SH1909

The Cell Theory

• postulated by Schleiden, Schwann, and
Virchow CELL
• is composed of three (3) tenets:

1. Cells are the smallest and most basic unit of

structure and function of organisms Prokaryotic Eukaryotic

2. All organisms are composed of cells

3. Cells arise from pre-existing cells Archaea Bacteria Eukarya

H. walsbyi E. coli H. sapiens

Cells – Identification and Classification Figure 1.0 Classification of Organisms Based on Cell
Structure
• First record of seeing a cell and identifying it Pro= before, Eu= true, karyon= kernel. The main difference
between prokaryotes and eukaryotes, therefore, is the presence
belongs to Robert Hooke of an enclosed structure to separate the genetic material of the
• All cells share common structural features: cell, known as the Nucleus.

1. Cell/plasma membrane Prokaryotic Cells

-the outer boundary of the cell • Earliest and most primitive cells
which separates its contents from the environment. • Contains only simple structures with very little
It varies in composition. differentiation
• Size varies from 0.1-5 µm (with few exceptions)
2. Cytoplasm
• Consists of organisms from the Domain
-a gel-like substance that
Archaea and Bacteria
constitutes the cells internal environment and holds
all of the structural components of the cell. For Structure
Capsule The outermost layer that encases the
3. Genetic material entire cell for additional protection.
-Deoxyribose nucleic acid (DNA) is Usually composed of polysaccharides
the genetic material which holds information for cell Cell wall A rigid case that encloses the entire cell
activities and function and gives it shape. For
Bacteria: Peptidoglycans are present,
4. Ribosomes while for Archaea: No peptidoglycans
-structures that manufacture are present.
proteins which are needed for cell function Plasma A semipermeable membrane that
membrane encloses the internal structures of the
• Cells can differ in number, size, components, cell that regulates the passage of
and composition molecules into and out of the cell. For
• Based on structural differences, cells can be Bacteria: Fatty acids are what
classified as either Prokaryotic or Eukaryotic composes this membrane, while for

02 Handout 2 *Property of STI

 [email protected] Page 1 of 13
 SH1909

Archaea: Non-fatty acid lipids are its For Genetic Material

composition. Nucleoid Region of the cell where DNA is present.

Mesosome Folds of the plasma membrane that Prokaryotes do not have an enclosed

enter the area of the cytoplasm. This is structure for its genetic material such as a

where the electron transport system for nucleus. Ribosomes and enzymes are

the creation of cell energy is located. seen near this region

Cytoplasm The gel-like substance that fills the Plasmid Small independent loops of DNA which
& Cytosol interior of the cell. It holds the other are separate from the chromosomal DNA

components of the cell. The cytosol is found in the nucleoid. This is important for

the liquid portion of the cytoplasm the genetic advantages of prokaryotes.

Table 1.2 Components of a Prokaryotic Cell used for
Table 1.0 Components of a Prokaryotic Cell used for
Structural Integrity Genetic Function

For Activities and Function

Ribosome Small structures that are scattered
throughout the cytoplasm for the
process of protein synthesis.
Prokaryotes have a 50s and 30s subunit,
forming a 70s ribosome.
Pili Tubular structures present in the cell
surface for cell-to-cell communication
and passing of genetic material.
Flagellum A tail-like appendage anchored to the
Image 1.0 A Labeled diagram of a Prokaryotic Cell
cell membrane and wall that allows a Source: https://owlcation.com/stem/Biolog-101-Cells

prokaryote locomotion through a circular

motion. This can either be seen at the
end of the cell or scattered randomly.
Fimbriae Additional small and bristle-like fibers
scattered throughout the cell surface.
They are used for attachment,
navigation, and propelling certain
molecules or objects toward the cell.
Table 1.1 Components of a Prokaryotic Cell used for Cell
Activities and Motor Function

Image 1.1 A Labeled micrograph of a E. coli

Source: http://ibbiology.wikifoundry.com/

02 Handout 2 *Property of STI

 [email protected] Page 2 of 13
 SH1909

Eukaryotic Cells ▪ Three carbon glycerol molecule

• Highly evolved, complex structures, and larger ▪ Two fatty acid tails
size compared to prokaryotes
• Size varies from 10-100 µm (with few o The charged phosphate group and the
exceptions) glycerol molecule form the
• Exhibits heavy Compartmentalization of phospholipids polar head
internal structures known as Organelles o The two (2) fatty acids makeup the non-

