Chapter 2

Cells
Siti Sabrina Kasri

Learning Objectives
State the cell theory.
Compare and contrast the structures of prokaryotic

and eukaryotic cells.

Describe the structure and function of organelles.

CHAPTER FOCUS
Subtopics

You should be able to understand:

1. Prokaryotic and Eukaryotic (with cell

theory

-Differences between prokaryotic and eukaryotic.

-Differences between plant and animal cells
-Plasma membrane and cytoplasm

*2. Cells Genetic Control Center

Structure and function

-Nucleus
-Ribosomes

*3. The Endomembrane System

Structure and Function for Organelle:

-Nuclear envelope
-Endoplasmic reticulum
-Golgi apparatus
-Lysosomes
-Vacoules
-Peroxisome

*2 and 3: Cell Structures Involved in

Manufacturing and Breakdown
4. Energy Converting Organelles

Structure and Function for Organelle:

-Mitochondria
-Chloroplasts

5. Internal and External Support

Structure and Function of Cytoskeleton (microtubules,

microfilaments, intermediate filaments), Extracellular
Structure (Cell Wall, ECM and Intercellular Junctions)
3

Cells Theory
All organisms are made of cells.

smallest structural unit, simplest collection of matter that can live.

independent functioning cells.
- consists of a nucleus, cytoplasm and various organelles surrounded by
selectively permeable membrane.
Cells= basic unit of life.

all living organisms are made up of one or more cells (unicellular, multicellular).
new cells are formed by the division of pre-existing cells.
cells contain genetic material of an organism which is passed from parent to
daughter cells.
all metabolic reactions takes place within the cells.
Cell structure is correlated to cellular function.

life at cellular level arises from structural order (still remember macromolecules? )
4

1. Prokaryotic and Eukaryotic Cells

1. Prokaryotic and Eukaryotic Cells

The basic structural and functional unit of every organism is one of two types of cells:
prokaryotic or eukaryotic.

Pro: before , Eu: true, Karyon: kernel which refer to the nucleus.
Prokaryotic cells- Only organisms of the domains Bacteria and Archaea.

Eukaryotic cells- Protists, Fungi, Animals, and Plants.

All cells have several basic features in common:
Bounded by a membrane-plasma membrane.
2. Enclosed in the membrane is cytoplasm.
3. Contain chromosomes which carry genes.
4. Have ribosomes- tiny complexes that make proteins according to instructions from gene.
1.

Prokaryotic cells
Prokaryotic cells are characterized by having:
No nucleus not enclosed by nuclear membrane.
DNA in an unbound region called the nucleoid (region where the cellss DNA is

located).
as DNA is not enclosed by nuclear membrane - the DNA coils on itself to form highly
compact supercoiled structure.
the nucleoid - usually found in the center of the cell
- represents about 20% of the cells total volume.
DNA in plasmid- exists separately, contain genes to help cell to survive in different
environment.
No membrane-bound organelles- eg. Mitochondria, chloroplast.

Ribosomes- smaller and differ from those of eukaryotes, synthesize protein.

Cytoplasm bound by the plasma membrane.
Range in size: 1.0-10 m (refer to figure 4.2A, pg no 54, Biology)

Fimbriae/ Pili
Nucleoid
Ribosomes
Plasma membrane
Bacterial
Chromosome

Cell wall
Capsule
0.5 m

(a) A typical
rod-shaped
bacterium

Flagella

(b) A thin section

through the
bacterium
Bacillus
coagulans (TEM)

Structure of prokaryote Description

(Bacteria)
1. Bacterial chromosomes

- Carrying genes containing DNA.

2. Fimbriae/ Pili

- Help attach prokaryotes to the surface.

3. Nucleoid

- Regions where DNA is located.

4. Ribosomes

- Synthesize protein.

5. Plasma membrane

- Membrane enclosing the cytoplasm that function as a selective

barrier.

6. Cell wall

- Rigid and chemically complex cell wall that helps protect the cell
and maintain its shape.

7. Capsule

- A sticky outer coat that surround the cell wall and protects the cell
surface.
- Also help glue prokaryotes to surface (eg sticks, rocks or tissues
within the human body)

8. Flagella

- Locomotion organelles of some bacteria (propel the prokaryotic

cell through its liquid environment).
9

Eukaryotic Cells
Eukaryotic cells are generally much larger than prokaryotic cells- 10 to 100 m.
Eukaryotic are characterized by having basic features of all cells:
Plasma membrane.

function as a selective barrier.

Semifluid substance called cytosol (refer to Raven, pg no 62, part The cytoplasm)

cytoplasmic solution that is semi fluid.

consists of various components (eg water, sugars, amino acids, enzymes, fatty
acids, nucleotides, ATP ,dissolved gas, proteins, microfilaments, microtubule etc).
Chromosomes contain DNA that carry genes.
DNA in a nucleus that is bounded by a membranous nuclear envelope
Membrane bound organelles.
10

Comparison of Prokaryotic and Eukaryotic Cells.

Prokaryotes

Eukaryotes

Size: 1.0-10 m

Size: 10-100 m

No membrane bound organelle

Have membrane bound organelles

No nucleus. The DNA region is called the

nucleoid

True nucleus bounded by a double

membrane.

Has one circular chromosomes composed

of DNA not associated to histone proteins

Most DNA are associated with histone

proteins to form chromosomes

Some bacteria contain plasmids

No plasmid

Most prokaryotes have flagella and they do

not have cilia

May have flagella or cilia

Small size ribosomes: consists of a 50S

subunit and a 30S subunit forming a 70S
ribosome.

Ribosomes are composed of a 60S subunit

and a 40S subunit forming an 80S
ribosome

Rigid cell walls containing murein

(peptidoglycan)

Cell walls: cellulose (plants and algae),

fungi (chitin).
Animal cells have no cell walls.

