Cell Structure (Module 2, Section 1)

Prokaryotes and eukaryotes:

Prokaryotic organisms are prokaryotic cells (i.e. they're single-celled organisms) and eukaryotic organisms are made up of eukaryotic cells. Both types contain organelles. Eukaryotic cells are complex and include all animal and plant cells. Prokaryotic cells are small and simpler, e.g. bacteria.

Organelles:  Organelles are parts of cells. Each one has a specific function. I f you examine a cell through an electron microscope you can see it's organelles and the internal structure of most of them - this is known as the cell ultrastructure.

Animal and plant cells:

Both eukaryotic. More complicated than prokaryotic cells and have more organelles.

Animal cells: Typical animal cell organelles = Plasma (cell surface) membrane, Lysosome, Rough endoplasmic reticulum (RER), Ribosome, Nuclear envelope, Nucleolus, Nucleus, Golgi apparatus, Cytoplasm, Smooth endoplasmic reticulum (SER), Mitochondrion.

Plant cells: plant cells have same organelles as animal cells but with a few added extras: A (cellulose) cell wall with plasmodesmata ('channels' for exchanging substances between adjacent cells), A vacuole (compartment containing cell sap), Chloroplasts.

Functions of Organelles:(description followed by function)

Plasma membrane = The membrane found on the surface of animal cells and just inside the cell wall of plant cells and prokaryotic cells. Made mainly of lipids abnd proteins. = Regulates movement of substances in and out of cell. Also has receptor molecules on it which allow it to respond to chemicals like hormones.

Cell wall = A rigid structure that surrounds plant xells. Made mainly of the carbohydrate cellulose. = Supports plant cells.

Nucleus = Large organelle surrounded by a nuclear envelope (double membrane), which contains many pores. Contains chromatin (made from DNA and proteins) and often a structure called the nucleolus. = Controls cell's activities ( by controlling the transcription of DNA). DNA contains instructions to make proteins. The pores allow substances (e.g. RNA) to move between nucleus and cytoplasm. The nucleolus makes riobosomes.

Lysosome = Round organelle surrounded by membrane with no clear internal structure. = Contains digestive (hydrolytic) enzymes. These are kept separate from cytoplasm by the surrounding membrane, and can be used to digest invading cells or to break down worn out components of the cell.

Ribosome = Very small organelle that either floats free in cytoplsam or is attached to the RER. Made up of proteins and RNA. Not surrounded by a membrane. = Site where proteins are made.

Rough endoplasmic reticulum (RER) = A system of membranes enclosing a fluid-filled space. Surface is covered in ribosomes. = Folds and processes proteins that have been made at ribosomes.

Smooth endoplasmic reticulum (SER) = Similar to RER, but with no ribosomes. = Synthesises and processes lipids.

Vesicle = A small fluid filled sac in the cytoplasm, surrounded by a membrane. = Transports substances in and out of cell (via plasma membrane) and between organelles. Some are formed by Golgi apparatus or the endoplasmic reticlum, while others are formed at cell surface. 

Golgi apparatus = Group of fluid-filled, membrane-bound, flattened sacs. vesicles are often seen at edges of the sacs. = It processes and packages new lipids and proteinbs. Also makes lysosomes.

Mitochondrion = Usually oval-shaped. Has double membrane - the inner one is folded to form structures called cristae. Inside is the matrix, which contins enzymes involved in respiration. = The site of aerobic respiration, where ATP is produced. Mitochondria are found in large numbers in cells that are very active and require a lot of energy.

Chloroplast = Smell, flattened structure found in plant cells. Surrounded by double membrane, and also has membranes inside called thylakoid membranes. Thes membranes are stacked up in some parts of the chloroplast to form grana. Grana are linked together by lamellae - thin, flat pieces of thylakoid membrane. = Site where photosynthesis takes place. Some parts of photosynthesis happen in the grana, other parts happen in the stroma ( a thick fluid found in chloroplasts).

Centriole = Small, hollow cylinders, made of microtubules (tiny protein cylinders). Found in animal cells, but only some plant cells. = Involved with separation of chromosomes during cell division.

Cilia = Small, hair-like structures found on surface membrane of some animal cells. In cross-section, they have an outer membrane and a ring of nine pairs of protein microtubules inside, with a single pair of microtubules in the middle. = The microtubules allow cilia to move. This movement is used by cell to move substances along cell surface.

Tip: Cilia in trachea are used to sweep dust and dirt out of the lungs.

Flagellum = Flagella on eukaryotic cells are like cilia but longer. They stick out from cell surface and are surrounded by the plasma membrane. Inside they're like cilia too - two microtubules in centre and nine pairs around edge. = The microtubules contract to make flagellum move. Flagella are used like outboard motors to propel cells forward.

