Cell structure

In a nutshell

Every living thing is built from cells. This subtopic is about what those cells are made of, how the two cell types (eukaryotic and prokaryotic) differ, why viruses are not cells at all, and how scientists actually look at and separate the parts inside a cell.

The whole topic rests on one idea: structure is matched to function. Almost every mark here comes from linking a structure to the job it does.

Assumed knowledge: Proteins, Lipids, Carbohydrates.

Core content

The eukaryotic cell

A eukaryotic cell is a cell that has a nucleus and membrane-bound organelles. Animal, plant, fungal and algal cells are all eukaryotic.

An organelle is a distinct structure within a cell that carries out a specific function. Dividing the cell into membrane-bound compartments lets different reactions happen in different places at the same time.

You must know the structure and function of each organelle below. Learn them as structure-then-job, because that is how the marks are written.

A closer look: mitochondria and chloroplasts

Examiners often ask you to draw or label these two, so learn the named parts and what each part does.

• The inner membrane is folded into cristae, which give a large surface area for the reactions of aerobic respiration.
• The matrix contains the enzymes for respiration.

• The thylakoid membranes (stacked into grana) give a large surface area of membrane holding chlorophyll, for the light-dependent reactions.
• The stroma contains the enzymes for the light-independent reactions.

Both organelles also contain their own small (70S) ribosomes and a loop of circular DNA.

Plant cells versus animal cells

All the organelles in the table are found in a typical plant cell too. A plant cell has three extra structures an animal cell does not:

• a cell wall (cellulose) outside the cell-surface membrane,
• one or more chloroplasts,
• a large, permanent vacuole with its tonoplast.

How organelles work together: making and exporting a protein

No organelle works alone. A cell that secretes a protein (for example an enzyme) uses several organelles in sequence. This is a favourite exam question because it tests whether you can link functions.

1. The nucleus holds the DNA; the base sequence of a gene codes for the amino acid sequence of the polypeptide.
2. Ribosomes on the rough endoplasmic reticulum assemble the polypeptide (translation).
3. The rough ER folds and processes the protein, then buds off a vesicle carrying it.
4. The vesicle fuses with the Golgi apparatus, which modifies (for example adds carbohydrate), then packages the protein into a secretory vesicle.
5. The secretory vesicle moves to the cell-surface membrane and fuses with it, releasing the protein by exocytosis.
6. Mitochondria supply the ATP needed for protein synthesis and to move the vesicles.

Specialised cells and levels of organisation

In a multicellular organism, cells become specialised (differentiated) for particular jobs. Specialised cells are then organised into a hierarchy:

cells → tissues → organs → organ systems.

Prokaryotic cells

Prokaryotic cells (bacteria) are much smaller than eukaryotic cells and have no nucleus and no membrane-bound organelles.

Compare a prokaryotic cell with a eukaryotic cell:

Many prokaryotic cells also have one or more of the following (you are not required to know their detailed structure):

• plasmids: small circular DNA loops carrying extra genes, for example antibiotic resistance,
• a capsule surrounding the cell,
• one or more flagella for movement.

Viruses

Viruses are acellular (not made of cells) and non-living: they have no cytoplasm, no ribosomes and no organelles, and can only replicate inside a host cell.

You only need three structures, all present in every virus particle:

Studying cells: magnification and resolution

Cells are too small to see with the naked eye, so we use microscopes. Two separate ideas decide how useful a microscope is:

• Magnification: how many times larger the image is than the real object.
• Resolution: the ability to distinguish (tell apart) two separate points as two, rather than as one blur.

Resolution is the one that limits how much detail you can see, and it is set by the wavelength used. A shorter wavelength gives a higher resolution.

Still don't get it? · magnification vs resolution

Imagine a small, blurry photo on your phone. You can pinch to zoom in as far as you like, making it bigger and bigger. That is magnification: it just makes the image larger.

But zooming in does not add any new detail. Past a certain point the photo is just big and blurry, because the camera only captured so much detail in the first place. That fixed limit on detail is resolution.

In the exam version: an optical microscope can magnify a lot, but it cannot resolve very small organelles because the wavelength of light is too long. An electron microscope uses electrons, whose wavelength is much shorter, so it has a much higher resolution and reveals fine detail. The key phrase examiners want is that the higher resolution is due to the shorter wavelength of the electrons (the beam), not of the microscope.

