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Model Organisms & Tools of Cell Biology. Lecture 3 Autumn 2007. Learning the Unknown. You are a car mechanic Would you rather know a little bit about the working of every car every constructed… … or everything about a representative one from each category? Science is no different!.

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learning the unknown
Learning the Unknown
  • You are a car mechanic
  • Would you rather know a little bit about the working of every car every constructed…
  • … or everything about a representative one from each category?
  • Science is no different!
what is a model organism
What is a Model Organism?
  • Many aspects of biology are similar in most or all organisms
  • It is much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans!
  • The most popular model organisms have strong advantages for experimental research
  • They become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information.
how many are there
How many are there?
  • Many (about 80)
  • Mouse, rat, zebra fish, viruses, chicken, dog, hamster, slime mould, maize, tetrahymena, etc.
  • Many scientists have worked on all these over the years, and shared information extensively
which are the main ones
Which are the main ones?
  • 1)E. coli (bacterium)
  • 2)Saccharomyces cerevisiae(yeast)
  • 3) Arabidopsis thaliana(weed)
  • 4) Drosophila melanogaster (fruit fly)
  • 5) Mus musculus (mouse)
  • 6) Homo sapiens (Man)
01 33 model plant jpg

Arabidopsis thaliana (mustard plant)

This is now the main model plant system for genetics.

Its small genome, and the recent application of classical genetics has put it far ahead of other models of agricultural importance (tomato, tobacco, corn etc.)

It's genome has been fully sequenced.

01_33_model plant.jpg
01 34 drosophila jpg
01_34_Drosophila.jpg

Drosophila sp. ‘Fruit Fly’

Usually the species Drosophila melanogaster -

Easily raised in lab, rapid generations, mutations easily induced, many observable mutations.

Many clues to development and genetics

01 38 c elegans jpg
01_38_C.elegans.jpg
  • Caenorhabditis elegans, a nematode
  • (Usually called just C. elegans)
  • an excellent model for understanding the genetic control of development and physiology.
  • C. elegans was the first multicellular organism whose genome was completely sequenced
  • First to show fixed cell count in body
  • Gave important clues on programmed cell death
01 32 model eucaryote jpg

Saccharomyces cerevisiae, baker's yeast or budding yeast (used in brewing and baking)

01_32_model eucaryote.jpg

Early studies on this enabled us to get a great grasp on the cell cycle

humans
Humans
  • Regardless of how thoroughly we may understand other animal systems, sometimes there is no alternative but to study humans directly - i.e. breast cancers
  • The human animal is the most medically analyzed and documented of any species.
  • We have now completely sequenced our own genome too
  • Over the next decade or so we will understand more about our biology than ever before!
where has knowledge of cells come from
Where has knowledge of cells come from?
  • Can we see cells?
  • Yes and no, most are too small, but some we can see easily - the egg of a chicken is a large single cell
  • What are ‘The tools of Cell Biology’?
  • How big is the average egg?
  • Lets put it in perspective…
size perspective
Size perspective

1X

10X -tissues

100X - cells

1000X - organelles

10,000X - organelles

100,000X - proteins

1,000,000X - atoms

microscopes aid us in seeing
Microscopes - aid us in seeing
  • First cells seen by Robert Hook, who made the first compound microscope
  • He looked at cork cells
  • The detail was lacking and limited by the quality of the instrument
  • Light microscopes are now much better
light microscopes
Light Microscopes
  • Many types exist
  • Light is either reflected from the specimen (Oblique illumination) or transmitted through the specimen (Bright field optical microscopy)
  • How small can we see? We can see all cells.
  • The lens are so good now that the limiting factor is now the wavelength of light itself.
    • The wavelength of the visible light used in optical microscopes is between 400 and 700 nanometers (nm).
    • The resolving powers of high-quality light microscopes are limited by the wavelength of imaging light to about 200 nanometers
electron microscopes
Electron Microscopes
  • Sample placed in vacuum - thus dead
  • Four main types all using electron streams instead of light waves;
    • Transmission Electron Microscope (TEM)
    • Scanning Electron Microscope (SEM)
    • Reflection Electron Microscope (REM)
    • Scanning Transmission Electron Microscope (STEM)
  • Resolutions as low as 70pm have been obtained - single atoms
      • Read all about these on the course web site
centrifugation for analysis
Centrifugation - for analysis
  • Allows separation of
    • Cells
    • Organelles
    • DNA and other macromolecules
  • Uses gravitational and centrifugal forces to separate items based on density and size - one spins things at high speeds
  • Many types are used in cell biology…
differential centrifugation
Differential centrifugation
  • This is the most common method of fractionating cells
    • Fractionation is the separation of the different organelles within the cell
  • The speed determines which size and mass (density) of material is pelleted.
isopycnic centrifugation
Isopycnic centrifugation
  • Isopycnic centrifugation or equilibrium centrifugation is a process used to isolate nucleic acids such as DNA.
  • Much high speeds and duration
  • Separates DNA based on base composition
sucrose gradient centrifugation
Sucrose gradient centrifugation
  • Uses a decreasing concentration of sucrose in a tube
  • The particles travel through the gradient until they reach the point in the gradient at which their density matches that of the surrounding sucrose.
mutation analysis an important mechanism for discovery
Mutation analysis - an important mechanism for discovery
  • Any organism which is different from the norm can be a candidate for biochemical analysis
  • Mutations are generally the cause of such differences
  • By analysis of these mutations one can gain insights or deduce the biochemical basis of important pathways…
01 35 yeast mutation jpg

Conditional Mutation Analysis - e.g. Temperature conditional

The organism grows at one temperature (permissive) but fails to do so at a different one (restrictive).

01_35_Yeast mutation.jpg

All the yeast colonies grow at one temperature (23C), but if one places the same cells at 35C some of the colonies fail to grow - what is wrong with the ones that fail to grow?

01 37 amino acid sequ jpg

Sequence analysis has taught us that there are about 200-300 genes required for the most basic cell survival.

Comparisons across species shows that many genes are common from simple bacteria to complex life forms, and that life uses similar processes

01_37_amino acid sequ.jpg
slide25

Genome sizes - a genome is the total haploid amount of DNA

Amoeba proteus

290,000,000,000 (100 times the size of a human genome)

Bufo bufo (cane toad)

6,900,000,000

Homo sapiens (Man)

3,000,000,000 (3 billion base pairs - 24 chromosomes - [22, X, Y])

Muntiacus muntjak vaginalis (Indian deer)

2,521,500,000

Boa constrictor (snake)

2,100,000,000

Rhinolophus ferrumequinum (bat)

1,929,400,000

Plasmodium falciparum (malaria parasite)

25,000,000

Human immunodeficiency virus type 1 (HIV)

19,750

slide27

Genome size and number of genes

Among the organisms whose genomes are sequenced, genome size does not correlate with the number of genes.

Species Size of genome Number of genes

Human

3.0 billion base pairs 25,000 ?

Fruit fly (Drosophila melanogaster)

120 million base pairs 13,601

Baker's yeast (Saccharomyces cerevisiae)

12 million base pairs 6, 275

Worm (Caenorhabditis elegans)

97 million base pairs 19,000

E. coli

4.6 million base pairs 4,403

Arabidopsis (Arabidopsis thaliana)

125 million base pairs 25,000

study
Study…
  • Please read chapter 1 entirely, if you have not done so already
  • Sample questions for the exams will start appearing on the supporting web site this week!
  • Bye!