Microscopes-

Optical Microscopes-
Stereo(dissecting)-basic 3d image, 100x max resolution
Compound(Brightfield)-1000x max resolution using an objective and ocular lens
Confocal Laser Scanning Microscope-produces a 3d image of the specimen using computer
software, for research institutions
Electron Microscope-high energy electrons are shot at the specimen, usually a cell or particle
and can magnify up to 2mil times. Specimen needs to completely dehydrate and is sometimes
covered in a metal coating for protection
Scanning electron- specimen is stained with gold and palladium and produces a 3d
black and white image(lower magnifying power)
Reflection electron- they track how the electrons have been scattered elastically to
produce an image
X-ray microscope-in between electron and optical in magnification and resolution, but it has an
advantage with being able to look at live specimens. It can slice together 1000s of images to
create a cohesive 3d model
Scanning helium ion microscope-helium ions to create a high quality image comparable to
electron but with ions of low energy, so specimen is left intact
Neutron microscope-still experimental but can use neutrons to create better images than
electron
Scanning Probe Microscope- it individualizes atoms and creates a 3d image based on how high
the atom is(if its sticking out of the surface) it slowly combs through the specimen and creates a
detailed 3d image, lots of computer usage and electrical signals
Confocal microscopy-identifies fluorescent particles in specimens and creates 3d models
Phase Contrast Microscopy-Uses variations in light when passing through a transparent
specimen
Inverted-the nosepiece and illuminator have basically switched spots and the arm comes
straight from the base.

Parts of compound microscope:

Ocular-magnifies the image from the objective lens
Nosepiece-holds the objectives and lies below the arm and body tube
Base-supports the microscope
Objective-lens that creates the first image by receiving light from the field of view
Arm-connects to the base and holds up all the above parts
Body tube-connects the ocular and objectives
Coarse Adjustment and fine adjustment- the knobs to enhance viewing
Stage-supports the slide and specimen
Clips-holds lens in place
Illuminator-source of light, sometimes lumarod(rod that collects light) is used if it’s not electric
Diaphragm controls how much light reaches the specimen
Principles of Microscopy
-if something is moved up and right, it will look like it moved down and left in the microscope
-total magnification is found by multiplying ocular and objective
-when changing to a higher magnification, size of field view decreases, field view darkens, the
size and resolution increase, the depth of focus and working distance decreases
-Some microscopes refract light with their lenses, which depends on temperature and different
mediums biconvex lenses causes light to converge, biconcave lenses causes light to diverge
Field of view determination: field number/magnification number
Scales

Topic 2:
https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(Boundless)/01%3A_Introducti
on_to_Microbiology/1.02%3A_Microbes_and_the_World/1.2.01%3A_1.2A_Types_of_Microorga
nisms
Prions-pathogenic misfolded versions of normal proteins PrP(major prion protein) encoded by
gene PRNP-provides an evolutionary benefit
Normal PrPc becomes PrpSc, which form clumps of protein called amyloid fibrils a bunch of
these fibrils called amyloid plaques clump in the CNS and the prions undergo
vacuolation-which forces the prions into the vacuoles and makes them look like holes
-Prions can be random, genetic, or from something outside

Prion Like Proteins

-different from prions because they are missing some of the steps: an infectious agent* (these
proteins may cause or be associated with disease, but are not necessarily infectious as they do not
enter new hosts), reservoir, portal of exit*, mode of transmission*, portal of entry*, and susceptible
host. Infectious transmission of prion-like proteins from one host to a new susceptible host has never
been recorded,

Viroids
-infect flowering plants(angiosperms) and don’t have a protein coating
-they have circular RNA that replicates using RNA Polymerase II and they can disrupt cell processes

