Lesson 1: The Cell Theory

Cells are the basic building blocks of all living things. The human body is composed of
trillions of cells. They provide structure for the body, take in nutrients from food, convert
those nutrients into energy, and carry out specialized functions. Cells also contain the
body’s hereditary material and can make copies of themselves.
Cells have many parts, each with a different function. Some of these parts,
called organelles, are specialized structures that perform certain tasks within the cell.
In this lesson, you are to explain the postulates of the cell theory. The three
postulates of the cell theory offer the basis on how an organism is considered as a living
thing.
 Prior to the invention of the very first microscope, everything that could not be
seen by the naked eye was unexplainable. In 1665, English physicist Robert Hooke
used of the first light microscopes to look at thin slices of plant tissues. One of these, a
slice of cork, especially caught his eye. Under the microscope, cork seemed to be made
of thousands of tiny chambers. Hooke called this chambers “cells” because they
reminded him of a monastery’s tiny rooms, which were also known as cells. Until 1676,
Anton van Leeuwenhoek published his observations on tiny living organisms which he
named animalcules. It was believed that Leeuwenhoek was the first to observe under
his microscope the structure of a red blood cell of different animals as well as a sperm
cell.

One of the leading botanists in his time, Robert Brown in 1831 was able to
compare diverse kinds of plant specimens under the microscope. He markedly indicated
that there is a common thing about them-they are all composed of cells, and inside the
cell is a dark dense spot which he termed as the nucleus. A few years later, German
botanist Matthias Schleiden (1838) concluded that all plant parts are made of cells.
Theodor Schwann (1839), a zoologist and a close friend of Schleiden, stated that all
animal tissues are composed of cells, too. In 1858, Rudolf Virchow concluded that all
cells come from pre-existing cells.

Figure 1.1. Structure of cork using a microscope as seen by Robert Hooke (1665)

The discoveries made by Hooke, Leeuwenhoek, Schleiden, Schwann, Virchow,

and others led to the formulation of the cell theory. The cell theory describes the
properties of all cells. This theory can be summed up into three basic components: (1)
all living things are composed of one or more cells; (2) the cell is the basic unit of life;
and (3) all cells arise from pre-existing cells.
Now, that you have an understanding of the history of the cell theory, answer the
activity that follows.
 Lesson 2: Cell Structure and Functions
All living organisms are made up of one or many cells. The cells are the building
block of life just as atoms are the basic building blocks of all matter. Each cell contains
materials that carry out basic life processes. Cell structures can only be observed under
high magnification electron microscope and are separated internally into numerous
membranous compartments called organelles (little organs). These organelles perform
a variety of functions like production of proteins, storage of important materials,
harvesting energy, repairing cell parts, digestion of substances, and maintaining the
shape and structure of the cell.
 In this lesson, you will describe the structure and function of major subcellular
organelles.

Cell Structure and Functions

Cells’ Functions
Structures
1. Cell 1. Separates cell from external environment; controls passage of
Membrane organic molecules, ions, water, oxygen and wastes into and out of
the cell
2. Cytoplasm 2. Provides structure to cell; site of many metabolic reactions;
medium in which organelles are found
3. Nucleolus 3. Location of DNA
4. Nucleus 4. Cell organelle that houses DNA and directs synthesis of
ribosomes and proteins
5. Ribosomes 5. Protein synthesis
6. Mitochondria 6. ATP production or cellular respiration
7. Peroxisomes 7. Oxidizes and breaks down fatty acids and amino acids and
detoxifies poisons
8. Vesicles and 8. Storage and transport; digestive function in plant cells
Vacuoles
9. Centrosome 9. Unspecified role in cell division in animal cells; organizing
center of microtubules in animal cells
10. Lysosomes 10. Digestion of macromolecules; recycling or worn out organelles
11. Cell wall 11. Protection, structural support and maintenance of cell shape
12. Chloroplast 12. Photosynthesis
13. Endoplasmic 13. Modifies proteins and synthesizes lipids
reticulum
14. Golgi 14. Modifies, sorts, tags, packages and distributes lipids and
 apparatus proteins
15. Cytoskeleton 15. Maintains cell’s shape, secure organelles on specific positions,
allows cytoplasm and vesicles to move within the cell, and enables
unicellular organisms to move independently
16. Flagella 16. Cellular locomotion
17. Cilia 17. Cellular locomotion, movement of particles along extracellular
surface of plasma membrane, and filtration

Lesson 3: Prokaryotic vs Eukaryotic Cells

Prokaryotes vs Eukaryotes
Most living things you know such as animals and plants are multicellular
organisms. Some living things are made up of only single cell. Single-celled or
unicellular organisms include the bacteria, some protists, and some fungi. Even though
composed of single cells, these organisms carry out all the functions necessary for life.
In different organisms, cells also vary in sizes, shapes, parts, and functions. But they all
have one thing in common: they make up all living things and they are living.
There are two kinds of organisms according to their cell structure, the
prokaryotes and eukaryotes. The difference between prokaryotic and eukaryotic
organisms is said to be the most important distinction among the groups of living things.
Prokaryotes are single-celled organisms that lack a membrane-bound nucleus,
mitochondria, and all other organelles. Its name comes from the Greek words pro,
which means “before”, and karyon, which means “nut or kernel”. Eukaryotes are
organisms with cells that contain membrane-bound nucleus and other membrane-bound
organelles. The nucleus of a eukaryotic cell contains the genetic material (DNA),
enclosed by a nuclear envelope. Other membrane-bound organelles are mitochondria,
Golgi apparatus, and chloroplast found in photosynthetic organisms such as algae and
plants. There are also unicellular eukaryotes known as protozoa. All other eukaryotes
are multicellular organisms such as plants, animals, and fungi.

