Microbiology and Parasitology - Prelim CAMPOS ELLA

Microbiology and Parasitology Villegas and Patete (2021)
Course Number: Bio120
Course Title: Microbiology and Parasitology
Number of Units: Lecture – 3.0 units
Laboratory – 1.0 unit
Course Description:
This course covers the anatomy, physiology, and genetics of microorganisms such as
bacteria, algae, fungi, and protozoans. It also introduces the mechanisms of parasitology,
focusing on the common diseases that have impacts on the community. The primary goal is to
equip the future science teachers with critical knowledge about microbial diversity and their
interactions with humans.
Authors:
Jhonnel P. Villegas
Lovely May B. Patete
This course pack is intended for institutional use only. Reproduction of this
material is NOT ALLOWED without written permission from the authors.
This module is NOT FOR SALE.

CONTENTS
Module I: Fundamentals of Microbiology and Parasitology
Lesson 1: Introduction to Microbiology and Parasitology
Lesson 2: Anatomy of Prokaryotic and Eukaryotic Cells
Lesson 3: Microbial Metabolism and Growth
Lesson 4: Microbial Genetics
Module II: Microbial Diversity
Lesson 5: Classification of Microorganisms
Lesson 6: The Prokaryotes: Domains Bacteria and Archaea
Lesson 7: The Eukaryotes: Fungi, Algae, Protozoa, and
Helminths Lesson 8: Viruses, Viroids, and Prions
Module III: Microbe-Host Interaction
Lesson 9: Principles of Disease and Epidemiology
Lesson 10: Microbial Mechanisms of Pathogenicity
Lesson 11: Innate and Adaptive Immunity
Lesson 12: Microorganisms and Human Disease

Lesson I: Introduction to Microbiology and
Parasitology OBJECTIVES
1. Define microbiology and parasitology;

2. List several ways on how microbes affect human lives;
3. Name and classify microorganisms;
4. Trace the historical origin of microbiology; and
5. Determine the relationship between microbes and human disease.
INTRODUCTION
Welcome to microbiology: the study of the great variety of living organisms that are too
small for us to see without a microscope—the microbes, or microorganisms. For many people,
the words microbe and germ bring to mind a group of tiny creatures that do not quite fit into any
of the categories in that old question, “Is it animal, vegetable, or mineral?”
Germ actually comes from the Latin word germen, meaning to spout from, or germinate.
Think of wheat germ, the plant embryo from which the plant grows. It was first used in relation to
microbes in the nineteenth century to explain the rapidly growing cells that caused disease.
Microbes, also called microorganisms, are minute living things that individually are usually too
small to be seen with the unaided eye. The group includes bacteria, fungi (yeasts and molds),
protozoa, and microscopic algae. It also includes viruses, those noncellular entities sometimes
regarded as straddling the border between life and nonlife.
ACTIVITY
Directions: Determine the classification of these organisms as Microbes or Parasites. rewrite
them on each box of their respective group.
Tapeworms bacteria Barnacles Molds Fleas Yeast Roundworms Algae
algae Tapeworms
Barnacles
yeast
Roundworms
Fleas
molds Bacteria
ANALYSIS
Directions: Using a Venn diagram, differentiate microbiology from parasitology.
It is the branch of
It is the study of all living Beneficial and detrimental in nature.

organisms that are too small to
be visible with the naked eye.
Deals with
-It includes bacteria, fungi, microbiology that is
protozoa, algae, archaea, concerned with the study of
viruses and prions, collectively parasites.
known as microbes.
Present in Focused more on parasitic organisms

flora and such protozoa, helminths, and
fauna arthropods(ectoparasites).
Branch of biology microorganisms Branch of

microbiology
Microbiology Parasitology
ABSTRACTION
Microbiology and Parasitology
Microbiology is the study of all living organisms that are too

small to be visible with the naked eye. This includes bacteria,
archaea, viruses, fungi, prions, protozoa and algae,
collectively known as 'microbes'.

Parasitology is the branch of microbiology that is concerned with the study of parasites. In the
process, it gives focus to various characteristics of the parasite (morphology, life-cycle, ecology,
taxonomy, etc), the type of host they infect/affect and the relationship between the two.
Microbes and Human Welfare
In the world of microorganisms only a minority are pathogenic. Microbes that cause food
spoilage— such as soft spots on fruits and vegetables, decomposition of meats, and rancidity of
fats and oils— are also a minority. The vast majority of microbes benefit humans, other animals,
and plants in many ways.
1. Food production:
Many food products employ microorganisms in their production. These include the
microbial fermentation processes used to produce yogurt, buttermilk, cheeses, alcoholic
beverages, leavened breads, sauerkraut, pickles, and kimchi.
2. Recycling vital elements
● bacteria and fungi, return carbon dioxide to the atmosphere when they decompose
organic wastes and dead plants and animals.
● Algae, cyanobacteria, and higher plants use the carbon dioxide during
photosynthesis to produce carbohydrates for animals, fungi, and bacteria.
● Only bacteria can naturally convert atmospheric nitrogen to a form available to
plants and animals.
3. Bioremediation
● a system that utilizes microorganisms to degrade the pollutants present in
wastewater and in soil environments with technological innovations.
● It is a technique that removes biodegradable complex toxic substances into
harmless and acceptable end products i.e., CO 2 and H2O through cellular
metabolisms.
4. Insect Pest Control
Some farmers use Bacillus thuringiensis in their crops. It is incorporated into a dusting
powder that is applied to the crops these insects eat. The bacteria produce protein
crystals that are toxic to the digestive systems of the insects. The toxin gene also has
been inserted into some plants to make them insect resistant.
5. Biotechnology and Recombinant DNA Technology

● Production of useful natural gene products or products from
bioengineering. Examples include specific enzymes, antibiotics,
vaccines,
and medications such as human insulin, interferons, and growth
hormones.

● In gene therapy, viruses are used to carry replacements for defective or
missing genes into human cells.
● Genetically modified bacteria are used in agriculture to protect plants
from frost and insects and to improve the shelf life of produce.
Nomenclature
Carolus Linnaeus in 1753 established the system of nomenclature (naming) for

organisms. Scientific names are latinized because Latin was the language traditionally
used by scholars. Scientific nomenclature assigns each organism two names
● the genus (plural: genera) is the first name and is always capitalized
● specific epithet (species name) follows and is not capitalized.
The organism is referred to by both the genus and the specific epithet, and both names
are underlined or italicized.
Escherichia coli Escherichia coli
Klebsiella pneumoniae Klebsiella pneumoniae
Mycobacterium tuberculosis Mycobacterium tuberculosis
By custom, after a scientific name has been mentioned once, it can be abbreviated with
the initial of the genus followed by the specific epithet.
Types of Microorganisms
1. Bacteria (singular: bacterium)

● are relatively simple, single- celled (unicellular) organisms. Because their
genetic material is not enclosed in a special nuclear membrane,
bacterial
cells are called prokaryotes, from Greek words meaning prenucleus.
Prokaryotes include both bacteria and archaea.
2. Archaea
● Like bacteria, archaea consist of prokaryotic cells, but if they have cell walls, the
walls lack peptidoglycan. Archaea are not known to cause disease in humans. ●
Archaea, often found in extreme environments, are divided into three main groups. ○
methanogens produce methane as a waste product from respiration.
○ extreme halophiles (halo = salt; philic = loving) live in extremely salty
environments such as the Great Salt Lake and the Dead Sea.
○ extreme thermophiles (therm = heat) live in hot sulfurous water, such as
hot springs at Yellowstone National Park.
3. Fungi (singular: fungus)