Viruses
-Have RNA or DNA in a capsid which is made up of capsomeres and protomers
-Viral particles are called virions
-Viruses affect all kingdoms, ones that infect bacteria are called bacteriophages
-Capsoids
-helical ones look rod-shaped(tobacco)
-polyhedral ones look like icosahedron
-Spider looking bacteriophages have an elongated icosahedron
-viral envelopes can make non-spherical viruses look like spheres
Baltimore classification
● Class I viruses are double-stranded DNA viruses
● Class II viruses are single-stranded DNA viruses
● Classes III viruses are double-stranded RNA viruses
● Class IV viruses are positive-sense single-stranded RNA viruses
● Class V viruses are negative-sense single-stranded RNA viruses
● Class VI viruses are RNA retroviruses
● Class VII viruses are DNA retroviruses
Lytic
-Virus injects its genome and the cell unwittingly makes mRNA from the virus and then makes viral
proteins that destroys the host cells DNA, the virus still uses the cell parts to make viruses until the
cell eventually lyses
Lysogenic
-Virus integrates its DNA into the host in a section called the prophage where it lays dormant until it’s
active after a few generations where it leaves the cell’s DNA and starts protein synthesis.

Satellite Viruses and Nucleic Acids

Needs a helper viruses the genomes are circular or linear and have no double stranded RNA.
Difference between them is whether there is a capsid around the genetic material, nucleic acids
need the helper virus for thier capsule. Hepatitis D is a satellite with Hepatitis B as a helper.
Virophages:
Virophages only have circular or linear double stranded DNA. They are similar to satellite viruses,
but they hijaack the cytoplasmic virus factories that their helper virus created. The helper viruses are
nucleocytoplasmic Giant viruses generally. This makes the virophage kill the giant virus and kinda
screw itself over. Examples are Sputnik and Zamilon.

Virusoids:
Considered to be a type of satellite. They are basically viroids that have been enclosed in the capsid
of another virus. They use botht he hlper virus and host cell’s Rna Polymerase II for replication and
they are ciruclar single stranded RNA.

Prokaryotes:
-Bacteria and archaea(are not pathogenic) are prokaryotes
-Divide by a process of binary fission, and no chromosomes are formed so after DNA replication
cytokinesis immeadiately happens
-There are sphere, rod, spiral, club, comma, and pleomorphic bacteria that alter shape based on
their environment
Bacterial Transcription Trnaslation DNA replication and gene regulations via operons

Gram Staining:
-Classify bacteria on the basis of cell wall structure
-Bacteria are first heat treated to hold the pirmary stain and keep them in place and then are treated
with 4 different reagents
1.Cationic primary stain(usually crystal violet, which stains cells purple or methyl blue) is taken up by
both gram pos and gram neg cells. Crystal violet will seperate into pos and neg ions and the pos
ions associate with the negatively charged particles on bacterial cell walls
2.A mordant (usually Gram’s iodine solution) contain anions that cover cells with the positive
particles on the surface, which make it harder to wash out the primary stain with decolorizer. It acts
as a color trapper.
3.A decolorizer(acetone or ethanol usually) is used to wash off the primary stain, which will only work
on the nagtive ones because the psoitive ones are trapped by the mordant.
4.A counterstain(often safranin, basic fuchsin, or carbol fuchsin all pink/red) will stain both gram
positive and negative cells, but because the positve stain is dark and purple, you can’t really see it.

Gram Positive: thicker walls of peptidoglycan, lack periplasmic space, lack an outer membrane,
example is Lactobacilli
Gram Negative: thinner walls of peptidoglycan, periplasmic space, and generally aerobic, more
difficult to kill gram negative with antibiotics
Limitations:
Not effective for acid-fast bacteria, they stain weakly gram negative and although similar to gram
negative bacteria have totally different cell surfaces. Cells without cell walls(L-form) are also unable
to have a proper gram stain.