Lesson 4: Cell Types and Cell Modification

There are hundreds of types of cells, but the four main types are epithelial cells,
connective tissue cells, muscle cells and nerve cells.
Epithelial Tissue—This type of tissue is commonly seen outside the body as coverings
or as linings of organs and cavities. Epithelial tissues are characterized by closely-
joined cells with tight junctions (i.e., a type of cell modification). Being tightly packed,
tight junctions serve as barriers for pathogens, mechanical injuries, and fluid loss.

Cells that make up epithelial tissues can have distinct arrangements:

• cuboidal—for secretion
• simple columnar—brick-shaped cells; for secretion and active absorption
• simple squamous—plate-like cells; for exchange of material through diffusion
• stratified squamous—multilayered and regenerates quickly; for protection
• pseudo-stratified columnar—single layer of cells; may just look stacked because of
varying height; for lining of respiratory tract; usually lined with cilia (i.e., a type of cell
modification that sweeps the mucus).

Figure 1: Epithelial Tissue (Source: Reece JB, U. L. (2010). Campbell Biology 10th. San Francisco (CA).)

Connective Tissue—These tissues are composed of the following:

BLOOD —made up of plasma (i.e., liquid extracellular matrix); contains water, salts,
and dissolved proteins; erythrocytes that carry oxygen (RBC), leukocytes for defense
(WBC), and platelets for blood clotting.

CONNECTIVE TISSUE PROPER (CTP)—made up of loose connective tissue that is

found in the skin and fibrous connective tissue that is made up of collagenous fibers
found in tendons and ligaments. Adipose tissues are also examples of loose connective
tissues that store fats which functions to insulate the body and store energy.
CARTILAGE —characterized by collagenous fibers embedded in chondroitin sulfate.
Chondrocytes are the cells that secrete collagen and chondroitin sulfate. Cartilage
functions as cushion between bones.

BONE —mineralized connective tissue made by bone-forming cells called osteoblasts

which deposit collagen. The matrix of collagen is combined with calcium, magnesium,
and phosphate ions to make the bone hard. Blood vessels and nerves are found at a
central canal surrounded by concentric circles of osteons.

Figure 2: Connective Tissue (Source: Reece JB, U. L. (2010). Campbell Biology 10th. San Francisco
(CA).)

Muscle Tissue—These tissues are composed of long cells called muscle fibers that
allow the body to move voluntary or involuntary. Movement of muscles is a response to
signals coming from nerve cells. In vertebrates, these muscles can be categorized into
the following:
• skeletal—striated; voluntary movements
• cardiac—striated with intercalated disk for synchronized heart contraction; involuntary
• smooth—not striated; involuntary
Figure 3: Muscle Tissue (Source: Reece JB, U. L. (2010). Campbell Biology 10th. San Francisco (CA).)

Nervous Tissue—These tissues are composed of nerve cells called neurons and glial
cells that function as support cells. These neurons sense stimuli and transmit electrical
signals throughout the animal body. Neurons connect to other neurons to send signals.
The dendrite is the part of the neuron that receives impulses from other neurons while
the axon is the part where the impulse is transmitted to other neurons.

Figure 4: Neurons and Glial Cells (Source: Reece JB, U. L. (2010). Campbell Biology 10th. San Francisco
(CA).)

Lesson 5: Cell Cycle

How much did you weigh when you were in quarantine periods due to pandemic COVID
19? Did you increase in weight or in height? Probably, much of growth happens to you
because you are just staying at home and all you can do are eating, watching television,
and sleeping. Your body needed millions of new cells to become as large as you are
now!
Have you experienced to get cuts and bruises and few days after, they are
healing? Have you noticed your worn-out cells on the sole of your feet are being
replaced?
How does this happen? Your cells throughout your body are growing, dividing
and repairing through the process called cell division which involves the distribution of
identical genetic material or DNA to two daughter cells. There are two ways by which
cells increase in number: a somatic cell division in which each daughter cell is
genetically identical to the parent cell (mitosis), and a reproductive cell division, in
which, the number of chromosomes in the daughter cells is reduced by half to produce
haploid gametes (meiosis).

In the previous activity, you were asked to color the cell cycle, which is the
process a cell undertakes to replicate all of its material and divide into two identical
cells. Cell cycle is comprised of a 4-stage-process consisting of Gap 1 (G1), Synthesis,
Gap 2 (G2) and mitosis. The Cell Cycle control system is driven by a built-in clock that
can be adjusted by external stimuli (i.e., chemical messages). The progression of cells
through the cell cycle is controlled by checkpoints at different stages. Checkpoint is a
critical control point in the Cell Cycle where ‘stop’ and ‘go-ahead’ signals can regulate
the cell cycle. Animal cells have built-in ‘stop’ signals that halt the cell cycles and
checkpoints until overridden by ‘go-ahead’ signals. • The three major checkpoints are
found in the G1, G2, and M phases of the Cell Cycle.
The G1 Checkpoint (the Restriction Point) ensures that the cell is large enough
to divide and that enough nutrients are available to support the resulting daughter cells.
If a cell receives a ‘go-ahead’ signal at the G1 checkpoint, it will usually continue with
the Cell Cycle. • If the cell does not receive the ‘go-ahead’ signal, it will exit the Cell
Cycle and switch to a non-dividing state called G0. Most cells in the human body are in
the G0 phase.
The G2 Checkpoint ensures that DNA replication in S phase has been
successfully completed.
The Metaphase Checkpoint ensures that all of the chromosomes are attached
to the mitotic spindle by a kinetochore.
Kinase is a protein which activates or deactivates another protein by
phosphorylating them. Kinases give the ‘go-ahead’ signals at the G1 and G2
checkpoints. The kinases that drive these checkpoints must themselves be activated.
The activating molecule is a cyclin, a protein that derives its name from its cyclically
fluctuating concentration in the cell. Because of this requirement, these kinases are
called cyclin-dependent kinases or CDKs. Cyclins accumulate during the G1, S, and G2
phases of the Cell Cycle. By the G2 checkpoint, enough cyclin is available to form MPF
complexes (aggregations of CDK and cyclin) which initiate mitosis. MPF functions by
phosphorylating key proteins in the mitotic sequence. Later in mitosis, MPF switches
itself off by initiating a process which leads to the destruction of cyclin. CDK, the non-
cyclin part of MPF, persists in the cell as an inactive form until it associates with new
cyclin molecules synthesized during the interphase of the next round of the Cell Cycle.
 Mitosis (apparent division) is nuclear division; the process by which the nucleus
divides to produce two new nuclei. Mitosis results in two daughter cells that are
genetically identical to each other and to the parental cell from which they came. Prior to
mitosis, the DNA replicates, and this is referred to as S or synthesis stage. The period
before and immediately after S are referred to as G1 and G2, respectively (G1-
presythetic and G2-postsynthethic). The major event in cell division is the splitting of the
nucleus (karyokinesis) followed by cytokinesis, which is the division of the cytoplasm.
Both mitosis and cytokinesis last for around one to two hours. Mitosis can be described
as occurring in four major phases:
Prophase—is the preparatory stage, during prophase, centrioles move toward opposite sides
of the nucleus. The initially indistinct chromosomes begin to condense into visible
threads. Chromosomes first become visible during early prophase as long, thin,
and intertwined filaments but by late prophase, chromosomes are more
compacted and can be clearly discerned as much shorter and rod-like structures.
As the chromosomes become more distinct, the nucleoli also become more
distinct. By the end of prophase, the nucleoli become less distinct, often
disappearing altogether.

