Chapter 4: Cell Structure

PROKARYOTIC & EUKARYOTIC CELLS

Cell Theory
The cell theory includes the following three principles:
1. All organisms are composed of one or more cells, and the life processes of
metabolism and heredity occur within these cells.
2. Cells are the smallest living things, the basic units of organization of all
organisms.
3. New cells arises only by division of pre-existing cells.

Cells vary in size and shape. Except for vertebrate eggs, which can typically be seen with the
unaided eye, most cells are microscopic in size. Prokaryotic cells are generally 1 to 10 μm
across. Eukaryotic cells are 10 to 100 μm.

Common unit of length measurement:

1 m = 102 cm = 103 mm = 106 μm = 109 nm
To overcome the limitations of our eyes, modern microscopes use 2 magnifying lenses. The
first lens focuses the image of the object of the second lens which magnifies it again and
focuses it on the back of the eye. Microscopes that magnify in stages are known as
compound microscopes

Electron microscopes are also used.

All cells:

 Have centrally located genetic material:

 Nucleoid in prokaryotes
 Membrane bound nucleus in eukaryotes

 Contain a semi-fluid matrix

 Called the cytoplasm
 Made up of organelles and cytosol

 Have a plasma membrane

 A Phospholipid bilayer
 About 5-10nm thick with proteins embedded in it

There are two basic cellular architectures:

1. Prokaryotic cells
Absence of membrane-bounded nucleus that contains genetic material

2. Eukaryotic cells
Presence of membrane-bounded nucleus that contains genetic material
Structural Characteristics of Prokaryotic Cells

 Prokaryotes are the simplest organisms, all are unicellular

 Have centrally-located nucleoid (a region that contains most of the genetic material),
most of the genetic material exists as a single circular molecule of DNA.
 Consist of cytoplasm surrounded by a plasma membrane, encased within a rigid cell
wall
 Have no distinct interior compartments
 Contain ribosomes but most lack the membrane-bounded organelles
 The plasma membrane of a prokaryotic cell carries out some functions organelles
perform in eukaryotic cells such as photosynthesis.
 Two main domains of prokaryotes:
o Archaea
o Bacteria

The General Structure of Bacteria

 They have a centrally located nucleoid, and their genetic material exist as a single
circular DNA molecule
  Nucleoid is not segregated from the cytoplasm with a membranous structure
 Contains ribosomes in the cytoplasm
 Encased by a cell wall composed of peptidoglycan (carbohydrates matrix cross-linked
by short polypeptide units/amino acids), which protect the cell, maintain its shape,
and prevent excessive uptake or loss of water
 Some bacteria also secrete a jelly-like, protective capsule of polysaccharide around
the cell
 Some bacteria possess a flagella which is long threadlike structures for locomotion
 Some bacteria have hair-like growths, called pili, on the outside of the cell

Archaea
 Archaea do not have peptidoglycan cell walls
 Their cell walls are composed of various chemical compounds, including polysaccharides
and proteins, and possibly inorganic components

Structural Characteristics of Eukaryotic Cells

For the first 1 billion years of life on Earth, all organisms were prokaryotes, cells with very
simple interiors. About 1.5 billion years ago, a new kind of cell appeared for the first time,
the eukaryotic cell. Eukaryotic cells are much larger than and profoundly different from
prokaryotic cells, with a complex interior organization. All cells alive today, except bacteria
and archaea, are of this new kind.

 Unicellular (e.g. protozoa, algae) or multicellular (e.g. plants, animals)

 Have membrane bound nucleus which contains the DNA
 Possess cytoplasm, plasma membrane and ribosomes (similar to prokaryotic
cells)
 Highly compartmentalized: Contains membrane bound organelles and
extensive endomembrane system
 Possess a cytoskeleton for support and to maintain cellular structure
Structure of an animal cell:
The plasma membrane encases the animal cell, which contains the cytoskeleton and various
cell organelles and interior structures suspended in a semifluid matrix called the cytoplasm.
Structure of a plant cell:

Most mature plant cells contain large central vacuoles that occupy a major portion of the
internal volume of the cell, as well as organelles called chloroplasts, within which
photosynthesis takes place.

**Note:
 The cells of plants, fungi, and some protists have cell walls.
 Contrast to animal cells, centrioles are absent in plant and fungal cells.
Structure and function of cells

Nucleus

 Mostly spherical in shape

 Typically located in the centre of the cell
 Bounded by nuclear envelope
 Contains genetic material (DNA) in the form of chromatin
 Site of transcription, for synthesis of messenger RNA (mRNA)
 Nucleolus: area within the nucleus which represent region of intensive ribosomal
RNA (rRNA) synthesis and site where ribosomes are produced

The large rounded structure is surrounded by a double membrane. Nuclear pores can be
seen clearly at intervals along the nuclear membrane. The lighter portions represents the
chromatin. The dark structure is the nucleolus.

