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Miltiadis-Spyridon Kitsos
1. Cell Biology
Miltiadis-Spyridon Kitsos
The guide
Miltiadis-Spyridon Kitsos
The guide part 2
Miltiadis-Spyridon Kitsos
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
Miltiadis-Spyridon Kitsos
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
Miltiadis-Spyridon Kitsos
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.
Miltiadis-Spyridon Kitsos
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 Kitsoshttps://titirangilifechurch.files.wordpress.com/2010/05/reef-fish-corals.jpg
Consider the following statement: All marine organisms breath with gills
Miltiadis-Spyridon Kitsos
Now, is this a trend or a discrepancy?
http://www.sciencedump.com/content/first-blue-whale-heart-ever-preserved-size-golf-cart
Miltiadis-Spyridon Kitsoshttps://commons.wikimedia.org/wiki/File:Onion_Cells.jpg
All living things are made of cells
Miltiadis-Spyridon Kitsoshttps://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_pAhttps://youtu.be/8bEhkBwiyos
Miltiadis-Spyridon Kitsoshttps://commons.wikimedia.org/wiki/File:Onion_Cells.jpg
All living things are made of cells
Consider that we may be able to examine all available tissues. Would we be able to prove this statement?
NoS
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.
Miltiadis-Spyridon Kitsos
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
Miltiadis-Spyridon Kitsos
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
Miltiadis-Spyridon Kitsos
Cells come only from preexisting cells
Cancer Cells Dividing, Biology, McDougal Littell, 2008
http://ibbio.pbworks.com/w/page/59801244/Cell%20Division
Miltiadis-Spyridon Kitsos
http://www.slideshare.net/gurustip/cell-theory-presentation-845660?ref=http://i-biology.net/ibdpbio/02-cells/cell-theory/
Stephen Taylor i-biology
Miltiadis-Spyridon Kitsos
A brief timeline of the cell theory
http://ed.ted.com/lessons/the-wacky-history-of-cell-theory
Miltiadis-Spyridon Kitsos
A brief timeline of the 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
Miltiadis-Spyridon Kitsos
A brief timeline of the cell theory
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
Miltiadis-Spyridon Kitsos
A brief timeline of the cell theory
Robert Brown (1773 –1858) gave the first description of the cell nucleus and cytoplasmic streaming
https://upload.wikimedia.org/wikipedia/commons/thumb/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/thumb/0/0a/PSM_V22_D156_Matthias_Jacob_Schleiden.jpg/220px-PSM_V22_D156_Matthias_Jacob_Schleiden.jpg
Miltiadis-Spyridon Kitsos
A brief timeline of the cell theory
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/commons/thumb/9/9c/Rudolf_Virchow_NLM3.jpg/220px-Rudolf_Virchow_NLM3.jpg
Rudolf Ludwig Carl Virchow (1821 – 1902)
Miltiadis-Spyridon Kitsos
A brief timeline of the cell theory
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.svg/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
Miltiadis-Spyridon Kitsos
A brief timeline of the cell theory
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
Miltiadis-Spyridon Kitsos
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 Painehttps://bioknowledgy.wikispaces.com
Miltiadis-Spyridon Kitsos
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
Looking for discrepancies in the cell theory
https://youtu.be/tjDjHV_d2HQ
Miltiadis-Spyridon Kitsos
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
Looking for discrepancies in the cell theory
Chris Painehttps://bioknowledgy.wikispaces.com
Miltiadis-Spyridon Kitsos
Looking for discrepancies in the cell theory
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/article/are-viruses-alive-2004/
Are viruses alive?“Virophage” suggests that viruses are alive
http://www.nature.com/news/2008/080806/full/454677a.html
Vs
Miltiadis-Spyridon Kitsos
Looking for discrepancies in the cell theory
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/article/are-viruses-alive-2004/
Are viruses alive?“Virophage” suggests that viruses are alive
http://www.nature.com/news/2008/080806/full/454677a.html
Vs
Miltiadis-Spyridon Kitsos
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 Panehttps://bioknowledgy.wikispaces.com
Miltiadis-Spyridon Kitsos
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 Panehttps://bioknowledgy.wikispaces.com
Miltiadis-Spyridon Kitsos
How does this algae show the functions of life?
Source: http://www.algae.info/Algaecomplete.aspx
Slide by Chris Panehttps://bioknowledgy.wikispaces.com
Chlorella, a unicellular alga exhibits all characteristics of life.