Metaphase—is when chromosomes become arranged so that their centromeres become

aligned in one place, halfway between the two spindle poles. The long axes of
the chromosomes are 90 degrees to the spindle axis. The plane of alignment is
called the metaphase plate.

Anaphase—is initiated by the separation of sister chromatids at their junction point at the
centromere. The daughter chromosomes then move toward the poles.

Telophase—is when daughter chromosomes complete their migration to the poles. The two
sets of progeny chromosomes are assembled into two-groups at opposite ends
of the cell. The chromosomes uncoil and assume their extended form during
interphase. A nuclear membrane then forms around each chromosome group
and the spindle microtubules disappear. Soon, the nucleolus reforms.

Meiosis is a reproductive cell division. While in mitosis all your body cells
develop, meiosis form all your germ cells—the sperm and the egg cells. It is the type of
cell division which reduces the amount of genetic information. While mitosis in diploid
cells produces daughter cells with a full diploid complement, meiosis produces haploid
gametes or spores with only one set of chromosomes. During sexual reproduction,
gametes combine in fertilization to reconstitute the diploid complement found in parental
cells. The process involves two successive divisions of a diploid nucleus.

First Meiotic Division The first meiotic division results in reducing the number of
chromosomes (reduction division). In most cases, the division is accompanied by
cytokinesis.
 Prophase I—has been subdivided into five substages: leptonema, zygonema,
pachynema, diplonema, and diakinesis.
Leptonema—Replicated chromosomes have coiled and are already visible. The
number of chromosomes present is the same as the number in the diploid cell.
Zygonema—Homologue chromosomes begin to pair and twist around each
other in a highly specific manner. The pairing is called synapsis. And because the pair
consists of four chromatids it is referred to as bivalent tetrad.
Pachynema—Chromosomes become much shorter and thicker. A form of
physical exchange between homologues takes place at specific regions. The process of
physical exchange of a chromosome region is called crossing-over. Through the
mechanism of crossing-over, the parts of the homologous chromosomes are
recombined (genetic recombination).
Diplonema—The two pairs of sister chromatids begin to separate from each
other. It is at this point where crossing-over is shown to have taken place. The area of
contact between two non-sister chromatids, called chiasma, become evident.
Diakinesis—The four chromatids of each tetrad are even more condensed and
the chiasma often terminalize or move down the chromatids to the ends. This delays the
separation of homologous chromosomes.

In addition, the nucleoli disappear, and the nuclear membrane begins to break
down.

Metaphase I—The spindle apparatus is completely formed and the microtubules

are attached to the centromere regions of the homologues. The synapsed tetrads are
found aligned at the metaphase plate (the equatorial plane of the cell) instead of only
replicated chromosomes.

Anaphase I—Chromosomes in each tetrad separate and migrate toward the

opposite poles. The sister chromatids (dyads) remain attached at their respective
centromere regions.

Telophase I—The dyads complete their migration to the poles. New nuclear
membranes may form. In most species, cytokinesis follows, producing two daughter
cells. Each has a nucleus containing only one set of chromosomes (haploid level) in a
replicated form.

Second Meiotic Division The events in the second meiotic division are quite
similar to mitotic division. The difference lies, however, in the number of chromosomes
that each daughter cell receives. While the original chromosome number is maintained
in mitosis, the number is reduced to half in meiosis.

Prophase II—The dyads contract.

Metaphase II—The centromeres are directed to the equatorial plate and then divide.
Anaphase II—The sister chromatids (monads) move away from each other and migrate
to the opposite poles of the spindle fiber.
Telophase II—The monads are at the poles, forming two groups of chromosomes. A
nuclear membrane forms around each set of chromosomes and cytokinesis follows. The
chromosomes uncoil and extend.

Cytokinesis—The telophase stage of mitosis is accompanied by cytokinesis. The two

nuclei are compartmentalized into separate daughter cells and complete the mitotic cell
division process. In animal cells, cytokinesis occurs by the formation of a constriction in
the middle of the cell until two daughter cells are formed. The constriction is often called
cleavage, or cell furrow. However, in most plant cells this constriction is not evident.
Instead, a new cell membrane and cell wall are assembled between the two nuclei to
form a cell plate. Each side of the cell plate is coated with a cell wall that eventually
forms the two progeny cells.

