Class notes
Class notes Micr 271 (MICR271)
- Course
- Micr 271 (MICR271)
- Institution
- Queen’s University (QU )
Comprehensive course notes for MICR 271.
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Module 1 - Microbial Evolution and Diversity:Evolution and the Role of Microbes:
Connections Between Prokaryotes and Eukaryotes:
Life can be categorized into 3 interconnected domains:
1. Bacteria (Prokaryote): Less complex life
2. Archaea (Prokaryote)
3. Eukaryota (Eukaryote): Most complex than prokaryotes. Have nucleated cells
Evolutionary theory shows that prokaryotes developed first, followed by more advanced eukaryotes
that built off the design of prokaryotes. Microbes are microscopic organisms that can be either single or
multi-cellular. These microbes are responsible for many functions that without more complex life would
not survive.
Endosymbiont Hypothesis:
This states that eukaryotes evolved from prokaryotes, based on the similarities found between
mitochondria and bacteria. Mitochondria and chloroplasts evolved from free-living bacteria via
symbiosis within a key eukaryotic host cell to have two key differences:
- These organelles contain their own DNA
- These organelles have a distinct translation system
Two theories of mitochondrial symbiosis currently exist:
1. Archezoan Scenario: An early eukaryote cell phagocytosed an a-proteobacterium. This then led
to the evolution of the mitochondrion. This theory has fallen out of favour due to errors in the
original phylogenetic analysis.
2. Symbiogenisis Scenario: This theory states that the defining features of a eukaryotic cell
developed after the mitochondrial symbiosis. This suggests that an a-proteobacteria was
uptaken into an archaeal cell which then led to the generation of the mitochondria, followed by
the nucleus and compartmentalization of organelles.
Categorizing Organisms – Phylogeny:
While there are distinct aspects of the three domains, there is also a significant amount of gene transfer.
This, paired with horizontal gene transfer complicates the “tree of life” into more of a “web of life”. Still,
generally speaking, the more similar one organism is to another, the closer their genetic relationships
are.
Characteristics Bacteria Archaea Eukaryota
Nucleus No No Yes
RNA Polymerase 3-4 Subunits 8-12 Subunits 12-14 Subunits
Ribosomes 70S 70S 80S
Cell Wall Murein No Murein No Murein
,Where Did Viruses Come From?:
Viruses are obligate intracellular parasites and are important contributors to the web of life. Viruses are
able to carry and transfer information between all three domains of life. Viruses have varied ways of
storing genetic material and can infect many different lifeforms. When not in a living cell, viruses exist in
the form of “Virons” complete virus particles composed of three parts:
1. Genetic Material (DNA or RNA)
2. Capsid (Protein Coat)
3. Envelope (Lipid Coat found on some virons)
Origin of Viruses:
There is intense debate as to how viruses came into being, with many prevailing theories:
- Virus-First Theory: Proposes viruses are ancestral to cells. Viruses evolved from combinations of
macromolecules before the first cells appeared on earth, making them the first self-replicating
units.
- Escape Theory: Cells came before Viruses. Viruses are derived from genetic material that
escaped from cells called retrotransposons.
- Reduction Theory: Cells came before viruses. Viruses are an offshoot of cellular evolution that
became dependent on other cells for reproduction and lost their cellular elements.
The Generation and Impact of Microbial Biodiversity:
Microbes are a part of every possible niche on earth. They are capable of living in any environments and
make up a large part of the biodiversity on the planet.
Diversity Of the Human Microbiome:
The human microbiome is dominated by four phyla:
1. Actinobacteria: A group of gram-positive bacteria that are aerobic and mostly found in soil
2. Bacteroidetes: Diverse Gram-Negative phylum which can be found in all environments
3. Firmicutes: Phylum of bacteria which are gram-positive and can form endospores
4. Proteobacteria: Major Gram-Negative phylum, includes a diverse array of bacteria
The bacteria in the human microbiome are classified as either pathogenic or commensal:
- Pathogenic: Harmful bacteria that cause infection
- Non-pathogenic bacteria that have a symbiotic relationship with the host
Horizontal Gene Transfer:
HGT occurs in microbes when the genetic material of two different organisms comes into contact with
one another. This can occur in three different ways:
1. Transformation: The uptake of naked genetic material from the surrounding environment
2. Conjugation: The direct transfer of genetic material from one cell to another
3. Transduction: The process by which bacterial DNA is moved from one species to another by a
virus.
4. Transposition: The use of transposons to increase or decrease gene expression
,HGT can affect human health when typically commensal microbes acquire virulence genes that make
them more likely to infect human cells.