● are eukaryotes organisms whose cells have a distinct nucleus containing the
cell’s genetic material (DNA), surrounded by a special envelope called the
nuclear membrane. Organisms in the Kingdom Fungi may be unicellular or
multicellular.
○ Large multicellular fungi, such as mushrooms, may look somewhat
like plants, but unlike most plants, fungi cannot carry out
photosynthesis.
○ True fungi have cell walls composed primarily of a substance called
chitin.
○ The unicellular forms of fungi, yeasts, are oval microorganisms that
are larger than bacteria.
4. Protozoa (singular: protozoan) are unicellular eukaryotic microbes. ● Protozoa
move by pseudopods, flagella, or cilia. Amebae move by using extensions of
their cytoplasm called pseudopods (false feet).
● Other protozoa have long flagella or numerous shorter append- ages for
locomotion called cilia.
● Protozoa have a variety of shapes and live either as free entities or as
parasites (organisms that derive nutrients from living hosts) that absorb or
ingest organic compounds from their environment
5. Algae (singular: alga) are photosynthetic eukaryotes with a wide variety of
shapes and both sexual and asexual reproductive forms.
● Algae are abundant in freshwater and saltwater, in soil, and in association
with plants.
● As photosynthesizers, algae need light, water, and carbon dioxide for food
production and growth, but they do not generally require organic compounds from
the environment.
6. Viruses
● These are microorganisms that are so small that most can be seen only with an
electron microscope, and they are acellular (that is, they are not cells). ● a virus
particle contains a core made of only one type of nucleic acid, either DNA or RNA.
This core is surrounded by a protein coat, which is sometimes encased by a lipid
membrane called an envelope.
● Viruses can reproduce only by using the cellula machinery of other organisms.
Thus, on the one hand, viruses are considered to be living only when they
multiply within host cells they infect.
● Viruses are parasites of other forms of life. On the other hand, viruses are not
considered to be living because they are inert outside living hosts.
7. Multicellular Animal Parasites

● Animal parasites are eukaryotes. The two major groups of parasitic worms are the
flatworms and the roundworms, collectively called helminths. During some stages
of their life cycle, helminths are microscopic in size. Laboratory identification of
these organisms includes many of the same techniques used for identifying
microbes.
Golden Age of Microbiology (1857 to 1914)
● During this productive period, microbiologists studied the chemical activities of

microorganisms, improved the techniques for performing microscopy and culturing
microorganisms, and developed vaccines and surgical techniques.
● Discoveries included both the agents of many diseases and the role of immunity in
preventing and curing disease.
These are the scientists who have made contributions in early
microbiology: Rudolf Virchow (1858).
- introduced the concept of biogenesis: living cells can arise only from preexisting
cells
Louis Pasteur (1861).

- demonstrated that microorganisms are in the air everywhere and
offered proof of biogenesis.
- His discoveries led to the development of aseptic techniques used in
laboratory and medical procedures to prevent contamination by
microorganisms.
Joseph Lister (1827–1912)

- Performed surgery under aseptic conditions using phenol. Proved that microbes
caused surgical wound infections.
Robert Koch (1843–1910)

- Established experimental steps for directly linking a specific microbe to
a specific disease.
Infectious Disease
An infectious disease is a disease in which pathogens invade a susceptible host, such

as a human or an animal. In the process, the pathogen carries out at least part of its
life cycle inside the host, and disease frequently results. Some emerging infectious
diseases

(EIDs) are the result of increased human exposure to new, unusual infectious agents
in areas that are undergoing ecologic changes such as deforestation and construction
(e.g., Venezuelan hemorrhagic virus). Some EIDs are due to changes in the
pathogen’s ecology. For example, Powassan virus (POWV) was transmitted by ticks
that don’t usually bite humans. However, the virus recently became established in the
same deer ticks that transmit Lyme disease. An increasing number of incidents in
recent years highlights the extent of the problem.
Microbes and Human Disease
1. The disease-producing properties of a species of microbe and the host’s resistance
are important factors in determining whether a person will contract a disease. 2.
Bacterial communities that form slimy layers on surfaces are called biofilms. 3. An
infectious disease is one in which pathogens invade a susceptible host. 4. An
emerging infectious disease (EID) is a new or changing disease showing an increase
in incidence in the recent past or a potential to increase in the near future.
APPLICATION
1. Research three species that are under each classification of microorganisms. Follow the
correct naming system if you are using scientific names.
Classification Organisms
Bacteria Escherichia coli (abbreviated as E. coli)

are bacteria found in the environment,
foods, and intestines of people and
animals.
Streptococcus canis is important to the skin

and mucosal health of cats and dogs, but
under certain circumstances, these bacteria
can cause opportunistic infections.
Lactiplantibacillus plantarum commonly

found in many fermented food products as
well as anaerobic plant matter.

Archaea Thermococcus litoralis is a species of
Archaea that is found around deep-sea
hydrothermal vents as well as shallow
submarine thermal springs and oil wells. It is
an anaerobic organotroph hyperthermophile
that is between 0.5–3.0 µm in diameter.
Halobacterium salinarum resides in

extremely salty environments and uses
energy from the sun in the photosynthetic
process.
Methanocaldococcus jannaschii the first

hyperthermophilic chemolithotrophic
organism that was isolated from a deep-sea
hydrothermal vent.
Fungi Batrachochytrium dendrobatidis is a fungus

that causes the disease chytridiomycosis in
amphibians.
Penicillium chrysogenum It is common in

temperate and subtropical regions and can
be found on salted food products.
Agaricus bisporus is one of the most

commonly and widely consumed
mushrooms in the world.
Protozoa Balantidium coli is a parasitic species of

ciliate alveolates that causes the disease
balantidiasis.
Plasmodium falciparum is a unicellular

protozoan parasite of humans, and the
deadliest species of Plasmodium that
causes malaria in humans.

Trichomonas vaginalis it is the most common
pathogenic protozoan infection of humans in
industrialized countries.
Algae Arthrospira platensis is a planktonic

filamentous cyanobacterium composed of
individual cells (about 8 μm diam.), which
grows in subtropical and alkaline lakes.
Pelvetia canaliculata is a type of brown

seaweed also known as Channeled wrack.
This hearty, upper shore-growing seaweed
is known to survive in harsh conditions,
including extended periods of low tide,
although it requires submersion for
maximum nutrient uptake.
Caulerpa lentillifera, is a seaweed that is one

of the favored species of edible Caulerpa
due to its soft and succulent texture.
Viruses Canine parvovirus is a contagious virus

mainly affecting dogs. It is highly contagious
and is spread from dog to dog by direct or
indirect contact with their feces.
Coxsackieviruses are RNA viruses that may

cause hand, foot, and mouth disease
(HFMD).
Human alphaherpesvirus 3 is one of nine

herpesviruses known to infect humans. It
causes chickenpox (varicella), a disease
most commonly affecting children, teens,
and young adults, and shingles (herpes
zoster) in adults.
Multicellular Animal Parasites Haemonchus contortus, also known as the

barber's pole worm, is a quite common
parasite and one of the most pathogenic
nematodes of
ruminants.
Echinococcus granulosus, also called the

hydatid worm, hyper tapeworm or dog
tapeworm, is a cyclophyllid cestode that
dwells in the small intestine of canids as an
adult, but which has important intermediate
hosts such as livestock and humans, where
it causes cystic echinococcosis, also known
as hydatid disease.
Ascaridia galli is a parasitic roundworm

belonging to the phylum Nematoda.
Nematodes of the genus Ascaridia are
essentially intestinal parasites of birds.
2. Create a timeline of major events and/or contributions of scientists in the development of

Microbiology.
Year Events
1677 Observed "little animals" (Antony

Leeuwenhoek)
1796 First scientific smallpox vaccination

(Edward Jenner)
1850 Advocated washing hands to stop the

spread of disease (Ignaz Semmelweis)
1858 Introduced the concept of biogenesis:

living cells can arise only from
preexisting cells (Rudolf Virchow)
1861 Disapproved spontaneous generation

(Louis Pasteur)
1862 Supported Germ Theory of Disease

(Louis Pasteur)
1867 Practiced antiseptic surgery (Joseph Lister)
1876 First proof of Germ Theory of Disease with

B. anthracis discovery (Robert Koch)
1881 Growth of Bacteria on solid media

(Robert Koch)
1882 Developed acid-fast Stain (Paul
Ehrlich) Outlined Kochs postulates
(Robert Koch)
1884 Developed Gram Stain (Christian Gram)
1885 First Rabies vaccination (Louis Pasteur)
1892 Discovered viruses (Dmitri