Table 1: Comparison of Mitosis and Meiosis

Meiosis
1. Requires two nuclear divisions
2. Chromosomes synapse and cross over
3. Centromeres survive Anaphase 1
4. Halves chromosome number
5. Produces four daughter nuclei
6. Produces daughter cells genetically
different from parent and each other
7. Used only for sexual reproduction
Mitosis
1. Requires one nuclear division
2. Chromosomes do not synapse and
cross over
3. Centromeres dissolve in mitotic
anaphase
4. Preserves chromosome number
5. Produces two daughter nuclei
6. Produces daughter cells genetically
identical to parent and to each other
7. Used for asexual reproduction and
growth

(Source:http://courses.washington.edu/bot113/spring/WebReadings/PdfReadings/
TABLE_COMPARING_MITOSIS_AND.pdf)

Disorders and Diseases

• Incorrect DNA copy (e.g., cancer)
• Chromosomes are attached to string-like spindles and begin to move to the middle of
the cell (e.g., Down Syndrome, Alzheimer’s, and Leukemia)

Other chromosome abnormalities:

• arise from errors in meiosis, usually meiosis I;
• occur more often during egg formation (90% of the time) than during sperm formation;
• become more frequent as a woman ages.
• Aneuploidy—is the gain or loss of whole chromosomes. It is the most common
chromosome abnormality. It is caused by non-disjunction, the failure of chromosomes to
correctly separate:
• homologues during meiosis I or
• sister chromatids during meiosis II
Lesson 6: Transport Mechanisms
6.1: Structural Components of the Cell Membrane
REVIEW: The Structural Components of the Cell Membrane

The modern understanding of the cellular or plasma membrane is referred to as

the fluid mosaic model or fluid mosaics of lipids and proteins. It is composed of a bilayer
of phospholipids, with their hydrophobic, fatty acid tails in contact with each other (Fig.
7.d). The landscape of the membrane is studded with proteins, some of which span the
membrane. Some of these proteins serve to transport materials into or out of the cell.
Carbohydrates are attached to some of the proteins and lipids on the outward-facing
surface of the membrane (Fig. 7.b.), forming complexes which function is to identify the
cell to other cells. Cell membranes enclose and define the borders of cells, but rather
than being a static bag, they are dynamic and constantly in flux.

Fig. 7.b. Structural Component of Cellular Membrane

Fig. 7.c. In 1935, Davson-Danielli, the sandwich model of membrane structure stated that the membrane
was made up of a phospholipid bilayer sandwiched between two protein layers.

Fig. 7.d. In 1972, S. J. Singer and G. Nicolson proposed that the membrane is a mosaic of proteins
dispersed within the bilayer, with only the hydrophilic regions exposed to water.

The Fluidity of the membrane is due to temperature, the configuration of the

unsaturated fatty acid tails (some kinked or form a sharp twist by double bonds), the
presence of cholesterol embedded in the membrane, and the mosaic nature of the
proteins and protein-carbohydrate combinations, which are not firmly fixed in place.

Key Takes of the Fluid Nature of the CM:

• Phospholipids in the plasma membrane can move within the bilayer (Fig. 7.e)
• Most of the lipids, and some proteins, drift laterally
• Rarely does a molecule flip-flop transversely across the membrane

Fig. 7.e.
• As temperatures cool, membranes switch from a fluid state to a solid state.
• The temperature at which a membrane solidifies depends on the types of lipids.
• Membranes rich in unsaturated fatty acids are more fluid than those rich in
saturated fatty acids. (Fig. 7.f.)
• Membranes must be fluid to work properly; they are usually about as fluid as salad
Oil.
Fig. 7.f. The type of hydrocarbon tails in phospholipids – Affects the fluidity of the cell membrane

• The steroid cholesterol has different effects on membrane fluidity at different

temperatures.
• At warm temperatures (such as 37°C), cholesterol restrains movement of
Phospholipids.
• At cool temperatures, it maintains fluidity by preventing tight packing.

Structural Component of the Cell Membrane (Plasma Membrane)

COMPONENT LOCATION FEATURE/FUNCTION

 the most abundant lipid in
the plasma membrane
Phospholipids Main fabric of the membrane
 are amphipathic
molecules
 Tucked between the hydrophobic
Dampen effects of
Cholesterol tails of the membrane
temperature
phospholipids

Embedded in the phospholipid

Integral Transport of substance
bilayer; may or may not extend
Proteins through membrane
through both layers

On the inner or outer surface of

Peripheral
the phospholipid bilayer, but not Cell recognition
Proteins
embedded in its hydrophobic core
Attached to proteins or lipids on  Cell recognition
Carbohydrate the extracellular side of the  Effective interaction with
Chains membrane (forming glycoproteins the acqueous
and glycolipids environment

Terminology:

Amphiphilic or Amphipathic
 molecule possessing a polar or charged area and a nonpolar or uncharged area
capable of interacting with both hydrophilic and hydrophobic environments

Fluid mosaic model

 describes the structure of the plasma membrane as a mosaic of components
including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar
chains attached to proteins or lipids, respectively), resulting in a fluid character
(fluidity)

Glycolipid
 combination of carbohydrates and lipids

Glycoprotein
 combination of carbohydrates and proteins

Hydrophilic
 molecule with the ability to bond with water; “water-loving”

Hydrophobic
 molecule that does not have the ability to bond with water; “water-hating”

Integral protein
 protein integrated into the membrane structure that interacts extensively with the
hydrocarbon chains of membrane lipids and often spans the membrane; these
proteins can be removed only by the disruption of the membrane by detergents
Peripheral protein
 protein found at the surface of a plasma membrane either on its exterior or interior
side; these proteins can be removed (washed off of the membrane) by a high-salt
wash

6.2: The Relationship of the Structure and Composition of the

Cell Membrane to its Function

REVIEW: The Structure and Composition of the Cell Membrane relation

to its Function

The plasma membrane protects the cell from its external environment, mediates
cellular transport, and transmits cellular signals.

 The principal components of the plasma membrane are lipids (phospholipids and
cholesterol), proteins, and carbohydrates.
 The plasma membrane protects intracellular components from the extracellular
environment.
 The plasma membrane mediates cellular processes by regulating the materials
that enter and exit the cell.
 The plasma membrane carries markers that allow cells to recognize one another
and can transmit signals to other cells via receptors.