Cell divides by binary fusion

Cell divides by mitosis and/or meiosis

11

A Panoramic View of the Eukaryotic Cell

A eukaryotic cell has internal membranes that partition the cell into organelles
There are four life processes in eukaryotic cells that depend upon structures and organelles.

i. Manufacturing- nucleus, ribosomes, endoplasmic reticulum, Golgi apparatus.

ii. Breakdown of molecules- lysosomes, vacoules, peroxisome.
iii. Energy processing- mitochondria, chloroplast.
iv. Structural support, movement, and communication- cytoskeleton, plasma membrane,
extracellular structure (cell wall, ECM, intercellular junctions) .

Plant and animal cells have most of the same organelles.

Although there are many similarities between animal and plant cells, differences exist
Lysosomes, centrioles/ centrosome , cilia and flagella are not found in plant cells.
Plant cells have a rigid cell wall and plasmodesmata, chloroplasts, and a central vacuole

that are not found in animal cells.

12

INTRODUCTION OF
CELL

Manufacturing and
breakdown
organelles

Energy
converting
organelles

Network of
fibres
structures
(cytoskeleton

Extracellular
structures

Oxidative
organelle

Peroxisome

Endomembrane
system

Nucleus

Nuclear
envelope

Endoplasmic
reticulum

Golgi
apparatus

Lysosome

Vacuole

Plasma
membrane

Ribosome

Mitochondria

Microtubules

Cell wall

Chloroplast

Microfilaments

Extracellular
matrix

Intermediate
filaments

Intercellular
junctions

ANIMAL CELLS
ENDOPLASMIC RETICULUM (ER)
Flagellum

Rough ER

Nuclear
envelope
NUCLEUS

Nucleolus

Smooth ER
Chromatin

Centrosome
Plasma
membrane
CYTOSKELETON:
Microfilaments
Intermediate
filaments
Microtubules
Ribosomes
Microvilli

Golgi
apparatus

Peroxisome
Mitochondrion

Lysosome
14

NUCLEUS

Nuclear envelope
Nucleolus
Chromatin

Rough endoplasmic
reticulum

PLANT CELLS

Smooth endoplasmic
reticulum
Ribosomes

Central vacuole

Golgi
apparatus

Microfilaments
Intermediate
filaments
Microtubules

CYTOSKELETON

Mitochondrion
Peroxisome

Chloroplast

Plasma
membrane
Cell wall
Plasmodesmata
Wall of adjacent cell

15

Comparison of Animal Cells and Plant Cells.

Animal cells

Plant cells

No cell wall, only plasma membrane

Has cell wall composed of cellulose

Irregular shape that is not fixed

Has fixed, regular shape due to presence

of cell wall.

No chloroplast

Has chloroplast

Small vacuoles which may be numerous

Has a large central vacuole with various

function

No tonoplast

Tonoplast around vacuole

Centrioles/ centrosome are present

No centriole

Lysosomes present

Lysosomes absent

No plasmodesmata

Has plasmodesmata

Some cells have cilia or flagella

No cilia and flagella

16

*The Structure of Membranes Correlates With Their FunctionsPlasma Membrane

The plasma membrane controls the movement of molecules into and out of the cell,
a trait called selective permeability.
The structure of the plasma membrane with its component molecules is responsible for

this characteristic.
Plasma membranes are made of lipids, proteins, and some carbohydrate, but the most
abundant lipids are phospholipids.

Phospholipids form a two-layer sheet called a phospholipid bilayer.

Hydrophilic heads face outward, and hydrophobic tails point inward.
Thus, hydrophilic heads are exposed to water, while hydrophobic tails are shielded from

water.

Proteins are attached to the surface, and some are embedded into the phospholipid
bilayer.

17

Hydrophilic head

Phosphate
group

Phospholipid molecule

Symbol

Hydrophobic tails
18

Hydrophilic
heads

Outside cell
Hydrophobic
region of
protein

Hydrophobic
tails
Inside cell

Proteins

Hydrophilic
region of
protein

Phospholipid Bilayer with Associated Proteins.

19

*Cytoplasm
Cytoplasm is the entire region between the nucleus and the plasma membrane.
Jelly like subtance consists of two parts: cytosol (cytoplasmic solution) and cell

organelles (organs of the cell).

Cytosol= semi fluid portion.
Organelles = Structures in the cell that carry out specialised functions.
= All organelles (except nucleus) is part of the cytoplasm.

nucleus is considered as a discrete cellular component due to its

characteristics and important role in the cell.

20

2. Cells Genetic Control Center

21

2. Cells Genetic Control Center

The Eukaryotic cells genetic instructions are housed in the nucleus and carried

out by the ribosomes.

The nucleus contains most of the DNA in a eukaryotic cell.

- The nucleus is spherical in shape and in animal cells, it is typically located

in the central region of the cell.
Ribosomes use the information from the DNA to make proteins.

22

The Nucleus = Cells Genetic Control Center

The nucleus contains most of the cells genes and is usually the most conspicuous
organelle.

The nuclear envelope (that separates nucleus from the cytoplasm) is a double
membrane (each membrane consists of a lipid bilayer that are separated by space of
20-40 nm ) with pores complex (diameter: 100 nm) that allow material to flow in and
out of the nucleus.
It is attached to a network of cellular membranes called the endoplasmic reticulum.

Pores complex regulate the entry and exit of molecules from the nucleus.
At the lip of the each pore, the inner and the outer membrane of nuclear envelope are

continous.
The shape of the nucleus is maintained by the nuclear lamina, which is composed of protein.
Nuclear lamina lines the inner surface of the two nuclear envelope.

