Lecture 1-2: Structural and Functional Compartmentalisation
Definiton of a cell: a long lived structure with an overall function typically
bounded by membrane(s) or phase separated from the surrounding medium in
order to include some specific function and/or exclude other functions
Why compartmentalise?
1) Capacity for complexity
Eukaryotes: Clearly compartmentalised
Prokaryotes: Compartments are less obvious though still present
2) Include/Exclude specific functions
What is an organelle?
A long-lived sub-cellular structure with an overall function typically
bounded by membrane(s) or phase separated from surrounding cell
To divide a cell into organelles allows a cell to physically segregate
activities/ environments
As a concept, it enables biologists to link location to function – allows
simplification (create a model for hypothesis testing and experimentation)
Major Nucleus, secretory pathway
(ER/Golgi/endosomes/lysosomes), mitochondria,
peroxisomes, lipid droplets
Sub-divisions ER, SER, RER, Sarcoplasmic Reticulum
Mitochondria: several sub-compartments, cristae
Lysosomes: lysosome related organelles, melanosomes, lytic
granules, α- granules
Protein Assemblies with Nucleolus, P-body, aggresome, Sec body
contents but without
limiting membranes
Cell-type specific Melanosome, rod outer-segment, elliposime, acrosome
NOT organelles Cytoskeletal elements, ribosome, proteasome (complexes),
argosome, (chromosome)
, Controls cell activity – contains more than 99.5% of
genetic material (DNA)
Has many subdomains not separated by membranes
– only the nucleolus can be clearly seen using light
microscopy – others are visualised by
immunofluorescence microscopy
Nucleus allows protection of DNA and complex gene
regulation
Nuclei range from 1 -10 micrometres – vary in size and shape
Nuclear Envelope
Is a double membrane
Outer membrane is continuous with Rough
ER, conspicuously perforated with nuclear
pores (3000-4000)
Nuclear pore complexes (NPCs) serve as
channels for the exchange of
macromolecules between the nucleus and
the cytoplasm
Nucleolus (outside of this is the nucleoplasm)
Manufactures ribosomes using the information in its own DNA
Area rich in ribosomal RNA, ribosomal proteins (imported from cytoplasm)
Usually 1-2 in a nucleus
Shapes and presence are different
depending on organism/condition –
yeast cells can destroy its nucleolus
in adverse conditions
Nucleolus only present if ribosomal
units are being produced – disappears
if rRNA transcription is inhibited
tRNA genes (clustered around nucleoli) also transcribed here, as well as
processing
,Chromatin
Coils of DNA bound to proteins – they occupy specifc domains
Cell division: chromatin aggregates to form chromosomes
Heterochromatin (found near periphery) and euchromatin – chromsomes
within the nucleus are arranged spatially and do not intertwine
Telomeres are anchored to the nuclear envelope – likely to avoid
entanglement
Areas chromatin-free are interchromosomal domains
Genes adjacent to interchromosomal domains vary depending on cell type
– in situ hybridisation and other techniques allow the location of
transcripts to be identified in the nucleus – facilitates the diffusion of
abundant mRNAs to NPCs
Genes abundantly transcribed placed close to NPCs
*Diffusion in the cytoplasm is a slow process (slower than water) – around 1s
Nuclear Bodies
Other smaller subcompartments of the nucleus, believed to increase
biological efficiency of certain processes by concentrating
macromolecules
RNA splicing factors: arranged spatially in speckles – concentration of
splicing factors
Cajal/colied body: contain protein coilin , small nucleolar RNAs (snoRNA),
small nuclear RNAs (snRNA) – thought to be sites of post-transcriptional
RNA modification
Gemini Body (GEM): not found in all cells but share some components of
Cajal bodies
PML bodies: function unknown – has proteins that recruit other proteins
, Structure and Function
Embedded into cytoplasm
Wall: two thin membranes – finger like
cristae that project into the matrix
Site of cellular (aerobic) respiration
- Cristae : LARGE S/A – more work done,
more energy released, more efficient
- Stalked particles – ATP made
- Enzymes in matrix: final stages of
respiration = glucose to CO2 and H2O
- Ribosomes and loops of DNA allow the
mitochondria to replicate themselves when the cell divides, so daughter
cells will have enough
Cristae
Cristae form a complex three
dimensional network – attempts
to map out cristae in 3D
achieved through tomography
of mitochondria in chick
cerebellum
The mitochondrial site is
complex – there are new views of how the network/mitochondrial
architecture is exactly arranged
Definiton of a cell: a long lived structure with an overall function typically
bounded by membrane(s) or phase separated from the surrounding medium in
order to include some specific function and/or exclude other functions
Why compartmentalise?
