs straight into the membrane of the rough ER, and like the RER it has ribosomes on its cytoplasmic face. At every pore it is joined to the inner membrane.
Inner membrane: Faces the nucleoplasm and has no ribosomes. A mesh of proteins lining it supports the envelope and anchors chromatin. At every pore it is joined to the outer membrane.
Space between the membranes: The perinuclear space, only a few tens of nanometres wide (drawn much wider here). Because the outer membrane is continuous with the RER, this space is continuous with the ER lumen.
Nuclear pore: A channel through the envelope. Mature mRNA and ribosome subunits leave the nucleus through pores; proteins needed inside, such as histones and RNA polymerase, enter through them.
Nuclear pore complex: A large structure built from many proteins, arranged with eightfold symmetry, that fills each pore. Small molecules diffuse through it, but large ones such as proteins and mRNA are let through selectively.
Chromatin: DNA wound around histone proteins. Loosely packed euchromatin (threads) holds most of the genes being transcribed; densely packed heterochromatin (dark patches) lies mostly against the envelope.
Nucleolus: A dense region with no membrane where ribosomal RNA is made and ribosome subunits are assembled. The subunits leave through the pores and only join into working ribosomes in the cytoplasm.
Rough ER: Flattened sacs of membrane (cisternae) with ribosomes on their cytoplasmic surface. Here the sheets branch off the outer nuclear membrane, so their lumen and the space between the nuclear membranes are one compartment.
Ribosomes on the ER: Ribosomes attached to the cytoplasmic face of the rough ER and the outer nuclear membrane. They make proteins that pass into the ER, for secretion, the plasma membrane, lysosomes, and the ER and Golgi.
mRNA being translated: Mature mRNA, already modified inside the nucleus, leaves through a pore and is translated by several ribosomes at once in the cytoplasm. Unmodified pre-mRNA never reaches the ribosomes.
Free ribosomes (80S): Ribosomes in the cytoplasm that are not attached to a membrane. All translation takes place outside the nucleus, in the cytoplasm.
Cytoplasm: The region outside the nucleus and inside the plasma membrane, where translation happens. Other organelles divide it into further compartments.

Mitochondrion

Outer membrane: A smooth membrane that separates the contents of the mitochondrion from the cytoplasm, creating a compartment where conditions suit aerobic respiration. With the inner membrane it forms a double membrane.
Inner membrane: Holds the electron transport chains and ATP synthase, which work together to make ATP by chemiosmosis. It is impermeable to protons, so they return to the matrix mainly through ATP synthase.
Cristae: Folds of the inner membrane that project into the matrix. They give a large surface area for electron transport chains and ATP synthase, so more ATP can be made. Very active cells have mitochondria with many cristae.
Intermembrane space: The narrow space between the two membranes, continuous with the space inside each crista. Its volume is very small (drawn wider here), so protons pumped into it quickly build up a high concentration.
Protons (H⁺): Pumped from the matrix into the intermembrane space by the electron transport chain. Because the space is so small, their concentration there soon becomes much higher than in the matrix.
Matrix: The fluid inside the inner membrane. Enzymes and substrates of the link reaction and Krebs cycle are concentrated here, kept apart from glycolysis in the cytoplasm, so these reactions run quickly.
ATP synthase: An enzyme in the inner membrane whose head projects into the matrix. Protons diffuse back into the matrix through it, down their concentration gradient, and the energy released is used to make ATP.
Electron transport chain: Protein complexes in the inner membrane that pass electrons from one to the next and use the energy released to pump protons into the intermembrane space.
70S ribosomes: Ribosomes like those of bacteria, smaller than the 80S ribosomes of the cytoplasm. With the mitochondrion's own DNA they allow it to make some of its own proteins.
Circular DNA: A small, naked loop of DNA carrying a few genes, including some for proteins of the inner membrane. Most mitochondrial proteins are coded by genes in the nucleus and imported.