The nucleoplasm is the semifluid subtances in the nucleus

23

 The nucleolus is located within the nucleus and is the site of ribosomal RNA
(rRNA) synthesis.
Synthesis of rRNA is according to instructions in the DNA.
- Proteins imported from the cytoplasm are assembled with rRNA into large and small
ribosomal subunits.
- These subunits exits nucleus via nuclear pores to the cytoplasm, where both subunits
(large and small) assembled into a functional ribosome.
-

The nucleus controls the cells activities and is responsible for inheritance
Inside is a complex of proteins + DNA = chromatin, which condense to makes up the

cells chromosomes chromatin appears as diffuse mass.

DNA (in chromosomes) is copied within the nucleus prior to cell division.
Act as a control centre that directs all activities of cell by regulating protein and enzyme
synthesis
- Directs protein synthesis by making messenger RNA (mRNA).
- Assist production of ribosomes (rRNA)

24

1 m

The Nucleus and Its Envelope

Nucleus

Nucleolus
Chromatin
Nuclear envelope:
Inner membrane
Outer membrane

Nuclear pore
Nucleoplasm
Pore
complex

Surface of
nuclear envelope

Rough ER
Ribosome

1 m

0.25 m

Close-up of nuclear
envelope

Pore complexes (TEM)

Nuclear lamina (TEM)

25

Ribosomes Make Proteins for Use in the Cell and Export

Ribosomes are involved in the cells protein synthesis.
It is particles made of ribosomal RNA and protein.
Ribosomes are synthesized in the nucleolus, which is found in the nucleus.
Cells that must synthesize large amounts of protein have a large number of ribosomes.

eg cells that secrete digestive enzyme in pancreas

Some ribosomes are:

Free ribosomes that are suspended in the cytoplasm.

Bound ribosomes that are attached to the endoplasmic reticulum (ER) associated with the

nuclear envelope.
Both are structurally identical.

26

 Ribosomes carry out protein synthesis in two locations:

In the cytosol (free ribosomes).
On the outside of the endoplasmic reticulum or the nuclear envelope (bound ribosomes).

Free ribosomes

proteins made by these ribosomes function within the cytosol.

eg, enzymes that catalyze the first steps of sugar breakdown.

Bound ribosomes

proteins made by these ribosomes:

1. are destined for insertion into membranes
2. for packaging within certain organelles such as lysosomes or
3. for export from the cell (secretion).
eg, cells of pancreas that secrete digestive enzymes.

27

Ribosomes
ER

Cytoplasm
Endoplasmic reticulum (ER)
Free ribosomes
Bound ribosomes
Large
subunit

TEM showing ER
and ribosomes

Diagram of
a ribosome

Small
subunit

28

Cytosol
Endoplasmic reticulum (ER)
Free ribosomes
Bound ribosomes

Large
subunit

0.5 m
TEM showing ER and ribosomes

Small
subunit

Diagram of a ribosome
29

3. The Endomembrane System

30

3. The Endomembrane System

The endomembrane system consists of set of organelles that involved in synthesis of
proteins and their transport into membranes and organelles or out of the cell.
- One of the fundamental distinctions between eukaryotes and prokaryotes.

The membranes within a eukaryotic cell are physically connected and compose the
endomembrane system.
regulates protein traffic and performs metabolic functions in the cell.
1. Synthesis of proteins and their transport into membranes and organelles or out
of the cell.
2. Metabolism and movement of lipids.
3. Detoxification of poisons.

Components of the endomembrane system:

Nuclear envelope
Endoplasmic reticulum
Golgi apparatus
Lysosomes
Vacuoles
Plasma membrane (not actually an endomembrane in physical location but nevertheless

related to the endoplasmic reticulum and other internal membrane).

These components are either continuous or connected via transfer by vesicles.

31

The Endoplasmic Reticulum: Biosynthetic Factory

The endoplasmic reticulum (ER) accounts for more than half of the total membrane in
many eukaryotic cells.

Endoplasmic: within the cytoplasm, reticulum: little net

The ER membrane is continuous with the nuclear envelope.
- It consists of a network of membranous tubules and flattened sacs called cisternae.
- The ER membrane separates the internal compartment of the ER= ER lumen/ cisternal space.

There are two distinct regions of ER:

Smooth ER, which lacks ribosomes, in the form of interconnected tubes and not

flattened sac.
Rough ER, with ribosomes studding its surface.

Both smooth ER and rough ER:

They differ in structure and function.
However, they are connected.

32

Smooth ER
Rough ER

ER lumen
Cisternae
Ribosomes
Transport vesicle
Smooth ER

Nuclear
envelope

Transitional ER
Rough ER

200 nm

33

 The smooth ER:

Functions of Smooth ER

Synthesizes lipids

- has enzymes in smooth ER for the synthesize of lipids including oils, phospholipids and steroid.
Metabolizes carbohydrates

- certain enzymes in smooth ER in the liver help regulate the amount of sugar released from liver
cells into the bloodstream.
Detoxifies drugs and poisons

- enzymes in the smooth ER help detoxify drugs and poisons especially in the liver cells.
- detoxification involves adding hydroxyl groups to drug molecules, making them more soluble and
easier to flush out from the body.
-eg alcohols, sedative phenobarbital and other barbiturates are examples of drugs metabolized in
this manner by smooth ER and its associated detoxification enzymes.
Stores calcium

- due to specialised form of smooth ER known as the sarcoplasmic reticulum, it is the site of
storage and release of calsium ions in muscle cells important in contraction of the cell & cell
signalling.
34

Functions of Rough ER
The rough ER:
1.

Has bound ribosomes, synthesize protein.