The plasma membrane (also known as the cell membrane or cytoplasmic

membrane) is a biological membrane that divides the interior of a cell from its outside
environment. (Figure 7.g)

The primary function of the plasma membrane is to protect the cell from its
surroundings. Composed of a phospholipid bilayer with embedded proteins, the plasma
membrane is selectively permeable to ions and organic molecules and regulates the
movement of substances in and out of cells. Plasma membranes must be very flexible
in order to allow certain cells, such as red blood cells and white blood cells, to change
shape as they pass through narrow capillaries.

The plasma membrane also plays a role in anchoring the cytoskeleton to provide
shape and integrity to the cell, and in attaching to the extracellular matrix and other cells
to help group cells together to form tissues. The membrane also maintains the cell
potential.

In short, if the cell is represented today as a COVID FREE-CAGAYAN DE ORO

CITY, then the plasma membrane is the checkpoints with the frontliners and law
enforcers that provides protective and territorial structure for the city inside, depicting
separation or barrier, regulates which people leave and enter the city, and conveys
messages to and from neighboring cities.

Just as an unguarded check point in the surrounding barrier can be a disaster for
the city in today’s crisis, like a rupture in the plasma membrane causes the cell to lyse
and die.

Cellular Signaling/ Recognition’s Relation to the Plasma Membrane

Among the most sophisticated functions of the plasma membrane is its ability to
transmit signals via complex proteins. These proteins can be receptors, which work as
receivers of extracellular inputs and as activators of intracellular processes, or markers,
which allow cells to recognize each other.

Membrane receptors provide extracellular attachment sites for effectors like

hormones and growth factors, which then trigger intracellular responses. Some viruses,
such as Human Immunodeficiency Virus (HIV), can hijack these receptors to gain entry
into the cells, causing infections.

Membrane markers allow cells to recognize one another, which is vital for cellular
signaling processes that influence tissue and organ formation during early development.
This marking function also plays a later role in the “self”-versus-“non-self” distinction of
the immune response. Marker proteins on human red blood cells, for example,
determine blood type (A, B, AB, or O).

Terminology:

Receptor- A protein on a cell wall that binds with specific molecules so that they can be
absorbed into the cell.

Cellular Transport Mechanisms’ Relation to the Plasma Membrane

The movement of a substance across the selectively permeable plasma

membrane can be either “passive”—i.e., occurring without the input of cellular energy —
or “active”—i.e., its transport requires the cell to expend energy.

The cell employs a number of transport mechanisms that involve biological

membranes:

1. Passive osmosis and diffusion: transports gases (such as O and CO and other
2 2)

small molecules and ions

 2. Transmembrane protein channels and transporters: transports small organic
molecules such as sugars or amino acids

3. Endocytosis: transports large molecules (or even whole cells) by engulfing them

4. Exocytosis: removes or secretes substances such as hormones or enzymes.

Fig. 7.g. Detailed Image of Cell Membrane Structure in a Cell

6.3: Transport Mechanisms in Cells

REVIEW: Transport Mechanisms in Cells (Diffusion, Osmosis,

Facilitated Transport, Active Transport) to its Function

Plasma membranes must allow certain substances to enter and leave a cell, and
prevent some harmful materials from entering and some essential materials from
leaving. In other words, plasma membranes are selectively permeable—they allow
some substances to pass through, but not others. If they were to lose this selectivity, the
cell would no longer be able to sustain itself, and it would be destroyed. Some cells
require larger amounts of specific substances. They must have a way of obtaining these
materials from extracellular fluids. This may happen passively, as certain materials
move back and forth, or the cell may have special mechanisms that facilitate transport.
Some materials are so important to a cell that it spends some of its energy, hydrolyzing
adenosine triphosphate (ATP), to obtain these materials. Red blood cells use some of
their energy doing just that. Most cells spend the majority of their energy to maintain an
imbalance of sodium and potassium ions between the cell's interior and exterior, as well
as on protein synthesis.

The most direct forms of membrane transport are passive. Passive transport is
a naturally occurring phenomenon and does not require the cell to exert any of its
energy to accomplish the movement. In passive transport, substances move from an
area of higher concentration to an area of lower concentration. A physical space in
which there is a single substance concentration range has a concentration gradient.

Selective Permeability

Plasma membranes lack symmetry: the membrane's exterior is not identical to its
interior (Fig. 7.h). There is a significant difference between the arrangement of proteins
and phospholipids and between the two leaflets that form a membrane. On the
membrane's interior, some proteins serve to anchor the membrane to cytoskeleton's
fibers. There are peripheral proteins on the membrane's exterior that bind extracellular
matrix elements. Carbohydrates, attached to lipids or proteins, are also on the plasma
membrane's exterior surface (Figure 7.b). These carbohydrate complexes help the cell
bind required substances in the extracellular fluid. This adds considerably to plasma
membrane's selective nature.
Fig. 7.h. molecular view of the cell membrane. Intrinsic proteins penetrate and bind tightly to the lipid
bilayer, which is made up largely of phospholipids and cholesterol and which typically is between 4 and
10 nanometers (nm; 1 nm = 10 metre) in thickness. Extrinsic proteins are loosely bound to the
−9

hydrophilic (polar) surfaces, which face the watery medium both inside and outside the cell. Some
intrinsic proteins present sugar side chains on the cell's outer surface. 2007 Encyclopædia Britannica,
Inc.

