lOMoARcPSD|2392027
Week 1
Lecture Chapter 1: Cells, The Fundamental Units of Life
Cell theory
1. All living organisms are composed of one or more cells
2. Cells are the fundamental units/building block that provide structure and organization to
organisms.
3. All cells arise from pre-existing cells by growth and division (evolution). They do not arise
spontaneously.
Cells are diverse, but their chemistry is remarkably similar:
o DNA (genetic information), RNA (transcription) and protein (translation) synthesis
o Building blocks & enzymes are very similar.
Evidence -> swapping genes between organisms
Model systems = Organisms of which we exploit the similarity between cell types
o Requirements:
Replicate quick
Easy to maintain
Can be modified or has other properties that make them easy to study (e.g. translucent)
o E.coli = fundamental mechanisms of life, e.g. transcription (DNA -> RNA) and translation
(RNA -> protein)
o Single cells: Yeast and mammalian cell lines (internal organization and cell cycle control)
o Arabidopsis, Drosophila, C.elegans: mechanisms of development of multicellular organisms
o Not just chemistry is conserved but also organizing mechanisms (e.g. growing microtubules
push nuclei into position)
Microscopes
o Observing cell division provided evidence for the cell theory
o Electron microscopes (EM)
Highest resolution/resolving power
Shows features that are < 200 nm apart
Very expensive
Light microscopes (LM)
0,61∙ λ 0.61∙ λ
Resolution = d = =
N.A n sin α
λ = wavelength in nm
n = refractive index of medium
N.A = numerical aperture (≈ 1)
Gedownload door Michou Weimar ()
, lOMoARcPSD|2392027
EM LM
1. Absorption and scattering of electrons 1. Absorption and scattering of photons
(light)
2. Cells in vacuum (fixated) 2. Cells in liquid (live cell imaging)
3. Contrasting agents (e.g OSO 4) 3. Dynamic processes visualized
6
4. High magnification (×10 ) 4. ×10 3
5. Magnetic lenses 5. Glass lenses
Low image contrast because of limited absorption and light scattering
Histological stains improve contrast, but are often incompatible with live cells (I 2KI stains
starch blue)
Techniques that rely on differences in refractive index between cell compartments
increase contrast for live cells
Microscopy methods:
1. Scanning EM (surface)
2. Transmission EM (inside of 50 nm thin-section)
3. Fluorescent LM (translucent)
4. Confocal fluorescence (virtual thinsectioning)
o Nobel prizes microscopy, do we need to know these???
Fluorophore
o Fluorescent molecules absorb photons of a specific color (= excitation) and produces
photons with a longer wavelength/less energy (emission)
o To observe the fluorophore only, we use a color filter
o Select fluorophores bind to specific cellular structures (DAPI to DNA and DIOC 6 to lipid
membranes)
o In the inside of the cell there is constant stirring: Brownian motion and active processes (e.g.
DNA replication)
GFP
o Green Fluorescent Protein -> a DNA construct that codes for a fusion protein can be inserted
in cells
o Cells express their own fluorophore
o Used to investigate dynamic interactions between cellular components
o The organization of cells is remodeled continuously
Gedownload door Michou Weimar ()
, lOMoARcPSD|2392027
Prokaryotes (bacteria and archaea)
o Simple internal organization: no nucleus, no membrane-bound organelles
o The plasma membrane forms a barrier between the cytosol and external space
o DNA concentrated in the nucleoid (nucleus in eukaryotes), which lacks a nuclear membrane
and is irregularly shaped
o Ribosomes perform protein synthesis in the cytosol and on the plasma membrane
o Cyanobacteria make complex organic molecules and O 2 from water and CO2 by
photosynthesis (Carbon fixation):
6CO2 + 6H2O + light C6H12O6 + 6O2
carbon dioxide water glucose oxygen
o There are also nitrogen fixing bacteria (such as cyanobacteria) which covert N 2 to NH3
(ammonia). Ammonia is needed for the biosynthesis of the basic building blocks of many
organisms, such as DNA, RNA and proteins.
o Some bacteria can survive on air, water and inorganic minerals alone
Eukaryotes
o Evolved from prokaryotes (endosymbiosis)
o Have a nucleus with a nuclear envelope which consists of a double membrane: inner and
outer membrane
DNA is compacted by proteins to fit in nucleus
Chromatin complex of DNA and proteins in the nucleus
Euchromatin a lightly packed form of chromatin that is enriched on genes
Is often under active transcription (active)
Heterochromatin a tightly packed form of DNA that plays a role in gene expression
(inactive)
Gedownload door Michou Weimar ()
, lOMoARcPSD|2392027
o They also contain other membranes (e.g. ER), these membranes are probably evolved by
folding of the plasma membrane
o The nucleus enables complex gene regulation
o RNA processing (5’ cap and poly-A-tail) and RNA splicing (removing introns) in nucleus
provides differential control over protein function enabling e.g. cell differentiation
o The nucleolus is the largest substructure inside the nucleus. In the nucleolus, the first step of
ribosome synthesis occurs by combining ribosomal proteins and transcribed rRNA
o The internal membranes create distinct environments that enable different chemical
processes:
1. Peroxisomes ( containment of H2O2 )
2. Lysosomes ( acidic specialized vesicles that digest large molecules with the aid of
hydrolytic enzymes)
3. Cytoplasm (= everything a cell consists of, except the nucleus, cell membrane and cell
wall )
4. Cytosol ( cytoplasm without the organelles )
o Having compartments with different conditions optimizes cellular processes and elongates
life, but much energy is needed to prevent disorder
o ER (endoplasmic reticulum)
Gedownload door Michou Weimar ()
Week 1
Lecture Chapter 1: Cells, The Fundamental Units of Life
Cell theory
1. All living organisms are composed of one or more cells
2. Cells are the fundamental units/building block that provide structure and organization to
organisms.