The three microscopes

You do not need to memorise exact magnification or resolution values, but you must be able to compare the three using words like higher and lower.

Because both electron microscopes need a vacuum, the specimen must be dead, and preparing it can introduce artefacts (structures that are not really part of the living cell). It took scientists a long time to work out which structures seen under the microscope were real organelles and which were artefacts.

Measuring the size of a cell

The magnification equation links the three quantities:

$\text{magnification} = \frac{\text{size of image}}{\text{size of real object}}$

Rearrange it depending on what you are asked for:

$\text{real size} = \frac{\text{size of image}}{\text{magnification}} \qquad \text{image size} = \text{real size} \times \text{magnification}$

• Magnification has no units (it is a ratio).
• Image size and real size must be in the same unit before you calculate. The usual conversions are 1 mm = 1000 µm and 1 µm = 1000 nm.

To measure a cell under an optical microscope you use an eyepiece graticule (a scale in the eyepiece with no fixed units) that you first calibrate against a stage micrometer (a slide with a scale of known length). Once you know what one graticule division is worth in µm, you can measure any cell.

Cell fractionation and ultracentrifugation

Cell fractionation is the process of breaking open cells and separating the organelles so they can be studied. It has two stages.

1. Homogenisation. The tissue is broken up (for example in a blender) to release the organelles into solution, giving a homogenate. This is then filtered to remove any whole cells and large debris.

The solution is kept cold, isotonic and buffered:

2. Ultracentrifugation. The homogenate is spun in a centrifuge, and the organelles separate out in order of density (densest first):

1. Spin at a low speed: the densest organelles (nuclei) are forced to the bottom as a pellet. The liquid above is the supernatant.
2. Remove and re-spin the supernatant at a higher speed: the next densest organelles (mitochondria, and chloroplasts in plant cells) form the next pellet.
3. Repeat at progressively higher speeds to pellet smaller, less dense organelles, ending with the ribosomes.

Still don't get it? · why cold, isotonic and buffered (and why organelles, not cells)

Think of the homogenate as a bag of delicate glass baubles (the organelles) floating in water. You have already smashed the box they came in (that was homogenisation breaking open the cells), so the thing you are now protecting is the baubles, not the box.

Cold: enzymes are like tiny scissors that snip things up. Chilling them slows the scissors right down, so they cannot cut up your baubles while you work.

Isotonic: if the water outside a bauble is more or less watery than the inside, water rushes in or out by osmosis and the bauble swells and bursts or shrivels. Matching the water potential stops water moving either way.

Buffered: a swing in pH would change the shape of the proteins and enzymes (denature them). A buffer holds the pH steady.

The exam trap: because the cells are already broken open, you must say the cold and isotonic conditions protect the organelles, not the cells. Writing "to stop the cells bursting" loses the mark.

Worked examples

Worked example 1: a magnification calculation with a unit conversion.

An electron micrograph shows a chloroplast measuring 30 mm long. The image was taken at a magnification of ×5000. Calculate the real length of the chloroplast in µm.

1. Rearrange for real size:

$\text{real size} = \frac{\text{size of image}}{\text{magnification}} = \frac{30 \text{ mm}}{5000}$

2. Calculate:

$\text{real size} = 0.006 \text{ mm}$

3. Convert to µm (× 1000):

0.006 \text{ mm} \times 1000 = 6 \text{ µm}

The real length is 6 µm. Notice the two places students throw the marks away: dividing the wrong way round, and forgetting to convert mm to µm.

Worked example 2: calibrating an eyepiece graticule.

A student lines up the eyepiece graticule with a stage micrometer on which 1 division = 10 µm. They find that 10 eyepiece divisions line up exactly with 5 stage-micrometer divisions. A cell then measures 8 eyepiece divisions long. Find its real length.

1. Work out the real length covered by the stage divisions:

5 \text{ stage divisions} \times 10 \text{ µm} = 50 \text{ µm}

2. This equals 10 eyepiece divisions, so one eyepiece division is:

\frac{50 \text{ µm}}{10} = 5 \text{ µm per eyepiece division}

3. The cell is 8 eyepiece divisions long:

8 \times 5 \text{ µm} = 40 \text{ µm}

The real length of the cell is 40 µm.