Fig. 7.i. Structural Component of Cellular Membrane

The plasma membrane's exterior surface is not identical to its interior surface.
Recall that plasma membranes are amphiphilic: They have hydrophilic and hydrophobic
regions. This characteristic helps move some materials through the membrane and
hinders the movement of others. Non-polar and lipid-soluble material with a low
molecular weight can easily slip through the membrane's hydrophobic lipid core.
Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the
plasma membranes in the digestive tract and other tissues. Fat-soluble drugs and
hormones also gain easy entry into cells and readily transport themselves into the
body’s tissues and organs. Oxygen and carbon dioxide molecules have no charge and
pass through membranes by simple diffusion.
Polar substances present problems for the membrane. While some polar
molecules connect easily with the cell's outside, they cannot readily pass through the
plasma membrane's lipid core. Additionally, while small ions could easily slip through
the spaces in the membrane's mosaic, their charge prevents them from doing so. Ions
such as sodium, potassium, calcium, and chloride must have special means of
penetrating plasma membranes. Simple sugars and amino acids also need the help of
various transmembrane proteins (channels) to transport themselves across plasma
membranes.

Key Takes of the Permeability of the Lipid Bilayer:

• Hydrophobic (nonpolar) molecules, such as hydrocarbons, can dissolve in the lipid
bilayer and pass through the membrane rapidly.
• Hydrophilic (Polar) molecules, such as sugars, do not cross the membrane easily.
Fig. 7.i. Substances highly impermeable to cross membrane like large uncharged polar molecules
(glucose and fructose), charged molecules and finally ALL IONS. But, Transport proteins are used to
transport ions across membrane.

The Transport Mechanisms

The transport of molecules across cell membrane may vary in rates, depending
upon molecular size, structure and composition of membrane, pressure gradient, and
internal and external conditions. The mechanisms fall into these five categories:
Diffusion, Osmosis, Facilitated Transport, Active Transport and Bulk Transport.

Diffusion is passive movement of molecules from a region of high concentration

to a region of low concentration. (Concentration gradient is the difference in
concentration between the two regions). Small, uncharged molecules like O , CO and 2 2

H O can move easily through the membrane. This works well over short distances.
2

Once molecules enter the cell, the rate of diffusion slows. It limits cell size.

Fig. 7.j. Diffusion through a permeable membrane moves a substance from a high concentration area
(extracellular fluid, in this case) down its concentration gradient (into the cytoplasm).

Osmosis is diffusion of the solvent across a semi-permeable membrane

separating two solutions (Diffusion of water). Water molecules move from a region of
high concentration to a region of low concentration. Direction depends on the relative
concentration of water molecules on either side of the cell membrane. External and
internal conditions arise from a variety of concentrations of solutes and solvent in and
out of the cell. Such conditions may be the following:
 Isotonic: Water inside the cell equals the water outside the cell and equal
amounts of water move in and out of the cell.

Hypotonic: Water outside the cell is greater than that inside the cell, water
moves into the cell, may cause cell to burst (lysis)

Hypertonic: Water inside the cell is greater than outside. Water moves out of the
cell, may cause the cell to shrink (plasmolysis)

Fig. 7.k. Movement of water molecules from high concentration to low concentration, through a semi-
permeable membrane
Facilitated Transport (Also Known as Facilitated Diffusion or Passive-Mediated
Transport) assists with the movement of large molecules like glucose into or out of the
cell by means of carrier proteins, which transports noncharged molecules with a specific
shape or channel proteins, which serve as tunnel shape that transports small charged
molecules. This usually happens when molecules move from high to low regions of
concentration and it does not require water molecules for other molecules to transfer.
 .

Fig. 7.l. Facilitated diffusion in cell membrane, showing ion channels and carrier proteins.

Active Transport is the process of moving substances against their

concentration gradients. Thus, it requires energy.
Examples:
• Kidney cells pump glucose and amino acids out of the urine and back into
the blood.
• Intestinal cells pump in nutrients from the gut.
• Root cells pump in nutrients from the soil.
• Gill cells in fish pump out sodium ions.
Fig. 7.m. Active transport: Requires the use of chemical energy to move substances across a
membrane, against a concentration gradient. Active transport proteins may be uniports, symports, or
antiports.

A sodium-potassium pump is an active transport pump where 3 sodium ions

inside the cell and 2 potassium ions outside the cell bind to. This allows the release of
energy from ATP and causes the protein complex to change shape. The change in
shape allow the Na+ and K+ ions to be transported in and out of the cell.
Fig. 7.n. In Primary active transport, energy from the hydrolysis of ATP is used to move ions into or out
of cells against their concentration gradients. The sodium-potassium pump is an important example
Fig. 7.o. Secondary active transport couples the passive movement of one substance with its
concentration gradient to the movement of another substance against its concentration gradient. Energy
from ATP is used indirectly to establish the concentration gradient that results in the movement of the first
substance

Bulk Transport Mechanisms are needed by cells when large particles are
moved across the cell membrane. There are different modes of bulk transport such as
endocytosis and exocytosis.
Endocytosis happens when the cell membrane folds inward, traps and encloses
a small amount of matter from the extracellular fluid.
Exocytosis is the reverse of endocytosis, in which, a vesicle from inside the cell
moves to the cell membrane. The vesicle fuses to the membrane and the contents are
secreted.
 Fig. 7.p. Exocytosis and Endocytosis
Difference between Endocytosis and Exocytosis

Exocytosis refers to the

Endocytosis refers to the transportation of
transportation of
macromolecules, large particles, and polar
molecules or particles
Definition substances into the cell
from the cell to the
from the external
outside of the cell
environment

Involved with up taking Involved in removing waste

Process
nutrients into the cell from the cell

Occurs by constitutive and

Type Occurs by both phagocytosis and pinocytosis regulated secretory
pathway

Secretory vesicles are

Vesicle Internal vesicles like phagosomes are formed
formed

Cell Wall
Not involved Involved
Formation

Engulfing bacteria by phagocytes is an Releasing of hormones out

Example
example of the cell is an example

Endocytosis can be further subdivided into the following categories:

Pinocytosis: The intake of a small droplet of extracellular fluid. This occurs in nearly all
cell types.
Phagocytosis: The intake of a large droplet of extracellular fluid. This occurs in
specialized cells.

