The Microstructure of Cells

Dr Sandile Buthelezi
Email: Sandile.Buthelezi@wits.ac.za
A Panoramic View of the Eukaryotic Cell

• External plasma membrane

• Internal membranes that partition the cell into
compartments (organelles)
• Different local environments
• Surface
• Plant and animal cells have mostly the same organelles –
key differences
 Nuclear
envelope
ENDOPLASMIC RETICULUM (ER)
Nucleolus NUCLEUS
Rough ER Smooth ER
Flagellum Chromatin

Centrosome
Plasma
membrane

CYTOSKELETON:
Microfilaments
Intermediate
filaments
Microtubules
Ribosomes

Microvilli

Golgi
Peroxisome apparatus

Mitochondrion
Lysosome
 Nuclear envelope Rough endoplasmic
reticulum
NUCLEUS Nucleolus
Chromatin
Smooth endoplasmic
reticulum
Ribosomes

Central vacuole
Golgi
apparatus
Microfilaments
Intermediate
filaments CYTO-
SKELETON
Microtubules

Mitochondrion
Peroxisome
Chloroplast
Plasma
membrane

Cell wall
Plasmodesmata
Wall of adjacent cell
Eukaryotic cells

• More complex than prokaryotic cells

• Membrane surrounded organelles
• WHY IS THIS IMPORTANT?
• Microenvironment
• Incompatible processes
• Embedded enzymes

• Internal membrane system unique lipids and proteins

Genetic instructions are housed in the
nucleus and carried out by the ribosomes

• The nucleus contains most of the DNA in a eukaryotic

cell (where is the rest?)
• The information in the DNA is transferred to a specific type
of RNA called messenger RNA (mRNA) which is exported
through pores in the nuclear envelope to the cytoplasm

https://commons.wikimedia.org/wiki/File:Antisense_DNA_oligonucleotide.png
 The Nucleus: Information Central

• The nucleus contains most of the cell’s genes and is

usually the most conspicuous organelle – function =
control and reproduction
• First described in 1831 – Robert Brown
• In animal cells located in the central region of the cell.
• Most cells have ONE nucleus BUT
• Some fungi: several
• Erythrocytes (red blood cells) : no nucleus
 Fungi

Erthrocytes
• Mammalian erythrocytes have nuclei during early
phases of erythropoiesis, but extrude them during
development as they mature in order to provide more
space for haemoglobin.
• They also lose all other cellular organelles
• No DNA = cannot divide - limited repair capabilities.
• No virus can evolve to target mammalian red blood
cells – why?
• The nuclear envelope is a membrane that encloses the nucleus,
separating it from the cytoplasm
• This is a double membrane
• Each membrane consists of a lipid bilayer which is continuous with
the endoplasmic reticulum
• Pores regulate the entry and exit of molecules from the nucleus
• Pores are lined by proteins (pore complex) that controls the
movement of materials into and out of the nucleus (what
materials?)

• The shape of the nucleus is maintained by the nuclear

lamina, which is composed of protein – net of protein filaments
Fig. 6-10

Nucleus
1 µm Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane

Nuclear pore

Pore
complex

Rough ER
Surface of
nuclear envelope
Ribosome 1 µm

0.25 µm

Close-up of nuclear
envelope

Pore complexes (TEM) Nuclear lamina (TEM)

• The nucleolus is located within the nucleus and is
the site of ribosomal RNA (rRNA) synthesis
• DNA is found in units called chromosomes
• Chromosomes carry genetic information - genes
• In the nucleus, DNA and proteins form genetic
material called chromatin - DNA wound around
proteins
During cell division
chromatin condenses to
form discrete
chromosomes
 Ribosomes: Protein Factories

• Ribosomes are particles assembled from ribosomal

RNA and many different proteins
• Ribosomes are made up of 2 subunits, a large subunit
and a small subunit

Is it an Organelle?
 Ribosomes: Protein Factories

• Ribosomal RNA (rRNA) synthesis takes place in the

nucleolus
• Ribosomal proteins are imported into the nucleolus
from the cytoplasm and combine with rRNA to form
ribosomes in the nucleus
 Ribosomes: Protein Factories
• The two ribosome subunits attach to mRNA in order
to synthesise proteins

https://commons.wikimedia.org/wiki/File:Ribosome_Translation.jpg
 Ribosomes: Protein Factories

