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. Biochemistry of the Cell

A. Water, the aqueous environment

Water is the biological medium here on Earth, and is the most abundant substance in living
systems, making up 70% or more of the weight of most organisms. Water is the only common
substance to exist in the natural environment in all three physical states of matter. Acknowledging
that life adapts to its environment through natural selection , Henderson emphasized that for life to
exist at all , the environment must first be suitable and that leads to water.

Water has four emergent properties which are stated below:

1. Cohesion and Adhesion of Water Molecules

Water molecules stay close to each other as a result of hydrogen bonding and these bonds
that hold the water together, is a phenomenon called cohesion. Cohesion contributes to the
transport of water and dissolved nutrients against gravity in plants. Water from the roots reaches
the leaves through a network of water conducting cells. Combined with cohesion is adhesion
which is the clinging of one substance to another. This adhesion of water to cell walls by
hydrogen bonds helps counter the downward pull of gravity.

2. Moderation of Temperature by Water.

Water moderates air temperature by absorbing heat from air that is warmer and releasing the
stored heat to air that is cooler. It relates to which heat must be absorbed in order to break
hydrogen bonds ; by the same token, heat is released when hydrogen bonds formed. This property
of water also helps warm the air when it is nighttime and tends to stabilize the ocean temperature,
creating a favorable environment for marine life. Thus, because of this property, the water that
covers most of the Earth keeps temperature fluctuations on land and in water within limits that
permit life. As for organisms which are made primarily of water , they are better able to resist
changes in their own temperature than if they were made of a liquid with a lower specific heat.

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3. Evaporative Cooling of Water

As a liquid evaporates, the surface of the liquid that remains behind cools down. This
evaporative cooling occurs because the “hottest” molecules, those with the greatest kinetic
energy, are the most likely to leave as a gas. Evaporative cooling of water contributes to the
stability of temperature in lakes and ponds and also provides a mechanism that prevents
terrestrial organisms from overheating. Evaporation of water from the leaves of a plant helps
keep the tissue in the leaves from becoming too warm in the sunlight. It also helps human to
prevent overheating on a hot day or when excess heat is generated by strenuous activity by
evaporation of sweat from human skin dissipating body heat.

In addition, the ability of ice to float due to its lower density is an important factor in the
sustainability of the environment since if ice sank, then eventually all bodies of water would
freeze solid, making life to be impossible. Also, during summer, only the upper few inches of the
ocean would thaw, then the floating ice would act as an insulator to the liquid water below,
preventing it from freezing and allowing life to exist under the frozen surface.

4. Water as the Solvent of Life

Water acts as solvent on a mixture of two or more substances which is called a solution. Being
the solvent, there is much more water than the solute. The solvent is then involved in the
dissolving of ions which contributes to processes happening in the body such as the formation of
the hydration shell, a sphere of water molecules around each dissolved ion.

B. Biomolecules and their Properties

B.1. Nucleic Acids

Nucleic acids are macromolecules that exist as polymers called polynucleotides

(consist of monomers called nucleotides). They store, transmit, and help express hereditary
information. A nucleotide is composed of three parts: a nitrogenous base, a five-carbon
sugar, and one or more phosphate groups. In a polynucleotide, each monomer has only one
phosphate group. The portion of the nucleotide without any phosphate groups is called a
nucleoside.

There are two families of nitrogenous bases:

a. Pyrimidine: has one six-membered ring of carbon and nitrogen atoms. The members of
pyrimidine are cytosine, thymine, and uracil.
b. Purines: are larger, with a six-membered ring fused to a five-membered ring. The purines
are adenine, and guanine.

NOTE: Adenine, guanine, cytosine are found in both DNA and RNA; thymine is only found
in DNA and uracil only in RNA. The complementary base pairing states that adenine
always pairs with thymine in DNA or uracil in RNA, while guanine always pairs with
cytosine.
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 In terms of sugar, in DNA, it is called deoxyribose and RNA has the sugar, ribose. The two
sugar phosphate backbones run in arrangement called “antiparallel”. DNA and RNA are
types of nucleic acids. DNA is double-stranded forming a double helix while RNA is single-
stranded. DNA stores hereditary information while RNA performs various functions,
during gene expression, including carrying instructions from DNA to ribosomes.