Chloroplast

Outer membrane: The outer membrane of the chloroplast envelope. With the inner membrane it encloses the stroma, creating a compartment with conditions suited to photosynthesis.
Inner membrane: The inner membrane of the envelope (a double membrane). Its transport proteins control what enters and leaves the stroma, such as the sugar phosphates made by the Calvin cycle.
Stroma: The fluid inside the envelope. Rubisco and the other enzymes of the Calvin cycle, and their substrates, are concentrated here, right next to the thylakoids that supply the ATP and NADPH.
Granum: A stack of thylakoids. Stacking packs a very large area of membrane, with its photosystems, into a small volume, so the light-dependent reactions can happen at a high rate.
Thylakoid: A flattened sac of membrane, separate from the envelope. Its membrane holds the photosystems, electron carriers and ATP synthase needed for the light-dependent reactions.
Thylakoid lumen: The fluid inside a thylakoid. Its volume is very small, so a high proton concentration builds up after relatively few photons have been absorbed. This gradient drives ATP synthesis.
Stroma lamella: A single, unstacked thylakoid that links one granum to another. Its lumen is continuous with theirs, so all the thylakoids form one connected membrane system.
Photosystems: Large complexes of proteins and pigments, including chlorophyll, set in the thylakoid membranes. They absorb light and pass excited electrons to the electron transport chain.
ATP synthase: Set in the thylakoid membrane with its head in the stroma. Protons diffuse from the lumen into the stroma through it, so ATP is made in the stroma, where the Calvin cycle uses it.
Starch grain: A store of starch made from sugars produced by the Calvin cycle. Starch is insoluble, so it can be stored without drawing water into the chloroplast by osmosis.
70S ribosomes: Bacterium-sized ribosomes in the stroma. With the chloroplast's own DNA they make some of its proteins, including the large subunit of Rubisco.
Circular DNA: Naked, circular DNA in the stroma (there are several copies) carrying genes for some chloroplast proteins. Most chloroplast proteins are coded in the nucleus and imported.

Secretory pathway

Rough ER: A network of flattened sacs (cisternae) whose outer surface is studded with ribosomes. Proteins made by these ribosomes enter the lumen, fold and are first modified before being sent on.
Bound ribosome: An 80S ribosome attached to the ER. A signal sequence at the start of the polypeptide directs the ribosome to the ER, and the growing chain is fed through the membrane into the lumen.
ER lumen: The space inside the rough ER. Proteins for secretion, for the plasma membrane and for lysosomes are folded here, kept separate from the cytosol.
Free ribosome: An 80S ribosome that is not attached to a membrane. Its protein (purple) is released into the cytosol, for example an enzyme of glycolysis. Free ribosomes also make proteins later imported into mitochondria, chloroplasts, the nucleus and peroxisomes.
Transport vesicle: A small sac of membrane that buds from the rough ER with proteins inside it and fuses with the cis face of the Golgi apparatus.
Cis face: The convex side of the Golgi stack, facing the ER. Vesicles from the rough ER fuse with the cisterna on this side, delivering their proteins.
Trans face: The concave side of the stack, facing the plasma membrane. Vesicles bud from it carrying finished proteins to the plasma membrane or to other organelles such as lysosomes.
Golgi apparatus: A stack of separate, flattened, curved sacs (cisternae). Enzymes in the cisternae modify proteins as they pass from cis to trans, for example by adding carbohydrate, and sort them into vesicles.
Secretory vesicle: Buds from the trans face and carries finished protein to the plasma membrane. Some are stored until a signal triggers release, as in pancreatic β cells, which secrete insulin when blood glucose rises.
Plasma membrane: The secretory vesicle fuses with it (exocytosis), releasing the protein outside the cell. The vesicle membrane becomes part of the plasma membrane.
Outside the cell: Secreted proteins, such as digestive enzymes, antibodies and peptide hormones, are released into the fluid outside the cell.