Function:

 Directs cellular function (growth and reproduction)

 Contains DNA (genetic materials) in the form of chromatin
 Site of mRNA synthesis by transcription, which carries genetic material out of the
nucleus (in the cytoplasm)
Nuclear Envelope

 Made up of two phospholipid bilayer: inner and outer membrane

 Outer membrane of the nuclear envelope is continuous with the endoplasmic
reticulum (ER) in the cytoplasm
 Nuclear pores allows ions and small molecules to diffuse freely between the nucleus
and the cytoplasm

Ribosomes

 Found in all 3 domains of life: archaea, bacteria, eukaryotes

 Attach to mRNA and serve as the site of protein synthesis in the cytoplasm
 The ribosomes associated with membranes AKA Membrane-associated ribosomes
synthesize: Integral membranous proteins, Lysosomal proteins, Proteins destined for
export out of the cell.
 The ribosomes lying freely in the cytoplasm AKA Free Ribosomes synthesize: Proteins
that are destined for the cytoplasm nucleus and mitochondria
 Prokaryotes have smaller ribosomes (70S)
  Eukaryotes have larger ribosomes (80S)
 Composed of 2 subunits: 1 large and 1 small
 Each subunit is composed of many:

1. ribosomal RNA (rRNA)

2. ribosomal proteins

Endomembrane System

The endomembrane system of eukaryotic cells is composed of:

1. Rough endoplasmic reticulum (RER)

2. Smooth endoplasmic reticulum (SER)
3. Golgi apparatus

Endoplasmic Reticulum (ER)

 The largest network of internal membranes in eukaryotic cells

 Made up of phospholipid bilayer embedded with proteins
 Two types of ER:

1. Rough endoplasmic reticulum (RER)

2. Smooth endoplasmic reticulum (SER)
 Rough endoplasmic reticulum Smooth endoplasmic reticulum
Network of membranes that form into Appears like a network of tubules
flattened sacs
Studded with ribosomes on the surface Relatively few bound ribosomes

**organelles with a membrane :MCPLVV -> mitochondria , chloroplasts,

peroxisome, lysosome ,vacuoles, vesicles (Most Clever People Love “Vix
Vapor rub”)

Functions of Endoplasmic Reticulum

Rough endoplasmic reticulum (RER)

 Membrane-bound ribosomes are site of protein synthesis
 The RER modifies newly synthesized proteins by the addition of short-chain
carbohydrates to form glycoproteins
 Proteins are folded into their tertiary structures
 The proteins are transported in vesicles which bud off the RER and are
transported to the Golgi apparatus for further modification.
Smooth endoplasmic reticulum (SER)
 The membranes of SER contains many embedded enzymes, which catalyse the
synthesis of a variety of carbohydrates, lipids
 Assembly site of the majority of membrane lipids
 Lipids are packaged in transport vesicles which then migrate to the Golgi apparatus.
 Site of:
o steroid hormones synthesis and storage
o calcium ion (Ca2+) storage
o detoxification by modifying foreign substances such as toxins and drugs
with the enzyme of SER

RER SER
Has Ribosome on membrane surface Has no ribosomes on membrane surface
(ribosomes) produces proteins Produce lipids (E.g. fatty acids, phospholipids,
steroids)
Within the membrane: Within the membranes:
 proteins are folded into their tertiary structures  Lipid hormones are produced/stored (E.g. testes
 Short carbohydrate chains may be attached to cells -> testosterone)
the proteins -> glycoproteins  Drugs and toxins are detoxifies (e.g. liver cells)
 Stores Ca2+ ions (E.g. muscle cells)
Proteins are packaged in transport vesicles which Lipids are packaged in transport vesicles which then
then migrate to Golgi apparatus, the cell surface or migrate to the Golgi apparatus.
secreted outside the cell.
Golgi apparatus

 Flattened stacks of membranes, often interconnected with one another. Concave in

shape on the trans face and convex in the shape on the cis face.
 Proteins and lipids manufactured from the rough and smooth ER membranes are
transported in transport vesicles into the Golgi apparatus through the cis face of the
GA
 Short sugar chains are added to proteins and lipids to form glycoproteins and
glycolipids as they pass through the Golgi apparatus
 The modified proteins or lipids are packaged into membrane bound secretory
vesicles or digestive vesicles that pinch off from the trans face of the GA
Protein transport through the endomembrane system: Proteins synthesized by ribosomes
on the RER are translocated into the internal compartment of the ER. These proteins may be
used at a distant location within the cell or secreted from the cell.

