What is it?

The term organism is applied to all living beings. To be considered an organism, one must have
at least one cell. A cell is the simplest and smallest unit of life. Cells join together and create the
biological levels of organization of living beings, as seen in Figure 1. Cells organize into tissues. Tissues
organize to form an organ. Different organs having similar or related functions group together to form an
organ system. The different organ systems make up an organism.

Source: Caroline Biological Supply Company. (n.d.). Infographic: The Hierarchy of Life. Pinterest. Retrieved June 6, 2022, from
https://www.pinterest.ph/pin/200199145914019142/.

Figure 1. Biological Levels of Organization

Cells were discovered when microscopes were invented and became available. The scientists who were
first to observe cells were Robert Hooke and Anton van Leeuwenhoek. Early studies of cells were
independently conducted by Matthias Schleiden, Theodor Schwann, and Rudolf Virchow until they
proposed the Cell Theory.
1.1. Cell Theory

The Cell Theory is one of the known foundations of biology as it explains the organization of life.
It covers three principles:

1) All organisms are composed of one or more cells. 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) Cells arise only be division of a previously existing cell.

1.2. Prokaryotic Cells vs. Eukaryotic Cells

Prokaryotic cells and eukaryotic cells are two basic cell architectures. Each is characterized by
distinct features and structures with specialized functions, but they also have something in common.

1.2.1 Prokaryotes

Organisms characterized by prokaryotic cells are called prokaryotes. They exhibit a relatively
simple cell structure due to the lack of membrane-bound organelles and an endomembrane system.
Prokaryotes are unicellular which means they rely on a single cell to perform all metabolic processes
necessary for life. Organisms under the domain bacteria and archaea are examples of prokaryotes.
Bacteria are characterized by peptidoglycan in their cell walls. Peptidoglycan is composed of polymers of
sugars and some proteins that help protect prokaryotic cells, maintain their shape, and prevent the
excessive uptake or loss of water. Most bacteria are considered pathogens or disease-causing organisms.
Archaea, on the other hand, lack peptidoglycan in their cell walls. This makes them distinct from
bacteria. Domain archaea includes organisms that are extremophiles or organisms that can live in
environments with extreme conditions.

1.2.2 Eukaryotes

Eukaryotes are organisms with eukaryotic cells. They are multicellular, which means that
they are composed of more than one and different cell types. Eukaryotes include protists, fungi,
plants, animals, and humans. Eukaryotic cells are characterized by the presence of
membrane-bound organelles and the endomembrane system that result to
compartmentalization. Compartmentalization separates in the interior of eukaryotic cells into
different regions allowing its different specialized functions or activities to occur at different
places simultaneously. Examples of eukaryotic cells are animal cells and plant cells.
1.3. Subcellular Structures and Organelles

1.3.1 Basic Structural Similarities in Prokaryotic cells and Eukaryotic cells

Prokaryotic cells and eukaryotic cells share four common features:

1) Genetic Material

Both prokaryotes and eukaryotes have DNA, which acts the genetic material. DNA holds the
genetic information of organisms and is the blueprint of life. The DNA in prokaryotes appears
circular and is located in the nucleoid, an irregularly shaped structure found at the center of the
cell. A nucleoid does not have a membrane. On the other hand, the DNA in eukaryotes is linear
and can be found inside the nucleus, a membrane-bound organelle at the center of the cell. It is
the largest organelle in a eukaryotic cell. The structure of a nucleus is shown in Figure 2. The
following are key features in a nucleus:

● Nucleolus – site of ribosomal synthesis

● Nuclear envelope – two phospholipid bilayer membranes characterized by nuclear
pores; protects the DNA inside the nucleus
● Nuclear pores – regulate the passage of molecules between the nucleus and cytoplasm

Source: Mason, K. A., Losos, J. B., Duncan. T. The nucleus. Biology 13th Edition

Figure 2. Structure of a Nucleus (found only in eukaryotic cell)

2) Cytoplasm

Cytoplasm is a jelly-like, semifluid matrix that fills the interior of both prokaryotic and eukaryotic
cells. Subcellular structures may be suspended in the cytoplasm. It also contains
macromolecules such as carbohydrates and proteins, and also dissolved ions.
3) Ribosomes

Ribosomes are made of RNA and proteins. Each ribosome is made of the small subunit and the
large subunit, as seen in Figure 3. In both prokaryotes and eukaryotes, ribosomes are sites for
protein synthesis. Ribosomes may be free (floating in the cytoplasm) or bound
(membrane-associated). Proteins needed inside the cells are synthesized in the free ribosomes.
Bound ribosomes are usually observed in eukaryotic cells and are attached to the rough
endoplasmic reticulum. This is where proteins meant for export from the cell are synthesized.

Source: Mason, K. A., Losos, J. B., Duncan. T. A ribosome. Biology 13th Edition

Figure 3. Structure of a Ribosome

4) Plasma Membrane

Plasma membrane, also known as the cell membrane, is made of a phospholipid bilayer
embedded with different types of proteins. The phospholipid bilayer is amphiphilic/amphipathic
which means that it is made up of hydrophilic heads and hydrophobic tails. The plasma
membrane is a selectively permeable barrier that regulates what comes in and out of the cell. It
separates the interior of a prokaryotic cell and eukaryotic cell from their surroundings. The
structure of a plasma membrane is shown in Figure 4.

