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Title: Microbiology
Description: The document are organised into clear and concise sections, covering the key concepts and topics in microbiology. These include the structure and function of microorganisms, microbial growth and metabolism, microbial genetics and evolution, and the role of microbes in infectious disease and public health. Each section would likely include detailed notes on the key points and concepts, as well as summaries of important studies and experiments in the field. By providing clear and concise summaries of complex concepts, the document makes it easier for individuals to quickly grasp the key ideas and build a strong foundation in the subject.
Description: The document are organised into clear and concise sections, covering the key concepts and topics in microbiology. These include the structure and function of microorganisms, microbial growth and metabolism, microbial genetics and evolution, and the role of microbes in infectious disease and public health. Each section would likely include detailed notes on the key points and concepts, as well as summaries of important studies and experiments in the field. By providing clear and concise summaries of complex concepts, the document makes it easier for individuals to quickly grasp the key ideas and build a strong foundation in the subject.
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Introduction to Microbiology
Welcome to the first lecture of microbiology this semester
...
We will
discuss the history behind microbiology, the ways we classify
microorganisms, and two main characters that have changed the face of
microbiology
...
What is Microbiology?
Microbiology is the study of organisms that are too small to be seen
without magnification
...
We will primarily focus on bacteria and viruses in the lab
...
We will also look at two main
figures in microbiology, Louis Pasteur and Robert Koch, who have had a
significant impact on the field
...
This is an important process that is similar to what we see
in biology, but we are focusing on the small things that we cannot see
without a microscope
...
These fields offer many job opportunities and can be
highly controversial
...
The study of microbiology is
important because these microorganisms play a significant role in our
lives, from causing diseases to helping with food production
...
It took time for
the planet to cool down and form solid rock, water, and other necessary
ingredients for life
...
These cells ruled the
world for about two billion years until more complexity led to the
evolution of eukaryotic cells
...
Throughout the semester, we will be
examining different types of cells, including prokaryotes, eukaryotes,
viruses, fungi, algae, protozoa, and worms
...
Bacteria come in different shapes and sizes, and we will be
discussing them in Chapter 4
...
Algae
Algae are not parasites on humans, but they can cause problems by
releasing toxic agents into water
...
Viruses
Viruses are tiny particles that can cause infections, such as the herpes
simplex virus that causes cold sores
...
Protozoa and Worms
Protozoa are unicellular animal cells that can have parasites associated
with them and cause infections
...
Understanding Microorganisms
This passage provides an overview of the different types and sizes of
microorganisms
...
Sizes of Microorganisms
•
Cysts of round worm that causes trichinella are visible to the naked eye
•
Most microorganisms are very small, ranging in size from micrometers
to nanometers
•
A meter is about three feet long
•
A micrometer is one millionth of a meter
•
A nanometer is one billionth of a meter
•
Bacteria are anywhere from 1 to 10 micrometers in size
•
Viruses are about a thousand times smaller than bacteria
How Humans Use Microbes
The passage discusses the ways in which humans use microbes to our
advantage
...
•
Free living microorganisms are harmless and found in air, soil, water,
and on surfaces
•
Parasites are microorganisms that live on or in the body of another
organism and can cause damage to the host
Diseases and Pathogens
When we talk about diseases, we refer to pathogens, which are microbes
that cause harm
...
Roughly 10 billion new infections occur every year
worldwide
...
AIDS and HIV are also major diseases, and diarrheal diseases and
food poisoning can cause problems
...
However, the United States is more developed and has a
healthcare system that works pretty well, so we do not see a lot of
infectious diseases
...
Before microscopes, people did not know anything about
microorganisms
...
With the
microscope, people could study microorganisms and develop medical
microbiology
...
Microscopy has advanced over
time, and now we have electron microscopes that can see even smaller
things
...
The Scientific Method
The scientific method is a way of testing things to see if they are true
...
The scientific method is essential for
discovering new things about microorganisms
...
It is essential for developing treatments and vaccines for diseases
...
Microbiology Techniques
There are many techniques that microbiologists use to study
microorganisms
...
These techniques are essential for studying microorganisms and
developing treatments for diseases
...
The scientific method emerged around the
same time, allowing scientists to formulate hypotheses based on
observations and test them through experiments
...
Spontaneous Generation and Biogenesis
Spontaneous Generation was the theory that non-living things could
generate living things, but Louis Pasteur disproved this theory with his
experiment using gooseneck flasks
...
The Germ Theory
The Germ Theory is the idea that germs cause disease, and the human
body is the source of infection
...
Oliver Wendell Holmes
...
Louis Pasteur and Robert Koch were two of the
main contributors to this theory
...
He also showed that
spontaneous generation does not occur and developed the process of
pasteurization
...
Robert Koch
Koch established Koch's postulates, a set of experimental steps to
determine what causes a disease
...
Taxonomy
Taxonomy is the system of organizing, classifying, and naming organisms
in biology
...
Introduction to Chemistry and Biomolecules
Atoms and Elements
All matter is made up of atoms, which are composed of protons, neutrons,
and electrons
...
Elements are substances composed of atoms with a
specific number of protons, neutrons, and electrons, which determine their
chemical behavior
...
For example, ionic bonds often involve the transfer of electrons
between elements such as sodium and chlorine
...
Carbohydrates, lipids, proteins, and nucleic
acids are the four main types of biomolecules
...
Each
atom also has a mass number, which is the sum of the protons and
neutrons in its nucleus
...
The mass number of an
element on the periodic table is typically a decimal because it takes into
account all the isotopes that exist for that element
...
The
atomic weight of an element is the sum of the mass numbers of all the
isotopes that exist for that element
...
The number of electrons in each
shell is important for bonding
...
•
The mass number is the sum of the protons and neutrons in an
element's nucleus
...
•
Radioactive isotopes release energy when they degrade and can be
used for nuclear energy
...
•
Electrons are arranged in shells around the nucleus of an atom
...
The octet rule states that elements will bond
together so that they both have eight electrons in their outer shell to make
it stable
...
Most other elements are missing one electron or have extra
electrons, which they want to get rid of by bonding with another element
to fill their outer shell to eight
...
Compounds are molecules or combinations of two or more different
elements
...
Nonpolar covalent bonds
have equal sharing of electrons, while polar covalent bonds have an
unequal sharing of electrons, resulting in a partial charge
...
Nonpolar covalent bonds have equal
sharing of electrons, while polar covalent bonds have unequal sharing of
electrons, resulting in a partial charge
...
Examples of Covalent Bonds
•
Oxygen has six electrons in its outer shell and bonds with two hydrogen
atoms to fill its shell
...
•
Carbon has four electrons in its outer shell and bonds with one
hydrogen atom
...
The first one is covalent bonds, where atoms share electrons
...
And the third
one is hydrogen bonds, which are weak interactions between the positive
and negative charges of different molecules
...
•
Ionic bonds involve atoms donating or accepting electrons
...
Covalent bonds are the strongest type of bond, while hydrogen bonds are
the weakest
...
Covalent Bonds
In covalent bonds, atoms share electrons
...
In a polar covalent bond, electrons are shared
unequally between the atoms, creating a positive and negative end
...
Ionic Bonds
In ionic bonds, atoms donate or accept electrons
...
Sodium chloride
(table salt) is an example of an ionic bond
...
When the water evaporates, the salt crystals reform
...
They are important in biological molecules like proteins and
nucleic acids
...
Synthesis reactions combine two or more
reactants into one product, while decomposition reactions break down
one reactant into two or more products
...
The solutes
are the substances that get dissolved while the solvent is the substance
that does the dissolving
...
Hydrophilic substances like sugars and
carbohydrates like water while hydrophobic substances like salts and oils
repel water
...
Acidic solutions have more hydrogen ions
while basic solutions have more hydroxide ions
...
Some examples of acidic substances are
hydrochloric acid and lemons, while sodium hydroxide is one of the
strongest bases known
...
Comparing the strength of two solutions is easy by
subtracting their pH values and adding that number of zeroes to 1
...
The more acidic a solution is, the higher
the concentration of H+ ions and the lower the concentration of OH- ions
...
Organic compounds are molecules that contain carbon and hydrogen
atoms
...
Organic molecules are essential for life and are
often associated with living organisms
...
For example, solution A has a pH of 2 and solution B has a pH of 4
...
We can use the subtraction rule to find the
answer
...
Alternatively, we
could say that the difference between 2 and 4 is 2, and 10 multiplied by 10
is 100
...
It is highly versatile and can form
single, double, and triple bonds with other atoms
...
Accessory molecules, known
as R-groups or side chains, add reactive properties to organic compounds
...
There are four types of macromolecules: carbohydrates,
lipids, proteins, and nucleic acids
...
They are categorized as
monosaccharides (simple sugars), disaccharides (two monosaccharides),
and polysaccharides (many monosaccharides)
...
g
...
g
...
g
...