1. They are transported within vesicles that bud off the rough ER. These transport
vesicles travel to the cis face of the Golgi apparatus. 
2. There they can be modified and packaged into vesicles that bud off the trans face of
the Golgi apparatus. 
3. Vesicles leaving the trans face transport proteins to other locations in the cell, or
they fuse with the plasma membrane, releasing their contents to the extracellular
environment.
Membrane Bound Organelles

Four types of membrane bound organelles will be discussed in this lesson which can
be divided into two groups.

Organelles responsible for degradation and recycling:

 Lysosomes
 Peroxisomes

Energy-processing organelles:

 Mitochondria
 Chloroplasts

**Organelles with double membrane are: Nucleus, mitochondrion and chloroplast.

Lysosomes

 Membrane bound digestive vesicles

 Formed from vesicles budding off the Golgi apparatus
 Contains large amounts of hydrolytic enzymes for the breakdown of proteins,
nucleic acids, lipids and carbohydrates
 Help to breakdown old organelles (autophagy) and phagocytized particles
 Lysosomes are activated by fusing with a food vesicle produced by
phagocytosis or by fusing with an old or worn-out organelle
 The fusion event activates proton pumps in the lysosomal membrane resulting
in a lower internal pH 
 Digestive enzymes within the lysosomes will be activated at low pH and
perform their digestive function

Peroxisomes

 An important type of microbody

 Small, spherical, membrane-bound, enzymes containing organelle
 They are made by the ER and the enzymes are synthesised in the cytoplasm
 Involved in the oxidation of fatty acids and the detoxification of harmful
chemicals
 Generating hydrogen peroxide as a by-product which is harmful to the cell
 Contains the enzyme catalase, which breaks down the harmful hydrogen
peroxide into water and oxygen

Lysosome Peroxisome
Appearance Small, spherical organelle with Small, spherical organelle with
single membrane single membrane
Size 0.5-1.0 micrometres 0.2-1.0 micrometres
Made by? Golgi apparatus Endoplasmic reticulum, with
proteins synthesised in the
cytoplasm
Contents Many types of enzymes Many types of enzymes
Function Break down various Break down (oxidise) fatty acids.
macromolecules. Also break This results in production of
down old (or damaged) organelles hydrogen peroxide (toxic).
and phagocytized particles Detoxification of harmful
containing food or foreign bodies chemicals. E.g. catalase (enzyme)
(like bacteria or viruses that could to further break down hydrogen
harm the cell) peroxide into harmless products
(H20 and O2)
Optimal pH for enzyme activity ~pH5 ~pH 6.9 - 7.1
Mitochondria

 Tubular in shape
 About the size of a bacteria
 Found in all types of eukaryotic cells
 Organelle that metabolizes sugar (glucose) to generate energy-rich molecule
called adenosine triphosphate (ATP)
 Contains circular DNA and protein synthesis machinery
 Mitochondria is able to divide

Mitochondrial membrane

 Surrounded by a double membrane

 Outer membrane: smooth
 Inner membrane: 
o folded with numerous continuous layers called cristae (increase surface area) 
o embedded with proteins that carry out oxidative metabolism
 The inner membrane divide the mitochondria into two compartments: 
 1. Matrix
2. Intermembrane space

Chloroplasts

 Found in plant cells and eukaryotic cells that carry out photosynthesis

 Use light to generate ATP and sugars
 Contains the photosynthetic pigment chlorophyll
 Surrounded by 2 layers of membranes: outer and inner
 Contains DNA

Inside the chloroplast

 Contains closed compartments known as grana which lie inside the inner

membrane (A chloroplast may contain a hundred or more grana)
 Each granum may contain from a few to several dozen disk-shaped structures
called thylakoids
 On the surface of the thylakoids are the light-capturing photosynthetic
pigments
 Surrounding the thylakoid is a fluid matrix called the stroma
  Enzymes used to synthesize glucose during photosynthesis are found in the
stroma

The Cytoskeleton of Cells

Eukaryotic cells can take on an amazing array of shapes, from neurons with projections
running from your spinal cord to your toes to skin cells that appear as compact, elongated
cubes. This flexibility of shape is made possible by a complex internal skeleton, a structure
made even more impressive by the cell’s ability to reorganize portions of it, depending on
the cell’s needs.

