CHAPTER 3

ULTRASRTUCTURE AND
FUNCTION OF THE CELL

HMM/SCM1414 1
3.1 The Cell
Basic Unit of structure & function.

Basic
Lowest level of biological

Lowest
organization that can perform
activities for life.

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 Level Definition
Biosphere All the environment of plane Earth that is inhabited
↑ by life.
Ecosystem Biotic factors in an area together with abiotic factors
↑ of the environment.
Community All the organisms in the system.
↑
Population All interbreeding individuals of one species.
↑
Organism An individual living thing (entity).
↑
Organ systems A group of organs that work together in performing
↑ vital body functions.
Organ A specialized center of body function composed of
↑ several types of tissues.
Tissue An integrated group of cells with a common
↑ function, structure, or both.
Cell Life’s fundamental unit of structure and
↑ function.
Macromolecule A giant molecule formed by joining smaller
↑ molecules, usually by a condensation reaction.
Molecule Two or more atoms held together by covalent
↑ bonds.
Atom The smallest unit of matter that retains the
↑ properties of an element.
Sub-atomic particle An elementary particle smaller than an atom
(Protons, neutrons, electrons).

(Refer Figure 1.3, Campbell)

(Also: http://fig.cox.miami.edu/~cmallery/150/scimeth/levels.htm)
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 3.1.1 Characteristics of Cells
All cells have:
1. Plasma membrane
Regulates passage of materials.
Selectively permeable.
2. Cytosol
Cytoplasm – entire cell’
cell’s content, minus
nucleus, & bounded by plasma membrane.
Cytosol – semi- fluid portion of cytoplasm.
3. Chromosome
DNA – genetic information.
4. Ribosome
Protein synthesis.
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3.1.2 The Cell Theory
From: http://fig.cox.miami.edu/~cmallery/150/unity/cell.text.htm

Matthias Schleidon & Theodor Schwann (1839):

“All organisms are composed of similar

units of organization called cells.”
• Three conclusions (tenets):
1. The cell is the unit of structure, physiology,
& organization in living things.
2. The cell retains a dual existence as a
distinct entity, & a building block in the
construction of organisms.
3. Cells form by free- cell formation
(spontaneous generation).
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• Tenet # 3 corrected by Rudolph Virchow:
Virchow:
“Omnis cellula e cellula”
cellula”

All cells only arise from pre-
pre-existing cells.

Modern tenets of cell theory:

1) All known living things are made up of cells.
2) The cell is the structural & functional unit of all
living things.
3) All cells come from pre-
pre-existing cells by
division.
4) Cells contain hereditary information which is
passed from cell to cell during cell division.
5) All cells are basically the same in chemical
composition.
6) All energy flow of life occurs within cells.

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Two main forms of cells:

I. Eukaryotic
Larger in size.
DNA in nucleus.
Membrane-
Membrane-bound organelles in
cytoplasm.
2. Prokaryotic
Simpler & smaller.
DNA in nucleoid.
No membrane-
membrane-bound organelles.
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3.1.3 Prokaryotic Cell
Example: 10µm diameter
Bacteria: 1 - 10µ
Mycoplasma: 0.1 - 1 µm
Mycoplasma:
Internal structure:
1) Nucleoid
Single circular DNA. No membrane.
2) Ribosomes
Smaller than in eukaryotes.
3) Storage granules
Stores nutrients & reserves.
4) Endospore
Highly resistant.
5) Cytoplasm
Gel-
Gel-like matrix - contains cell structures,
including plasmids in some prokaryote.
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Surface Structure:
1) Capsule
Jelly-like outer coating - polysaccharide,
protein.
For protection.
2) Plasma membrane
Lipid bilayer.
Proteins – transport across membrane.
3) Cell Wall
Peptidoglycan (polysaccharide + protein).
Maintains shape of bacteria.

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Appendages
1) Pili (fimbriae)
fimbriae)
Hollow hair-
hair-like attachment
structures.
Specialized pilus (singular)–
(singular)– sex
pilus.
pilus
2) Flagella
Locomotion.
One, a few, or many per cell.

