Lecture 1:

 What is a microbe?
o Very small and have to be grown in a medium
o Examples of exceptions
 Fungi
 Some groups when they produce their fruiting bodies / sexual structures, they
form mushrooms that are visible (with naked eye) although they are microbes
o Acellular
 Neither prokaryotic nor eukaryotic
 Virus and prions are examples
 Plasmids are acellular agents that can move
o Can’t grow on their own
o Microorganisms don’t generally grow by getting bigger but generally grow in populations
(increasing their numbers)
 Microorganism in the three domains of life
o All identification of all microbes is unclear (there is a cluster of microorganisms that aren’t
identified)
o Bacteria are often used interchangeably with eubacteria
 Prokaryotic microbes
o Grown in medium (solid)
 Agar plate which has nutrients in the medium and blood agar to solidify
 Blood agar to show the morphology of the eubacteria
o The morphology of the colonies is different
 A colony isn’t a single entity (millions of cells)
o Liquid culture
 Measuring turbidity instead of dry counting for colony count
o Colonies can have different pigments
 Observation that can be used to identify the bacteria
o Common morphology amongst eubacteria (general shapes)
 Streptococcus
 Found in clusters and also in chains
 Spherical (characteristic of cocci)
 Bacilli (rod shaped)
 Different variations
o Can be curved shaped or comma shaped
 Spiral bacteria
 Focus on bacilli and spiral shaped because the others are usually pathogens
(including spiral bacteria)
o Level 1 microbiology safety labs
 Different cell shape
o Different ways in which the microbes can be organized
 Individually, in chains, in clusters or tetrads
 Bacteria on a plate of growth medium/ morphology of colonies change/colour
o An isolated colony has risen from a single colony
 2 colonies touching = don’t know if they have risen from more than one starting cell
  That’s why you must isolate colonies when plating them so that you can be
sure that the cells are separated enough when they grow
o Sterilize the loop and streak each time (but sterilize each time for different colonies)
 Isolates the colonies
 Then able to pick an isolated colony for further research
o Two ways to get isolated colonies
 Streak plating and spread plating
 Cyanobacteria (within group of eubacteria)
o Photosynthetic bacteria (carry photosynthesis in the same way as plants)
o Evolved out of anaerobic photosynthetic bacteria
 Prospered and started the process of oxygenating the world
 Using CO2 as a carbon source and by product is oxygen
o Come in various different shapes
o Unique cell types in amongst their group as indicated by the heterocyst
 Not only able to perform photosynthesis but have unique cells that are good at
nitrogen utilization
 Able to take nitrogen in different forms and convert it for plant usage
o Largest population of nitrogen is in form of nitrogen gas which is
converted by cyanobacteria
 Ammonia and nitrate can be used by plants
 Archaebacteria
o Share similar qualities as eubacteria
 Prokaryotic, have no membrane-bound nucleus, have no true membrane bound
organelles (except for ribosomes)
o However, differ in the way they make their cell well
o The descriptor used called “extreme” has a classification problem because extreme
environment differs person to person
 For example
 Many thermophile bacteria can grow in 65-70 C which can be considered
“extreme”
o Considered growing in extreme conditions means their cell walls are different due to the vast
temperature difference (live in extreme temperatures and high methane conditions)
 Their membranes are made different and the way their proteins are made differ
 Eukaryotic microbes
o Fungi = heterotrophic (not equivalent to algae)
 Example
 In colonies, they have aerial hyphae that give the surface a fuzzy appearance
 The moulds and yeasts are able to make use of organic material in manner that higher
eukaryotes can’t and carry out detoxification of the environment
 Top 5 acquired infections in hospitals
 Al least 2 are fungal infections
 There are 2 classification of fungi pathogens
 Primary pathogens
o Can make everybody sick
 Mortality and mobility of these fungi are relatively low
  Not good at killing people
 Another group of fungi
o Good at making immunocompromised people very sick
 Mortality and mobility of these fungi are very high
o Immune system compromised due to autoimmune diseases and the
accommodating treatment as well as steroid treatment for
transplantations
o Fungi (like bacteria) are good at developing antimicrobial resistance to combat medications
 Protozoa
o Diatoms surprisingly have a cell wall
o Heterotrophic
o Often have a flagella because they are mostly growing in liquid environment
 Swamps and lakes
 Concept of microbial communities
o Community can be composed of just eubacteria, or bacteria and fungi or bacteria, fungi, and
protozoa
o Important to understand that they organize and create complex communities
 Communicate together and grow differently
 Create extracellular material that cause foreign and antimicrobial agents from
working
o Example
 Communities of cyanobacteria with algae
 Cyanobacteria (known as blue-green algae) aren’t algae but prokaryotic
organisms
 Human oral bacterial community
o Found in mouth and teeth
 Ability to fill holes; cavities
 Play off the glucose that is consumed
o Sugarless gum work because they aren’t ready form glucose
 Stops them from forming capsules and other polymetric substances that they can
secrete
 Less likely to form communities that can stick to the teeth
 Sites
o Common site is the catheter placed by the hospital
 Is contaminated by a single bacterial cell that overtime create a huge community of
bacteria and forming biofilms
 Catheter is siting close to blood stream; thus able to move around = death
eventually
o Other important sites are mouth, artificial hip and knee transplants
 Often time when you have an infection from the artificial hip, they have to clean the
bacterial community by taking out the artificial hip, so the person is left with open
wound for the cleaning up process
 After the artificial hip is inputted back
 Living microbes
o Do everything that living cells do
  They can compartmentalize and carry out metabolism
 Although don’t have distinct organelles, they have distinct areas that are
responsible of doing different functions
 Ability to grow and divide
 Increase cell number
 Undergo changes in their genetic material overtime (evolve)
 Many microorganisms have ability to self-propulsion
 Some can differentiate (not really simple organisms)
 Example
o Form endospores that allow bacteria to withstand variant climates
and able to stay dormant
 Then germinate when conditions resume
 Ability to communicate
 Release material outside the cell to communicate with other cells
 Catalytic and genetic functions of cells
o Do replication, transcription, and translation to grow
 Same thing as humans
o There is nothing you are doing that they aren’t doing to grow
 Non-cellular (acellular) microbes
o Plasmids and transposons carry extra DNA in a cell
 Important for bacteria to share genetic material with other cells
 Relative position of evolution of the 6 kingdoms / 3 domains
o In the same domain of plants and animals are fungi
 Microorganisms are within each domain
 What does this dendrogram indicate about the bacterial?
o Line of evolution from eubacteria are predicted to come from the same evolution as
archaebacteria
 Overview of micro-organisms contribution
o Ability to breaking down grass and poor quality of straw are done by microorganisms that sit
in the gut of cows
 Same with human gut bacteria helping with digesting food in the intestine
o Break down of toxic material and radioactive substances are done by microorganisms
o A lot of food preservations make use of some products of microorganisms
 Food additives are products of microorganisms
 The Carbon Cycle
o Decomposed nitrogen from animal dying
 Microorganisms key in breaking down the nitrogen (usable form) into the soil for the
plant to use
 Nitrogen cycle
o N2 fixation bacteria (as well as fungi)
 Specifically help the plant (critical for plant survival)
 Often in symbiotic
 Sulphur cycle
o Sulfur reduction (not necessarily good in certain environment)
o A lot of byproducts aren’t beneficial for organism
 Used in bioremediation
o Important in bioremediation of sewage
 Before it ends up as chemical treatment
 Bioremediation by microorganisms
o Microorganisms can eat oil (in oil spills) using their plasmas
 Have genes that can do it
 Constructed wetland for wastewater treatment
o Wetlands are critical to helping materials from getting into lakes
 Plants and bacteria pull out the toxic materials
 Make the lake cleaner
o Plants are good at taking out the phosphates and nitrates out of the water
 Stopping algal blooms (love phosphates and nitrates)
 Healthy balance of green and blue algae as well as water
o Not dangerous
o Essentially, plants, bacteria and fungi can be to create wetland wastewater treatment process
 Bacteria/human interaction
o Human is actually community of organisms (not a single entity)
 Eukaryotes and prokaryotes
 Required for survival
o Gut’s ability to grow appropriate microorganisms is the main important structure for immune
system to work well
o Symbiotic organisms within the human gut = human gut microbiome
 Include viruses, protists, and bacteria
 Have bacteriophages and viruses within the body
o Have certain bacteria in the gut microbiome
 Need to have some important ones to avoid certain diseases
 But individual gut microbiome can differ with different bacteria
o Don’t know the exact # of bacteria within us
 But there is a lot of them
 Rely on them for survival and health
o Metagenomics; use of sequencing to know what microorganisms are present within the gut
 Timescale Diagram
o 100x objective + 10x Ocular lens = 1000 fold magnification
 Must use oil to reduce the refraction of the light
 Usually, 100x with oil emergent lens is needed
o Transmission and electron microscope is the modern technology
 Antony van Leeuwenhoek
o Developed the first microscope (simplistic)
 No concept of sanitization and microorganisms prior
 Plagues = brought by gods
 Aminalcules = modern microorganisms
o Renewed 2 controversies
 Where did microorganisms come from?
 Believed in spontaneous generation
o There was a formation of living organism from non-living materials
  What is the true cause of a contagious disease?
 Didn’t believe in microorganisms (things that they couldn’t see)
 Didn’t believe either in the contagious (infectious and transmissible) diseases
o Didn’t accept that notion at all
 Some of the researchers that attempted to deal with the 2 major controversies
o Spallanzani
 Took broth that looked clear and boiled it over the flame
 A lot of the micrograms were killed
o We now know that
 2 groups
 Put a cap vs cap off (left opened)
o The cap off
 The liquid was turbid after the initial boiling and smelled
bad (characteristics of bacterial growth)
o Cap on
 Liquid (broth) was clear and didn’t smell
 Microorganisms in the air got into the jar
o Indicated that growth was occurring
 Smell from the microorganisms
 Experiment conclusions
 Turbidity was indication of bacterial growth occurring
 The smell is the breakdown of products in the media; happens with bacterial
growth
 With microscope, can see microorganisms within the media
 Conclusions of Spallanzani’s experiments
o To be turbid needs to be 10 million cells
o Evidence that spontaneous generation is wrong (didn’t evolve suddenly)
 The microbial cells seen in the unboiled broth arose from pre-existing microbial cells
in the broth
 Microorganisms were always there, just not in high numbers
o Also showed that you can get rid of microorganisms by boiling
 Concept of canning (storage of food)
 Boil the jar and then capping the food stuff inside; keeps it preserved from
microorganisms until cap is opened
o Sealed off microorganisms
 Now can move further and migration because it allowed
access to fresh food more (storage was easier)
 More conquering of civilisations
 Schroder and von Dusch
o Made it better by using a cotton plug (instead of a solid plug) because most bacteria are
aerobes (require air)
 Now plugging the flask will eventually use up the air needed, and they weren’t going
to grow as well
o Same observation but used a cotton plug
 Same conclusion found
 o The use of cotton plug blocked the microbes moving in and allows it to be filtered out of the
air
o Applications
 Can’t boil glucose (breakdown and caramelize)
 Instead use a filter to remove the bacteria
 Louis Pasteur
o Father of microbiology
o Asked to be a in wine business because he studied the role of silkworm diseases
 Figured out that the difference between pasteurization and sterilization
o Key in development of vaccine
 Nowadays, we introduce the individual to the mRNA of the microorganism which is
delivered by a vesicle that can be integrated to make proteins
 Ultimately, delivering the protein that the immune system responds to
 Pasteur’s experiment
o Used a neck flask that wasn’t blocked
 Took a broth infusion and boiled it
 As long as the swan neck stayed upright, it was not contaminated by
microorganisms
o There was free passage of air but anytime the microorganisms from
the air passed thru, they were stuck in the bend (couldn’t make the
turn)
 If tipped to the side, the bend was in a different orientation which allowed the
bacteria in the air to come into the broth
o In another bend orientation, the microorganism growth happened
 Pasteur's achievements continued:
o Nowadays, we use an autoclave that uses a hot steam in high pressure and speed
 Sterilization
o Use of chlorine is situational
 It stops bacteria from growing (if that’s what you want)
o 15 minutes is not absolute
 As the volume increase, so does the time for sterilization
Lecture 2:

 Culture and pure culture techniques

o Became clear that they needed a way that properly isolate individual representation of
bacteria
 Therefore, required the growth of culture
 In labs, given a culture inside a nutrient agar slant (ideal temperature) to take
samples
o Ideal incubation (different growth rate for different bacteria)
o Preparation of a pure culture
 First must streak for isolated colonies, and then pick the single colony of that type of
organism
 After that, must streak it onto nutrient agar slant
o Now know that its only that specific organisms that will grow inside
 o How do we stop contamination of our culture when we are working with other bacteria?
 Use sterilization techniques and inoculation (flaming the loop but waiting enough
until it cools to not kill the bacteria)
 The germ theory of “infectious” disease
o Neisseria (genus) = diplococci (has one flat side with 2 cocci together)
o Bacillus (genus) = rod-shaped
 The circles seen in the images are the endospores forming in the stained areas
o Vibrio (genus) = comma-shaped
 Microbe Hunting
o Figured out different types of microbiological mediums
 Because not all bacteria grow equally well in all medium
 Fastidious bacteria; require higher need for specific amino acids and
nutrients
o Require specific medium
 Unlike simple bacteria that require normal nutrients and
amino acids
o Petri dish (for plating the bacteria)
 Lots of surface area = able to see a nice spread of the organism and the isolated
colony
o Staining techniques
 Simple stain = stains all the bacteria
 Gram’s stain
 Differentiates the bacteria based on their types of cell wall
 Acid fast
 Only stains certain types of cell walls
 Koch’s postulates
o Susceptible animal = animal that hasn’t yet been exposed to the disease (not yet affected)
o Rule 4
 Able to then, isolate the same bacteria from the susceptible individual and get the
same organism
 Ability to know which organism is causing the disease
o Relies on the important concept; they must be isolated and grown in culture
 Some microorganisms can only grow in their hosts (can’t grow in culture)
 Now use PCR and primers at times
o To look at the organism present
o Diagram
 (1) Start with the disease infected animal and a healthy animal
 (2) Only the disease infected animal has the suspected pathogen
 (3) Must streak for colonies and get the colony that only contains the bacteria likely
to cause the disease
 Stain to make sure it’s only one type of bacteria
 (4) Inoculate the bacteria into the susceptible animal
 Must re-identify the same bacteria as b4
 Some examples of infectious diseases and causative agents identified soon after Koch’s postulates
o Typhoid fever, major problem in overcrowded cities (historically)
 o Tuberculosis, is now very resistance to many modern medications and drugs
 Problematic
o Tetani
 Gram positive anaerobic rod
 Tetanus shot every 10 years
 Likes to grow in deep roots

o Pestis
 Not caused by rats but the bacteria that used the rats as hosts
 Koch’s postulates are still used in the identification of the causes of disease: Emerging and remerging
diseases
o Earlier versions of Covid-19
 MERS
 SARS; major house of disease in Toronto, traveling from Hong Kong
 Very severe so not able to be transmitted as easily; damage was done in
hospitals only
o Not able to spread around the community
 Original version
o Lyme disease; transmitted by ticks
 Problematic in southern Ontario
 Becomes more problematic as climate change occurs; increasing ticks niches (as they
move upwards)
 Due to increasing temperature
o Legionnaires disease
 Happened in legionnaires meeting
 Represents the first leading emerging pathogens that exploits man-made niches
 Natural bacteria that happened in lakes
o AC collecting water, collects legionnaires which like to grow in the
AC units
 Result of man made niches
o Difficile
 All of us have it but it is controlled by our natural floral bacteria
 But when sick, the prescribed antibiotics wipe out all the bacteria within us
o Also, causing the beneficial floral bacteria to die
 Increasing the population of difficile bacteria
 Diagram
 Not active in the gut (in a spore)
o It’s a gram positive anaerobic rod and the forming of endospore is a
dormant form of the bacteria
 But due to the change in makeup of the gut microbiome, it
starts to germinate (starting to form spores)
 Dysbiosis happens; outgrowth of spores
o The difficile is taking over; makes u very ill
 The morbidity and mortality is very
high
  Now, we must reconstitute the gut bacteria; get all the good bacteria back
(need the appropriate diet which takes a long time and is hard)
o Instead use fecal microbiota transplantation
 Give healthy feces from healthy people (remove the
bacteria) and put it back inside into the infected individuals
 Able to now reconstitute the microbiota
 If left untreated, it damages membrane of the gut that are responsible for the
absorption of nutrients and supporting of the immune system is hindered
o Develop a form of colitis
 Serious and difficult disease of the gut
 Example of irritable bowel disease
 Most are predisposed and predetermined to colitis
o There are diseases that are now resistant to antibiotics
o Streptococcus
 All of us have streptococcus pyogenes and taken care of by normal floral bacteria
within the gut (and immune system)
 But with the number of respiratory infections around like the COVID, the
immune system is dampened; allowing its growth
o Tuberculosis
 Common wherever tuberculosis is endemic
 In order to clear it, it requires expensive drugs and many months
 Even with it, people are multi-drug resistant to the antibiotics and infected
people live closely to other people
o 2 scenarios that are not good for the treatment
 Always must complete the treatment plan correctly and in timely fashion
o If not followed thru, the bacteria will be exposed to the antibiotic and
will develop antibiotic resistance
 Therefore, the next time it flares up, it will be already
resistant to it, so the drugs won’t be effective
o VRE
 Tested if you have and tested when leaving to make sure you don’t have it
 In hospitals
o MRSA
 Gram positive cocci
 Methicillin-resistant
 One of the antibiotics developed for bacteria that are resistant to penicillin,
ampicillin and etc.
o ESBLs
 Some bacteria make beta lactamases which means antibiotics won’t affect them
 Now only antibiotics from the carbanenem family (from a beta-lactamase family) are
effective
o Candidemia
 Fungi are becoming more problematic as they are developing resistance to anti-
fungal drugs
 Becoming hospital acquired infections
 Flu
 o Why is flu vaccine needed every year?
 Covid has subtypes (small changes)
 The first vaccine still help protect you from the new variants and subtypes of
COVID
 But with flu, it changes many genetic materials with other influenza viruses and have
many different diverse subtypes
 Now exposed to a very different virus each year
 Need many new vaccine every year
 Investigate different mixes of H (hemoglobin) and N (neuraminidase) for the
vaccine
o These are surface proteins onto the coat of the virus
o Worried about birds because the different viruses that affect birds, humans and pigs can
combine
 They can communicate together
 Therefore, when a bird is infected with one type of influenza and gets
exposed to another influenza type, it can recombine together to create a new
virus
o But fortunately, the infection from birds is hard to spread from
human to human
o H1N1
 Humans were common target (mix of bird/swine type and human type virus)
 Young healthy adults were the main targets for virus
 As well as elderly but not as negatively impacted because they were exposed
to Spanish flu so had built in protection
o The Spanish flu was similar in nature to the H1N1
 Graphs
o In 1900, major cause of death were microbial infections and less of human cause
o Today, its flipped; bacteria infections are not major cause of death and human caused
incidents are
 However, as we lose antimicrobial agents for microbial infections as they become
more resistant, it could change again
 Microbial infections can be the leading cause of death
 Chronological discoveries
o In 1940s, DNA was found to be genetic material and streptomycin was developed as one of
the first antibiotics
 In molecular biology
 Trying to understand the genetic coding
o Now in era of cellular microbiology on top of the molecular microbiology, genomics, and
proteomics
 What are microorganisms interacting with in nature that is helpful to us?
 Understanding what they are interacting with the host
 How are they getting into the host and the interaction with the immune
system?
 Current hypotheses of the origins of cells
o Living cells didn’t spontaneously appear
 No spontaneous generation on planet Earth
 o In first evolution of prokaryotes, they were anaerobic and heterotrophic (characteristic of
prokaryotes) that still exist today in prokaryotes
 They share these same characteristics
o However, the first organism to exist were not DNA-based organism but instead were RNA
based organism
 DNA-based organism evolved from RNA-based organism
 RNA can code for new proteins and act as enzymes
 Current theories
o Between 4 to 3.8 bya, it was first thought to be when the first cell-like systems evolved
 They were very different from now
 But at some point, when the first universal ancestor was developed, the
similarities of the present day organisms became more consistent with the
first universal DNA-based ancestor
o From research, know prokaryotic-like organisms lived for 3.7-.3.8 bya
 Based on sedimentary rocks called stromatolites (which lived 3.8 bya)
 Estimate of when different cell types and organisms are though to have evolved
o Starting with the lower eubacteria like the protists and fungi, you notice that fungi are more
animal-like than plant-like
 As can be seen from the evolutionary tree
o Prokaryotes shaped the evolution within the planet
o When bacteria first developed anaerobic photosynthesis as they were anaerobic, they needed
only a slight change in their Calvin cycle so that ultimately the product of the Calvin cycle
was oxygen
 Leading to oxygenation of the world with evolution of the cyanobacteria
 Cyanobacteria sits between anaerobic and aerobic world
o Now cyanobacteria can live in both worlds and still can perform
photosynthesis
 Timeline scale
o Just as we were able to tear down oxygen, oxygenic photosynthesis developed as a result of
the cyanobacteria
 Even though, plants were critical in providing oxygen but oxygen was really just a
byproduct of metabolic processes
 The cyanobacteria were really the ones that allowed the evolution to progress
o Starting the oxygenation of the world
 From anoxic world (oxygen wasn’t available in a form that
can be used) into an oxygenic world
 Changed the Earth to becoming a reducing
environment rather than the environment it had in
earlier development
 What happened in the first billion years on earth?
o At some point, a self duplicating systems evolved that had a living-like characteristic and was
thought to evolve by prebiotic processes
 Wasn’t carrying metabolic processes but using chemical reactions that were occurring
in absence of organisms
 Remember any reaction that can take place within a living organism can be
made chemically without enzymes)
 o Thus, it could make small amounts of amino acids
o However, the Earth could only make small amino acids and proteins in limited quantities
which the organisms will use up (rather fast)
 Therefore, these organisms must develop the metabolic pathways that allow them to
make their own amino acids, nucleic acids and etc.
 Thus, early organisms utilized chemical reactions rather than biological
processes (at first)
 The evolution of the cengenote or universal ancestor:
o Random abiogenic chemical reactions came together on certain surfaces (over thousands of
years) produced the building blocks of the first organism
 But remember, they were accumulating with absence of any users and under anoxic
conditions (no oxygen available)
o With the concentrated organic and inorganic substances, there were interactions at a much
higher rate
o Initial reaction interactions were in hot sulfur rich environment (now found in specific
environment; where archaebacteria inhabit and grow now)
 These microenvironment proposed to give rise to RNA
 Only molecule that is able to and capable of self-duplication (whereas
enzymic reaction isn’t)
o First cell like systems were RNA based organisms
 Some theories:
o Again, not spontaneously occurring
 Different reactions occurred in different places on the planet
o Tested in experiment
 Taking an RNA and forming a membrane around it whilst giving it the building
blocks (amino acids, etc.)
 It can survive
 Therefore, in order to create a self-duplicating organism, it needs lipophosphate
membrane around RNA
 Allowing potential cell-like systems
o Sophisticated prokaryotes (those that can perform photosynthesis)
 Fossils resembling present day cyanobacteria are from 3.1 bya
 Diagram
o Chemical reactions taking place in a hot hypothermal vent in oceans
 Prebiotic chemistry leading to RNA life
o Mounds are being created where RNA can make more RNA and encode for genome and
proteins
o Eventually, there were set of cell-like organism that made DNA instead of RNA
 Those organisms were better at surviving
 RNA already existed and DNA was a copy of that RNA
o But DNA was more stable than RNA
 Tends to not be easily degraded
 Thus, the world switched to a more predominately DNA based environment
 Led to the first universal ancestor which then led to diversity of organism and
development of cell membrane (& cell walls)
 As well as diversification of habitats
  Allowing early bacteria and archaebacteria
 Diagram
o The DNA replaced the RNA that was sitting in a lipophosphate membrane and DNA
ultimately led to development of organisms
 (1) RNA self-duplicated or replicated which becomes encased in membrane
 (2) RNA makes proteins that carry out catalytic functions
 But this won’t allow for an efficient organism due to the limited catalytic
ability caused by RNA
o As RNA is instable in the genome
 (3) Ultimately some organisms evolved into DNA-based systems
 Eventually becoming universal ancestor
o Replacing the concept of RNA being catalytic and coding genome
 Instead, DNA -> RNA -> Protein (central dogma)
 The first billion years continued
o Cell systems did in fact evolve from non-living materials but based on the environment the
planet was left upon as it was created
 In hot thermal vents and sulfur events (etc.)
o This was able to take place because chemical reactions occurred over time in the absence of
users whereby there were almost no systems that could use up the accumulating chemically
created materials
 A proposed timeline
o The anaerobic photosynthetic autotrophic ultimately evolved to generate the aerobic
photosynthetic autotrophs
 Of course, ultimately those autotrophs needed to develop aerobic heterotrophs to
support the catalytic ability of aerobic heterotrophs
o Once that took place, there were non-photosynthetic aerobic organisms that were autotrophic
but not carrying out photosynthetic
 Instead, where chemolithotrophs
o Again, the development of aerobic photosynthetic autotrophs led to oxygenation of the world
 Once oxygen started to form because of aerobic photosynthesis, it led to oxygen
revolution
 Leading to ozone layer formation
o Ozone layer formation protects the sun ray’s damage; meaning
reducing the amount of mutations that can occur
 Mutation rate of organisms dropped
o Nowadays, ozone layer is decreasing in size = increase in mutation
 Skin disease on the rise
 Characteristics of the Universal ancestor (cenancestor)
o Again, anaerobic because the world was anoxic
o Anaerobic doesn’t mean it can’t use oxygen for metabolism but rather oxygen is toxic
 It kills the anaerobic organisms
 Not evolved the important enzymes that can allow living in oxygenated
world
o Metabolism of oxygen creates ROS (reactive oxygen species) which
damages cells
 Need enzymes (superoxide dismutase or catalase)
 o Characteristics of todays bacteria are primarily eubacteria
 Archaebacteria have some of these characteristics but also have characteristics that
are for bacteria that live in extreme environment
o The majority of bacteria today is aerobic (not anaerobic)
 Current day prokaryotes
o Eubacteria also be in between aerobic and anaerobic
 Microaerophilic
 Likes only very little oxygen
 Aerotolerant
 Tolerate oxygen but don’t really need it
o Don’t die of it tho
o Remember, the non-photosynthetic, heterotrophic and anaerobic eubacteria have evolved b4
the aerobic photosynthetic bacteria
o Archaebacteria evolution (splitting) is unclear
 Split immediately or archaebacteria split off the eubacteria???
o Cyanobacteria
 Not really algae just named that way
 They are prokaryotic organism that carry out anaerobic photosynthesis (in
addition to aerobic photosynthesis)
 Can be aerobic or anaerobic depending on conditions
 Also have the ability to fix nitrogen
 Common features of modern prokaryotes
o Shapes likely evolved from different sets of genes that led to different kinds of cell division
 Characteristic of specific genus
 Coccus can’t become rod or spirillum (vice versa)
o E.coli
 Bullet shaped; coccus and bacillus (coccobacillus)
o Can have bacteria that undergo a change in morphology
 From growing as single rods or chains of rods to filaments (as if there was no cell
wall divisions between them)
 Key stains
o Differential stain is used to differentiate different types of bacteria
 Gram stain
 Differentiates gram positive and negative (major types of eubacteria)
o Based on their characteristics of their cell walls, they are stained
differently
 Image
o Gram negatives are the reds that take on the secondary dye (safranin)
and gram positives are the dark ones (crystal violet)
 Acid fast
 Most bacteria that are acid fast are pathogens
 Acid fast bacteria are a subset of bacteria that have a very unique cell wall
which have a high liquid content called mycolic acid
o Makes them resistant to simple gram stain
 Therefore, use phenol and heat to dry the stain
  Then use a more robust decolorizer
 Use acid alcohol in acid fast but alcohol in gram
stain to remove the stain more readily
 Staining abnormalities
o Sometimes, stain start to precipitate in the bottle (see uniform dots in the microscope =
problem with stain)
 They crystallized (because the dye was concentrated)
 The staining bottle must be changed
 Cell may have characteristics structures
o Negative stain (stains the background)
 True indication of size
 Heat fixing shrinks the cells (not true size)
o Can see the capsule by using capsule stain (culmination of negative stain and stain that stains
the bacteria)
 Leaves the capsule unstained
o Capsule
 Capsule is a polysaccharide; carbohydrate (provides ability for bacteria to attach to
surfaces)
 Good barrier for antimicrobials
o Sugarless gum works because it is a form of sugar that bacteria (or
you) can’t use so doesn’t form capsule that stick to teeth; not able to
create enamels
o When endospores are finally mature, they are released meaning there is no red vegetative
cells (dies)
 Allows the endospores that are dormant to be released; able to now survive in
climatic environment
o Tetani
 Has its spore at the end of its cell; wider than the cell
 The size and position of the endospore is genetically determined
o Can’t become thicker or thinner
 Some common features of modern prokaryotes
o Autonomously replicating types of DNA are the plasmids
o Bacteria are designed to carry out photosynthesis very fast
 Gram stain/ cell wall
o Air dry is critical
o Heat fixing (killing the bacterial cells)
 Don’t pass thru the flame too much (once is fine)
o Preparing the smear
 Needs to be a thin coat of bacteria (thin smear)
 Too many cells or bacteria = not able to stain properly = can’t be
differentiated
o Less is better in microbiology
 Some common features of modern prokaryotes continued
o There are no internal structures
o Left image
  Dividing bacteria going thru binary fission (no strong membrane)
o Right images (examples of bacteria that have membranes)
 Nitrifying bacteria
 Membranes that allow nitrification
 Photosynthetic bacteria
 Need membrane to carry out photosynthesis
o In general, the ribosome level is up to 25% of dry weight as they are good at doing protein
synthesis
o There is one bacterial chromosome
 Circular chromosome to which the origin of replication is opening and 2 replication
forks going around
o Plasmids are also autonomously replicating
o Inclusion bodies (fat deposits as well as sulfur polyphosphate depending on the growing
conditions)
 Inclusion bodies in bacteria
o (a) & (b)
 Grown in abundance of polyphosphate vs sulfur
o Right (a)
 Liquid droplets
 Bacteria have ability to store nutrients in different ways in inclusion bodies
 Some common features of modern prokaryotes continued
o RNA is continuous
 The introns if it exists, is removed without any additional help
o The different kinds of RNA (tRNA, mRNA and rRNAs) are made by one RNA polymerase
 Only for eubacteria and cyanobacteria
 Archaebacteria have many RNA polymerase
 Why they are considered the predecessor of nucleus
o Primase
 Used to make Okazaki fragments
 Special features of modern Archaebacteria
o Have unique cell walls and membrane lipids
 Makes sense because they live in such extreme environments
 They have to made differently
o The archaebacteria have evolved a very different way to grow and have their genes expressed
differently
 Again, makes sense due to the hot thermal environments
Lecture 3:

 Anaerobes and microaerophiles lack all or some of the enzymes that allow a cells to life in an
oxygenated environment
o Facultative anaerobe = like to grow in oxygen but can still grow in absence of oxygen
(E.coli)
o What does aerobes and facultative anaerobes have that anaerobes don’t?
 They have enzymes that can break down the oxygen free radicals formed
o Agar shake (liquidized medium) test
  Inoculate the tube with a bacteria throughout the entire tube and let it solidified
 Know what temperature it grows at
o Indicate the presence of oxygen at high level (pink indicator)
 Based on where they grow, it tells u the level of oxygen
needed
 Only grow at absolute top tube = obligate aerobe
o Absolutely require oxygen
 Only grow at the bottom tube = obligate anaerobe
o Can only grow in absence of oxygen
 Grows variably in the tube = facultative anaerobe
o Has the ability to grow anaerobically but
prefers oxygen
 E. coli
 Tends to grow where oxygen levels are slightly
lower than atmospheric oxygen = microaerophiles
o Evolved early in the usage of oxygen
 Tend to grow throughout the tube = aerotolerant
o Don’t even care if they’re in oxygen or not
 Pathogens use this to grow in
different places in hosts
o 2 important enzymes
 SOD (super oxide dismutase) takes the radical free oxygen and turn it into
hydroperoxide + O2
 Catalase takes the hydroperoxide and converts it into water + O2
 Obligate aerobes have both enzymes
o Anaerobes lack those 2 enzymes
 Facultative may lack catalase tho
 Microaerophiles don’t have a huge amount of these enzymes
o Tells us that when organisms first evolved they lacked some enzymes
 Evolved first abiotically without any ability to make the nutrients (nutrients were
already present in the environment)
 Thus, needed to evolve to make enzymes
 Third characteristics of the earliest cell type
o Heterotrophs
 Majority of organisms that exist today
 Photoheterotroph
 Uses sunlight as an energy source but uses organic carbon as source of
carbon
 Chemoheterotrophs
 Use organic compounds as energy source and source of carbon
o Most common
o Autotrophs
 CO2 isnt a direct carbon source
 Must go thru Kelvin cycle to generate building blocks of sugars and those
sugars are used in respiration thru other major cycles (TCA cycles)
 o Then the CO2 is fixed into carbohydrates
 Very high energy required cycle
 Photoautotrophs
 Remember anaerobic photosynthetic bacteria that don’t grow in presence of
oxygen and are still autotrophs
o Like cyanobacteria
 Which sit in margin between development of anaerobic and
aerobics; can sometimes grow and use anaerobic
photosynthesis in absence of oxygen or do normal
photosynthesis in presence of oxygen
 Chemoautotrophs
 Small group
 Organisms are usually subsets of predominately the eubacteria and
archaebacteria
o Chemolithotrophs
 Use unusually structures to carry out their growth
 Live in deep thermal hydro vents
 Because they can use hydrogen sulphide for their inorganic compound source
 Sulfur-oxidizing bacteria
 The SO4 ions can be problematic to atmosphere but useful for some
organisms
 Nitrogen-oxidizing bacteria
 The NO2- is beneficial to the plants (providing nutrients)
o Symbiotic relationship with plants
 Sometimes, their byproducts are positive or their inorganic use of compounds is
negative (toxic)
 Depends
 Hypotheses
o All reactions done by enzymes can be done chemically (enzymes just catalyze the speed of
reaction)
 Just would take a long time
o Glycolysis is identical in all organisms
 First energy producing pathway (not much)
 Anaerobic organisms still use glycolysis for energy production to this day
 How did heterotrophs give rise to autotrophs?
o (1) Building blocks were made already
 First cells didn’t have to carry out any metabolic pathways, since they existed (could
get nutrients from the environment)
o (2) Run out of these nutrients
o (3) Rate of nutrient usage was faster than the rate of abiogenic synthesis
 Chemically, it would take very long to create it abiogenetically
 Heterotrophs to autotrophs
o Overtime, the organisms that can make nutrient Z, it will dominate
 However, then precursor Y is depleted so another step of the pathway must be created
(and so on…)
 Another step of the pathway is created
 o Also, when organic nutrients were depleted, evolving the ability to be autotrophic from
heterotrophic will have selective advantage because they could use CO2 rather an organic
source of carbon (that’s depleted)
 How can aerobes evolve from anaerobes (how did autotrophic evolve from anaerobic organism)?
o Bacterial photosynthesis (anaerobic photosynthesis)
 Formula
 Is very similar to the normal aerobic photosynthesis
o Only H2S rather than water and S rather than O2
 Cyanobacterial photosynthesis
o There just had to be a change to use water rather than sulfur in the Calvin cycle
 Move towards aerobic photosynthesis
o As aerobic organisms evolved, as the cyanobacteria started to produce oxygen, it would result
in a thickening of the ozone layer
 Resulted in a decrease in mutation rate and evolution rate
 Cyanobacteria: anerobic to aerobic
o Anaerobic bacteria were just using H2S and producing elemental sulfur
 A mutation allowed bacteria to use water instead of H2S
 The rest of the pathway is identical in anaerobic and aerobic photosynthesis
 Endosymbiont pathway (how we first evolved the first eukaryotic cell)
o Rhizobium and roots of plants
 Rhizobia are nitrifying bacteria
 Provides nitrate
 Plants provide nutrients and protection
o Often the hypothesis starts with concept of a gulfing of a smaller bacterial cell by a larger one
or the interaction of 2 bacterial cells to basically give certain functions
o Example; Giardia
 Have to stay within the host to survive because it can’t generate its own energy
 Serial endosymbiosis
o Steps
 (1) An endosymbiotic event leads to the nucleus in ancestral anerobic eukaryote
 (2) A second bacterial cell is engulfed (aerobic bacterium)
 For a period of tine, its a classic endosymbiotic relationship
o Could leave the primitive eukaryote if it wanted to but at some point,
it becomes an organelle
 There is exchange of genetic material
 A lot of the genes from the organism moves out of
the organism into the nucleus; it maintains some of
its genetic material but not all genetic materials
o Can’t function as a living cell but rather is
incorporated into the organism
 Now gives it aerobic metabolism
providing the sufficient fuel for
growth in heterotrophs
 (3) The second symbiont allowed the development of mitochondria
 Mitochondria have a genome and can cell divide to do protein synthesis
 o Its ribosome is prokaryotic in size
o Subset of its genes is maintained (not enough to be an absolute
mitochondria) because most went to the nucleus
 (4) Now the ancestral eukaryote has evolved with the first endosymbiont engulfing
after the evolution of nucleus; get an aerobic eukaryote
 (5) The endosymbiotic (third endosymbiont relationship) becomes the photosynthetic
cyanobacteria that carry out photosynthesis
 It gets engulfed into the organism that has the mitochondria and nucleus,
wants to carry out photosynthesis
o Ends up developing the chlorophyll
 Engulfed cyanobacteria becomes an endosymbiont and
multiples to generate ATP using energy from sunlight
 At some point in time, cyanobacteria lose some of
its genome because there is a genome in chloroplasts
o It has ribosomes of prokaryotic type but
doesn’t encode all the genes that the
chloroplast needs to carry out its function
(some are lost to the nucleus)
 Ultimately get the photosynthetic
eukaryote
o Remember, a large portion of genetic material is transferred to the nuclear linage, but some
genes still remain within the particular engulfed symbiont
o Double membranes = suggestion of many engulfing events
 However, the traditional method doesn’t explain the double membrane in the nucleus
 Nor does it address the characteristics of the archaebacteria
 Circular chromosome that has multiple origins of replication, DNA that are
more histone like
 Therefore; modern thinking suggests that the genetic material from archaebacteria are
predecessor of the nucleus
 Hydrogen Hypothesis (taken over now)
o Difference is that 2 types of organism came together
 One was the methane producer and the other was producing hydrogen gas
 They formed a symbiotic relationship based on H2 and CO2 as fuel
o Eventually became as one organism
 Gene transfer occurred due to increased host interactions
 Led to archaebacteria host with its DNA and the
organism that ultimately led to mitochondria
engulfed into a cell that led to the various
characteristics
o We know that the mitochondria is for sure evolved from aerobic eubacteria and chloroplasts
evolved from the cyanobacteria
 Maybe nucleus was a product of 2 organism that came together but ultimately formed
1 organism because of the nuclear material in the nucleus (hypothesis)
 Nuclear acquisition: hypotheses
 o Became clear that genes that encode proteins similar to eukaryotes for carrying out DNA and
RNA synthesis and interaction with DNA and RNA are more similar to what we see in
archaebacteria than what we see in eubacteria
 Likely archaebacteria was the predecessor for the nucleus
o Genes from archaeal bacteria are those involved in RNA and DNA synthesis
o Genes coming from eubacteria are the more housekeeping genes that are involved in
metabolism
 Together came together to make up the nucleus today
 The first symbiont interaction
o Archaebacteria have actually more than 1 polymerases, that’s involved in making different
types of RNA (mRNA, tRNA and rRNA) but unlike eukaryotes, the polymerases don’t do
specific functions
 Both are involved in the same function; making all different types of RNA
 Family tree
o Archaea is coming off the same line as eukarya but just b4
 Reality is, archaebacteria lives in a lineage that is more like eukaryotes
o Eukarya
 Diplomonads
 Present day eukaryotes that have no mitochondria
o Close to the root of eukarya
o How have they found out?
 Isolate the DNA
 Amplify the ribosomal RNA for the bacteria (16S or 15S)
 Look at the size of the region of RNA
 Based on the sequence similarity, can determine which organisms evolved at
which rate
o Via PCR using specific primers
 Cellular and Acellular microbes
o There is more non-cellular than just viruses
 Plasmids & transposons are considered as acellular because bacteria can exchange
them with each other
 Conjugate plasmids
o Bacteria have transposons that literally jump from one bacterial cell
type to another and carry with it, genes that aren’t seen in any
eukaryotic cells
 Measles
o Very infectious; airborne (hangs in the air; 9 /10 people will be infected after infected people
leaves the room)
 Secondary effects; hospitalizations and death
 Brain loss, and loss of hearing
o Double shot of vaccinations needed (since 1990s) for complete coverage
 The viruses
o Are non-living
 No ability to grow by themselves
 Need the hosts building blocks to grow
 o Only have some genetic material and ancillary proteins to allow
genome to be replicated because sometimes, the replication process
isn’t the same in their host
o Transmissible between susceptible host
 Host specificity
 Viruses are held within kingdoms (bacterial virus can’t infect plants)
o Don’t have the same receptors to be infected
 Virion
o Can vary in size
o To identify them, need light microscope
o Image
 Some are really small or large enough
 Criteria used to group viruses
o All viruses have a capsid
 Capsid can be in various shapes (protein based)
 Encoded by a gene in the genome; viral protein
o Genetic material is enclosed in a capsid
o Naked virus (capsid surrounding the genetic material) vs enveloped virus (an envelope
around the capsid)
 The proteins that are placed into the envelope are encoded by the viruses
 Proteins encoded in the viral genome are spike and capsid proteins
o Sometimes, accessory polymerase that aren’t encoded by the host
genome
o Envelope
 Critical for virus to attach to the target host cell
 Can easily be destroyed via detergents and soaps (COVID-19)
o Harder to attach to host cell; no membrane = no spikes = no
attachment
o Naked virus
 Hard to get rid of it or destroy it because it’s made of proteins
o Not all viruses have an envelope, but all virus has capsids
o When envelope is made, the lipids come from the host when the virus buds off the host, after
its replicated
 Viruses that infect animals, bacteria, plants
o Complex shape
 Bacteriophage
 Capsid head
o Lands on membrane and tail fibers retract to expose the spikes
 The spikes poke a hole into the cell
 The viral genetic material is injected into cell
o Icosahedral shape
 Adenoviruses
 Protein coat
o Top left
 Classic isohedral capsid
 o Nucleic acid and viral genetic material found in capsids are either DNA or RNA
 Never both
 Viruses is either RNA or DNA based
o Can’t find both types of nucleotides
 Tobacco mosaic virus
o RNA based virus
 The capsid proteins are surrounding the RNA to create the helical structure
 Bacteriophage T4
o Structure is all about delivering the genetic material
o Right image
 E-coli cell to which many bacteriophages are attached
 Tail fibers attach, then shrink and the base plate is stuck to the cell wall
creating a hole for genome to be injected
o Complex because it has a tail fibers
 The head is isohedral shaped
o Viruses self-assembles
 Once the genetic material is injected, the genes that code for the separate components
of the structure (tail and head) will make each part separately and then self-assembles
into the structure without help from the host
 SARS-COV 2
o Helical shaped and RNA based
o Spike proteins
o M-proteins stabilizes the virus with the envelope allowing the attachment to specific
receptors
 Influenza virus
o Helical structure but has different segments
o Spikes are called hemoglobin neuraminidase
 Important for infection
o Due to the nature of the segmented genome, known as a pleomorphic shaped virus because it
can morph into slightly different shapes
 Viruses with capsids of complex symmetry
o Categorizes by the shape/structure of the capsid
 What kind of genetic material is in the capsid and what does the capsid look like?
 Criteria used to group viruses continued
o 2) Host specificity
 There is also cell-type specificity within the host as well
o 3) Type of nucleic acid present
 A larger class of bacterial viruses are double stranded DNA
 But there can be variations of different combinations
 Image
o Some viruses are RNA based that go thru a DNA intermediate and comes back as DNA based
once replicated
 There are a lot of viruses that infect the liver (hepadnaviruses)
 Can use cell type or location of infection as classification
 Table
 o A lot of variability and across all kingdoms
 The more common types of viruses that affect animals are RNA based viruses
 Criteria used to group viruses continued
o 4) Viral genomes consisting of single stranded RNA whereby the single strand is a sense or
anti sense RNA strand
 Single stranded positive
 The genome of the virus that is packaged in the capsid is the same as the
viral mRNA
o When genome enters the host, the genome can immediately make
messenger RNA
 In the process, has to make negative strand RNA to make
more positive RNA strands to be packaged
 Rubella vaccination is important because if pregnant
individuals are infected, it leads to massive
consequences onto the fetus
 Single stranded negative