Iosifovich Ivanovski)
1899 Recognized viral dependence on cells

for reproduction (Martinus Beijerinck)
1900 Proved mosquitoes carried the yellow

fever agent (Walter Reed)
1910 Discovered cure for syphilis (Paul Ehrlich)
1928 Discovered Penicillin (Alexander Fleming)
1977 Developed a method to sequence DNA

(W. Gilbert & F. Sanger)
1983 Polymerase Chain Reaction invented

(Kary Mullis)
Luc Montagnier and Robert Gallo
announce their discovery of the
immunodeficiency virus (HIV) believed to
cause AIDS.
L. W. Riley and colleagues describe for
the first time the involvement of E. coli
O:157 as an infectious diarrhogenic
agent.
1984 Ralph Isberg and Stanley Falkow clone a

gene (inv) from Yersinia
psuedotuberculosis that confers an
invasive phenotype on the non invasive
strain HB101 of E. coli. This is the first
demonstration of transfer of such a
virulence property by a single gene.
1985 Robert Gallo, Dani Bolognesi, Sam Broder,

and others show that AZT inhibits the
infectivity and cytopathic effects of HIV in
vitro. This discovery is a significant advance
in slowing the infective cycle of the virus.
1995 First microbial genomic sequence
published (H. influenzae) (TIGR)

3. Why is it important to do environmental sampling from time to time?
It is important to do environmental sampling to further investigate an area that may

provide a major public health risk due to microbiological dangers that may be present and
contributing to food contamination. Aside from that to check if there are prior suspected or
confirmed linkage to human illness, recalled or seized contaminated product, or prior
detection of environmental pathogens in the environment.
4. What suggestions can you give to prevent outbreaks of infectious disease?
It is undeniable that most of the infectious disease are caused by not strictly
following proper hygiene and improper waste disposal. I suggest is to observe
proper hygiene such as washing hands before eating, taking bath regularly and
ensuring that your room is cleaned and always disinfected. Aside from that, make
sure that waste is properly disposed and follows proper segregation to prevent
bacteria and viruses from spreading.
5. Why does some normal flora from the environment become pathogenic?
Some normal flora from the environment become pathogenic because of the
negative host-microbes relationship. Instead of sustaining energy and nutrients to
their host, the balance is disturbed, and microbes start to harm the health of the
host. Another factor is when the host resistance mechanism fail---either through
immunodeficiency or infection process, normal flora becomes pathogenic.
Lesson 2: Anatomy of Prokaryotic and Eukaryotic Cells
OBJECTIVES
1. Determine the size, shape, and arrangement of bacterial cells;

2. Cite structures external to the cell wall;
3. Determine the composition and characteristics of the cell wall;
4. Enumerate structures internal to the cell wall;
5. Identify the structures of the eukaryotic cell;
6. Differentiate the structures of the prokaryotic and eukaryotic cells; and
7. Discuss the evolution of eukaryotes.
INTRODUCTION
Despite their complexity and variety, all living cells can be classified into two groups,
prokaryotes and eukaryotes, based on certain structural and functional characteristics. In
general, prokaryotes are structurally simpler and smaller than eukaryotes. The DNA (genetic
material) of prokaryotes is usually a single, circularly arranged chromosome and is not
surrounded by a membrane; the DNA of eukaryotes is found in multiple chromosomes in a
membrane-enclosed nucleus.
Plants and animals are entirely composed of eukaryotic cells. In the microbial world,
bacteria and archaea are prokaryotes. Other cellular microbes—fungi (yeasts and molds),
protozoa, and algae—are eukaryotes. Both eukaryotic and prokaryotic cells can have a sticky
glycocalyx surrounding them. In nature, most bacteria are found sticking to solid surfaces,
including other cells, rather than free-floating. The glycocalyx is the glue that holds the cells in
place.
ACTIVITY
Directions: Draw and label the parts of a prokaryotic and eukaryotic cell.
Mic
robiology and Parasitology Villegas and Patete (2021)

ANALYSIS
Directions: Using a Venn Diagram, differentiate the structures and functions between a
prokaryotic and eukaryotic cell.
Lack membrane
enclosed organelles
(including a nucleus).
Have a membrane
bound nucleus and
other organelles Peptidoglycan is found

Chemical
and composition
and chemical
reactions
0.2 to 2.0 mm in diameter and 2 to 8

mm in length.
Have cilia or flagella for movement
No mucilaginous present
DNA is linear, thread like structure.

in prokaryotic cells flagella (for propulsion)
Have pili and fimbriae (for adhesion) Mucilaginous capsule DNA is circular
Prokaryote Eukaryote
ABSTRACTION
Comparing Prokaryotic and Eukaryotic Cells: An Overview
● Prokaryotic and eukaryotic cells are similar in their chemical composition and chemical
reactions.
● Prokaryotic cells typically lack membrane-enclosed organelles (including a
nucleus). ● Peptidoglycan is found in prokaryotic cell walls but not in eukaryotic cell
walls. ● Eukaryotic cells have a membrane-bound nucleus and other organelles.
The Prokaryotic Cell
● Bacteria are unicellular, and most of them multiply by binary fission.

● Bacterial species are differentiated by morphology, chemical composition, nutritional
requirements, biochemical activities, and source of energy.
The Size, Shape, and Arrangement of Bacterial Cells
● Most bacteria are 0.2 to 2.0 mm in diameter and 2 to 8 mm in length.

● The three basic bacterial shapes are coccus (spherical), bacillus (rod-shaped), and spiral
(twisted).
● Pleomorphic bacteria can assume several shapes.
Structures External to the Cell Wall
● Glycocalyx
● Flagella and Archaella
● Axial Filaments
● Fimbriae and Pili
The Cell Wall
● The cell wall surrounds the plasma membrane and protects the cell from changes in water
pressure.
● The bacterial cell wall consists of peptidoglycan, a polymer consisting of NAG and NAM
and short chains of amino acids.
● Gram-positive cell walls consist of many layers of peptidoglycan and also contain teichoic
acids.
● Gram-negative bacteria have a lipopolysaccharide-lipoproteinphospholipid outer
membrane surrounding a thin peptidoglycan layer.

● The outer membrane protects the cell from phagocytosis and from penicillin, lysozyme,
and other chemicals.
● Porins are proteins that permit small molecules to pass through the outer membrane;
specific channel proteins allow other molecules to move through the outer membrane. ● The
lipopolysaccharide component of the outer membrane consists of sugars (O
polysaccharides), which function as antigens, and lipid A, which is an endotoxin.
Structures Internal to the Cell Wall
● Plasma (Cytoplasmic) Membrane

● Cytoplasm
● The Nucleoid
● Ribosomes
● Inclusions
● Endospores
Structures in the Eukaryotic Cell
● Flagella and Cilia

● Cell Wall and Glycocalyx
● Plasma (Cytoplasmic) Membrane
● Cytoplasm
● Ribosomes
● Organelles
The Evolution of Eukaryotes
● According to the endosymbiotic theory, eukaryotic cells evolved from symbiotic

prokaryotes living inside other prokaryotic cells.
APPLICATION
1. Diagram each of the following flagellar arrangements:
a. lophotrichous
b. monotrichous
c. peritrichous
d. amphitrichous
e. polar

2. Draw the bacterial shapes listed in (a), (b), and (c). Then draw the shapes in (d), (e),
and (f), showing how they are special conditions of a, b, and c, respectively.
a. spiral
b. bacillus
c. coccus
d. spirochetes
e. staphylococci
f. streptobacilli

3. Answer the following questions using the diagrams provided, which represent cross
sections of bacterial cell walls.
a. Which diagram represents a gram-positive bacterium? How can you tell?
The diagram that presents a gram-positive bacterium is a because it consists
high amount of peptidoglycan than the diagram b. Many layers of peptidoglycan
are a major determinant of gram-positive bacterium.
b. Explain how the Gram stain works to distinguish these two types of cell walls.
The gram stain works to give a clearer idea of the differences in chemical
and physical properties of their cell walls. Gram-positive cells have a thick layer of
peptidoglycan in their cell wall with teichoic acid while gram-negative cells have a
outer membrane that covers around a thin peptidoglycan layer.
c. Why does penicillin have no effect on most gram-negative cells?

