BIO107 – CELL AND MOLECULAR BIOLOGY

LEARNING PACKETS

Department of Biological Sciences

College of Science and Mathematics

Mindanao State University- Iligan Institute of Technology

Iligan City, Philippines

Compiled by:

Johanna Marie Cuadra, M.Sc.

Maria Reina Suzette Madamba, Ph.D.

Mylah Tabelin, Ph.D.

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REFERENCES:

Alberts, B., Johnson, A., Lewis, J., Morgan, D., Raff, M., Roberts, K., and Walter, P. (2015). Molecular Biology of The Cell
(6th ed). Garland Science, NY: USA.

Atlas of Plant and Animal Histology. (September 23, 2019). Cell Membrane. Retrieved August 21,2020 from
https://mmegias.webs.uvigo.es/02-english/5-celulas/3-adhesion.php

BCUNY.(n.d.). Endocytosis. Retrieved August 21, 2020 from

http://www.brooklyn.cuny.edu/bc/ahp/LAD/C5/C5_Endocytosis.html

Bergtrom, G., “Cell and Molecular Biology: What We Know & How We Found It (Second Edition, An Annotated iText)”
(2016). Cell and Molecular Biology 3e: What We Know and How We Found Out-All Versions. 5. Retrieved from
https://dc.uwm.edu/biosci_facbooks_bergtrom/5.

Biology Dictionary. (2017, April 04). Animal Cell. Retrieved August 20,2020 from https://biologydictionary.net/animal-cell
Biology Dictionary. (2017, September 08). Extracellular Matrix. Retrieved August 21, 2020 from
https://biologydictionary.net/extracellular-matrix/

Biology Dictionary. (2020, June 18). Plant cell. Retrieved August 20, 2020, from https://biologydictionary.net/plant-cell/

BSCB. (n.d.). Endoplasmic Reticulum (Rough and Smooth). Retrieved from August 20, 2020 from
https://bscb.org/learning-resources/softcell-e-learning/endoplasmic-reticulum-rough-and-smooth/

Cain, M. L., Jackson, R. B., Minorsky, P. V., Reece, J. B., Urry, L. A., and Wasserman, S. A. (2011). A tour of the cell.
In Campbell biology (9th ed., p. 94). San Francisco, CA: Pearson.

Cain, M. L., Jackson, R. B., Minorsky, P. V., Reece, J. B., Urry, L. A., and Wasserman, S. A. (2011). Membrane structure and
function. In Campbell biology (9th ed., p. 125-139). San Francisco, CA: Pearson.

Cain, M. L., Jackson, R. B., Minorsky, P. V., Reece, J. B., Urry, L. A., and Wasserman, S. A. (2011). The structure and
function of large biological molecules. In Campbell biology (9th ed., p. 68-89). San Francisco, CA: Pearson.

Cain, M. L., Jackson, R. B., Minorsky, P. V., Reece, J. B., Urry, L. A., and Wasserman, S. A. (2011). Water and life.
In Campbell biology (9th ed., p. 46-50). San Francisco, CA: Pearson.

KhanAcademy.(n.d.).Structure of the plasma membrane. Retrieved August 21,2020 from

https://www.khanacademy.org/science/high-school-biology/hs-cells/hs-the-cell-membrane/a/structure-of-the-
plasma-membrane

LumenCandela. (n.d.). Structure and function of plasma membrane. Retrieved August 21, 2020 from
https://courses.lumenlearning.com/boundless-biology/chapter/components-and-structure/

ScienceProfOnline.(October, 2017). Prokaryotic structures. Retrieved August 20, 2020 from

https://www.scienceprofonline.org/cell-biology/prokaryotic-cell-parts-functions-diagrams-2.html

Tocris. (n.d.).Extracellular matrix and adhesion molecules. Retrieved August 21, 2020 from https://www.tocris.com/cell-
biology/extracellular-matrix-and-adhesion- molecules

Tocris. (n.d.). Signal Transduction. Retrieved August 21, 2020 from https://www.tocris.com/cell-biology/signal-
transduction

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MODULE 1:

At the end of this module, the students are expected to:

1. discuss the differences of prokaryotic and eukaryotic cells and its associated cell parts and
functions;
2. identify the biomolecules that composes the structures and properties of the cell;
3. discuss the parts of a plasma membrane and;
4. show the different components and functions of extracellular matrix.