Miltiadis-Spyridon Kitsos
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 – photosynthesis happens inside the chloroplasts to provide the algae with food
Slide by Chris Panehttps://bioknowledgy.wikispaces.com
Chlorella, a unicellular alga exhibits all characteristics of life.
Miltiadis-Spyridon Kitsos
2. Microscopy
Miltiadis-Spyridon Kitsos
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.html
Slides taken fromStephen Taylor’s
Miltiadis-Spyridon Kitsos
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 yourmicroscope using all available lens combinations.
Which is the highest magnification you calculated?
Miltiadis-Spyridon Kitsos
Converting sizesUnit 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 = micrometersWe usually use this in discussion of cells.
There are 1,000μm in one mm. Slides taken fromStephen Taylor’s
http://i-biology.net/ibdpbio/02-cells/cell-theory/
Miltiadis-Spyridon Kitsos
Working with microscopic images
Suppose you want to calculate the actual sizeof these mitochondria from this photo takenwith a Transmission Electron Microscope
Mitochondria from mammalian lung tissuehttps://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg
Miltiadis-Spyridon Kitsos
Working with microscopic images
Start from the scale bar, which is a means of visually showing the scale of a image, that is the magnification
Mitochondria from mammalian lung tissuehttps://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg
Miltiadis-Spyridon Kitsos
Working with microscopic images
Using a ruler measure the length of the bar. Lets assume its 12 mm
Mitochondria from mammalian lung tissuehttps://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg
Miltiadis-Spyridon Kitsos
Working with microscopic images
Now calculate the magnification of the image using the following formula
= 240.000 X
Mitochondria from mammalian lung tissuehttps://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg
Miltiadis-Spyridon Kitsos
Working with microscopic images
Now measure the size of the mitochondrion in the photo using a ruler. Assume its 117 mm
Mitochondria from mammalian lung tissuehttps://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg
Miltiadis-Spyridon Kitsos
Working with microscopic images
Mitochondria from mammalian lung tissuehttps://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg
Now calculate the actual size of the mitochondrion solving the formula for actual size
Miltiadis-Spyridon Kitsos
Working with microscopic images
Mitochondria from mammalian lung tissuehttps://upload.wikimedia.org/wikipedia/commons/0/0c/Mitochondria,_mammalian_lung_-_TEM.jpg
So here comes the easy part
= 0.48 μm
Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/
Slides taken fromStephen Taylor’s
Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/
Slides taken fromStephen Taylor’s
Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/
Slides taken fromStephen Taylor’s
Homework: Complete data-based question on page 6 of your OUP textbook.
Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/
Slides taken fromStephen Taylor’s
= 714 μm
250 mm
350 X
Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/
Slides taken fromStephen 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/
Miltiadis-Spyridon Kitsos
The problem of surface area to volume ratio
HeatWaste productsCO2
FoodO2
Cell are open systems constantlyexchanging 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 areato volume ration in these threecubes 1 cm 2cm 3cm
http://images.flatworldknowledge.com/stangor/stangor-fig04_012.jpg
Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/Slides taken fromStephen Taylor’s
Miltiadis-Spyridon Kitsos
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
Miltiadis-Spyridon Kitsos
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
Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/Slides taken fromStephen Taylor’s
Miltiadis-Spyridon Kitsos
Emerging properties: Consider these examples
https://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Levels_of_Organization.svg/220px-Levels_of_Organization.svg.png
http://www.wpclipart.com/animals/birds/_Miscellaneous/generic_colors/clip_art_bird_green.png
Individual bird Flock of birds
Emerging properties: defense, mating
Miltiadis-Spyridon Kitsos
Emerging properties: Consider these examples
https://upload.wikimedia.org/wikipedia/commons/thumb/3/38/Levels_of_Organization.svg/220px-Levels_of_Organization.svg.png
http://www.wpclipart.com/animals/birds/_Miscellaneous/generic_colors/clip_art_bird_green.png
Individual amino acidsProtein
Emerging properties: catalysis
https://upload.wikimedia.org/wikipedia/commons/thumb/c/ce/AminoAcidball.svg/2000px-AminoAcidball.svg.png
http://www.weightlossforall.com/wp-content/uploads/2010/08/amino-acid-chain.jpg
Miltiadis-Spyridon Kitsos
http://www.stepsinbiology.eu