Introduction to Molecular

and Cell Biology

Dr Sandile Buthelezi
ILS Course-Coordinator (Block 1 Lecturer)
Office: GH, first floor, room 11
Email: Sandile.Buthelezi@wits.ac.za
Contact me via email or the Ulwazi Inbox (for appointments and queries)
Cells and how we
study them
Fig. 1-4b

Levels of Biological Organisation

10 µm
Cells
Organs and
organ systems
Cell

Organelles

1 µm

Molecules
Tissues 50 µm
• Cells
• Hierarchy (levels) of structure and organisation
• Subcellular structures (organelles)
• Intracellular environment
• Molecules making up the organelles
• Molecules making up the environment
• Interaction of cellular molecules…

STRUCTURE, FUNCTION
and PROCESSES
Some of the questions we’ll address in this section

• What are cells?

• How did they get their name?
• What do they do?
• How big are they?
• Why are they small?
• If they are so small how do we study them?
What are cells?
Cells are an organism’s basic units of structure and
function
• The cell is the smallest unit of organization that can perform
all the activities required for life

• Cells:
• Are enclosed by a membrane
• Use DNA as their genetic information
• Cells can divide, this is the basis of all reproduction,
growth, and repair of uni- or multi-cellular organisms
• all cells arise from cells
Fig. 1-7

25 µm

A lung cell from a newt divides into two smaller cells

that will grow and divide again
• Some cells have additional specialised functions
• Complex organisms are made up of groups of cells
with specialised functions
Discovery and early study of
cells
Microscopy
• Robert Hooke (1665) first saw the cell wall
1665 – curator of instruments –
Royal Society of London
He wrote:
• . . . I could exceedingly plainly perceive it to be all
perforated and porous, much like a Honey-comb,
but that the pores of it were not regular. . . . these
pores, or cells, . . . were indeed the first
microscopical pores I ever saw, and perhaps,
that were ever seen, for I had not met with any
Writer or Person, that had made any mention of
them before this. . . Hooke had discovered
plant cells -- more precisely, what Hooke saw
were the cell walls in cork tissue (which was
dead).
 Hooke coined the
term "cells“
because the
boxlike cells of
cork which
appeared to be
empty reminded
him of the cells of
a monastery.

Question: why does

cork float?
Cell Theory states
• All organisms are composed of one or more cells
• Cells are the smallest living things – the basic units of structure
organisation of all organisms
• Cells arise only by division of a previously existing cell
Origin of Cell Theory
• First living cells: van Leeuwenhoek – “animalcules” (late 1600s)
• 1805 – Oken “All living things originate from and consist of
vesicles or cells”
• 1839: Cells basic unit of structure and function- Schleiden and
Schwann
• 20 years later: Virchow added: “all cells originate from cells”
What is a Cell?
• Fundamental unit of life
• Smallest unit that can carry out all life activities
• Life activities:
• Extraction of energy from raw materials
• Growth – organised manner
• Respond to stimuli
• Homeostasis
• Reproduce
• Adapt
How big are cells?
• Most cells – microscopically small – so small units
used
• Unit of measurement: μm
• 1 μm is: 1/1 000 000 of a meter (1 X 10 -6) (1/1000
of a mm)
• 1 nm is: 1/1 000 000 000 of a meter (1 X10 -
9m)

How many nm in 1mm?

And in 1 μm?
50 µm

0.136 nm
 Angstrom
• The angstrom or ångström is a unit of length
equal to 10−10 m or 0.1 nm.
• Å.
• Expresses the sizes of atoms, molecules, and
microscopic biological structures, lengths of
chemical bonds, arrangement of atoms in crystals,
wavelengths of electromagnetic radiation, and
dimensions of integrated circuit parts.
• Named after the Swedish physicist Anders Jonas
Ångström (1814–1874) – worked on spectroscopy.
Fig. 6-2
10 m
Human height
1m
The size
Length of some
nerve and muscle
cells

Unaided eye
0.1 m
range of Chicken egg

cells 1 cm

Frog egg
1 mm

Light microscope
100 µm
Most plant and
animal cells
10 µm
Nucleus
Most bacteria

Electron microscope
Mitochondrion
1 µm

Smallest bacteria
100 nm
Viruses

Ribosomes
10 nm
Proteins
Lipids
1 nm
Small molecules

0.1 nm Atoms
 Why are cells so small?

• The logistics of carrying out cellular metabolism

sets limits on the size of cells
• The surface area to volume ratio of a cell is critical
• As the surface area increases by a factor of n2, the
volume increases by a factor of n3
• Small cells have a greater surface area relative to
volume
Fig. 6-8
Surface area increases while
total volume remains constant

5
1
1

Total surface area

[Sum of the surface areas
6 150 750
(height ´ width) of all boxes
sides ´ number of boxes]

Total volume
[height ´ width ´ length ´
1 125 125
number of boxes]

Surface-to-volume
(S-to-V) ratio
6 1.2 6
[surface area ÷ volume]
• WHY is it important that cells have a large surface area?