-as polypeptide chain grows from a bound ribosome, it is threaded into the ER
lumen through a pore.
- in the ER lumen, the new protein (now known as secretory protein) folds into
its native shape and is stored there temporarily.
- a short carbohydrate chain (an oligosaccharide) is added to the protein
converting it to glycoproteins.

35

Functions of Rough ER
The rough ER:
2.

Distributes transport vesicles.

-The ER membrane keeps secretory protein separate from the proteins that
are produced by free ribosomes.
- Once secretory proteins are formed, the molecules are ready for export
from the ER.
- The secretory proteins will moved to specialised region of the rough ER=
transitional ER.
- At the transitional ER, the secretory protein packaged into tiny sacs called
transport vesicles.
- The transport vesicles then bud off from the ER membrane like bubbles and
travel to the Golgi apparatus for further processing.

36

Functions of Rough ER
Rough ER:

3. Is a membrane factory for the cell

- some of the proteins made by the ER ribosomes are inserted into the ER
membrane.
- it grows in place by adding membrane proteins (anchored there by its
hydrophobic portion) and phospholipids to its own membrane.
- as a result, the ER membrane enlarges and some of it can be transferred to
other organelles as well as the plasma membrane through transport vesicles.

37

Synthesis and Packaging of a Secretory Protein by the Rough ER.

Transport vesicle
buds off

Ribosome

Secretory
protein
inside transport vesicle
3

Sugar
chain

1
2 Glycoprotein

Polypeptide
Rough ER
38

The Golgi Apparatus: Shipping and

Receiving Center
Name after Camillo Golgi.

The Golgi apparatus finishes, sorts, and ships cell products.

- center of manufacturing, warehousing, sorting and shipping.

The Golgi apparatus consists of flattened membranous sacs (stack of pita bread) called
cisternae.

- contains 4-7 cisternae/stack that separated its internal space from cytosol.
- a Golgi stack has a distinct polarity:
cis face- convex shape cisternae, receiving departments, located near the ER.
trans face- concave shape cisternae, shipping departments of the Golgi apparatus.
-vesicles that bud from ER add its membrane and contents of its lumen to the cis face by fusion
with a Golgi membrane.
- the trans face give rises to vesicles, which pinch off and travel to the other sites.

39

 Functions of the Golgi apparatus:

Modifies products of the ER.

- Products travel in transport vesicles from the ER to Golgi apparatus.

- Products are modified as they go from cis face of the Golgi apparatus to the trans face
and travel in vesicles to other sites.
Golgi apparatus receives vesicles from ER. Vesicles that has glycoprotein shall be
modify by various enzyme in Golgi by modifying carbohydrate portion of
glycoprotein.
Manufactures certain macromolecules by itself.

- Like secretory proteins, non protein Golgi products that will be secreted depart from the
trans face of the Golgi (inside transport vesicles) will fuse with the plasma membrane.
- Eg: Many polysaccharides secreted by cells are Golgi products (such as pectin in plant)
Sorts and packages materials into transport vesicles.

- Before a Golgi stack dispatches its products by budding vesicles from the trans face,
molecular identification tags (eg, phosphate groups) are added to the Golgi products.
- Finally, transport vesicles budded from the Golgi have external molecules on their
membranes which recognized docking sites (on the plasma membrane), thus targetting
the vesicles destination (to plasma membrane or to cytosol) appropriately.
40

cis face
(receiving side of
Golgi apparatus)

0.1 m
Cisternae

Transport
vesicle from
the Golgi
trans face
(shipping side of Golgi apparatus)

TEM of Golgi apparatus

The Golgi apparatus is abundant in secretory cells and in rapidly dividing cells eg,
pancreatic cells, cells in testes and ovaries.

41

Lysosomes: Digestive Compartments

Lysosomes are digestive compartments within a cell.
Under the electron microscope, lysosomes appear as dark spherical bodies in the
cytoplasm.

- Diameters are smaller than mitochondria.

A membranous sac of hydrolytic enzymes that can digest macromolecules.
The fluid within the lysosome is highly acidic. It contain enzymes that work best in acidic

environment. What happen if this enzyme leaks to cytosol? Think!!!!!!

The enzymes and membrane of lysosomes are produced by the ER and transferred to the
Golgi apparatus for further processing.
The Golgi apparatus chemically refines the enzymes and releases mature lysosomes to
cytosol.
The membrane of lysosomes safely isolate these potent enzymes from the rest of the cell.
it has a single membrane that can prevent leakage of enzymes and able to resist digestion.
illustrate the main theme of the eukaryotic cell structure: compartmentalisation
this is important as excessive leakage of enzyme from a number of lysosomes can lead to
the autodigestion of the cell. However autodigestion is essential during embryonic
development.
42

 Main function (IMPORTANT !!!!)

- the lysosomes enzymes involves in

i. hydrolyzing macromolecules (food).

ii. breaking down the pathogens (defense system), eg bacteria.

iii. breaking down worn-out/damaged organelles.

- i and ii - via phagocytosis by forming a food vacuole.

- a lysosome fuses with the food vacuole and digests the molecules.
- iii via autophagy : Recycle the cells own organelles, thus helping cell to continually renews itself.
The damaged organelle is first enclosed in a double membrane (vesicle).
Then a lysosome fuses with the vesicle, dismantling its contents and breaking down the damaged

organelle.

43

Nucleus

1 m

Vesicle containing
two damaged organelles

Lysosome contains
active hydrolytic
enzymes.

1 m

Mitochondrion
fragment
Peroxisome
fragment

Lysosome

Lysosome

Digestive
enzymes

Lysosome

Plasma
membrane

Peroxisome
Digestion
Food vacuole

(a) Phagocytosis

Food vacuole fuses

with lysosome

Vesicle

Mitochondrion

Digestion

(b) Autophagy

Hydrolytic enzymes
digest food particles.