Cytoskeleton

 Network of protein fibres found in the cytoplasm of a cell

 A dynamic system in which the protein subunits are constantly assembling and
disassembling
 Made up of 3 types of protein fibres

1. Microfilaments (7nm)
2. Intermediate filaments (8 – 10 nm)
3. Microtubules (25nm)

Functions of Cytoskeleton

 Maintain/change the shape of cell

 Formation of mitotic spindle during mitosis
 Act as molecular motors
 Enable cell movement e.g. flagella, cilia
 Anchor organelles to fixed locations

Microfilaments:

 Long fibres about 7 nm in diameter

 Each filament is composed of two protein chains loosely twined together
 Each subunit on the chain is the globular actin protein
 Actin filaments exhibit polarity: plus (+) end and minus (-) end
o Plus end: the end at which the filament grow in length
o Minus end: the end at which the filament dissociate
 Assembling and disassembling of actin filaments enable cells to change shape quickly
which allow the cells to crawl in cellular processes such as inflammation or spread of
cancer
 Aids in movement of the cell (the actual cell, and it can “crawl” or contract in muscle
cells) Muscle cells also use actin filaments.
 Actin filaments (the network) in most animal cells are found in the region of
cytoplasm at the very edge of the cell. This network is linked to the plasma
membrane. Thus it play a role in structural roles in the cell.
 Actin filaments are also found on the leading edge of a crawling cell, in which rapid
polymerization moves the cell forward.
  For own knowledge: They serve as tracks for the movement of a motor protein
called myosin, thus actin is involved in many cellular events requiring motion such as
cell division

Intermediate filaments:

 A system of tough, fibrous protein molecules twined together in an overlapping

arrangement
 8-10 nm in diameter, between the size of microfilaments and microtubules
 Once formed, very stable and rarely breakdown
 Offers structural support and can mainly be found in the cytoplasm
 It specialises to bear tension and help maintain the shape of the cell and anchoring
the nucleus and other organelles in place.

Microtubules:
  Hollow tubes of about 25 nm in diameter
 Composed of a ring of 13 protein protofilaments
 The subunits of each protofilaments is consisted of the alpha-tubulin and beta-
tubulin dimer globular protein
 In a constant state of flux, continually polymerizing and depolymerizing
 The dimers align such that all the alpha tubulin tails are on one side, called the minus
end
 All the beta tubulin heads are at the other end called the plus end
 Plus end: away from the nucleation centre
 Minus end: towards the nucleation centre
 The dimers usually assemble by layers on top of the plus end.
 Found in centrioles, flagella, cilia
 Made up the mitotic spindle during mitosis
 Involved in intracellular transport, ciliary and flagellar motility, involved in nucleic
and cell division, organization of intracellular structure.
 Most of the microtubules come from the region centrosome which is found near
the middle of the cell, and microtubules radiate outward from it.
 Centrosomes and basal bodies are microtubule-organizing centres.
 Basal bodies are the nucleation site for cilia and flagella

The top figure below shows the basic subunits of microtubules which is a dimer of globular
protein α-tubulin and β-tubulin.
The bottom figure below is a very high magnification TEM picture showing the cross-section
of the microtubules. Count to see if there is 13 protofilaments. Indeed, the figure on top
also shows a total of 13 protofilaments.

This figure shows the 3 types of cytoskeleton in the cytoplasm of the cell and their
association with other cytoplasmic organelles.
Centrioles

 Barrel-shaped organelles found in the cells of animals and most protists

 Occur in pairs, usually located at right angles to each other near the nuclear
membrane
 Area around the centrioles is called centrosome which is found near the middle of
the cell
 Each centriole is composed of nine triplets of microtubules (1 centriole = 9 triplets of
microtubules)
 Involved in the organization of mitotic spindle during cell division
 Serve as the microtubule organizing centre e.g. during cell division
 The centrosomes of plants and fungi lack centrioles but still contain microtubule-
organizing centres.