Fungi:
-like animals, chitin cell walls
-in acidic environment to create a gradient for chemiosmosis for extracellular digestion
-usually humid environment
-sterols in plant, animal, and fungi to maintain the cytoplasm, most common in fungi is ergosterol
Lichen:
-symbiotic relationship between a mycobiont fungi and a photosynthetic organism
Protists:
The catch-all group of eukaryotic organisms, plant-like ones often called eukaryotic algae and
animal-like protozoa. Some are multi-cellular and do not have specialized tissue. Difference between
algae and protists are blurry
Eukaryotic algae:
Eukaryotic photoautotrophs that are not plants and cyanobacteria. They have different pigments, no
cuticles, and different plastids
Protozoa:
Very complex, some have two nuclei, they eat others and have some form of motion, they also can
form cysts, which is like a form of hibernation in a cocoon until they can get a good meal

Worms :(
Flatworms:
-no body cavity, excrete and nutrients through passive diffusion,only nervous system, bilateral
symmetry
-Turbelleria are basically worms that are parasites that also eat normal food, but the classification is
actually wrong phylogenetically
-Neodermata
-Cestodes-includes tapeworms and other worms that infect fish
-they have proglottids and chains of them form the strobilia which is the body
-they produce starting from the head(scolex), so the ones at the start are young and small and the
later ones are older and bigger, also hermaphroditic
-they have hooks and suckers near the head and the tegument is the skin coating that helps with
absorption
-Trematodes are leaf like and sometimes called flukes and specific ones infect certain organs no
hooks or suckers
-Monogeneans-infect fish not humans and are hermaphroditic

Roundworms(Nematode):
-they have a digestive tract with a mouth, and an excretory pore which is same for male
reproduction(cloaca) and a separate one for females
-they kinda have false body cavities because they only have mesoderm on one side instead of both
-hydrostatic skeleton and cuticle rich in collagen to stop expansion as hydrostatic pressure builds up
-the ones that go after plants have a spear called a stylet
-common ones are hookworm and pinworm

Thorny Headed Worms-spiny headed worms that are modified Rotifers that sometimes infect
digestive tract

Microbial Metabolisms:
-obligate aerobes need oxygen but obligate anaerobes can’t do high concentrations of it
-microaerophiles need some oxygen but can’t stand too much
-facultative anaerobes- can use oxygen or not depending on the environment their in
Aerotolerant anaerobes-don’t need oxygen but can live anywhere
Pasteur effect-help to distinguish between aerotolerant and facultative anaerobes based on the
amount of fermentation products there are

Bacterial Culture and Growth:

Batch culture vs. Chemostatic-batch means closed and no additional nutrients are added, for
chemostatic nutrients are continuously added to maintain a constant environmental level

Liquid vs Solid: liquid makes more uniform growth conditions, but harder to separate the bacteria
than in the agar conditions.

Defined media vs undefined media: You know what’s in it versus kinda but not really

Selective vs Differential media: selective encourages growth of a certain bacteria and may kill others;
differential will show indicators and certain growths in the presence of the target bacteria.

Lag Phase- stuff is in synthesis and getting ready to double

Exponential growth-constant doubling, better conditions mean longer slope, fast ones mean steeper
slope and generation time can be calculated here
Stationary phase-cell death and birth are about equal
Decline or death phase-accumulation of waste products or depletion of food
Long term stationary phase-sometimes observed in lab settings where cell birth and death rates are
high and can stay that way for a while at a steady population

If the efficiency of binary fission is assumed to be 100%, then the formula for modeling bacterial
growth is:
, where P = current population size at time t, Po = initial population size, t = time
elapsed since t = 0, and g = generation time. Note that
 number of generations since t = 0. If the efficiency of binary fission were instead less than 100%,
this would mean that there is a chance any given parent cell results in only one viable daughter cell.
In this case, the formula we would use is:
, where e = efficiency.
The Monod equation is as follows:
µ
µ