Tip: Only example of a flagellum found in humans is the 'tail' of a sperm cell.

Tip: The formation of microtubules inside flagella and cilia is known as the '9 + 2' formation becauses there are nine pairs of microtubules surrounding two central microtubules.

Tip: 'cilium' and 'flagellum' are singular. 'cilia' and 'flagella' are plural.

Protein production:

Proteins are made at the ribosomes - the ribosomes on the RER make proteins that are axcreted or attached to cell membrane, whereas free ribosomes in cytoplasm make proteins that stay in the cytoplasm. New proteins produced at RER are folded and processed (e.g. sugar chains are added) in the RER. They're then transported from the RER to the Golgi apparatus in vesicles. At the Golgi apparatus, the proteins may undergo further processing (e.g. sugar chains are trimmed or more are added). The proteins enter more vesicles to be transported around the cell. E.g. glycoproteins (found in mucus) move to cell surface and are secreted.

Tip: Protein production is slightly different in prokaryotes as they don't have the same organelles as eukaryotes.

Tip: Proteins may be stored at the RER until they are neeeded by the Golgi apparatus. 

The cytoskeleton:

Organelles in cells are surrounded by cytoplasm. Cytoplasm has a network of protein threads running through it. These protein threads are called the cytoskeleton. In eukaryotes the proteinthreads are arranged as microfilaments (very thin protein strands) and microtubules....

....(tiny protein cylinders). Cytoskeleton has four main functions:

1. The microtubules and microfilaments support the cell's organelles, keeping them in position.

2. Help to strngthen the cell and maintain it's shape.

3. They're responsible for the transport of organelles and materials within the cell. E.g. The movement of chromosomes when they separate during cell division depends on contraction of microtubules in the spindle. E.g. The movement of vesicles around the cell relies on cytoskeletal proteins.

4. The proteins of the cytoskeleton can also cause the cell to move. E.g. The movement of cilia and flagella is caused by the cytoskeletal protein filaments that run through them. So in the case of single cells that have a flagellum (e.g. sperm cells), the cytoskeleton propels the whole cell.

Tip: A cytoskeleton is found in prokaryotes as well as eukaryotes, but the prokaryotic cytoskeleton contains different proteins.

Tip: The asembly of microtubules and microfilament, and movement of materials along them, rquires energy from repiration. So microtubules and microfilaments can be prevented from functioning using respiratory inhibitors.

Prokaryotes vs eukaryotes:

Prokaryotic cells:

• Extremely small cells (less than 2 micrometres[µm]).
• DNA is circular. (complete ring)
• No nucleus - DNA free in cytoplasm.
• Cell wall made of a polysaccharide, but not cellulose or chitin.
• Few organelles and no membrane-bound organelles, e.g. no mitochondria.
• Flagella (when present) made of the protein flagellin, arranged in a helix.
• Small ribosomes (20nm or less).
• Example: E. coli bacterium, Salmonella bacterium.

Eukaryotic cells:

• Larger cells (about 10-100 micrometers [µm] in diameter)
• DNA is linear. (has two distinct ends - imagine  a long starnd of DNA)
• Nucleus present - DNA is inside nucleus.
• No cell wall (in animals), cellulose cell wall (in plants), chitin cell wall (in fungi).
• ......

• .... Many organelles - mitochondria and other membrane-bound organelles present.
• Flagella (when present) made of microtubules arranged in '9 + 2' formation.
• Larger ribosomes (over 20nm).
• Examples: Human liver cell, yeast, amoeba.

Tip: A micrometer (µm) is one millionth of a metre, or 0.001mm.

Tip: Prokarotes are single-celled organisms but eukaryotes can be single-celled or multicellular.

Bacterial cells:

Prokaryotes like bacteria are roughly a tenth the size of eukaryotic cells, meaning normal microscopes aren't really powerful enough to look at their internal structure.

Tip: Flagella and plasmids aren't always present in prokaryotic cells.

Bacterial cell organelles (example) = DNA (bacterrial chromosome), cell wall (peptidoglycan), Plasmid (ring of DNA), Plasma (cell surface) membrane, Flagellum (tail used to propel the cell).

Magnification and resolution of microscopes:

Magnification is how much bigger the image is than the specimen.

Magnification = Image size ÷ Object size

Tip: put this formula into a triangle! Image size on the top, magnification and object size on the bottom. If you want image size, cover it and multiply magnification and image size. I f you want magnification, cover it and divide image size by object size, etc.

When calculating magnification, you need to make sure that all lengths are in the same unit.

