1.1. Cell theory and microscopy

Miltiadis-Spyridon Kitsos
1. Cell Biology

The guide

The guide part 2

The cell theory..wait..what’s a scientific theory??
…a well-substantiated explanation of some aspect of the natural world that is
acquired through the scientific method, and repeatedly confirmed through observation
and experimentation...
As with most (if not all) forms of scientific knowledge, scientific theories are inductive
in nature and aim for predictive power and explanatory force. ..
https://en.wikipedia.org/wiki/Scientific_theory
Wikipedia.com
https://www.youtube.com/watch?v=d80Lf76Ht18

 It makes falsifiable predictions with consistent accuracy across a broad area of
scientific inquiry (such as biology).
 It is well-supported by many independent strands of evidence, rather than a single
foundation.
 It is consistent with pre-existing experimental results and at least as accurate in its
predictions as are any pre-existing theories.
 It can be subjected to minor adaptations to account for new data that do not fit it
perfectly, as they are discovered, thus increasing its predictive capability over time.
 It is among the most parsimonious explanations, economical in the use of
proposed entities or explanatory steps.
The criteria.
https://en.wikipedia.org/wiki/Scientific_theory
Wikipedia.com

Homework activity
https://www.youtube.com/watch?v=wNDGgL73ihY
 Please watch this video on the Bing
bang theory
 Then apply the criteria of the
previous slide and see whether the
Big bang theory is a true scientific
theory.
 Please provide a brief comment for
each criterion based on the
evidence taken from the video.

Trends and discrepancies
In all theories there are observations and data that are in general agreement with
the statements of the theory (Trends)
At the same time there are evidence and facts that might go against the basic
statements of the theory (Discrepancies) . Discrepancies might be able to wield
new testable hypotheses leading to changes in the theory.
Further reading
Patterns, trends and discrepancies
https://danielatok.wordpress.com/2015/03/30/patterns-trends-and-discrepancies/

Miltiadis-Spyridon Kitsos https://titirangilifechurch.files.wordpress.com/2010/05/reef-fish-corals.jpg
Consider the following statement: All
marine organisms breath with gills

Now, is this a trend or a discrepancy?
http://www.sciencedump.com/content/first-blue-whale-heart-ever-preserved-
size-golf-cart

https://commons.wikimedia.org/wiki/File:Onion_Cells.jpg
All living things are made of cells

Unicellular: one
cell that carries out all
the functions of life
Multicellular:
specialized cells that carry
out specific functions
https://youtu.be/7pR7TNzJ_pA
https://youtu.be/8bEhkBwiyos

Consider that we may be able to examine all available tissues. Would we
be able to prove this statement?
Suppose that life was discovered in another planet and living things were
not made of cells. How would this change the cell theory?
Allott, Andrew, and David Mindorff. <i>Biology: Course Companion</i>.
Oxford: Oxford UP, 2010. . Print.

The ciliated protozoan Paramecium caudatum.
By Deuterostome (Own work) [CC BY-SA 3.0
(http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
Cells are the smallest unit of life

The ciliated protozoan Paramecium caudatum.
By Deuterostome (Own work) [CC BY-SA 3.0
(http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons
Cells are the smallest unit of life
Evidence suggests that subcellular structures do not
exhibit the characteristics of life

Cells come only from preexisting cells
Cancer Cells Dividing, Biology, McDougal Littell, 2008
http://ibbio.pbworks.com/w/page/59801244/Cell%20Division

http://www.slideshare.net/gurustip/cell-theory-presentation-845660?ref=http://i-
biology.net/ibdpbio/02-cells/cell-theory/
Stephen Taylor i-biology

A brief timeline of the cell theory
http://ed.ted.com/lessons/the-wacky-history-of-cell-theory

http://ocw.mit.edu/ans7870/21l/21l.016/s07/assignments/hooke-cover.html
http://www.bl.uk/learning/timeline/external/hookeflea-
tl.jpg
Robert Hooke (1635-1703) was the first one to use the
term cells in 1665 in his publication Micrographia
(1665)
https://archive.org/details/mobot31753000817897ographia
Full text here

Antonie Philips van Leeuwenhoek (1632-1723) is
considered “the father of Microbiology”. He was the first
one to observe microorganisms (he called them
animalcules) in 1676
http://www.history-of-the-microscope.org/images/Anton-van-
Leeuwenhoek.jpg
http://upload.wikimedia.org/wikipedia/commons/0/0f/Van_Leeuwenhoek's_microscopes_by
_Henry_Baker.jpg
http://www.microbiomedigest.com/wp-
content/uploads/2015/01/o_Leeuwenhoek.jpg
Bacteria from the human mouth