Source: Mason, K. A., Losos, J. B., Duncan. T. Biology 13th Edition

Figure 4. The structure of a plasma membrane

1.3.2 Generalized Cell Organization of a Prokaryote
Shown in Figure 5 is a bacterial cell that represents the structure of a prokaryotic cell.
Prokaryotic cells have a relatively simple structure as they lack membrane-bound organelles and
the endomembrane system. Aside from the nucleoid, cytoplasm, ribosomes, and plasma
membrane, the key features of prokaryotic cells also include the following with their
corresponding functions:

● Cell Wall: a rigid structure composed of proteins and carbohydrates that supports and
protects the plasma membrane; characterized as porous allowing most nutrients from the
environment to reach the plasma membrane

● Glycocalyx/Capsule: a gelatinous, viscous covering that traps water and helps protect
bacteria from drying out; certain strains of bacteria that invade animals’ bodies produce a
very thick glycocalyx to help them avoid being destroyed by the animal’s immune system or
aid in the attachment to cell surfaces

● Pili (singular, pilus): hair-like projections that allow prokaryotic cells to attach to surfaces and
to each other

● Flagella (singular, flagellum): long appendages (tails) used by prokaryotic cells for motility

Source: Mason, K. A., Losos, J. B., Duncan. T. Structure of a prokaryotic cell. Biology Pics/Science Source, Biology 13th Edition

Figure 5. Structure of a Prokaryotic Cell

1.3.3 Generalized Cell Organization of a Eukaryote

Most of the subcellular structures and organelles comprising a eukaryotic cell are enclosed in a
membrane composed of lipids and proteins. The presence of the endomembrane system and the
various membrane-bound organelles result to compartmentalization, which is the hallmark of
the structure of a eukaryotic cell. Compartmentalization separates the interior of the eukaryotic
cell into different regions allowing its different specialized functions or activities to occur at
different places simultaneously.

1.3.3.1 The nucleus and the endomembrane system

● Nucleus: stores the eukaryotic DNA; site of DNA replication and transcription in
eukaryotes
o nuclear envelope: protects the DNA inside the nucleus
o nuclear pores: regulate the passage of materials between the nucleus and
the cytoplasm

● Endoplasmic Reticulum (ER): characterized by cisternae as seen in Figure 6

o Rough Endoplasmic Reticulum (rER): has ribosomes attached in its surface
where proteins meant for export from the cell are synthesized; sorts
synthesized proteins according to where they are needed; starting site of
glycosylation

o Smooth Endoplasmic Reticulum (sER): lack ribosomes in its surface;

involved in lipid synthesis, detoxification of organic molecules, and protein
and lipid modification; stores calcium ions

Source: Mason, K. A., Losos, J. B., Duncan. T. The endoplasmic reticulum. Biology 13th Edition

Figure 6. Structure of the rough endoplasmic reticulum and rough endoplasmic

reticulum

● Golgi Apparatus: also known as golgi body or golgi complex; functions in the
collection, packaging, and distribution of molecules synthesized at one location and
used at another within and outside the cell; involved in the modification of proteins
and lipids and in the synthesis of cell wall components (Refer to Figure 7)

o cis face: receiving side of golgi apparatus; located near the ER; materials
arrive in the golgi apparatus in transport vesicles
o trans face: exit of materials from golgi apparatus in secretory vesicles

Mason, K. A., Losos, J. B., Duncan. T. The golgi apparatus. Biology 13th Edition

Figure 7. Structure of the golgi apparatus

● Lysosomes: digestive vesicles; contains high level of enzymes (acid hydrolases) that
degrade biological macromolecules; involved in the break down of old organelles
and recycle their component molecules

● Vacuoles: mostly found in plant cells, fungal cells, and protists; helps maintain
tonicity and osmotic balance in plant cells; serves as storage of useful molecules
(sugars, ions, pigments); may participate in breakdown of macromolecules and
detoxification of foreign substances

● Peroxisomes: contains enzymes used to oxidize fatty acids; produces hydrogen

peroxide as by-product but is decomposed by the enzyme catalase
1.3.3.2 Cellular Generators
Mitochondria and chloroplast are the cellular generators of eukaryotic cells. Both are
membrane-bound organelles involved in energy metabolism or the process of
synthesizing ATP that is needed for many cellular processes.

● Mitochondria: found in both plant cells and animal cells; characterized by a smooth
outer membrane and inner membrane with numerous cristae as shown in Figure 8;
site of ATP synthesis

Source: Mason, K. A., Losos, J. B., Duncan. T. Mitochondria. Biology 13th Edition

Figure 8. Structure of a Mitochondrion

● Chloroplast: found in both plant cells but not in animal cells; characterized by an
outer and inner membrane; composed of chlorophylls, thylakoids, grana, and
stroma as shown in Figure 9
▪ chlorophylls: photosynthetic pigments responsible for the green color of plants

▪ thylakoids: disk-shaped structures; contains light capturing photosynthetic

pigments
▪ grana: stacks of thylakoids

▪ stroma: fluid matrix inside the chloroplast; contains enzymes used to

synthesize glucose

Source: Mason, K. A., Losos, J. B., Duncan. T. Chloroplast structure. Biology 13th Edition

Figure 9. Structure of a chloroplast

1.3.3.3 Cytoskeleton
The cytoskeleton is a distinct feature of eukaryotic cell. It is a network of protein fibers
that help maintain cell shape and anchor the organelles at their specific/fixed locations.
The protein fibers include actin filaments, microtubules, and intermediate filaments as
seen in Figure 10.

o actin filaments: responsible for cellular movements

o microtubules: organize the cytoplasm; responsible for moving materials within the
cell itself
o intermediate filaments: provide structural stability

Source: Mason, K. A., Losos, J. B., Duncan. T. Molecules that make up the cytoskeleton. Biology 13th Edition

Figure 10. Fibers composing the cytoskeleton

1.3.3.4 Centrioles
Centrioles are found in animal cells but not in plant cells. They come in pairs are
specifically located in the centrosome. Each centriole is composed of nine triplets of
microtubules. They function in organizing the microtubules during, for example, cell
division. See Figure 11.
Mason, K. A., Losos, J. B., Duncan. T. Centrioles. Biology 13th Edition
Figure 11. Structure of Centrioles

1.3.3.5 Extracellular Structures

The following are extracellular structures found in eukaryotic cells:

● Flagella: aid in cell movement and eukaryotic reproduction

● Cilia: short cellular projections characterized by a rhythmic waving or beating motion

