Structure of Eukaryotic & Prokaryotic

Cells 1 & 2

Suggested Reading:

Essential Cell Biology

Alberts et al. (4th ed)
Chapter 1, pages: 1-4, 12-
22, 25
More detail in chapter 11
(has also some material for
the macromolecule
lectures)
by
Dr. Martha Ludwig
Modified, revised (2022) and presented by
Dr Thomas Martin
 Structure of Eukaryotic & Prokaryotic Cells 1 & 2
– Learning outcomes

You will be able to

• memorize that cells are the basic unit of life sharing a basic chemistry,

• memorize, identify and contrast characteristics of prokaryotic and eukaryotic cells,

• describe the composition and roles of cellular membranes,

• explain the roles of cellular organelles and compartments,

• explain the origin of mitochondria and chloroplasts - endosymbiosis theory

• describe in detail mitochondrial and chloroplastic structures,

• describe the generation of cellular energy,

• explain the role of proton gradients in ATP production,

• describe the production of carbohydrates in chloroplasts

Cells - The Basic Unit of Life

➢ comprise all living things

➢ small membrane-bound units
➢ Cytosol: aqueous, gel like
solution of water and chemicals
➢ divide
➢ grow
➢ respond to stimuli
➢ energy conversion
➢ highly specialised
➢ Huge diversity
▪ single-celled organisms
▪ multi-celled organisms
o cells make up tissues, which
make up organs, which make
up organisms

Alberts et al. (10) Essential Cell Biology, Figs 1-3, 1-5

 Cells have a similar basic chemistry

➢ All composed of the same sorts of molecules

➢ All carry out the same basic chemistry

➢ All store their genetic material as DNA

➢ All have same basic genetic mechanisms
➢ genetic material is replicated & passed on to
next generation by cell division
➢ information flow uses the same chemical
machinery

➢ All contain the same set of 20 amino acids in their

proteins
 Why Are Cells So Similar?

Same common ancestor - 3.5 billion years ago

HOWEVER
Mutation & selection of
descendant cells
(evolution), resulted in
divergence, modification,
adaptation,
specialisation AND this is
on-going

Alberts et al. (10) Essential Cell Biology, Fig 1-29

 A Nucleus - The Fundamental Difference
Between Prokaryotes & Eukaryotes

Prokaryotes Eukaryotes
pro = “before” eu = “truly”

karyon =
‘kernel’ or
nucleus

Alberts et al. (10) Essential Cell Biology, Fig 1-29

 Prokaryotes

Escherichia coli - gut bacterium Beggiatoa - sulphurous environments

• “true • found in hostile
bacteria” Archea environments
Eubacteria • found in as well as in
environments bacteria more familiar
familiar to us ones

❖ Division between these two groups is based on molecular biological

characterisations.

❖ They are as different to each other as either is from eukaryotes.

Alberts et al. (08) Molecular Biology of the Cell, Fig 1-29; Alberts et al. (10) Essential Cell Biology, Fig 1-13
 Prokaryotes - Features

Alberts et al. (10) Essential Cell Biology, Fig 1-10

➢ most diverse group of cells

➢ successfully inhabit many different environments
➢ exhibit many different growth forms
o spherical, rod-shaped, spiral, chains, clusters, organised
multicellular structures
➢ may be
o organotrophic (use any organic molecule as an energy source)
o phototrophic (use light as an energy source)
o lithotrophic (use inorganic molecules as an energy source)
 Prokaryotes - Features

➢ “simple” cells
➢ a few micrometres (μm) long
➢ tough, protective cell wall
➢ plasma membrane
➢ essentially no membrane-bound organelles
o have no nucleus
o circular DNA free in cytosol
➢ ribosomes
➢ may have a flagellum
➢ can reproduce quickly, e.g. some divide every 20 min
Alberts et al. (08) Molecular
Biology of the Cell, Fig 1-18
 Eukaryotes

➢ Unicellular
▪ most protists
▪ yeast

➢ Multicellular
▪ animals, plants (including
multicellular algae) & fungi

Alberts et al. (08) Molecular Biology of the Cell, Figs 1-40, 1-42, 1-47, 1-48, 1-53; Raven et al. (05) Biology of Plants, Fig 15-53
Eukaryotes: Plant and animal cells have a
large number of organelles