1) Capacity for complexity
Eukaryotes: Clearly compartmentalised
Prokaryotes: Compartments are less obvious though still present
2) Include/Exclude specific functions
What is an organelle?
A long-lived sub-cellular structure with an overall function typically
bounded by membrane(s) or phase separated from surrounding cell
To divide a cell into organelles allows a cell to physically segregate
activities/ environments
As a concept, it enables biologists to link location to function – allows
simplification (create a model for hypothesis testing and experimentation)
Major Nucleus, secretory pathway
(ER/Golgi/endosomes/lysosomes), mitochondria,
peroxisomes, lipid droplets
Sub-divisions ER, SER, RER, Sarcoplasmic Reticulum
Mitochondria: several sub-compartments, cristae
Lysosomes: lysosome related organelles, melanosomes, lytic
granules, α- granules
Protein Assemblies with Nucleolus, P-body, aggresome, Sec body
contents but without
limiting membranes
Cell-type specific Melanosome, rod outer-segment, elliposime, acrosome
NOT organelles Cytoskeletal elements, ribosome, proteasome (complexes),
argosome, (chromosome)
, Controls cell activity – contains more than 99.5% of
genetic material (DNA)
Has many subdomains not separated by membranes
– only the nucleolus can be clearly seen using light
microscopy – others are visualised by
immunofluorescence microscopy
Nucleus allows protection of DNA and complex gene
regulation
Nuclei range from 1 -10 micrometres – vary in size and shape
Nuclear Envelope
Is a double membrane
Outer membrane is continuous with Rough
ER, conspicuously perforated with nuclear
pores (3000-4000)
Nuclear pore complexes (NPCs) serve as
channels for the exchange of
macromolecules between the nucleus and
the cytoplasm
Nucleolus (outside of this is the nucleoplasm)
Manufactures ribosomes using the information in its own DNA
Area rich in ribosomal RNA, ribosomal proteins (imported from cytoplasm)
Usually 1-2 in a nucleus
Shapes and presence are different
depending on organism/condition –
yeast cells can destroy its nucleolus
in adverse conditions
Nucleolus only present if ribosomal
units are being produced – disappears
if rRNA transcription is inhibited
tRNA genes (clustered around nucleoli) also transcribed here, as well as
processing
,Chromatin
Coils of DNA bound to proteins – they occupy specifc domains
Cell division: chromatin aggregates to form chromosomes
Heterochromatin (found near periphery) and euchromatin – chromsomes
within the nucleus are arranged spatially and do not intertwine
Telomeres are anchored to the nuclear envelope – likely to avoid
entanglement
Areas chromatin-free are interchromosomal domains
Genes adjacent to interchromosomal domains vary depending on cell type
– in situ hybridisation and other techniques allow the location of
transcripts to be identified in the nucleus – facilitates the diffusion of
abundant mRNAs to NPCs
Genes abundantly transcribed placed close to NPCs
*Diffusion in the cytoplasm is a slow process (slower than water) – around 1s
Nuclear Bodies
Other smaller subcompartments of the nucleus, believed to increase
biological efficiency of certain processes by concentrating
macromolecules
RNA splicing factors: arranged spatially in speckles – concentration of
splicing factors
Cajal/colied body: contain protein coilin , small nucleolar RNAs (snoRNA),
small nuclear RNAs (snRNA) – thought to be sites of post-transcriptional
RNA modification
Gemini Body (GEM): not found in all cells but share some components of
Cajal bodies
PML bodies: function unknown – has proteins that recruit other proteins
, Structure and Function
Embedded into cytoplasm
Wall: two thin membranes – finger like
cristae that project into the matrix
Site of cellular (aerobic) respiration
- Cristae : LARGE S/A – more work done,
more energy released, more efficient
- Stalked particles – ATP made
- Enzymes in matrix: final stages of
respiration = glucose to CO2 and H2O
- Ribosomes and loops of DNA allow the
mitochondria to replicate themselves when the cell divides, so daughter
cells will have enough
Cristae
Cristae form a complex three
dimensional network – attempts
to map out cristae in 3D
achieved through tomography
of mitochondria in chick
cerebellum
The mitochondrial site is
complex – there are new views of how the network/mitochondrial
architecture is exactly arranged