• Oxygen
• Nutrients
• Waste
 Microscopy
• There are different types of microscopes
• In a light microscope (LM), visible light is used to
illuminate the specimen, the light then passes
through glass lenses, magnifying the image
https://www.pxfuel.com/en/search?q=biology
What is required for a light microscope to
work
• The source of light.
• The specimen.
• The lenses that makes the specimen seem bigger.
• The magnified image of the specimen that you see.

https://microbiologynotes.com/differences-between-simple-and-compound-microscope/
Compound Light Microscope - More than one lens

Light from light source is

focused on the specimen by the
condenser lens.
After passing through the
specimen the light enters
objective lens (principal
magnifying lens).
Light rays then enter the
projector lens (if present) and
are directed to the ocular lens
(eyepiece) 2nd magnification.
•Total magnification: multiply
powers of 2 lenses together.
• The quality of an image depends on
• Magnification, the ratio of an object’s
image size to its real size
• Contrast, visible differences in parts of
the sample
• Resolution, the measure of the clarity of
the image, or the minimum distance of two
distinguishable points. No system can
resolve points that are closer together
than ½ λ of the light used to view them.
• The limitation is light itself
Resolution
• Light Microsopes can magnify effectively to about
1,000 times the size of the actual specimen (limit
of usefulness is ≈ 1400X)

• Most subcellular structures, including organelles

(membrane-enclosed compartments), are too small
for their details to be resolved by a Light
Microscope
More sophisticated microscopes
and/or staining techniques
improve images…..
• e.g some microscopes enhance contrast and cell
components may be stained or labeled
Fig. 6-3ab

TECHNIQUE RESULTS

Brightfield (unstained
specimen)
Passes light directly
through the specimen

Brightfield (stained 50 µm

specimen)
Staining enhances contrast
Disadvantage: cells must be fixed
– kills them
Fig. 6-3e

TECHNIQUE RESULTS

Fluorescence

Detect the locations of

specific molecules in cells
Fluorescent stains bind to
specific molecules, absorb
UV light and emit visible
light.
50 µm
Fig. 6-3cd

TECHNIQUE RESULTS

Phase-contrast
Enhances contrast in unstained cells
by amplifying variations in density;
especially useful for examining
living, unpigmented cells
Interfering waves of light may be used to
enhance the internal structures of cells
• e.g Phase contrast
Fig. 6-3cd

TECHNIQUE RESULTS

Differential-interference-
contrast (Nomarski)
Uses optical modifications to
exaggerate differences in density –
making the image appear almost
3-D
Fig. 6-3f

TECHNIQUE RESULTS

Confocal Confocal

Fluorescent “optical sectioning”

technique that uses a pinhole
aperture to eliminate “out-of
focus” light from a thick sample,
creating a single plane of
fluorescence in the image. Standard

By capturing sharp images at

many different planes, a 3-D
reconstruction can be obtained.

50 µm
Electron Microscopy
• Increases resolving power by > 10 000
• Object flooded with electrons
• Two basic types of electron microscopes (EMs)
are used to study cells
• Scanning electron microscopes (SEMs) focus a
beam of electrons onto the surface of a specimen,
providing images that look 3-D
• Transmission electron microscopes (TEMs)
focus a beam of electrons through a specimen
• TEMs are used mainly to study the internal
structure of cells
Summary of how an electron microscope
works
• The light source is replaced by a beam of very fast moving electrons.
• The specimen usually has to be specially prepared and held inside a vacuum
chamber (because electrons do not travel very far in air).
• The lenses are replaced by a series of coil-shaped electromagnets through which
the electron beam travels. In an ordinary microscope, the glass lenses bend (or
refract) the light beams passing through them to produce magnification. In an
electron microscope, the coils bend the electron beams the same way.
• The image is formed as a photograph (called an electron micrograph) or as an
image on a screen.
How a scanning
electron
microscope works

TEM or SEM??
How a
transmission
electron
microscope
works
 Transmission Electron Microscope

• Specimen embedded in plastic and cut very

thin.

Preparation • Stained with atoms of heavy metals, which

attach to certain structures – enhance
electron density different structures
of Samples • Preparation can introduce artifacts

Scanning Electron Microscope

• Sample is coated with a thin film of gold

Fig. 6-4
TECHNIQUE RESULTS

Scanning electron Cilia 1 µm

microscopy (SEM)
Show a 3-D
image of the
surface

Transmission electron Longitudinal Cross section

microscopy (TEM) section of of cilium
cilium 1 µm

Used to study the

ultrastructure of cells
• Microscopy is important in the study of cell structure
• Biochemistry is essential to study the function of each
structure

https://commons.wikimedia.org/wiki/File:Mitochondria,_mammalian_lung_-_TEM.jpg
Cell fractionation
• Cell fractionation enables scientists to
purify sub cellular structures like
organelles in large amounts
• This makes it easier to determine their
function(s) by various means, like
biochemistry
• Biochemistry together with cytology help
correlate cell function with structure
• Process used to separate cellular
components while preserving individual
functions of each component.
– centrifugation of broken up cells
– subcellular structures separate according to
their size and density
Bench centrifuge – swinging
bucket rotor

Ultracentrifuge
Supernatant
Fig. 6-5a

TECHNIQUE

Homogenization

Tissue
cells Homogenate

Differential centrifugation
Fig. 6-5b
1,000 g
(1,000 times the force
of gravity)
10 min
Supernatant poured
Increasing speeds
into next tube Different subset of cell
Components settle out
20,000 g
20 min

80,000 g
60 min
Pellet rich in
nuclei and cellular
debris
150,000 g
3 hr

Pellet rich in
mitochondria (and
chloro-plasts if cells
are from a plant)

Pellet rich in
“microsomes”
(pieces of plasma
membranes and
cells’ internal
membranes) Pellet rich in
ribosomes
Cells
• All living organisms are made of cells
• The cell is the simplest collection of matter
that can live independently
• NB: Cell structure is correlated to cellular function
• How does the molecular makeup of the various
organelles influence their structure and
function?
• Role of types of molecules in functioning of the
cell