They are a
source of energy and are involved in cellular processes such as cell
signaling and cell adhesion
...
However, laboratory tools and methods have been
developed to help in studying these organisms
...
•
Incubation: Allowing the microbe to grow in a warm, dark environment
...
•
Inspection: Looking at the microbe under a microscope or observing its
growth patterns
...
Inoculation and Growth Media
The medium is the substance used to grow the microbe
...
Inoculation
involves introducing the microbe to the growth medium using a loop or
other tools
...
Incubation
After inoculation, the growth medium is placed in an incubator, which
provides the warm and dark environment needed for the microbe to grow
...
This is
done by diluting the sample until only one colony of the microbe is left,
which can then be introduced to a new growth medium
...
Identification involves various tests such as
biochemical and immunologic tests, or even DNA analysis, to determine
the type of microbe
...
Lab Techniques: Sterilization and Culturing Microbes
In the lab, it is important to ensure that all instruments used are sterile
...
Clinical specimens can be blood, cerebrospinal
fluid, urine, feces, or diseased tissue
...
Atmospheric gases like oxygen and
carbon dioxide may also be required
...
Types of Cultures
•
Pure culture: contains only one species of microbe, allowing for the
study of its reaction to different stimuli
...
•
Contaminated culture: contains a known bacterium contaminated with
an unknown organism, which can occur through various means such as
touching unsterilized equipment or airborne transmission
...
Some
microbes require host organisms to grow, while others require artificial
media
...
Agar is
flexible, moldable, and can hold moisture and nutrients, making it ideal for
microbial growth
...
Types of Media for Microbial Growth
Media for microbial growth can vary widely in composition, from blood to
meat extracts to complex mixtures of nutrients that are impossible to
chemically define
...
General Purpose Media
General purpose media, such as nutrient agar, contain a wide range of
nutrients that can support the growth of many different types of bacteria
...
Defined Media
Defined media are highly specific and contain precise amounts of
individual nutrients, such as amino acids, to support the growth of specific
types of bacteria
...
This type of medium is useful for
isolating specific microorganisms from samples with many different
organisms present
...
Colonies may differ in
size, color, or gas production, among other characteristics
...
Reducing medium is a media that contains bio glycolic acid or cysteine
...
Carbohydrate
fermentation media contains sugars that can be fermented by bacteria,
with a pH indicator and a Durham tube
...
Isolation is the process of getting one specific type of organism to grow
...
A colony is a macroscopic cluster of cells that you can
see in the growth medium that all came from one cell
...
Loop dilution is also known as a poor plate because you
pour it into the petri dish
...
Bacterial Characteristics and Identification
Bacterial identification can be challenging due to the presence of enzymes,
genetic and immunological characteristics, and mechanisms for deriving
energy such as photosynthesis and thermogenesis
...
These tests make it possible to identify
bacteria quickly and accurately based on the byproducts they give off
...
Some
examples include:
•
Selective media: int arrow caucus, callous broth, tomato juice agar,
macconkey agar, salmonella shigella agar, and loan steamed ginseng
medium
...
•
Reducing agar: foul glycol a broth or agar cysteine reducing medium
...
Visualization of Microorganisms
Light microscopy is commonly used for visualization of microorganisms
...
Some
examples of sizes in science include macroscopic (visible with the naked
eye), microscopic (millimeters to micrometers or nanometers), and atomic
(tenth of a nanometer)
...
The objective lens is closest to the
specimen and forms the real image
...
The light
shines through the specimen, and the stage can be adjusted to bring it
into focus
...
The ocular lens is
typically always 10x, and the objective lenses are 4x, 10x, 40x, and 100x
...
The
resolving power of a microscope is its ability to distinguish two separate
points from each other, and higher resolution allows for better clarity
...
Visible Light Microscopes
Bright field microscopes are the most common, and they produce images
with different shades depending on the density of the object being
viewed
...
Phase contrast microscopes add contrast to similarly
dense objects, making it easier to see things inside or outside of a cell
...
Ultraviolet Light Microscopes
Fluorescent microscopes use ultraviolet light and a filter to dye and
fluoresce a specimen, enabling better identification of certain microbes
...
Introduction
What is Life?
When we talk about life, we refer to cells, which are either single or multicellular units that have common characteristics
...
Characteristics of Life
Some of the characteristics of life include the presence of DNA, growth
and development, movement and response, metabolism, transport, and
cell support
...
They
contain cytoplasm, DNA chromosomes, ribosomes, and inclusion bodies
...
Motility Appendages
The flagella and axial filaments are periplasmic flagella that help bacteria
move and twitch around
...
Bacterial Movement and Flagella
In the medical field, bacteria tend to stick to plastics, catheters, and other
medical devices
...
Two main functions of bacteria are movement and attachment
...
Depending on the direction they want to go, they spin clockwise or
counterclockwise
...
There are also bacteria that do not move at all
...
Bacteria can be attracted or repelled by chemicals and light
...
If it is an antibiotic, they move
away from it
...
Bacteria spin their flagella
either clockwise or counterclockwise, and depending on the direction they
spin, it is called a run or a tumble
...
There are many different ways that bacteria can move, such as flagella,
periplasmic flagella, and gliding motility
...
Prokaryotic Flagella
The prokaryotic flagella rotates to allow the cell to move in one direction
...
Fimbriae and Pili
Fimbriae and pili are hair-like structures that allow bacteria to stick and
attach to surfaces
...
Glycocalyx
Glycocalyx is a sugar coating that surrounds bacteria
...
The capsule is a more organized structure that protects bacteria
from the immune system
...
They consist of different types of organisms that function together and
create an environment for metabolic activities
...
Bacteria and Biofilms
In hospital settings, bacterial infections in plastics such as catheters can
cause clogging and infections due to the growth of biofilms
...
Cell Envelope
The cell envelope is the protective layer that surrounds bacteria
...
Bacteria have a cell wall made of a protein-sugar molecule called
peptidoglycan, which is different from human cells
...
Gram-Positive vs Gram-Negative
Gram-positive cell walls are thick and brick-like, while gram-negative cell
walls are thin and weak
...
Gram staining is a technique used to differentiate
between gram-positive and gram-negative bacteria
...
•
Gram-negative cell walls are very thin and have only one layer of nan
and nag, but they have an additional outer membrane layer containing
LPS
...
This technique is used to
distinguish between the two types of bacteria - Gram-positive and Gramnegative - based on the color of their cell walls
...
The Gram Stain Technique
The Gram stain technique involves the use of crystal violet, grams iodine,
decolorizer, and a red stain to distinguish between the two types of
bacteria
...
The decolorizer is a crucial step in the
technique, as it removes the color from one of the bacteria
...
Non-Typical Cell Walls
There are some bacteria that have non-typical cell walls and do not stain
well with the Gram stain technique
...
For these
bacteria, an acid-fast staining technique is used instead
...
Internal Structures of Bacterial Cells
Inside bacterial cells, we find the cytoplasm, which is mostly water with
some dissolved proteins, sugars, amino acids, and salts
...
Bacteria also have plasmids, small pieces of DNA
that contain one or two genes that are not important for normal
metabolism but make the bacterias life easier
...
Bacteria also have an internal skeleton, the actin
and microfilaments, and some can make endospores that store their DNA
until the time is right to form new bacterial cells
...
They contain one or two genes that
are not important for normal metabolism, but they can help break down
certain toxins, proteins, and carbohydrates
...
Endospores in Bacteria
Endospores are like time capsules that bacteria make when the time is not
right for them
...
When the time is right, the
endospore erupts, and the bacteria form new bacterial cells
...
Video on Sporeforming Bacteria
Sporeforming bacteria grow as vegetative cells and divide by binary fission
when nutrients are available and environmental conditions are not
adverse
...
The mother cell divides into two
complete copies, and the mother cell membrane invaginates to form the
developing forespore
...
Peptidoglycan is laid down between the two membranes, and the
developing spore is now ready to form new bacterial cells when the time is
right
...
The Origin of Eukaryotic Cells
Eukaryotic cells did not exist until about two billion years after prokaryotic
cells
...
The DNA in prokaryotic cells became encapsulated in a bilipid membrane,
forming the nucleus
...
Some of these cells then ate up
photosynthetic bacteria, leading to the development of plant cells that can
produce their own glucose through photosynthesis
...
One large
prokaryotic cell engulfed a smaller one, forming the mitochondria, and
another prokaryotic cell, capable of photosynthesis, was engulfed later,
forming the chloroplasts in plant cells
...
We will briefly cover these organisms in this lecture
...
They are similar in size to photosynthetic and aerobic bacteria, and
there is evidence supporting the theory that eukaryotes evolved from
these types of bacteria
...
In this article,
we will explore the internal structures of eukaryotic cells, including
mitochondria, golgi apparatus, chloroplasts, rough ER, and centrioles
...