● Plant Cell walls: chemically and structurally different from the cell wall of
prokaryotes; made up of carbohydrate polymers like cellulose and hemicellulose;
see Figure 12
o Primary Cell wall: provides flexibility and allow the cell to increase in size,
mainly made of cellulose, hemicellulose, glycans, and pectins

o Secondary Cell wall: formed between the primary cell wall and the plasma
membrane

Brooker, R. et al. Structure of Plant Cell Walls. Biology 5th Edition

Figure 12. Structure of Plant Cell Walls

● Extracellular matrix (ECM): a mixture of glycoproteins secreted by animal cells as
seen in Figure 13; embedded with collagen fibers and elastin fibers; acts as a
protective layer over the cell surface; provides cell strength and structural support;
acts a scaffold; involved in cell signaling

Mason, K. A., Losos, J. B., Duncan. T. The extracellular matrix. Biology 13th Edition

Figure 13. The extracellular matrix of animal cells

. Plant cells vs Animal Cells

Plant cells and animal cells are examples of eukaryotic cells. They share structural similarities but
there are some subcellular structures and organelles that are present in one but not in the other.
Shown in Figure 14 and Figure 15 are the structure of plant cells and animal cells, respectively. A
summary of these is provided in the table below. Included in the table are features that are
absent and present in prokaryotes too.

Source: Mason, K. A., Losos, J. B., Duncan. T. Structure of a plant cell. Biology 13th Edition

Figure 14. Structure of a Plant Cell

Mason, K. A., Losos, J. B., Duncan. T. Structure of an animal cell. Biology 13th Edition

Figure 15. Structure of an animal cell

Table 1. A comparison of prokaryotic cells, animal cells, and plant cells

Prokaryote Animal Plant

EXTERIOR STRUCTURES

Present
Cell wall (protein- Absent Present (cellulose)
polysaccharide)

Cell membrane Present Present Present

Flagella may be Absent except in sperm of a few

Flagella/cilia May be present
present species

INTERIOR STRUCTURES

Endoplasmic
Absent Usually present Usually present
reticulum

Ribosomes Absent Present Present

Microtubules Absent Present Present

Centrioles Absent Present Absent

Golgi apparatus Absent Present Present

Nucleus Absent Present Present

Mitochondria Absent Present Present

Chloroplasts Absent Absent Present

Multiple;
Multiple;
Chromosomes single; circular DNA DNA-protein
DNA-protein complex
complex
Lysosomes Absent Usually present Present

Vacuoles Absent Absent or small Usually a large single vacuole

What I can do (Activity 6: McGraw-Hill Connect SmartBook)

Directions:

1. Open your Cardinal Edge – Blackboard account.

2. Access McGraw-Hill Connect.
3. Click CO1 – Cell Structure Activity 6.
4. Answer the SmartBook questions related to the endomembrane system, cellular
generators, cytoskeleton, centriole, and extracellular structures.

1.5. Cell-to-Cell Interaction

Cells are physically connected to form a tissue. The connections are important in determining the type of
tissue formed and in maintaining cell-to-cell communication. There are three types of cell junctions as
shown in Figure 14.

Source: Mason, K. A., Losos, J. B., Duncan. T. Cell junction types in animal epithelium. Biology 13th Edition

Figure 14. Types of Cell junctions

MODULE

Cell Cycle vs Cell Division

The Cell Cycle is a series of events involving growth, synthesis, and regulations in a cell that results in
cell division. Cell division refers to the reproduction of cells or a process where a parent cell produces
new, daughter cells. In the succeeding sections of this module, the reproduction of cells in both
prokaryotes and eukaryotes is discussed. Generally, the reproduction of cells in prokaryotes is relatively
simpler compared to that occurring in eukaryotes.

Prokaryotic Cell Division: Binary Fission

Recall that prokaryotic cells such as bacterial cells are characterized by a circular and naked DNA.
During binary fission, the chromosome is replicated, and the two products are partitioned to each end of
the cell prior to the actual division of the cell. One key feature of bacterial cell division is that
replications and partitioning of the chromosome occur as a concerted process. In contrast, DNA
replication in eukaryotic occur erly in division, and chromosome separation occurs much later.

At the start of the binary fission and prior to cell division, the DNA of a parent cell replicates to produce
its identical copy. Replication of the bacterial DNA begins at a specific site - the origin of replication
and proceeds both directions around the circular DNA to a specific site of termination. At this point, all
other parts of the cell duplicates. During DNA replication, the bacterial cell also increases its length and
enlarges.

The cell's other components are partitioned by the growth of new membrane and production of the
septum. This process, known as septation, usually occurs at the midpoint of the cell. It begins with the
formation of a ring composed of many copies of the FtsZ protein. Next, accumulation of a number of
other proteins occurs, including ones embedded in the membrane. This structure contracts inward
radially until the cell pinches off into two new daughter cells.

Figure 1: Binary fission

The process of binary fission can continue wherein each daughter cell formed can now act as parent
cells that will each undergo DNA replication, elongation, and cell division to produce 2 daughter cells
each, a total of 4. Through binary fission, prokaryotic cells has an exponential growth. Reproduction of
cells in prokaryotes is affected by several conditions such as the medium where they are growing,
temperature, and nutrients available.

Eukaryotic Chromosome

Chromosomes have been found in the cells of all eukaryotes, although their numbers vary enormously
between different species. When defining the number of different chromosomes in a species, geneticist
count the haploid (n) number of chromosomes. This refers to on complete set of chromosomes
necessary to define an organism. For humans and many other species, the total number of
chromosomes in a cell is called diploid (2n) number, which is twice the haploid number. For humans,
the haploid is 23 and the diploid is 46. Diploid chromosomes reflect the equal genetic contribution that
each parent makes to offspring. We refer to the maternl and paternal chromosomes as being
homologous, and each of the pair is termed a homologue.

