Cellular Organisation (4 lectures) Medicinal Biology 2009

Contact details: Room 639, Chemistry;

e.tate@imperial.ac.uk
To provide an overview of cellular organisation,
Molecular Cell Biology 6th edition, Eds. Lodish et al.,
Freeman press
This textbook provides a lot of background material to
the course and would be a useful resource for the future.
In the main library, buy or borrow it from a biochemistry
student; parts of the material are also available online at
the NCBI website: http://www.ncbi.nlm.nih.gov/books/.
In the exam you will not be expected to provide more
detail than is provided on these handouts
Cellular Organisation: Course structure
A recap on your previous studies in
biology
Cell signalling
o Signalling in disease
Common features of all cells
Prokaryotic vs Eukaryotic cells
Overview of important cellular structures
o Endocrine, paracrine, autocrine
Signal transduction
o Signalling networks and systems biology
Overview of important cellular structures
g g y gy
o Receptors, amplification and bifurcation,
modulation and integration, transduction
o Mode of action of GPCRs
Transcription and splicing
mRNA export and translation
Protein sorting to organelles
Examples of signal transduction in
cellular organisation
o In development: Sonic hedgehog
g g
Overview of trafficking
V i l d d t i t i
p g g
o In regulated cell death: apoptosis
Building on: Macromolecule structure o Vesicles and endocytosis vs exocyctosis
Secretory pathway
o Role of the rough ER
Building on: Macromolecule structure
and biosynthesis, Molecular biology of
the gene & cell (yr 1)
B ildi t d M di i l h i t
o Role of the Golgi
Building towards: Medicinal chemistry
(yr 2), Biological Chemistry (yr 3)
Part 1: Cellular Structure
Common features of all cells
A general (re)introduction to cells, classes of organisms, cellular structure, organelles g ( ) g g
Understanding of the fundamental similarities and differences between Pro/Eukaryotes at
a morphological and genetic/complexity level a morphological and genetic/complexity level
Refresher on cellular structure: structure and general function of key organelles and other
cell components
Compare and contrast prokaryotic and eukaryotic organisms
Identify the main cellular structures and understand their general function
Some cells
Di iding east cells These single
E li i lt l t
Dividing yeast cells. These single-
celled eukaryotes divide rapidly by
budding off new daughter cells. A
widely-used model organism, especially
E. coli in culture on an agar plate,
expressing various colours of fluorescent
protein. A prokaryote (bacterium), and the
model organism in which our basic knowledge
y g , p y
valuable for studies of the cell cycle
ode o ga s c ou bas c o edge
of cellular processes was (and often still is) first
discovered
1.1 Common features of all cells
Subject to a degree of epigenetic variation
Replicate DNA by templated polymerization Replicate DNA by templated polymerization
Use proteins (enzymes) as catalysts
Use the same molecular building blocks (primary metabolites)
One gene can give rise to many proteins (splicing, protein modification)
Multiple genes can code for identical or near-identical proteins (multi-copy)
Require chemical energy to maintain structure
Allows cell to control internal environment, take up and retain nutrients,
and dump waste into external environment
1.1 And some fundamental differences
Karyon (Gr.) = nut/kernel
Pro (Gr.) = before, Eu (Gr.) = true ( ) ( )
Virus (lat.) = toxin; obviously, these are not cells! Can infect both pro- and eukaryotes.
Feature Prokaryotes Eukaryotes Viruses Feature Prokaryotes Eukaryotes Viruses
Genome size
10
6
base pairs
0.16 x10
6
4 x10
6
10
9
base pairs
0.02 x10
9
670 x10
9
10
3
base pairs
3 x10
3
50 x10
3
Genes 500-5,000 5,000-50,000 4-100
Proteins (proteome) 1000s 100,000s 10s Proteins (proteome) 1000s 100,000s 10s
Morphology
Single-cell, no
nucleus
1+ nuclei (Single- or
Multi-cellular)
Encapsulated RNA
or DNA genome
Examples
Archea, Bacteria.
e.g. causative
agents of
Fungi (e.g. yeast),
Plants, Protozoa
(e g malaria
Influenza virus,
chickenpox, HIV,
SARS
tuberculosis,
typhoid
(e.g. malaria
parasite), Animals
SARS,
bacteriophage
1.2 Some model organisms
C ll l bi h i t C ll l t b t Cellular biochemistry,
molecular biology
Cell cycle,
signalling, genetics
vertebrate
and mammalian biology
genetics,
gene function development gene function, development
Rapid life cycle, easily maintained in
large numbers
Relatively straightforward genetic y g g
manipulation (engineering)
Genome sequence available
Widely available strains standardise Widely-available strains standardise
experiments
1.3 Prokaryotes
No recognizable intracellular organelles
Cytoplasm does not have much structure even Cytoplasm does not have much structure even
at very high magnification
Have an outer cell wall and inner cell membrane
Store DNA in a amorphous region called the Store DNA in a amorphous region called the
nucleoid; bacterial genomes are almost always
circular, which enables rapid replication
Biochemistry simpler than eukaryotes
Many important basic mechanisms are very Many important basic mechanisms are very
similar (transcription, translation, energy
generation, etc.)
Rapid replication (minutes) and evolution (e g
Lower image: Electron micrograph of
Rapid replication (minutes) and evolution (e.g.
of resistance)
Lower image: Electron micrograph of
a longitudinal section through the
widely studied bacterium Escherichia
coli (E. coli). The cell's DNA is
At least 99% of all prokaryotic species remain to
be characterised!
concentrated in the lightly stained
region (termed the nucleoid)
1.4 Eukaryotes
Many models have been proposed, based on morphology and on phylogenetic trees (i.e.
degree of conservation of genetic sequences between organisms)
Early eukaryotes with no photosynthesis or aerobic metabolism enveloped aerobic
bacteria or photosynthetic bacteria and formed endosymbiotic associations.