•
Cilia: long, hair-like structures that whip back and forth, used for
motility, feeding, and filtering
...
•
Cell walls: found only in fungi and algae, provide structure and support
...
•
Golgi apparatus: processes and packages proteins for transport
...
•
Rough ER: site of protein synthesis and modification
...
Overall, eukaryotic cells are complex structures with a variety of internal
and external components that work together to sustain life
...
These
internal structures include the nucleus, endoplasmic reticulum, Golgi
apparatus, lysosomes, and vacuoles
...
Cell Wall
The cell wall provides structural support and shape to the cell
...
The
cell wall is absent in all other eukaryotic cells
...
It is composed of a phospholipid bilayer and proteins, which are
fluid and can move around the cell
...
Nucleus
The nucleus is where the genome is kept
...
The nucleolus is responsible for
encoding RNA
...
The rough endoplasmic reticulum produces proteins, while the
smooth endoplasmic reticulum produces lipids
...
Lysosomes and Vacuoles
Lysosomes contain digestive enzymes that break down materials, while
vacuoles are membrane-bound sacks that store various materials
...
•
Chloroplasts: found in plant cells and used for photosynthesis
...
Eukaryotic cells have
larger ribosomes (40s and 60s) compared to prokaryotic cells (30s and
50s)
...
•
Golgi apparatus: responsible for transporting vesicles inside and
outside the cell
...
The ER is involved in protein synthesis, lipid synthesis, and
detoxification
...
•
Nucleus: contains the cell's genetic material and is responsible for DNA
replication, transcription, and gene expression
...
Prokaryotes vs
...
•
Reproduction: eukaryotes reproduce by mitosis, while prokaryotes use
binary fission
...
•
Photosynthesis: eukaryotes have chloroplasts for photosynthesis, while
prokaryotes do something different
...
Common Microorganisms
Some common microorganisms that can cause illness include:
•
Fungi: can cause infections such as athlete's foot and ringworm
...
•
Bacteria: can cause a wide range of infections such as strep throat,
tuberculosis, and pneumonia
...
Fungi
Fungi are single-celled organisms, and there are over 100,000 species
...
Macroscopic fungi include mushrooms and puffballs, while microscopic
fungi are the ones that can make people sick, such as mold
...
Yeast and
hyphae are the two morphologies of microscopic fungi
...
Fungi excrete their digestive enzymes outside the cell, digest the food
outside the cell, and then take it back up
...
Fungal infections are
called mycosis or mitosis ease
...
Fungi grow in
warm and dark places, and spores in the air transmit them
...
Impacts of Fungi
Fungi can cause diseases, allergies, toxins, and destruction of crops and
food storages
...
They are also used in making foods and genetic studies
...
Protists
Protists belong to the kingdom Protista and are the "junk drawer" of the
biology world
...
Protists are divided into two main types: plant-like and animal-like cells
...
They are mostly microscopic and found in water
...
However, some algae
can cause blooms that release toxins in the water, which can poison and
kill fish, dogs, and even humans if ingested
...
However, some can cause diseases as parasites in the
human body
...
There
are around 65,000 species of protozoa, and some can cause serious
diseases such as malaria, toxoplasmosis, and cryptosporidiosis
...
African sleeping sickness is caused by
trypanosomes, which are carried by black flies in Africa and can lead to
neurological issues and death
...
Dysentery is mostly associated with
amoebas that can cause severe gastrointestinal issues and can be
asymptomatic
...
Some amoebas can even cross the nose and infect the
brain, causing serious brain infections
...
Avoid swimming in stagnant water, and always use caution when
using neti pots or drinking tap water in areas where these organisms are
prevalent
...
Introduction to Viruses
Viruses are tiny infectious particles that can cause severe illness and even
death
...
We will explore
their structure, function, and infection process, and also touch on prions,
which are protein particles that cause mutations in other proteins
...
The name was first used to describe substances that caused illness
and death in people
...
Virus Classification
Viruses do not fit into the five kingdom system or three domains, so they
are not universally classified
...
Viruses are obligate intracellular
parasites, meaning they need a host to grow, multiply, and infect
...
Are Viruses Alive?
There is a debate among biologists on whether viruses should be
considered a live entity or not
...
They also do not have any
metabolism and cannot grow on their own
...
Virus Structure and Size
Viruses are not considered alive because they lack metabolism and cannot
reproduce outside of host cells
...
In this class, we will consider them as infectious particles
...
They can only
be seen with electron microscopes and are typically much smaller than
bacterial cells
...
Capsids are made up of
protein subunits and can be either helical or icosahedral in shape,
depending on the virus
...
Capsids and Spikes
Capsids are the solid outer structure of the virus and are made up of
protein subunits
...
The nucleic acid core and the capsid
together make up the nucleocapsid
...
Virus Shapes
There are two main shapes of viruses: helical and icosahedral
...
Icosahedral viruses have a spherical shape,
with the capsid subunits forming a closed shell around the nucleic acid
core
...
Another type is the helical, like the rabies
virus
...
Enveloped viruses steal a
membrane from the host cell, which becomes their coat and allows them
to detach from the cells and protect their nucleic acid
...
Types of Viruses
•
Naked viruses: either cubical or rod-shaped, or icosahedral
•
Enveloped viruses: either helical or icosahedral
•
Complex viruses: have more than just an envelope and a capsid
Virus Nucleic Acids
Viruses can have either DNA or RNA, and they usually have one or the
other
...
Chapter 24 is
dedicated to DNA viruses like herpes and hepatitis B, while chapter 25
covers RNA viruses like flu and HIV
...
There are three orders, 63 different families, and about 263 different
genera of viruses
...
" RNA viruses are more common than DNA
viruses
...
Some viruses have enzymes
associated with them, such as reverse transcriptase, which allows HIV to
convert its RNA genome to DNA and integrate into the host
...
Virus Multiplication
Viruses that infect bacteria go through similar stages as animal viruses
...
The lytic cycle is
the process of virus replication in which the virus enters the cell,
synthesizes new virus particles, assembles them, and finally releases them
out of the cell
...
•
•
Bacterial viruses follow the lytic cycle, which involves the following
stages:
•
Binding/absorption
•
Penetration
•
Biosynthesis
•
Synthesis/assembly
•
Maturation and lysis/release
Some viruses undergo the lysogenic cycle, in which they hide inside the
cell and incorporate their DNA into the chromosome
...
In the lytic cycle, the virus infects the host cell, replicates, and
causes the cell to die
...
The virus can
even be passed down to future generations of the cell
...
Lysogenic viruses can also cause mutations in host cells, leading to cancer
or other health issues
...
Differences Between Bacterial and Animal Viruses
While both bacterial and animal viruses go through absorption,
penetration, and synthesis assembly, there are some differences in how
they operate
...
Bacterial viruses
often cause the host cell to explode, releasing thousands of new viruses
...
Understanding the Lytic and Lysogenic Cycles
It's important to understand the lytic and lysogenic cycles when studying
viruses
...
By
understanding how viruses operate, we can better understand how to
prevent and treat viral infections
...
Some animal viruses are
very specific, infecting only certain cells, while others have a more broad
range
...
For example, hepatitis B only
infects liver cells, while polio virus can infect intestinal and nerve cells
...
Once the virus enters the cell, it can either be taken in by endocytosis or
fuse with the plasma membrane and release the nucleocapsid into the
cytoplasm
...
The virus can then replicate and make new virus particles,
either incorporating into the lysogenic phase or making new viruses in the
lytic phase
...
There are differences in where DNA and RNA viruses replicate in cells, but
the focus should be on understanding the general mechanisms of virus
entry and release
...
They are often referred to as the power tools of the
biological world
...
Aerobic Respiration
Aerobic respiration generates ATP, which is the energy currency of the cell
...
Anaerobic Respiration
Bacteria can perform anaerobic respiration using molecules other than
oxygen
...
Metabolism
Metabolism includes catabolism, which is the breaking down of
substances, and anabolism, which is the building up of substances
...
Photosynthesis
Photosynthesis is the process by which plants convert light energy into
chemical energy in the form of glucose
...
Enzymes: The Power Tools of the Biological World
Enzymes are like motorized carts or power tools that make biological
reactions faster, more efficient, and with less energy
...
The substrate is always on the left-hand side, while the product is on the
right
...
Enzyme Structure
Enzymes are proteins, but not all proteins are enzymes
...
Enzymes only have one role in life, and that is to do the one thing
they are made to do
...
" For
example, catalase breaks down hydrogen peroxide, oxidase adds electrons
to oxygen, and hexokinase transfers phosphate to glucose
...
How Enzymes Work
Enzymes work by binding to specific substrate molecules at the active site,
which is a special region on the enzyme
...
The
product is released from the active site, and the enzyme assumes its
original shape, ready to work again
...
Cofactors play a role in binding and
assisting in enzyme activity, acting as battery packs for proteins to work
...