Receptor-assisted endocytosis: The intake of specific molecules that attach to special

proteins in the cell membrane. These proteins are uniquely shaped to fit
the shape of a specific molecule.

Fig. 7.q. Secondary active transport couples the passive movement of one substance with its
concentration gradient to the movement of another substance against its concentration gradient. Energy
from ATP is used indirectly to establish the concentration gradient that results in the movement of the first
substance.

Lesson 7: Structures and Functions of

Biological Molecules- Enzymes
Introduction:

When you were very young and played under the heat of the sun, were
you able to experience sweat dripping in your neck, head and then like some acid that
went in your eyes, it feels burning and stingy right? But don’t you worry. Now, we all
know that the burning and stingy sensation in our eyes was due to dust and oils that
came in contact with the sweat and to an anti-microbial enzyme fighting off germs called
Lysozyme.
 So, enzymes are vital for life and serve a wide range of important
functions in the body, such as aiding in fighting germs, digestion, and metabolism.

Some enzymes help break large molecules into smaller pieces that are more
easily absorbed by the body. Other enzymes help bind two molecules together to
produce a new molecule. Enzymes are highly selective catalysts, meaning that each
enzyme only speeds up a specific reaction.

Peeling, bruising, or cutting fruits cause them to release enzymes like polyphenol
oxidase (PPO, phenolase) that, with the presence of oxygen (oxidation) in the
surrounding air, goes into chemical reactions of plant compounds. These chemical
reactions produce brown pigments through the process of enzymatic browning (Fig.
8.a.)

Oxidation and reduction occur in tandem and it occurred when peeling or

cutting fruits resulting to an enzymatic browning. Because oxidation and reduction
usually occur together, these pairs of reactions are called oxidation reduction reactions,
or redox reactions.

Think of people passing balls back and forth, and the balls are balls of negativity.
So if I'm holding the ball, I'm reduced. If I pass you the ball, you get reduced, and I
become oxidized. The passing of the ball was the reduction-oxidation reaction.

An oxidation-reduction (redox) reaction is a type of chemical reaction that

involves a transfer of electrons between two species. An oxidation-reduction reaction
is any chemical reaction in which the oxidation number of a molecule, atom, or ion
changes by gaining or losing an electron. A classic example of a redox reaction is
rusting. When rusting happens, oxygen steals electrons from iron. Oxygen gets
reduced while iron gets oxidized.
Fig. 8.a. Enzymatic browning of a sliced apple.

7.1: Transport Mechanisms in Enzymes

REVIEW: Description of the Components of Enzyme

What is an enzyme?

 Enzymes are protein macromolecules.

 They have a defined amino acid sequence, and are typically 100-500
amino acids long.
 They have a defined three-dimensional structure.
 Enzymes are catalysts.
 They act as a catalyst to a chemical or biochemical reaction, with a
defined mechanism.
 They increase the speed of that reaction, typically by 10 -10 times faster
6 14

than the rate of the uncatalyzed reaction.

 They are selective for a single substrate.
 They speed up rate of reaction by lowering the activation energy (Ea).
 They are stereospecific, meaning the reaction produces a single product.

Common mistakes and misconceptions

 Enzymes are "specific." Each type of enzyme typically only reacts with one (Fig
8.b.), or a couple, of substrates. Some enzymes are more specific than others
 and will only accept one particular substrate. Other enzymes can act on a range
of molecules, as long as they contain the type of bond or chemical group that the
enzyme targets.

Fig. 8.b. A substrate entering the active site of the enzyme.

Image modified from "Enzymes: Figure 2," by OpenStax College, Biology, CC BY 3.0.

 Enzymes are reusable. Enzymes are not reactants and are not used up during
the reaction. Once an enzyme binds to a substrate and catalyzes the reaction,
the enzyme is released, unchanged, and can be used for another reaction. This
means that for each reaction, there does not need to be a 1:1 ratio between
enzyme and substrate molecules.

Nomenclature

Typically add “-ase” to name of substrate

e.g. lactase breaks down lactose (dissacharide of glucose and galactose)

Enzymes based upon the class of organic chemical reaction catalyzed:

1. Oxidoreductase - catalyze redox reactions; dehydrogenases, oxidases,

peroxidases, reductases.
2. Transferases - catalyze group transfer reactions; often require coenzymes.
3. Hydrolases - catalyze hydrolysis reactions.
4. Lyases - lysis of substrate; produce contains double bond.
5. Isomerases - catalyze structural changes; isomerization.
6. Ligases - ligation or joining of two substrates with input of energy, usually from ATP
hydrolysis; often called synthetases or synthases.

ENZYME COMPONENTS

An enzyme as illustrated on Fig. 8.c. has different components which follow:

 Apoenzyme- is an inactive enzyme, which activation occurs upon binding of an
organic or inorganic cofactor. This enzyme is a protein that lack its necessary
cofactor(s) for proper functioning

Holoenzymes-are the active forms of apoenzymes, (Apoenzyme plus cofactor).

DNA polymerase and RNA polymerase are examples (see Fig. 8.d.).

Cofactors are mostly metal ions or small organic molecules. They are inorganic
and organic chemicals that assist enzymes during the catalysis of reactions.
These are nonprotein component (e.g. magnesium, zinc)

Coenzymes are non-protein organic molecules that are mostly derivatives of

vitamins soluble in water by phosphorylation. Examples are organic cofactor
(e.g., NADH, FADH)

Many enzymes can catalyze a reaction only if coenzymes, or cofactors are present.