Common units: (conversions)

   Unit:                                                 How many mm it is:     mm to µm = × 1000

   Millimetre (mm)                                 1mm                              µm to nm = × 1000

   Micrometre (µm)                                0.001 mm                      nm to µm = ÷ 1000

   Nanometre (nm)                                0.000001 mm                µm to mm = ÷ 1000

Resolution:

Resolution is how detailed the image is/how well a microscope distinguishes between two points that are close together. If a microscope lens cannot separate two objects, then increasing thee magnification won't help. E.g. a far away car, headlights seem to be one light (low resolution). As it gets closer, two lights (higher resolution). (A microscope cannot distinguish between objects smaller than it's max resolution)

Types of microscope:

Light microsopes: Use light. Lower resolution than electron microscopes. Maximum resolution of about 0.2 micrometres (µm). Useful to look at whole cells or tissues. Maximum useful magnification of a light microscope is about ×1500.

Laser scanning confocal microscopes: Special type of light microscope, uses laser beams (intense beams of light) to scan specimen that's usually tagged with fluorescent dyes. Laser beam is focussed through a lens which is aimed at a beam splitter. This splits beam and some of light is directed yo specimen. When laser hits dyes, it causes them to give of fluorescent light. This light is then focussed through a pinhole onto a detector. Detector is hooked up to computer, generates image. Pinhole means any out-of-focus light is blocked, so much slearer image than normal light microscopes. Can be used to look at objects at different depths in thick specimens. Multiple images produced can be combined to generate 3D images of specimen.....

...Electron microscopes: Use electrons instead of light. Higher resolution than light microscopes so give more detailed images.

Types of electron microscope:

Two types:

1. Transmission electron mcroscope (TEM): Use electromagnets to focus beam of electrons, which is then transmitted through specimen to produce 2D images. Denser parts of specimen absorb more electrons, making them darker on image you end up with. Provide high resolution images, can be used to look at very small organisms (e.g ribosomes). Can also be used to look at internal structures of organelles in detail. However, specimens need to be thinly sliced. Angle at which specimens are cut can affect how they appear.

2. Scanning electron microscope (SEM): Scan a beam of electrons across specimen. This knocks off electrons from specimen, which are gathered in a cathode ray tube to form an image. Images produced show surface of specimen and can be 3D but give lower resolution images than TEMs.

Interpretation of electron micrographs:

Micrographs produced from transmission and scanning electron microscopes are different - due to how they're produced. 

Producing electron micrographs:

To prepare samples for use with electron microscopes they are treated with a solution of heavy metals (like lead) - this process is the equivalent of stainingsamples tthat are to be viewed with a light microscope. The metal ions act to scatter te electrons that are fired at the sample and give contrast between different structures. The images produced by electron microscopy are always black and white, colour can be added to images after they've been made to make them easier to interpret.         

Comparing types of microscope:                                                                                   

                             Light microscope            TEM                                  SEM

Max resolution         0.2µm                          0.0002µm                         0.002µm

Max magnification     ×1500           Can be more than ×1000000      Usually less than                                                                                                                               ×500000

You need to know:

• How to prepare a slide for use with lighr microscope - including the use of stains.
• How to use light microscope - including using eyepiece graticule and stage micrometer to work out size of specimens you're looking at.
• How to produce and interpret drawings and annotated diagrams of cells viewed under light microscope.

Staining samples:

Sometimes the object being viewed is completely transparent. This makes the whole thing look white because the light rays just pass straight through. Hence, the need to stain. For the light microschope, this means using some kind of dye - called stains. Common stains include methylene blue and eosin. The stain is taken up by some parts of the object more than others, meaning some parts are more heavily stained than others. The contrast between heavily stained and more lightly stained parts means that the different parts of cells can be seen. Different stains can be used to make particular parts of cells show. E.g. Methylene blue can be used to stain DNA and Giemsa stain is commonly used to differentiate between different types of blood cells. It is poossible to use more than one stain at once. E.g. The stains haematoxylin and eosin are often used together (H&E staining). Eosin stains cytoplaasm pink. Haematoxylin stains RNA and DNA present in cells a purple/blue colour - this highlights cell structures where these molecules are found (e.g. the nucleus and ribosomes).

How to prepare a microscope slide:

There are two main ways of preparing a microscope slide:

1. Dry mount: Simplest way. Particularly useful for observing specimens such as hairs, parts of insects, pollen, parts of flowers, etc.

• Firstly, specimen needs to let light through it for you to be able to see it clearly under microscope. You will need to take a thin slice of specimen.
• Use tweezers to pick up specimen and put in middle of a clean slide.
• Pop a cover slip (a square of thin, transparent plastic or glass) on top. Slide now ready to use.
• (Tip: In a dry mount there's just a (relatively) dry specimen under cover slip)

2. Wet mount: Involve specimen being in liquid (usually water). More difficult to carry out than dry mount but can produce slides that give reeally clear view. This technique can be used with variety of specimens including living samples (i.e. tiny aquatic organisms).