 Genome must first be made into plus strand in order to be translated into the
proteins that are needed
 Image
o Double stranded DNA (dsDNA) viruses have 2 different classes
 Just know that they undergo transcription and replication a little different
o Single stranded DNA (ssDNA)
 There is no way that a eukaryotic host can replicate a ssDNA so it must go thru a
double stranded intermediary to form dsDNA
o DNA viruses by definition are exclusively replicated within the host’s nucleus
 Anything replicated into the host’s nucleus can be embedded into the host DNA; can
then lead to transformation of the cell
 Leading to cancer
o Increase the likelihood of mutations
o dsRNA viruses are class III
 First thing, is to make an mRNA and then make more of the genome
 Class III makes a plus ssRNA by transcribing it to give the single stranded
negative strand (partner) to make the genome
o Single stranded plus RNA can be used to directly make mRNA but then its used as the
template to make negative RNA
 As an intermediate, make more plus RNA for packaging
 Because if viral RNA injects plus RNA, it doesn’t inject enough of plus RNA
to package into all viral genomes
o Need to replicate genome so you have multiple copies of the
genomes to make the necessary proteins
o Minus ssRNA are class V
 Has to make ss plus to transcribe and then it also needs to take it to give rise to
ssRNA genome for repackaging
 o ssRNA plus, are retrovirus
 Unique
 Make ds DNA intermediate which means that go from RNA to ds
intermediate
o The ds intermediate enters the nucleus and gets replicated multiple
times
 Meanwhile, the mRNA has to come back out of the nucleus
to make the viral proteins
 Therefore, retroviruses are entering the nucleus and can be incorporated into the
genome
 Infections with retroviruses can cause transformation in eukaryotic cells
towards a cancerous state
 Criteria used to group viruses continued
o 5) Disease state (not ideal classification for viruses)
 Question
o E
 SARS
o Identical to Covid virus
 Question
o D

Lecture 4:

 Host range
o Viruses don’t cross kingdoms
o Many host are specific and attach to specific tissues
 Rhino viruses wont make the dog sick because they don’t have the right receptors to
be infected
o Different ways viruses can move
 Directly infect the hosts
 Respiratory infections that come into contact mostly with respiratory droplets
make people sick
 Some are airborne and direct contact like measles
 Some come into contact with blood or secretion form one individual
 Via a vector
 West Nile virus
o Move between birds and animals via mosquitos
 Directly from another host
 Rather contact with the rodent and human
 Example
o Being in contact with primates = HIV
o Determined by
 Without the virus signals on its surface and the right receptors responding
 There is no interaction and no invasion
o Thus, if u can remove the receptors on the target cells = no infections
  However, viruses usually use important receptors that are
required for functionality of most cells
 Virus needs the host everything
 Only encode spike proteins and special accelerating genetic replicons to help
with replication
 For most DNA based virus
o Most proteins will exist in the cell
 For retrovirus s
o They need reverse transcriptase (doesn’t exist the animal cell)
 Must encode this reverse transcriptase
 Generalized illustration
o Reinforces that viruses needs to attach
 In this case, it’s a non-envelope virus where the spikes are on the capsid
 Its showing that the capsid never enters
o The genetic materials enters and causes making of viral proteins
 Needs transcription, translation, and synthesis of proteins
 Viruses self-assemble
o The proteins come together to make the
virus
 Then the virus is released
o If it’s capsid based non-envelope virus
 It often means total destruction of the cell for the virus to exit
o If its enveloped
 It can bud off, without severely damaging the cell but it does cause damage
 Viral infection
o Attachment
 Not random
 Its random that u inhaled the virus but the attachment of the specific viral
component to the specific surface component (receptor site) isn’t random
 Generally, a lot of different receptors are used in all viruses
 Receptors are always on the host cell surface
 Examples of receptors in bacteria
o Bacteriophage lambda
 LamB protein on E. coli surface are important for transport of sugars
 If lost; it will no longer be susceptible to bacteriophage lambda but it wont be
able to move variety of sugars into the cell
o Detrimental effect; if lost the protein
o Other viruses that can affect E. coli is also t4
o The receptor for bacteriophage is actually in the cell membrane bitt other receptors can be on
the pili or flagella
 So anything on the surface that can encode for particular proteins can be receptors for
different bacteria
 Images
o Top
 Isohedral shapes (bacteriophages) are attaching to the pili
 o Bottom
 See that as it lands on the cell wall; it empties the capsid head for the DNA to enter
the cell
 Bacteriophage is one example of a virus that doesn’t enter the bacteria but
they her inject its DNA
o Rarer event in animal viruses
 Capsid or envelope spike interaction with receptor
o Again, all about the spikes that are encoded by the viral genome (whether on the capsid or on
the envelope)
 It attaches to the cell membrane of host and allows entry
 Examples of viral receptors
o Polio virus (has been eradicated in certain places)
 Has a specific glycoprotein intercellular adhesion molecule (ICAM)
 Attaches to the ICAM in the human nasal pharynx, gut and respiratory
epithelium
 There is relapse of polio later in life (had it when they were a child)
 Remerges issues in gut and spinal cord
o Being attacked by the virus and now in wheelchair
o Rhinovirus
 Makes sense why the cold centers around the sneezing, stuffiness, watery eyes and
coughing
 Attacking the upper respiratory system
o Measles
 One of the most infectious virus
 Symptoms are more broad because the protein it attaches are found on number of
tissues
 Effect on different locations in the body
o Broad symptoms
o HIV
 On white blood cells (particularly in CD4 protein; which is fund in the plasma
membrane of leukocytes)
 Quick engagement with WBC and leads to depletion of functionality of
immune system
o Rabies virus
 Attaches to acetylcholine receptors in the brain
o SARS
 ACE 2 can also be found in the gut
 Leads to expression of severe gastrointestinal infection
o Long lasting symptoms
o Influenza
 Hemagglutinin and neuraminidase are involved in binding to the host
 The key interaction between hemoglobin and surface of the host is sialic
residue (sugars; specific type of glycosylation proteins that is found on
surface of cells)
o Uses these sugars to attach to the host
 o The common or widespread nature of these receptors are important
o Gene therapy
 Use modified viruses to deliver treatment for certain diseases
 Have a virus that directs itself to a particular cell type and then if u can
activate the ability to multiply in the host; can add a gene theoretically
o The gene being administered is non functional and can rescue them
from the disease
 Its possible
 For neurological disease = successful
 However, many viruses can interact together
o No way to know without a lot of genetic sequencing what dormant
viruses are inside our bodies
 Don’t all have the same viruses
 Inactivated viruses can be activate via exchange of gnetic
material
 Penetration of host cells
o Once attached; must penetrate
 Diagram
 Virus lands
o Tail fibers attach to the receptor and then the tail fibers pull the
structure of the surface
o Tail pins interact with cell wall (I this case a gram negative cell wall
of E. coli)
 Moves into the outer membrane (made of lipids and other
structures)
o Sends the tail fibers thru the peptidoglycan layer and has enzymes
(lysosome) to help destroy the peptidoglycan
o Once done, have a direct entry for the virus into the cytoplasm
 Again, the virus must carry genes and protein products it needs to carry out the
infection
 Animal virus
o Virus just has to go thru the plasma but in fungus or bacteria or plant; must go their the
plasma membrane with the cell wall
 The cell wall creates issues with easy endocytosis event to bring the virus into the
cell
o Thus, initial contact is critical
o Then, the virus binds tightly
o After, have induction
 (1) The viral genome only enters the cell
 Common in fungal and plant world
 Rare in animal world
 (2) Viral capsid with the viral genome or the entire enveloped virus is endocytosed
into the target host
o As a result, there is a number of different mechanism of endocytosis and phagocytosis for the
virus to enter
 Entry mechanisms
 o Diagram
 (a) If it’s a non-enveloped virus and using a endocytic route
 Its demonstrating clathrin-mediated endocytosis
 (b) Non-endocytic route
 Simple fusion at the cell surface and delivery of the capsid into the cell
o Since the envelope virus has a membrane, it can simply fuse with the
membrane of host
o There is caveolin mediated
o Basic endocytosis
 Doesn’t require anything at the pit
 Diagram
o Can have ….
 Simple fusion
 Coded pits
 Caveolin
 Clathrin
o Both enveloped and non enveloped virus can enter
 Non-clathrin, non-caveolin endocytosis; simple endocytosis
 No need for coded pits
 Bulk-phase endocytosis
 Can bring viruses in
 Phagocytosis
 By cells that carry out phagocytosis
o Only method of entry where if the envelope is within the enclosed
vesicle, then there doesn’t need to be a complete disassembly of the
coated vesicle in order to get to the right location
 Generally, a fusion with lysosomes to form phagolysosome
o At some point that they try to destroy the virus
 The virus will uncoat themselves and release themselves so
they can replicate
o The type of genetic material that is in virus determines where it ends up
 Entry of HIV and influenza
o HIV
 Spikes attach to the CD4 receptors with assistance by another cell surface protein
 Leads to fusion of the envelope of the virus to the target of the host cell
 The capsid with genetic material is released into the cell
 Causes destruction of the capsid
 First thing to perform is reverse transcription to create ds DNA that will enter the
nucleus
o Influenza
 Blue = hemoglobin and yellow = neuraminidase
 Sialic acid residues attach to the receptors that have the same kinds of carbohydrates
on them
 Unlike a fusion at the cell surface; see the entire enveloped virus become
engulfed in a vesicle
  As a it moves, it has to be broken apart in order to release DNA
o It becomes an endosome; pH becomes lower due to activities
 The genetic material is decoded
 i.e. removal of envelope and capsid
 Continues on with process of making more genome and protein so it can exit
later
o One viral protein enters but millions of viral proteins (virions) will
leave the cell
 Replicates quickly = increased symptoms
 Potential to attack many different cells
 Question
o D
 Can use many methods of entry but use a particular mode to get in
 Replication, packaging and exit from the host cell
o After being inside; must replicate genome for transcription of proteins (spikes and specific
polymerase)
o In almost all cases in animals, the nucleocapsid is going to enter (capsid is intact)
 Often the envelope is present as well
o Steps
 (1) nucleic acid genome must be released from the nucleocapsid structure
 Needs function of the host cell which the host in the process of getting rid of
it will remove the capsid
o Allows release of genetic material
 (2) generally, viral genome is replicated first because need to make more genome
 Exception
o Plus strand RNA can enter and immediately start transcribing
 Not able to make all proteins needed
o Often needs an assistance protein (not came with the virus) for
replication of its genome
 (4) may need to add the envelope if an enveloped virus
 What machinery do viruses use for replication and transcription?
o Whole process is different for different viruses
 Often times needs accessory proteins if not ds DNA for transcription and replication
 Sometimes; that protein is brought into the host cell (like in HIV)
o Precursor is usually, hijacking the host cell
 Nucleotides to make RNA, and amino acids to make proteins
o If an envelope virus, envelope is made from lipids from host cells
 Via process of interacting with either the plasma membrane, nuclear membrane,
Golgi membrane or ER membrane
o If the membrane that has gone around the virus occurs b4 the plasma membrane, then there is
no pinch off at the plasma membrane
 Its not adding another membrane onto the virus
 Virus will break out by breaking the plasma membrane
o But if the envelope source is the plasma membrane, then it’s a simple exocytosis
  The exocytotic vesicles pinch off the plasma membrane like how cells secrete
proteins
 Diagram
o All proteins needs for viral replication aren’t made at the same region
 Usually, a sequential synthesis of various proteins are needed
o (1) Once lambda infects and DNA is injected into the cell
 The nuclease, DNA polymerase and sigma factors are made
 Those then are needed to make phage DNA
o (2) Once phage DNA is made, now makes use of the early mRNA of the infection to make
what they need to undergo phage DNA replication
o (3) Once phage replication is done, need to carry out what’s needed for packaging
 Need middle and late mRNA to encode for those proteins that put the capsid around
the viral DNA
o Phage is completely assembled after entry into cell is between 20 and 25 mins
 Why in labs; need time to allow the interaction with new cells so u can see the actual
plagues forming b4 plating
 One plaque is given rise to by an infection of one bacteriophage into the
E.coli
 Lytic and lysogenic cycles
o In lab; make use of lytic cycle (all about infection and release of phage particles)
 Mix the bacteria with the phage together
 After short incubation, add the mix to some molten top agar (50 C)
 It will solidify
o End up with only a lawn of E. coli if there is no infection
o See clear zones (representing the phage) if there is infection
 Lytic cycle; killing the bacterial cells that it infects and the
reason you see a plaque is because as it goes thru the first
round of infection, it gets released; able to now infect the
cells next to them
 Keeps on going, plaque becomes bigger
o To see a plaque (kill millions of bacterial
cells)
o Lysogenic pathway
 Ability of certain viruses that have right type of genetic material (DNA) to actually
integrate into the host chromosome and become a prophage
 Silent and no longer carry out a lytic cycle
o But have their DNA incorporated into the genome of organism
 As so, genome has now acquired new genes
 Bacteriophages can give bacterial cells new function
including antibiotic resistance
 Since the DNA integration is random; it could integrate into genes that result in miss
functionality
 Importance; why many viruses that are able to integrate into the host
chromosome (being a DNA virus or having a DNA intermediatory) have
been shown a connection to transforming cells to cancerous state
o Knocking out important genes
  May knock tumor suppression genes; no control over cell
division
 Predation
o Body has many bacteria but also bacteriophages
 Phages aren’t there to make us sick but can alter the microbiome
 In multiple ways…
o By predation alone; killing bacterial cells
 Can deplete population of specific bacterial taxa to change
bacterial communities
 Modulate bacterial communities
o Over many generations of these interactions the bacteria phages can
carry ancillary genes that encode for different functions (including
antibiotic resistance)
 Over time, as these infections continue (infecting the
bacterial cells in the body (not really u))
 Lead to phage resistant phenotypes
o Can exchange genetic material and give bacteria antibiotic resistance
 New traits of being able to produce particular toxins or
antimicrobial agents
o Phages have ability to cross the gut cell epithelial membrane to get