• Divided into Protista, Fungi, Plantae, and polar hydrophobic tail

Animalia o The hydrophobic tails move away from

• Derivations vary per classification, but all have the environment and cluster together

the general components of a typical eukaryotic forming the middle portion of the lipid

cell bilayer of the plasma membrane, while

• Cell structures can be categorized as either for: the hydrophilic heads are faced toward

1. Structures for protection the environment.

2. Genetic control organelles o Because the middle portion of the

3. Manufacturing, Storing, Distributing, and membrane is non-polar, this causes it

Breakdown organelles to have selective permeability,

4. Energy processing organelles meaning non-polar molecules such as

5.Organelles for structural support, glucose cannot pass freely through the

movement, and communication between cells cell

I. STRUCTURES FOR PROTECTION Membrane Proteins

Cell Membrane • The cell membrane is also composed of
• Functions as a barrier to separate the proteins and other molecules which are
environment and the internal structures of the randomly scattered
cell • The presence of membrane proteins and other
molecules is why the cell membrane is termed
• Also regulates the passage of molecules to and
as Fluid Mosaic (coined by Nicolson and
from the cell Singer).
• Composed of two (2) sheets of phospholipids,
hence the name Phospholipid bilayer
o Phospholipids are organic molecules
that exhibit both polar (hydrophilic) and
non-polar (hydrophobic) ends.
o The cause of its bipolar nature is due to
the three (3) key structures it
Image 2.0 A Fluid Mosaic Model Showing the
possesses: Structures of the Cell Membrane
▪ Charged Phosphate group Source: https://biofoundations.org/repairing-the-cell-
membrane/

02 Handout 2 *Property of STI

 [email protected] Page 3 of 13
 SH1909

• Only found in plant cells (but also present

Structures Embedded in Cell Membrane
in prokaryotic bacteria)
Create passageways for ions
• Composition varies per classification.
Transport and non-polar molecules to
Some examples would be:
Proteins pass freely through the cell
membrane
1. Plants and algae: Polysaccharide
Channel Form tunnels for the import
cellulose
Proteins and export of materials and
Because cellulose is rigid and does
wastes
not allow free passage of molecules, plants
Cell Enable cells to distinguish own
and algae have openings which allow water
Recognition cells from that of other
and molecules to diffuse
Proteins organisms
Junction Assist in cell-to-cell adhesion 2. Fungi: Chitin
Proteins and communication between
cells Cytoplasm
Receptor Facilitate exchange of signals • It is the jellylike substance contained within the
Proteins between cells by changing its cell membrane. Generally composed of the cell
shape to allow specific organelles (not including the nucleus) and
molecules (ligands) to bind to cytosol
it
• Cytosol is the liquid component of the
Enzymatic Participate in metabolic
cytoplasm and is largely composed of water
Proteins reactions such as degradation
• Organelles are compartmentalized structures
and synthesis to sustain life in
which offer efficiency and provides the cell the
the cell
ability to do different complex metabolic
Carbohydrate Serve as identification tags for
reactions in localized areas
Chains the cell recognition proteins
1. Membranous organelles (single
Cholesterol Strengthens the cell membrane)
membrane by making it more Golgi body, lysosomes, smooth
flexible but less fluid. It also and rough endoplasmic reticulum, vesicle,
makes the membrane less vacuole
permeable to water-soluble
substances 2. Membranous organelles (double
Table 2.0 Structures Embedded in the Cell Membrane and
their Functions membrane)
Nucleus, mitochondria, plastids
Cell Wall
• An additional boundary between the cell
3. Non-membranous organelles
membrane and the environment for added
Ribosome, centriole
structural support and protection

02 Handout 2 *Property of STI

 [email protected] Page 4 of 13
 SH1909

II. GENETIC CONTROL ORGANELLES DNA

Nucleus • The long-chain molecule of inheritance made of
• The storehouse of genetic information (DNA). It segmented portions called genes which
functions to prevent damage to the DNA and contains the information needed for cell
direct all cell activity. activities (such as protein synthesis)
• Numerous proteins are needed for genetic • The molecule is compacted by proteins called
function, so the nucleus has specialized histones which form a condense structure
structures to facilitate their entry: called chromatin and condenses further into
1. Nuclear envelope chromosomes when cell division is occurring.
A two (2) membrane structure that • There are two types of chromatin seen in the
encloses the nucleus and separates it from nucleus:
the cytoplasm 1. Euchromatin
Contains active DNA, stains lightly
2. Perinuclear space when viewed under the microscope
The space between the two (2)
membranes of the nuclear envelope 2. Heterochromatin
Contains inactive DNA, stains
3. Nucleoplasm deeply when viewed under the microscope
The semifluid substance inside the
nucleus