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3.1.3 Prokaryotic
Pili Cell

Nucleoid

Ribosomes

Plasma
membrane

Cell wall
Bacterial
chromosome Capsule
0.5 µm
Flagella

A typical A thin section through the

rod-shaped bacterium Bacillus
bacterium coagulans (TEM)

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3.1.4 Eukaryotic Cell
Eukaryotic cell contains:
1. Plasma membrane
2. Cytoplasm
3. Membrane-
Membrane-bound organelles
4. Cytoskeleton.

 Plant & animal cells have most

of the same organelles.
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Eukaryotic cells:
• 10- 100 µm.
• Chromosomes within nuclear membrane.
• Membrane - bound organelles – partition cell
into compartments:
Membrane participates in metabolism.

Membrane
Compartments – different local environment

Compartments
→ facilitate specific metabolic function.
Structure:

Structure:
 Lipid bilayer
 Other lipids & proteins – embedded or
attached.

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 ENDOPLASMIC RETICULUM (ER
Nuclear envelope
Flagellum Rough ER Smooth ER
Nucleolus NUCLEUS

Chromatin

Centrosome
Plasma membrane

CYTOSKELETON

Microfilaments

Intermediate filaments

Microtubules

Ribosomes:

Microvilli

Golgi apparatus

Peroxisome

Mitochondrion
Lysosome

In animal cells but not plant cells:

Lysosomes
Centrioles
Flagella (in some plant sperm)
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 Nuclear
envelope Rough
NUCLEUS Nucleolus endoplasmic
reticulum
Chromatin
Smooth
Centrosome endoplasmic
reticulum

Ribosomes
(small brown dots)

Central vacuole
Golgi
apparatus
Microfilaments
Intermediate CYTOSKELETON
filaments
Microtubules

Mitochondrion
Peroxisome
Plasma Chloroplast
membrane

Cell wall
Plasmodesmata
Wall of adjacent cell
In plant cells but not animal cells:
Chloroplasts
Central vacuole and tonoplast
Cell wall
Plasmodesmata
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 3.1.5 Organelles – Structure & Functions

1) Nucleus
• 5 µm diameter.
a) Nuclear envelope

Double membrane.

Space between membrane: 20- 40 µm.

Perforated by pores 100 nm diameter.

Pore complex – regulates entry/exit of
macromolecules & particles

Inner surface lined by nuclear lamina.
lamina.

Contiguous with ER.

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b) Chromosomes
 Carry genes.
 Made up of chromatin = DNA +
proteins.
 Coils (condense) & thickens
during division.
 Specific chromosome number:
 Human: 46
 Drosophila: 8

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c) Nucleolus
 Densely stained granules & fibers.
 Non-
Non-membranous.
 One or more per nucleus.
 Synthesizes rRNA & ribosomal
subunits.

d) Nucleoplasm (Nuclear sap)

 Nucleus cytoplasm
 Highly viscous.
 Contains nucleotides, enzymes, &
nuclear matrix.

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 Nucleus

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)

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2) Ribosomes
 Made of rRNA + proteins.
 Protein synthesis.
i. Free ribosomes
• In cytosol.
• Proteins for use in cytosol.
ii. Bound ribosomes
• On ER or nuclear envelope.
• Protein for membranes,
packaging, or export.
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Ribosomes ER Cytosol
Endoplasmic
reticulum (ER)
Free ribosomes

Bound ribosomes

Large
subunit

0.5 µm Small
subunit
TEM showing ER Diagram of
and ribosomes a ribosome

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3) Endomembrane system

 Internal membranes system:

a) Plasma membrane
b) Nuclear envelope
c) Endoplasmic reticulum (ER)
d) Golgi apparatus
e) Lysosomes
f) Vacuoles
 Directly continuous or connected via
vesicles.
vesicles.
 Diverse functions & structure

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a) Endoplasmic Reticulum (ER)

Network of membranous tubules and

cisternae (sacs).

Membranes continuous with nuclear
envelope.

Lumen (cisternal space) continuous
with space of nuclear envelope.

Two types:
i. Smooth ER – no ribosomes.
ii. Rough ER – ribosomes on outer
surface.
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Smooth ER

Rough ER Nuclear
envelope

ER lumen
Cisternae

Ribosomes Transitional ER
Transport vesicle
200 nm
Smooth ER Rough ER

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Functions of smooth ER:

• ER rich in metabolic enzymes.