Chromosomes vary in size, staining properties, the location of a visible constricted region called the
centromere, and the relative length of the two arms on either side of the centromere. The particular
array of chromosomes an individual oorganism possesses is called karyotype.

When DNA is replicated, the single molecule in each chromosome becomes two identical DNA
molecules held together at their centromere by cohesins. As each chromosome becomes more
condensed, it becomes visible as the X-shaped structure in a karyotype. At this point, we still call this
on chromosome, but it is composed of two sister chromatids.

Figure 2: Homologous chromosome vs sister chromatids

Eukaryotic Cell Division

Eukaryotic cell cycle is more complex than the cell cycle in prokaryotes. This is because eukaryotes
have sets of chromosomes, which require proper sorting. The eukaryotic cell cycle is divided into
phases based on the key events of genome duplication and segregation:

​ Interphase (preparatory phase)

​ G1 (Gap Phase 1) is the primary growth phase of the cell. The term gap phase refers to its
filling the gap between cytokinesis and DNA synthesis. For most cells, this is the longest phase.
​ S (Synthesis) is the phase in which the cell synthesizes a replica of the genome.
​ G2 (Gap Phase 1) - is the second growth phase, and preparation for separation of the newly
replicated genome. This phase fills the gap between DNA synthesis and the beginning of
mitosis. During this phase microtuble begin to form a spindle
​ M phase (dividing phase)
​ Mitosis is the phase of the cell cycle in which the spindle fiber assembles, binds to
chromosomes, and moves the sister chromatids apart. It is an essential step in the separation
of the two daughter genomes. It is traditionally subdivided into five stages: Prophase,
Prometaphase, Metaphase, Anaphase, Telophase
​ Cytokinesis is the phase of the cell cycle when the cytoplasm divides, creating two daughter
cells. In animal cells, the microtuble spindle helps position a contracting ring of actin that
contricts like a drawsting to pinch the cell in two. In cells with a cell wall, such as plant cells, a
plat forms between the dividing cell.

Figure 3: The cell cycle

Mitosis

Mitosis is conventionallly divided into five stages which act to separate duplicated chromosomes. This
is followed by cytokinesis, which divides the cell into two separate cells.

Figure 4: Mitosis and cytokinesis

Five stages of mitosis:

​ Prophase
​ chromosomes that start phrophase as minute threads appear quite bulky
​ spindle fiber begins to form
​ nuclear envelope breaks down and endoplasmic reticulum reabsorbs its components
​ Prometaphase
​ transition from prophase to prometaphase occurs following the disassembly of the nuclear
envelope
​ condensed chromosomes becomes attached to the spindle by their kinetochores resulting to
each sister chromatid being connected to the opposite poles of the spindle
​ Metaphase
​ alignment of the chromosomes in the center of the cell
​ an imaginary plane perpendicular to the axis of the spindle that passes through this circle is
called the metaphase plate
​ Anaphase
​ removal of cohesin proteins that holds together the sister chromatid
​ sister chromatids are rapidly pulled toward the opposite poles to which their kinetochores are
attached
​ Telophase
​ spindle fiber disassembles as the microtubule are broken down into tubulin monomers that can
be used to construct the cytoskeletons of the daughter cells
​ nuclear envelope forms around each set of sister chromatids
​ chromosomes begin to uncoil into the more extended form that permits gene expression

Cytokinesis

​ Animal Cells
​ cytokinesis is achieved by means of constricting belt of actin filaments
​ as actin filaments slide past one another, the diameter of the belt decreases, pinching the cell
and creating a cleavage furrow around the cell's circumference.
​ Plant Cells
​ plant cells are far too rigid to be squeezed in two by actin filaments
​ cells assemble membrane components in their interior, this expanding membrane creates a
partition called a cell plate (forms from the fusion of Golgi-derived vesicles) continues to grow
outward until it reaches the interior of the plasma membrane and fuses with it, effectively
dividing the cell in two.
​ cellulose is then laid down on the new membranes, creating two new cell walls
Membrane Transport

Membrane Transportis a vital process done by cells for many important reasons. It occurs in various
mechanisms that allow cells to move food, water, and other important molecules, ions, and substances
in and out of cell. Membrane Transport follows a monitored and regulated way of transporting proteins,
lipids, and other molecules synthesized by the cell to the different compartments within it or even
transport these materials out of the cell. Membrane Transport also enables the selective passage of
materials from the external environment to inside of the cell. Membrane Transport also serves as a way
for cells to get rid of materials that are considered as wastes and/or toxins.

Most of these molecules, ions, substances, and other materials being transported in and out of the cell
are necessary to keep it healthy and surviving, and have the ability to perform its many cellular
functions. There are several structures in cells that participate in membrane transport. This includes the
plasma membranes, the membranes of the different membrane-bound organelles especially in
eukaryotic cells, and also transport vesicles. We are going to cover these structures in the succeeding
sections in this module.

Cell Membrane

Cell Transport is a highly regulated process. One of the specialized structures in cells that participates
in this highly regulated process is the plasma membrane. ThePlasma Membrane, also known as the
cell membrane, acts as a semi-permeable barrier in cells. As a barrier, it separates the interior of the
cell from its external or outside environment. Being semi-permeable, it indicates that it is selective of
what goes in and what goes out of the cell. The plasma membrane carefully monitors and chooses
what materials can or should enter and exit the cell. The key to this vital function of the plasma
membrane is its structure. It has components that are each characterized by distinct features and tasks.

Shown in Figure 1 is the biochemical organization of a plasma membrane. Below are the key structural
components of the plasma membrane following the Fluid-Mosaic Model.