Animal cell Plant cell

Figure by LadyofHats, Public Domain,

https://commons.wikimedia.org/w/index.php?curid=4266142 Figure by LadyofHats, Public Domain,
https://commons.wikimedia.org/w/index.php?curid=844682
 Ribosomes
➢ prokaryotes and eukaryotes
➢ sites of protein synthesis
➢ large complexes of
▪ proteins &
▪ ribosomal RNAs = rRNAs
➢ eukaryotic larger (80S) than prokaryotic
(70S)
➢ two populations in eukaryotes
▪ cytosolic
o free or attached to Endoplasmic
Reticulum (80S)
▪ in mitochondria & chloroplasts (70S)
= bacterial size

More in topic 2 lectures on DNA to Proteins

Alberts et al. (10) Essential Cell Biology, Figs 7-30, 7-31

 Membranes - Composition

Alberts et al. (10) Essential Cell Biology, Fig 11-4

➢ Prokaryotes and eukaryotes

➢ Bilayer of phospholipids ➔ see L3
➢ asymmetrical arrangement in the two halves
➢ Proteins
➢ integral - embedded in the bilayer
➢ peripheral - attached loosely to the bilayer
 Plasma Membrane

Alberts et al. (10) Essential Cell Biology, Figs 1-24, 11-2

Plasma membrane involved in

▪ cell signalling
▪ transport of solutes
Theme 5 and 6
▪ cell growth & motility
 Membranes
- Selectivity

➢ Selectively permeable

▪ Small hydrophobic &

small uncharged
molecules can cross
freely.

▪ Larger uncharged polar

molecules & charged
solutes must interact
with transmembrane
proteins (transporters)
to cross phospholipid
bilayer.
More under topic 5, 6 Alberts et al. (10) Essential Cell Biology, Fig 12-2
Plasma Membrane - Carbohydrate groups

Alberts et al. (10) Essential Cell Biology, Fig 11-35

▪ Carbohydrate groups attached to lipids - glycolipids

▪ Carbohydrate groups attached to proteins - glycoproteins
➢ on external (non-cytosolic) side of plasma membrane
➢ play roles in:
o cell-to-cell communication
o protection from chemical & mechanical damage
o adhesion
 Membranes
– Create Compartments

➢ Compartmentalise cells
▪ separate cells from their
environments
▪ separate organelles from each
other & from the cytosol

➢ Double membranes surround

▪ nucleus
▪ mitochondria
▪ chloroplasts

Alberts et al. (10) Essential Cell Biology, Figs 1-24, 11-2

 Eukaryotes Cells
- Single Membrane bound Organelles

o Endoplasmic
reticulum (ER)
o Golgi apparatus
o Vesicles:
o Secretory vesicles
o Endosomes
o Lysosomes
o Microbodies (e.g.
peroxisomes)
o Vacuoles - plants (not
shown here as it is an
animal cell)

Figure by LadyofHats, Public Domain,

https://commons.wikimedia.org/w/index.php?curid=4266142
 Endomembrane system

Red arrows = exocytic path

Green arrows = endocytic path
Alberts et al. (10) Essential Cell Biology, Fig 15-18

➢ Includes: nuclear envelope, ER, Golgi apparatus, transport vesicles,

plasma membrane, and endosomes and lysosomes (animal cells) or
vacuoles (plant cells)
 Endomembrane System:
Endoplasmic Reticulum - ER
➢ network of sacs & tubules
(cisternae)
➢ throughout the cytosol
➢ synthesis of most cell
membrane components &
molecules exported from a
cell
➢ Rough ER ➔ ribosomes
attached
▪ protein synthesis
▪ Carbohydrate addition
to proteins
▪ continuous with the
Alberts et al. (10) Essential Cell Biology, Fig 1-22
nuclear membrane
➢ Smooth ER ➔ no ribosomes
▪ lipid synthesis
 Endomembrane System:
Golgi Apparatus

