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

http://en.wikipedia.org/wiki/Inductive_reasoning












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.


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 Kitsoshttps://titirangilifechurch.files.wordpress.com/2010/05/reef-fish-corals.jpg

Consider the following statement: All marine organisms breath with gills

https://titirangilifechurch.files.wordpress.com/2010/05/reef-fish-corals.jpg





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

https://commons.wikimedia.org/wiki/File:Onion_Cells.jpg






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





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?

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.






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

https://commons.wikimedia.org/wiki/File:Paramecium_caudatum_Ehrenberg,_1833.jpg








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




https://www.preceden.com/timelines/46013-contributions-to-cell-theory


https://www.youtube.com/watch?v=dscY_2QQbKU



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/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

https://upload.wikimedia.org/wikipedia/commons/thumb/1/10/Robert_Brown_(young_-_larousse).jpg/170px-Robert_Brown_(young_-_larousse).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/commons/thumb/9/9c/Rudolf_Virchow_NLM3.jpg/220px-Rudolf_Virchow_NLM3.jpg

Rudolf Ludwig Carl Virchow (1821 – 1902)

https://upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Theodor_Schwann_Litho.jpg/200px-Theodor_Schwann_Litho.jpg















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








https://upload.wikimedia.org/wikipedia/commons/thumb/9/96/Louis_Pasteur,_foto_av_F%C3%A9lix_Nadar_Crisco_edit.jpg/220px-Louis_Pasteur,_foto_av_F%C3%A9lix_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 Painehttps://bioknowledgy.wikispaces.com

http://en.wikipedia.org/wiki/File:Skeletal_striated_muscle.jpg




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

http://www.apsnet.org/edcenter/intropp/pathogengroups/pages/introfungi.aspx















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 Painehttps://bioknowledgy.wikispaces.com

http://deptsec.ku.edu/~ifaaku/jpg/Inouye/Inouye_01.html





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

















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





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

http://umanitoba.ca/Biology/BIOL1030/Lab1/biolab1_3.html#Ciliophora







How does this algae show the functions of life?

Source: http://www.algae.info/Algaecomplete.aspx


Chlorella, a unicellular alga exhibits all characteristics of life.





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


Chlorella, a unicellular alga exhibits all characteristics of life.





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.html

Slides taken fromStephen Taylor’s



















http://i-biology.net/


Calculating the magnification


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?






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/








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

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

= 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










So here comes the easy part

= 0.48 μm







Miltiadis-Spyridon Kitsos http://i-biology.net/ibdpbio/02-cells/cell-theory/










Homework: Complete data-based question on page 6 of your OUP textbook.







http://platon.managebac.com/



= 714 μm

250 mm

350 X









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

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








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





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








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















Emerging properties: Consider these examples



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






























http://www.stepsinbiology.eu

http://www.stepsinbiology.eu/

http://www.stepsinbiology.eu/

http://www.stepisinbiology.eu/

1.1. Cell theory and microscopy

Education

Transcript of 1.1. Cell theory and microscopy