Penicillin has no effect on gram-negative cells because it contains a
lipopolysaccharide-lipoproteinphospholipid that surrounds the peptidoglycan layer
of the cell wall; thus it prevents penicillin from attacking and entering the cells.
d. How do essential molecules enter cells through each wall?
Essential molecules diffuse through the gram-positive wall, porins, and
specific channel proteins while in the gram-negative wall, outer membrane allow
passage of small water-soluble molecules.
e. Which cell wall is toxic to humans?
The outer membrane of Gram-negative bacteria contains a unique
component called lipopolysaccharide (LPS) in addition to proteins and
phospholipids. The LPS molecule is toxic to human and is classified as an
endotoxin that elicits a strong immune response when the bacteria infect
animals.

Lesson 3: Microbial Metabolism and Growth
OBJECTIVES
1. Differentiate catabolic and anabolic reactions;
2. Discuss the mechanisms in microbial energy production;
3. Categorize the metabolic diversity among organisms;
4. Explain the metabolic pathways of energy use;
5. List the physical and chemical requirements for microbial growth; and
6. Determine the physical and chemical methods of microbial control.
INTRODUCTION
Now that you are familiar with the structure of prokaryotic cells, we can discuss the activities
that enable these microbes to thrive. The life-support processes of even the most structurally
simple organism involve a large number of complex biochemical reactions. Most, although not
all, of the biochemical processes of bacteria also
occur in eukaryotic microbes and in the cells of
multicellular organisms, including
humans. Through their metabolism, bacteria
recycle elements after other organisms have
used them. Still other bacteria can live on diets of
inorganic substances such as carbon dioxide, iron,
sulfur, hydrogen gas, and ammonia. Microbial
metabolism allows some microorganisms to grow
in or on the human body, as shown in dental
plaque in the photograph. An example of the
bacterial metabolism that contributes to our pool
of knowledge in its growth.
This chapter examines some

representative chemical reactions that either
produce energy (the catabolic reactions) or use energy (the anabolic reactions) in
microorganisms. We will also look at how these various reactions are integrated within the cell.
This also includes how these microorganisms grow in number and how they can be controlled
using physical and chemical means.

ABSTRACTION
Microbial Metabolism
Metabolism refers to all chemical reactions that occur within a living

organism. These chemical reactions are generally of two types:
● Catabolic: Degradative reactions that release energy by breaking down large,

complex molecules into smaller ones. Often involve hydrolysis, breaking bonds
with water.
● Anabolic: Biosynthetic reactions that build large complex molecules from simpler
ones. Require energy and often involve dehydration synthesis.
Coupling of Anabolic and Catabolic Reactions
❖ Catabolic reactions provide the energy needed to drive anabolic reactions. ❖ ATP stores
energy from catabolic reactions and releases it to drive anabolic reactions. ❖ Catabolic reactions
are often coupled to ATP synthesis:
ADP + Pi + Energy -----------> ATP
❖ Anabolic reactions are often coupled to ATP hydrolysis:
ATP -----------> ADP + Pi + Energy
❖ Efficiency: Only part of the energy released in catabolism is available for work, the rest is lost as
heat. Energy transformations are inefficient.
Anabolic and Catabolic Reactions are Linked by ATP in Living Organisms

Enzymes
● Protein molecules that catalyze chemical reactions.

● Enzymes are highly specific and usually catalyze only one or a few closely related
reactions Sucrase
Sucrose + H2O -----------> Glucose + Fructose

(substrate) (products)
● Enzymes are extremely efficient. Speed up reaction up to 10 billion times more than
without enzymes.
● Turnover number: Number of substrate molecules an enzyme molecule converts to
product each second. Ranges from 1 to 500,000
● The rate of a chemical reaction depends on temperature, pressure, substrate
concentration, pH, and several other factors in the cell.
● Activation Energy: energy required to bring all molecules in chem. rxn into reactive stage ●
Enzymes speed up chemical reactions by decreasing their activation energy without
increasing the temperature or pressure inside the cell.
○ Example: Bring reactants together, create stress on a bond, etc.
● Enzymes lower the energy of activation of a chemical reaction
Naming Enzymes
● Enzyme names typically end in -ase.

● There are six classes of enzymes
○ Oxidoreductases: Catalyze oxidation-reduction reactions. Include dehydrogenases
and oxidases.
○ Transferases: Transfer functional groups (amino, phosphate, etc).
○ Hydrolases: Hydrolysis, break bonds by adding water.
○ Lyases: Remove groups of atoms without hydrolysis
○ Isomerases: Rearrange atoms within a molecule.
○ Ligases: Join two molecules, usually with energy provided by ATP hydrolysis.
Mechanism of Enzymatic Action

Surface of enzymes contains an active site that binds specifically to the substrate.
1. An enzyme-substrate complex forms.
2. Substrate molecule is transformed by:
● Rearrangement of existing atoms
● Breakdown of substrate molecule
● Combination with another substrate molecule
3. Products of reaction no longer fit the active site and are released.
4. Unchanged enzyme is free to bind to more substrate molecules.
Factors Affecting Enzymatic Action
Enzymes are protein molecules and their three- dimensional shape is essential for their
function. The shape of the active site must not be altered so that it can bind specifically to the
substrate. Several factors can affects enzyme activity:
➔ Temperature: Most enzymes have an optimal temperature. At low temperatures most reactions
proceed slowly due to slow particle movement. At very high temperatures reactions slow down
because the enzyme is denatured.
➔ Denaturation: Loss of three-dimensional protein structure. Involves breakage of H and
noncovalent bonds.
Energy Production
Oxidation-Reduction or Redox Reactions: Reactions in which both oxidation and reduction occur.

Oxidation: Removal of electrons or H
atoms
Addition of oxygen
Associated with loss of energy
Reduction: Gain of electrons or H atoms
Loss of oxygen
Associated with gain of energy
Examples: Aerobic respiration & photosynthesis are redox processes.
Aerobic Respiration is a Redox Reaction
Carbohydrate Catabolism
● Most microorganisms use glucose or other carbohydrates as their primary source

of energy.
● Lipids and proteins are also used as energy sources.
Two general processes are used to obtain energy from glucose: cellular respiration and
fermentation.
Carbohydrate Catabolism
I. Cellular respiration:
➔ ATP generating process in which food molecules are oxidized.
➔ Requires an electron transport chain.
➔ Final electron acceptor is an inorganic molecule:
◆ Aerobic respiration final electron acceptor is oxygen. Much more efficient
process.
◆ Anaerobic respiration final electron acceptor is another inorganic molecule.
Energetically inefficient process.
II. Fermentation:
➔ Releases energy from sugars or other organic molecules.
➔ Does not require oxygen, but may occur in its presence.

➔ Does not require an electron transport chain.
➔ Final electron acceptor is an organic molecule.
➔ Inefficient: Produces a small amount of ATP for each molecule of food. ➔
End-products are energy rich organic compounds:
● Lactic acid
● Alcohol
Cellular Respiration
A. Aerobic Respiration
C6H12O6 + 6 O2 -----> 6 CO2 + 6H2O + ATP
Glucose oxygen oxidized reduced
➔ Most energy efficient catabolic process.