.
where P = population size, t = time, µ = growth rate of population (negative values indicate
population is decreasing), µmax = the maximum possible growth rate, [S] = the concentration of the
limiting nutrient, and KS = the concentration of the limiting nutrient at which the current growth rate is
half of the maximum (i.e., [S] at which μ/μmax = 0.5).
Symbiogenesis:
Mitochondria, chloroplasts, plastids, and other organelles descended from prokaryotes. Mitochondria
from alphaproteobacteria and chloroplasts are descended from cyanobacteria
They have their own dna, replicate separately, have cell walls like bacteria, similar inner and outer
structure to bacteria
Scientists believe that they came into eukaryotic cells through symbiosis, but even cells who have
lost their symbiotes still have lasting evolutionary change, which could be the reason for major
evolutionary events

-antibiotics
-metagenomic 16/18s
-bacteria transcription translation replication
-bacterial gene regulation with operons
-horizontal gene transfer(transduction, transformation, conjugation)

Extra Notes:
Protists are MOSTLY single celled eukaryotic organisms with dna in plasmids while archaea and
bacteria are single celled prokaryotic organisms

Mychorrhizae- mutualistic relationship between plants and fungi

Gram Positive - has a cell membrane covered by a thick wall of peptidoglycan, called murein that
protects itself from hydrophobic chemicals because those are usually the dangerous ones. They are
totally unique to bacteria which is why antibiotics work so well on them! The walls also have proteins
on the surface along with techoic acids for bonding with other bacteria
Gram Negative - Has inner membrane, thin murein layer, then outer membrane and between the two
membranes is 2 periplasm spaces which is super unique made of lipopolysaccharide. It only allows
hydrophilic compounds through the outer membrane. Most have pili which are like smaller flagella

Bacterial DNA Exchange:

Transformation-one cell donates dna to another and it integrates into their genome
Conjugation-the small plasmid contains dna separate from the genome that transfers using pili
Transduction-bacteriophages will infect a bacteria, but they might pick up some DNA from one
bacteria and spread it to another when it tries to infect a new one.

Viruses have envelopes made of a phosphlipid bilayer that fuses with the animal cell and allows it to
release the capsid into the cell.

Bacteria-plasmids often carry resistant genes. The proteins synthesized from those genes will help
in different ways. Sometimes antibiotic degrading enzymes, efflux pump on the membrane to push
out antibiotics from the bacteria, some of the proteins modify the antibiotic binding protein.

Modes of action:
If antibiotic kills-bactericidal if it slows down growth-bacteriostatic

Some of them target the cell membrane and mess up osmosis-such as polymyxins
Some of them target cell wall by inhibiting cell wall synthesis-bactericidal and are penicillin
Some inhibit dna and rna synthesis - quinolenes and rifamycine
Some inhibit protein synthesis - erythromycin - bacteriostatic
Some inhibit folic acid metabolism by stopping conversion of PABA to folate - sulfonamides

Acidophile-neutrophiles-alkiliphiles
Obligate aerobe→facultative anaerobe grows w or w/o oxygen but is better with→aerotolerant
anaerobes-doesn’t matter to them →obligate anaerobes can’t survive in presence of oxygen

Prokaryotic transcription and translation: They happen together, as soon as mRNA is created
through RNA polymerase, the ribosomes are translating it immediately and part of it is because there
are no separate organelles or anything, so those two steps take place in the same place as opposed
to eukaryotes
Prokaryotic DNA Replication - it starts at oriC, it’s basically eukaryotic just in a loop. Ligase repairs
okazaki fragments and it moves 5’ to 3’ direction.