I. Introduction

A. Cells as Building Blocks

A cell is the smallest unit of living thing. A living thing, whether made of one cell (like bacteria)
or many cells (like human), is called an organism. Thus, cells are the basic building blocks of all
organisms. Several cells of one kind that interconnect with each other and perform a shared function
form tissues; several tissues combine to form an organ (your stomach, heart or brain); and several
organs make up an organ-systems that functions together to form an organism. There are many types
of cells all grouped into one of two broad categories: prokaryotic and eukaryotic. Both animal and plant
cells are classified as eukaryotic cells, whereas bacterial cells are classified as prokaryotic.
Types of Specialized Cells
Your body has many kinds of cells, each specialized for a specific purpose. For example,
epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone
cells help to support and protect the body. Cells of the immune system fight invading bacteria.
Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing
carbon dioxide. Each of these cell types plays a vital role during growth, development, and day-to-day
maintenance of the body. In spite of their enormous variety, cells from all organisms share certain
fundamental characteristics.

Cell Theory
The microscopes we use today are far more complex than those used in the 1600s by Antony
van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of
his now-ancient lenses, he observed the movements of protista (a type of single-celled organism) and
sperm, which he collectively termed “animalcules.”
In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the
term “cell” for the box-like structures he observed when viewing cork tissue through a lens. In the
1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope
construction, and staining techniques enabled other scientist to see some components inside cells.

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 By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying
tissues and proposed the unified cell theory. The cell theory states that: all living things are composed
of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells. Rudolf
Virchow later made important contributions to this theory.
Schleiden and Schwann proposed spontaneous generation as the method for cell origination,
but spontaneous generation (also called abiogenesis) was later disproven. Rudolf Virchow famously
dispelled the theory of spontaneous generation by proving that living things do not come from nothing.
All living things, which are made of cells, come from other living thing as enunciated by his powerful
dictum, "Omnis cellula e cellula" or "All cells only arise from pre-existing cells". Thus, through
extensions research, Virchow supported the claim that all cells arise from other cells, completing the
third statement prominent in the Cell Theory in1855.

The parts of the theory that did not have to do with the origin of cells, however, held up to
scientific scrutiny and are widely agreed upon by the scientific community today. The generally
accepted portions of the modern Cell Theory are as follows:

1. The cell is the fundamental unit of structure and function in living things..
2. All organisms are made up of one or more cells.
3. Cells are from other cells through cellular division.

The expanded version of the cell theory can also include:

1. Cells carry genetic material passed to daughter cells during cellular division
2. All cells are essentially the same in chemical composition
3. Energy flow (metabolism and biochemistry) occurs within cells

B. Cell Parts and Functions

Each cell is surrounded by a membrane and contains parts called cellular organelles. These
cellular organelles has specific functions on different parts of a cell which are involved in converting
energy from nutrients in the food you eat into a form of energy that the cell can use. Some are also
involved in storing the genetic information that serves as the blueprint and others are responsible for
building the proteins that enable the cell to perform its tasks. Though these parts comprises the cell,
it still differs on whether it is a prokaryotic cell or a eukaryotic cell.

C. Different Cell Types

Cells are the basic structural and functional units of every organism, and are of two distinct
types: prokaryotic and eukaryotic cells. Even though all cells share certain features, prokaryotic cells
are found in organisms of the domains Bacteria and Archaea, calling them prokaryotes while protists,
fungi, animals, and plants all consist of eukaryotic cells, making them eukaryotes.

C.1. Prokaryotic Cells

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 Prokaryotic cells or prokaryotes share a certain similarity to parts found in eukaryotes. The
major thing that differs is that prokaryotic cells has an absence of nucleus, making its DNA location
different and can travel openly around the cell, since it was believed that prokaryotic cells evolved
before eukaryotic cells. Even though some parts differ, stated below are the parts of a prokaryotic
cell and its associated functions:

a. Plasma Membrane: The plasma membrane or also known as the cell membrane is a double-
layer of phospholipids with associated proteins and other molecules. It is essentially the “bag”
that holds all of the intracellular material and regulates the movement of materials into and
out of the cell.
b. Cytoplasm: This is the gel-like fluid that the cell is filled with, and is inside the plasma
membrane. The cytoplasm is where all of the cellular organelles suspended within.
c. Cytoskeletal Proteins: Unlike eukaryotic cells, which has a cytoskeleton, prokaryotic cells
such as the rod-shaped bacteria and archaea possess cytoskeletal proteins that function
similarly to the cytoskeleton of eukaryotic cells. This scaffolding provides structural support to
the cell and plays a role in cell division.
d. Ribosomes: A similarity to both prokaryotic and eukaryotic cells is that they have multiple
ribosomes within. These are the tiny protein-making machines that carry out the genetic
instructions of the cell.
e. Nucleoid: In replacement of the nucleus, prokaryotic cell has the nucleoid which is the region
of the prokaryotic cytoplasm that contains the genome—the main genetic material (DNA) of
the cell and typically have a single, circular chromosome.
f. Plasmids: In addition to the nucleoid, prokaryotic cells such as in bacteria may contain one or
more plasmids. A plasmid is a non-essential piece of DNA that confers an advantage to the
bacteria, such as antibiotic resistance, virulence (the ability to cause disease)
and conjugation (a bacterium’s ability to share its plasmids with other bacteria).
g. Glycocalyx: The glycocalyx is a layer outside of the cell wall, and present in some bacteria.
There are two types of glycocalyces which are the slime layers and capsules.