➔ Oxygen is the final electron acceptor.
➔ Aerobic Respiration occurs in three stages:
◆ Glycolysis
◆ Kreb’s Cycle
◆ Electron Transport & Chemiosmosis
1. Glycolysis: “Splitting of sugar”.
● Glucose (6 C) is split and oxidized to two molecules of pyruvic acid (3C).
● Most organisms can carry out this process.
● Does not require oxygen.
● Net yield per glucose molecule:
★ 2 ATP (substrate level phosphorylation)
★ 2 NADH

2. Krebs Cycle (Citric Acid Cycle):
● Before the cycle can start, pyruvic acid (3C) loses one carbon (as CO2) to
become acetyl CoA (2C).
● Acetyl CoA (2C) joins oxaloacetic acid (4C) to form citric acid (6C). ● Cycle
of 8 oxidation-reduction reactions that transfer energy to electron carrier
molecules (coenzymes NAD+ and FAD).
● 2 molecules of carbon dioxide are lost during each cycle.
● Oxaloacetic acid is regenerated in the final step.
● Net yield per glucose molecule:
★ 2 ATP (substrate level phosphorylation)
★ 8 NADH
★ 2 FADH2
3. Electron Transport Chain and Chemiosmosis:

● Electrons from NADH and FADH2 are released to chain of electron carriers.
● Electron carriers are on cell membranes (plasma membranes of bacteria or
inner mitochondrial membrane in eukaryotes).
● Final electron acceptor is oxygen.
● A proton gradient is generated across membranes as electrons flow down
the chain.
● ATP is made by ATP synthase (chemiosmosis) as protons flow down
concentration gradient.

● Net ATP yield:
★ 2 FADH2 generate 2 ATPs each: 4 ATP
★ 10 NADH generate 3 ATPs each: 30 ATP
Total Yield from Aerobic Respiration of 1 Glucose molecule: 36-38 molecules of
ATP In prokaryotes:
C6H12O6 + 6 O2-----> 6 CO2 + 6 H2O + 38 ATP
B. Anaerobic Respiration
● Final electron acceptor is not oxygen.

● Instead it is an inorganic molecule:
● Nitrate (NO3-): Pseudomonas and Bacillus. Reduced to nitrite (NO2-):, nitrous
oxide, or nitrogen gas.
● Sulfate (SO42-): Desulfovibrio. Reduced to hydrogen sulfide (H2S).
● Carbonate (CO32-): Reduced to methane.
● Inefficient (2 ATPs per glucose molecule).
● Only part of the Krebs cycle operates without oxygen.
● Not all carriers in the electron transport chain participate.
● Anaerobes tend to grow more slowly than aerobes.
1. Fermentation
● Releases energy from sugars or other organic molecules.
● Does not require oxygen, but may occur in its presence.
● Does not require Krebs cycle or an electron transport chain.
● Final electron acceptor is organic molecule.
● Inefficient. Produces a small amount of ATP for each molecule of food. (1
or 2 ATPs)
● End-products may be lactic acid, alcohol, or other energy rich organic
compounds.

● Lactic Acid Fermentation: Carried out by Lactobacillus and Streptococcus.
Can result in food spoilage. Used to make yogurt, sauerkraut, and pickles.
● Alcohol Fermentation: Carried out by yeasts and bacteria.
Fermentation is Less Efficient Than Aerobic Respiration
Alcohol and Lactic Acid Fermentation
Microbial Growth
● Refers to an increase in cell number, not in cell size.

● Bacteria grow and divide by binary fission, a rapid and relatively simple
process. 4 Key Factors To Control The Growth Of Microorganisms

1. Temperature
2. pH
3. Water Availability (Osmosis)
4. Oxygen
Physical Requirements
1. Temperature: Microbes are loosely classified into several groups based on their
preferred temperature ranges.
A. Psychrophiles: “Cold-loving”. Can grow at 0oC. Two groups:
◆ True Psychrophiles: Sensitive to temperatures over 20oC. Optimum
growth at 15oC or below. Found in very cold environments (North
pole, ocean depths). Seldom causes disease or food spoilage.
◆ Psychrotrophs: Optimum growth at 20 to 30oC. Responsible for
most low temperature food spoilage
B. Mesophiles: “Middle loving”. Most bacteria.
● Include most pathogens and common spoilage organisms.
● Best growth between 25 to 40oC.
● Optimum temperature commonly 37oC.
● Many have adapted to live in the bodies of animals.
C. Thermophiles: “Heat loving”.
● Optimum growth between 50 to 60oC.
● Many cannot grow below 45oC.
● Adapted to live in sunlit soil, compost piles, and hot springs.
● Some thermophiles form extremely heat resistant
endospores.
○ Extreme Thermophiles (Hyperthermophiles):
Optimum growth at 80oC or higher. Archaebacteria.
Most live in volcanic and ocean vents.
Growth Rates of Bacterial Groups at Different Temperatures
2. pH:

● Most bacteria prefer neutral pH (6.5-7.5).
● Molds and yeast grow in wider pH range, but prefer pH between 5 and 6. ●
Acidity inhibits most microbial growth and is used frequently for food
preservation (e.g.: pickling).
● Alkalinity inhibits microbial growth, but not commonly used for food
preservation.
● Acidic products of bacterial metabolism interfere with growth. Buffers can
be used to stabilize pH.
Organisms can be classified as:
A. Acidophiles: “Acid loving”.

● Grow at very low pH (0.1 to 5.4)
● Lactobacillus produces lactic acid, tolerating mild acidity.
B. Neutrophiles:
● Grow at pH 5.4 to 8.5.
● Includes most human pathogens.
C. Alkaliphiles: “Alkali loving”.
● Grow at alkaline or high pH (7 to 12 or higher)
● Vibrio cholerae and Alkaligenes faecalis optimal pH 9.
● Soil bacterium Agrobacterium grows at pH 12.
●
3. Osmotic Pressure: Cells are 80 to 90% water.
A. Hypertonic solutions: High osmotic pressure removes water from cell, causing
shrinkage of cell membrane (plasmolysis).
● Used to control spoilage and microbial growth.
● Sugar in jelly.
● Salt on meat.
B. Hypotonic solutions: Low osmotic pressure causes water to enter the cell. In most
cases cell walls prevent excessive water entry. Microbe may lyse or burst if the
cell wall is weak.
C. Halophiles: Require moderate to large salt concentrations. Ocean water contains

3.5% salt.
D. Extreme or Obligate Halophiles: Require very high salt concentrations (20 to
30%). a. Bacteria in the Dead Sea, brine vats.
E. Facultative Halophiles: Do not require high salt concentrations for growth, but
tolerate 2% salt or more.
Chemical Requirements
1. Carbon: Makes up 50% of the dry weight of the cell.

● Structural backbone of all organic compounds.
● Chemoheterotrophs: Obtain carbon from their energy source: lipids, proteins, and
carbohydrates.
● Chemoautotrophs and Photoautotrophs: Obtain carbon from carbon dioxide.
2. Nitrogen, Sulfur, and Phosphorus: .
a. Nitrogen: Makes up 14% of dry cell weight. Used to form amino acids, DNA, and
RNA.
Sources of nitrogen:
● Protein: Most bacteria

● Ammonium: Found in organic matter
● Nitrogen gas (N2): Obtain N directly from atmosphere. Important nitrogen
fixing bacteria, live free in soil or associated with legumes (peas, beans,
alfalfa, clover, etc.). Legume cultivation is used to fertilize soil naturally.
● Nitrates: Salts that dissociate to give NO3-.
b. Sulfur: Used to form proteins and some vitamins (thiamin and biotin).
Sources of sulfur:
● Protein: Most bacteria

● Hydrogen sulfide
● Sulfates: Salts that dissociate to give SO42-.
c. Phosphorus: Used to form DNA, RNA, ATP, and phospholipids.