• Start by pipetting a small drop of water onto slide. Then use tweezers to place specimen on top of water drop......

• ..... To put cover slip on, stand slip upright on slide, next to water droplet. Then carefully tilt and lower it so it covers specimen. Try not to get any air bubbles - they'll obstruct view of specimen.
• Once cover slip is in position, you can add a stain. Put a drop of stain next to one edge of cover slip. Then put a bit of paper towel next to opposite edge. The stain will get drawn under the slip, across the specimen.

Tip: Wet mounts are also used for liquid specimens (e.g. pond water sample). For these you will not need to add any water as sample itself will provide the liquid. This is an eexample of when you might use a slide that has a well. 

Tip: A smear slide is a special type of wet mount. Often used for blood samples. Involves spreading the liquid thinly over the central area of slide. A cover slip can then be applied and any excess liquid wiped off the slide.

How to use a light micoscope:

To view specimen:

• Start by slipping slide containing specimen onto the stage......

• Select the lowest-powered objective lens (i.e. the one that produces the lowest magnification).
• Use the coarse adjustment knob to move the objective lens down to just above the slide.
• Look down the eyepiece (which contains the ocular lens) and adjust the focus with the fine adjustment knob, until you get a clear image of whateverr's on slide.
• If you need to see the slide with greater magnification, swap to a higher-powered objective lens and refocus.

If you are asked to draw what you can see when using a microscope to look at a specimen, make sure the relative sizes of objects in drawing are accurate and that you write down the magnification the specimen was viewed under. Also, label drawing and give title.

Tip: Use sharp pencil, take up at least half the spcae given, do not colour or shade, make sure outlines are drawn neatly, not sketched. Pencil lines of labels need to be straight, should not cross over each other and should touch the part you are labelling, no arrowheads.

How to use eyepiece graticule and stage micrometer:

• Eyepiece graticule = fitted onto the eyepiece. its's like a transparent ruler with numbers, but no unts. So when you look through the eyepiece you'll see a scale.....

• Stage micrometer = Placed on the stage. it's a microscope slide with an accurate scalee (it has units) and it's used to work out the value of the divisions on the eyepiece graticule at a particular magnification. 

This means that when you take the stage micrometer away and replace it with the slide containing your specimeen, you'll be able to measure the size of the specimen. This works because you'll have worked out what lengths the divisions on your eyepiece graticule actually represent. 

Tip: An eyepiece graticule is just a transparent disc with a scale on it. They can be slotted inside the eyepiece or some eyepieces have them already built-in.

Example: Maths skills.

• 1.Line up eyepiece graticule and stage micrometer.
• 2.Each division on the stage micrometer is 0.1 mm long.
• 3.At this magnification, 1 division on the stage micrometer is the same as 4.5 divisions on the eyepiece graticule.
• 4.To work out the size of 1 division on the eyepiece graticule, you need to divide 0.1 by 4.5:    1 division on eyepiece graticule = 0.1 ÷ 4.5 = 0.02... mm 
• ...

• 5.So if you look at an object under the microscope at this magnification and it's 20 eyepiece divisions long, you know it measures:      20 × 0.02.... = 0.4 mm (1 s.f.) 

If you look at a different object under the microscope and it's 37 eyepiece divisions long, you know it measures:       37 × 0.02... = 0.8 mm (1 s.f.)

But don't forget, if you change to a different magnification you'll need to re-do the calibration.

Tip: If you change the magnification, 1 division on the stage micrometer will be equal to a different number of divisions on the eyepiece graticule - so the eyepiece graticule will need to be re-calibrated.

Tip: Each division on an eyepiece graticule can be called an eyepiece unit (epu). 

Equations you may need to know:

You need to know how to calibrate a graticule and the maths around that topic.

Magnification 

Magnification = Image size ÷ Object size

Common units and converstions:

   Unit:                                                 How many mm it is:     mm to µm = × 1000

   Millimetre (mm)                                 1mm                              µm to nm = × 1000

   Micrometre (µm)                                0.001 mm                      nm to µm = ÷ 1000

   Nanometre (nm)                                0.000001 mm                µm to mm = ÷ 1000

Side notes:

1: Check the OCR specification to make sure you have covered everything.

2: Practice questions and test papers!

3: Find pictures and diagrams to correspond to each topic/sub-topic as i could not include them. The picture will be very helpful and may be good to use as cues to prompt recall. Drawing them yourself may help you remember more!

(All information taken from the CGP A-level Year 1 & AS Biology OCR A text book)

Thank you!