Fig. 8.c. Parts of an Enzyme

 Fig. 8.d. Component of a Holoenzyme

Terminology:

Catalyst
 A substance that speeds up a chemical reaction without being changed

Enzyme
 A biological catalyst (usually a protein)

Substrate
 The reactant molecule that an enzyme works on

Active Site
 The part of the enzyme where the substrate binds

Enzyme-substrate complex
 formed when the substrate molecule collides with the active site of its
enzyme

Endoenzymes(intracellular) / Exoenzymes (extracellular)

Activation energy
 the minimum energy required to start a chemical reaction

Transition state
 the intermediate stage in a reaction in which the old bonds break and new
bonds are formed

7.2: Oxidation/Reduction Reactions

 REVIEW: Oxidation-Reduction Reactions

An oxidation-reduction (redox) reaction is a type of chemical reaction that involves a

transfer of electrons between two species. An oxidation-reduction reaction is any
chemical reaction in which the oxidation number of a molecule, atom, or ion changes by
gaining or losing an electron. Redox reactions are common and vital to some of the
basic functions of life, including photosynthesis, respiration, combustion, and corrosion
or rusting.

Oxidation-reduction reactions are also called REDOX reactions. All redox reactions
involve the transfer of electrons from one atom to another. Spontaneous redox reactions
are generally exothermic, and we can use their released energy as a source of energy
for other applications.

Redox reactions are comprised of two parts, a reduced half and an oxidized half,
that always occur together. The reduced half gains electrons and the oxidation number
decreases, while the oxidized half loses electrons and the oxidation number increases.
Simple ways to remember this include the mnemonic devices OIL RIG, meaning
"oxidation is loss" and "reduction is gain," and LEO says GER, meaning "loss of e = -

oxidation" and "gain of e = reduced." There is no net change in the number of electrons
-

in a redox reaction. Those given off in the oxidation half reaction are taken up by
another species in the reduction half reaction.

A good example of a redox reaction is the thermite reaction, in which iron atoms in
ferric oxide lose (or give up) O atoms to Al atoms, producing Al O .
2 3

Fe2O3(s)+2Al(s)→Al2O3(s)+2Fe(l)

What do you mean by oxidation and reduction?

OXIDATION can be defined as addition of oxygen/electronegative element to a

substance or removal of hydrogen/ electropositive element from a substance.

REDUCTION can be defined as removal of oxygen/electronegative element from a

substance or addition of hydrogen/ electropositive element to a substance.
*oxidation occurs when an atom’s oxidation
state increases during a reaction
 *reduction occurs when an atom’s oxidation
state decreases during a reaction

Development of oxidation and reduction reaction concept______________________

Reaction of reduction oxidation based on releasing (losing) and gaining of oxygen (capturing).

a. Oxidation reaction is a reaction of gaining (capturing) of oxygen by a substance

Ex.
CH4(g) + 2O2(g) 🡪 CO2(g) + 2H2O(g)
P4(s) + 5O2(g) 🡪 2P2O5(s)
b. Reduction reaction is a reaction of releasing (losing) of oxygen from an oxide
compound
Ex.
CuO(s) + H2(g) 🡪 Cu(s) + H2O(g)
Fe2O3(s) + 3CO(g) 🡪 2Fe(s) + 3CO2(g)
What is an oxidizing and reducing agent?

• Oxidizing agent: a reagent which increases the oxidation number of an element of a

given substance. These reagents are called oxidants. It contains the element that is
reduced.

• Reducing agent: a reagent that lowers the oxidation number of a given element.
These reagents are also called reductants. It contains the element that is oxidized.
2 Na(s) + Cl2(g) 🡪 2 Na+Cl–(s)
Na is oxidized, Cl is reduced
Na is the reducing agent, Cl2 is the oxidizing agent

Terminologies:

Reactant is a substance or compound added to a system to cause a chemical reaction,

or added to test if a reaction occurs.

Reagent is more specifically a substance consumed in the course of a chemical

reaction.
7.3: Determining the Factors Affecting Enzyme Activity
REVIEW: Factors Affecting Enzyme Activity

Enzyme activity can be affected by a variety of factors, such as temperature, pH,

concentrations and inhibitors.

Enzymes work best within specific temperature and pH ranges, and sub-optimal
conditions can cause an enzyme to lose its ability to bind to a substrate.

Determinants of the Factors Affecting Enzyme Activities

A. Temperature: Raising temperature generally speeds up a reaction, and lowering

temperature slows down a reaction. However, extreme high temperatures can
cause an enzyme to lose its shape (denature) and stop working. Most enzymes
have an optimum temperature, near normal body temperature at which they

catalyze a reaction most rapidly

B. pH (abbr. power of hydrogen or potential for hydrogen ): Each enzyme has an
optimum pH range. Changing the pH outside of this range will slow enzyme
activity. Extreme pH values can cause enzymes to denature. Even small pH
changes can alter the electrical charges on various chemical groups in enzyme
molecules, thereby altering the enzyme’s ability to bind its substrate and catalyze
a reaction.
 Enzymes catalyze a reaction most rapidly at an optimum pH, near neutral.

C. Substrate concentration: Increasing substrate concentration also increases the

rate of reaction to a certain point. Once all of the enzymes have bound, any
substrate increase will have no effect on the rate of reaction, as the available
enzymes will be saturated and working at their maximum rate. At the saturation
point, the reaction will not speed up, no matter how much additional substrate is
added. The graph of the reaction rate will plateau.

D. Enzyme concentration: Increasing enzyme concentration will speed up the

reaction, as long as there is substrate available to bind to. Once all of the
substrate is bound, the reaction will no longer speed up, since there will be
nothing for additional enzymes to bind to.

The higher the concentration of an enzyme the greater should be the initial
reaction rate. This will last as long as substrate present
E. Enzyme Inhibitors (Inhibition):

 Competitive inhibitor: A molecule similar in structure to a substrate can

bind to an enzyme’s active site and compete with substrate
 Noncompetitive inhibitors: attach to the enzyme at an allosteric site,
which is a site other than the active site distort the tertiary protein structure
and alter the shape of the active site.
 Feedback inhibition: regulates the rate of many metabolic pathways
when an end product of a pathway accumulates and binds to and
inactivates the first enzyme in the metabolic pathway. Product (usually
ultimate product) of a pathway controls the rate of synthesis through
inhibition of an early step (usually the first step). Conserves material and
energy by preventing accumulation of intermediates.