BIOB10
Lecture 1
Microscopes
• Robert Hooke- examined cork under microscope,
cork is made up of cells
• Anton van Leeuwenhoek- examined pond water
under microscope
• Matthias Schleiden, Theodor Schwann, and Rudolf
Virchow- proposed the cell Theory
o Cell theory (3):
▪ All organisms are composed of one
or more cells
▪ The cell is the structural unit of life
Cells can arise only by division from a pre-existing cell
Universal features of cells (6)
• Cells possess a genetic program and the means to use
it
• Cells are capable of producing more of themselves
(Mitosis and meiosis)
• Cells carry out chemical reactions
• Cells can acquire and utilize energy
• Cells are enclosed by a membrane
Cells respond to stimuli, carry out mechanical activities and
more
Cells differ in different ways (2)
1. Obtain free energy in different ways
o Phototrophic (sunlight)
o Lithotrophic (inorganic chemicals in
environment)
o Organotrophic (other living things and the
organic chemicals they produce)
2. Some cells specialize in fixing nitrogen and carbon
dioxide and other cells reply on such cells/organisms
o Plants fix CO2
Nitrogen fixing bacteria helps plants fix N2
The tree of life
(two prokaryotes and one eukaryote)
o Bacteria
, o Archaea
o Eukaryotes
Horizontal gene transfer is a big component for evolution
Types of cells:
Prokaryotes
o Types:
o Archaea “extremophiles” thermophiles that grow @80-105
o Bacteria: cyanobacteria (most complex), archaea are actually closer to eukaryotes than eubacteria- archaea and
eykaryota share a common ancestor not shared by bacteria
o Pro means before and karyon meaning nucleus
o Some unique characteristics-
o Nucleoid- Genetic material not bounded by a membrane
o Structurally simpler
o Less DNA than eukaryotes
o No mitosis or meiosis- binary fission instead
Eukaryotes
o Eu means true
o Model eukaryotes- yeast is a model single celled eukaryote
a. Humans are close to yeast and yeast can be used to study pathogens
o Model eukaryotes
a. Worm- see cell division and cell death
b. Fruit fly- best model for vertebrate development (cheap and fast to grow, key is that they have small genome and
this comes from the fact that not all genes are mutated)
c. Cell movement understanding can be seen by frog and zebrafish
i. Frog cells are developed outside of animal so development is easy to follow Zebrafish are transparent for
first 2 weeks of life so you can watch behaviour of the cell
d. Mouse- most used vertebrate model
o Ex: protists, fungi, plants, animals
o Some unique characteristics
a. Nuclear membrane
b. More complex
c. More DNA than prokaryotes
d. Division by mitosis or meiosis
Similarities of pro and euk
o Genetic code is identical
, o Shared metabolic pathways like synthesis of ATP
o Shared structural elements- cell membrane
What came first?
Prokaryotic came first, cyanobacteria, which can be found
through fossil record
But… did eukaryotic cells arise from prokaryotes?
Endosymbiont theory: combination of 2 cells living together
in a symbiotic relationship; one cell lives “inside” the other
cell. “endo” meaning inside or within. Eukaryotic cells may
have originated as predators
Ribosome protein don’t mutate that much
Housekeeping cells: ubiquitin
Studying cells: cell culture
o Cells are grown outside the body “in vitro”
o Cells are grown in plastic flasks filled with defined media (liquid bath, typically looks red when cells are healthy and will
look yellow if cells are unhealthy in the media)
o Primary culture: obtained directly from the organism (mostly embryonic tissues)
o Divide them up to 25 to 100 times, this is called passages
o Why there is a finite limit? Telomere starts to shrink which tell the cell to go through cell death, adding too many
growth factors which can cause damage to fix this issue we can use cell line
o Cell line are primary cultures that have undergone genetic modifications to allow them to grow indefinitely in culture- can
occur spont. And tumour tissue can be used
o Tumour tissue (HeLa cells) can grow indefinitely and is called transformed cell lines
o In order for cells to thrive in culture, it is important to have similar environments outside of the body, hence we introduce
ECM (extracellular matrix)
Lecture 2
Studying cell microscope
Angstrom: diameter of the cell which is around å10^(-7)mm
o Bright field light microscopy
o Resolution- how true is what we see to be actual details present to that specimen view. It is relied on wavelength of
light and numerical aperture
▪ Resolution=061y/nsino
o Dark field microscopy
o Incident light is oblique
o Only scattered light rays enter objective
o Background is dark, object is light, high contrast allows us to see the object better
o Phase contrast
o Different parts of the cell have different refractive index which results in change in intensity
, o Change in colour
o Differential interference contrast
o rate of change calculation done
o exterior of the cell
Stains used in light microscopy
o Fix cells- Immobilize everything in the context of the cell
o Freeze the cell- flash freeze to the point where water does not freeze
o Haemotoxylin & Eosin staining (H&E)
o H stains nucleic acids
o E stains proteins
o Ex: checking normal brain vs. CJD brain- holes inside
a. bright field
b. phase contrast
c. differential interference contrast
d. dark field
Electron microscopy (EM)
o Electrons used instead of light source due to short wavelength
o Short wavelength produce high resolution
o Magnets are used instead
Transmission electron microscope (TEM)
o Most things in our body are not electron dense like C, H, N hence we stain them with heavy metals
o Metals scatter electron path and this is where the image is caught; parts of the image will appear dark where electrons have
been scattered away by metal atoms
Cryoelectron microscopy