Free and bound ribosomes. Translation always starts on a free ribosome. The purple protein has no signal sequence, so its ribosome stays free and the protein is released into the cytosol. The red proteins start with a signal sequence, so their ribosomes bind to the rough ER and each growing polypeptide is fed into the ER lumen.
Folding in the rough ER. In the lumen each polypeptide folds into its three-dimensional shape. The proteins collect at the edge of a cisterna, and a small region of the ER membrane buds off as a transport vesicle with the proteins inside it.
To the cis face of the Golgi. The transport vesicle moves through the cytoplasm to the convex cis face of the Golgi apparatus and fuses with its first cisterna, so the proteins enter the Golgi without ever crossing a membrane.
Processing from cis to trans. The proteins pass from cisterna to cisterna towards the trans face. Enzymes in the cisternae modify them, here by adding carbohydrate chains (green) to make glycoproteins. Some proteins are also cut to their final length.
Secretion by exocytosis. A secretory vesicle buds from the trans face and carries the finished proteins to the plasma membrane. Its membrane fuses with the plasma membrane and the proteins are released outside the cell.

In a eukaryotic cell the chromosomes are enclosed in the nucleus, bounded by the nuclear envelope. This divides the cell into two compartments with different jobs:

Transcription (making RNA from DNA) happens in the nucleus.
Translation (making polypeptides on ribosomes) happens in the cytoplasm. No ribosomes translate mRNA inside the nucleus.

The advantage: mRNA is modified before it meets ribosomes

The RNA first made by transcription is pre-mRNA. While it is still in the nucleus it undergoes post-transcriptional modification. Most importantly, non-coding sequences called introns are cut out and the remaining exons are joined together; the two ends of the molecule are also modified. Only this mature mRNA is exported through the nuclear pores to the cytoplasm.

Because the ribosomes are on the other side of the envelope, they cannot start translating pre-mRNA. If they did, the introns would be translated, giving a polypeptide with the wrong amino acid sequence that would usually not function. Keeping the two processes apart makes sure modification is finished first. (The details of splicing are in D1.2 Protein synthesis.)

Prokaryotes: no separation

Prokaryotes have no nucleus: their DNA lies in the cytoplasm. Ribosomes can attach to an mRNA molecule and begin translating it while it is still being transcribed, so there is no opportunity to modify the mRNA first. Most bacterial genes have no introns, so this does not cause errors for them, and it lets bacteria make new proteins very quickly.

Eukaryote: separated by the nuclear envelope

Prokaryote: no nucleus, no separation

Left: in a eukaryote, pre-mRNA is modified inside the nucleus, and only mature mRNA passes out through a pore to the ribosomes. Right: in a prokaryote, ribosomes begin translating each mRNA while RNA polymerase is still making it.

Advantages of compartments in the cytoplasm

SL & HLSyllabus understandings: B2.2.3

The membranes of organelles divide the cytoplasm into many separate compartments. Each compartment can have its own set of enzymes and its own internal conditions. This compartmentalization has three main advantages.

Enzymes and metabolites are concentrated. If the enzymes and substrates of a pathway are packed into a small organelle rather than spread through the whole cell, their concentrations are higher, they collide more often and the reactions are faster. The product of one enzyme is also made close to the next enzyme in the pathway.
Incompatible processes are kept apart. Some processes would interfere with each other if they shared a space. Hydrolytic enzymes would digest the cell’s own proteins and nucleic acids; fatty acids are built up in the cytosol but broken down inside mitochondria, so the two pathways do not undo each other.
Conditions can be optimized. Each compartment can be kept at conditions that suit its enzymes, such as a particular pH.

Lysosomes

Lysosomes are vesicles bounded by a single membrane and filled with dozens of different hydrolytic enzymes (proteases, lipases, nucleases and carbohydrases). Proton pumps in the membrane use ATP to keep the inside at about pH 4.5–5, the optimum for these enzymes, while the cytosol is about pH 7.2. Lysosomes digest material taken into the cell by endocytosis and break down worn-out organelles, so their contents can be recycled. If a lysosome leaks, its enzymes are much less active at the pH of the cytosol, which protects the cell further.