3. All cells arise from pre-existing cells by growth and division (evolution). They do not arise
spontaneously.
Cells are diverse, but their chemistry is remarkably similar:
o DNA (genetic information), RNA (transcription) and protein (translation) synthesis
o Building blocks & enzymes are very similar.
Evidence -> swapping genes between organisms
Model systems = Organisms of which we exploit the similarity between cell types
o Requirements:
Replicate quick
Easy to maintain
Can be modified or has other properties that make them easy to study (e.g. translucent)
o E.coli = fundamental mechanisms of life, e.g. transcription (DNA -> RNA) and translation
(RNA -> protein)
o Single cells: Yeast and mammalian cell lines (internal organization and cell cycle control)
o Arabidopsis, Drosophila, C.elegans: mechanisms of development of multicellular organisms
o Not just chemistry is conserved but also organizing mechanisms (e.g. growing microtubules
push nuclei into position)
Microscopes
o Observing cell division provided evidence for the cell theory
o Electron microscopes (EM)
Highest resolution/resolving power
Shows features that are < 200 nm apart
Very expensive
Light microscopes (LM)
0,61∙ λ 0.61∙ λ
Resolution = d = =
N.A n sin α
λ = wavelength in nm
n = refractive index of medium
N.A = numerical aperture (≈ 1)
Gedownload door Michou Weimar ()
, lOMoARcPSD|2392027
EM LM
1. Absorption and scattering of electrons 1. Absorption and scattering of photons
(light)
2. Cells in vacuum (fixated) 2. Cells in liquid (live cell imaging)
3. Contrasting agents (e.g OSO 4) 3. Dynamic processes visualized
6
4. High magnification (×10 ) 4. ×10 3
5. Magnetic lenses 5. Glass lenses
Low image contrast because of limited absorption and light scattering
Histological stains improve contrast, but are often incompatible with live cells (I 2KI stains
starch blue)
Techniques that rely on differences in refractive index between cell compartments
increase contrast for live cells
Microscopy methods:
1. Scanning EM (surface)
2. Transmission EM (inside of 50 nm thin-section)
3. Fluorescent LM (translucent)
4. Confocal fluorescence (virtual thinsectioning)
o Nobel prizes microscopy, do we need to know these???
Fluorophore
o Fluorescent molecules absorb photons of a specific color (= excitation) and produces
photons with a longer wavelength/less energy (emission)
o To observe the fluorophore only, we use a color filter
o Select fluorophores bind to specific cellular structures (DAPI to DNA and DIOC 6 to lipid
membranes)
o In the inside of the cell there is constant stirring: Brownian motion and active processes (e.g.
DNA replication)
GFP
o Green Fluorescent Protein -> a DNA construct that codes for a fusion protein can be inserted
in cells
o Cells express their own fluorophore
o Used to investigate dynamic interactions between cellular components
o The organization of cells is remodeled continuously
Gedownload door Michou Weimar ()
, lOMoARcPSD|2392027
Prokaryotes (bacteria and archaea)
o Simple internal organization: no nucleus, no membrane-bound organelles
o The plasma membrane forms a barrier between the cytosol and external space
o DNA concentrated in the nucleoid (nucleus in eukaryotes), which lacks a nuclear membrane
and is irregularly shaped
o Ribosomes perform protein synthesis in the cytosol and on the plasma membrane
o Cyanobacteria make complex organic molecules and O 2 from water and CO2 by
photosynthesis (Carbon fixation):
6CO2 + 6H2O + light C6H12O6 + 6O2
carbon dioxide water glucose oxygen
o There are also nitrogen fixing bacteria (such as cyanobacteria) which covert N 2 to NH3
(ammonia). Ammonia is needed for the biosynthesis of the basic building blocks of many
organisms, such as DNA, RNA and proteins.
o Some bacteria can survive on air, water and inorganic minerals alone
Eukaryotes
o Evolved from prokaryotes (endosymbiosis)
o Have a nucleus with a nuclear envelope which consists of a double membrane: inner and
outer membrane
DNA is compacted by proteins to fit in nucleus
Chromatin complex of DNA and proteins in the nucleus
Euchromatin a lightly packed form of chromatin that is enriched on genes
Is often under active transcription (active)
Heterochromatin a tightly packed form of DNA that plays a role in gene expression
(inactive)
Gedownload door Michou Weimar ()
, lOMoARcPSD|2392027
o They also contain other membranes (e.g. ER), these membranes are probably evolved by
folding of the plasma membrane
o The nucleus enables complex gene regulation
o RNA processing (5’ cap and poly-A-tail) and RNA splicing (removing introns) in nucleus
provides differential control over protein function enabling e.g. cell differentiation
o The nucleolus is the largest substructure inside the nucleus. In the nucleolus, the first step of
ribosome synthesis occurs by combining ribosomal proteins and transcribed rRNA
o The internal membranes create distinct environments that enable different chemical
processes:
1. Peroxisomes ( containment of H2O2 )
2. Lysosomes ( acidic specialized vesicles that digest large molecules with the aid of
hydrolytic enzymes)
3. Cytoplasm (= everything a cell consists of, except the nucleus, cell membrane and cell
wall )
4. Cytosol ( cytoplasm without the organelles )
o Having compartments with different conditions optimizes cellular processes and elongates
life, but much energy is needed to prevent disorder
o ER (endoplasmic reticulum)
Gedownload door Michou Weimar ()
