The Microscope

The Microscope



Using the microscope

1. Mount slide on stage using stage clips

2. Turn on light source – adjust so it is bright but doesn’t hurt your eyes

3. Adjust diaphragm – try it out

4. Put the stage to the lowest setting and put the slide in

5. Start with lowest power objective lens and focus using coarse adjustment knob (turn it until the stage reaches the top then go back one turn)

6. Adjust focus on eyepiece for your eyes

7. Move the slide around the stage adjustment knobs

8. If you wish, move up to a higher magnification and use the fine adjustment knob ONLY to focus – IMPORTANT

9. Make further adjustments if necessary

10. To put the microscope away turn to the lowest lens, put the stage to the lowest setting and take the slide out.

11. Cover, tie up the cord and put back in the cupboard as you found it



















Magnification and Measurements



Measurement Symbol Power/m How many in proportion to 1m? How many in 1m? Written as a number
1 millimetre


mm 10-³ metre 1/1000m One thousand  
1 micrometre


μm   1/1 000 000m    
1 nanometre


nm 10-⁹ metre   One billion 0.000000001




Calculation of sizes and magnification values in biology questions

Magnification = measured size divided by actual size




Measured size

Actual size






If two of the figures are available then these can be used to work out the third one. Numbers on the top are divided by number on the bottom. Numbers beside each other are multiplied.



· If you know the magnification and the actual size you can multiply them to give the measured size

· If you know the measured size and the actual size you can divide the measured size by the actual size to give the magnification

· If you have measured the size in the picture and know the magnification you can divide the measured size by the magnification to give the actual size



Drawing for Biology


· Use a pencil

Figure 1: The Eukaryotic Cell.

Magnification x400


· Draw in two dimensions (unless 3D is needed to make a point clearer for example for SEM)

· Blank paper

· Lines should not have breaks

· Drawings should be approximately half an A4 page

· Use line to annotate. The lines should not cross

· Drawings should have:

· A figure number – at the bottom

· A title – at the bottom after the figure number

· A legend (not always required)

· Magnification or size (required for microbiology assessment)

· Annotations and labels


Drawings should ‘stand alone’, there should be enough information for the reader to understand what is going on in the picture without having to refer to the main text.

BUT in reports and essays drawings are referred to in the main text to make the text clearer. For example, an essay text contains the sentence: eukaryotic cells contain a number of organelles (see figure 1).



Note, figure number and title at the bottom

Figure 1. The eukaryotic cell.

Some organelles are labelled.

Original magnification x400



Note figure number, title and legend at the bottom


What's the Difference Between Prokaryotic and Eukaryotic Cells? |  HowStuffWorks Cells






Organelle Description Function Diagram/TEM
Cell wall, membrane and cytoplasm
Cellulose cell wall · On the outside of the plant cells

· Three layers: the primary cell wall, the middle lamellae and the secondary cell wall.

· Contains cellulose microfibrils in a criss-cross pattern

· Supports the cell

· Helps maintain cell shape with turgor pressure

· Prevents the cell from busting in times of high osmotic pressure

Image result for cellulose cell wall

Plasma Membrane (Cell surface membrane)




· Present in all living cells

· Consists of a double layer of phospholipids studded with proteins

· Called the fluid mosaic model

· Controls the passage of substances into and out of the cell

· Regulates the internal environment of the cell.

· Provides a selective barrier between the cell’s contents and the external environment

Image result for Cell membrane

Cytoplasm · Gel-like substance in which the organelles and structures are suspended.

· Contains the cytoskeleton – a network of fibres that link organelles

· Organelles are suspended in the cytoplasm

· Numerous biochemical reactions occur here

Image result for cytoplasm TEM Image result for expasy biochemical reactions

Centrioles · Small tubes of protein fibres.

· There is a pair of them next to the nucleus in animal cells and some protists.

· Part of the cytoskeleton

· Take part in cell division.

· The spindle fibres used to move chromosomes grow from this organelle.

accessdayunit1booklet centrioles
Cytoskeleton · Network of string-like proteins

· .

· Centrioles/cilia and flagella: all part of the cytoskeleton.


· Involved in maintaining and changing cell shape and movements in animal and bacteria cells

· organelles to move propelled by contractile proteins attached to their various surfaces

accessdayunit1booklet Project III 15-16 (Modelling the Cytoskeleton)

Vacuole and tonoplast · A large membrane bound sac containing water and solutes.