Sources: Mainly inorganic phosphate salts and buffers.
3. Other Elements: Potassium, magnesium, and calcium are often required as enzyme
cofactors. Calcium is required for cell wall synthesis in Gram positive bacteria.
4. Trace Elements:
Many are used as enzyme cofactors.
Commonly found in tap water.
● Iron
● Copper
● Molybdenum
● Zinc
5. Oxygen: Organisms that use molecular oxygen (O2), produce more energy from
nutrients than anaerobes.
Can classify microorganism based on their oxygen requirements:
A. Obligate Aerobes: Require oxygen to live.
Example: Pseudomonas, common nosocomial pathogen.
B. Facultative Anaerobes: Can use oxygen, but can grow in its absence. Have a
complex set of enzymes.
Examples: E. coli, Staphylococcus, yeasts, and many intestinal bacteria.
C. Obligate Anaerobes: Cannot use oxygen and are harmed by the presence of toxic
forms of oxygen.
Examples: Clostridium bacteria that cause tetanus and botulism.
D. Aerotolerant Anaerobes: Can’t use oxygen, but tolerate its presence. Can break
down toxic forms of oxygen.
Example: Lactobacillus carries out fermentation regardless of oxygen presence.
E. Microaerophiles: Require oxygen, but at low concentrations. Sensitive to toxic

forms of oxygen.
Example: Campylobacter
Control of Microbial Growth
➔ Early civilizations practiced salting, smoking, pickling, drying, and exposure of food and clothing
to sunlight to control microbial growth.
➔ Use of spices in cooking was to mask taste of spoiled food. Some spices prevented spoilage.

➔ Semmelweiss and Lister (1800s ) aseptic techniques to prevent contamination of surgical wounds.
Before then:
◆ Nosocomial infections caused death in 10% of surgeries.
◆ Up to 25% mothers delivering in hospitals died due to infection
Physical Methods of Microbial Control:
1. Heat: Kills microorganisms by denaturing their enzymes and other proteins. Heat
resistance varies widely among microbes.
★ Thermal Death Point (TDP): Lowest temperature at which all of the microbes in a
liquid suspension will be killed in ten minutes.
★ Thermal Death Time (TDT): Minimal length of time in which all bacteria will be
killed at a given temperature.
★ Decimal Reduction Time (DRT): Time in minutes at which 90% of bacteria at a
given temperature will be killed. Used in the canning industry.
A. Moist Heat: Kills microorganisms by coagulating their proteins.

➔ In general, moist heat is much more effective than dry heat.
a. Boiling: Heat to 100oC or more at sea level. Kills vegetative forms of
bacterial pathogens, almost all viruses, and fungi and their spores within
10 minutes or less. Endospores and some viruses are not destroyed this
quickly. However brief boiling will kill most pathogens.
➢ Hepatitis virus: Can survive up to 30 minutes of boiling.
➢ Endospores: Can survive up to 20 hours or more of boiling.
b. Autoclave: Chamber which is filled with hot steam under pressure.
Preferred method of sterilization, unless material is damaged by heat,
moisture, or high pressure.
➢ Temperature of steam reaches 121oC at twice atmospheric
pressure.
➢ Most effective when organisms contact steam directly or are
contained in a small volume of liquid.
➢ All organisms and endospores are killed within 15 minutes.
➢ Require more time to reach center of solid or large volumes of liquid.
c. Pasteurization:
● prevent the spoilage of beverages.
● Used to reduce microbes responsible for spoilage
➢ Classic Method of Pasteurization: exposed to 65oC for 30 minutes.
➢ High Temperature Short Time Pasteurization (HTST): Used today.
Milk is exposed to 72oC for 15 seconds.
➢ Ultra High Temperature Pasteurization (UHT): Milk is treated at
140oC for 3 seconds and then cooled very quickly in a vacuum
chamber.

B. Dry Heat: Kills by oxidation effects.
1. Direct Flaming: inoculating loops and needles. Heat metal until it has a red
glow.
2. Incineration:
● Effective way to sterilize disposable items (paper cups, dressings)
and biological waste.
● Carcasses
3. Hot Air Sterilization: Place objects in an oven. Require 2 hours at 170oC for
sterilization. Dry heat is transfers heat less effectively to a cool body, than
moist heat.
C. Filtration:
● Removal of microbes by passage of a liquid or gas through a screen like material

with small pores. Used to sterilize heat sensitive materials like vaccines,
enzymes, antibiotics, and some culture media.
○ High Efficiency Particulate Air Filters (HEPA):
-Used in operating rooms and burn units to remove bacteria from
air. D. Desiccation
● In the absence of water, microbes cannot grow or reproduce, but some may remain
viable for years. After water becomes available, they start growing again.
Susceptibility to desiccation varies widely:
❖ Neisseria gonorrhoeae: Only survives about one hour.

❖ Mycobacterium tuberculosis: May survive several months.
❖ Viruses are fairly resistant to dessication.
❖ Clostridium spp. and Bacillus spp.: May survive decades.
E. Osmotic Pressure:
● The use of high concentrations of salts and sugars in foods is used to increase the
osmotic pressure and create a hypertonic environment.
Plasmolysis: As water leaves the cell, plasma membrane shrinks away from the
cell wall. Cell may not die, but usually stops growing.
★ Yeasts and molds: More resistant to high osmotic pressures.

★ Staphylococci spp. that live on skin are fairly resistant to high
osmotic pressure.
F. Ionizing Radiation
● X-rays, -rays, electron beams dislodge e- from atoms production of free radicals
and other highly reactive molecules

● Commonly used Cobalt-60 radioisotope
● Salmonella and Pseudomonas are particularly sensitive
● Sterilization of heat sensitive materials: drugs, vitamins, herbs, suture material
Chemical Methods of Microbial Control:
A. Use-dilution test (Disk-diffusion Method)

● Metal rings dipped in test bacteria are dried.
● Dried cultures of S. choleraesuis, S. aureus, and P. aeruginosa are placed in
disinfectant for 10 min at 20C.
● Rings are transferred to culture media to determine whether bacteria survived
treatment.
B. Disinfectants
1. Phenols and Phenolics:
➔ Phenol (carbolic acid) was first used by Lister as a disinfectant.
➔ Rarely used today because it is a skin irritant and has strong odor.
➔ Used in some throat sprays and lozenges.
➔ Acts as local anesthetic.
2. Halogens: Effective alone or in compounds.
a. Iodine:
➔ Tincture of iodine (alcohol solution) was one of the first antiseptics used. ➔
Combines with amino acid tyrosine in proteins and denatures proteins. ➔ Stains
skin and clothes, somewhat irritating.
➔ Iodophors: Compounds with iodine that are slow releasing, take several minutes to
act. Used as skin antiseptic in surgery. Not effective against bacterial endospores.
3. Alcohols:
➔ Kill bacteria, fungi, but not endospores or naked viruses.

➔ Act by denaturing proteins and disrupting cell membranes.
➔ Evaporate, leaving no residue.
➔ Used to mechanically wipe microbes off skin before injections or blood drawing.
➔ Not good for open wounds, because they cause proteins to coagulate.
● Ethanol: Drinking alcohol. Optimum concentration is 70%.
● Isopropanol: Rubbing alcohol. Better disinfectant than ethanol.
Also cheaper and less volatile.
4. Heavy Metals:
➔ Include copper, selenium, mercury, silver, and zinc.

➔ Oligodynamic action: Very tiny amounts are effective.

a. Silver- 1% silver nitrate used to protect infants against gonorrheal eye
infections until recently.
b. Mercury-Organic mercury compounds like merthiolate and mercurochrome
are used to disinfect skin wounds.
c. Copper- Copper sulfate is used to kill algae in pools and fish tanks.
5. Quaternary Ammonium Compounds (Quats):
➔ Widely used surface active agents.

➔ Cationic (positively charge) detergents.
➔ Effective against gram positive bacteria, less effective against gram negative
bacteria.
➔ Also destroy fungi, amoebas, and enveloped viruses.
6. Aldehydes:
➔ Include some of the most effective antimicrobials.

➔ Inactivate proteins by forming covalent crosslinks with several functional groups.
7. Gaseous Sterilizers:
➔ Chemicals that sterilize in a chamber similar to an autoclave.

➔ Denature proteins, by replacing functional groups with alkyl groups.
APPLICATION
1. Give 2 examples of anabolic and catabolic reactions that occur in an
organism. Catabolism:
An example of a catabolic reaction is the breakdown of glucose during cellular

respiration, which releases energy that is needed by the cell to carry out life processes. Another
example is the process of food digestion, where different enzymes break down food particles so
that it can be absorbed by the small intestine.
Anabolism:
Examples of anabolic reactions is the synthesis of large proteins from amino acid
building blocks, and the synthesis of new DNA strands from nucleic acid building blocks.