• At the end of the process the ribosomes detach from

mRNA as free subunits
• They can then attach to a new mRNA strand
• Ribosomes are found in two cell locations:
• In the cytosol (free ribosomes)
• On the outside of the rough ER or the nuclear envelope (bound
ribosomes)
• Free ribosomes à internal (cytosolic) proteins
• Bound ribosomes à exported proteins
Fig. 6-11

Cytosol
Endoplasmic reticulum (ER)

Free ribosomes

Bound ribosomes

Large
subunit

Small
0.5 µm subunit
TEM showing ER and ribosomes Diagram of a ribosome
Concept: The endomembrane system regulates protein
traffic and performs metabolic functions in the cell

• Components of the endomembrane system:

• Nuclear envelope
• Endoplasmic reticulum
• Golgi apparatus
• Lysosomes
• Vacuoles
• Plasma membrane
• These components are either continuous or connected via
transfer by vesicles
The Endoplasmic Reticulum:
Biosynthetic Factory

• The endoplasmic reticulum (ER) accounts for

more than half of the total membrane in many
eukaryotic cells
• The ER membrane is continuous with the nuclear
envelope
• There are two distinct regions of ER:
• Smooth ER, which lacks ribosomes
• Rough ER, with ribosomes studding its surface
Fig. 6-12
Smooth ER

Rough ER Nuclear
envelope

ER lumen
Cisternae
Ribosomes Transitional ER
Transport vesicle 200 nm
Smooth ER Rough ER
Functions of Smooth ER
• Synthesizes lipids
• Metabolizes carbohydrates
• Detoxifies poison
• Stores calcium ions

• Functions differ with cell type

https://commons.wikimedia.org/wiki/File:Liver_(organ).png
Functions of Rough ER
• Has bound ribosomes, which make
proteins that are secreted out of the
cells
• Many secretory proteins are glycoproteins
(proteins covalently bonded to
carbohydrates)
• The carbohydrate portion is attached to the
secretory proteins by enzymes embedded in
the rough ER
After the RER
synthesizes a protein it
packages it in a vesicle
for transport
Functions of Rough ER

• After synthesis secretory proteins are isolated from the

cytoplasm by being wrapped in membranes
• These bud off from the rough ER and move to other
parts of the cell
• The membrane buds containing secretory proteins are
called transport vesicles
• Is also a membrane factory for the cell
The Golgi Apparatus: Shipping and
Receiving Center
• The Golgi apparatus consists of flattened
membranous sacs called cisternae
The Golgi Apparatus: Shipping and
Receiving Center

• The apparatus has 2 faces or sides:

• The cis (on the same side) face is close to the rough ER and
is the receiving site for transport vesicles
• The transport vesicles from the ER fuse with this face and release
their content

• The trans face is the dispatching site where modified and

sorted proteins are packaged into new vesicles and released
The Golgi Apparatus: Shipping and
Receiving Center

• Functions of the Golgi apparatus:

• Modifies products of the ER (e.g. glycoproteins and
phospholipids)
• Manufactures certain macromolecules
• Targets specific products for specific parts of receiving
cells by adding molecular identification tags
• Packages secretory products into transport vesicles
(Same as in RER)
Fig. 6-13

The Golgi Apparatus

cis face
(“receiving” side of Golgi 0.1 µm
apparatus) Cisternae

trans face
(“shipping” side of Golgi TEM of Golgi apparatus
apparatus)
 Lysosomes: Digestive
Compartments

• A lysosome is a membranous sac of hydrolytic enzymes that

can digest macromolecules
(What does this mean?)
• Lysosomal enzymes can hydrolyze proteins, fats,
polysaccharides, and nucleic acids
• Acid environment
• Hydrolytic enzymes and lysosome membrane are made in the
rough ER -Golgi
Processes which require lysosomes

• Some types of cell can engulf another cell or food

particles by phagocytosis à this forms a food vacuole
• A lysosome fuses with the food vacuole and digests the
molecules
• The products of digestion can be used as nutrients by the
engulfing cell
Fig. 6-14a
Nucleus 1 µm

Phagocytosis

Lysosome
Digestive
enzymes
Lysosome

Plasma
membrane
Digestion

Food vacuole

(a) Phagocytosis
• Lysosomes also use enzymes to recycle the
cell’s own organelles and macromolecules, a
process called autophagy
Fig. 6-14b
Vesicle containing 1 µm
two damaged organelles