➢ stacks of flattened
sacs (cisternae)
➢ one or more per cell
➢ synthesis and
packaging of
molecules to be
secreted from cell
➢ routing of newly
synthesised proteins to
Alberts et al. (10) Essential Cell Biology, Fig 1-23
their correct cellular
locations
➢ associated with many
transport vesicles
 Golgi Apparatus has
a distinct orientation

cis face - adjacent to ER,

vesicles arrive from the ER

trans face - points toward

plasma membrane
➢ transport vesicles pinch off &
fuse with cisternae
➢ carry proteins being modified
by the addition of sugar
groups
➢ correlation of enzyme
location (e.g. which cisterna)
& what step it catalyses in
sugar-modification pathway

Figure from: https://www.britannica.com/science/Golgi-apparatus

 Endomembrane System: Microbodies

Peroxisomes
▪ single-membrane bound
▪ contain oxidative enzymes

In animals
➢ sites of detoxification (e.g. lots in
liver)

In plants
➢ sites of detoxification
➢ photorespiration (carbon recycling)
➢ conversion of stored fats into
sucrose during germination of
some seeds (= glyoxysomes)

Raven et al. (05) Biology of Plants, Fig 3-16; http://nobelprize.org/educational

_games/physics/microscopes/tem/gallery/8.html
 Endomembrane system
– Exocytic Pathway

Membrane growth,
secretion
➢ Outward = exocytic pathway
➢ Proteins synthesised on rough
ER & glycosylated
➢ Vesicles containing glycoproteins
bud off ER & fuse with cis Golgi
cisternae
➢ Glycoproteins are further
glycosylated as they travel
through Golgi cisternae by
vesicle budding & fusion Red arrows = exocytic path
Green arrows = endocytic path
➢ At the trans face of the Golgi,
Alberts et al. (10) Essential Cell Biology, Fig 15-18
vesicles are directed to plasma
membrane or lysosome/
vacuole
Endomembrane system
– Endocytic Pathway
➢ Inward = endocytic
pathway
➢ Ingestion & degradation
(or recycling) of
extracellular molecules
▪ Regions of the plasma
membrane containing
molecules to be
degraded bud inward to
form vesicles
▪ Vesicles fuse with early
endosomes
▪ Ultimately molecules
are degraded in the
lysosome /vacuole
▪ Some degradation Red arrows = exocytic path
products can be reused Green arrows = endocytic path
by the cell
Alberts et al. (10) Essential Cell Biology, Fig 15-18
 Endomembrane System:
Vacuoles

➢ Vacuoles of plant cells are sites of

degradation

nucleus ➢ They also act as:

▪ storage organs (e.g. seed
proteins)
▪ detoxification sites (e.g.
vacuole tannins)
▪ pigment deposition (e.g.
chloroplast anthocyanins)

Raven et al. (05) Biology of Plants, Fig 3-3

 Eukaryotes Cells
- Double Membrane bound Organelles

o nucleus – double
membrane
o Mitochondria – double
membrane
o chloroplasts – double
membrane

Figure by LadyofHats, Public Domain,

https://commons.wikimedia.org/w/index.php?curid=844682
 Nucleus
➢ Surrounded by a double
membrane
• continuous with ER
• interrupted by pores
▪ allow passage of
selected molecules
between cytosol &
nucleus
➢ Contains most cellular DNA
• heterochromatin
▪ DNA + proteins - highly
condensed, even at
interphase
• euchromatin
nucleolus ▪ DNA + proteins - not
condensed until mitosis
Alberts et al. (10) Essential Cell Biology, Fig 1-15
➢ Typically contains a nucleolus
• site of ribosomal RNA
(rRNA) synthesis &
ribosomal subunit assembly
 Mitochondria

➢ sites of cellular respiration & major energy (ATP) production

in a process called oxidative phosphorylation

➢ surrounded by a double membrane

▪ smooth outer membrane
❖ permeable to ions & small
molecules
▪ inner membrane
❖ highly folded (into cristae)
❖ impermeable
❖ transport proteins control
substrate movement across the
inner membrane
❖ contains an electron transport
chain & ATP synthase Alberts et al. (10) Essential Cell Biology, Fig 1-18
 Mitochondrial Matrix