Relationship of Genetic Diversity to Resistance:
Antibiotic resistance genes occur naturally in microbes, but are more and more frequent due to use by
humans which creates selective pressure. This can create multi-antibiotic resistant strains that
negatively affect human health. There are many ways in which bacteria can become resistant to
antibiotics:
- Target Protection: Development of a protein that disrupts the interaction between an antibiotic
and it’s target
- Target Modification: Alters the target site of antibiotics
- Prevention of antibiotic accumulation: Increased bacterial efflux mechanisms that effectively
“bail out” the antibiotic faster than it can accumulate
- Antibiotic Detoxification: Ability to degrade the antibiotic, reducing it’s effects.
Human Influence in the Health and Environment:
Human impact such as climate change, antibiotic use, and vaccinations affect the diversity of microbes.
Module 2 - Impact of Microbial Structure on Survival:
Microbial Structures:
The more complex an organism is, the more genes it requires to store and pass on that information.
Parasitic creatures also tend to have smaller genomes than non-parasitic ones as they can use their
host’s.
Viral Structures:
They are obligate, intracellular parasites. This means they are completely reliant on their host to
reproduce. Viral genetic material enters a cell and is taken up into the nucleus. The viral genome then
codes for new viral particles called virions. These then leave the cell and hangout until they enter a new
cell and the process repeats. There are two main virus structures:
1. Nonenveloped structures: Simple viruses made up of nucleic acid and a capsid. Taken into the
cell by endocytosis.
2. Enveloped structures: The virus is coated in a lipid layer permeated with spike proteins. Inject
genetic material directly into the cell.
Bacteriophages:
Phages are a type of virus that exclusively infects bacteria. These can be either nonenveloped or
enveloped and often have a “tail” structure that facilitates binding to the host cell. The phage lifecycle is
well studied and serves as an example for other viruses:
1. A phage attaches to the surface of the bacterial cell and injects its genetic material into the
bacterium.
2. The genetic information replicates using host cell machinery
3. Host machinery make the component parts for new virions
4. Using the new component parts, new virions are created
, 5. The bacterium cell wall degrades due to the phage protein lysin, and the new phages are
released to infect new cells.
Some phages do not lyse the host cell with each infection, but instead incorporate their genetic material
with the hosts DNA. This allows newly formed cells to be infected with the phages DNA, and eventually
lyse at some point in the future. This is known as Lysogenic infection.
Bacterial Structures:
Bacteria are much more complex than viruses are. There are two main classifications of bacteria:
Gram Positive:
These bacteria stain dark purple. They have thick peptidoglycan cell walls that provide structural, but
not barrier functions. This wall is attached to the cell envelope by teichoic and lipoteichoic acid. The
space in between the wall and envelope (periplasmic space) is also much smaller than in gram negative
bacteria. Peptidoglycan is made of alternating N-acetylglucosamine (NAG), and N-acetylmuramic acid
(NAM) these two compounds form tight bonds and covalent cross links. Because of the strong bonding,
the PG structure must be cleaved open by enzymes to add new subunits.
Gram Negative:
Stain light red. The periplasmic space on these cells is much larger than in gram-positive bacteria. They
also have an outer membrane that contains porins, lipoproteins and liposaccharides (endotoxin). The
liposaccharides produce a highly reactive immune response and are composed of three parts:
1. O-antigen: repeating polysaccharide chain that is external to the cell, allowing it to interact with
immune cells
2. Core: Formed by an array of sugars including ketodeoxyoctonate (KDO). It is external, but close
to the membrane and cross-links with other membrane components
3. Lipid A: anchors the molecule to the OM
Cytoplasmic Membrane:
The cytoplasmic membrane of bacterial cells is a fluid mosaic of phospholipids. They typically lack
steroid-containing lipids like cholesterol but contain sterol-like compounds called hopanoids. Bacteria
gain nutrients through passive diffusion, facilitated diffusion, and primary and secondary active
transport. They also require iron, which is typically found in transferrin proteins in a host. The iron in this
protein can be stripped off by bacteria. Some bacteria also have high affinity scavenger proteins called
siderophores that can grab iron and bring it back to the cell.
Endospores:
These are small forms that allow bacteria to survive extended periods of low nutrition or water. The
creation of an endospore is complex:
1. Vegetative bacterium begins to divide
2. Asymmetric division of the cell leads to the creation of a mother cell and a forespore.
3. Peptidoglycan barrier between the two is degraded, the forespore enters the mother cell.
4. The cortex, a layer of peptidoglycan is formed
5. Coat synthesis begins. The proteins provide strong resistance to degradation from chemicals and
enzymes.