- Slime layers help bacteria stick to things and protect them from drying out,
particularly in hypertonic environments.

- Capsules allow bacteria to stick to things, but have the added benefit of helping
encapsulated bacteria hide from the host's immune system.

h. Cell Extensions: Cell extensions are made of delicate protein strands and there are several
different types of cell extensions associated with bacteria, including flagella and endoflagella.

- Flagella: These are long whip-like extensions that help bacteria move about the
environment.

- Endoflagella (axial filaments): These are also flagella but are wrapped around
corkscrew-shaped bacteria and move in waves making the bacteria spin.

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C.2. Eukaryotic Cells

Eukaryotic cells or eukaryotes have much more organelles than what comprises prokaryotic
cells. Its organelles are membrane-bound making it intact unlike the prokaryotes which are freely
flowing around the cell. Eukaryotic cells are much bigger in size and its nucleus is present containing
DNA. To further understand eukaryotic cells and its parts, an animal cell and a plant cell is then put
into a comparison.

C.2.1. Animal Cell

Animal cells and plant cells are both eukaryotic. Thus, they both have a defined nucleus
and other membrane-bound organelles. Unlike plant cells, animal cells do not have a cell
wall. Instead, multicellular animals have other structures that provide support to their tissues and
organs, such as skeleton and cartilage. Animal cells are generally smaller than plant cells and come in
various sizes and tend to have irregular shapes. Animal cells also contain structures such as
centrioles, lysosomes, cilia, and flagella that are not typically found in plant cells.

Animal cells have a variety of different organelles that work together to allow the cell to
perform its functions, but not every animal cell has all types of organelles. Here are the parts of an
animal cell and its associated functions:

a. Nucleus : The nucleus contains all the genetic material called DNA in a cell. DNA contains all the
instructions for making proteins, which control all of the body’s activities. Therefore, the nucleus is
like the manager’s office of the cell, having individual parts

- Nuclear envelope: This is a double membrane enclosing the nucleus and is continuous
with the endoplasmic reticulum . It is perforated by pores which permit the entry and
exit of some molecules.

- Nucleolus: It is a non-membranous structure involved in the synthesis of ribosomes. It

is within the nucleus and the nucleus has one or more nucleoli.

- Chromatin: It is a material consisting of DNA and proteins, and is visible in a dividing

cell as individual condensed chromosomes.

b. Ribosomes: These are organelles that are like mini machines that synthesize all the proteins in the
cell, and form the manufacturing department of the cell. It is free in the cell’s cytoplasm or bound to
the rough ER or nuclear envelope.

c. Endoplasmic Reticulum: The endoplasmic reticulum (ER) is a network of flattened, membrane-

bound sacs and tubes that are involved in the production, processing, and transport of proteins that
have been synthesized by ribosomes. The endoplasmic reticulum is like the assembly line of the cell,

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where the products produced by the ribosomes are processed and assembled. There are two kinds of
endoplasmic reticulum: smooth and rough.

- Rough ER : has ribosomes attached to the surface of the sacs and is involved in some
protein production, protein folding, quality control and dispatch.

- Smooth ER: does not have ribosomes attached and is associated with the production
and metabolism of fats and steroid hormones.

d. Golgi apparatus: The Golgi apparatus, also called the Golgi complex or Golgi body, receives
proteins from the ER and folds, sorts, and packages these proteins into vesicles. The Golgi apparatus
is like the shipping department of the cell, as it packages proteins up for delivery to their
destinations. It is an organelle active in synthesis, modification , sorting and secretion of cell
products.

e. Lysosomes: These are specialized vesicles that contain digestive enzymes and are used extensively
within the cell for metabolism and transport of large molecules that cannot cross the membrane
unaided. These enzymes can break down large molecules like organelles, carbohydrates, lipids, and
proteins into smaller units so that the cell can reuse them. Therefore, they are like the waste
disposal/recycling department of the cell.