➢ Region not taken up by membranes

➢ Contains:
▪ DNA ➔ mitochondrial genome
❖ codes for
o mitochondrial tRNA
o mitochondrial rRNA
o mitochondrial mRNA
• proteins for DNA
synthesis & oxidative
reactions
▪ Mitochondrial ribosomes (70S)
▪ Enzymes for the tricarboxylic
acid (citric acid, Krebs) cycle Alberts et al. (10) Essential Cell Biology, Fig 1-18
 Chloroplasts
– Organelle with a double membrane
http://unisciencenet.org/IBHbio
➢ sites of photosynthesis 3_frameset.html

❖ two sets of reactions:

▪ light harvesting
▪ carbohydrate production

➢ surrounded by a double
membrane:
❖ outer membrane
▪ permeable to ions & small
molecules

❖ inner membrane
▪ impermeable
▪ transport proteins control
movement of substrates
across internal membrane
system

Alberts et al. (10) Essential Cell Biology, Fig 1-20

 Chloroplasts
– Thylakoids and Lumen
http://unisciencenet.org/IBHbio3_frameset.html

Thylakoids
▪ formed by a folded
internal membrane system
▪ folded into stacks – grana
➢ light-harvesting
pigments
➢ electron transport chain
➢ ATP synthase
Lumen http://m.eb.com/assembly/45552

➢ space between
thylakoids
 Chloroplasts - Stroma

➢ region not taken up

by thylakoid membranes

➢ contains
❖ DNA codes for
▪ tRNA
▪ rRNA
▪ mRNA ➔ proteins
for DNA synthesis &
photosynthesis
❖ ribosomes (70S)
❖ enzymes for
carbohydrate production http://www.tutorvista.com/biology/chloroplasts#
 Mitochondria & Chloroplasts
are Products of Endosymbiosis

Figure from: https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/endosymbiosis

• An ancestral eukaryotic cell ingested, but did not digest an aerobic bacterium,
which over time evolved into a mitochondrion. ➔ eukaryotic cells

• Eukaryotic cells later ingested a photosynthetic bacterium without digesting it.

Over time, this ingested bacterial cell evolved into a chloroplast ➔ plant cells
 Energy Production Overview

➢ Digestive enzymes
breakdown:
• proteins to amino acids
• polysaccharides to simple
sugars
• fats to fatty acids & glycerol

➢ Breakdown products enter cell

cytosol for gradual oxidation
& production of some energy
(ATP) and reducing
molecules (NADH)
➢ The final stages and the
majority of energy production
takes place in the
mitochondria.

Alberts et al. (10) Essential Cell Biology, Fig 13-2

 Cytosol
Energy Production: Early Stages

Alberts et al. (10) Essential Cell

Biology, Fig 13-2

cytosol

Alberts et al. (10) Essential Cell Biology, Fig 13-2

CYTOSOL:
➢ Glucose & other sugars are converted to pyruvate through
glycolysis.
➢ This generates some energy molecules (ATP, NADH)
➢ Some amino acids are converted to pyruvate.
 Mitochondria
Energy Production: Early Stages

mitochondrion
Alberts et al. (10) Essential Cell Biology, Fig 13-2

➢ Pyruvate, some amino acids and fatty acids enter the

mitochondrion.
➢ Pyruvate, fatty acids and some amino acids are oxidised
to acetyl CoA in the mitochondrion.
 Mitochondria
Production of Reducing Molecules

➢ Acetyl CoA is further oxidised by some

the citric acid cycle amino
acids
Produces:
o CO2 , diffuses out of
mitochondria via membranes
o NADH & FADH2 (FADH2 not
shown)
o NADH and FADH2 are
molecules with strong
reducing power
Note: some amino acids can enter
the citric acid cycle at intermediate
steps & be oxidised directly
CO2
Alberts et al. (10) Essential Cell Biology, Fig 13-2
 Electron Transport Chain (ETC)
Using reducing power to generate ATP
- overview
➢ NADH & FADH2 have strong
reducing power = ‘high energy
electrons’
➢ NADH & FADH2 donate
electrons to electron transport
chain (ETC) in the inner
mitochondrial membrane.
➢ The electrons move through the
electron transport chain ➔
consist of multiprotein
complexes
➢ This results in:
▪ oxidation of NADH & FADH2
▪ reduction of O2 to H2O Alberts et al. (10)
Essential Cell Biology,
Fig 14-7
▪ ATP production.
 Mitochondria – Finally, ATP production