1. Amphipathic Phospholipid Bilayer

​ The plasma membrane is composed of two layers of phospholipids, which are characterized
to be amphiphilic. Each layer of phospholipids is called a leaflet. One leaflet faces the outside of
the cell and the other faces the cytosol inside the cell. Each leaflet has hydrophobic tails and
hydrophilic heads. The hydrophobic tails of each layer are non-polar and water-fearing. They
are found in the interior of the plasma membrane facing towards each other. The hydrophilic
heads, on the other hand, are polar, water loving, and are found on the surfaces of the plasma
membrane.
​ Cholesterols affect the fluidity and the stability of the plasma membrane. How it affects the
plasma membrane depends on the temperature. Cholesterols make the plasma membrane less
fluid at high temperatures. On low temperatures, cholesterol makes the plasma membrane
more fluid and prevents it from freezing. Cells alter the amount of cholesterols present in their
plasma membrane depending on the temperature to keep the balance/homeostasis and restrict
the passage of molecules going in and out cells.

2. Transmembrane Protein

​ Actively or passively transport molecules across membrane; transmit information into cell
​ Integral membrane proteins - can span or insert themselves in the phospholipid bilayer. These
are tightly positioned in the plasma membrane and can only be removed if the plasma
membrane is disrupted.

3. Interior Protein Network

​ Structurally supports membrane by reinforcing the membrane’s shape

​ Peripheral or intracellular membrane proteins

4. Cell Surface Markers

​ Act as cell identity markers

​ These are carbohydrate chains found in the plasma membrane that are either attached to its
proteins or to the phospholipids.
​ Carbohydrate chains attached to lipids are called Glycolipids.
​ Carbohydrate chains attached to protein are called Glycoproteins
​ The carbohydrate chains are vital in stabilizing the structure of the plasma membrane
​ They also play key roles in cell recognition, which is important in selecting which materials enter
​ and exit the cell

Membrane Transport

Membrane Transportis a vital process done by cells for many important reasons. It occurs in various
mechanisms that allow cells to move food, water, and other important molecules, ions, and substances
in and out of cell. Membrane Transport follows a monitored and regulated way of transporting proteins,
lipids, and other molecules synthesized by the cell to the different compartments within it or even
transport these materials out of the cell. Membrane Transport also enables the selective passage of
materials from the external environment to inside of the cell. Membrane Transport also serves as a way
for cells to get rid of materials that are considered as wastes and/or toxins.

Most of these molecules, ions, substances, and other materials being transported in and out of the cell
are necessary to keep it healthy and surviving, and have the ability to perform its many cellular
functions. There are several structures in cells that participate in membrane transport. This includes the
plasma membranes, the membranes of the different membrane-bound organelles especially in
eukaryotic cells, and also transport vesicles. We are going to cover these structures in the succeeding
sections in this module.

Cells follow different mechanisms of membrane transport like Passive Transport, Active Transport, and
Vesicular Transport. These types of membrane transport are discussed in the succeeding sections of
this module. To fully understand how each type of membrane transport occurs, it is important that we
know what concentration gradient means. A concentration gradient refers to the difference in
concentration of a certain material between two different areas. Specifically in cells, a concentration
gradient means that the concentration of a solute is higher on one side of a membrane than on the
other. A type of concentration gradient is the chemical gradient. For example, you ate a meal with
carbohydrates. Immediately after eating, the concentration of carbohydrates like glucose is higher
outside of the cell than those found inside of the cell. Concentration gradient may also refer to
electrochemical gradient, which involves differences in both charge and chemical concentration
across a membrane. The electrochemical gradient mostly occurs if the materials being transported are
ions. The movement of ions in and out of a cell can cause electrochemical gradient.

Passive Transport

Passive Transport is a type of membrane transport in which the movement of a material across the
membrane is from an area of higher concentration to an area with lower concentration. Passive
transport follows the movement of materials down the concentration gradient. This type of membrane
transport does not require an energy input. The passive transport has two main mechanisms – Simple
Diffusion and Facilitated Diffusion.

​ Simple Diffusion is a transport mechanism that occurs when a substance passes directly
through the phospholipid bilayer of the plasma membrane. The substances moves from an area
with a high concentration to an area with low concentration, without the help of other structures
like proteins. An example of simple diffusion is when oxygen moves from the alveoli in our lungs
to the blood vessels. Simple diffusion also occurs when carbon dioxide moves from the blood
vessels to the alveoli in our lungs to be exhaled. Oxygen and carbon dioxide move directly
across plasma membrane.
​ Facilitated Diffusion is another type of passive transport. In this transport mechanism, a
substances needs help from a transport protein to cross the biological membrane. Most of
these substances are those that cannot pass through the hydrophobic region of the membrane
and hence they need a help from transport proteins that act as passageways/channels. The
movement of substances is still from an area with higher concentration to an area with lower
concentration. An example of facilitated diffusion is the transport of glucose. Glucose is a large
and polar molecule. Because of its size and polarity, it cannot simply or directly pass through
the cell membrane. Hence, it uses a carrier protein to help it enter the cell.
​ Osmosis is a type of passive transport that involves the movement of water molecules. In
osmosis, water moves from an area where there is low solute concentration to an area with a
high solute concentration. This occurs in order to balance the solute concentrations in the two
areas.

A cell is said to be isotonic when the solute concentration inside it is equal to the solute concentration
outside of it. A cell is hypertonic if the solute concentration is higher outside of the cell than inside. A
cell is hypotonic if the solute concentration outside of it is lower compared to that in the inside.

How does osmosis affect the different types of cells? If healthy red blood cells are, for example, placed
in a hypertonic solution, the cells may soon start to shrink because water keeps exiting the cell. This is
known as crenation. If, on the other hand, red blood cells are placed in a hypotonic solution, water
goes into the cell and so the result will be swelling of the cells. When cells swell, it can lead to osmotic
lysis wherein cells are ruptured.

Another example is the case for plant cells. When plant cells are placed in a hypertonic solution, the
volume inside the plasma membrane shrinks and so the membrane moves away from the cell wall
resulting to plasmolysis. When plant cells are placed in a hypotonic solution, only a small amount of
water enters the cell but the cel wall prevents major expansions.