Robert Brown (1773 –1858) gave the
first description of the cell nucleus and
cytoplasmic streaming
https://upload.wikimedia.org/wikipedia/commons/t
humb/1/10/Robert_Brown_%28young_-
_larousse%29.jpg/170px-
Robert_Brown_%28young_-_larousse%29.jpg
Matthias Jakob Schleiden (1804 –1881).
In Contributions to Phytogenesis (1838),
he stated that the different parts of the
plant organism are composed of cells.
https://upload.wikimedia.org/wikipedia/commons/t
humb/0/0a/PSM_V22_D156_Matthias_Jacob_Sch
leiden.jpg/220px-
PSM_V22_D156_Matthias_Jacob_Schleiden.jpg

Theodor Schwann (1810 – 1882) made
similar observations with Schleiden in animal
cells.
In his work Microscopic Investigations on the Accordance in
the Structure and Growth of Plants and Animals he stated "All
living things are composed of cells and cell products:
https://upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Theodor_Schwann_Litho.jpg
/200px-Theodor_Schwann_Litho.jpg
Omnis cellula e cellula
est,
https://upload.wikimedia.org/wikipedia/co
mmons/thumb/9/9c/Rudolf_Virchow_NLM3
.jpg/220px-Rudolf_Virchow_NLM3.jpg
Rudolf Ludwig Carl Virchow (1821
– 1902)

Louis Pasteur (1822 –1895), French chemist,
well known for developing the principles of
vaccination and pasteurization.
https://upload.wikimedia.org/wikipedia/commons/thumb/0/02/Louis_Pasteur_Experiment
vg/220px-Louis_Pasteur_Experiment.svg.png
Pasteur is also known for the disproval of the
theory of spontaneous generation
https://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Louis_Pasteur%2C_foto_av_
Félix_Nadar_Crisco_edit.jpg/220px-Louis_Pasteur%2C_foto_av_Félix_Nadar_Crisco_edit.jpg

Homework – The theory of spontaneous generation
Prepare a presentation outlining the main
principles of the theory spontaneous generation
and try answering the following questions.
(a) What are the main principles underlying this
theory?
(b) Is is a “true” scientific theory (criteria)
(c) Which scientists contributed to the rejection
of this theory?
(d) How is it related with the cell theory? https://upload.wikimedia.org/wikipedia/commons/thumb/4/44/
Louis_Pasteur_experiment.jpg/220px-
Louis_Pasteur_experiment.jpg

The striated muscle
• challenges the idea that a cell
has one nucleus
• Muscle cells have more than
one nucleus per cell
• Muscle Cells called fibres can
be very long (300mm)
• They are surrounded by a
single plasma membrane but
they are multi-nucleated
(many nuclei).
• This does not conform to the
standard view of a small single
nuclei within a cell
Source: http://en.wikipedia.org/wiki/File:Skeletal_striated_muscle.jpg
Looking for discrepancies in the cell theory
Chris Paine
https://bioknowledgy.wikispaces.com

Aseptate fungal hyphae
• challenges the idea that a cell is a
single unit.
• Fungal hyphae are again very large
with many nuclei and a continuous
cytoplasm
• The tubular system of hyphae form
dense networks called mycelium
• Like muscle cells they are multi-
nucleated
• They have cell walls composed of
chitin
• The cytoplasm is continuous
along the hyphae with no end cell
wall or membrane
Source: http://www.apsnet.org/edcenter/intropp/pathogengroups/pages/introfungi.aspx
https://youtu.be/tjDjHV_d2HQ

Giant algae (Acetabularia)
• Acetabularia is a single-celled
organism that challenges both
the idea that cells must be
simple in structure and small in
size
• Gigantic in size (5 – 100mm)
• Complex in form, it consists of
three anatomical parts:
– Bottom rhizoid (that resembles
a set of short roots)
– Long stalk
– Top umbrella of branches that
may fuse into a cap
• The single nucleus is located in
the rhizoid
Source: http://deptsec.ku.edu/~ifaaku/jpg/Inouye/Inouye_01.html
Chris Paine
https://bioknowledgy.wikispaces.com

https://youtu.be/ctpjjOkUtEU
Dr. Mark Young of Montana State
University addresses the question of
whether viruses are alive
http://www.ncbi.nlm.nih.gov/books/NBK8174/bin/ch41f1.jpg
Also read
Are viruses alive?
http://www.scientificamerican.com/a
rticle/are-viruses-alive-2004/
Are viruses alive?
“Virophage” suggests
that viruses are alive
http://www.nature.com/news/2008/080806/full/4
54677a.html
Vs