Operons:
Positive transcription factors make RNA polymerase make more and negative transcription factors
tell RNA polymerase to chill out
Operons are mostly in prokaryotes. DNA polymerase needs a primer to know where to start but RNA
polymerase needs a promoter to know where to start. The next part is the operator, and sitting on
top of the operator is the repressor, RNA polymerase cannot move forward if the repressor is
blocking it.
Lac - lactose binds to the repressor, which makes it unable to bind to the operator and unblocks it
Trp(from e coli genome) - when tryptophan is not bonded with the repressor, the repressor is unable
to fit onto the operator, when trp is connected to the repressor, then it can connect to the operator
and stop RNA polymerase from moving forward

Acid fast bacteria are just bacteria with some sort of property that makes it hard for the acidic
decolorizers in stainings to work on the bacteria

The great plate count anomaly - it is the difference between the amount of bacteria we know exist
and the amount we can actually grow. We know it exists because there are far more bacteria we can
count under a microscope than we can grow on a plate.

Industry applications
- kombucha fermentation - yeast is used to hydrolyze sucrose which turns into glucose and
fructose which are then metabolized to ethanol. From there, acetic acid bacteria(AAB)
oxidize the ethanol and create acetic acid, which gives kombucha a sour taste
- Algal biofuels - algae produce oil that can be used as replacements for common gasses like
renewable diesel and jet fuel. The already existing tanks can still be used for these new
fuels. The carbohydrates from the algae can be fermented to create ethanol and butanol and
biomass from algae can be used for pyrolysis oil or combined heat and power generation.
Advantages to using biofuels is that they can be farmed on non-arable land using saltwater
or brackish water. Even though they make up less than 2% of carbon plants, they fix up to
0% of atmospheric carbon into organic carbon, and they also produce up to 50% of our
oxygen.
- Bioremediation - the use of microbes to clean contaminated water or soil. It may take several
years for a place to undergo successful bioremediation. Harmful chemicals are consumed
and changed into water or harmless gasses. People need to make sure that first the helpful
bacteria are in the soil, known as the process of bioaugmentation. Then the bacteria need
ideal growth conditions such as temperature and nutrients, which can be fixed by adding
“amendments”
- Phage therapy - the use of bacteriophages to kill a bacteria. Has been used for the past 80
years and is advantageous because it helps kill bacteria that are antibiotic resistant. Usually
harmless to the host, the struggle is finding the perfect phage for a particular bacteria. Phage
cocktails are sometimes given if there is uncertainty. Antibiotics and phages have issues with
biofilms, which are basically a slimy layer of bacteria around wet surfaces. They form their
own Extracellular Polymerics Substances(EPS) that allows them to stick together and grow
to create a complex 3D structure that allows for waste removal and energy consumption and
it makes it harder to kill them.
Describe types of microbial interactions, ie competition, cooperation, and parasitism
- Mutualism - each organism receives a benefit but is obligatory so the relationship is
necessary for survival
- Cooperation - each organism receives a benefit but is non-obligatory
- Commensalism - one is benefited while the other gets nothing
- Amensalism - one organism is harmed while the other is normal
- Parasitism - one benefits at the cost of the other
- Predation - one eats the other
 - Competition - both competing for the same substrate and one might grow and crowd out the
other
xvi. Causes and effects of microbial population explosions in the context of algal blooms, thrush, and
Enterocolitis.
- Algal blooms - caused by wastewater, fertilizer, or some other chemical with ideal growing
conditions that cause algae to grow, it is often recognized by discoloration in water due to
algae pigments. They can lead to extinction events by preventing sunlight from reaching the
bottom zones of the ocean and it can take up other nutrients. HABs(Harmful algae blooms)
can release toxic chemicals that harm the environment.
- Thrush - caused by the fungus Candida Albicans where there is a multiplication of the fungus
all over the mouth and tongue that crowds out other organisms and occurs when something
throws the body off of equilibrium, like antibiotics.
- Enterocolitis - the pseudomembranous type is caused by the bacteria Clostridium difficile(C.
diff.) and is caused usually by taking antibiotics to fight another infection. Many antibiotics
don’t kill C. diff., but many antibiotics kill bacteria that would kill the C. Diff for you, which
causes it to grow unfettered.
Culture-independent methods to study microbial communities: 16/18s rRNA amplicon sequencing
and metagenomics, basic sample preparation and data analysis procedures for these techniques