4. Nuclear pores
Perforations in the nuclear
envelope that regulate the passage of
materials (usually proteins, ribosomes, and
RNA)

3. Nucleolus
Condensed region of the nucleus
where synthesis of ribosomal RNA (or
rRNA) and ribosomal subunits are
Image 2.1 A Micrograph of a Nucleus Showing its
centralized Specialized Structures
Source: https://www.histology.leeds.ac.uk /cell/nucleus.php
rRNA is combined with imported
proteins to form the large and small
ribosomal subunits. These subunits exit
through the nuclear pores and combine
once within the cytoplasm

02 Handout 2 *Property of STI

 [email protected] Page 5 of 13
 SH1909

III. MANUFACTURING, STORING, Secretory proteins made from the

DISTRIBUTING, AND BREAKDOWN RER are typically used by specialized cells
ORGANELLES (i.e. pituitary glands: hormones), or can
even be secreted outside the cell (i.e.
Endoplasmic Reticulum (ER) mammary glands: milk proteins)
• An extensive folded membrane that occupies a
large space in the cytoplasm. 2. Smooth ER (SER)
• Due to its large size, the ER is folded like a Region adjacent to the RER where
maze where the membranous tubules and no ribosomes are present and whose
flattened sacs are called cisternae, while the cisternae are membranous tubules
spaces between them are the cisternal space Its main functions are mostly
o The cisterna (singular) is continuous involving metabolic processes such as
with the nuclear envelope, and so the synthesis and transport of lipids,
perinuclear space is also continuous metabolism of carbohydrates, and
with the cisternal space detoxification of drugs and poisons.
A specialized form of SER in
o This connection allows the synthesized muscle cells is the sarcoplasmic reticulum
ribosomes from the nucleolus to be where calcium ions are stored and
transported directly to the ER released. When a nerve signal stimulates
the muscle the release of ions triggers a
The presence of ribosomes in the ER allows it to be contraction
classified into two (2) regions:
1. Rough ER (RER)
Region closest to the nucleus
whose cisternae are flattened sacs, and are
studded with ribosomes, giving it a rough
appearance when viewed from the
microscope
Proteins are formed and
temporarily stored in the cisternal space
A short carbohydrate attaches to
the formed protein (converting it into a
Image 2.2 Diagram of an Endoplasmic Reticulum Showing
glycoprotein, a secretory protein) thereby its Specialized Regions
Source: https://cellsorganelles.weebly.com/packaging-shipping-
making it ready for cell use and-producing.html
Secretory proteins are moved to
the specialized transitional ER, where
transport vesicles take them to the Golgi
body for further packaging

02 Handout 2 *Property of STI

 [email protected] Page 6 of 13
 SH1909

Golgi Apparatus/Body
o Stacks of cisternae which acts as a processing
system that sorts, modifies, and packages
products from the ER
o Proteins finish their folding here to become
functional
o Enzymes in the Golgi body manufacture and
attach carbohydrates that serve as name tags
for the cell
o The Golgi has specialized regions that interact
with the ER, the rest of the cell, and with each
Image 2.3 Micrograph of an Endoplasmic Reticulum other through vesicles budding off from the
Showing its Specialized Regions
Source: http://ibbio.pbworks.com/w/page/59800989/Prokaryotic Golgi cisternae
%20and%20Eukaryotic%20Cells
o These regions are arranged from the closest to
the ER up to the ones near the plasma
Ribosomes
membrane:
• Sites of protein synthesis
1, Cis-face
• Spherical granules composed of two subunits, The receiving end of the Golgi.
the large subunit and small subunit, Where transport vesicles from the ER are
synthesized in the nucleolus. These subunits fused with the cisterna of the Golgi. Also
exit to the cytoplasm and combine to form responsible for the returning incorrectly
ribosomes sent proteins back to the ER
• Each ribosome consists of ~70 proteins and
several ribosomal RNA (rRNA) 2. Dictyosome/medial-face
• Found as either bound ribosomes attached to Bulk or main stacks of cisternae.
the RER and nuclear membrane, or free Responsible for processing proteins and
ribosomes suspended in the cytosol lipids and directing them to their
o They are structurally identical and can destinations.
alternate roles depending on the needs
of the cell 3. Trans-face
• Proteins synthesized by free ribosomes The shipping end of the Golgi.
function as enzymes or structural proteins Sorts and directs the modified proteins to
• Proteins synthesized by bound ribosomes their destination by budding off secretory
function as secretory proteins or hormones vesicles