2. Using the diagrams below, show the following:
a. where the substrate will bind? Active site of the enzyme
b. where the competitive inhibitor will bind? Active site of the enzyme, competing with the
substrate.
c. where the noncompetitive inhibitor will bind? Allosteric site separate from the active
site of substrate binding.
d. which of the four elements could be the inhibitor in the feedback inhibition?
Competitive Inhibitor
e. what effect will the reactions in (a) (b) and (c) have?
(a) the substrate and binds to the enzymes active site.
(b) The substrate is prevented from binding to the same active site due to competitive
inhibitor that competes with the substrate.
(c) A competitive inhibitor reduces the rate of catalysis by lowering the proportion of
enzyme molecules connected to a substrate.
3. By deep-freezing, bacteria can be stored without harm for extended periods. Why do
refrigeration and freezing preserve foods?
By stopping bacteria from multiplying and reducing the enzyme activity that causes food
to decay, freezing delays spoiling and keeps goods safe. Water in food freezes into ice crystals,
making it unavailable to microbes that require it for growth.
4. Nitrogen and phosphorus added to beaches following an oil spill encourage the growth of
natural oil-degrading bacteria. Explain why bacteria do not grow if nitrogen and phosphorus are
not added.
Higher nitrogen source concentrations could encourage greater bacterial development since
nitrogen source is involved in the biochemical synthesis of nucleic acids, lipids, and proteins in
bacteria cells. However, too much nitrogen can inhibit bacterial growth; on the other hand, all
bacteria require some phosphorus for cell maintenance and growth, which allows them to
solubilize inorganic phosphorus from insoluble compounds. Therefore, nitrogen and phosphorus
play such an important role in bacterial growth.

5. Use the following diagrams (a), (b), and (c) for question 3.
a. Name pathways diagrammed in parts (a), (b), and (c) of the figure.
(a) Calvin-Benson Cycle
(b) Glycolysis pathway
(c) Krebs Cycle or Citric Acid Cycle
b. Show where glycerol is catabolized and where fatty acids are catabolized.
In glycolysis, Glycerol is catabolized as dihydroxyacetone phosphate while in Krebs

cycle fatty acids is catabolized as acetyl group.
c. Where is ATP required in pathways (a) and (b)?
ATP is required in between glucose and glyceraldehyde 3-phosphate.
d. Where is CO2 released in pathways (b) and (c)?
CO2 is released during the conversion of pyruvic acid to acetyl, isocitric acid to
a ketoglutaric acid, and ketoglutaric acid to succinyl CoA.

e. Where is NADH (or FADH2 or NADPH) used and produced in these pathways? In
the second stage of Calvin-Benson Cycle, the organic molecule is reduced using
electrons supplied by NADPH.
In the second half of glycolysis, there is an involvement of phosphorylation

without ATP investment and produces 2NADPH and 4-ATP molecules per glucose.
During the process of the Krebs cycle or citric acid cycle, 3NADH, 1FADH2 AND
1- ATP is produced by substrate-level phosphorylation.
f. Identify four places where anabolic and catabolic pathways are integrated.
• Dihydroxyacetone phosphate
• Acetyl
• Oxaloacetic acid,
• Ketoglutaric acid
Lesson 4: Microbial Genetics
OBJECTIVES
1. Define the structures and functions of the genetic material;

2. Discuss the regulation of bacterial gene expression;
3. Analyze the changes in genetic materials;
4. Explain the mechanisms of genetic transfer and recombination; and
5. Elaborate the link between genes and evolution.
INTRODUCTION
The inherited characteristics of microbes include shape, structural features, metabolism,

ability to move, and interactions with other organisms. Individual organisms transmit these
characteristics to their offspring
through genes.
The development of antibiotic

resistance
in microorganisms is often carried on
plasmids
such as those in the photo, which are
readily
transferred between bacterial cells.
They are
responsible for the emergence of
methicillin
resistant Staphylococcus aureus and
the recent
emergence of carbapenem resistant
Klebsiella
pneumoniae. The emergence of vancomycin
resistant S. aureus (VRSA) poses a serious threat
to patient care. In this lesson, you will see how
VRSA acquired this characteristic.
Emerging diseases provide another

reason why it is important to understand
genetics. New diseases are the results of genetic changes in some existing organism; for
example, E. coli O157:H7 acquired the genes for Shiga toxin from Shigella.
Currently, microbiologists are using genetics to study unculturable microbes and the
relationship between hosts and microbes.
ACTIVITY
DNA, Chromosomes, and Cells

Directions: Study the figure above and describe the function(s) of the different genetic material
structures.
Structure Function
Nucleus The nucleus controls and regulates the

activities of the cell such as growth and
metabolism and carries the genes,
structures that contain the hereditary
information.
Chromosome Chromosomes carry the basic genetic

material DNA which is responsible to
provide hereditary characteristics and
genetic information to the various cells.
Histone Proteins Histones are the proteins strongly

associated with DNA molecules. They are
responsible for the structure of chromatin
and play important roles in the regulation of
gene expression.
Nucleosomes The nucleosome serves three primary

functions. First, it brings about the first level
of
genomic compaction, organizing ∼200 bp of
DNA. Second, the nucleosome acts as a
signaling hub for chromatin-templated
processes by providing a scaffold for the
binding of chromatin enzymes and
displaying a combinatorial array of post-
translational modifications (PTMs). Third,
the nucleosome can self-assemble into
higher-order chromatin structures, allowing
for further compaction of the genome.
Deoxyribonucleic Acid (DNA) It is a double helix carrying genetic

instructions responsible for the
development, functioning, growth and
reproduction of all known organisms and
many viruses.
Ribonucleic Acid (RNA) Ribonucleic acid (RNA) is a polymeric

molecule essential in various biological
roles in coding, decoding, regulation and
expression of genes. The main function of
RNA is cellular protein synthesis. RNA
converts the instructional genetic
information stored in deoxyribonucleic acid
(DNA) into proteins.
ANALYSIS
Directions: Answer the following questions comprehensively. Use additional sheets of paper if
necessary.
1. Briefly describe the components of DNA and explain its functional relationship to RNA and
protein.
DNA has Thymine, whereas RNA has Uracil. Nucleotides in RNA include sugar ribose,
rather than the Deoxyribose that is part of DNA. RNA, DNA as well as protein are all
closely related. DNA contains the information necessary for encoding proteins, although
it does not produce proteins directly. RNA carries the information from the DNA and
transforms that information into proteins that perform most cellular functions.
2. Why are mutation and recombination important in the process of natural selection and the
evolution of organisms?

Mutation is the ultimate source of all genetic variation and is required for natural
selection to occur as a matter of fact most of our genome has been shaped primarily by
mutation and random drift.
Mutation and recombination drive the evolution of most pathogens by generating

the genetic variants upon which selection operates. These variations can impart
resistance to the host immune system and pharmacological therapy, as well as cause
pandemic outbreaks.
3. Identify and mark each of the following on the portion of DNA undergoing replication:
replication fork, DNA polymerase, RNA primer, parent strands, leading strand, lagging
strand, the direction of replication on each strand, and the 5’ end of each strand.
OVERALL DIRECTION OF REPLICATION
DNA Replication
DNA helicase POLYMERASE
Single strand binding proteins fork
DNA
Leading strand
Lagging
strand
RNA primase
DNA Ligase
Parent strands
Polymerase
RNA primer
4. When iron is not available, E. coli can stop synthesis of all proteins, such as
superoxide dismutase and succinate dehydrogenase, that require iron. Describe a
mechanism for this regulation.
Iron deficiency may stimulate miRNA that is complementary to RNA encoding

iron required proteins.

