Micro Notes For Practicals
Micro Notes For Practicals
UNIT 1
MICROSCOPY
Structure
1.1 Introduction Scanning Transmission
Electron Microscopy (STEM)
Objectives
Environmental Scanning
1.2 Imaging Techniques
Electron Microscopy (ESEM)
(Microscopy)
Comparative account of
Principles of Microscopy
different types of microscopes
Light Microscopy
1.4 Techniques for preparing
Phase Contrast Microscopy tissue for Electron Microscopy
Fluorescence Microscopy Negative Staining
Confocal Microscopy Freeze Fracture
Polarization Microscopy Freeze-Etching
1.3 Electron Microscopy (EM) Shadow Casting
Transmission Electron 1.5 Summary
Microscopy (TEM)
1.6 Terminal Questions
Scanning Electron Microscopy
1.7 Answers
(SEM)
1.1 INTRODUCTION
Cell biology is the branch of biology which deals with the study of cell
structure, their architectural details, major cellular as well as subcellular
processes, and the interactive processes between the cells. Various
techniques have been used to study the structural details and functioning of
the cell. Imaging techniques such as microscopy have proven very useful in
studying various aspects related to the architecture of cells, tissues and
various organelles present in them. The minute structural details of the cell,
cellular processes and other characteristics can be easily studied with the help
of microscopy techniques. The information procured via these techniques
provides a better understanding of the various cellular processes taking place
in a living being. Our knowledge about cellular structures and their functions
has improved manifold by using microscopy and biochemical techniques. In
this unit you will study about the various aspects of the microscopy techniques
and how microscopy helped to understand the structure of cell. An update
about various types of microscopy will also be provided to you. 9
Block 1 Techniques in Cell Biology
Objectives
Objectives
After studying this unit, you would be able to:
The most commonly used microscope is the optical or light microscope. In this
microscope the glass lenses are used to magnify the image.
History of Microscope
The concept of magnification came into existence long back in 1267 A.D. An
English philosopher R. Bacon invented eyeglasses in 1235 A.D. In his book
Perspectiva, he mentioned about the small size of dust and sand particles. In
1538, an Italian physician Girolamo Fracastoro observed that an object
appears much larger when seen with two spectacle glasses one
superimposed on the other. He mentioned these facts in his book
Homocentrica. The first simple microscope was invented by two Dutch
scientists, Zaccharias Janssen and his father, Hans in 1590. They were the
first to combine two concave lenses within a tube. They noted that nearby
objects appeared closer and larger. They developed a microscope made up of
wood and cardboard with an eyepiece and an objective lens. Antonie van
Leeuwenhoek, a Dutch microbiologist made first simple microscope in the
year 1668. He was able to see the presence of tiny living organisms present in
pond water. The organisms appeared like dots. His microscope was made up
of a double convex glass lens that was held between two silver plates (Fig.
1.1). Leeuwenhoek was the one who made microbiology popular throughout
10 the world.
Unit 1 Microscopy
Single lens microscopes were first used by English natural philosopher Robert
Hooke in 1665 (Fig. 1.2).
(a) (b)
Fig. 1.2: a) The microscopes used in earlier times by Robert Hooke; b) image of
cover page of Micrographia.
Fig. 1.3: Images of two single lens microscopes used in older times.
d = λ / 2 NA
It has been noted that resolving power of the lens is higher if the wavelength is
short. Hence smaller the value of resolving power, higher the resolution and
more the clarity.
The magnification of the objective lens and eyepiece manage the magnifying
power of the compound microscope. 13
Block 1 Techniques in Cell Biology
Parts of a Microscope
Objective
The objective lens gathers light from the specimen, magnifies the image of the
specimen and projects this magnified image. Objective lenses show
magnifications in the range of 2 to 100X. Objective is designed to minimize
aberrations.
The focal length regulates the optics of the objective. The focal length is
inversely proportional to the magnification. This means that focal length of an
objective decreases with the increase in magnifying power. .
In some objectives special glasses are used. These are called apochromats
and were first produced commercially by Abbe in the 1870s.
Eyepiece is the lens which is used to observe the image. These lenses are
usually of 10X or 15X magnification. The eyepiece helps in forming enlarged
14 virtual image that can be seen by the observer.
Unit 1 Microscopy
Body Tube
A hollow tube through which light travels from the objective to the ocular lens
is called as body tube (Fig. 1.5). It connects eyepiece to the objective. It
contains a prism that bends the light rays so they can enter the tube. The
upper end of body tube possesses ocular or eyepiece lens, while the lower
portion consists of a movable nosepiece containing the objective lenses.
Base
Stage
It is a flat platform having clips that supports the slides (Fig. 1.4). In case of
mechanical stage, the slide kept in position with the help of two knobs. One
knob moves the slide left and right, the other moves it forward and backward.
Nosepiece
The circular structure that screws the objective lenses is called nose piece.
Objective lenses of varying magnification and numerical aperture are mounted
on the rotating nosepiece.
Condenser Lens
The condenser is mounted below the stage (where the specimen is placed)
and focuses beam of light onto the specimen. When it provides uniform
illumination in the region of the object under observation, it is referred to as
critical illumination. Alternatively, when the image is focused on the condenser
followed by objective of the microscope, it is referred to as Köhler illumination.