You probably know:
• Movement
• Reproduction
• Sensitivity
• Homeostasis
• Growth
• Respiration
• Excretion
• Nutrition
A short explanation
• Metabolism - the web of all the enzyme-catalysed
reactions in a cell or organism, e.g. respiration
• Response - Living things can respond to and interact
with the environment
• Homeostasis - The maintenance and regulation of
internal cell conditions, e.g. water and pH
• Growth - Living things can grow or change size /
shape
• Excretion – the removal of metabolic waste
• Reproduction - Living things produce offspring, either
sexually or asexually
• Nutrition – feeding by either the synthesis of organic
molecules (e.g. photosynthesis) or the absorption of
organic matter
So which are the functions of life? Slide by Chris Pane
https://bioknowledg
y.wikispaces.com

Source: http://umanitoba.ca/Biology/BIOL1030/Lab1/biolab1_3.html#Ciliophora
Homeostasis – contractile vacuole fill up
with water and expel I through the plasma
membrane to manage the water content
Reproduction – The
nucleus can divide to
support cell division by
mitosis, reproduction is
often asexual
Metabolism –
most
metabolic
pathways
happen in the
cytoplasm
Growth – after consuming
and assimilating biomass
from food the paramecium
will get larger until it divides.
Response – the
wave action of
the cilia moves
the
paramecium in
response to
changes in the
environment,
e.g. towards
food.
Excretion – the plasma
membrane control the entry
and exit of substances
including expulsion of
metabolic waste
Nutrition – food vacuoles
contain organisms the
parameium has
consumed
Paramecium, a unicellular organism exhibits all
characteristics of life.
Slide by Chris Pane
https://bioknowledg
y.wikispaces.com

How does this algae show the functions of life?
Source: http://www.algae.info/Algaecomplete.aspx
Slide by Chris Pane
https://bioknowledgy.
wikispaces.com
Chlorella, a unicellular alga exhibits all

Source: http://www.algae.info/Algaecomplete.aspx
Homeostasis –
contractile
vacuole fill up
with water and
expel I through
the plasma
membrane to
manage the
water content
Reproduction – The nucleus can divide
to support cell division, by mitosis (these
cells are undergoing cytokinesis)
Metabolism –
most
metabolic
pathways
happen in the
cytoplasm
Growth – after consuming and assimilating
biomass from food the algae will get larger until
it divides.
Response – the
wave action of
the cilia moves
the algae in
response to
changes in the
environment,
e.g. towards
light.
Excretion – the plasma
membrane control the
entry and exit of
substances including the
difussion out of waste
oxygen
Nutrition –
photosynthes
is happens
inside the
chloroplasts
to provide
the algae
with food
Slide by Chris Pane
https://bioknowledgy.
wikispaces.com
Chlorella, a unicellular alga exhibits all

2. Microscopy

The parts of the microscope
http://www.microscope-microscope.org/images/BWScope.jpg
http://www.biology.ualberta.ca/facilities/multimedia/uploads/alberta/
microscope.swf
http://www.udel.edu/biology/ketcham/microscope/scope.ht
ml
Slides taken from
Stephen Taylor’s

Calculating the magnification
http://www.microscope-microscope.org/images/BWScope.jpg
Overall Magnification = magnification of eyepiece lens X
magnification of objective lens
TASK: Calculate the overall magnification of your
microscope using all available lens combinations.
Which is the highest magnification you calculated?

Converting sizes
Unit abbr. Metric equivalent
kilometer km 1,000m 1 x 103m
meter m 1m 1m
centimeter cm 0.01m 1 x 10-2m
millimeter mm 0.001m 1 x 10-3m
micrometer μm 0.000 001m 1 x 10-6m
nanometer nm 0.000 000 001m 1 x 10-9m
÷1,000
÷1,000
÷1,000
X 1,000
μm = micrometers
We usually use this in discussion of cells.
There are 1,000μm in one mm.
Slides taken from
Stephen Taylor’s
http://i-biology.net/ibdpbio/02-cells/cell-theory/

Working with microscopic images
Suppose you want to calculate the actual size
of these mitochondria from this photo taken
with a Transmission Electron Microscope
Mitochondria from mammalian lung tissue
https://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg

Start from the scale bar, which is a means of
visually showing the scale of a image, that is the
magnification

Using a ruler measure the length of the bar. Lets
assume its 12 mm

Now calculate the magnification of the image using the following formula
𝑀𝑎𝑔𝑛𝑖𝑓𝑖𝑐𝑎𝑡𝑖𝑜𝑛 =
𝑠𝑐𝑎𝑙𝑒 𝑏𝑎𝑟 𝑎𝑐𝑡𝑢𝑎𝑙 𝑠𝑖𝑧𝑒
𝑠𝑐𝑎𝑙𝑒 𝑏𝑎𝑟 𝑙𝑎𝑏𝑒𝑙
=
12.000.000 𝑛𝑚
50 𝑛𝑚
= 240.000 X

Now measure the size of the mitochondrion in the photo using a ruler.
Assume its 117 mm

Now calculate the actual size of the mitochondrion solving the formula for
actual size
𝑀𝑎𝑔𝑛𝑖𝑓𝑖𝑐𝑎𝑡𝑖𝑜𝑛 =
𝑚𝑎𝑔𝑛𝑖𝑓𝑖𝑒𝑑 𝑠𝑖𝑧𝑒
𝑎𝑐𝑡𝑢𝑎𝑙 𝑠𝑖𝑧𝑒
→ Actual size =
𝑀𝑎𝑔𝑛𝑖𝑓𝑖𝑐𝑎𝑡𝑖𝑜𝑛

So here comes the easy part
Actual size =
=
117000 𝜇𝑚
240000
= 0.48 μm

Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/
Slides taken from
Stephen Taylor’s

Slides taken from
Stephen Taylor’s
Homework: Complete data-based question on page 6 of your OUP textbook.

Slides taken from
Stephen Taylor’s
Actual size =
=
250.000 𝜇𝑚
350
= 714 μm
250 mm
350 X

Slides taken from
Stephen Taylor’s
How big is it? Understanding the relative sizes of structures
http://www.cellsalive.com/howbig_js.htm
http://www.biology.arizona.edu/cell_bio/tutorials/cells/graphics/size_comp.gif
http://learn.genetics.utah.edu/content/cells/scale/

The problem of surface area to volume ratio
Heat
Waste products
CO2
Food
O2
Cell are open systems constantly
exchanging energy an matter
with the environment
This exchange is happening
through the plasma membrane
The problem is that as a cell
increases in size there is an
unproportionate increase of the ratio
surface area to volume
Outline changes in the surface area
to volume ration in these three
cubes
1 cm 2cm 3cm
http://images.flatworldknowledge.com/stangor/stangor-fig04_012.jpg

Systems Biology: The Inductive vs the Reductionist approach
Scientists usually have a reductionist approach in the hypotheses tested. Consider the
following flow chart
System under study
Examine and
understand the
structure and function
of the subunits
Combine this
knowledge to
understand the
structure and function
of the system

Systems Biology: The Inductive vs the Reductionist approach
However, the reductionist approach is not always effective since systems are very complex and
dynamic and thus, its very difficult to forecast their properties by solely studying the
properties of the individual parts.
Systems biology is the study of systems of biological components, which may be molecules,
cells, organisms or entire species or even ecosystems.
System under study
Systems biology is using a more inductive
reasoning thus, moving from specific
observations to broader generalizations and
theories. (bottom-up)
http://www.socialresearchmethods.net/kb/dedind.php

Emerging properties: Consider these examples
https://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Levels_of_Organ
ization.svg/220px-Levels_of_Organization.svg.png
http://www.wpclipart.com/animals/birds/_Miscellaneous/generic_colors/clip_art_bi
rd_green.png
Individual bird Flock of birds
Emerging properties: defense, mating

Emerging properties: Consider these examples
https://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Levels_of_Organ
ization.svg/220px-Levels_of_Organization.svg.png
http://www.wpclipart.com/animals/birds/_Miscellaneous/generic_colors/clip_art_bi
rd_green.png
Individual amino acids
Protein
Emerging properties: catalysis
https://upload.wikimedia.org/wikipedia/co
mmons/thumb/c/ce/AminoAcidball.svg/200
0px-AminoAcidball.svg.png
http://www.weightlossforall.com/wp-content/uploads/2010/08/amino-acid-
chain.jpg

http://www.stepsinbiology.eu

1.1. Cell theory and microscopy

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1.1. Cell theory and microscopy