f. Mitochondria: These are the energy-producing organelles, commonly known as “the powerhouse
of the cell.” This is where the process of cellular respiration happens. During this process, sugars and
fats are broken down through a series of chemical reactions, releasing energy in the form of
adenosine triphosphate (ATP).

g. Cytoplasm: It is the gel-like liquid contained within cells. The cytosol and all the organelles within
it, except for the nucleus. Its cytosol consists primarily of water, but also contains ions, proteins, and
small molecules, with a pH level of 7.

h. Cytoskeleton: The cytoskeleton is a network of filaments and tubules found throughout the
cytoplasm of the cell. It gives the cell shape, provides strength, stabilizes tissues, anchors organelles
within the cell, and has a role in cell signaling. It also provides mechanical support to allow cells to
move and divide. There are three types of cytoskeletal filaments: microfilaments, microtubules, and
intermediate filaments.

i. Cell Membrane: The cell membrane surrounds the entire cell and separates its components from
the outer environment. The cell membrane is a double layer made up of phospholipids (called
the phospholipid bilayer) and is selectively permeable, meaning it only allows certain molecules to
enter and exit. Oxygen and carbon dioxide pass through easily, while larger or charged molecules
must go through special channels, bind to receptors, or be engulfed.

j. Peroxisome: It is the organelle with various specialized metabolic functions and produces hydrogen
peroxide as a by-product, the converts it to water.

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k. Microvilli: These are projections that increase the cell’s surface area.

l. Centrosome: This is the region where the cell’s microtubules are initiated and it contains a pair of
centrioles.

m. Flagellum: It is the motility structure present in some animal cells, composed of a cluster of
microtubules within an extension of the plasma membrane.

C.2.2. Plant cell

Plant cells are the basic unit of life in organisms of the kingdom Plantae. They are eukaryotic
cells, which have a true nucleus along with specialized structures called organelles that carry out
different functions. They are differentiated from the animal cells by their cell walls, chloroplasts,
and central vacuole. Plant cells are more similar in size and are typically rectangular or cube shaped
than eukaryotic cells.

Plants are considered autotrophic because they produce their own food and do not have to
consume any other organisms. Specifically, plant cells are photoautotrophic because they use light
energy from the sun to produce glucose. Plant cells store water in the central vacuole, which
expands the vacuole into the sides of the cell. The cell wall then pushes against the walls of other
cells, creating a force known as turgor pressure. While animals rely on a skeleton for structure,
turgor pressure in plant cells allows plants to grow tall and reach more sunlight. The parts of a plant
cell with each respective function is stated below:

a. Chloroplasts : These are specialized disk-shaped organelles surrounded by a double membrane

which is found only in plants and some types of algae. These organelles carry out the process of
photosynthesis, which turns water, carbon dioxide, and light energy into nutrients from which
the plant can obtain energy.

- Stroma: It is a fluid matrix at the center of the chloroplast that is enclosed by the
double membrane.
- Thylakoids: These are flattened disks within the stroma, and when stacked, is called
grand. Thylakoids have a high concentration of chlorophyll and carotenoids, which are
pigments that capture light energy from the sun.

b. Vacuoles: A vacuole is a small sphere of plasma membrane within the cell that can contain fluid,
ions, and other molecules. Vacuoles are essentially just large vesicles. The central vacuole of a
plant cell helps maintain its turgor pressure, which is the pressure of the contents of the cell
pushing against the cell wall.
c. Cell Wall: It is a layer found on the outside of the plant cell that gives it strength and also
maintains high turgidity. In plants, the cell wall contains mainly cellulose, along with other
molecules like hemicellulose, pectin, and lignins, unlike bacterial cell wall which
contains peptidoglycan. It is classified into two: primary cell wall and secondary cell wall.

- Primary cell wall: is a flexible layer formed on the outside of a growing plant cell.

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 - Secondary cell wall: a tough, thick layer formed inside the primary plant cell wall when
the cell is mature.

d. Plasmodesmata: cytoplasmic channels through cell walls that connect the cytoplasms of
adjacent cells.

NOTE : For the following parts, refer other functions from the animal cell section since
both animal and plant cells are similar in these parts.