· Found in plant cells

· The membrane surrounding it is called a tonoplast

· Storage of water and solutes.

· Maintenance of cell turgidity

· Involved in cell elongation during growth

Making Proteins
Nucleus · The Largest organelle (10-20m in diameter).

· Roughly spherical.

· It is double membrane bound

· The membrane has pores and is linked on the outside to the endoplasmic reticulum

· There is an area which appears darker under the microscope called the nucleolus (see below)

· Contains chromosomes – long linear DNA structures.

· The chromosomes are packed into chromatin – a mixture of DNA and associated proteins.

· It carries the genetic code for all of the proteins

· It controls protein synthesis by making messenger RNA (mRNA)

· During cell division and reproduction, the DNA is duplicated then divided between daughter cells to ensure the code is passed on.

cell_nucleus1.gif accessdayunit1booklet

Nucleolus · Area of dense chromatin within the nucleus

· It is a granular structure and is not membrane bound

· The nucleolus makes ribosomal RNA (rRNA) and assembles ribosomes  
Ribosome · Very small organelle

· Can be attached to the rough ER or free in the cytoplasm

· Key components are RNA and proteins (ribonucleoproteins)

· Consists of two subunits

· Size: in eukaryotes the ribosome is 80s whereas in prokaryotes the ribosomes is 70s

· The site of protein synthesis, called translation.

· mRNA from the nucleus is read and used to assemble amino acids in the correct order.

· Multiple ribosomes can attach to the same mRNA at once (see picture)

Image result for ribosome polysome

Processing Proteins
Rough Endoplasmic Reticulum · Consists of flattened sacs called cisternae

· Cisternae are made of membrane

· The inside of the tubes is called the lumen

· Continuous with the outer nuclear membrane.

· Studded with Ribosomes

· Closely linked with the Golgi apparatus

· The ribosomes make protein which is then transported

· Some of the proteins are secreted by the cell, others are used within the cell.

· Proteins which are embedded in the membrane are produced here

· Protein modification occurs in the lumen such as the addition of sugar groups (glycosylation) or quaternary folding with metal ions such as haemoglobin with iron


Smooth Endoplasmic Reticulum · Consists of tubes called cisternae

· Cisternae are made of membrane

· The inside of the tubes is called the lumen

· No ribosomes

· Production of lipids

· Production of steroid hormones

· Release of calcium in the muscles

· Detoxification of organic molecules in the liver

smooth er

vesicles · The membrane at the end of the ER or Golgi pinches off to make a small sac containing proteins


· Vesicles are transported within the cell to various organelles

· Vesicles from the rough ER travel to the Golgi

· Vesicles from the Golgi go to various destinations such as the lysosome, mitochondria and outer membrane

· Vesicles that reach the outer membrane fuse with it causing their contents to be released

vesicular transport Image result for vesicles TEM er golgi
Golgi apparatus · A stack of flattened sacs

· Sacs are made of membrane

· The inside of the sacs is called the lumen

· Characteristic curved form on one side, flatter on the side closest to the rough ER

· Vesicles can be seen on either side


· Receives proteins packaged in vesicles from the ER.

· The cis side accepts vesicles (which contain a cargo of protein)

· Modifies proteins e.g. by the addition of sugars, sulphur or phosphate

· Packages modified proteins into vesicles for transportation to the cell surface membrane and secretion out of the cell.

· Vesicles leave for their destination on the trans side

Lysosome · Spherical sacs surrounded by a single layer of membrane.

· Contain powerful digestive enzymes

· The pH is more acidic than the cytoplasm (pH4.8)

· Protects the cell from enzymes contained within.

· Enzymes are used in the breakdown of materials e.g. cells taken up by white blood cells taken up in phagocytosis or proteins that are not functioning properly


Energy Processing
Mitochondria · Spherical sausage shaped organelle formed from two membranes.

· The inner membrane is highly folded to form cristae.

· Site of aerobic respiration

· Produce adenosine triphosphate (ATP)

mitochondria mitochondriaem






Chloroplast · Found only in plant cells

· Two layers of membranes

· The inner layer is continuous and forms flattened membrane sacs called thylakoids.

· Site of photosynthesis a process in which Glucose is produced.

· Contain chlorophyll: a photosynthetic pigment.




There are resources below to get you started and you can visit these websites for more information: – interactive but basic



Tissue Types Features & Functions Examples


Usually forms a barrier between the external and internal environment or between two internal tissues or organs.

Endothelium is a type of epithelium which lines the blood vessels.