** Centrioles are usually not found in plant cells. In animal cells they help to organize
microtubules.
Molecular motors

 All eukaryotic cells must move materials from one place to another in the cytoplasm
 Materials can be moved using vesicles
 Vesicles can be transported along microtubules using motor proteins that use ATP to
generate force
 The vesicles are attached to motor proteins by connector molecules
 For example: Dynein (motor protein) and dynactin complex (binding protein
between vesicle and dynein) moves vesicles to the minus end of microtubules
(toward the centre of the cell)

Flagella and Cilia

 Made up of microtubules in a 9+2 structure (A circle of 9 microtubule pairs

surrounding 2 central microtubules) in eukaryotic cells
 The base of flagella, known as the basal body is made up of an outer circle of 9
microtubule triplets but don’t have 2 central microtubules in the centre
 Move in an undulating motion
 Cilia is shorter than flagella

DIFFERENCES Centrioles Flagella

Appearance Barrel-shaped organelle Whip-like organelle
Occurrence In pairs , located at right Occur singly, in tufts or along the
angles to each other within circumference, external of the cell
the cell cytoplasm
 SIMILARITIES Centrioles Flagella
Structure Consists of 9 triplets of Basal body (9+0)
microtubules
- A circle of 9 triplets of
microtubules

Flagellum (9+2)

- A circle of 9 pairs of
microtubules+ 2 central
microtubules

Flagella and cilia. A eukaryotic flagellum originates directly from a basal body. The flagellum
has two microtubules in its core connected by radial spokes to an outer ring of nine paired
microtubules with dynein arms (9 + 2 structure). The basal body consists of nine
microtubule triplets connected by short protein segments. The structure of cilia is similar to
that of flagella, but cilia are usually shorter.
Plant Cell Wall

The cells of plants, fungi, and many types of protists have cell walls, which protect and
support the cells. The cell walls of these eukaryotes are chemically and structurally different
from prokaryotic cell walls. In plants and protists, the cell walls are composed of fibres of
the polysaccharide cellulose, whereas in fungi, the cell walls are composed of chitin.

Component of cell wall:

1. Plants and protists – cellulose

2. Fungi – chitin
3. Bacteria - peptidoglycan

Plant cell wall

 Thick, strong and rigid

 Made up of the polysaccharide cellulose
 Primary cell wall: outer layer, laid down when the cell is still growing
 Secondary cell wall: inner layer, deposited inside the primary wall of fully expanded
cell
 Middle lamella: sticky substance that glue the cells together
Cell Communication Junctions

There are 3 categories of cell junctions: 

1. Adhesive junctions 
2. Septate/tight junctions
3. Communication junctions

Adhesive junctions

 Mechanically attaches cytoskeleton of a cell to the cytoskeleton of other cells or to

the extracellular matrix
 Found in tissue subject to mechanical stress, such as muscle and skin epithelium

3 types of adhesive junctions:

a) Adherens junctions
b) Desmosomes
c) Hemidesmosomes

Septate/Tight junction

 Form a barrier that can seal off a sheet of cells

 Occlude substances from passing between cell

Communication junction

 Allow communication between cells through small openings

 Small molecules like glucose, amino acids or ions can diffuse across between cells
(but not organelles)

a) Gap junction (in animal)

b) Plasmodesmata (in plant)
The diagram of gut epithelial cells on the right illustrates locations of common cell junctions
between 2 adjacent cells.

The detailed models on the left show the structures of the three major types of cell
junctions:
(a) Tight junction
(b) Adhesive junction—the example shown is a desmosome
(c) Communicating junction—the example shown is a gap junction
Adherens Junction

 A type of adhesive junction

 Cells are connected together through the interaction of extracellular domains of
the cadherin molecules on the cell surface
 The cytoplasmic domain of the cadherin molecule interact with actin filaments in the
cytoplasm
 The cadherin molecule is anchored to actin in the cytoskeleton and passes through
the membrane to interact with the cadherin of an adjoining cell.
 Cadherin is a type of cell adhesion molecule important in the formation of adherens
junction that bind cells together
Gap Junction

 Communication junction found in animals

 Small openings/channels found on the plasma membrane
 Allow diffusion of small molecules such as glucose, amino acids or ions between
adjacent cells
 Formed by 6 identical transmembrane proteins known as connexons which are
arranged in a circle to create a channel through the plasma membr ane

Plasmodesmata

 Found in plant cells

 Specialized openings in their cell walls
 Due to openings in cell walls, cytoplasm of adjoining cells is connected
 Allow diffusion of small molecules such as glucose, amino acids or ions between
adjacent cells
 Lined with plasma membrane and contain a central tubule that connects the ER of
the two cells
 Cell to cell connections summary

Adhesive junctions Septate or Tight Communication

junctions junctions

Examples a) Adherens junctions a) Gap junctions

b)Desmosomes b)Plasmodesmata

c)Hemidesmosomes

Examples Mechanically attach Form a barrier that Allow communication

cytoskeletons of can seal off a sheet of between cells by
neighbouring cells, cells. diffusion through
mediated (helped) by small openings.
cadherin.