B.2. Proteins

Nearly every dynamic function of a living being depends on proteins. Proteins account
for more than 50% of the dry mass of most cells, and they are instrumental in almost
everything organisms do. A protein is a biologically functional molecule that consists of one
or more polypeptides (polymers of amino acids), each folded and coiled into a specific three-
dimensional structure. Many proteins are roughly spherical (globular proteins), while others
are shaped like long fibers (fibrous proteins). Folding of proteins are done by chaperonins and
when proteins are transferred from an aqueous environment to a non-polar solvent, it
unravels and loses its native shape by a process called denaturation.

The structure of a protein is composed of:

a. Primary structure: It is a linked series of amino acids with a unique sequence. The primary
structure of a protein is determined not by the random linking of amino acids, but by
inherited genetic information.
b. Secondary structure: This is collectively referred to as coils and folds, which are the result
of hydrogen bonds between the repeating constituents of the polypeptide backbone.

- a- helix : a delicate coil held together by hydrogen bonding between every fourth amino
acid.

- b pleated sheet: two or more strands of the polyopeptide chain lying side by side (called
b strands) are connected by hydrogen bonds between parts of the two parallel
polypeptide backbones.

c. Tertiary structure: It is the overall shape of a polypeptide resulting from interactions

between the side chains (R groups) of the various amino acids.

Kinds of interactions:

- Hydrophobic interaction: caused by the exclusion of nonpolar substances by the

water molecules

- Hydrogen and ionic bonds: Hydrogen bonds are between polar side chains and ionic
bonds are between positively and negatively charged side chains.

- Disulfide bridges: These further reinforce the shape of a protein. Disulfide bridges
are formed when two cysteine monomers which have sulfhydryl groups (-SH) on their side
chains are brought closer together by the folding of protein.
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 d. Quaternary structure: It is the overall protein structure that results from the
aggregation of these polypeptide subunits, the a and b subunits.

Proteins function as:

enzymes , selectively accelerating chemical reactions, such as digestive enzymes

on hydrolyzing bonds inn food molecules.
storage of amino acids, such as the ovalbumin, protein of egg white serve as
storage of amino acid for the developing embryo.
coordinator of an organism’s activities such as insulin regulating blood sugar
concentration.
motor proteins for movement such as actin and myosin for the contraction of
muscles.
protection against disease such as antibodies inactivating bacteria and viruses.
transport of substances, such as hemoglobin transporting oxygen.
response of cell to a chemical stimuli
support such as collagen and elastin providing a fibrous framework in connective
tissues.

B.3. Lipids

Lipids are the one class of biomolecules that does not include true polymers, and they
are generally not big enough to be considered as macromolecules. They are grouped together
because they mixed poorly with water. Their hydrophobic behavior is based on their
molecular structure and the three types of lipids are fats, phospholipids and steroids.

• Fats – These are not polymers but are large molecules assembled from smaller molecules by
dehydration reaction. A fat is constructed from two kinds of smaller molecules: glycerol and
fatty acids. Glycerol is an alcohol; each of its three carbons bear a hydroxyl group. A fatty acid
has a long carbon skeleton, having a carbon at one end which is a part of the carboxyl group.
Fatty acids are hydrophobic(away from water) due to the nonpolar C-H bonds. In making a fat
or triacylglycerol, three fatty acid molecules are each joined to glycerol by an ester linkage, a
bond between a hydroxyl group and carboxyl group. The major function of fats is energy
storage. The hydrocarbon chains are similar to gasoline molecules and rich in energy. They
also cushion such vital organs as the kidneys, and layer beneath the skin insulates the body.