It is useful in getting sharp images of magnification 400X and above. For a
microscope with a power of 1000X or above, condenser lens with an N.A. of
1.25 or greater is needed. Such microscopes are generally equipped with an
Abbe condenser. 15
Block 1 Techniques in Cell Biology
Diaphragm or Iris
The diaphragm or iris regulates the amount of light entering the condenser i.e.
helps in adjusting the intensity of light. It is located under the stage or between
the light source and condenser.
IIluminator
A steady light source is used for illumination in the microscope. Mirrors were
used as a source of light in early microscopes. Mirror reflected light up from an
external light source located at the bottom of the stage. Generally, a tungsten
lamp is used as a light source. Effective illumination is required for getting
good magnification and resolving power. The amount of light entering the
microscope needs to be regulated as excessive illumination may obscure the
specimen.
The modern theory of image formation in the microscope was given by German
physicist Ernst Abbe in 1873. According to this theory, convergent light obtained from
a condenser helps in visualization of objects or specimens in the focal plane of the
microscope. A collection of plane waves propagating in a specified set of directions is
called as convergent light. The superimposition of waves produces incident
illumination. The diffracted waves are collected by the objective and directed to the
focal plane. Interference between the diffracted waves produces an image of the
object.
16
Unit 1 Microscopy
Abbe showed that more is the number of diffracted waves reaching the objective, finer
is the details of the image. The objective’s ability to collect diffracted light was
considered as the N.A. Greater is the magnification of the objective, greater is N.A. of
the objective.
Metallographic microscope
In this type of microscope, vertical source of light (illumination) is used. The
light source is generally present below the eyepiece in the tube. Light is
focused through the objective onto the specimen. The reflected light or
scattered light gets back to the objective which is imaged back at the
eyepiece. This type of microscope is used to identify defects in metal surfaces,
determine crystal grain boundaries in metal alloys, and study rocks and
minerals. They also have applications in forensic science and diagnostics.
Reflecting microscope
Microscopes of this type possess reflecting objectives. An objective usually
consists of two components: a relatively large, primary concave mirror and a
smaller, secondary convex mirror which is located between the primary mirror
and the object. The objective lens of this type does not produce chromatic
aberration and needs no correction. The objects can be observed over a wide
range of visible light and also in the ultraviolet or infrared regions.
Brightfield microscope
Two lens systems are used for magnifying specimens. This includes ocular
lens located in the eyepiece and objective lens located in the nosepiece. The
beam of light obtained from tungsten lamp helps in illumination of the
specimen. The light is focused on sub-stage lens called a condenser. This
microscope provides a high-resolution image. These microscopes are used for
observing non-viable, stained samples. We cannot observe living cells
because of the absence of contrast between the specimen and the
surrounding medium. 17
Block 1 Techniques in Cell Biology
Darkfield microscope
In this type of microscope, the condenser is modified which directs light
obliquely on the specimen. This results in deflection or scattering of light,
hence making object appear bright against a dark background. This type of
microscope is suitable for observing living specimens.
Interference microscope
Two beams of light are used in this microscope. One beam of light passes
through the specimen while the other bypasses it. The combination of two
beams results in interference between them, thus revealing the structure of the
specimen. The difference between interfering beams of light is used to create
the image. This type of microscopy was developed by British microscopist
Francis Smith and French physicist Maurice Françon in 1947. Quartz lenses
were used by them to produce two beams of light that were perpendicularly
polarized.
SAQ 1
a) Fill in the blanks with the appropriate word :
i) Eyepiece
ii) Diaphragm
1. The vacuum system creates strong vacuum in the entire column i.e.,
along the path of electron beam. This is required for making the
electrons travel as they do not travel easily in air.
(a) (b)
a b
c d
Fig.1.11: Image showing a) Knife Maker; b) Glass knife; c) Boats; d) Glass knife
with boat.
An Ultramicrotome
TEM shows enhanced resolution but the electron beam used is very weak and
pass an appreciable distance through air, therefore high vacuum is required
inside the internal chamber of electron microscope. The photographs of cells
taken using an electron microscope are called electron micrographs. You
can see that the picture below shows the minute structural details of the
cellular entities (Fig. 1.13).
Fig. 1.13: Electron Micrograph showing two plant cells (X 45, 000). CW - Cell
wall; ER- Endoplasmic, M-Mitochondria, PM- Plasma membrane, PP-
Proplastids, T-Tonoplast.
Generally, the image resolution of SEM is less than that of TEM. The SEM
image depends upon the surface processes. SEM can produce images of bulk
samples up to many centimeters in size. It produces images of three-
dimensional shape of the sample (Fig 1.15). This microscope has proved very
dimensional
useful in studying the minute structural details of the cell surface (Fig. 1.16).
The increasing popularity of SEM among cell biologists is because of its
remarkable ability to provide details
details about surface topography, show 3D
structure and improved resolution (30-100 Å).
Fig. 1.16: Pollen structure of Cineraria plant showing spines as observed under
scanning electron microscope (image magnified 1,500X).