6. Coat synthesis is completed, increasing refractility and heat resistance
, 7. Lysis of mother cell releases the endospore.
Extracellular Structures:
Many bacteria use them to provide protection from the immune system:
- Capsules: A polysaccharide layer firmly attached to a single cell
- Slime: A polysaccharide material that is diffuse and easily removed
- Biofilm: A polysaccharide structure that contains multiple organisms. Important for colonization.
Biofilms can harbour very high concentrations of bacteria and are therefore the primary sites for deeper
tissue infections.
Proteinaceous Structures:
The Surface layer (s-layer) is a glycoprotein component of the cell envelope. They are 2-D crystalline
arrays that coat the entire cell. They are made of one or more S-layer proteins (SLP’s). S-layers are found
on the surface of bacteria and archaea.
Motility Structures:
Microbes other than viruses have developed methods of moving around their environment.
- Flagella: Tail-like structures used for moving around liquid environments
- Pili/fimbriae: Type IV pili are used to move around on solid surfaces by twitching. Sex pili can
transmit genetic information via conjunction
The number and location of flagella are distinctive for different types of bacteria:
- Peritrichous: Flagella surround entirety of cell
- Lophotrichous: Tufts of flagella at one end
- Single/Polar: Single flagellum
- Bipolar: One flagellum at each end of the cell.
Archaeal Structures:
Similar to bacteria, archaea have slight differences in the arrangement of their cell envelopes and in
their motility structures. They are well adapted to adhering to structures and their appendages show
this.
Archaeal membranes have various compositions. Most have an S-layer, but may also include other
components such as polysaccharides, protein sheaths, and pseudomurein, which has a similar function
to the peptidoglycan layer in bacteria. Some archaea have a lipid monolayer rather than a bilayer. The
lipids used by archaea are very heat and chemical resistant, which allows them to be extremophiles.
Archaea show a variety of traits associated with both bacteria and eukaryota. They have different rRNA
from bacteria and a different arrangement of ribosomes that make them immune to some antibiotics.
They also have an archaeal chromosome like a eukaryotic nucleosome.
Movement Structures:
Archaea use a structure called archaella to move around. It rotates like a flagellum but can also adhere
to surfaces like type IV pili and are similarly constructed.
,Eukaryotic Microbe Structures:
Eukaryotes demonstrate immense diversity. Their main similarity is their compartmentalisation of
specific processes into organelles. The eukaryotic cytoskeleton is formed of three components:
1. Actin: allows for cellular movement
2. Intermediate filaments: Provide structure to the cell
3. Microtubules: Creates the spindle apparatus during mitosis. Also directs movements of
organelles and vesicles.
Eukaryotic flagella are more complex and wave rather than spin. They also use cilia which allow them to
move themselves or surrounding objects.
Structural Targets for Therapy, Immunity, and Phage Infection:
Preventing Viral Infection at Initial Interaction:
Viruses must bind to a host to reproduce. These interaction sites are vital to viral infection and are thus
a good target to prevent viral entry.
HIV:
HIV initially interacts with host cells in one of two ways:
1. Non-specifically interacts with negatively charged proteins on the host cell surface
2. Specifically interacts with host receptor proteins such as CD4 on immune cells.
The former is thought to pull the virus in close enough so that the latter can interact with the specific
receptors on the cells surface. The HIV Env Spikes are made up of GP41 and GP120. GP120 binds to CD4.
This causes a conformational change that allows GP41 to insert into the cell membrane. Eventually, this
process allows the two membranes to fuse together, depositing the viral genetic material inside the cell.
Adenoviruses:
These have large double stranded DNA genomes and do not possess an envelope. The protein spikes on
adenoviruses play a key role in their initial interaction with host cells. The spikes bind to coxsackievirus
and adenovirus receptors (CAR’s). The virus particles are then taken up by endocytosis. Once
internalized, the genetic material is released directly into the cell. CAR’s are found on most cell types,
allowing adenoviruses to cause many different illnesses.
The Role of Pili in Infections:
Pili are essential for the formation of biofilms. Without them, bacteria could not initially stick to
surfaces. If biofilm cannot form, it becomes much easier for the immune system to attack and destroy
the bacterium. Pili are also used by phages to infect bacteria, they attach to the pili and are brought to
the cell membrane when they retract. Phages could potentially be used as treatment for bacterial
infections in this way. The phage would cause cell lysis and would effectively take out the pathogen.