into bloodstream
 Interact with immune cells
 Confuses the immune systems = doesn’t know what
to do with the bacteriophages
o Eventually, be a movement towards using phages to treat diseases because running out of
antibiotics
 Nowadays, we develop antimicrobials that are small peptides that can destroy them
but hard to do so moving forward
 Diagram (herpes simples virus = ds DNA virus)
o Virus that enters by fusion
 It’s a membrane bound ds DNA
 The spikes are left behind in the eukaryotic cell and ds DNA enters
 Its decoded and enters the nucleus to make the mRNA
o Moves to the cytosol to make the proteins
 Early and late mRNA are making different proteins
 In this case, it requires an extra enzyme to be made in order to replciate the genetic
material
o Remember; ds DNA will never leave the nucleus because in eukaryotic cell it doesn’t
 Thus, all the proteins that make up the capsid and envelope are transported back to
the nucleus
 Then, genetic material can be surrounded by the capsid while the spike
proteins can be put into the nuclear membrane
o Exocytotic events in the nucleus takes place; leading to membrane
being formed with the spikes
o In this herpes simples virus; once the viral particles accumulate near the host cell, it raptures
the cells in order to release the viral particles
 o There are other cases where the assembly can take place in the ER or Golgi
 Then pinched off the membrane of those compartments
o Since herpes simple’s virus can integrate into the host chromosome, it can lead to
transformation of cells
 Attached to different kinds of disease
 Example; causes herpes disease or cells become cancerous state
 Severe acute respiratory
o The receptor being attached to the spikes
 Is a receptor mediated interaction
 Endocytic event
o After, there is removal of the membrane and capsid
 mRNA is released
 Because its plus strand, the hosts’ ribosomes can immediately transcribe
o The first thing being made is a replicate to make more of the genome
 Because since it’s a plus mRNA genome, it has to make
minus RNA intermediary to make more plus mRNA
 Thus, replications are able to be carried out with
production of viral proteins
 They form a complex and start to replicate the minus
genome (transcription)
 Now a combo of minus and plus RNA
 The minus RNA are used to make more plus RNA
o Ultimately, the plus RNA will end up in the nuclear capsid
 Theres important genes being made involved in making of spikes
 Eventually, this structure has to be put into the membrane
 The packaging takes place in the cytosol and specifically, the ER (after the
translation of viral structural proteins)
o The spikes are put into the membrane
o The ER membrane will pinch off a vesicle
 The vesicle will engulf the genetic material with the capsid
forming the mature virion
 Leaves the cell via exocytosis
o To clarify…
 The proteins are put into the ER but the fusion with the genome happens after the
vesicle formation in the ER/Golgi intermediate
 This virus is different from herpes
 Host cells has no ability to make minus RNA from plus RNA, so the proteins
have to encoded by the virus itself
o Thus, have to be made early to start creating more plus mRNA so
that it can be used to make more proteins and packaging of the
genome
 Again, diagram is not realistic
 Many genomes are replicated and multiple viruses are formed/matured
 HIV (retrovirus example)
o Scanning EM images
 HIV at the cell membrane is being uncoated so it can enter the cell
  Via fusion
 The first thing being released is the RNA with the reverse transcriptase attached
 Viral RNA has to undergo a reverse transcription to make a DNA/RNA
hybrid to create a ds DNA intermediate
o ds DNA intermediate enters the nucleus and incorporated into the
host chromosome to be replicated/transcribed
 The early and late mRNA are used to make capsid, and proteins required to be put
into the envelope
 Go to the ER and form the right spikes proteins on the vesicles
o The vesicles (has glycoproteins) because many spikes are
glycoproteins
 Which are made into the ER and go into the Golgi
 Thus, anything that sits internal to the ER or Golgi vesicle when it fuses with the
plasma membrane
 Those proteins hanging in the vesicles are now outside the cell
 The genetic material is encapsulated by the capsid and then as it leaves via
exocytosis, it forms a bud (pinches off)
 All the spikes are put into the virus
 Retrovirus structure
o Remember, eukaryotic cells (host) don’t have reverse transcriptase to make the ds DNA (from
DNA/RNA hybrid to ds DNA)
 Thus, reverse transcriptase have to be brought into the host cell by the virus (first
step) and be encoded by the viral genome
 Then those required proteins are packaged to the genetic material for new
replicated cells
o List of important proteins required are…
 Envelope and gag protein
 Key in forming the capsid and spikes for the envelope
 Unique accessory proteins needed for replication of genetic material if it doesn’t exist
into the host cell
 Once again; to be infectious, the virus must enter the host cell
o It can only be infectious if host has the polymerase to replicate the
virus or it must bring with it the polymerase that can be encoded by
the genome
 Spike proteins and capsid proteins
o The remainder of enzymes will be provided by the host
 General viral packaging for release
o Viral capsid moves towards the plasma membrane, nuclear membrane or ER membrane
 Gets put into the vesicle and pinches off that region
 If it pinches off the plasma membrane, its released into the environment
o If it doesn’t need a envelope; then the capsid will have the spikes and the spikes will be added
during the process of self-assembly of the capsid
 There will be no budding but rather lysing of the cell
 See plaques only when it completely lyses the cell (lab)
 Mechanism of viral release
o Influenza diagram
  As the genetic material surrounded by the capsid and often a matrix protein
 It moves towards the membrane where already the host proteins are starting
to be pushed away
o In case of influenzas, the neuraminidase and hemoglobin are
replaced post release
 As you can see, the host proteins (green) are being pushed out of the way by the viral
proteins
 The areas where virus pinch off in the plasma membrane are in what’s called
lipograph
 When the virus pinch off the plasma membrane, the only proteins that are in the
envelope are spike proteins
 What happens if all the host proteins aren’t cleared from area of pinching;
few host proteins also get out?
o Now envelope has spike proteins and few host proteins
 Thus when immune system tries to destroy the virus; it can
make antibodies for ur own host proteins as well
 Therefore, due to incorrect budding; can develop
autoimmune response to certain host proteins
 Thinking question
o Virus manages to get out but has no envelope nor spikes
 What happens?
 Virus is not virulent
o But virus still exists in the cell (since it was released)
 No virulence ability
 But if it finds a way back into a cell and has viral DNA that can be integrated
into the host chromosome
o It can cause damage to host cell (still) because if it can integrate into
the host chromosome
 It can possibly lead to damage to different genes in the
chromosome leading to movement towards transforming
those cells towards a cancerous state
 Its only not infectious but doesn’t mean its
completely innocuous
o Over rounds of cell division; get damage
 Mature influenza virus
o Again influenzas has neuraminidase and hemagglutinin (spike proteins), viral RNA
polymerase (unique; needs it bc host doesn’t have it), RNA endonuclease
 All the proteins are packaged with the RNA genome (in a eight segments)
 Not a single linear genome but arranged into 8 individual segments
o It allows it easily to exchange genetic material with other influence
viruses that can lead to genetic drift
o Neuraminidase sialidase helps with escape from the host
 Neuraminidase spikes are important for finding the receptor and causing the
membrane to invert inwards to form the vesicles that bring the virus in
o 3 types of influenza
 A
  Epidemics or pandemics don’t describe the severity of disease but rather
where or how far it spreads
o Pandemics means it spread further than what an epidemic would do
 Most important types because it has ability to change its surface proteins
 A lot of variations in hemoglobin and neuraminidase
 B
 No clear subtypes
o See an influenzas but don’t know the different H and N subtypes
 C
 Not really a concern
 Antigenic shift versus drift (2 aspects of genetic modifications in a virus)
o Antigenic shift (reserved for influenza but for other viruses are called viral shift or
reassortment)
 2 different strains with different spikes come together and exchange genetic material
 Now virus loos completely different than it did b4
o Antigenic drift
 How virus try to evade immune systems
 Via natural mutations (base pair changes, change in AA or spike proteins (not
able to be recognized by antibody or stronger attachment to receptors))
o Since influenzas A can infect more than just humans, it can have major reorganizations (bird,
pig or human)
 B and C only infect humans, so it limits the re assortments
 Influenza
o H1N1
 Made the lungs very leaky and people died of severe pneumonia very quickly
o It was found that when we have flu pandemic similar to the pandemics of 1918 or late 1960s
(H1N1)
 Older people have more immunity against those viruses than younger people
 Drift and shift
o Drift
 Single point mutations may change up the way the virus interacts with the host cells
 But small changes in genetic material
o Overall genetic material has not changed
o Shift
 Diagram
 2 different virus (with different H and N subtypes) come together in a host
cell
o Exchange genetic material
 Not just single point mutations but rather a whole strand of
DNA is moved into it
 Yellow and red genome combination
o Completely different setup of surface spike
proteins
 Causes great problem; different
virus than u started with (why hard
 to create vaccines that work each
year bc have to predict which
subtypes will emerge)
 Image
o Reassortment virus
 Completely different spike proteins (not a single point mutation in the spike proteins)
 Sars Covid movement
o First emerged in 2020 (orange) emerged in China
 The one in NA came from China
o The blue is a variant developed in Europe
 Chinese variant went to Europe and a mutation led to the European variant
o Now replaced the Chinese variant with European variant
 It was just due to a simple change in AA D614 (aspartate) to G614 (glycine)
 Changed ability of the receptive function to be recognized
o Made it more infectious than the original variant
 Types of viral infections
o Persistent
 Chronic viral infections
 Must be treated constantly with meds
 It can spread easily amongst people because people are unaware that they
carry the infection (hepatis B)
 Latent viral infections
 Virus infects and then stops replicating for long periods of time (HIV)
o Dormancy period but activated later in several years
 Example are members of Herpesviridae
o Herpes
 Dormant but has an outburst later
 Then goes quiet again
o Meet people with constant recurrence of
cold sores
 Emerged due to stress (immune
system is stressed by other
infections)
 Can use antiviral treatments during outbreaks
o EBV (DNA based virus)
 Usually doesn’t make u sick if exposed
 But can develop due to illness, stress or having
autoimmune diseases
 Due to the fact that it can integrate into host chromosome, it
can lead to Burkitt’s lymphoma
o varicella zoster
 An acute infection (chickenpox) that can lead to latent
infection (shingles)
 Cant get shingles without having chickenpox
 Its viral group is varicella zoster
 Children with chickenpox can get shingles as adults
  Because their antibody production will drop and
now virus can multiply
 Shingles (old people) vs chickenpox (most young)
 Shingles
 Everywhere can have burning sensation
 Hides in nervous system
 Graph (blue line = virus production and red bar = symptoms)
o Acute infection
 Symptoms and virus are paired
 Disappear together and don’t come back
o Chronic infection
 Viral numbers increases immediately but not significant damage to host until later on
(have severe symptoms)
o Latent infection
 Starts with few viral increases and small symptoms
 Virus disappears
 Then have different burst with symptoms and sometimes; no symptoms
 Further subdivided into
 Slow infection
o It disappears due to little virus
o Until it finally emerge to defeat the host
 Why get cold sores?
o Get HSV-1 as a child and becomes latent
 It sits in the neuron of root ganglion (hides) and often move to trigeminal nerve
(jawline)
 Where it reemerges
o By anything that stress your body
 Critical thinking
o Just a benign virus
o Can such latent virus be considered safe?
 It will never be considered safe bc it has integrated into host chromosomes so it can
at the least created one mutation of some sorts
 May need one more mutations = leading to a transformation of cells into
cancerous cells
o Cancer isn’t a single mutation but a series of mutations; need one to
start it tho
 Transmission of virus
o Usually…
 In surfaces
 Tests papers
 Money bills
o Hard to treat SARS Cov2 and influenza
 Bc need to be treated with antivirals as soon as you are infected
 More than 48 hr after symptoms emerge because too many viral particles for
the antiviral to work against
 Anti-viral targets
o Any steps from entry, encoding to nucleic acid synthesis to packaging can be targets of
antivirals
 Vaccines
o Historically, don’t use mRNA based vaccines
 When entered, mRNA disappears but have the spike proteins
 To which the body releases antibodies that lead to memory cells capturing it
o Used recently in SARS Cov2
 Developed the first time to use mRNA vaccines
 Less dependence on heat activated vaccines (not bad; just another tool)
Lecture 5:

 Remember concept of cellular agents

o They too have an ability to move and infect organisms
 Plasmids and transposons move
 Allow bacteria to survive environmental conditions and be good pathogens
 Gene therapy
o Since viruses attach to specific tissue cells (tissue specificity) it can be used therapeutically
 To incorporate gene changes into appropriate cells
o Concept of tropism is what makes virus a great tool for modifying genome without it being
capable to replicate within but only for delivering a gene that will rescue the cell from being
abnormal
o Key things to consider…
 Virus must be able to enter the cell using the receptor and spikes interaction
 But cant have the organisms respond as an immune response
 Cause it will make a person sick with the virus
o First successful gene therapy using virus
 In SCID patients (babies w/o immune systems)
 Took the bone marrow cells out and treated it with the relevant virus
 Then put bone marrow cells or stem cells back into the patient
o The viral addition now has the appropriate gene to allow for immune
system to function
o Its potential in treating neurological conditions as being tested
 To rescue the cells to work normally
 Concept of gene therapy
o Diagram
 Using a vector that has spikes (in this case a naked virus)
 Viral DNA is modified by putting in a new gene and perform other
manipulations
o Take out any genes that help the virus repackage (don’t want it to
replicate in the genome or repackage)
 Just deliver
 The new gene is placed into the nucleus (virus isn’t infectious)
 Now hopefully, the cell type will eliminate the results of the disease
 In this case, adenovirus (DNA based) can be incorporated into the host chromosome
  It can stay there forever
 Common mechanisms for gene therapy DNA entry
o 3 ways
 Retroviral
 Functions like a retrovirus (RNA based)
o Has a ds DNA intermediary that’s gets integrated into the genome
 Again, virus wont replicate its genome but rather integrates the gene of
interest into the genome
o To target mutations that might have occurred
 To now be able to make the proper therapeutic proteins
 Adenoviral
 It endocytoses in the cytosol (in a vesicle)
 Endosome breaks down and virus attaches to the nuclear pores to deliver the
virus
 Virus is not infectious, and the therapeutic gene is incorporated into the
genome
 Makes a new protein
o Making the right proteins to carry out normal functioning
 Nonviral
 Vectors that are DNA surrounded by a lipid (liposomes)
o Carries the DNA and enters the nucleus (same process)
 Viroids
o Transmission is said to likely be either as a cargo with pollen, attached to insects or fungi
vectors (that take it to the plant)
o It exists as a closed circle
 The circle is closed so it will base pair between large partial portions of the circle
 End up with closed rod like structure via strand base pairing
o Its actually the naked RNA doing the moving between cells
 Completely naked genetic material
 Viroids continued
o Can’t encode mRNA or proteins
o It replicates in the nucleolus
o They replicate via rolling circle type of replication
 RNA is mistaken for piece of DNA
 Also, one way in which viral DNA can be replicated
o The RNA has enzymatic activity
 May use to cleave specific plant mRNA that plant needs for proper functioning
 Leading to silencing of those gens which disallow protein production = leads
to disease
o Usually aren’t found in humans but a variation exists
 Hepatitis D virus (viroid that infects the liver)
o Categorized (they all have different genomes but also their means of infection is different)
 Hep A
 Acquired via fecal, oral or food prep
 Hep B
  Hep C
 Hep E
o Hep D
 Originally not considered a viroid but was when it had similarities to plant virus
 Unique structure since its circular
 Smaller than RNA of smallest picornaviruses (common cold)
 The encoding of hep D antigen causes a super infection if you get an infection with
one of the other hep viruses
 Protein is encoded as a nuclear localization signal
o It is detected by infected liver cell nucleus (can go into the nucleus)
 Able to then help the HDV RNA be replicated by animal
hosts RNA polymerase II
 Not only does it make a protein but its RNA also has ribozyme activity
 Can only spread if you had been infected with Hep B or if infected by Hep B and
Hep D at the same time (co-infection)
 Reason
o The Hep B provides the missing function
 Needs the Hep B’s spike to get to the liver to infect it
o Once it is Hep D moves thru the infected cell, its packaged up like a
Hep B
 It can then infect
 Thus, it needs it to be already infected by Hep B so
it knows the information of how to do so
 HDV is packaged into envelope since HBV is also an
envelope virus
 You can be a carrier of HBV (no symptoms); these are prime suspects for spreading
HBV
 Reason why travellers tend to be vaccinated against hep B so that they never
have issue with hep D since they never had hep B
 Also even if u don’t show symptoms, it isn’t benign, it can cause serve issues
with functioning of liver and lead to transformation that causes liver cancer
o When liver functioning isn’t functioning, it tends to be identified late
in the disease
 Liver has the ability to function until the entire liver is
damaged
 Often when u have symptoms, the liver has already
gone thru severe damage (destroyed by infection or
compromised)
 Prions
o Acellular infectious agents
 Small
 Categorized under acellular microorganisms
o Can’t function alone, need host
o Cause plaques due to the modifications of the prion proteins
o When first found; no one wanted to believe that proteins can be infectious because it broke
the central dogma
  But failed to deny; no evidence of nucleic acid basis
o TSEs
 U can have genetic mutations that lead to Creutzfeldt-Jakob disease
 The prion protein was a natural protein in our cells, but it underwent some
mutations; became infectious proteins
o The infectious prion protein takes all our proteins that we need to
function in a cell and changes its conformation so it can’t function
 Usually resulted from eating contaminated meat
 Meat that was sold contained spinal cord
o Ground beef (lowest grade and cheapest)
 Has residues of spinal cord and brain; which prions like to
reside in
 Odds of manifesting in large numbers are minimized
(controlled)
 Eating a sheep that had the prion disease; then the prion will go and attack
the prion proteins in ur own body
o Kuru was identified when studying cannibals
o All the examples are the same; just different variation of constitutive PRP proteins to an
abnormal PRP protein that leads to severe issues with functioning
o Infectious form detected in genetic disease is called PrP (sc)
 Initially identified in a sheep (SC initials justified)
 Abnormally formed protein that undergoes a massive conformational change
 Also, can become chemically modified = changes in post translation
o The normal PRP has multiple alpha helicases
 The mutated version has a lot of beta sheets; makes it more stable and causes them to
congregate
 Results in protein tangles = cells unable to function properly
o Many neurological disease are a cause of protein tangles
 Big complexes of cells are unable to function properly
o (2)
 Corneal transplant (corneas can take the infected genes with them)
 Donor with genetic CJD can donate the infected corneal to the receiver that
ca develop CJD at a very late stage in their life
 Including those patients that were treated with non recombinant human
growth hormones
o Since it was human growth hormones taken from other humans (not
lab grown)
 Came with potential genetic disease that individual was
carrying
 Now use recombinant human growth hormone
(never collected from humans)
 Have controlled the rise in infected transmission of all feeds (not only cow feed)
 Reduced spread
 Just the cook the meat appropriately; no chance but it will be destroyed by the heat
 Neuronal cell
o Have a normal PRP made by gene in the nucleus in a cell
  Carries important functions
o At some point, obtained a misfolded protein
 Either due to mutations or eating tainted meat
o It will misfold any protein it interacts
 Converting all normal proteins into misfolded form
o Results in abnormal functioning protein
 Really caused by change in secondary protein structure
 Plasmids
o Conjugative bacteria lab
 Ability to infect cells (may not cause disease in bacterial cell) but moves from
bacterial cell to another
 So it can transport antibiotic resistance gene or other antimicrobial
protections or metabolic functions
o Characteristics it didn’t have b4
o Automonous plasmid
 Can do anything without help of host chromosome
o Integrated plasmid
 Inserted into the genomic DNA of bacteria
o Example
 E. coli can have a plasmid (that can under exchange with other cells), a quiescent
bacteriophage lambda/t4 (integrated into host chromosome; will replicate when host
chromosome replicates), and transposons (integrated into genome host, plasmids, or
virus)
o Plasmids are rare bc lost during process of evolution of eukaryotic cells
 Only fungi have some plasmids and only select # actually have plasmids
 Plasmids continued
o Plasmid vectors that are used to insert genes into different organisms = engineered plasmids
 Nothing like a natural plasmid; except has an origin of replication similar to natural
ones
o Engineered plasmids
 Remember anytime an organism is given a new gene; isn’t not a wild organism so it
cant be allowed to share information with other organisms
 Thus, have to develop plasmids that disallow exchange with certain other
organisms (controlled vectors)
o Natural plasmids
 Found exclusively in bacteria and fungi
 Bacterial conjugation
 One way direction of transmission (donor to recipient only)
 Bacterial transformation
 Chemically induced transformation of engineered plasmid called pGLO into
E. coli
o With genes attached; arabinose promoter (to induce expression of
protein that’s encoded in the plasmid) and GFP (those cells
transformed with the engineered plasmid will fluorescent under UV
light)
 Artificial transformation in lab
 o Weaken the cell wall with calcium chloride which has a positive
charge while gram-negative cell wall is negative
 Bonds to the cell wall; alters its integrity
 Plasmid DNA will attach to the calcium chloride
 Add heat and it forms transitory holes; it drives the plasmid
into the host cell
o Generally, genes encoded in plasmids are not essential for the bacteria to survive
 Provide ancillary proteins and co- ancillary proteins that give them greater benefits to
survive in particular environments
 Examples
 Deg plasmid
o Pseudomonas is a psychrophilic organism so it can grow in colder
temperatures
 Can make products that break down oil
 Nif-nod plasmid
o Rhizobium forms symbiotic relationships with root hairs
 This ability to carry out nitrogen fixation is in plasmids not
in genome
 R factor
o Found in many bacteria and it’s a resistance factor plasmid
 Allows bacteria to go from no to complete antibiotic
resistance in quick time
 If placed under selective pressure of growing in
antibiotics
o Overuse and bad use of antibiotics =
problem with lack of useful antibiotics today
 R-factor
o Understand; plasmid has its own origin of replication that controls rate of which its copied
into the cell
 If it’s a conjugative plasmid; it also has an origin of transfer
 Thus, it can carry out 2 types of replication
o Classic theta replication
 Origin and replication port going around in a circle
o Rolling circle for transfer of conjugative plasmid
o tra genes needed for conjugation plasmids transfer
o Imagine if we had a transposon on a plasmid that carries antibiotic resistance genes and a
chromosome
 The transposon will jump to the chromosome
 Now, the plasmid has no antibiotic resistance genes which the cell loses
 However, the transposons and its antibiotic resistance (in chromosomes) are
not lost
o Transmission of plasmid carrying antibiotic resistance genes allows many bacteria to be
resistant to antibiotics
 If u use antibiotics; the entire bacterial population within the body will be exposed to
the antibiotics, creating the ideal antibiotic stress
 If one of the bacteria has an antibiotic resistance gene
 o Makes it advantageous to acquire the resistance genes (it will
multiple and multiply = whole population is resistant)
 Next time = antibiotic doesn’t work anymore (only for real
bacterial infection)
 Move to reduce antibiotics
o Removed in Canadian farming (not in US
completely)
 Plasmid origin of replication continued
o Origin of replication determines how many copies of plasmid can accumulate in a cell
o Plasmids make use of hosts replication machinery to replicate the plasmid
o Example (looking at different origins)
 In the f plasmid which is a conjugative plasmid);
 oriV allows replication of 1 copy of f plasmid per cell
 ColE plasmid
 oriC generate up to 20 plasmid per cell
o This origin was used in recombinant vectors
 Bc when used in transformation to express gene, it will lead
to multiple copies of the plasmid in the cell
o Faster growth rate means cells with no plasmids (or smaller plasmids)
 Competes with replication machinery; cells divide much slower
 So, if interested in dividing; lose plasmid
 If introduced antibiotic resistance stress; keeps plasmids bc can’t survive
otherwise
 Autonomous versus integrated plasmid
o Autonomous
 Has its own functional origin so it can divide many times by itself
 Many copies of plasmids
o Integrated
 Only replicate when host chromosome replicates
 Which is when cell divides
 Some retain ability to be autonomous even after they become a physical part of the
chromosome
 If the plasmid goes out of the host chromosome, it can go back to
autonomous replicate
o Plasmids that are integrated are called episomes (just like how virus and bacteriophage
lambda t4 is called so when integrated into host chromosome)
 Example
 Certain retroviruses like HIV
o Can be integrated into host chromosomes (defined as episomes)
 Cartoon
o Series of genes can be passed across cells
 Horizontal gene transfer between bacteria (what conjugation is)
o Can be done in many ways (not just conjugation)
 Transformation
 DNA is released which can be picked up by the recipient cell
 o Not random
 Only certain cells can
 Basis of the Griffith experiment
 Conjugation
 Conjugative plasmid moves; receiver receives additional information
 There is a transposon that could jump into conjugative plasmid = end up in a
recipient cell
 Transduction
 Bacteriophage (virus) can land on host cell and it picks up the gene from the
chromosome
o That gene can be transferred to a recipient cell once that virus
becomes lysogenic virus
 Integrated into recipient’s host chromosomes
 CT
o Allows significant exchange of genetic material that allows bacteria to acquire new abilities
that it couldn’t by itself
 Capable to adapt to new environment
 Natural transformation
o Streptococcus makes use of secretion of competence factor which allows transformation of
mid log cells
 Basically, the movement of plasmid to another cell requires the recipient to be in
mid-log (not any stage of growth)
o DNA fragments can also be exchanged as its released from one cell types
 A dying streptococcus can release some of its genome
 If the right info and right partner is there, it can be picked up by another cell
o Generally passed thru a pilin
 Protein that forms a pili (allows bacteria to attach to surfaces)
 Griffith experiment
o Shows that genetic material of encoded proteins is a classic example of transformation
 There are 2 types of S. pneumonia; S and R form
 S cells have a capsule (smooth) while R cells don’t have the capsule (rough)
o Presence of capsule makes the organism; infectious agent
 Virulent factor that makes S. pneumonia a good pathogen
o If we inject S form into a mouse, it kills the mouse
 If we use heat; the ability of this capsule containing bacteria, can no longer kill the
mouse
o If we inject R cells, they have no ability to kill the mouse
 If we instead inject R cells and heat killed S cells, they now can exchange genetic
information (capsule is taken up by the R cells)
 It kills the mouse
o The genes encoding the capsule was released from the dead cells and
picked up by the R cells
 Example of Natural transformation of pieces of DNA
 Streptococcus pneumonia and other gram positives
o (a)
 DNA released from a dead or dying donor cell
  That DNA can binds to the DNA binding protein (in plasma membrane of
bacterial cell)
o Once it does bind, inside the cell, there are competence-specific,
single-strand DNA-binding protein
o (b)
 The associated nuclease in the plasma membrane cell wall will breaking it into single
stranded piece of DNA
 The free nucleotides in the extracellular environment will be destroyed
 The single stranded DNA will enter the cell
o (c)
 Competence-specific, single-stranded DNA-binding protein will interact and recruit
other proteins needed (like RecA protein)
o (d)
 The piece of DNA is integrated into the chromosomes and gets replicated as the
chromosome divides
 As long as the cell has the right machinery associated with its plasma
membrane and cell wall, it can take up the DNA in (for streptococcus
pneumonia example)
o Have one strand be integrated into the chromosome
o Other organisms (second diagram)
 (b) B. subtilis (gram positive) vs (a) N gonorrhoeae (gram -)
 There is a pore that allows movement for B. subtilis
 See that there is ornate differences of pores in gram – and + cell wall
o Based on characteristics
 Gram positive has a thick peptidoglycan cell wall
 Pore helps the DNA thru the plasma membrane and
peptidoglycan (only)
 For gram negative cell, the pore has to traverse the outer
membrane and inner membrane
 Outer membrane is composed of lipopolysaccharides
and peptidoglycan sits between outer membrane and
plasma membrane
o See that it requires more complexity and
structure when gram negatives move things
thru
 Needs to cross 2 membranes
 Both have the same kind of proteins but the gram – has many more proteins
that make up the pores to allow the DNA into the cell
 Conjugative versus non-conjugative plasmids (not all plasmids can go from cell to cell = non-
conjugative)
o Transmissible
 Requires 2 partners; donor (has the conjugative plasmid) and recipient (doesn’t have
the conjugative plasmid)
 There is a signal on the surface of recipient that tells the donor that they are
compatible
 Thus, able to form conjugative bridge for transfer
 o No donor to donor because their surface changes indicate they have
the conjugative plasmids
o Non-conjugative plasmids
 They can’t bc they don’t have the genes necessary for transfer (no cluster of tra
genes)
o Examples of ability to move (conjugative plasmids)
 R factors
 Carry antibiotic resistance genes that will affect eukaryotic cells that it enter
 F factor
 For our lab purposes; it can show conjugation and carry not too many
resistance genes
 Col factors
 This is what one antimicrobial bacterial cell secretes to kill other bacterial
cell
o Example; protein that kills E. coli
 Bacterial cells exchange with other bacteria that will kill the other bacteria
 The normal flora of skin has bacteria that produce bacteriocins to kill pathogens
 Don’t remove all the bacteria from the skin (major protection)
o Don’t over wash the hand; destroy the natural flora of the skin
 Help the host cells by increasing bacterial
o Support the host immune system; help kills the bad bacteria
 A conjugative plasmid
o Process of transfer
 One strand moves to the conjugative bridge (also called sex pili)
 As the strand is displaced, it is replaced in the donor
o End up still keeping the plasmid in the donor
 On the recipient, the machinery of DNA replication will make the other
strand
o Now have the double stranded DNA (complete conjugative plasmid)
o Sometimes the whole conjugative plasmid (relatively large) can integrate into host
chromosome which makes the chromosome really big
 It can still move to another cell while it is still being integrated in the chromosome
 The ability of conjugative plasmids
o Transfer is done by a different origin of replication (caries out the concept of rolling circle
replication)
 The best studied example of conjugative plasmid
o A conjugative plasmid that’s separate (has the F plasmid) = F+ cell or RTF plus cell
 F – cell = recipient
o An integrated conjugative plasmid, it is given the hfr signal meaning there is an integrated
conjugative plasmid (called hfr cell)
 Defined as such because it has a high frequency of recombination
 Hfr formation
o If the f plus cell integrates the fertility factor and its integrated into another cell, it becomes
hfr cell
 Not random
  Specific sequences in the conjugative plasmids that find similar sequences in
the chromosome to undergo homologous recombination events
 The F plasmid
o Minimum things requires for a conjugative plasmid
 OriV allows replication autonomously
 OriT for transfer
 Entire tra region of conjugative plasmid
 30 genes needed to make the sex pili and other gene products needed for
plasmid to go from donor to recipient
o None of the transfer genes are apart of the chromosome itself, its carried by the conjugative
plasmid
o There are presence of transposon
 IS2 and IS3; insertional sequences (simple transposons)
 Same insertional sequences found in E. coli which can be used for
homologous recombination
 Can have Tn1000 (more complicated transposon)
 Other genes for encoding to make the plasmid a vector for transferring a lot
of genes to different places
 F plasmid
o All the genes and proteins need for the transfer
 Genes that…
 Encode pili
 Encode the actual pore complex that allow DNA to move into recipient
o Type IV secretion system
 Circular replication
o A single origin of replication and 2 replication forks going around the circle
 Lead to 2 copies of chromosome when cell undergoes cell division
 Sometimes, the origin is called OriS
o This is classic example of replication that is identical in all organisms that have 2 replication
forks
 Same is true for non-conjugative plasmids; they replicate in the same way by classic
theta replication
 Rolling circle replication
o For transfer
 Not only need to copy something but also need to displace a strands so that it can go
somewhere else
o Diagram
 A nicking enzyme comes in to make a nick, creating ends
 3’ hydroxyl end needed to add new DNA to the strand
o Light green (original strand) while dark green (new DNA replication
taking place)
 New synthesis is taking place and displaces the other strand
 The displaced strand will move to the recipient cell thru the pili
 The donor still has a double stranded DNA
o Thus, contact is absolutely necessary
  Pili can break b4 transfer (common)
 In that case, the recipient cell wouldn’t be a plus cell but it can still receive
some genetic information (some was transferred; just not the entire sequence
encoding the content of the plasmid)
o Now have a prime cell (not really a donor)
 May still provide new abilities it didn’t have b4
 Type IV secretion system (conjugation requires it)
o Special types of pores that can form in the bacterial cells
 Same system is required for natural transformation of pieces of DNA
o Many effectors’ molecules (considered as virulent factors make pathogens better pathogens)
 Enter into the host cell
o Diagram
 Use type IV secretion
 Considered intracellular pathogens bc they enter the host cell and damage the host
cell once inside
 Use type IV secretion to move their effectors out of the endosome and into
the eukaryotic cell to be damaged
o Type IV secretion system is common and found in plasma membrane of bacterial cells
 Diagram
o Same explanation as b4
o Important to point out
 This is a gram – cell wall
 In the donor cell, there has to be complex secretory pathways to allow exit
and entry
 Conjugative plasmids can integrate into host chromosome
o Diagram
 There is homologous recombination happening between IS3 sequences or other
insertional elements (like simple transposons)
 There are 2 genes on the chromosome make proline and lac operon
 When integration of plasmid occurs, can see how far apart the genes are
o New DNA between the 2 genes (in the chromosome)
 Formation of high frequency recombination cells
o Occasionally, if the entire chromosome becomes transferable
 The whole thing moves meaning the donor will send a copy of its entire chromosome
and entire content of its plasmid to a recipient that already has a chromosome
 After transfer, now the recipient cell has any duplicated genes; the duplicated
genes will be removed
o But in the process, if the recipient doesn’t have important functions
on the chromosome (didn’t exist b4), they are gain genes from
conjugative plasmid and chromosome as well
 Another way they can exchange genetic information
 Transfer of chromosomal genes by a hfr strain
o Why can’t it just transfer the conjugative plasmid?
 It depends since, the nick occurs in the middle of the conjugative plasmid
 There will be rolling replication; as the replication occurs using the bottom
strand, it will be displaced
 o Now have a part of the conjugative plasmid transfers, then the entire
chromosome and then the remaining part of the conjugative plasmid
transferred
 Odds of this happening is really small
 That’s a lot of DNA transfer so normally some of it
only transfers
o Recipient gets only some new genetic
information and becomes a prime cell (never
got the whole copy of the conjugative
plasmid)
 Transfer of chromosomal DNA by conjugation
o Again normally, there is a break in pili
 Results in some of plasmid and chromosome being transferred = prime cell
 Still f- since it didn’t receive the entire plasmid
 Conjugation with HFR strain
o Again, the recipient cell will be diploid for the duplicated genes; one of them will be lost
 Any new genes will be retained
o Since it received only some part of the plasmid (and some of chromosome), its still f- cell
 Thus, can undergo conjugation with another donor and get the entire conjugative
plasmid (at a later point)
 F plasmids are episomes…
o Important; need specific nicking and control of transfer for the right conjugation
 Sometimes, when an episome that has an incorrect incision can lead to f prime cell
because it didn’t get the full transfer of plasmid but still got new genes
 Certain naturally occurring plasmids can transfer between different kingdoms
o Agrobacterium has a T DNA that found on a Ti plasmid
 T-DNA is what makes it infectious
 Once integrated into plant host chromosome; bacterial cell infected the plant,
leads to disease in plant
 Role in genetic modifications
o Modify the Ti plasmid so that it can enter the plant but not damage or replicate
 Put a cloning site into the T region and the gene of interest
 It disrupts the T-DNA region; no longer infectious
o Plasmid can deliver the new gene to the plant and into its
chromosome
o Samething is happening for frost protection, drought protection and making plants more
colourful
 Delivers the gene using a modified plasmid (transgenic plant)
Lecture 6:

 Col plasmids
o Found in E. coli
 They are conjugative plasmids
 Bacteriocins; they are toxic metabolites to inhibit the growth another bacterial group
 Even tho, it is E.coli; it can move to different species
 o Because the toxins are proteinaceous, different species of different
strains will develop ability to kill bacteria
 Natural flora of skins have bacteriocins
 Some examples of bacteriocins
o Gram positive = thick peptidoglycan (really only the plasma membrane)
o Gram negative = outer membrane with pores to allow movement; peptidoglycan in the
middle and plasma membrane
 Making it more difficult for any kind material to go from outside to inside compared
to gram positive cells
o (a) Gram positive targets
 Class I bacteriocins
 Can do 2 things
o Interact with the lipids that get embedded in the membrane
 By changing it, it can alter the way in which things moves
from cytoplasm to the extracellular space to make
peptidoglycan
 Inhibiting peptidoglycan synthesis
o Organism won’t survive because without
cell wall; its not osmotically stable (will die)
o Can engage with transmembrane proteins and lipids in the membrane
 Can create pores; large enough in the plasma membrane
 Very damaging; things can leak out and things can
get in easily
 Class II bacteriocins
 Involved in making more complex pores
o As you can see, bacteriocins in gram positive cells are trying to
disrupt the plasma membrane in some way (often by making a pore)
 Don’t really get into the cytoplasm
o (b) Gram-negative targets
 Three types of bacteriocins (secreted by different bacteria)
 In gram negative, must go thru pores in the outer membrane called Ompf
(outer membrane protein)
o Different bacteriocins interact with different protein embedded in the
outer membrane
 It is moved to the periplasmic space (where peptidoglycan
is)
 Then they have to move thru other pores
o Some immediately move thru target pore
and get into the cytoplasm; affecting the
DNA gyrase
 DNA gyrase = critical in taking out
super coils so that genome can be
replicated
 Targeting DNA gyrase means that
its effecting its ability to replicate;
going to die
 o Some affect the RNA polymerase
 RNA polymerase = involved in
making mRNA (eukaryotes have 3
different RNA pol while bacteria
only have one major one)
 Targeting the RNA pol = kills the
cells ultimately
o Some have ability to engage with
transmembrane proteins in the membrane;
will inhibit aspartate tRNA synthase
 If cant make aspartate tRNA then
cant make proteins that need
aspartate
o Bacteriocins in the skin are secreted to lower the # of “bad” bacteria compared to the good
ones
o People are now looking into antimicrobial peptides to drill holes into bacteria plasma
membrane
 Not relying on antibiotics
 Bacteria is killed
 Metabolic plasmids
o

Lecture 8:

 Mycobacterium leprae
o Leprosy
 People was isolated and put into leprosy chambers
 Within a subpopulation can end up with autoimmune disease
 Problematic = hard to treat
o There may be a genetic proneness towards the disease
 Hypothesis
o The tissue destruction caused prior to the disease are not cured
 Side effects can remain
o It’s a acid fast…
 If acid fast cell walls are made into vaccines = trigger immune response
 Acid fast bacterial
Lecture 9:

 Location of synthesis of teichoic acids

o Precursors will crosses the membrane
 It needs carriers
 Teichoic acids and lipoteichoic acids continued
o S. mutans = common in the mouth
o Includes the genus; Streptococcus, Enterococcus and Lactococcus
 Lancefield system
o Antigenic nature
 o Group A is most important
 Lancefield groups of selected streptococci
o Table
 Group A
 As time as passed, more virulent strains of group A is developed
o Today, causing severe throat infection
 Able to destroy red blood cells
 Group D
 Commensal (under some conditions can be infectious)
 Opportunistic pathogen
o It makes only people
 Example
o Enterococcus faecalis
 It is resistance to mitomycin
 Streptococcus mutans
o Major component of cavities
 Without sucrose in the mouth, less likely to make capsule
 Cant stick very well; less likely to have an infection
 Group N
 Used for fermentation of milks and yogurts
o Good bacteria
 Group A strep
o Sore throat different from a fever
 Back of mouth covered with white
 It can spread to organs
o Scarlet fever
o Attachment to rashes and deeper tissues
o Rhematic fever
 Damage to heart
o Glomerulonephritis
 Damage to liver if
o Can be put into septic shock
 Some disease caused…
o Cutaneous
 Impetigo
 Crusty rash
o Invasive
 Sequele = secondary infection (without antibiotics in timely fashion)
 Spreads…
o Pharynx
o Tonsils
 Severe sore throat plus fever
 Exotoxin A encoded by lysogenic phage
 TSLS
 First TSLS was identified from staphylococci
  Necrotizing fasciitis
 Bacteria get into facia (separates the muscle from the skin)
o It eats thru it; lose limbs
o Streptococcus pneumonia
 90 serotypes
 Changes its capsule; body not able to recognize new capsule
o Many antibiotics required
 Group A strep continued
o TSLS
 Infection process
 (4)
o Cytokine burst
o Too much infection
 Problem to host
 (5)
o Septic shock
 Sepsis
 Everything is moving thru the body; leads to shock
symptoms (eventually death if unmonitored)
 Septic shock
o Drop in blood pressure
 120/80 is the cutoff value
o Extreme drop in blood pressure
 Muscles won’t work
 Necrotizing fasciitis
o Cellulitis
 Milder form; eats at the cutaneous layer only
o Separates the muscle from the fat
 Not able to get blood
 Black color
o Rate of destruction is 1 in per hr
 Red line moves
o Wash ur cuts
 Symptoms of necrotizing fasciitis
o Hot to the touch
 Caused by the ongoing damage at the site
 What makes S. pyogenes infections so destructive?
o Enzymes
 Streptokinase
 Destroys the blood clot
 Hemolysins