xi. Contrasting photoautotrophic vs. heterotrophic metabolic strategies, describe metabolic strategies
of
green sulfur bacteria, iron oxidizing, heterotrophic, and cyanobacteria based on energy and carbon
Source.
[1]
How the organism obtains carbon for synthesizing cell mass:
● autotrophic – carbon is obtained from carbon dioxide (CO2)
● heterotrophic – carbon is obtained from organic compounds
● mixotrophic – carbon is obtained from both organic compounds and by fixing carbon
dioxide
2. How the organism obtains reducing equivalents (hydrogen atoms or electrons) used either in
energy conservation or in biosynthetic reactions:
● lithotrophic – reducing equivalents are obtained from inorganic compounds
● organotrophic – reducing equivalents are obtained from organic compounds
3. How the organism obtains energy for living and growing:
[2]
● phototrophic – energy is obtained from light
[citation needed]
● chemotrophic – energy is obtained from external chemical compounds
In practice, these terms are almost freely combined. Typical examples are as follows:
● chemolithoautotrophs obtain energy from the oxidation of inorganic compounds and
carbon from the fixation of carbon dioxide.
● photolithoautotrophs obtain energy from light and carbon from the fixation of carbon
dioxide, using reducing equivalents from inorganic compounds.
● chemolithoheterotrophs obtain energy from the oxidation of inorganic compounds, but
cannot fix carbon dioxide (CO2).
 ● chemoorganoheterotrophs obtain energy, carbon, and hydrogen for biosynthetic
reactions from organic compounds.
● photoorganoheterotrophs obtain energy from light, carbon and reducing equivalents
for biosynthetic reactions from organic compounds. Some species are strictly
heterotrophic, many others can also fix carbon dioxide and are mixotrophic.

Photoautotrophic - they use photons for energy to create organic materials from sunlight, water, and
carbon dioxide. They fix carbon dioxide into carbon by using biosynthesis and respiration. Carbon is
fixed into PGA through the Calvin cycle
Heterotrophic - gets carbon from organic materials and uses that for biomass production
heterotrophic bacteria aka chemoorganoheterotrophic bacteria make up the majority and they use
organic compounds as carbon and energy sources. They are able to digest more organic materials
than bigger creatures
Green sulfur - photolithoautotroph and is gram negative. They reduce sulfur as an energy source
and use light
Iron oxidizing - chemolithoautotroph and reduces dissolved iron and produces a reddish brown slime
wasteproduct
Cyanobacteria - photolithoautotroph that reduces nitrogen and carbon while using water as an
electron donor

Identification of bacterial cell shapes (i.e., rods, cocci, spirochetes);

Cocci - spherical shaped are monococcus, diplococcus where they are arranged in pairs,
streptococcus are arranged in a chain like pattern on a plane, tetrads are groups of 4,
staphylococcus looks like grapes, sarcinae are groups of 8.
Bacilli - rod shaped there are many taxonomic groups of rod-shaped bacteria, those belonging to
bacillus are gram positive, can form endospores, they are the most abundant bacteria, can withstand
extreme heat, and only two known species are pathogenic, anthracis(anthrax) and cereus(food
poisoning) diplobacilli are pairs, streptobacilli are arranged in a chain, coccobacilli are oval shaped,
palisades are a fence like structure.
Spiral bacteria - they are spiral or helical in shape, the gram negative spirillum are generally more
rigid and have flagella on the outside, spirochetes are thin and flexible and pathogenic.
Vibrio - they are comma shaped and generally gram negative that cause foodborne illnesses.
Extra - filamentous, star shaped, rectangular, sheathed, lobed, pleomorphic change their shape
based on different factors, appendaged have budding bacteria, trichome is chain of vegetative cells
covered in slimy substance, fusiform are spindle shaped that bulged in the middle and tapered at the
end, stalked where a stalk forms due to asymmetrical cell division