Constitutive enzymes are constantly made, while regulated
enzymes are turned on and off
...
Enzyme sensitivity is affected by temperature, osmotic pressure, and
growth factors
...
Enzyme inhibition can be
competitive, where a substrate fights for the same active site as the
enzyme, or noncompetitive
...
Competitive inhibition involves blocking the active site of the
enzyme, while noncompetitive inhibition involves blocking a different site
on the enzyme
...
Noncompetitive inhibition can be
demonstrated using scissors, where blocking a different site on the
scissors prevents cutting
...
•
Repression through binding to DNA: Binding to the DNA can block the
transcription of enzymes and inhibit their activity
...
The end product of the pathway binds
to the first enzyme unique to the pathway, causing a conformational
change and preventing the enzyme from reacting with its substrate
...
Metabolism and Energy Production
Energy is the capacity to work and cause change, and can take different
forms such as thermal, radiant, electrical, mechanical, atomic, and
chemical
...
Exergonic reactions release energy,
while endergonic reactions consume energy
...
Electron Carriers and Reduction
The link between glycolysis and Krebs to the electron transport chain is
through electron carriers
...
Reduction means making
something more negative, which occurs when a molecule gains electrons
and hydrogen
...
Phosphorylation occurs through substrate level phosphorylation and
oxidative phosphorylation
...
Photophosphorylation happens during photosynthesis
...
Bacteria do aerobic respiration, anaerobic respiration, or
fermentation depending on their metabolic strategies
...
In anaerobic respiration, a
different molecule such as nitrate or nitrite is used instead of oxygen
...
Aerobic vs Anaerobic Respiration and Fermentation
In aerobic respiration, oxygen is used to generate ATP through glycolysis,
Krebs cycle, and electron transport
...
However, when oxygen is not available, anaerobic respiration takes place
using sulfate, nitrate, or carbonate
...
Fermentation, on the
other hand, involves the process of generating ethanol and CO2, which is
used to make bread and wine
...
•
Aerobic respiration: glucose in, pyruvate out, 2 ATP generated in
glycolysis, Krebs cycle produces CO2, electron transport occurs in the
mitochondria
•
Anaerobic respiration: uses sulfate, nitrate, or carbonate, 2 ATP
generated, produces lactic acid
•
Fermentation: generates ethanol and CO2, used to make bread and wine
Glycolysis and Krebs Cycle
Glycolysis is the process of breaking down glucose into pyruvate, which
generates 2 ATP
...
The Krebs cycle involves the conversion of
pyruvate to acetyl coenzyme A (acetyl coa), which goes through a cyclic
process to generate intermediates for electron transport
...
It is
important to know what goes in, what comes out, and where it takes place
...
Essential nutrients can be
broken down into two groups: macronutrients and micronutrients
...
Micronutrients or trace
elements, such as iron, magnesium, and zinc, act as cofactors for enzymes,
allowing them to function properly
...
Organic molecules require both carbon and
hydrogen, while inorganic molecules do not have both
...
Transport and Conditions
The difference between active and passive transport and hypotonic,
hypertonic, and isotonic conditions will be discussed
...
Growth Rate Factors
Temperature, oxygen, and pressure are among the factors that affect
bacterial growth
...
Growth Curve
Bacterial growth can happen quickly, with some bacteria multiplying from
one to two within 20 minutes
...
Cell Composition
Approximately 70% of a cell's contents is water
...
Other important elements found in smaller amounts
include sodium, calcium, magnesium, chloride, zinc, and iron
...
•
Autotrophs can use CO2 from the air and convert it into organic
molecules through the process of photosynthesis
...
•
Chemoheterotrophs, including most organisms, obtain their energy
from consuming organic matter and their carbon from other living
organisms
...
•
Autotrophs can use CO2 from the air and are mostly photoautotrophs
...
•
Photoheterotrophs can use sunlight to get energy, but must consume
organic matter for their carbon source
...
Transport Across Cell Membrane
Transport across the cell membrane can be either passive or active
...
Passive transport can be further classified into three types; simple
diffusion, osmosis, and facilitated diffusion
...
Passive Transport
Diffusion is the process where molecules move from high concentration to
low concentration without the need for energy
...
Osmosis is the
movement of water towards the area where solute concentration is higher
...
Facilitated diffusion requires a protein to help molecules cross the
membrane
...
Group translocation is found in bacteria, while
vault transport involves endo- and exocytosis
...
Human cells lack a cell wall, making them sensitive to
changes in osmotic pressure
...
Cellular Solutions and Transport
In cellular biology, there are three types of solutions: isotonic, hypotonic,
and hypertonic
...
Hypotonic solutions have more solute inside the cell
than outside, causing water to move into the cell and potentially lead to
cell lysis
...
Bacteria cells have cell walls that allow them to tolerate changes in solute
concentration better than eukaryotic cells
...
In hypertonic
solutions, the plasma membrane pulls away from the cell wall, causing
some dehydration but not cell death
...
Active transport, on the other hand,
requires ATP and moves molecules against the concentration gradient
...
Transport Across the Cell Membrane
Molecules can enter the cell through phagocytosis (eating) and pinocytosis
(drinking), both of which are types of endocytosis
...
Passive transport processes include diffusion, osmosis, and
facilitated diffusion
...
Exocytosis is another active process that involves
moving waste and other materials out of the cell
...
There are three temperature ranges for
any organism: minimum, maximum, and optimum
...
The optimum temperature for bacterial growth is around 37°C, which
is the same as the human body temperature
...
Oxygen is essential for most organisms, but
there are bacteria that can survive without it
...
Bacterial Growth and Survival
Bacteria have different requirements for growth and survival, including
oxygen, pH, osmotic pressure, and pressure
...
There are also bacteria that can
survive in both oxygen and non-oxygen environments, known as
facultative anaerobes
...
The pH level is also an important factor for bacterial growth and survival
...
Bacteria that grow in acidic environments are called
acidophiles, while those that grow in alkaline environments are called
alkalinophiles
...
Halophiles are bacteria that can survive in high salt
concentrations, while osmotolerant bacteria have mechanisms to keep
water in to survive in low water concentrations
...
Bacteria can also form associations with other organisms, either symbiotic
or nonsymbiotic
...
Genetics: Understanding DNA, Transcription, Translation,
and Replication
Basics of Genetics
The study of heredity, genetics, involves the transmission of biological
traits
...
We will look at the structure of the bacterial chromosome, which is a
single circular piece of DNA
...
Overall, genetics is the study of heredity and the transmission of biological
traits
...
Protein Synthesis and Genes
Protein synthesis involves DNA as the blueprint, RNA as the messenger,
and protein as the product
...
Genotypes refer to the genetic
makeup, while phenotypes refer to the appearance of an organism
...
Size Comparison
Viruses have the smallest genome size, with about 100 to a couple
thousand base pairs
...
coli has about 4,000 genes, which is equivalent to
about 4-5 million base pairs
...
DNA Structure
DNA is made up of nucleotides, which include sugar, phosphate, and
nitrogenous base (adenine, guanine, thymine, and cytosine)
...
The backbone of DNA is
connected by covalent bonds, while bases are connected by hydrogen
bonds
...
DNA runs antiparallel, with one side running in one direction and the other
side running in the opposite direction
...
It involves about 30 enzymes, but the most critical one is
helicase, which unzips the DNA by breaking the hydrogen bonds
...
This allows for error correction if mistakes are made during
replication
...
The
arrangement of the four nucleotides (adenine, thymine, guanine, and
cytosine) provides variety, and that's what makes each organism unique
...
The Process of Replication
Replication occurs in both strands simultaneously, creating a
complementary strand
...
DNA polymerase binds to and builds the new
strands, with one strand being the leading strand and the other being the
lagging strand
...
Concept Check: Complementary Bases
In DNA, thymine is complementary to adenine, and cytosine is
complementary to guanine
...
DNA Replication
DNA replication begins at the origin of replication site
...
The enzyme complex DNA
polymerase engages the separated portion of the molecule and initiates
the process of replication
...
Therefore, replication
begins as an enzyme called primase assembles an RNA primer at the origin
of replication site
...
DNA polymerase is then able to add DNA
nucleotides to the RNA primer and thus begin the process of constructing
a new complementary strand of DNA
...
Because the two complementary strands of the DNA molecule are oriented
in opposite directions and the DNA polymerase can only accommodate
replication in one direction, two different mechanisms for copying the
strands of DNA are employed
...
Each Okazaki fragment requires a separate RNA
primer
...
Transcription and Translation
Transcription is involved with making proteins and takes place all the time
...
The proteins determine the phenotype, and the
DNA is the blueprint that tells you what the cell is going to do, how it's
going to function, and what it's going to make
...
The central dogma of biology states that DNA is converted to RNA, which
then builds the protein
...
The DNA tells you what the protein is going to look like by
telling you what amino acid is going to go in what order
...