Lysosome fuses with

vesicle containing
damaged organelles.

Hydrolytic enzymes
digest organelle
components.
44

Vacuoles: Diverse Maintenance Compartments

Vacuoles are membranous sacs that are found in a variety of cells and possess an
assortment of functions. It is bounded by single membrane.

- eg vacuoles: central vacuole, contractile vacuole and food vacuole.

Central Vacoule
A plant cell or fungal cell lack lysosomes. Thus, they have central vacuole.
- Single membrane that surrounds the vacuole is called the tonoplast. The fluid within the vacuole
is called cell sap.
- Central vacuole carry out hydrolysis (like lysosome), however they play other roles as well.
- The other roles:
= Hold important organic compounds, eg proteins stockpiled in the vacuoles of storage
cells in seeds.
= Main repository inorganic ions, eg pottasium, sodium.
= Disposal sites for metabolic by product that would endangered in the cell if they
accumulated in cytosol. Eg, Tannin.
= Colour the cell because they hold pigment.
= Protect the plant against predators by containing compound that are poisonous or
unpalatable to animals .
45

 Tonoplast

- Semipermeable membrane.
- Actively transport of certain ions into the vacuole.
-As vacuole contain hydrolytic enzyme too, the tonoplast just like other
membranes will lose its semipermeability after cell death and release enzymes
from the vacoule, causing autolysis of the cell.
Cell sap

- is a concentrated solution of mineral salts, sugars, amino acid, wastes (tannin)

and pigments (eg to provide color to flowers).
- generally hypertonic relative to the external medium. This helps plants to absorb
water from its environment by osmosis.

46

Central vacuole

Cytosol

Cell sap
Tonoplast

Nucleus

Central
vacuole

Cell wall
Chloroplast
5 m
47

Contractile Vacoule
Found in many freshwater protists.
Pump excess water out of cells

Nucleus

Contractile
vacuoles
48

Food Vacuole
Formed by phagocytosis. (refer to slide 44 for figure phagocytosis)
Animals and many single cell protozoa (protist) have food vacuoles that contain
food that undergoing digestion.

49

Peroxisomes: Oxidation
A specialized metabolic compartments bounded by a single membrane.
It is not part of the endomembrane system but involved in various metabolic

functions.
Peroxisomes do not bud from the endomembrane system. It grow larger by:

1. Incorporating proteins made primarily in the cytosol

2. Lipids made in the ER, and
3. Lipids synthesized within the peroxisome itself.
Peroxisomes may increase in number by splitting in two when they reach a certain

size.

50

Peroxisomes involvement in Various Metabolic Functions.

To detoxify alcohol and other harmful substances (eg Hydrogen),

peroxisomes produce hydrogen peroxide and convert it to water.

How?
- enzyme in peroxisomes transfer hydrogen from various substrates to oxygen,
producing hydrogen peroxide.
- the hydrogen peroxide is toxic but the organelle also has an enzyme that
converts hydrogen peroxide to water.
Some peroxisomes use oxygen to break down different types of molecules.

- eg, fatty acids are break down into smaller molecules that can be transported
to mitochondria to be used as fuel in cellular respiration.

51

Chloroplast
Peroxisome
Mitochondrion

1 m
52

The Endomembrane System: A Review

The endomembrane system is a complex and dynamic player

in the cells compartmental organization.

53

Nucleus

Rough ER

Smooth ER

Plasma
membrane
54

Nucleus

Rough ER

Smooth ER
cis Golgi

trans Golgi

Plasma
membrane
55

Nucleus
1
Rough ER
2
Smooth ER
cis Golgi

3
Plasma
membrane

trans Golgi
4

6
56

Review Relationships Among Organelles of the Endomembrane

1.

Nuclear envelope is connected to rough ER, which is also continous with smooth ER.

2.

Membranes and proteins produced by the ER flow in the form of transport vesicles to the
Golgi.

3.

Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes, (other
types of specialized vesicles).

4.

Lysosome is available for fusion with another vesicle for digestion.

5.

Transport vesicle carries proteins to plasma membrane for secretion.

6.

Plasma membrane expands by fusion of vesicles; proteins are secreted from cell.

57

CHAPTER FOCUS

Subtopics

You should be able to understand:

4. Energy Converting Organelles

Structure and Function for Organelle:

-Mitochondria
-Chloroplasts

5. Internal and External Support

Structure and Function of Cytoskeleton (microtubules,

microfilaments, intermediate filaments), Extracellular
Structure (Cell Wall, ECM and Intercellular Junctions)

58

4. Energy Converting Organelles

59

Chloroplasts and Mitochondria 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 (a

process of converting light energy to the chemical energy).

60

Mitochondria and Chloroplasts

Are not part of the endomembrane system- both are

semiautonomous organelles that grow and reproduce within

the cell.
- evolved by endosymbiosis.
Have a double membrane.
Contain their own DNA.
Have proteins made by free ribosomes.

61

Mitochondria: Chemical Energy Conversion

Mitochondria occur in all eukaryotic cells.
The word mitochondria means thread granule.
Under the light microscope- it appear as a tiny, rod like

structure in the cytoplasm of almost all cell.

Under the electron microscope- cylindrixal organelles.

The mitochondria

are abundant in cells which are

metabolically active. Eg skeletal muscle cells, spermatozoa,
liver and pancreatic cells.
62

 Mitochondrion structure includes:

1. Bound by a double membrane.

2. They have a smooth outer membrane and an inner membrane folded
into cristae.
- Cristae present a large surface area for enzymes that synthesize ATP due to stalked
particles (sites for ATP synthesis) .