1. Synthesize lipids
2. Detoxify poisons & drugs.

-OH groups added to drug, making
them soluble.
3. Stores calcium ions.

Specialized ER in muscles –
Sarcoplasmic reticulum.
4. Metabolizes carbohydrates.
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Functions of rough ER:

1. Bound ribosomes synthesize

proteins.
2. Produces membrane.
 Membrane factory for cell.

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b) Golgi Apparatus

• Stacks of flattened membranous disks

(cisternae).
• cis face near ER receives materials from
ER.
• trans face buds off vesicles.

• Functions:
1. Modifies products from ER.
2. Manufactures certain macromolecules.
3. Sorts & packages materials into
transport vesicles.
HMM/SCM1414 27
 Golgi
apparatus
cis face
(“receiving” side of
Golgi apparatus)

Vesicles coalesce to
Vesicles move
form new cis Golgi cisternae
0.1 µm
Vesicles also from ER to Golgi
transport certain
proteins back to ER Cisternae
Cisternal
maturation:
Golgi cisternae
move in a cis-
to-trans
direction

Vesicles form and

leave Golgi, carrying
specific proteins to
other locations or to
the plasma mem-
brane for secretion
Vesicles transport specific trans face
proteins backward to newer (“shipping” side of
Golgi cisternae Golgi apparatus) TEM of Golgi apparatus

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c) Lysosomes
• Sac bounded by single membrane.
• Contains hydrolytic enzymes –
work best at pH 5.0.
Hydrolyzes macromolecules.
Hydrolyzes
• Synthesized by rough ER &
modified in Golgi apparatus.

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Functions:
Carry out intracellular digestion.

i. Engulf smaller organisms or

other food particles by
phagocytosis.
phagocytosis.
ii. Recycles cell’
cell’s organelles &
macromolecule by autophagy.
autophagy.
iii. Programmed cell death –
apoptosis.
apoptosis
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 Nucleus 1 µm

Lysosome

Lysosome contains Food vacuole Hydrolytic

active hydrolytic fuses with enzymes digest
enzymes lysosome food particles

Digestive
Plasma enzymes
membrane
Lysosome

Digestion
Food vacuole

Phagocytosis: lysosome digesting food

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 Lysosome containing
two damaged organelles 1 µm

Mitochondrion
fragment
Peroxisome
fragment

Lysosome fuses with Hydrolytic enzymes

vesicle containing digest organelle
damaged organelle components

Lysosome

Digestion
Vesicle containing
damaged mitochondrion
Autophagy: lysosome breaking down
damaged organelle
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d) Vacuoles
• Larger version of vesicles.
• Bounded by single membrane.
• One or more per cell.

HMM/SCM1414 33
Functions of vacuoles:
1.Food
1.Food vacuoles
 Hydrolyzes food particles.

2.Contractile
2.Contractile vacuoles
 Pump excess water out of cell.

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 Central vacuole

Cytosol

Tonoplast

Nucleus Central
vacuole

Cell wall

Chloroplast

HMM/SCM1414 5 µm 35
Functions of vacuoles:

3. Central vacuoles
 In mature plant cells.
 Formed from many smaller
vacuoles.
 Surrounded by tonoplast.
tonoplast.

HMM/SCM1414 36
Functions of central vacuole

1. Stockpiling proteins.
2. Repository of inorganic ions.
3. Disposal site for metabolic by-
by-
products.
4. Stores pigments.
5. Stores defensive compounds.
6. Growth of plant cells.

HMM/SCM1414 37
 Review of the endomembrane system
• Example: Flow of protein destined for secretion
from cell

Protein synthesized on ribosomes


Carbohydrate component added in lumen of ER

(cis
Transport vesicles move glycoprotein to Golgi (cis
face)

Protein further modified in Golgi

(trans
Vesicle transports glycoprotein from Golgi (trans
face) to plasma membrane

Contents released from cell
HMM/SCM1414 38
4) Mitochondria & Chloroplast

 Both convert energy to usable forms.