02 Handout 2 *Property of STI

 [email protected] Page 7 of 13
 SH1909

packaged by the Golgi body where it fuses with

transport vesicles carrying cell debris
o The main function of lysosomes is intracellular
digestion by means of autophagy

Peroxisome
o Structurally identical to lysosomes however, the
enzymes present are from the Golgi body and
have much higher concentrations than
lysosomes
o Mainly function to dispose of toxic substances
Image 2.4 Diagram of Golgi Body and lipids
Source: http://animalia-life.club/other/golgi-apparatus-labeled-
diagram.html

IV. ENERGY PROCESSING ORGANELLES

Mitochondria
o Double membranous structures that supply
energy to the cell by means of cellular
respiration

medial o Consists of their own ribosomes and DNA,

which is the basis of the endosymbiotic theory
o The space between the double membranes is
cis called the intermembrane space
Vesicles trans o The two membranes of the mitochondria allow
vacoules it perform functions for cellular respiration:
lysosomes
1, Outer Membrane
peroxisome
Smooth continuous boundary that
Image 2.5 Micrograph of Golgi Body encapsulates all the contents of the
Source: https://www.thinglink.com/scene/
698921523674611713 mitochondria

Lysosomes 2. Inner Membrane

o Free floating organelles that contain enzymes Has intricately folded structures

that dismantle and recycle food particles, called cristae where enzymes responsible

captured bacteria, worn-out organelles, and for cellular respiration are located. The

debris number of cristae is proportional to the

o The enzymes, known as lysozyme, originates energy requirements of the cell In between

from the RER, is recognized, refined, and these folds is the mitochondrial matrix

02 Handout 2 *Property of STI

 [email protected] Page 8 of 13
 SH1909

This region also contains DNA and

ribosomes for the genetic function of the
mitochondria

o Mitochondria are the sites of energy production

where adenosine triphosphate (ATP), the cell’s
source of chemical energy, is synthesized
o The process of converting energy-rich
molecules (e.g. pyruvate) is known as the
Kreb’s Cycle which makes use of pyruvate
oxidation and produces carbon dioxide as a
waste product
Image 2.7 Micrograph of Mitochondria
o Mitochondria are considered semi-autonomous Source: https://www.thestudentroom.co.uk/show
organelles because they can grow and divide thread.php?t=1422067
on their own

Plastids
o A group of large organelles only found in plant
cells and not animal cells. Can be divided into 3
groups:
1. Chloroplasts
Green colored plastids due to the
green pigments: chlorophyll a and
bChloroplasts are the sites of energy
production in plants because this is where
photosynthesis occurs. This process
makes use of solar energy and transforms
Image 2.6 Diagram of Mitochondria
Source: https://biology.tutorvista.com/animal-and-plant- it into energy-rich molecules
cells/mitochondria.html
Chloroplasts are parallel to
mitochondrion due to their double
membrane features and the presence of
their own DNA. It has other specialized
structures such as:
a. Outer Membrane
b. Inner Membrane
c. Thylakoid

02 Handout 2 *Property of STI

 [email protected] Page 9 of 13
 SH1909

The third membrane system folded 3. Leucoplasts

into flattened sacs. Photosynthetic Non-colored plastids that do not
pigments such as chlorophyll a and b are contain pigments. They function mainly as
found here, which is why this is where light- storage for nutrients
dependent reactions occur here Starch filled leucoplasts are called
The thylakoid membrane Amyloplasts. Those that store oil are called
separates the stroma and the grana Elaioplsts, and those that store proteins are
called Aleuroplasts
d. Granum
Stacks of thylakoids that increase
the surface area for the attachment of
chlorophyll
Each chloroplast has around 50
grana, and each granum is made of around
50 thylakoids
Each granum is connected to the
other by an intergranal lamellae
Image 2.8 Micrograph of Chloroplast

S: Stroma, EM: Envelope Membrane, GT: Granular Thylakoid,

e. Stroma ST: Stroma thylakoid
Source: https://www.researchgate.net/figure/Thin-section-
An enzyme-rich gel-like matrix electron-micrograph-of-a-young-tobacco-chloroplast-Two-
found inside the chloroplast. It contains envelope-membranes_fig2_7536996

DNA, ribosomes, photosynthetic enzymes,

lipid droplets, and starch.
This is where light-independent
reactions occur via the enzymes present

V. ORGANELLES FOR STRUCTURAL

2. Chromoplasts SUPPORT, MOVEMENT, AND
Colored plastids rich in pigments COMMUNICATION BETWEEN CELLS
such as carotenoids instead of chlorophyll
Cytoskeleton
which give fruits, flowers, and leaves their
o A flexible network of protein threads and fibers
orange, yellow, and red colors
that provide mechanical and structural
Chromoplasts can arise from
framework of support throughout the cell.
chloroplasts that have lost their chlorophyll
Additionally, it helps in directing cell movement,
(i.e. ripening of fruits)
transport, and responses
o There are three (3) major protein components
of the cytoskeleton:

02 Handout 2 *Property of STI

 [email protected] Page 10 of 13
 SH1909

1. Microtubule o Centrosome division is crucial in preceding and

The thickest and longest filament stimulating cell division:
composed of tubulin assembled into hollow 1. Division of Centriole
tubes that can rapidly add or remove tubulin Each centriole will divide into two
molecules (2), and each of the two (2) pairs will move
It can function as a trackway where into opposite poles of the cell
specialized proteins use it as a path to carry
cargo such as vesicles 2. Formation of asters and spindle fibers
From the pair of centrioles, asters
2. Intermediate Filament will form and will be the source of a system
Smaller than microtubules and of microtubules called spindle fibers where
appears ropelike. Provides the cell tensile chromosomes can attach and be pulled
strength, thus allowing it to stretch without toward the respective poles. Plant cells do
breaking. It is composed of multiple protein not form asters when dividing
subunits Centrioles can also divide to form
basal bodies where cilia and flagella are
3. Microfilament formed:
The thinnest filament composed of
actin which is present in nearly all cell types a. Cilia
of eukaryotes. It can provide strength to Both cilia and flagella have a 9+2
resist stretching, compression, and assists pattern regarding the microtubules that
in anchorage compose them
Actin filaments are especially Short, numerous extensions that
notable in muscle cells, where it works move in a coordinated to propel the cell
together with myosin to produce muscle
contractions b. Flagella
Longer extensions which occur
Centrosomes and Centrioles singly or in pairs. Movement is done by
o A small dense region in the cytoplasm where means of a propeller motion.
microtubules are assembled and arranged,
thus termed the Microtubule Organizing Center
(MTOC)
o Inside the centrosome are two hollow cylinders
made of filaments (which are microtubule
triplets) called the centriole
o The centriole is composed of 9 filaments
arranged in a circular pattern

02 Handout 2 *Property of STI

 [email protected] Page 11 of 13
 SH1909

Cell Surface and Junctions

o Cells are joined to each other by structures
A
called junctions. In plants, the plasma
B
membrane and cytoplasmic fluid extend
specialized structures between cells called
C
plasmodesmata to communicate and pass D

molecules effectively
o Animal cells have different types of junctions E

depending on their location and function:

F
1. Tight Junctions
Fuses cells together to form an G
H
impassable barrier using actin fibers
attaching to membrane-anchored
Image 2.9 Micrograph of Animal Cell
proteins, forming cell sheets
A: Plasma membrane, B: Golgi body, C: Centrosome, D:
Important in controlling Mitochondria, E: Lysosome, F: Nucleus, G: Endoplasmic
Reticulum, H: Cytoplasm
biochemical movement (e.g. stomach Source: https://quizlet.com/219495003/aice-biology-chapter-1-
animal-cell-electron-micrograph-labeling-diagram/
fluids should not seep into the
surrounding tissue)

2. Adhesion Junctions
Connects two (2) neighboring cells References
together or a cell to the extracellular
References
matrix. Acts like screws using Hofnagels, M. (2016). General Biology Books I and
cytoskeletal fibers to form strong II. Quezon City: McGraw-Hill Education.
Morales-Ramos, A., & Ramos, J. A. (2017).
sheets with spaces between them Exploring Life Through Science: General
Biology 1. Quezon City: Phoenix Publishing
House, Inc.
3. Gap Junctions
Similar to plasmodesmata, wherein
a channel protein links with the cytoplasm
of an adjacent cell to allow exchange of
ions and nutrients

02 Handout 2 *Property of STI

 [email protected] Page 12 of 13
 SH1909

DEFINITIONS BOX

Cell membrane DNA

Cytoplasm RNA
Cytosol Genes
Ribosomes Histones
Prokaryote Ribosomal subunits
Eukaryote Secretory protein
Electron transport system Glycoprotein
Compartmentalization Transitional ER
Organelles Transport vesicles
Hydrophilic Enzymes
Hydrophobic Hormones
Phospholipids rRNA
Fluid Mosaic Model Endosymbiotic Theory
Chlorophyll Photosynthesis
Krebs Cycle Tubulin
Actin and Myosin Centrosomes
Centrioles Cilia
Flagella Asters and Spindle Fibers

02 Handout 2 *Property of STI

 [email protected] Page 13 of 13