3. The inner membrane creates two compartments: intermembrane space

(narrow region between the inner and outer membrane) and mitochondrial
matrix. Both compartments filled with fluid.

63

Intermembrane space
Outer
membrane

Free
ribosomes
in the
mitochondrial
matrix

Inner
membrane
Cristae
Matrix

0.1 m

64

cristae (fold)

Intermembrane
space

65

 Functions of the mitochondria:

1. Sites of cellular aerobic respirationCellular Power Plants.

-Generate ATP for cellular work from food (eg, glucose).
-Some metabolic steps of cellular respiration are catalyzed in the mitochondrial matrix
( that contains many different enzymes)
- As highly folded surfaces, the cristae give the inner mitochondrial membrane a large
surface area.
ennhancing the productivity of cellular respiration.

2.Replicate during cell division.

66

Chloroplasts: Capture of Light Energy

Plastids are a group of large organelles found in the cytoplasm of all plants but

not in animal cells.

Divided to 3 categories; chloroplasts, chromoplasts and leucoplasts.

Type of Plastids

Descriptions

Chloroplasts

Green coloured plastids, play role in photosynthesis.

Chromoplasts

Coloured plastids rich in pigment (eg carotenoid) that

give fruits, flowers and leaves their orange, red and
yellow colours.

Leucoplasts

Non coloured plastids such as amyloplasts stored starch

in root and tuber, elaioplast stored oil, aleuroplasts stored
protein.

67

 Chloroplast: the most studied due to its important role in photosynthesis.

Chloroplasts are found in leaves and other green organs of plants and in

algae.

Chloroplast structure includes:

1.Size: bigger than mitochondrion (measuring about 2 m and 5 m).
2.Shape: bioconvex disc.
3.Chloroplasts contain the green pigment chlorophyll, as well as enzymes and
other molecules that function in photosynthesis.

68

 Chloroplast structure includes :

4.Consists of an envelope of two membranes (outer membrane and inner
membrane ) separated by a very narrow intermembrane space.
5.Thylakoids
- Membranous system in the form of flattened and interconnected sacs. The
compartment inside these sacs thylakoid space.
- Thylakoids are stacked (like poker chips) to form a granum (plural: grana).
- Connecting one granum to another granum are intergranal lamellae.
- Granum: solar power pack- chlorophyll embedded in membrane.

6. Stroma
- The internal thick fluid of the chloroplast.
- Contains the chloroplast DNA and ribosomes as well as many enzymes.

69

Ribosomes
Stroma
Inner and outer
membranes
Granum
Thylakoid

Intergranal
lamellae

1 m

70

Functions of chloroplasts:
The one and only PHOTOSYNTHESIS as it absorb light

energy and convert to chemical energy.

71

5. INTERNAL AND EXTERNAL

SUPPORT

Cytoskeleton,
Extracellular
Structure
(Cell Wall, ECM and
Intercellular Junctions)
72

Cytoskeleton
The cytoskeleton:

- a network of fibers that organizes structures and activities in the cell,

anchoring many organelles.
- (refer to Fig 4.4A, pg 56, Biology. Look at GA, Rough ER and Plasma
membrane, can you identify cytoskeleton?).
- a network of fibers extending throughout the cytoplasm.
The cytoskeleton is composed of three kinds of fibers

1. Microtubules are the thickest of the three components of the

cytoskeleton
2. Microfilaments, also called actin filaments, are the thinnest components
3. Intermediate filaments are fibers with diameters in a middle range

73

74

Four Roles of the Cytoskeleton in Support, Motility, and

Regulation
1. The cytoskeleton helps to support the cell and maintain its shape.
-important to animal cells that lack cell walls.
-provides anchorage for many organelles and even cytosolic enzyme
molecules.
-cytoskeleton more dynamic to an animal skeleton
can be quickly dismantled in one part of the cell and reassembled in a
new location, thus changing the shape of the cell. Eg: actin filaments that
responsible for amoeboid movement.

75

2. It interacts with motor proteins to produce motility.

- with motor protein, the whole cells moves along fibers outside the cell.
-eg, motor proteins bring about the bending of cilia and flagella by
gripping microtubules within those organelles and sliding them against each
other.
3. Regulating biochemical activities in the cell in response to mechanical
stimulation.
- eg, if plasma membrane proteins that attached to the cytoskeleton were
pull, there were instantaneous rearrangements of nucleolus and other
structures in the nucleus.

76

4. Inside the cell, vesicles can travel along monorails provided by the
cytoskeleton.
- eg, vesicles that bud off from the ER travel to the Golgi along cytoskeletal
track.

77

1. Microtubules
Microtubules are hollow rods about 25 nm in diameter and about 200 nm to

25 m long.
Two types of microtubules
- Centrosome and centrioles.
- Cilia and flagella.

Constructed from a globular protein called tubulin.

- A tubulin dimer consists of -tubulin and -tubulin.
- It grow in length by adding tubulin dimers.

Functions of microtubules:
Shaping and support the cell.
Motility. Eg; Flagella and cilia.
Guiding movement of organelles- serve as tracks (which organelles equipped with

motor proteins can move). Eg vesicles move from GA to plasma membrane with the
help of microtubule.
Separating chromosomes during cell division thru centrioles.

78

10 m

Structure and Function of the Cytoskeleton

Column of tubulin dimers

25 nm

Tubulin dimer
79

Centrosomes and Centrioles

The centrosome is a microtubule-organizing center.
In many cells, microtubules grow out from a centrosome near the nucleus.
Function as compression-resisting girders of the cytoskeleton.

In animal cells, the centrosome has a pair of centrioles, each with nine triplets

of microtubules arranged in a ring.