Techniques to determine antibiotic susceptibility, mechanisms of antibiotic resistance and resistance

transfer, Distinguish between bacteriostatic and bactericidal antibiotics(see above)
Techniques - the Kirby Bauer method basically puts the microbe in different levels of concentration of
an antibiotic and determines if the growth on the agar plate is sufficient enough to say resistant,
intermediate, or susceptible.
Mechanisms and transfer - The antibiotic is unable to enter into the bacteria(cough cough gram
negative), the bacteria produces pumps that flush out the antibiotic, change or destroy the drug
through enzymes or proteins made by the bacteria, change the targets of the drug, for example if the
drug targets a certain protein on the cell wall, the bacteria may stop producing it, the bacteria could
also stop using the process that the antibiotic targets, if the antibiotic disrupts process A, the bacteria
may have another way to survive without that process

viii. Bacterial transcription, translation, and genome replication

i. Culture-independent methods to study microbial activity (i.e., metatranscriptomics, proteomics,

metabolomics)
Metatranscriptomics - Metatranscriptomics is dealt with the study of extraction and analysis of
metagenomic mRNA (metatranscriptome) that provides the information about the regulation and
expression profiles of complex microbial communities present in the environmental sample.
Metatranscriptomics provides a snapshot of the gene expression in a given sample at a given
moment and under specific conditions by capturing the total mRNA
Proteomics - Proteomics is the study of the interactions, function, composition, and structures of
proteins and their cellular activities[2]. Proteomics provides a better understanding of the
structure and function of the organism than genomics. However, it is much more complicated
than genomics because the protein expression is altered according to time and environmental
conditions. Gel electrophoresis is an example of proteomics mostly looks at the protein
interactions and expressions of certain genes.
Metabolomics - Metabolomics is the large-scale study of small molecules, commonly known as
metabolites, within cells, biofluids, tissues or organisms. Collectively, these small molecules and
their interactions within a biological system are known as the metabolome. metabolomics is the
study of substrates and products of metabolism, which are influenced by both genetic and
environmental factors (Figure 1).Metabolomics is a powerful approach because metabolites and
their concentrations, unlike other “omics” measures, directly reflect the underlying biochemical
activity and state of cells / tissues. Thus metabolomics best represents the molecular
phenotype.
-Transcriptomics - Transcriptomics is the study of the transcriptome—the complete set of RNA
transcripts that are produced by the genome, under specific circumstances or in a specific
cell—using high-throughput methods, such as microarray analysis. Comparison of
transcriptomes allows the identification of genes that are differentially expressed in distinct cell
populations, or in response to different treatments.

ii. Phage lambda cro repressor system

-Bacteriophage lambda infects e.coli and possibly more bacteria when c1 is active, cro is repressed
and vice versa. When cro is expressed, the virus does the lytic cycle, when c1 is active, the virus
does the lytic cycle

iii. Control of lac and trp operons for research applications

iv. Functions of microbes in lakes and oceans, soil, and the gut microbiome
Lakes and oceans - viruses kill algal blooms(awwww) microorganisms make up between 70 and 90
percent of all biomass in the ocean and they act as decomposers. They do most of the
photosynthesis in the ocean and they are responsible for cycling of carbon , nitrogen, and
phosphorous. In lakes they convert detritus to nitrate, phosphate, and sulfate.
v. Describe metabolic strategies of sulfate reducing, purple sulfur, and purple non-sulfur based on
energy and carbon source
Purple sulfur - phototrophic and they use sulfide, sulfur, thiosulfate, or hydrogen as electron donors.
They are mostly photoautotrophic though
Purple non sulfur - typically use hydrogen as an electron donor, sometimes sulfide, thiosulfate or
ferrous iron however they are mostly photoheterotrophic and can use a variety of organic
compounds as both electron donor and carbon source
vi. Phylogenetic methods to detect horizontal gene transfer (i.e., comparing gene and species
phylogenies)