These endosymbionts eventually lost most of their genes, many of which were transferred
to their host, and became the specialised mitochondria and chloroplasts.
1.5 Recap on (eukaryotic) cellular structure
100 trillion cells in
the human body
There is no such
thing as a typical
eukaryotic cell! y
Size can range from
10-100 m
Very many types; Very many types;
there are over 100
types of neuronal
cells alone cells alone
1.5 Nucleus
The major defining organelle of
eukaryotic cells
Surrounded by nuclear envelope
containing many nuclear pores
Contains most of the DNA in the
cell
The vast majority of DNA is
transcriptionally silent (either transcriptionally silent (either
switched off or non-transcribed)
When a cell is dividing, the DNA and surrounding protein condense into chromosomes
that are visible by microscopy.
The structure of the nucleus is complex (figure for reference only!) The structure of the nucleus is complex (figure for reference only!)
The most prominent structure in the nucleus is the nucleolus, which is the site of
transcription of ribosomal RNA (rRNA) and ribosome assembly
Specialised cells can be enuculeated (e.g. erythrocytes) or polynucleated (myocytes).
Polynucleation is also implicated in the progression of cancer.
1.5 Cytosol, Cytoplasm, Cytoskeleton
The "soup" within which cell
organelles reside; very viscous due to
hi h lt d t i t t high salt and protein content
Cytoplasm is the collective term for
the cytosol plus the organelles
Network of protein fibres that
pervades the cytoplasm pervades the cytoplasm
Gives the cell its shape and provides
the basis for movement
K f ll l d Key component of cell cycle and
protein transport
Contains three types of fibres and
Blue: microfilaments; Yellow: microtubules; Green: nuclei
molecular motors that pull on them:
o Fibres (smallest to largest):
microfilaments, intermediate filaments,
microtubules microtubules
o Motors: Kinesin, Dynein, Myosin
1.5 Plasma membrane
A double layer of lipids (lipid bilayer); very complex structure, high protein content
(receptors, pores, enzymes)
Responsible for the controlled entry and exit of ions (Na, K, Ca, Cl), nutrients, signalling
molecules
Electron micrograph and cartoons of the plasma membrane of a human red blood cell in
cross section.
1.5 Mitochondria
elongate cylinders to spheroids, 3-5 m
long by 0.5-1.0 m diameter. g y
20 to 1,000/cell, depending on activity
required; up to 20% of cell volume
Double membrane: inner membrane Double membrane: inner membrane
contains numerous folds (cristae)
Regenerates ATP by oxidative
phosphorylation. Major centre of cellular
respiration
I k i ith it d bi ti i i t i Mit h d i l DNA (16 kb b t 37 In keeping with its endosymbiotic origin, contains Mitochondrial DNA (16 kb, about 37
genes) and prokaryote-like ribosomes (mitoribosomes)
Matrix contains most of the enzymes of the tricarboxylic acid cycle and the urea cycle.
Inner membrane contains the components of the electron transport chain.
1.5 Ribosomes
Small particles (18-22nm), in cytosol and studding the surface of the rough ER
The site for all protein synthesis in the cell p y
Often in clusters called polyribosomes or polysomes held together by a strand of mRNA
Ribosome Nascent Ribosome
mRNA
Nascent
peptide
chain
1.5 Endoplasmic reticulum (ER)
Found in all non-enucleated eukaryotic
cells, and has structural continuity with
the nucleus; 50% of the total membrane
of a cell
Composed of flattened sheets, sacs, & p
tubes of membranes in a convoluted 3D
membrane network enclosing internal
spaces
Internal volume is called the Lumen (up
to 10% of cell's volume)
Smooth ER: lipid and bile biosynthesis
(e.g. prostaglandins), and detoxification
f t i of toxins
Rough ER: studded with ribosomes,
makes, transports, and packages
proteins into membrane vesicles
1.5 Golgi
Size: 1-3 m by 4-7 m; formed of
membranes stacks (cisternae), up to
100 per cell, with three parts: cis-
medial- and trans-Golgi
Constantly in flux (cisternal maturation): y ( )
vesicles from ER join to form the cis-
Golgi and mature through to the trans-
Golgi where they reform into new
vesicles.
A key part of the endo and exocytotic A key part of the endo- and exocytotic
pathways.
Endocytosis: packaging of
t ll l l l f i t l extracellular molecules for internal use.
Exocytosis (secretion): packaging and
delivery of newly synthesised proteins
f
The Golgi. a) under a light microscope; b)
tomographic reconstruction (blue: cisternea;
purple: vesicles)
and carbohydrates for extra-cellular
secretion
1.5 Lysosomes
A cytoplasmic single-membrane vesicle, containing hydrolytic enzymes that operate at
pH 5.0. The lysosomal membrane has an ATP-driven proton pump that lowers the internal
pH.
Protein and organelle recycling/degradation: recycle intact and non-functional cell Protein and organelle recycling/degradation: recycle intact and non functional cell
components (autophagy), and break down food/foreign bodies (phagocytosis).
However, the major regulatory protein-degradation pathway occurs in the cytoplasm via
proteosomes proteosomes.
1.6 Summary
Prokaryotes have a much simpler cellular
organisation
How do these organelles come together
to orchestrate cellular organisation?
Eukaryotes (in a generic sense) are the
focus of this course
o Synthesis, sorting and trafficking of proteins
o Controlling cellular processes via cell
signalling
Nucleus
Cytoskeleton
Pl b
o Programming cell division and cell death
Plasma membrane
Mitochondria
Ribosomes
Endoplasmic Reticulum
Golgi
Lysosomes Lysosomes
We will discuss others, such as vesicles
and centrioles later in the course.