e. Nucleus: The nucleus contains deoxyribonucleic acid (DNA), the cell’s genetic material, which
contains instructions for making proteins, controlling all of the body’s activities. The nucleus
also regulates the growth and division of the cell.
f. Ribosomes: The synthesis of proteins happen in the ribosomes.
g. Endoplasmic Reticulum: In the endoplasmic reticulum, proteins are modified.
h. Golgi Apparatus : The proteins are folded, sorted, and packaged into vesicles in this region.
i. Mitochondria: These are also found in plant cells. They produce ATP through cellular
respiration. Photosynthesis in the chloroplasts provides the nutrients that mitochondria break
down for use in cellular respiration.
j. Cytoplasm : This contains the organelles except the nucleus and the liquid within the cells called
the cytosol. The cytosol is mostly made of water, and also contains ions, proteins, and small
molecules.
k. Cytoskeleton: The cytoskeleton is a network of filaments and tubules found throughout the
cytoplasm of the cell. It gives the cell shape, provides strength, stabilizes tissues, anchors
organelles within the cell, and has a role in cell signaling. The cell membrane, a
double phospholipid layer, surrounds the entire cell.
l. Plasma Membrane: The plasma membrane is the “bag” that holds all of the intracellular
material and regulates the movement of materials into and out of the cell.

Go to the following link for the introduction of cells:

https://www.youtube.com/watch?v=URUJD5NEXC8&feature=youtu.be&t
=5

Explore more about Eukaryotic cells:

Animal cells:
https://www.youtube.com/watch?v=cj8dDTHGJBY&feature=youtu.be

Plant cells:
https://www.youtube.com/watch?v=9UvlqAVCoqY&feature=youtu.be

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D. Techniques and Methods in Studying Cells

Light Microscopy – This is done by having visible light pass through the specimen and then
through glass lenses. The lenses refract(bend) the light in such a way that the image of the
specimen is magnified as it is projected into the eye or into a camera. The three important
parameters in LM are magnification (ratio of an object’s image size to its real size), resolution
(clarity of the image), and contrast (accentuates differences in parts of the sample).

Different Types of Light Microscopy:

1. Brightfield(unstained specimen) : Light passes directly through the specimen. Unless the cell
is naturally pigmented or artificially stained, the image has little contrast
2. Brightfield (stained specimen) : Light also passes directly through the sample but staining
with various dyes enhances contrast. (NOTE: Most staining procedures require cells to be
fixed or preserved)
3. Phase-contrast: Variations in density within the specimen are amplified to enhance contrast
in unstained cells, which is useful for examining unpigmented , living cells.
4. Differential-interference-contrast(NOMARSKI) : Optical modifications are used to
exaggerate differences in density, making the image appear almost 3-D as in phase-contrast
microscopy.
5. Fluorescence : Locations of specific molecules in the cell can be revealed by labelling the
molecules with fluorescent dyes or antibodies, yet for some cells have molecules that
fluoresce on their own. Fluorescent substances absorb ultraviolet radiation and emit visible
light.
6. Confocal : Using a laser, this “optical sectioning” technique eliminates out of focus light from
a thick sample, creating a single plane of fluorescence in the image. By capturing sharp
images at many different planes, a 3-D reconstruction can be created.
7. Deconvolution : Using the deconvolution software, blurry images of reconstructed cell from
many different planes was processed. This process digitally removes out-of-focus light and
reassigns it to its source, creating a much sharper 3-D image.
8. Super-resolution : Sophisticated equipment is used to light up individual fluorescent
molecules and record their position. Combining information from many molecules in
different places “breaks” the limit of resolution, increasing the sharpness of the image

Electron Microscopy – It focuses a beam of electrons through the specimen or onto its
surface.

Two Types of Electron Microscopy:

1. Scanning electron microscopy(SEM) : This is useful for a detailed study of the topography
of a specimen. The electron beam scans the surface of the sample, usually coated with a
thin film of gold. The beam excites electrons on the surface, and these secondary electrons
are detected by a device that translates the pattern of electrons into an electronic signal to
a video screen. The result is an image of the specimen’s surface that appears three-
dimensional.

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 2. Transmission electron microscopy(TEM) : It is used to study the internal structure of cells.
The TEM aims an electron beam through a very thin section of the specimen, similar to the
way a light microscope transmits light through a slide. The specimen has been stained with
atoms of heavy metals, which attach to certain cellular structures, thus enhancing the
electron density of some parts of the cell more than others. The electrons passing through
the specimen are scattered more in the denser regions, so fewer are transmitted. The
image displays the pattern of transmitted electrons.

Cell Fractionation

The process takes cells apart and separates major organelles and other subcellular structures
from one another. The instrument used is the centrifuge, which spins test tubes holding mixtures of
disrupted cells at a series of increasing speeds. At each speed, the resulting force causes a fraction of
the cell components to settle to the bottom of the tube forming a pellet. At lower speeds, the pellet
consists of larger components, and higher speeds yield a pellet with smaller components. This is for
preparing cell components in bulk and identifying their functions, a task not possible with intact cells.

Go to the following link that will help you understand the different techniques for studying cells:

https://www.youtube.com/watch?v=8mMiz0My3vw&feature=youtu.be

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