Once there is no more bacteria to infect, the phage would be cleared out by the immune system without
causing harm.
Peptidoglycan as an Antimicrobial Target:
Because human cells do not contain peptidoglycan, it makes it a perfect target for antibiotics, as they
should have no effect on human cells.
,Beta-lactams are a group of antibiotics including penicillin that contain a b-lactam ring in their structure.
These antibiotics look like amino acids used to make peptidoglycan. They therefore interfere with the
enzymes that form cross-links between amino acids in different glycan chains. Of the beta-lactams,
penicillin’s and cephems are the most used.
Immune Response to Bacteria:
The innate immune system triggers a non-specific, fast acting response while the adaptive immune
system begins preparing to specifically target the pathogen. In extracellular bacterial infections, the
neutrophils can directly attack the pathogen without waiting for the adaptive immune system. With
intracellular infections. The body must produce antibodies specifically designed to locate and destroy
the pathogen.
The immune system detects invaders by picking up proteins used for essential components like flagella.
The benefits of having these far outweigh the cost so pathogens continue to have them despite
triggering the immune system. Some have evolved ways to get around this. Salmonella for example, can
build its flagella out of a different protein called FliJB instead of FLiC to avoid detection by an immune
system with FliC antibodies.
Module 3 – Microbial Metabolism and Environmental
Influences:
Metabolic Attributes of Microbes:
General Introduction to Microbial Growth:
Like all living organisms, microbes require nutrients to generate energy and produce the
macromolecules used for new cell components.
Binary Fission:
Bacterial populations grow by binary fission, which is like mitosis. Binary fission happens at a much
slower rate when nutrient levels are low. Bacteria exploit osmotic pressure to expand their cell wall
during binary fission
Bacterial Aging:
Bacteria do undergo senescence just like higher organisms. At each binary event, one pole of the
bacteria is made of older material while the other is mostly new material. Damaged DNA also tends to
gather at the older pole. This leads to the older cell focusing more on repair than growth, which leads to
fewer and fewer divisions.
Eating, Processing, and Elimination:
Bacteria use several transmembrane uptake systems to take in nutrients which can then be used by
anabolism to create new components such as proteins. They can also break down molecules to obtain
energy using catabolism.
Physical Requirements for Growth:
Temperature, pH, and hydration can all have an affect on microbial metabolism. If the environment is to
far from what the bacteria is used to, it’s enzymes and proteins can become denatured and will cease to
function.
Oxygen Concentration:
, Bacteria have evolved to require specific levels of oxygen in their environment:
- Obligate Aerobe: Undergo aerobic respiration
- Facultative Aerobe: Grow better in the presence of oxygen but do not require it for growth.
- Aerotolerant Anaerobe: Can tolerate oxygen, but do not use it.
- Strict Anaerobe: Oxygen is toxic, and they produce energy by fermentation
- Microaerophiles: Require oxygen concentrations between 2-10% but are damaged by levels
above 20%.
Microbial Metabolism:
Required Nutrients:
Some nutrients required for growth cannot be synthesized by microbes. These are instead obtained
from the environment to support energy production and cellular biosynthesis. The most important
components are carbon and nitrogen, while hydrogen, vitamins, and other trace elements are also
important.
Metabolic Groupings:
Organisms can be grouped by how they obtain carbon, energy, and electrons.
Energy Source:
- Chemotrophic: Obtain energy from external chemical compounds
- Phototrophic: Obtain energy from sunlight
Carbon Source:
- Autotrophic: Obtain carbon from carbon dioxide
- Heterotrophic: Obtain carbon from other organisms
- Mixotrophic: Can use both organic compounds and carbon dioxide
Electron Source:
- Lithotrophic: Obtain electrons from inorganic compounds
- Organotrophic: Obtain electrons from organic compounds
Most pathogenic bacteria are chemoautotrophs as they use the natural compounds found within the
body to facilitate their growth.
Adaptive Metabolism in Bacterial Populations:
Infectious bacteria must constantly adapt to the environment of their host and alter their biological
pathways accordingly in order to ensure the synthesis of needed components.
Persister Cells:
These are dormant antibiotic-resistant cells that escape the effects of antibiotics without undergoing
any genetic changes. They do this by radically changing their antibiotic pathways so that they are just
making enough ATP to survive. Because there is no metabolic activity, the antibiotics have nothing to
target. Once the antibiotic has left the system, they revert to their normal metabolism and began
reproducing. This is different from resistant bacteria which continue growing in the presence of
antibiotics.
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