Common exam mistakes

• Saying a mitochondrion "produces energy" or "makes energy", or that ATP is "used for respiration". Energy is not made; the mark needs releases energy / produces ATP (by or in aerobic respiration). Many answers also forget the word aerobic.
• Confusing the chloroplast (the organelle) with chlorophyll (the green pigment inside it). They are not the same thing.
• Saying lysosomes "store enzymes". The mark needs the active role: they release hydrolytic (digestive) enzymes that break down material.
• Saying the Golgi apparatus "makes proteins". It modifies, sorts and packages them; the ribosomes make them. The Golgi is also the organelle most often misidentified in a diagram.
• Explaining an electron microscope's higher resolution as due to "the short wavelength of the microscope". It is the shorter wavelength of the electrons (the beam), not of the instrument.
• Blaming low magnification for why a light microscope cannot show small organelles. The limit is resolution (set by the long wavelength of light), not magnification.
• Thinking an electron microscope can view living specimens, or that an SEM gives colour. Both electron microscopes need a vacuum, so specimens are dead, and both give black-and-white images. A black-and-white image is therefore not evidence that an SEM was used; a 3D image is.
• In magnification calculations: dividing real size by image size (inverted), multiplying measured size by magnification, or failing to convert between mm, µm and nm (answers end up a factor of ten or more out).
• In cell fractionation, saying the cold or isotonic solution protects the cells. The cells are already broken open, so it protects the organelles. Also: "cold prevents denaturation" is wrong (cold slows enzymes; it is the buffer that prevents denaturation), and forgetting that it is the supernatant that is re-spun at a higher speed.
• Writing that prokaryotic DNA is "single-stranded". Prokaryotic DNA is still a double helix; it is just circular and not associated with proteins.
• Listing a eukaryotic feature (like a nucleus or mitochondria) as something a prokaryote has, or giving "ribosomes" as a difference without qualifying them as smaller (70S).
• Confusing the capsule of some bacteria with the capsid of a virus, and confusing the bacterial cell-wall material murein with the plant material cellulose.

Key definitions

• Eukaryotic cell: a cell that contains a nucleus and membrane-bound organelles.
• Prokaryotic cell: a cell with no nucleus and no membrane-bound organelles; its DNA is a single circular molecule, free in the cytoplasm and not associated with proteins.
• Organelle: a distinct structure within a cell that has a specific function.
• Magnification: how many times larger the image is than the real object; magnification = size of image / size of real object.
• Resolution: the ability to distinguish between two separate points as two, rather than as one; the shorter the wavelength used, the higher the resolution.
• Cell fractionation: the process of breaking open cells and separating out the organelles.
• Homogenisation: breaking open cells to release the organelles.
• Ultracentrifugation: separating organelles by spinning the homogenate at increasing speeds, so that they settle out in order of density.
• Capsid: the protein coat that surrounds and protects the genetic material of a virus.
• Attachment protein: a protein on the surface of a virus that binds to a specific receptor on a host cell.

Specification

• I can describe the structure and function of each eukaryotic organelle: cell-surface membrane, nucleus (with chromosomes and nucleolus), mitochondria, chloroplasts, Golgi apparatus and vesicles, lysosomes, ribosomes, rough and smooth ER, cell wall and cell vacuole.
• I can explain how organelles work together to produce and secrete a protein.
• I can explain how the structure of a specialised cell is adapted to its function.
• I can state that cells are organised into tissues, tissues into organs, and organs into systems.
• I can describe how a prokaryotic cell differs from a eukaryotic cell (no membrane-bound organelles, smaller ribosomes, circular DNA not associated with proteins, murein cell wall) and name the extra features some prokaryotes have (plasmids, capsule, flagella).
• I can state that viruses are acellular and non-living, and describe their structure (genetic material, capsid, attachment protein).
• I can state the principles and limitations of the optical microscope, TEM and SEM, and explain the difference between magnification and resolution.
• I can use the magnification formula, measure an object under an optical microscope, and convert between mm, µm and nm.
• I can describe the principles of cell fractionation and ultracentrifugation, and explain why the solution is kept cold, isotonic and buffered.

Related notes

• All cells arise from other cells
• Transport across cell membranes
• Cell recognition and the immune system
• Proteins