Phagocytic vacuoles

White blood cells such as macrophages and neutrophils engulf bacteria by endocytosis, enclosing each in a phagocytic vacuole (see B2.1 Membranes and membrane transport). Lysosomes fuse with the vacuole and release their enzymes into it. The bacterium is digested inside the vacuole, and the small products, such as amino acids and sugars, are absorbed into the cytoplasm. Unicellular organisms such as Amoeba digest their food in the same way, in food vacuoles.

1. Concentrated in a small volume

2. Incompatible processes kept apart

3. Digestion inside a phagocytic vacuole

Three advantages of compartmentalization: enzymes and substrates concentrated in a small volume; a lysosome keeping its hydrolases, at their low optimum pH, apart from the rest of the cell; and a bacterium digested inside a phagocytic vacuole after lysosomes fuse with it.

Advantage	How the membrane helps	Example
Concentration of enzymes and substrates	Small volume, so collisions are more frequent	Krebs cycle enzymes in the mitochondrial matrix
Separation of incompatible processes	Enzymes kept away from molecules they would destroy	Hydrolases in lysosomes
Optimal conditions	Pumps keep the inside different from the cytosol	pH 4.5–5 inside lysosomes
Safe digestion of engulfed material	Digestion is confined to a membrane-bound sac	Bacteria digested in phagocytic vacuoles

The mitochondrion: adapted for ATP production

AHLSyllabus understandings: B2.2.4

Mitochondria carry out the aerobic stages of cell respiration. Glycolysis happens in the cytoplasm; the pyruvate it produces enters the mitochondrion, where the link reaction and Krebs cycle take place in the matrix, and ATP is made by the electron transport chain and chemiosmosis in the inner membrane (see C1.2 Cell respiration). The structure of the mitochondrion is closely related to these functions, an example of adaptation produced by natural selection.

Structure	Adaptation	How it helps ATP production
Double membrane	The outer membrane encloses a separate compartment; the inner membrane holds the electron transport chains and ATP synthase	Conditions inside can suit respiration; the inner membrane is impermeable to protons, so they return to the matrix mainly through ATP synthase
Small intermembrane space	A very small volume between the two membranes	Relatively few protons pumped into it give a high concentration, so a steep proton gradient builds up quickly
Cristae	Inner membrane folded into shelves or tubes	A large surface area for electron transport chains and ATP synthase, so more ATP can be made
Matrix	Enzymes and substrates of the link reaction and Krebs cycle are compartmentalized in it	High concentrations give fast reactions, separate from glycolysis in the cytoplasm

The electron transport chains use energy from electrons to pump protons from the matrix into the intermembrane space. Protons then diffuse back down their concentration gradient through ATP synthase, whose head projects into the matrix, and ATP is made in the matrix.

Cells that use a lot of ATP, such as muscle cells, have many mitochondria with densely packed cristae. Mitochondria also contain 70S ribosomes and a loop of naked DNA, so they can make some of their own proteins.

The chloroplast: adapted for photosynthesis

AHLSyllabus understandings: B2.2.5

A chloroplast is bounded by a double membrane (the chloroplast envelope) around the fluid stroma. Inside is a third, separate system of membranes: the thylakoids, flattened sacs that are stacked into grana and joined by single stroma lamellae. The light-dependent reactions happen in the thylakoid membranes and the light-independent reactions (Calvin cycle) in the stroma (see C1.3 Photosynthesis).