Squamous Thin, paving stone appearance. These cells are adapted for diffusion as they are thin and this reduces the diffusion distance. Squamous epithelium in the lungs: squamous epithelium lines the alveoli – the small sacs at the end of the airways where gas exchange occurs. File:1SHEmbryo44.jpg - StudyingMed
  Cuboidal These cells can be both secretory and for absorption. They resemble rounded cubes. Found in the kidneys and other organs.    
  Columnar Columnar epithelium is where the height of the cell is four times the width. They usually have a secretory function such as mucus in the lungs and digestive enzymes in the small intestine. They also can also be involved in absorption, particularly in the digestive tract. Stratified epithelium in the oesophagus. The cells are being continuously made at the basement membrane and move upwards. The upper layers of cells are dead and full of the protein keratin. When food passes the top cells can be sloughed off without damaging the tissue below. accessdayunit1booklet
  Stratified Stratified epithelium has multiple layers of cells. The layers provide a strong protective surface.    
  pseudostratified Pseudostratified epithelium appears to be stratified columnar cells but in fact all cells are attached to the basement membrane. It has a secretory function. Pseudo stratified ciliated epithelium in the upper respiratory tract. The secretory goblet cells produce mucus which traps unwanted microorganisms.

The cilia aid movement of the mucus back up the respiratory tract.

  Ciliated Ciliated epithelium has tiny hair-like cilia on the top (apical) surface. Cilia can move and are involved in the movement of substances such as mucus.    
Connective tissue


Mostly tissue with a structural component such as fibres. Blood is included in this category as it is made in the bone marrow.

Loose: areolar, reticular, adipose Areolar connective tissue has cells and fibres creating a loose matrix. It connects skin to the surrounding tissue; holds organs in place and provides support for nervous tissue. Elastic tissue. The fibres in this tissue can stretch without breaking when needed. They can be found in the larger blood vessels such as the aorta which expands when blood is pumped through from the heart. C:UsersjwebbAppDataLocalMicrosoftWindowsINetCacheContent.MSO9C97F582.tmp
  Dense: fibrous & elastic Fibrous connective tissue is found in tendons and ligaments. It contains bundles of the protein collagen which are very strong.    
  Blood: red and white cells, lymph White blood cells fight pathogens either by engulfing them (phagocytes) or by producing neutralizing antibodies (B-lymphocytes) Red blood cells are adapted to carrying oxygen around the body. The middle is thinner than the outside giving them a donut like shape. They are flexible and can squeeze through the smallest blood vessels. As they mature they lose their nucleus so they can pack in more of the oxygen carrying protein haemoglobin. Red Blood Cells, Sem Photograph by Ami Images
  Structural: cartilage & bone Cartilage is a smooth but flexible layer which covers the end of the bones and provides the structure for organs such as the ear. Bone has calcium deposits and collagen fibres which makes it very strong.    
Nervous tissue


Neuronal cells present in the CNS and the PNS

Neurons: sensory, relay and motor Sensory neuron: detects changes in the environment. Conveys impulse to the brain or spinal cord To convey electrical impulses, which act as communication, between the body and the brain. Purkinje Nerve Cell, Sem Photograph by David Mccarthy
    Relay neuron: connects sensory and motor neurons    
    Motor neuron: conveys impulse to effector organs such as muscle and glands    
Muscle tissue


Cell are adapted for movement

Smooth muscle Smooth muscle is found in sheets surrounding the tubes of the body such as the digestive system and the blood vessels. The sheets are often layered with the cells organised in different directions. Smooth muscle responds to the autonomic nervous system. In the digestive system it causes peristalsis which moves the food through the digestive tract. In blood vessels it controls how much blood flows through various tissues. Chapter 7, Page 11 - HistologyOLM
  Striated muscle Striated muscle is skeletal muscle which, along with the skeletal system, allows movement. The cells fuse end to end during development to form long fibrils. Multiple fibrils form a muscle. These are packed with the proteins actin and myosin which slide against each other to lengthen or shorten the fibril and so the muscle. The stripes or striations formed by actin and myosin can be seen under the light microscope. accessdayunit1booklet
  Cardiac muscle Cardiac muscle cells also have striations but the cells are not fused. They have intercalated discs which are linked to the nervous system and ensure all of the muscle cells contract at the same time. Cardiac Muscle - Lippincott Illustrated Reviews: Physiology (Lippincott  Illustrated Reviews Series)


Differences between Light Microscope and Electron Microscope


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