Active Transport

Active Transport is a type of membrane transport characterized by the movement of substances from
an area of low concentration to an area of high concentration with the help of specialized transport
proteins. The mechanism of transport is against the concentration gradient. Unlike passive transport
mechanisms, active transport requires an energy input from an energy-carrying molecules like ATP or
adenosine triphosphate. Examples of Active Transport are sodium-potassium pump, exocytosis and
endocytosis.

​ Sodium-Potassium Pump. The same carrier protein transports sodium ions (Na+) to the
ourside of the cell and potassium ions (K+) to the inside of the cell, because it undergoes an
ATP-dependent change in shape. Three sodium ions are carried outward for every two
potassium ions carried inward. Therefore, the inside of the cell is less positively charged
compared to the outside.

​
​
​ Exocytosis is a type of membrane transport in which the materials inside the cell are placed in
vesicles usually secreted/produced by the golgi body. Once the materials are packed in the
vesicles, they are then ready to be transported into the extracellular environment. An example
of how exocytosis occurs is when our neurons or nerve cells release neurotransmitters. A
neuron sends signals and information to another neuron by releasing neurotransmitters. These
neurotransmitters initially enclosed in synaptic vesicles. Then, these synaptic vesicles fuse with
the plasma membrane to release the neurotransmitters.

​ Endocytosis is a type of membrane transport wherein a material from the extracellular

environment is brough into the cell. The plasma membrane folds inward to create a vesicle that
will carry and release the material into the cell. Three different types of endocytosis are
receptor-mediated endocytosis, pinocytosis, and phagocytosis.
​ Receptor-mediated Endocytosis – In this type of membrane transport, receptors are found in
the plasma membrane of the cell. These receptors are only able to bind to a specific ligand.
When the receptors are already bound to the ligands, the plasma membrane then creates the
vesicles carrying them and eventually release them into the cell.
​
​ Pinocytosis (Cell-Drinking) – This is a type of membrane transport in which the plasma
membrane creates vesicles that carry fluids from the extracellular environment and then release
them inside the cell. This type of membrane transport is most common for cells whose function
is the absorption of nutrients and other important molecules needed for survival.
​
​ Phagocytosis (Cell-Eating) – This type of membrane transport involves the formation of large
vesicles from the plasma membrane enough to engulf large materials and pathogens like
bacteria. Phagocytosis is a common type of membrane transport in cells that are part of the
immune system. Cells of the immune system like macrophages undergo phagocytosis to kill
pathogens or stop them from infecting the body.

Contents:

​ Polymer vs Monomer
​ Dehydration Synthesis vs Hydrolysis
​ Carbohydrate
​ Lipids

The term organic is used to identify those molecules and compounds that contain both carbon and
hydrogen atoms. Living organisms contain only four classes of organic molecules: carbohydrates,
lipids, proteins, and nucleic acids. Collectively these are called biomolecules, and despite the limited
number of types, their functions in a cell are quite diverse. The diversity of life is possible because of
the diversity of organic molecules. Despite their functional differences, the variety of organic molecules
is based on the unique chemical properties of the carbon atom.

The Carbon Atom

Carbon is the basis of life as we know it. What is there about carbon that makes organic molecules the
same but also different? Carbon is quite small, with only a total of six electorin: two electrons in the first
shell and four electrons in the outer shell. To acquire four electorns to complete its outer shell, a carbon
atom almost always forms covalent bonds. Carbon can form covalent bonds with as many as four other
elements. Generally, carbon forms those bonds with other atoms of carbon, plus hydrogen, nitrogen,
oxygen, phosphorus, and sulfur - the same elemetns that make up most of the weight of living
organisms. The ability of carbon to share electrons with other carbon atoms plays an important role in
establishing the shape, and therefore the function, of the biomolecules. This is because the C-C bond is
very stable and allows the formation of long carbon chains. The molecules termed hydrocarbons, such
as the octane molecule below, are chains of carbon atoms that have additional bonds exclusively with
hydrogen atoms.

In addition to long, linear molecules, hydrocarbons may also form a ring structure when placed in a
water environment:

In addition to forming single bonds, carbon can form double bonds with itself and other atoms. Double
bonds aren't flexible as single bonds, and they restrict the movement of bonded atoms. Double bonds
affect a molecule's shape and therefore influence its function. The presence of double bonds is one
way to distinguish between saturated and unsaturated fats, which are important to heart health. Carbon
is also capable of forming triple bonds with itself. Branches may also form at any carbon atom, allowing
the formation of long, complex carbon chains. This flexibilty makes carbon the ideal building block for
biomolecules, and it plays an important role in establishing the diversity of organic molecules we
observe in nature.

The Biomolecules of Cells

Many biological molecules you are familiar with, such as carbohydrates, lipids, proteins, and nucleic
acids, are macromolecules, meaning they contain smaller subunits joined together. The carbohydrates,
proteins, and nucleic acids are referred to as polymers (macromolecule consisting of covalently bonded
monomers), because they are constructed by linking together a large number of the same type of
subunit, called a monomer (small molecule that is a subunit of a polymer). Lipids do not form polymers,
because they contain two different types of subunits (glycerol and fatty acids).

Category Subunit (monomers) Polymer

Carbohydrates Monosaccharide Polysaccharide

Lipids Glycerol and fatty acids Does not form polymer

Proteins Amino Acids Polypeptide

Nucleic Acids Nucleotides DNA, RNA

Assembly and Disassembly of Polymers

To build, or synthesize, a macromolecule, the cell uses a condensation reaction in which subunits are
joined to form a larger structure. This is commonly called a dehydration reaction, because the
equivalent of a water molecule – that is, an -OH (hydroxyl group) and an-H (hydrogen atom) – is
removed as subunits are joined. Therefore, water molecules are formed as biomolecules are
synthesized.