Instead, it has uracil
...
mRNA makes the message from the DNA, transcribes the DNA code into
RNA, and then binds to the ribosome so that it can be made into protein
...
rRNA is a
part of the ribosome
...
Messenger RNA
(mRNA) carries the DNA message and is used to make a copy from the
DNA in the transcription process
...
•
rRNA: builds subunits
•
tRNA: brings amino acids
•
mRNA: carries DNA message
•
rRNA: subunits in prokaryotes and eukaryotes
RNA polymerase is used in transcription, building an RNA copy by binding
to the DNA upstream of the gene in the promoter region
...
Messenger
RNA molecules can be anywhere from 100 to 1,200 base pairs depending
on the size of the gene
...
This takes place at the ribosome in both prokaryotes and
eukaryotes
...
Understanding Translation Process in DNA
The translation process in DNA involves five stages that help to interpret
the genetic code
...
The first step is to
understand that mRNA is a collection of three-letter words that mean the
same thing
...
This redundancy helps to ensure that mutations do not affect
the protein too much
...
The start codon is AUG, which codes for methionine,
and the ribosome binds to this site to start the process
...
The initiation process involves the small ribosomal subunit
binding to the mRNA near its 5' end
...
Initiation Process
The initiation process involves the binding of the 30s subunit and mRNA
complex, facilitated by initiation factor 3
...
The large ribosomal subunit binds, and the
initiation factors are released
...
The
acquired immunity adapts to what you are exposed to and is acquired over
your lifetime
...
Let's take a look at the specifics:
•
B cells: Mature in bone marrow, produce antibodies, and respond to
antigens
•
T cells: Mature in the thymus, help with response, and kill cells with their
response
•
Antigen: A molecule that stimulates the response by B or T cells
•
Specificity: Each B and T cell responds to a different antigen
•
Memory: Each exposure to a disease or pathogen gives some type of
immunity or response
The acquired immunity provides needle competence to the body
...
The specificity and memory are the important features of the
third line of defense
...
Lymphocytes respond to antigen processing and
cooperate with antigen presentation
...
Overall, the acquired or adaptive immunity is a dual system of B and T cells
that provide specificity and memory to the body
...
The immune system works in
the following way:
•
B and T cells develop in the bone marrow and thymus, respectively
...
•
T cells leave the bone marrow before they get receptors and go to the
thymus, where they become mature and then go to lymph nodes to
wait
...
•
When an antigen comes in contact with a B or T cell, it gets activated
...
•
An activated T cell can become a memory cell, cytotoxic T cell, or helper
T cell to help the B cells respond
...
MHC class 1 is found on all cells and tells the
immune system that this is "you
...
Understanding B and T Cells
There are two types of cells in the immune system: B cells and T cells
...
B cell receptors bind to antigens while T cells help
present and bind to other cells to attack and kill cells
...
This is known as the clonal selection theory, where one stem cell can
produce different types of cells, resulting in millions of unique cells that
recognize a million different receptors
...
Once
they gain the receptor, they respond only to that one antigen
...
Eliminating Clones
During the process of making clones, some receptors may bind to self and
are eliminated right away
...
However, some cells that recognize self may still get through,
leading to autoimmunities such as lupus, Crohn's disease, and rheumatoid
arthritis
...
This process helps the immune system fight against
pathogens
...
The B cells or T cells respond to the antigen,
and we start to make thousands of B cells
...
Each B cell and T cell has different specificity for different antigens, and
the B cell receptor is called an antibody, which is shaped like a Y and has
four polypeptide chains
...
The
antigen and antibody need a specific lock-and-key mechanism to fit
perfectly and trigger an immune response
...
B Cell Specificity and Memory
•
B cells are specific to outside things outside the cells
...
•
The constant region always binds to the cells, and the variable region
changes and gives specificity to the antigen
...
•
The B cells become activated once they come in contact with the
specific antigen, and the response takes place
...
•
Anything that can cause a response is called an antigen
...
•
Properties that can cause an immune response include foreignness, size,
shape, accessibility, and how it can bind
...
Understanding Antigens and Epitopes
An antigen is any foreign substance that the body recognizes and
responds to
...
Antigens that are large
and over 10,000 molecular weight are the most energetic
...
Each antigen can have
multiple epitopes, and the more epitopes an antigen has, the more
antigenic it is
...
Antibodies and Epitopes
Individual antibodies are not made against the entire antigen molecule,
but rather to specific chemical groups known as antigenic determinants or
epitopes
...
Complex structures,
such as bacterial cell surfaces, may have many different epitopes, and each
different antibody binds only to the correct epitope
...
A lot of times, haptens need to be
attached to a carrier molecule to cause an immune response
...
Special Categories of Antigens
There are special categories of antigens, including alloantigens, super
antigens, and allergens
...
Super antigens provide a potent T-cell stimulator, causing an
overwhelming response that can be dangerous
...
Types of Antigens and Immune Responses
In the human body, there are different types of antigens that can cause an
immune response
...
Autoantigens can lead to diseases like lupus,
rheumatoid arthritis, and skin infections
...
Once an antigen and antibody response occurs, there is a proliferation of B
cells, which create memory cells for long-term storage
...
Opsonization
Opsonization occurs when antibodies flag a microbe and tell white blood
cells to attack it
...
Neutralization
Antibodies can neutralize viruses and toxins by blocking their ability to
attach to cells
...
Agglutination
Agglutination occurs when antibodies cause antigens to clump together
...
Understanding these different types of antigens and immune responses is
crucial for understanding vaccines and how they work
...
There are microbes everywhere, and we need
to make things clean and sterile to prevent infections
...
These methods kill microorganisms
...
There are different types of
chemicals, and we will survey through them
...
The least resistant are easily wiped out with
soaps and chemicals used around the house
...
Prions and bacterial spores are the most resistant, while protozoan cysts,
Pseudomonas, Mycobacterium tuberculosis, and Staphylococcus aureus
have moderate resistance
...
Microbes and Their Elimination
Eliminating all microbes is not possible, and some microbes are actually
beneficial
...
However, some
microbes need to be eliminated to prevent harm
...
The hardest
to eliminate are endospores
...
Sterilization means eliminating all microbes, while
disinfection means reducing microbes, and antiseptic means killing
microbes on the body
...
Determination reduces the number of microbes
through mechanical means
...
The permanent loss of reproductive capability leads to
microbial death, even if the bacteria is still metabolizing
...
Low loads are easier to sterilize than high loads
...
Other factors include
the concentration or dosage, mode of action, and presence of solvents
and organic matter
...
In a hospital setting, it is crucial to think about the best ways to kill
microbes
...
Additionally, the method used must be suitable for the job and penetrate
effectively, while also being cost-effective and safe for the patient
...
Destroying these targets effectively eliminates the ability of bacteria to
grow and reproduce
...
Cell Membrane
Surfactants such as soap can destroy the cell membrane, allowing for
effective elimination of bacteria
...
Proteins
Heat and chemicals can denature proteins and affect enzyme activity,
while acids and bases can affect the shape and structure of proteins
...
Moist Heat vs
...
Dry heat, on the
other hand, requires much higher temperatures and longer exposure times
and is effective by desiccating or drying out everything
...
Radiation
Radiation can be used to effectively eliminate microbes, but can also be
harmful to humans if not used properly
...
Conclusion
Choosing the best method for eliminating microbes requires consideration
of various factors such as temperature, pH, concentration, mode of action,
and presence of inhibitors
...
Understanding Sterilization Methods: Thermal Death
Time and Thermal Death Point
In microbiology, it is essential to sterilize equipment and materials to
prevent contamination by microorganisms
...
However, the effectiveness of each method depends on the type of
material and microorganism involved
...
This method is suitable for
most materials and takes about 10 to 40 minutes at 121 degrees Celsius
and 15 psi
...
Thermal Death Time
Thermal death time is a test that determines the amount of time required
to kill a particular microbe at a constant temperature
...
After boiling, the solution is plated to
determine the time required to kill all the bacteria
...
Thermal Death Point
Thermal death point is a test that determines the temperature required to
kill a particular microbe in a constant time, typically 10 minutes
...
The solution is then plated to determine the temperature that
kills all bacteria within the time limit, and that temperature is the thermal
death point
...
Free-Flowing Steam
Free-flowing steam is an intermediate sterilization method used for
substances that cannot withstand autoclaving, such as canned foods
...
This sterilization method is also suitable for media
...
Nevertheless, it is crucial to maintain
a sterile environment to prevent contamination
...
Some of these methods include:
•
Canned Food
•
Boiling Water
•
Pasteurization
•
Dry Heat
•
Cold
•
Preserve Fruit Media and Cultures
•
Desiccation
Canned Food
Canned food is a great way to preserve food, but it's important to
remember that these canned foods may sit around for a long time
...