Structure	Adaptation	How it helps photosynthesis
Thylakoid membranes	A very large total surface area, packed into grana	Room for many photosystems, electron carriers and ATP synthase molecules, so light is absorbed and ATP made at a high rate
Thylakoid lumen	A very small volume of fluid inside each thylakoid	A high proton concentration builds up after relatively few photons have been absorbed, driving ATP synthesis
Stroma	The enzymes of the Calvin cycle, including Rubisco, and their substrates are compartmentalized here	High concentrations give fast reactions, right next to the thylakoids that supply ATP and NADPH
Double membrane	Encloses a compartment separate from the cytoplasm	Conditions inside can be kept suitable for photosynthesis

Protons are moved into the thylakoid lumen during the light-dependent reactions. They diffuse back into the stroma through ATP synthase, so ATP is made in the stroma, exactly where the Calvin cycle uses it. Chloroplasts also contain starch grains (a store of the sugar they make), 70S ribosomes and naked, circular DNA.

Mitochondrion and chloroplast compared

	Mitochondrion	Chloroplast
Membrane with the ATP synthase	Inner membrane (cristae)	Thylakoid membrane
Small space where protons accumulate	Intermembrane space	Thylakoid lumen
Compartment where ATP is made	Matrix	Stroma
Enzymes concentrated in the fluid	Link reaction and Krebs cycle	Calvin cycle (e.g. Rubisco)

The double membrane of the nucleus

AHLSyllabus understandings: B2.2.6

The nuclear envelope consists of two membranes, each a phospholipid bilayer, separated by a narrow perinuclear space. The outer membrane is continuous with the membrane of the rough ER, and like the RER it has ribosomes on its cytoplasmic face; the perinuclear space is continuous with the ER lumen. The inner membrane is lined by a mesh of proteins that supports the envelope and anchors chromatin.

Nuclear pores

At nuclear pores, the outer and inner membranes are joined, so the pore is a channel through the envelope lined with membrane. Each pore is filled by a nuclear pore complex, a large ring-shaped structure made of many proteins. A nucleus in a typical mammalian cell has a few thousand pores. They are needed because:

mRNA and ribosome subunits are made in the nucleus but used in the cytoplasm, so they must move out;
proteins needed in the nucleus, such as histones, DNA polymerase, RNA polymerase and the proteins of ribosomes, are made in the cytoplasm, so they must move in, along with nucleotides.

Small molecules diffuse through the pores freely, but large molecules are let through selectively.

Benefits of a double membrane

Pores can be formed by joining the outer membrane to the inner membrane around an opening, linking nucleoplasm and cytoplasm without exposing the space between the membranes.
The envelope can break up into vesicles during mitosis and meiosis. At the end of prophase the envelope breaks down, releasing the chromosomes so that spindle microtubules can attach to them and move them. At telophase, the membrane vesicles are used to rebuild a nuclear envelope around each group of chromosomes, forming the daughter nuclei.

Free ribosomes and the rough ER

AHLSyllabus understandings: B2.2.7

Eukaryotic ribosomes in the cytoplasm are 80S, made of a large (60S) and a small (40S) subunit, each built from ribosomal RNA and proteins. They are found in two places:

Free ribosomes float in the cytosol.
Bound ribosomes are attached to the cytoplasmic surface of the rough endoplasmic reticulum (RER).

The two kinds are identical. Translation of every protein coded by nuclear genes begins on a free ribosome. If the polypeptide begins with a signal sequence, the ribosome is directed to the RER and binds to it, and the growing polypeptide is fed through the membrane into the ER lumen. Without a signal sequence, the ribosome stays free.

	Free ribosomes	Ribosomes on the rough ER
Location	Cytosol	Cytoplasmic face of the RER
Where the polypeptide goes	Released into the cytosol	Into the lumen of the RER (or into its membrane)
Proteins made	Proteins that work in the cytosol, e.g. enzymes of glycolysis, and proteins later imported into the nucleus, mitochondria, chloroplasts and peroxisomes	Proteins for secretion, for the plasma membrane, for lysosomes, and for the ER and Golgi apparatus themselves

Structure and function of the rough ER

The RER is a network of flattened, membrane-bound sacs called cisternae, with ribosomes on their outer surface; the space inside is the lumen, and the network is continuous with the outer nuclear membrane. In the lumen, polypeptides fold into their three-dimensional shape and begin to be modified, for example by the addition of carbohydrate. They are then carried to the Golgi apparatus in transport vesicles that bud from the RER.