80

Centrosome

Microtubule
Centrioles
0.25 m

Longitudinal section Microtubules Cross section

of one centriole
of the other centriole

81

Cilia and Flagella

Microtubules control the beating of cilia and flagella, locomotors appendages
of some cells.
The length and quantity of these microtubules are differ.
- Cilia: occur in large number, about 0.25 m in diameter and about 2-20 m long.
- Flagella: limited to just one or a few per cell, same diameter like cilia but longer,
about 10-200 m.

Cilia and flagella differ in their beating patterns.

- Cilia: Back and forth motion. The rapid power stroke moves the cell in a direction
perpendicular to the axis of the cilium. Then during the slower recovery stroke, the
cilium bends and sweeps sideways, closer to the surface.

- Flagella: Undulating motion that generates force in the same directions as the
flagellums axis. Its snakelike motion driving a cell in the same direction as the axis of
the flagellum.
82

Direction of swimming

(a) Motion of flagella

5 m

Direction of organisms movement

Power stroke Recovery stroke

(b) Motion of cilia

15 m
83

 Cilia and flagella share a common ultrastructure though both different in

length, number per cell and beating pattern:

A core of microtubules sheathed by the plasma membrane.

An arrangement of 9+2 pattern .

- Nine doublets of microtubules, the member of each pair sharing part of their
walls are arranged in ring.
- In the center of the ring are two single microtubules.
A basal body that anchors the cilium or flagellum with the arrangement of 9+0

pattern.
- Composed of nine sets of triplet microtubules arranged in ring (just like
centrioles.
A motor protein called dynein, which drives the bending movements of a cilium

or flagellum.
- The movements caused by changes in the shape of the protein with ATP
providing the energy for these changes.
84

Core of microtubules for each cilia and

flagellum sheathed in an extension of the
plasma membrane
85

Outer microtubule
doublet

0.1 m

Plasma
membrane

Dynein proteins
Central
microtubule
Radial
spoke
Protein crosslinking outer
doublets

Microtubules

Plasma
membrane
Basal body

(b) Cross section of

cilium

9+2 pattern

0.5 m

(a) Longitudinal
section of cilium

0.1 m
Triplet

9+0
pattern
(c) Cross section of basal body
86

2. Microfilaments (Actin Filaments)

Microfilaments are solid rods about 7 nm in diameter, built as a twisted

double chain of actin (globular protein) subunits.

The structural role of microfilaments is to bear tension (resisting pulling forces

within the cell).

They form a 3-D network just inside the plasma membrane to help support the

cells shape. This network gives the outer cytoplasmic layer of a cell, called the
cortex (semisolid consistency of gel) .

87

 Bundles of microfilaments make up

the core of microvilli of intestinal

cells.

88

Structure and Function of the Cytoskeleton

10 m

Actin subunit

7 nm

89

Microfilaments and Motility

1 .Microfilaments are well known in cell
motility, as part of the contractile
apparatus of the muscle cells and
contain the protein myosin (muscle
contraction)
- Thousands of actin filaments are
arranged parallel to one another along the
length of a muscle cell, interdigitated with
thicker filaments made of protein myosin.
- Myosin acts as a microfilament-based
motor protein.
- Contraction of the muscle cell results
from the actin and myosin filaments
sliding past one another in this way,
shortening the cell.

90

2. Localized contraction brought about by

actin and myosin also drives amoeboid
movement. (changes in cell shapes and cell
motility)
- Pseudopodia (cellular extensions) extend
and contract through the reversible
assembly and contraction of actin subunits
into microfilaments.

3. Cytoplasmic streaming is a circular flow

of cytoplasm within cells.
- This streaming speeds distribution of
materials within the cell
- In plant cells, actin-myosin interactions
and sol-gel transformations drive
cytoplasmic streaming

91

3. Intermediate Filaments
Intermediate filaments range in diameter from 812 nanometers, larger than

microfilaments but smaller than microtubules.

Intermediate filaments are more permanent cytoskeleton fixtures than the

other two classes.

- even after cells die, intermediate filament networks often persist.

They support cell shape and fixing the position of certain organelles in

place.
- eg, the nucleus commonly sits within a cage made of intermediate filaments, fixed in
location by branches of the filaments that extend into the cytoplasm.
- eg, nuclear lamina that lines the interior of the nuclear envelope are made from
intermediate filaments.

92

Structure and Function of the Cytoskeleton

5 m

Keratin proteins
Fibrous subunit (keratins
coiled together)
812 nm

93

Extracellular Components and Connections between

Cells Help Coordinate Cellular Activities
Most cells synthesize and secrete materials that are external to

the plasma membrane

These extracellular structures include:
Cell walls of plants
The extracellular matrix (ECM) of animal cells
Intercellular junctions

94

Cell Walls of Plants

The cell wall is an extracellular structure that distinguishes plant cells from

animal cells.
Prokaryotes, fungi, and some protists also have cell walls.
The cell wall protects the plant cell, maintains its shape, and prevents excessive

uptake of water.
Plant cell walls are made of cellulose fibers embedded in other polysaccharides

and protein.
- cellulose fibers are synthesized by an enzyme called cellulose synthase and secreted to the
extracellular space (embedded in other polysaccharides and protein.)

95

 Plant cell walls have multiple layers:

Primary cell wall: relatively thin and flexible.

- This is the wall that been secreted first in young tree.

Middle lamella: thin layer between primary walls of adjacent cells.

- A thin layer rich in sticky polysaccharides called pectins.

- With pectin, middle lamella glues adjacent cells together.
Secondary cell wall (in some cells): added between the plasma membrane

and the primary cell wall.