Lecture 1
Microscopes
• Robert Hooke- examined cork under microscope,
cork is made up of cells
• Anton van Leeuwenhoek- examined pond water
under microscope
• Matthias Schleiden, Theodor Schwann, and Rudolf
Virchow- proposed the cell Theory
o Cell theory (3):
▪ All organisms are composed of one
or more cells
▪ The cell is the structural unit of life
Cells can arise only by division from a pre-existing cell
Universal features of cells (6)
• Cells possess a genetic program and the means to use
it
• Cells are capable of producing more of themselves
(Mitosis and meiosis)
• Cells carry out chemical reactions
• Cells can acquire and utilize energy
• Cells are enclosed by a membrane
Cells respond to stimuli, carry out mechanical activities and
more
Cells differ in different ways (2)
1. Obtain free energy in different ways
o Phototrophic (sunlight)
o Lithotrophic (inorganic chemicals in
environment)
o Organotrophic (other living things and the
organic chemicals they produce)
2. Some cells specialize in fixing nitrogen and carbon
dioxide and other cells reply on such cells/organisms
o Plants fix CO2
Nitrogen fixing bacteria helps plants fix N2
The tree of life
(two prokaryotes and one eukaryote)
o Bacteria
, o Archaea
o Eukaryotes
Horizontal gene transfer is a big component for evolution
Types of cells:
Prokaryotes
o Types:
o Archaea “extremophiles” thermophiles that grow @80-105
o Bacteria: cyanobacteria (most complex), archaea are actually closer to eukaryotes than eubacteria- archaea and
eykaryota share a common ancestor not shared by bacteria
o Pro means before and karyon meaning nucleus
o Some unique characteristics-
o Nucleoid- Genetic material not bounded by a membrane
o Structurally simpler
o Less DNA than eukaryotes
o No mitosis or meiosis- binary fission instead
Eukaryotes
o Eu means true
o Model eukaryotes- yeast is a model single celled eukaryote
a. Humans are close to yeast and yeast can be used to study pathogens
o Model eukaryotes
a. Worm- see cell division and cell death
b. Fruit fly- best model for vertebrate development (cheap and fast to grow, key is that they have small genome and
this comes from the fact that not all genes are mutated)
c. Cell movement understanding can be seen by frog and zebrafish
i. Frog cells are developed outside of animal so development is easy to follow Zebrafish are transparent for
first 2 weeks of life so you can watch behaviour of the cell
d. Mouse- most used vertebrate model
o Ex: protists, fungi, plants, animals
o Some unique characteristics
a. Nuclear membrane
b. More complex
c. More DNA than prokaryotes
d. Division by mitosis or meiosis
Similarities of pro and euk
o Genetic code is identical
, o Shared metabolic pathways like synthesis of ATP
o Shared structural elements- cell membrane
What came first?
Prokaryotic came first, cyanobacteria, which can be found
through fossil record
But… did eukaryotic cells arise from prokaryotes?
Endosymbiont theory: combination of 2 cells living together
in a symbiotic relationship; one cell lives “inside” the other
cell. “endo” meaning inside or within. Eukaryotic cells may
have originated as predators
Ribosome protein don’t mutate that much
Housekeeping cells: ubiquitin
Studying cells: cell culture
o Cells are grown outside the body “in vitro”
o Cells are grown in plastic flasks filled with defined media (liquid bath, typically looks red when cells are healthy and will
look yellow if cells are unhealthy in the media)
o Primary culture: obtained directly from the organism (mostly embryonic tissues)
o Divide them up to 25 to 100 times, this is called passages
o Why there is a finite limit? Telomere starts to shrink which tell the cell to go through cell death, adding too many
growth factors which can cause damage to fix this issue we can use cell line
o Cell line are primary cultures that have undergone genetic modifications to allow them to grow indefinitely in culture- can
occur spont. And tumour tissue can be used
o Tumour tissue (HeLa cells) can grow indefinitely and is called transformed cell lines
o In order for cells to thrive in culture, it is important to have similar environments outside of the body, hence we introduce
ECM (extracellular matrix)
Lecture 2
Studying cell microscope
Angstrom: diameter of the cell which is around å10^(-7)mm
o Bright field light microscopy
o Resolution- how true is what we see to be actual details present to that specimen view. It is relied on wavelength of
light and numerical aperture
▪ Resolution=061y/nsino
o Dark field microscopy
o Incident light is oblique
o Only scattered light rays enter objective
o Background is dark, object is light, high contrast allows us to see the object better
o Phase contrast
o Different parts of the cell have different refractive index which results in change in intensity
, o Change in colour
o Differential interference contrast
o rate of change calculation done
o exterior of the cell
Stains used in light microscopy
o Fix cells- Immobilize everything in the context of the cell
o Freeze the cell- flash freeze to the point where water does not freeze
o Haemotoxylin & Eosin staining (H&E)
o H stains nucleic acids
o E stains proteins
o Ex: checking normal brain vs. CJD brain- holes inside
a. bright field
b. phase contrast
c. differential interference contrast
d. dark field
Electron microscopy (EM)
o Electrons used instead of light source due to short wavelength
o Short wavelength produce high resolution
o Magnets are used instead
Transmission electron microscope (TEM)
o Most things in our body are not electron dense like C, H, N hence we stain them with heavy metals
o Metals scatter electron path and this is where the image is caught; parts of the image will appear dark where electrons have
been scattered away by metal atoms
Cryoelectron microscopy