To break down biomolecules, a cell uses a degradation type of reaction. During a hydrolysis reaction
(Gk. Hydro, “water”; lyse, “break”), an OH- group from water attaches to one subunit, and an -H from
water attaches to the other subunit. In other words, hydrolytic reactions break down biomolecules by
adding water to them. These reactions rarely occur spontaneously. Usually, special molecules called
enzymes act as catalyst, speeding up the rate of the reaction and allowing it to occur in a functional
amount of time.

NUCLEIC ACIDS AND PROTEINS

Contents:

​ Nucleic Acid
​ Proteins
​ Summary

NUCLEIC ACIDS

Nucleic acids are the biomolecules in charge of the storage, expression, and transmission of genetic
information. Genetic information refers to the inheritable and unique identity of organisms. Nucleic acids
include DNA and RNA. DNA stands for deoxyribonucleic acid while RNA means ribonucleic acid. DNA
contains genes that provide the direction for its own replication. It also directs the synthesis of RNA
needed for protein synthesis. RNA also plays a major role in protein synthesis. Both DNA and RNA are
polymers of nucleotides. Nucleotides are the repeating monomer units in nucleic acids. Each nucleotide
is composed of three parts: 1) phosphate group, 2) pentose (composed of 5 carbon atoms) sugar, and
3) nitrogenous base. The phosphate groups and pentose sugars form the backbone in the structure of
nucleic acids. The nitrogenous bases form the rungs (ladder).
DNA vs RNA

The nucleotides in DNA are called deoxyribonucleotides while those for RNA are called ribonucleotides.
The phosphate groups in both DNA and RNA link the 3' carbon of one nucleotide to the 5' carbon of
another nucleotide. The sugar in DNA is called deoxyribose while the sugar in RNA is called ribose.
Both deoxyribose and ribose are classified as pentose, a monosaccharide with 5 carbon atoms. In
ribose, each carbon atom is linked to an oxygen atom. In deoxyribose, its 2' carbon is not linked to an
oxygen atom, hence the term "deoxy'. This is illustrated in Figure 3. Both DNA and RNA have 4
nitrogenous bases. These nitrogenous bases are classified into two: purines and pyrimidines. In DNA,
the nitrogenous bases are adenine (A), guanine (G), cytosine (C), and thymine (T). In RNA, thymine is
replaced by uracil (U). Adenine and guanine are purines. Cytosine, thymine, and uracil are pyrimidines.
Purines are characterized to have 2 rings, a 6-membered ring fused with a 5-membered ring.
Pyrimidines, on the other hand, only have one 6-membered ring.

DNA has a double-helix structure. It has two strands that are connected via the complementary pairing
of the nitrogenous bases. The nitrogenous bases follow the Chargaffs rule of Nucleotide Base Pairing,
which states that in a DNA sample of any organism, the amount of adenine is equal to the amount of
thymine. Likewise, the amount of guanine in that DNA sample is equal to the amount of cytosine
present. In other terms, the Chargaffs rule of nucleotide base pairing also tells us that the total amount
of purines in that DNA sample is equal to the total amount of pyrimidines (A + G = T + C). This
suggests purines always pair with pyrimidines. To be specific, adenine pairs with thymine whereas
guanine pairs with cytosine. Adenine and thymine are held together by 2 hydrogen bonds. Guanine and
cytosine are held together by 3 hydrogen bonds. The connection between guanine and cytosine are
harder to break than that between adenine and thymine. These hydrogen bonds between nitrogenous
bases are what connects the two strands of DNA together. The two strands of DNA also follow an
antiparallel orientation, which means that the two strands run in opposite directions. One strand
stretches in the 3' to 5' direction. The other stretches in the 5' to 3' direction. RNA is single-stranded. It
is also made up of 4 nucleotides. Recall that in RNA, thymine is replaced by uracil. Thus, RNA contains
adenine, guanine, uracil, and cytosine. During the process of expressing the genetic information,
adenine pairs with uracil. Guanine still pairs with cytosine.

Comprehension Check: Consider the DNA nucleotide sequence below. What will be the
complementary base pairing in DNA? What will be the complementary base pairing in RNA?

​ ATG CCG ATT

​ CGC ACG GTA
​ CCC GGG GC
​ ATA TAA GAA

SUMMARY

PROTEINS

Proteins are polymers of amino acids. Amino acids are organic molecules with a carbon atom called
α-carbon) that is connected to a carboxyl group (-COOH) and an amino group (-NH2). They are also
linked to a hydrogen atom and to various side chains (R). See figure below:

Structure of an Amino Acid

In humans, for example, there are 20 amino acids that are all required to synthesize nearly all the
proteins needed by the body. These 20 amino acids differ from one another because each of them has
a unique side chain. These are also categorized into groups according to whether they are non-polar or
polar (charged / uncharged). See Figure S. The unique side chains of amino acids are what dictates
their chemical properties, structure, and functions. Non-polar amino acids are hydrophobic, which
means that they do not like interacting with water molecules. Other amino acids, on the other hand, are
polar which means that they are hydrophilic or water-leaving. Some polar amino acids are neutral
(uncharged) while the other polar amino acids are charged. Polar and charged amino acids may have
acidic or basic side chains.

Amino Acid

In the 20 amino acids that the human body needs, only 11 of them are naturally produced. The other 9
are called essential amino acids. Essential amino acids that cannot be produced naturally by the body
and so we obtain them from external sources such as food and supplements. Essential amino acids
include Methionine, Threonine, Histidine, Valine, Phenylalanine, Isoleucine, Tryptophan, Lysine,
and Leucine.

Polypeptides

When amino acids are covalently linked together by peptide bonds, a linear chain of polypeptide is
formed. Amino acids are linked together via a dehydration reaction wherein the carboxyl group of one
amino acid is connected to the amino group of another amino acid. One end of a polypeptide is called
the N-terminus (amino end) while the other end is called the C-terminus (carboxyl end). See Figure
below. The side chains of the amino acids are projecting from the backbone.

Proteins can be made from one or more polypeptides. When the polypeptides obtain a specific folding,
the 3-dimensional structure of a protein is formed. The structure of a protein is what dictates its
function.