Alberts et al. (10) Essential Cell Biology, Fig 14-11

➢ Pumping of electrons leads to a H+ (proton) gradient

▪ higher concentration of protons in the inter membrane space than in the
matrix
➢ ATP is synthesised as protons move through the ATP synthase from the
inter membrane space into the matrix.
➢ ATP is transported out of the mitochondrion for use by the cell.
 Chloroplasts
– Light Harvesting Reaction

PQ = plastoquinone
Fd = ferredoxin
Raven et al. (05) Biology of Plants, Fig 7-12

➢ Light energy is collected by pigments in the thylakoid membranes

➢ Converted to reducing power (NADPH) and chemical energy (ATP) via a
series of oxidation-reduction reactions
➢ H2O being the original electron donor and NADPH the final electron acceptor.
 The Chloroplast
- Electron Transport Chain

Stroma

Lumen
PQ = plastoquinone
Fd = ferredoxin
Raven et al. (05) Biology of Plants, Fig 7-12

➢ During electron transport, protons move across the thylakoid

membranes from the stroma into the thylakoid lumen, generating a
proton gradient.
➢ ATP is synthesised as protons move back across the membrane, from
the thylakoid lumen into the stroma, through the chloroplastic ATP
synthase.
 Carbohydrate Production
in the Chloroplast

➢ Calvin cycle uses

NADPH & ATP produced
during the light reactions
for the synthesis of
carbohydrates from
atmospheric CO2 in the
stroma.
➢ The enzyme Rubisco =
ribulose 1,5-bisphosphate
carboxylase/oxygenase
catalyses the first reaction
in the Calvin cycle
➢ Rubisco is the most
abundant enzyme in the
world.
Raven et al. (05) Biology of Plants, Fig 7-9
 Cytoskeleton
- Overview
➢ a network of protein filaments
that extends throughout the
cytoplasm

Functions:
➢ support, shape, motility,
intracellular transport,
chromosome movement, cell
division

➢ dynamic - continuously
reorganised

➢ three types of components -

each formed from protein
subunits
▪ actin filaments
▪ intermediate filaments
▪ microtubules Alberts et al. (04) Essential Cell Biology, Fig 17-2
 Cytoskeleton
- Actin Filaments
➢ found in all eukaryotic cells
Functions:
➢ cell shape, movement &
division, vesicular movement,
muscle contraction
Structure:
▪ subunits = globular actin
▪ filaments (7 nm diameter)
twisted into chains
▪ cross-linked bundles &
networks
➢ actin rearrangements within
cells is the molecular basis for
changes in cell shape &
movement Alberts et al. (10) Essential Cell Biology, Fig 17-28;
http://probes.invitrogen.com
 Cytoskeleton
- Intermediate Filaments

Actin 7nm < intermediate 10nm < microtubules 25nm

Structure:
➢ subunits = heterogeneous family of
proteins collectively called intermediate proteins
➢ twisted together into rope-like structures
➢ toughest of the cytoskeletal components

Found in:
➢ Cytoplasm of most animal cells
▪ network surrounding nucleus, extends
to cell periphery
➢ Nucleus
▪ make up the nuclear lamina, which
strengthens the nuclear envelope
▪ mesh-like
▪ attachment sites for chromatin

Alberts et al. (10) Essential Cell Biology, Figs 17-2, 17-7

 Cytoskeleton
– Microtubules

Found in all eukaryotic cells

Structure
➢subunits = tubulin - dimers of -
& - tubulin
➢dimers stack into filaments,
which form walls of stiff hollow
tubes (25 nm in diameter)
Function
➢ intracellular organisation &
transport, mitosis, cilia & flagella
Location
➢ extend from an organising
structure, e.g. centrosome,
spindle pole, basal body

Alberts et al. (10) Essential Cell Biology, Figs 17-8 17-9;

http://probes.invitrogen.com