Boiling Water
If there is a water main break, it's important to boil water before
consumption
...
This is also important when camping and collecting water from
streams or lakes
...
This method is not a sterilization technique, but it does kill most
pathogens
...
This includes
incineration and the use of dry ovens
...
This
is why refrigeration is important for preserving food, but it's important to
remember that cold does not eliminate microbes
...
Desiccation
Desiccation is the freeze-drying process, which is used to preserve food for
space travel
...
Freezing and Desiccation
Freezing and desiccation help eliminate microbes by removing water,
which is necessary for their growth
...
Incineration
Incineration is used to sterilize bacteria by killing everything, including
vegetative and endospores
...
This
method destroys DNA and is used in ultraviolet levels, x-ray, and gamma
rays
...
If you see a symbol on your fruit, it means that it has
been irradiated
...
Non-Ionizing Radiation
Non-ionizing radiation is based on UV rays
...
For instance, if you hold a piece of
paper over a UV light, none of the UV rays will get through
...
UV radiation is used in clean rooms and is effective in controlling
microorganisms in the air and on surfaces
...
Innate Immunity
Immunology and the innate immune system are considered nonspecific
immunity
...
What is Immunology?
Immunology is the study of the immune system, which defends against
foreign invaders
...
The three lines of defense are
the first line, mechanical barriers; the second line, white blood cells
responsible for phagocytosis and inflammation; and the third line, B and T
cells, which will be discussed in Chapter 15
...
Lymph is
the extracellular fluid that leaks out of our vessels and returns into
circulation through lymphatic vessels
...
Host Defenses
The innate immune system is our natural defense system, which attacks
viruses, bacteria, fungi, parasites, and any other organism that enters our
body
...
Understanding the Body's Defense System
Today, we're going to look at the first and second line of defense, which
are both innate, nonspecific, and have no memory associated with them
...
The first line of defense includes mechanical
barriers such as skin and mucous membranes, respiratory, general and
digestive tracts
...
The First Line of Defense
The first line of defense is any mechanical barrier around the portal of
entry
...
Sweating also helps eliminate
microbes by washing them away
...
Stomach acid is another
barrier that kills most microbes that enter our body
...
Chemicals like sebaceous secretions, lysozyme in tears
and saliva, high lactic acid and electrolyte concentration in sweat, skin's
acidic pH, hydrochloric acid, digestive juices and bile in the intestines,
fluids like semen and the vagina's acidic pH are some of the other
mechanical barriers that keep microbes from getting into our body
...
There is an idea of
the good genes surviving because some people are more resistant to
microbes than others
...
For example, about 1% of the
population can't get infected with HIV because they lack the right receptor
for the virus to bind to
...
Genetics plays a huge role in determining our health, as some individuals
have a better combination of genes that allow them to be healthier and
more resistant to microbes
...
However, if microbes penetrate this line of defense, the second line of
defense takes over
...
First Subdivision: Reticuloendothelial System
The reticuloendothelial system consists of connective tissue with cells that
sit ready to attack any foreign material that enters the body
...
Second Subdivision: Extracellular Fluid
The extracellular fluid is fluid that leaks out of our vessels and contains a
lot of white blood cells that attack and find foreign material that isn't
supposed to be there
...
Third Subdivision: Bloodstream
The bloodstream brings all the cells and fluid to the sites that need to be
attacked
...
The liquid portion of the blood is called plasma, and if you take out the
clotting proteins, it becomes serum
...
The system includes lymphatic vessels and lymph nodes that
act as security checkpoints to attack foreign material
...
Granulocytes
Granulocytes are white blood cells that have granules
...
•
Eosinophils (1-3% of white blood cells) - fight against eukaryotic
parasites
...
Agranulocytes
Agranulocytes are white blood cells that do not have granules
...
•
Monocytes - similar to neutrophils
...
Cancer treatment drugs can affect blood cell production because
they target rapidly dividing cells
...
Monocytes, also known as macrophages, are responsible for eating
pathogens and showing them to B and T cells
...
The delay in the acquired
immunity response occurs because macrophages need to eat first before
responding to T cells
...
They carry oxygen and have a limited lifespan before dying and being
removed by the spleen
...
Lymphatic System
The lymphatic system is a network of vessels that carries extracellular fluid
back to the heart
...
It also
monitors fluids for any infectious agents or debris
...
Lymph nodes are
checkpoints that survey the fluid for any microbes or pathogens
...
Lymphoid Organs
The lymphatic system is responsible for returning fluid back into
circulation
...
The bone marrow and thymus are primary lymphoid organs
where white blood cells are formed and matured
...
Primary Lymphoid Organs
The bone marrow and thymus are primary lymphoid organs where white
blood cells are formed and matured
...
As one gets older, the thymus gland
shrinks, leading to a weakened immune system
...
How White Blood Cells Work
Inflammation
Inflammation is an innate immune response where white blood cells attack
anything that enters the body
...
Neutrophils are the first responders and eat
bacteria, resulting in swelling and pus formation
...
Other Functions
White blood cells can also leave blood vessels on their own without injury
...
This is achieved through operands, which means
having multiple genes on one transcript
...
Mutations
Mutations in DNA can affect the overall protein produced by changing the
three-letter words that make up the genetic code
...
DNA Exchange Between Bacteria
Bacteria can exchange DNA through conjugation, transformation, and
transduction
...
Operons and Gene Regulation
In bacteria, operons play a crucial role in regulating gene expression
...
Inducible
operons are usually off but can be turned on when needed, while
repressible operons are normally on but can be turned off when the
process is not needed
...
Lactose Operon
The lactose operon is an example of an inducible operon
...
The regulator codes
for the repressor protein, which is bound to the DNA and prevents RNA
polymerase from binding and making mRNA
...
The structural locus
has the genes that code for the three enzymes needed to break down
lactose: beta-galactosidase, permeate, and beta-galactosidase transit
satellites
...
Arginine Operon
The arginine operon is an example of a repressible operon
...
The structural genes needed to
make arginine are always on because they are required
...
When arginine is present,
the repressor binds to the DNA and stops transcription and translation,
preventing the production of enzymes needed to make arginine
...
Inducible operons are usually off but can be turned on when needed, while
repressible operons are normally on but can be turned off when the
process is not needed
...
Synthesis and Regulation of Catabolic Pathways
When microorganisms such as E
...
In the absence of lactose, the regulatory protein called a
repressor binds to the operator site and blocks transcription
...
The repressor can no longer bind to the
operator site, and transcription can proceed
...
The lac operon gets turned down when lactose is present, while arginine is
normally needed when arginine is present
...
Mutations
Mutations refer to any change in the phenotype due to the change in the
sequence of the DNA
...
If it has some type of mutation and it
does some other phenotype, then we call this a mutant string
...
We either change the DNA physically by
actually manipulating the bases or expose it to different chemicals,
radiation, or other things to physically change the DNA bases
...
Types of Mutations
•
Missense: changes the amino acid
•
Silent: does not change the amino acid
•
Back: changes the amino acid, but it goes back to the original
•
Frameshift: insertion or deletion of a nucleotide, which changes the
reading frame
Types of Mutations
Mutations can occur in DNA, which can lead to changes in the amino acid
sequence of a protein
...
This is called a missense
mutation
...
This can halt protein production,
leading to incomplete proteins
...
•
Back mutation: A mutated DNA sequence can revert back to the
original wild-type sequence
...
Examples of Mutations
Here are some examples of how mutations can affect a sentence:
•
Missense mutation: Changing "fat" to "fit" changes the meaning of the
sentence
...
•
Frameshift mutation: Adding or deleting a letter can cause the
sentence to become incomprehensible
...
•
Mismatch repair: This enzyme can fix mismatches in DNA sequences
...
DNA Repair Mechanisms
Our DNA is constantly being damaged by various factors like UV radiation,
chemicals, and errors during transcription and replication
...
These checks and balances
ensure that mistakes are fixed before they lead to mutations such as
cancer
...
If a
mismatch occurs, the DNA polymerase pauses and removes several
nucleotides from the growing strand, including the one with the
mismatched base
...
Excision Repair
If a mismatch is not corrected by proofreading, another repair mechanism
called excision repair comes into play
...
The
enzymes then remove the mismatched nucleotides and fill the gap with
the correct ones
...
It
involves exposing a culture of Salmonella bacteria to the chemical and
seeing if they can now utilize histidine, which they normally cannot
...
Positive Mutations
While mutations are often associated with negative effects, some
mutations can be positive and provide an advantage to bacteria
...
DNA Recombination Events
Bacteria exchange DNA with each other through three mechanisms:
conjugation, transformation, and transduction
...
Conjugation
Conjugation is also known as bacterial sex and involves the transfer of a
plasmid or a chromosomal fragment from one bacterium to another
...
Transformation
Transformation involves physically adding naked DNA to a bacterium,
which allows it to acquire new genes
...