• Mitochondria:
Mitochondria:
 Cellular respiration.
• Chloroplasts
 In plants & algae only.
Photosynthesis
Photosynthesis
 Have own DNA.
 Semi-
Semi-autonomous organelles.

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a) Mitochondria

• In almost all eukaryotes.

• Size: 1 – 10 µm long.
• Smooth outer membranes &
convoluted inner membranes
infolded into cristae.
cristae.

HMM/SCM1414 40
• Inner membrane creates two
compartments:
i. Intermembrane space
ii. Mitochondrial matrix
• Some metabolic steps of cellular
respiration catalyzed by enzymes
in matrix.
• Cristae provide large surface area
for enzymes that synthesize ATP.

HMM/SCM1414 41
 Mitochondrion

Intermembrane space
Outer
membrane

Free
ribosomes
in the
mitochondrial Inner
matrix membrane
Cristae
Matrix

Mitochondrial
DNA 100 nm
HMM/SCM1414 42
b) Chloroplasts

• A member of a family of organelles

called plastids:
i. Amyloplasts
ii. Chromoplasts
iii. Chloroplasts – contains chlorophyll,
enzymes, & other molecules
involved in photosynthesis.
• 2 x 5 µm.
• In leaves & other green organs of
plants & algae.
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Three compartments:
i. Intermembrane space
ii. Stroma
 Fluid-
Fluid-filled space.
 Contains DNA, ribosomes, &
enzymes.
iii. Thylakoids
 Interconnected sets of flat
membranous sacs.
 Some are stacked atop one another
= grana.
grana.
 Chlorophyll in thylakoid membranes.
HMM/SCM1414 44
 Chloroplast

Ribosomes
Stroma
Chloroplast
DNA Inner and outer
membranes

Granum

1 µm
Thylakoid

HMM/SCM1414 45
c) Perioxisomes
• Specialized metabolic compartments
bounded by single membrane.
• Have enzymes that produce H2O2 &
convert it to H2O.
• Other functions:
i. Break down fatty acids.
ii. Detoxify alcohol & other harmful
substances in liver.
iii. Glyoxysomes convert fatty acid to
sugars in seeds.
HMM/SCM1414 46
 Chloroplast

Peroxisome

Mitochondrion

HMM/SCM1414 1 µm 47
5) Cytoskeleton
• Network of fibers extending
through cytoskeleton.
• Organizes structures & activities
of cell.
• Three types:
a) Microtubules
b) Microfilaments
c) Intermediate filaments

HMM/SCM1414 48
Roles of cytoskeleton:
i. Support

Mechanical support, maintain cell
shape, & provides anchorage.
ii. Motility

Interacts with motor proteins to enable
movement of whole cell, movement of
cilia & flagella, & muscle contraction.

Moves vesicles along microtubules
(“monorails”).

Enables formation of food vacuoles.

Enables cytoplasmic streaming.
iii. Regulation

Regulate biochemical activities.
HMM/SCM1414 49
 Vesicle
ATP
Receptor for
motor protein

Motor protein Microtubule

(ATP powered) of cytoskeleton

HMM/SCM1414 50
a) Microtubules
• Thickest fiber.
• Hollow rod.
• 25 nm diameter; 200 nm – 25 µm long.
• tubulin α- & β-tubulin.
Made of tubulin:

HMM/SCM1414 51
• Functions:
i. Give shape & support to cell.
ii. Guides movement of
organelles.
iii.Separates chromosome
during cell division.
iv.Cell motility – cilia & flagella

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Centrosomes & Centrioles

• In many cells, microtubules grow out of

centrosomes near nucleus.
• Centrosome = “microtubule-organizing
centre”.
• In animal cells, centrosome has a pair
of centrioles, each with 9 triplets of
microtubules arranged in a ring.