4. Replication of the E. coli chromosome takes 40 to 45 minutes, but the organism has a
generation time of 26 minutes. How does the cell have time to make complete
chromosomes for each offspring cell?
The cell does not take control the rate of DNA synthesis, but it controls the rate at
which replication forks on the chromosome are initiated. The cell initiates multiple
replication forks, likely to result in a daughter cell having inherited a complete
chromosome and other additional portions from multiple replication forks. The replication
of chromosomes tends to begin during or immediately after division.
ABSTRACTION
Structure and Function of the Genetic Material
● Genetics is the study of what genes are, how they carry information, how their information
is expressed, and how they are replicated and passed to subsequent generations or
other organisms.
● DNA in cells exists as a double-stranded helix; the two strands are held together by
hydrogen bonds between specific nitrogenous base pairs: AT and CG.
● A gene is a sequence of nucleotides, that encodes a functional product, usually a protein.
● The DNA in a cell is duplicated before the cell divides, so each offspring cell receives the
same genetic information.
The Regulation of Bacterial Gene Expression
● Regulating protein synthesis at the gene level is energy-efficient because proteins are
synthesized only as they are needed.
● Constitutive genes are expressed at a fixed rate. Examples are genes for the enzymes in
glycolysis.
Changes in Genetic Material
● Mutations and horizontal gene transfer can change a bacterium’s genotype.

Genetic Transfer and Recombination
● Genetic recombination, the rearrangement of genes from separate groups of genes,

usually involves DNA from different organisms; it contributes to genetic diversity.

● In crossing over, genes from two chromosomes are recombined into one chromosome
containing some genes from each original chromosome.
● Vertical gene transfer occurs during reproduction when genes are passed from an
organism to its offspring.
● Horizontal gene transfer in bacteria involves a portion of the cell’s DNA being transferred
from donor to recipient.
● When some of the donor’s DNA has been integrated into the recipient’s DNA, the resultant
cell is called a recombinant.
Genes and Evolution
● Diversity is the precondition for evolution.

● Genetic mutation and recombination provide diversity of organisms, and the process of
natural selection allows the growth of those best adapted to a given environment.
APPLICATION
Directions: Read the Review Article titled Genetics of COVID-191 by Salmo Raskin (2020)
published in Jornal de Pediatria and answer the questions below:
1. Where did SARS-CoV-2 come from?
The SARS-CoV-2 exited when the SARS-CoV-2 shares 79.5% of its genome with SARS
CoV-1 and exhibits a remarkable 93.1% homology with the sequence of the RaTG12
virus isolated from a bat (Rhinolophus affinis) from Yunnan province, China, 2,000 km
from Wuhan.
2. How SARS-CoV-2 tries to evade immune defenses?
Among all the coronaviruses that existed, only SARS-CoV-2 has a genetic sequence
featuring an insertion of 12 base pairs (4 amino acids) in the spike, called the polybasic
site. The four amino acids inserted into the sequence form an exposed loop, increasing
the susceptibility of the S protein to cleavage mediated by protease, which facilitates
infection by SARS-CoV-2.
3. Does the SARS-CoV-2 have a high mutation rate?
SARS-CoV-2 has a slow mutation rate. Its average mutation rate is approximately 8 × 10−4
substitutions per nucleotide per year. Due to the fact that proofreading proteins like ExoN
(encoded by the non-structural protein Nsp14) have the capability to correct some errors.
1
Link: https://www.sciencedirect.com/science/article/pii/S0021755720302114

4. Could SARS-CoV-2 have been created in a laboratory?
The claims stating that SARS-Cov-2 that it is created in a laboratory is not true
and it lacks evidence. Here is the following evidence that nullifies this claim. The bat
coronavirus RaTG13 is the virus with the greatest genetic homology in which only 96% of
its genome with the SARS-CoV-2 (1200 different nitrogenous base pairs). There is no
laboratory technology that can simultaneously handle 1200 nitrogenous base pairs.
Another clue that the virus is natural is the presence of unique sugar-fixing sites (O
glycosidic bonds) in the SARS-CoV-2 genome. Because Malayan pangolins have an
RBD that is extremely like SARS-CoV-2, we can deduce that this happened in the virus
that was transmitted to humans, implying that the polybasic insertion at the cleavage site
happened during human-to-human transmission. Also, The RBD in the SARS-CoV-2 is
different from that of the SARS-CoV-1, and the SARS-CoV-2’s connection to ACE2 is
not ideal, meaning connection mechanisms is a result of natural selection.
5. How does the SARS-CoV-2 selects the target cells, fuses its membrane with the host, and
injects its RNA into the human cell?
The spike binds the virus with the human cell, causing the viral membrane to fuse with
the human cell's cytoplasmic membrane, allowing viral RNA to be injected into the
human cell. The spike, through its receptor-binding domain (RBD), recognizes the
membrane receptor of angiotensin-converting enzyme 2 (ACE2), a protein expressed
mainly in the lungs, heart, kidneys, and intestine. By selecting ACE2 as a target, the
virus has the right to choose the main tissues it will infect. After such, the human
transmembrane protease serine 2 (TMPRSS2) cleaves and activates the spike protein,
which through its fusion peptide fuses the viral membrane with the membrane of the
target cell, allowing injection of the SARS
CoV-2 RNA into the human cell.

Microbiology and Parasitology - Prelim CAMPOS ELLA

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Microbiology and Parasitology Villegas and Patete (2021)

Course Number: Bio120

Course Title: Microbiology and Parasitology

Number of Units: Lecture – 3.0 units

Laboratory – 1.0 unit

Lovely May B. Patete

Microbiology and Parasitology Villegas and Patete (2021)

Lesson 4: Microbial Genetics

Module II: Microbial Diversity

Lesson 5: Classification of Microorganisms

Lesson 6: The Prokaryotes: Domains Bacteria and Archaea

Lesson 7: The Eukaryotes: Fungi, Algae, Protozoa, and

Helminths Lesson 8: Viruses, Viroids, and Prions

Module III: Microbe-Host Interaction

Lesson 9: Principles of Disease and Epidemiology

Lesson 10: Microbial Mechanisms of Pathogenicity

Lesson 11: Innate and Adaptive Immunity

Lesson 12: Microorganisms and Human Disease

Microbiology and Parasitology Villegas and Patete (2021)

1. Define microbiology and parasitology;

Tapeworms bacteria Barnacles Molds Fleas Yeast Roundworms Algae

It is the study of all living Beneficial and detrimental in nature.

Present in Focused more on parasitic organisms

Branch of biology microorganisms Branch of

Microbiology is the study of all living organisms that are too

Microbiology and Parasitology Villegas and Patete (2021)

Microbes and Human Welfare

5. Biotechnology and Recombinant DNA Technology

Microbiology and Parasitology Villegas and Patete (2021)

Carolus Linnaeus in 1753 established the system of nomenclature (naming) for

1. Bacteria (singular: bacterium)

3. Fungi (singular: fungus)

7. Multicellular Animal Parasites

Microbiology and Parasitology Villegas and Patete (2021)

Golden Age of Microbiology (1857 to 1914)

● During this productive period, microbiologists studied the chemical activities of

These are the scientists who have made contributions in early

microbiology: Rudolf Virchow (1858).

Louis Pasteur (1861).

Joseph Lister (1827–1912)

Robert Koch (1843–1910)

An infectious disease is a disease in which pathogens invade a susceptible host, such

Microbiology and Parasitology Villegas and Patete (2021)

Bacteria Escherichia coli (abbreviated as E. coli)

Streptococcus canis is important to the skin

Lactiplantibacillus plantarum commonly

Microbiology and Parasitology Villegas and Patete (2021)

Halobacterium salinarum resides in

Methanocaldococcus jannaschii the first

Fungi Batrachochytrium dendrobatidis is a fungus

Penicillium chrysogenum It is common in

Agaricus bisporus is one of the most

Protozoa Balantidium coli is a parasitic species of

Plasmodium falciparum is a unicellular

Microbiology and Parasitology Villegas and Patete (2021)

Algae Arthrospira platensis is a planktonic

Pelvetia canaliculata is a type of brown

Caulerpa lentillifera, is a seaweed that is one

Viruses Canine parvovirus is a contagious virus

Coxsackieviruses are RNA viruses that may

Human alphaherpesvirus 3 is one of nine

Multicellular Animal Parasites Haemonchus contortus, also known as the

Echinococcus granulosus, also called the