Transduction
Transduction involves the use of viruses to transfer DNA between bacteria
...
Bacterial Gene Transfer
Bacterial gene transfer involves three mechanisms: conjugation,
transformation, and transduction
...
Transformation is the uptake of DNA from the
environment and its integration into the host DNA
...
Conjugation
Conjugation involves direct contact between donor and recipient cells
...
Recipient cells that lack an F plasmid are referred to as
F-
...
The plasmid then becomes
mobilized for transfer when a plasmid-encoded endonuclease cleaves one
strand of the plasmid at a specific nucleotide sequence called the origin of
transfer
...
A complementary strand to the single-stranded
plasmid remaining in the donor is synthesized via the rolling circle
mechanism
...
When F+ and F- cells are mixed
together, eventually all of the cells become F+
...
Some cells can naturally do this, while
others need to be artificially made competent by adding magnesium or
calcium chloride
...
Transformation was shown early on
in the early days of DNA as an effective process of changing the DNA from
one type of bacteria to another
...
Transduction
Transduction involves the transfer of bacterial DNA from one cell to
another using a virus as a carrier
...
The phage attaches to the bacterial cell
and injects its nucleic acid into it
...
Then those
viruses with the bacterial DNA go and infect another bacteria and inject
the new bacterial DNA into the bacteria
...
Infections that Target the Cardiovascular and
Lymphatic Systems
The cardiovascular and lymphatic systems are prone to systemic infections
that can easily spread throughout the body
...
The cardiovascular system is a closed circulatory
system that transports oxygen and nutrients to cells and tissues while
removing carbon dioxide and other waste products
...
Infections in these systems can
cause widespread edema, inflammation, and septic shock
...
Immune cells are present in the
bloodstream and lymphatic system and are activated quickly in response
to infection
...
Infectious Diseases in the Cardiovascular System
Endocarditis is the inflammation of the endocardium, the smooth tissue
lining the inside of the heart, heart valves, and interior chambers of the
heart
...
Acute endocarditis can be
life-threatening, while subacute endocarditis can take months to develop
into a serious condition
...
Septicemias occur when organisms actively grow in the bloodstream,
causing disease within the bloodstream
...
Prophylactic
antibiotics may be prescribed before dental work or surgeries to prevent
infections in individuals with heart problems
...
Here are some common
bacterial infections and their symptoms:
•
Septicemia
Fever is the most prominent symptom of septicemia, which is associated
with hospitals and nosocomial infections
...
Septicemia is rare for healthy individuals, and mostly
affects those who are immunocompromised or have other
complications
...
It is transmitted to humans through flea bites
...
This can grow and
perpetuate inside the body, eventually moving into the bloodstream
and then into the lungs
...
•
Tularemia
Tularemia, also known as rabbit fever, is similar to plague, but instead of
rodents, it is transmitted through lagermorphs or rabbits
...
Symptoms include a high-grade fever and bubo-like
formations, which are necrotic lymph nodes
...
•
Lyme Disease
Lyme Disease is caused by a spiralio organism of Irelia Border Fury and
is transmitted through a biological vector, a deer tick or the Ixodes
...
If left untreated, it can result in a chronic
infection due to the organism's ability to constantly change its surface
and evade the immune system
...
Early
symptoms include a bullseye rash, fever, headache, stiff neck, and
dizziness
...
Lyme disease can be chronic and slowly worsen
over time, resulting in autoimmune-like illness
...
Tick Life Cycle
•
Larval tick - bites infected mouse and becomes infected
•
Nymphal tick - bites humans and becomes infected
•
Adult tick - mates on a deer and continues the life cycle
If treated early with doxycycline, Lyme disease can be cured
...
It is important to save the tick if possible to help with
identification and testing
...
Symptoms include fatigue,
fever, and flulike symptoms
...
It is not life-
threatening and does not cause major problems, but it can make you very
tired and affect your ability to focus
...
They are transmitted primarily by mosquitoes and
include:
•
Yellow fever - causes a nasty fever disease
•
Dengue fever - causes severe joint pain and flulike illness
•
Ebola - results in severe hemorrhage in up to 100% of people that
become infected
Because hemorrhagic fever diseases cause such severe symptoms, it is
relatively easy to quarantine people and slow the spread down
...
Non-Hemorrhagic Fever Diseases
Non-hemorrhagic fever diseases cause high-grade fever without bleeding
and are generally treated with antibiotics
...
Symptoms include fever,
chills, headache, muscular pain, and a distinctive red blotchy rash
...
Common Pathogens and Diseases
There are several common pathogens and diseases that affect people
globally
...
It is easily treatable with doxycycline
...
It is treatable with ciprofloxacin
...
It is transmitted through the Anopheles mosquito and caused by
Plasmodium falciparum or Plasmodium bybax
...
Viruses
•
HIV: This is a retrovirus that targets CD4 cells and weakens the
immune system causing AIDS
...
Malaria
Malaria is transmitted through the Anopheles mosquito and is
characterized by symptoms such as malaise, fatigue, diarrhea, fever, and
sweating every 48-72 hours
...
It has both an asexual and sexual phase, and reproduces
within the liver and red blood cells
...
It is treatable
with ciprofloxacin and is primarily found in cattle
...
HIV and AIDS
HIV weakens the immune system by targeting CD4 cells and causing AIDS
...
The symptoms associated with HIV are directly tied
to the amount of virus present in the body and the amount of CD4 T cells
that have been lost due to infection
...
Once infected,
the virus replicates by integrating into the host cell's genome and
releasing RNA that reverse-transcribes into DNA
...
The initial symptoms of HIV infection are vague and may not appear for
years, but as the virus replicates and destroys T cells, the immune system
becomes weakened, leading to AIDS
...
HIV is
primarily transmitted through direct contact with contaminated bodily
fluids, such as blood, semen, vaginal fluid, and breast milk
...
As the virus progresses and destroys T cells, individuals may experience
flu-like symptoms, weight loss, and neurological changes
...
Transmission of HIV
HIV is primarily transmitted through direct contact with contaminated
bodily fluids, such as blood, semen, vaginal fluid, and breast milk
...
Men who have sex with men and engage in anal sex have a higher risk of
transmission than heterosexual individuals
...
HIV Transmission and Statistics
While HIV is relatively difficult to contract, it only takes one instance of
exposure to become infected
...
These groups tend to be more
promiscuous, and their sexual practices make the virus more easily spread
...
Treatment for HIV
Highly active antiretroviral therapy (HAART) is the primary treatment for
HIV
...
HAART involves taking
three antiretroviral drugs, two nucleoside inhibitors, and one protease
inhibitor for the rest of one's life
...
However, it is crucial to take these
drugs every day and not stop because HIV is highly mutation-prone
...
PrEP drugs prevent the
virus from establishing itself in the body, wiping it out before it can cause
an infection
...
Natural Resistance to HIV
Long-term nonprogressors either lack a receptor required by the virus or
have an immune system that keeps it at bay permanently
...
Researchers study these
individuals to learn more about how to prevent HIV infection, but their
antibody responses are often unique to HIV and not helpful for other
infections
...
The upper respiratory tract comprises all the cavities of
the face, nose, sinuses, mouth, and the upper part of the throat
...
The entire tract is
lined with a mucous membrane, and the trachea has cilia that work to trap
any inhaled microorganisms or foreign matter
...
There is also secretory immunoglobulin A, which is an antibody
that is released from the mucous membranes and binds to antigens and
targets them for destruction
...
The presence of cytokines can communicate
messages between immune cells and recruit immune cells to the area if
needed
...
However, in the very lower part of the respiratory tract, the
lung alveoli, there should not be any microorganisms growing, making it
an area of the body free from microbes
...
It can also
cause a more advanced pharyngitis known as scarlet fever
...
It has several virulence factors,
including antigens that mimic host proteins, m protein that helps the
bacteria resist phagocytosis and promotes adherence to host tissue, and a
capsule that helps it resist phagocytosis
...
To diagnose pharyngitis or scarlet fever, a physician
would take a pharyngeal swab and perform a rapid diagnostic test to
detect the presence of strep pyogenes bacteria
...
Influenza Virus
The influenza virus is an RNA virus that causes seasonal circulation and
spikes every winter with varying virulence
...
The virus is transmitted through respiratory droplets or fomites, and
its virulence factors include its ability to mutate rapidly, especially its
hemagglutinin and neuraminidase spikes on its surface
...
Signs and symptoms of the flu include headaches, chills, dry cough,
body ache, fever, stuffy nose, sore throat, and fatigue
...
Prevention and
treatment include the flu vaccine and antiviral drugs such as Tamiflu
...
Streptococcus pyogenes and the
influenza virus are two microorganisms that can cause respiratory diseases
and have specific virulence factors that make them dangerous
...
Flu and Mycobacterium Tuberculosis
Flu is caused by two types of viruses, influenza A and influenza B
...