Autophagy
Mitochondrion
fragment

Peroxisome
fragment

Lysosome

Peroxisome

Mitochondrion Digestion
Vesicle

(b) Autophagy
The Endomembrane System
continued…

• The endomembrane system is a complex and

dynamic player in the cell’s compartmental
organization
Fig. 6-16-1

Nucleus

Rough ER

Smooth ER

Plasma
membrane
Fig. 6-16-3

Nucleus

Rough ER

Smooth ER
cis Golgi

Plasma
membrane
trans Golgi
Vacuoles: Diverse Maintenance
Compartments

• A plant cell or fungal cell may have one or several

vacuoles
• Essentially a large vesicle
• Contents vary according to cell – or organisms (may
contain H2O, stored food, salts, pigments and wastes)
• Surrounded by a membrane called the tonoplast
• Vacuoles larger in plant cells
Fig. 6-15

Central vacuole

Cytosol

Nucleus Central
vacuole

Cell wall

Chloroplast

5 µm
• Food vacuoles are formed by phagocytosis
• Contractile vacuoles, found in many freshwater
protists, pump excess water out of cells
• Central vacuoles, found in many mature plant
cells, hold ions and organic compounds and water
 Functions of vacuoles
• In plants = structural roles
• Toxic substances may be recycled in the vacuole
• Storage for inorganic compounds in plants
• Noxious compounds – stored in vacuoles as means of
defense against herbivores
• Role in plant growth and development (Immature plant cells –
small and numerous; mature plants – coalesce to form central
vacuole)
• Protozoa – specialized = food vacuoles or phagosomes; also
contractile vacuoles – pump out water.
Now, for the
Energy: Meet
Mitochondria
and Chloroplasts
Concept : Mitochondria and Chloroplasts
change energy from one form to another

• Mitochondria are the sites of cellular respiration,

a metabolic process that generates ATP
• Chloroplasts, found in plants and algae, are the
sites of photosynthesis
• Mitochondria and chloroplasts:
• Are not part of the endomembrane system
• Have a double membrane
• Have proteins made by free ribosomes
• Contain their own DNA which codes for some of
their proteins and ribosomes
Mitochondria: Chemical Energy Conversion

• Mitochondria are found in nearly all eukaryotic cells

• They have a smooth outer membrane and an inner
membrane folded into cristae

https://commons.wikimedia.org/wiki/File:Animal_mitochondrion_diagram_en.svg
Mitochondria: Chemical Energy Conversion

• The inner membrane creates two compartments:

intermembrane space and mitochondrial matrix
• Some metabolic steps of cellular respiration are
catalyzed in the mitochondrial matrix
• Cristae present a large surface area for enzymes
that synthesize ATP
Fig. 6-17

Intermembrane space
Outer
membrane

Free ribosomes
in the
mitochondrial
matrix
Inner
membrane
Cristae
Matrix

0.1 µm
Chloroplasts: Capture of Light Energy

• The chloroplast is a member of a family of

organelles called plastids
• Chloroplasts contain the green pigment
chlorophyll, as well as enzymes and other
molecules that function in photosynthesis
• Chloroplasts are found in leaves and other green
organs of plants and in algae
• Chloroplast structure includes:
• Thylakoids, membranous sacs,
stacked to form a granum
• The internal fluid is the stroma
 Peroxisomes: Oxidation

• Peroxisomes are like specialized lysosomes -

metabolic compartments bounded by a single
membrane
• Oxygen is used to break down different types of
molecules
• Peroxisomes oxidize other molecules and produce
hydrogen peroxide which is then broken down -
convert it to water
 Peroxisomes cont.d

• Peroxisomes are found in organisms including plants ,

animals (liver & kidney) and protozoa

• Originate from SER

 Glyoxysomes
• These are specialised peroxisomes
• Occur in lipid–storing regions of
seeds
• When seeds sprout, enzymes of
glyoxysomes convert stored lipids
to sugars
Fig. 6-19

Chloroplast
Peroxisome
Mitochondrion

1 µm
Relative sizes of cell organelles
•Next week we will be looking at:
• the cytoskeleton
• the ECM, Adhesion and Junctions