HMM/SCM1414 53
 Centrosome

Microtubule

Centrioles

0.25 µm

Longitudinal section Microtubules Cross section

of one centriole HMM/SCM1414of the other centriole 54
Cilia & Flagella
• Cilia:
 Numerous per cell.
 0.25 µm diameter; 2 – 20 µm long.
 Produces “back-and-forth”
movement.
• Flagella:
 One or few per cell.
 0.25 µm diameter; 10 – 200 µm long.
 Produces undulatory (wave-like)
movement.
HMM/SCM1414 55
 Direction of swimming

Motion of flagella 5 µm

Direction of organism’s movement

Direction of Direction of
active stroke recovery stroke

Motion of cilia
15 µm
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Structure of cilia & flagella
• Core microtubules sheathed by plasma
membrane.
• Nine doublets of microtubules arranged
in a ring around a central pair = “9+2”
pattern.
• Outer doublet and central pair held
together by cross-linking proteins &
radial spokes.
• Outer doublets connected by motor
proteins, the dynein arms.

HMM/SCM1414 57
 0.1 µm Outer microtubule Plasma
doublet membrane
Dynein arms
Central
microtubule
Cross-linking
Microtubules proteins inside
outer doublets
Plasma
membrane Radial
Basal body spoke

0.5 µm 0.1 µm
Triplet

Cross section of basal body

HMM/SCM1414 58
b) Microfilaments
• Solid rods - 7nm diameter.
• Consists of twisted chain of
actin subunits.

HMM/SCM1414 59
Role:

i. Structural
 To bear tension – resist pulling
forces within cell.
 Form 3-D network inside plasma
membrane to help support cell’s
shape.

HMM/SCM1414 60
ii. Motility
 Contraction of muscle cells
 Change in cell shape.
 Cleavage furrow in animal cells
during cell division.
 Amoeboid movement.
 Cytoplasmic streaming in plant
cells

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 Muscle cell
Actin filament

Myosin filament
Myosin arm

Myosin motors in muscle cell contraction

Cortex (outer cytoplasm):

gel with actin network
Inner cytoplasm: sol
with actin subunits

Extending
pseudopodium

Amoeboid movement

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 Nonmoving
cytoplasm (gel)
Chloroplast

Streaming
cytoplasm
(sol) Vacuole

Parallel actin
filaments Cell wall

Cytoplasmic streaming in plant cells

HMM/SCM1414 63
c) Intermediate filaments

• 8 -12 nm diameter.
• Fibrous protein supercoiled into
thicker cables.
• Built from keratins.
• More permanent fixtures of
cytoskeleton.

HMM/SCM1414 64
• Functions:
i. Support shape (bearing
tension).
ii. Fix nucleus & organelles in
place.
iii.Forms nucleus lamina.
HMM/SCM1414 65
6) Extracellular Components

• Most cells synthesize and secrete

materials external to plasma
membrane.
• Extracellular structures include:
a) Cell walls
b) Intercellular junctions

HMM/SCM1414 66
a) Cell Wall
• In plants, prokaryotes, fungi, & some
protists.
• 0.1 to several µm thick.
• Made of cellulose microfibrils
embedded in matrix of proteins &
other polysaccharides.
• Mature cell wall –middle lamella,
primary cell wall, & secondary cell
wall.
• Walls perforated by plasmodesmata.

HMM/SCM1414 67
Functions of cell wall:

i. Protects cell.
ii. Maintains its shape.
iii. Prevents excessive uptake of
water.
iv. Supports plant against force of
gravity

HMM/SCM1414 68
 Central
vacuole Plasma
of cell membrane
Secondary
cell wall

Primary
cell wall

Central Middle
vacuole
lamella
of cell

1 µm

Central vacuole
Cytosol

Plasma membrane

Plant cell walls

Plasmodesmata
HMM/SCM1414 69
b) Intercellular Junctions
• Specialized regions of connection
between cells.
Enables neighboring cells to adhere,
interact, and communicate through
direct physical contact.
• Types:
 Plants cells: plasmodesmata
 Animal cells: tight junctions,
desmosomes, & gap junctions

HMM/SCM1414 70
i. Plasmodesmata
Enables cytosol to pass between
cells.
• Water & small solutes (and sometimes
proteins and RNA) pass freely between
cells.

HMM/SCM1414 71
ii. Tight Junctions
 Prevents leakage of extracellular
fluid.

HMM/SCM1414 72
ii. Desmosomes (anchoring junctions)
 Fastens cells together into strong
sheets.

HMM/SCM1414 73
ii. Gap Junctions (Communicating
junctions)
 Provides cytoplasmic channels
between cells for passage of
small molecules.

HMM/SCM1414 74