Cells that secrete large amounts of protein, such as the cells of the pancreas that secrete digestive enzymes and plasma cells that secrete antibodies, are packed with rough ER.

From ribosome to secretion, and clathrin-coated vesiclesAHL

Free and bound ribosomes. The free ribosome makes a protein (purple) that is released into the cytosol and stays in the cell. Ribosomes bound to the rough ER make proteins (red) that are fed through the membrane into the ER lumen as they are made.

A transport vesicle buds from the rough ER. Inside the ER lumen the polypeptides fold. A small patch of ER membrane bulges out and pinches off as a transport vesicle with the proteins inside it. The purple protein folds in the cytosol.

Fusion with the cis face. The transport vesicle moves to the Golgi apparatus and its membrane fuses with the first cisterna on the convex cis face, which faces the ER. The proteins are now inside the Golgi.

Processing in the Golgi. The proteins pass from cisterna to cisterna towards the trans face. Enzymes in each cisterna modify them, here by adding carbohydrate (green) to make glycoproteins, so their final form is gradually produced.

A secretory vesicle leaves the trans face. A secretory vesicle containing the finished proteins buds from the concave trans face and moves to the plasma membrane.

Exocytosis. The vesicle membrane fuses with the plasma membrane, and the proteins are released outside the cell. The vesicle's membrane becomes part of the plasma membrane.

A clathrin coat assembles. Receptor proteins in the plasma membrane bind particular cargo molecules outside the cell. Three-legged clathrin molecules gather on the cytoplasmic side and link into a curved lattice, which starts to pull the membrane inwards into a coated pit.

The coated vesicle buds off. The pit deepens until only a narrow neck joins it to the plasma membrane. The neck is pinched off, and a clathrin-coated vesicle with the receptors and their cargo inside separates into the cytoplasm.

The coat is removed. Soon after the vesicle forms, the clathrin coat comes away and the clathrin is reused for new pits. The uncoated vesicle can now fuse with its target membrane inside the cell.

Text description of this animation

A slice through a secretory cell, with the plasma membrane along the bottom and the outside of the cell below it. At the top left is a flattened sac of rough ER with ribosomes on both of its outer surfaces; to the right is a free ribosome. In the middle is the Golgi apparatus, a stack of five curved cisternae with its convex cis face towards the ER and its concave trans face towards the plasma membrane. Red proteins are made by ribosomes on the ER and fed into its lumen, fold, and leave in a transport vesicle that fuses with the cis face. They are modified as they pass through the stack, gaining green carbohydrate chains, leave the trans face in a secretory vesicle, and are released outside the cell by exocytosis. The purple protein made by the free ribosome stays in the cytosol. On the right, receptors in the plasma membrane bind cargo outside the cell, three-legged clathrin molecules gather on the cytoplasmic side and pull the membrane into a pit, a coated vesicle pinches off into the cytoplasm, and the clathrin coat falls away.

Free and bound ribosomes. The free ribosome makes a protein (purple) that is released into the cytosol and stays in the cell. Ribosomes bound to the rough ER make proteins (red) that are fed through the membrane into the ER lumen as they are made.
A transport vesicle buds from the rough ER. Inside the ER lumen the polypeptides fold. A small patch of ER membrane bulges out and pinches off as a transport vesicle with the proteins inside it. The purple protein folds in the cytosol.
Fusion with the cis face. The transport vesicle moves to the Golgi apparatus and its membrane fuses with the first cisterna on the convex cis face, which faces the ER. The proteins are now inside the Golgi.
Processing in the Golgi. The proteins pass from cisterna to cisterna towards the trans face. Enzymes in each cisterna modify them, here by adding carbohydrate (green) to make glycoproteins, so their final form is gradually produced.
A secretory vesicle leaves the trans face. A secretory vesicle containing the finished proteins buds from the concave trans face and moves to the plasma membrane.
Exocytosis. The vesicle membrane fuses with the plasma membrane, and the proteins are released outside the cell. The vesicle's membrane becomes part of the plasma membrane.
A clathrin coat assembles. Receptor proteins in the plasma membrane bind particular cargo molecules outside the cell. Three-legged clathrin molecules gather on the cytoplasmic side and link into a curved lattice, which starts to pull the membrane inwards into a coated pit.
The coated vesicle buds off. The pit deepens until only a narrow neck joins it to the plasma membrane. The neck is pinched off, and a clathrin-coated vesicle with the receptors and their cargo inside separates into the cytoplasm.
The coat is removed. Soon after the vesicle forms, the clathrin coat comes away and the clathrin is reused for new pits. The uncoated vesicle can now fuse with its target membrane inside the cell.