Protein Structure and Function

The structure of a protein follows a hierarchy. It starts from a linear chain of polypeptide having a
specific sequence of amino acids that progresses to a 3-dimensional structure. See Figure 7. This
specific sequence of amino acids in a polypeptide is based on the specific sequences of nucleotides in
DNA and RNA. The specific sequence of amino acids in the polypeptide chain the primary structure of
a protein. The secondary structure of a protein is obtained when portions of the polypeptide chain form
hydrogen bonds that cause them to have a local folding that is categorized into two types: a-helices
(spiral) or pleated sheets (zigzag). When the secondary structure becomes stable, side chains of the
amino acids in the polypeptides begin to interact with each other. This causes the protein to do further
folding which results to a dimensional structure. The tertiary structure of a protein refers to the local
folding of the polypeptides (a-helices or pleated sheets) plus the interactions between side chains of
amino acids. When a protein is composed of two or more polypeptides that are each characterized by a
tertiary structure, each of these polypeptides are called protein subunits. When these protein subunits
interact with each other, the quaternary structure of a protein is formed.

Hierarchy of Protein Structure

The function of a protein depends on its structure. When the structure of a protein changes, its function
can also change. As mentioned, the primary structure of a protein depends on the specific sequence of
nucleotides in DNA and RNA. This means when a change in the sequence of nucleotides in the nucleic
acids occurs, it can affect the overall structure of the protein. Since the structure is changed, the
function can also change. This is evident, for example, in Sickle Cell Anemia. Sickle cell anemia is an
inherited disorder in which the body has no sufficient healthy red blood cells to carry and deliver oxygen
to the different parts of the body. Figure 8a shows a portion of the amino acid sequence for the protein
hemoglobin. Hemoglobin is a part of the red blood cells where oxygen binds. This the correct sequence
and so the hemoglobin works well and the red blood cells are healthy. When amino acid 6, glutamate,
has been changed to valine, as shown in , it means that the primary structure of hemoglobin has been
changed. This results to changing the function of the hemoglobin. Sickled red blood cells are then
present, which are unable to deliver oxygen properly.

The structure of proteins changes due to many factors. This includes changes in pH, salt concentration,
temperature, and other environmental factors. Exposing proteins to unfavorable conditions causes
them to denature and become inactive. When proteins denature, the structure changes. When the
structure changes and so does the function.

In living organisms, proteins have a wide range of functions that are critical to life processes. Some of
their functions are listed below:

​ Enzymes — proteins that speed up biological and chemical reactions.

​ Structural proteins — proteins that provide physical support and shape to cells and
organelles.
​ Motility Proteins — proteins that provide command or aid in the contraction and movement of
cells and intracellular structures.
​ Regulatory Proteins — proteins that control and coordinate cellular functions.
​ Transport Proteins — proteins that help monitor and regulate the movement of materials into,
out of, and within the cell.
​ Hormonal Proteins — proteins that mediate intracellular communication especially between
cells in distant parts of an organism.
​ Defensive Proteins — proteins that help in protecting an organism against a disease.
​ Storage Proteins — proteins that act as reservoirs.

Summary

Comprehension Check: Consider the DNA nucleotide sequences below. What will be the sequence of
the messenger RNA transcript? What will be the sequence of amino acids? Use the amino acid table
provided.

Translation table

DNA Nucleotide Sequence: TAC CCG AGG AGG CCA ATC

mRNA Sequence:

Amino Acid Sequence:

https://youtu.be/8oodcy8SEBk?si=GFKVmeSNEieSAgOr

Other Types of Photosynthesis: C4 and CAM

C3 PHOTOSYNTHESIS

​ C3 plants use the enzyme RuBP carboxylase to fix XO2 to RuBP in mesophyll (photosynthetic)
cells. The first detected molecule following fixation is the 3-carbon molecule 3PG: RuBP + CO2
-> 2 3PG
​ Leaves have small opening called stomata, through which water can leave and carbon dioxide
(CO2) can enter. If the weather is hot and dry, the stomata close, conserving water. (Water loss
might cause the plant to wilt and die). Now th concentration of CO2 decreases in leaves, while
O2 rises in C3 plants, RuBP carboxylase combines it with RuBP instead of CO2. The result is
one molecule of 3PG and the eventual release of CO2. This is called photorespiration,
because in the presence of light (photo), oxygen is taken up and CO2 is released (respiration)

C4 PHOTOSYNTHESIS

​ In a C3 plant, the mesophyll cells contain well-informed chloroplast and are arranged in parallel
layers. In a C4 lead, the bundle sheath, as well as the mesophyll cells, contain chloroplast.
Further, the mesophyll cells are arranged concentrically aroun the bundle sheet cells.
​ C4 plants fix CO2 to PEP (phosphoenolpyruvate, a C3 molecule) using the enzyme PEP
carboxylase (PEPCase). The result is oxaloacetate, a C4 molecule: PEP + CO2 ->
oxaloacetate.
​ In C4 plant, CO2 is taken up in mesophyll cells, and then malate, a reduced form of
oxaloacetate, is pumped into the bundle sheath cells. Only here does CO2 enter the Calvin
Cycle.

CAM PHOTOSYNTHESIS

​ CAM stands for crassulacean-acid metabolism: the Crassulaceae is a family of flowering

succulent (water-containing) plants, such as a pineapple plant, that live in warm, dry region of
the world.
​ During the night, CAM plants use PEPCase to fix some CO2, forming C4 molecules, which
are stored in large vacuoles in mesophyll cells.
​ During the day, C4 molecules (malate) release CO2 to the Calvin cycle when ADPH and ATP
are available from the light reactions.
​ The primary advantage for this partitioning again has to do with conservation of water. CAM
plants open their stomata only at night; therefore, only at that time does atmospheric CO2 enter
the plant. During the day, the stomata close; this conserves water, but CO2 cannot enter the
plant.