Sample preparation
2. The fixed specimen is washed thrice (for 5 to10 min) in 0.1 M Hepes
buffer (pH 7.2).
5. The sample is mounted on metal stub with double sided carbon tape.
(a)
(b)
Fig. 1.17: a) Scanning Transmission Electron Microscope (STEM); b) Schematic
diagram of STEM.
ESEM is useful for studying non-metallic and biological materials (Fig. 1.19).
(a) (b)
(c) (d)
Fig. 1.20: Image micrographs of an algal cell as seen under different
30 microscopes. a) Compound; b) Confocal; c) SEM; d) TEM.
Unit 1 Microscopy
SAQ 2
a) Match the items in column l correctly with those of Column ll.
Column I Column II
1.4.2 Freeze-fracture
The technique involves physical breaking (fracturing) of a frozen biological
sample along the planes of natural weakness that run through each cell.
These planes generally occur between the two layers of lipid molecules which
forms part of membrane and around various organelles of the cell. The main
steps involved in formation of a freeze-fracture replica are; (i) rapid freezing,
(ii) fracturing, (iii) formation of replica, and (iv) replica cleaning. The
pretreatment carried out before freezing comprises fixation of material in
glutaraldehyde followed by cryoprotection with glycerol. Cryoprotection is done
to reduce the formation of ice crystals during freezing. This kind of sample
preparation provides planar views of the internal organization of membranes.
Images provided by these samples have proved useful understanding the
functional morphology of the cell. This technique has been used to study
membranes and reveal the pattern of integral membrane proteins.
General outline of technique:
i) Cells are frozen in liquid Freon (-130º C). This results in instant
immobilization of cell components.
i)
ii) iii)
iv) v) vi)
1.4.3 Freeze-Etching
The freeze-etching technique of sample preparation is related to freeze
fracture. One more step is added to freeze fracture procedure. In this method,
the specimens are rapidly frozen in liquid Freon under vacuum and struck with
a sharp knife edge as in freeze fracture method (Fig. 1.23).
(a)
(b) (c)
Fig. 1.23: Freeze fracture views of organelles a) entire cell showing nucleus and
nuclear pores; b) Golgi apparatus; c) Mitochondria. 33
Block 1 Techniques in Cell Biology
Biological samples fracture along lines of natural weakness at low
temperature. The tissue is subjected to vaccum which results in sublimation of
water from the fractured surfaces. This removal of water produces an “etching”
effect. This etching will cause small areas of the cell surface around the
periphery of the fracture face to stand out against the background. A replica of
the specimen is made by heavy metal such as platinum, followed by backing it
with a carbon film. After dissolving the tissue in strong acid, the remaining
metal replica can be viewed with the electron microscope. Such preparations
provide a unique picture of cells. This procedure is useful because it avoids
exposure to fixatives, embedding agents, and stains which can deform
ultrastructure of cell (Fig. 1.23). This type of specimen treatment causes
minimal tissue distortion and permits immediate arrest of cell function
SAQ 3
a) Answer in one word:
iv) Focused beams of laser light are scanned across the sample and
light only from the desired focal plane can enter the detector.
1.5 ANSWERS
Self-Assessment Questions
1. a) i) magnification
ii) Frits Zernike
iii) fluorophore
iv) obliquely
v) microtome
vi) light
b) i) True; ii) False; c) True; d) False; e) True
c) i) Refer to Subsection 1.2.1
ii) Refer to Subsection 1.2.1
iii) Refer to Subsection 1.2.1
d) Refer to Fig. 1.4
2. a) i) uses a laser light as the source of illumination
ii) invented by Manfred von Ardenne
iii) uses electron as the source of illumination and 3-D image is
formed
ii) cooling
iii) tungsten
3. a) i) interference
iii) fluorescein
v) polarization microscopy
viii) freeze-fracture
Terminal Questions
1. a) Magnification is the measure of the ability of a lens or other optical
instruments to magnify. It is expressed as the ratio of the size of
the image to that of the object.
Acknowledgement
Fig 1.1 : Source:
https://www.google.co.in/imgres?imgurl=https%3A%2F%2Ffanyv88.com%3A443%2Fhttps%2F50
a8d2.medialib.edu.glogster.com
b) https://www.google.co.in/imgres?imgurl=https%3A%2F%2
Fthumbs-prod.si-cdn.com)
Fig.1.19 : Source:
https://www.google.co.in/imgres?imgurl=https%3A%2F%2Ffanyv88.com%3A443%2Fhttps%2Fars
.els-cdn.com%2Fcontent%2Fimage%2F1-s2.0-
S1369702110701437-
gr9.jpg&imgrefurl=https%3A%2F%2Ffanyv88.com%3A443%2Fhttps%2Fwww.sciencedirect.com
https://www.youtube.com/watch?v=icRQE73AUII
https://www.youtube.com/watch?v=CVusz4wHaic
https://www.youtube.com/watch?v=gyOIFWhvUn0
https://www.youtube.com/watch?v=NG44AEWHtRQ
https://www.youtube.com/watch?v=QFtZFbug1SA
40