- When cell matures and stop growing, its strengthens its walls by secreting
hardening substances into the primary wall.
- Other cell added a secondary cell wall. It is deposited in several laminated layers.
- The wall is strong and durable matrix that affords the cell protection and support.

96

Secondary
cell wall
Primary
cell wall
Middle
lamella

1 m

Central vacuole
Cytosol
Plasma membrane
Plant cell walls

Plasmodesmata
97

The Extracellular Matrix (ECM) of Animal Cells

Animal cells lack cell walls but are covered by an elaborate extracellular

matrix (ECM).
The ECM is made up of glycoproteins such as collagen, proteoglycans, and

fibronectin.
- collagen is the most abundant glycoprotein, form strong fibers outside the
cells and account about 40% of the total protein in the human body.
ECM proteins bind to receptor proteins in the plasma membrane called

integrins.
Functions of the ECM:

Support
Adhesion
Movement
Regulation
98

Collagen fibers are

embedded in a web
of proteoglycan
complexes.

Proteoglycan Complex
consists of hundreds of
proteoglycan molecules.
Polysaccharide
molecule

EXTRACELLULAR FLUID

Fibronectin
attaches the
ECM to integrins
embbeded in the
plasma
membrane

Carbohydrates

Core
protein

Plasma
membrane

Microfilaments

CYTOPLASM

Integrins
Membrane
proteins bind to
the ECM on one
side and to
Proteoglycan
associated
molecule
proteins attached
to microfilaments
on the other. This Proteoglycan complex
linkage can
transmit signal
between the
cells external
environment and
its interior.

99

Intercellular Junctions
Neighboring cells in tissues, organs, or organ systems often adhere,

interact, and communicate through direct physical contact.

How? Intercellular junctions facilitate these contacts.
There are several types of intercellular junctions.
Plasmodesmata
Tight junctions
Desmosomes
Gap junctions

100

Plasmodesmata in Plant Cells

Plasmodesmata are channels that perforate plant cell walls.
Through plasmodesmata, water and small solutes (and sometimes

proteins and RNA) can pass from cell to cell.

101

Secondary
cell wall
Primary
cell wall
Middle
lamella

1 m

Central vacuole
Cytosol
Plasma membrane
Plant cell walls

Plasmodesmata
102

Tight Junctions, Desmosomes, and Gap Junctions in Animal

Cells
At tight junctions, membranes of neighboring cells are pressed together,

preventing leakage of extracellular fluid.

- eg, Tight junctions between skin cells make us watertight by preventing leakage
between cells in our sweat gland.

Desmosomes (anchoring junctions) fasten cells together into strong sheets. At

desmosomes, the intermediate filaments anchor desmosomes in the cytoplasm.

- eg, Desmosomes attach muscle cells to each other in a muscle.

Gap junctions (communicating junctions) provide cytoplasmic channels

between adjacent cells and neccesary for communication between cells in

many types of tissues.
- The function is similar to the plasmodesmata.
- The junctions consist of membrane proteins that surround a pore where ions, sugars,
amino acids and small molecules may pass.
103

Tight junction
Tight junctions prevent
fluid from moving
across a layer of cells

0.5 m

Tight junction
Intermediate
filaments

Desmosome

Gap
junctions

Space
between
cells
Plasma membranes
of adjacent cells

Desmosome

1 m

Extracellular
matrix
Gap junction

0.1 m

104

SUMMARY- CELLS

Structure

Cell Component
Concept 6.3
The eukaryotic cells genetic
instructions are housed in
the nucleus and carried out
by the ribosomes

Nucleus

Function

Surrounded by nuclear
envelope (double membrane)
perforated by nuclear pores.
The nuclear envelope is
continuous with the
endoplasmic reticulum (ER).

Houses chromosomes, made of

chromatin (DNA, the genetic
material, and proteins); contains
nucleoli, where ribosomal
subunits are made. Pores
regulate entry and exit os
materials.

Two subunits made of ribosomal RNA and proteins; can be

free in cytosol or bound to ER

Protein synthesis

(ER)
Ribosome

105

Cell Component
Concept 6.4
Endoplasmic reticulum
The endomembrane system
(Nuclear
regulates protein traffic and
envelope)
performs metabolic functions
in the cell

Golgi apparatus

Lysosome

Vacuole

Structure

Function

Extensive network of
membrane-bound tubules and
sacs; membrane separates
lumen from cytosol;
continuous with
the nuclear envelope.

Smooth ER: synthesis of

lipids, metabolism of carbohydrates, Ca2+ storage, detoxification of drugs and poisons

Stacks of flattened
membranous
sacs; has polarity
(cis and trans
faces)

Rough ER: Aids in sythesis of

secretory and other proteins
from bound ribosomes; adds
carbohydrates to glycoproteins;
produces new membrane
Modification of proteins, carbohydrates on proteins, and phospholipids; synthesis of many
polysaccharides; sorting of
Golgi products, which are then
released in vesicles.

Breakdown of ingested subMembranous sac of hydrolytic stances cell macromolecules,

enzymes (in animal cells)
and damaged organelles for
recycling
Large membrane-bounded
vesicle in plants

Digestion, storage, waste

disposal, water balance, cell
growth, and protection

106

Cell Component
Concept 6.5

Mitochondrion

Mitochondria and chloroplasts change energy from

one form to another

Structure
Bounded by double
membrane;
inner membrane has
infoldings (cristae)

Function
Cellular respiration

Chloroplast

Typically two membranes

around fluid stroma, which
contains membranous thylakoids
stacked into grana (in plants)

Photosynthesis

Peroxisome

Specialized metabolic
compartment bounded by a
single membrane

Contains enzymes that transfer

hydrogen to water, producing
hydrogen peroxide (H2O2) as a
by-product, which is converted
to water by other enzymes
in the peroxisome

107