- Saturated fatty acid: These are formed if there are no double bonds between
carbon atoms composing a chain, then as many hydrogen atoms as possible are
bonded to the carbon skeleton. They lack double bonds, and their flexibility allows the
fat molecules to pack together tightly.

- Unsaturated fatty acid: It has one or more double bonds , with one fewer
hydrogen atom on each double-bonded carbon. Its double bonds are cis which has
kinks to prevent the molecules from packing together closely enough to solidify at
room temperature.

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• Phospholipids – Cells could not exist without phospholipids, since they are essential on
making up the cell membranes. A phospholipid is similar to a fat molecule but has only two
fatty acids attached to glycerol rather than three. The two ends of phospholipids show
different behavior toward water. The hydrocarbon tails are hydrophobic while its hydrophilic
head has an affinity for water. When phospholipids are added to water, they self-assemble
into double-layered structures called “bilayers”, shielding their hydrophobic portions from
water. The hydrophilic heads are on the outside of the bilayer in contact with the aqueous
solutions inside and outside of the cell. The hydrophobic tails point toward the interior of the
bilayer, away from the water. Phospholipids function as a boundary between the cell and its
external environment.
• Steroids – These are lipids characterized by a carbon skeleton consisting of four fused rings.
Different steroids are distinguished by the chemical groups attached to the rings. Cholesterol,
a steroid, is a crucial molecule in animals since it is a component of animal cell membranes
and is also the precursor from which other steroids are synthesized, such as the sex
hormones.

B.4. Carbohydrates

Carbohydrates include both sugars and polymers of sugars. The simplest

carbohydrates are the monosaccharides, or simple sugars; these are the monomers from
which more complex carbohydrates are constructed. Disaccharides are double sugars,
consisting of two monosaccharides joined by a covalent bond. Carbohydrates also include
macromolecules called polysaccharides, polymers composed of many sugar building blocks.

• Monosaccharides – these are simple sugars which generally have formulas that are some
multiple of the unit CH2O. Glucose (C6H12O6), the most common monosaccharide, is of
central importance in the chemistry of life. These sugars are classified by the location of
the carbonyl group (C=O) and the size of the carbon skeleton. Monosaccharides
particularly glucose, are major nutrients for cells. During cellular respiration, cells extract
energy in a series of reactions starting with glucose molecules. Simple – sugar molecules
not only function as a major fuel for cellular work, but their carbon skeletons also serve
as raw material for the synthesis of small organic molecules such as amino acids.
• Disaccharides – consists of two monosaccharides joined by a glycosidic linkage, a
covalent bond formed by a dehydration reaction. It is commonly found to the food that
we eat such as maltose, where malt sugar is used for brewing beer, or lactose which is in
the milk that we drink. Plants also transports= carbohydrates from leaves to roots by the
form of sucrose, which is also known as table sugar.
• Polysaccharides – are macromolecules, polymers with a few thousand monosaccharides
joined by linkages. Some polysaccharides serve a storage material, hydrolyzed as needed
to provide sugar for cells, or even used as a building material. Plants store starch, a
polymer of glucose monomers, within the plastids. Starch would then be synthesized,
enabling the plant to stockpile surplus glucose, and represents as a stored energy.

While animals store glycogen mainly in liver and this is released when the demand for
sugar is high, serving as a fuel. These sugars also act as structural polysaccharides where
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 organisms build strong materials from it such as the cellulose which is the major
component of the tough walls that enclose plant cells, and cellulose is also the major
constituent of paper and the only component of cotton. Another structural
polysaccharide is chitin where it is used by arthropods for their exoskeleton (hard case
protecting the soft parts of the body).

Go to the following links to learn more about the molecules of life using these voice-over
presentations:

Chemistry and the Molecules of Life:

https://www.youtube.com/watch?v=udvppplTq1w&feature=youtu.be

Biochemistry Part 1:
https://www.youtube.com/watch?v=wSKxCNcj6Ac&feature=youtu.be

Biochemistry Part 2:
https://www.youtube.com/watch?v=6JV-Iy80JKo&feature=youtu.be