The Golgi apparatus: processing and secretion

AHLSyllabus understandings: B2.2.8

The Golgi apparatus is a stack of flattened, curved, membrane-bound sacs (cisternae), usually about four to eight in animal cells. Unlike the RER, the cisternae in a stack are separate from one another, and they have no ribosomes. The stack has two distinct faces:

the cis face, which is convex and faces the rough ER: it receives proteins;
the trans face, which is concave and usually faces the plasma membrane: it ships them out.

Processing proteins

Transport vesicles from the RER fuse with the cisterna on the cis side, delivering their proteins.
The proteins are passed from cisterna to cisterna towards the trans side.
Enzymes in the cisternae modify them as they go. For example, carbohydrate chains are added or altered (making glycoproteins), and some polypeptides are cut or have other groups added. The final form of the protein is gradually produced: insulin, for instance, is made as a longer precursor, proinsulin. Most of it is cut to form active insulin only after it has left the trans face, inside immature secretory vesicles.
The finished proteins are sorted and packed into vesicles that bud from the trans face.

Secretion

Secretory vesicles from the trans face carry proteins to the plasma membrane and release them outside the cell by exocytosis. Some are released continuously; others are stored until a signal arrives, as when β cells of the pancreas release insulin when blood glucose rises. Other vesicles from the trans face carry proteins to lysosomes or to the plasma membrane itself.

Vesicles and clathrin

AHLSyllabus understandings: B2.2.9

A vesicle is a small, spherical sac of single membrane (a phospholipid bilayer) enclosing a droplet of fluid. Vesicles form by budding from a membrane, are moved through the cytoplasm along microtubules by motor proteins, and deliver their contents by fusing with a target membrane. This works because membranes are fluid (see B2.1 Membranes and membrane transport).

Roles of vesicles

Transport between organelles: from the RER to the Golgi apparatus, and from the Golgi to lysosomes.
Secretion: carrying proteins to the plasma membrane for exocytosis.
Taking materials in: endocytosis, including the phagocytic vacuoles of white blood cells.
Adding membrane: when vesicles fuse with the plasma membrane, their phospholipids and membrane proteins become part of it, so the cell can grow.

Clathrin and coated vesicles

Some vesicles are formed with the help of clathrin, a protein with three bent legs. At the plasma membrane:

Receptor proteins in the membrane bind particular molecules (cargo) outside the cell, such as cholesterol-carrying particles in the blood.
Clathrin molecules gather on the cytoplasmic side of that patch and link together into a curved, cage-like lattice of hexagons and pentagons. This pulls the membrane inwards into a coated pit.
The pit deepens until only a narrow neck remains, which is pinched off. A clathrin-coated vesicle, with the receptors and cargo inside, separates into the cytoplasm.
The coat is soon removed and the clathrin is reused. The uncoated vesicle then fuses with its target membrane inside the cell.

Clathrin-coated vesicles also bud from the trans face of the Golgi apparatus, for example carrying enzymes destined for lysosomes. Vesicles leaving the rough ER use different coat proteins. Steps 7–9 of the animation above show a clathrin-coated vesicle forming.

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