The virus can
undergo two types of genetic changes: antigenic shift and antigenic drift
...
Antigenic drifts are smaller changes in the H or N spikes that are caused
by point mutations in the RNA genome
...
It grows very slowly and has lipids and wax in its cell
wall
...
Its virulence factors
are its waxy surface which enables it to survive inside macrophages by
blocking phagosome formation
...
Signs and symptoms include tubercles form in the lungs, violent coughing,
fever, fatigue, and weight loss
...
Flu Virus
•
Influenza A and B viruses cause flu
...
•
Antigenic shift occurs when a flu virus found in ducks and a flu virus
found in humans recombine in a pig, creating an entirely different virus
...
Mycobacterium Tuberculosis
•
Mycobacterium tuberculosis is a gram variable bacteria that is positive
for acid fast staining
...
•
Its virulence factors are its waxy surface which enables it to survive
inside macrophages by blocking phagosome formation
...
•
Diagnosis can be done with culturing the bacteria, a tuberculous skin
test, acid fast staining, and a chest X-ray
...
Flu vaccination is recommended every
year
...
Treatment for tuberculosis involves antibiotics for six
months, and in the case of drug resistance, longer antibiotic treatment or
fewer effective treatments
...
The epidermis is the most superficial layer and is made up of dead
keratinized skin cells
...
The subcutaneous layer contains
adipose tissue and larger blood vessels
...
Defenses of the Skin
The skin's biggest defense is its barrier function, which blocks organisms
from entering the body
...
The skin also produces
oil and sweat, which make the environment inhospitable to
microorganisms
...
Normal Commensals on the Skin
The most common organisms found on the skin are fermicutes, which are
soil-dwelling microorganisms
...
Other organisms found on the
skin include gram-negative organisms, staphylococcal organisms, and
organisms that thrive in moist areas, such as under the arms and in the
groin region
...
Acne occurs when there is an overgrowth of the
organism due to excess oil secretion in hair follicles
...
Acne is harmless but can be disfiguring and cause scarring
...
These infections can be serious and potentially
life-threatening
...
These infections are caused by the release of exfoliative toxins and other
virulence factors by the bacteria
...
Furnacle
is an infected hair follicle that can result in the development of a boil,
while carbuncle is a larger and more painful infection of multiple hair
follicles
...
Staphylococcus Aureus
S
...
While it is found in the upper respiratory
tract as a commensal in most people, it can cause diseases if it acquires
virulence factors
...
The bacteria can be tested using a latex agglutination
test or beta hemolytic on a blood agar plate
...
pyogenes is responsible for causing strep throat and can also cause skin
infections
...
It can be
tested using a latex agglutination test or beta hemolytic on a blood agar
plate
...
In this article, we will focus on bacterial infections of the
skin and their treatment
...
It is primarily transmitted through a small
break in the skin
...
However, those who are
immunocompromised or have poor blood flow may be at risk
...
Gas Gangrene
Gas gangrene is caused by anaerobic soil-dwelling bacteria, such
as Clostridium perfringens, and usually enters the body through a cut or
wound
...
If left
untreated, the organism can spread and cause death
...
Other Bacterial Infections of the Skin
Pseudomonas aeruginosa is a common commensal bacterium found on
the skin that can become opportunistic in immunocompromised
individuals or burn victims
...
Staphylococcus
aureus can cause a variety of skin infections, including scalded skin
syndrome, which results in blister-like lesions all over the body
...
It can result
in disfiguration and death after many years of infection
...
These
infections can cause various symptoms, including blisters, warts, and
lesions
...
Common Viral Skin Infections
One of the most common viruses that cause skin infections is the varicello
zoster virus (VZV), which is also known as the herpes virus
...
The virus primarily targets peripheral nerves and can incubate for up
to 12 days before causing a pustular rash that tends to itch and release the
virus when scratched
...
Smallpox, caused by the variola major virus, is another viral skin infection
that was eradicated in 1977
...
Macro-papular rashes are a type of flat, red rash that does not raise the
skin
...
Measles can
be life-threatening in young children and can lead to a latent infection
that reactivates later in life and targets the brain
...
Rubella, also known as German measles, is a milder version of measles that
can cause deformities in unborn children if contracted by pregnant
women
...
Other viral skin
infections include fifths disease, roseola, and scarlet fever
...
This is a red rash
that forms all over the body and a high grade fever
...
Warts are caused by the human papillomavirus (HPV) and can be
transmitted through direct contact
...
Treatment involves stimulating the
immune response in the area, which can be done using acids, immune
stimuli, or by burning the skin
...
It causes
cutaneous leishmaniasis, which results in a big open rubbery sore that
occurs for a long period of time until eventually the organism works its
way into the lymphatic system, resulting in systemic leishmaniasis and
potential death
...
Cutaneous anthrax is caused by a bacterium found on cows and can infect
humans through a break in the skin
...
Early treatment with antibiotics is crucial
...
They form little rings on the skin and are called
ringworm, but they are fungal organisms
...
The
two most common are athlete's feet and jock itch
...
The Eye and Infectious Diseases
Unlike the skin, the eye is relatively well-protected from infections due to
its constant exposure to the environment
...
Blinking and the production of lysozyme, an enzyme that kills bacteria, aid
in preventing infections
...
Conjunctivitis
Conjunctivitis is the inflammation of the conjunctiva
...
Screening and treatment during
prenatal care and the administration of antibiotics to newborns can
prevent this from occurring
...
Herpes keratitis and Acanthamoeba keratitis are the two main
causes, with the latter resulting from the use of dirty contacts
...
It can lead to blindness,
but it can be eradicated through anti-helminthic drugs
...
It is essentially one long tube through which we ingest foods and
liquids, and release wastes
...
The oral cavity
is protected by saliva and lysozymes that are antimicrobial
...
Several groups of normal microbiota
protect the oral cavity by microbial antagonism
...
If pathogens are detected in the food or drink
we ingest, then the immune system can be alerted by these lymphoid
tissues
...
Gastritis and Gastric Ulcers
Gastritis or gastric ulcers are inflammations of the gastrointestinal tract
and sores on the stomach or upper portions of the intestine
...
H
...
Its mode of transmission is probably by fecal-oral or oral-oral route
...
pylori are its ability to adhere very strongly to
the epithelial cells that line the stomach and production of urease, which is
essential for converting urea to bases that can neutralize the acidic pH of
the stomach
...
pylori infection
and resulting gastric ulcers is due to the inflammatory response by the
host's immune system
...
pylori antigen in stool samples
...
pylori infection is over-the-counter for
symptom relief and antibiotics to clear the bacteria
...
It contaminates an estimated ten percent
of chickens destined for human consumption
...
Its mode of transmission is direct contact via
kissing, vehicle via food, and mechanical vector via reptiles, rodents,
poultry, or cattle
...
All of the
gastrointestinal tissues can be infected by Salmonella enterica
...
Prevention is
mostly to avoid eating the outside of food, cooking foods to the
recommended temperature, or boiling things to kill the presence of
bacteria that might be present
...
Cholera
Cholera is caused by the gram-negative bacteria Vibrio cholerae and is a
common-shaped gram-negative rod with a low pH
...
The mode of
transmission is vehicle, so you get cholera from food or water that
contains the bacteria
...
There have been several outbreaks of cholera after natural disasters, and
at points in time, half or a significant part of the world's population has
been wiped out by cholera epidemics or pandemics
...
The bacteria has flagella which help
it move and penetrate the mucus barrier of the small intestine
...
The diarrhea, called rice water stools, is
characterized by flecks of mucus and looks like rice water
...
Diagnosis is done through stool
samples and PCR to determine the source of infection
...
Treatment includes oral rehydration therapy and oral antibiotics
...
Prevention:
•
Proper sewage treatment and water purification
•
Detection and treatment of asymptomatic carriers
•
Vaccination for those in endemic regions or traveling
Treatment:
•
Oral rehydration therapy
•
Oral antibiotics
Title: Microbiology
Description: The document are organised into clear and concise sections, covering the key concepts and topics in microbiology. These include the structure and function of microorganisms, microbial growth and metabolism, microbial genetics and evolution, and the role of microbes in infectious disease and public health. Each section would likely include detailed notes on the key points and concepts, as well as summaries of important studies and experiments in the field. By providing clear and concise summaries of complex concepts, the document makes it easier for individuals to quickly grasp the key ideas and build a strong foundation in the subject.
Description: The document are organised into clear and concise sections, covering the key concepts and topics in microbiology. These include the structure and function of microorganisms, microbial growth and metabolism, microbial genetics and evolution, and the role of microbes in infectious disease and public health. Each section would likely include detailed notes on the key points and concepts, as well as summaries of important studies and experiments in the field. By providing clear and concise summaries of complex concepts, the document makes it easier for individuals to quickly grasp the key ideas and build a strong foundation in the subject.