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Microbiology 255 - Part 1 of course 2021
Module 1

Microorganisms - organisms that too small to be seen with just the eye - usually think of bacterial cells


-decompose organic waster


-producers in the ecosystem by photosynthesis


-produce industrial chemicals ie ethyl alcohol and acetone


-produce fermented foods ie vinegar, cheese, bread


-produce products used in manufacturing and treatment ie insulin


-a few are pathogenic, disease - causing

**Understand so allow humans to prevent disease occurrence — led to aseptic techniques in
labs and medicine

Germ- rapidly growing cell, generically used for microbes (pathogen)

Scienti c naming


-Linnaeus est
...
Organism has 2 names : the genus [broader category] and speci c epithet (species
- have most if not all same characteristics; ex
...
The genus is capitalized and the species name is lower
case


-Latinized and used worldwide


-May be descriptive or honor scientist


-After rst use, scienti c names may be abbreviated w/ rst letter of the genus and the
speci c epithet
...
coli) — problem is same letter but 2 di names

-3 domains of life (cell types):


-Bacteria (prokaryote)


-Archae (prokaryote)


-Eukarya



-protists (slime molds, protozoa)



-plants (mosses, ferns , owering plants)



-fungi (unicellular yeasts, multicellular molds, mushrooms)



-animal (sponges, insects , worms, vertebrates)



-algae

Woese-Fox classi cation system - 3 domains of life


-Phylogeny - degree of relatedness between groups of living things



-shows much better view of common ancestry and relatedness

Bacteria


-prokaryotes


-peptidoglycan cells walls
...
Pasteurization

Germ theory of disease: microorganisms cause disease


-Bassi - silkworm disease was caused by fungus


-Pasteur - another silkworm disease caused by protozoan


-Semmelweis - advocated hand washing to prevent transmission of puerperal fever
(uterine in ammation) from one OB patient to another during childbirth


-Lister - used chemical disinfectant to prevent surgical wound infections ; treat bandages and wounds with phenyl

-Koch - provided proof that a bacterium causes anthrax and provided the experimental steps , Koch’s postulates, used to provide that a speci c microbe causes a speci c disease (working w/cattle that died from bacterial infection/anthrax, cultured
microorganism that causes diseases’ and injected this into healthy cattle, harvested that
blood when cattle got sick and found same organism)

Edward Jenner and Immunity

-dairymaids who had mild cowpox infections were protected from smallpox

-Hypothesis: cowpox infection provides protection against smallpox

-Expt(1798): inoculated boy w/ cowpox uid and later challenged w/ smallpox uid

-Result: boy did NOT get smallpox

-Called Vaccination from vacca for cow [pasteur developed this name] —> lead to immunity


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Treatment w/ chemicals is chemotherapy:

Chemotherapeutic agents used to treat infectious disease can be synthetic drugs (prepared
from chemicals in the lab) or antibiotics (chemicals produced by bacteria and fungi that inhibit
or kill microbes)

-Ehrlich - developed synthetic arsenic drug , Salvarsan to treat syphilis


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-Hypothesis that living organisms arise from nonliving matter = spontaneous generation [a ‘vital
force’ forms life]

-Alternative hypothesis that living organisms arise from preexisting life = Biogenesis


-Sulfonamides were synthesized in 1930s - inhibit enzymes of folate metabolism in microbes
but humans don’t have same metabolic pathway

-Fleming - discovered 1st antibiotic; observed that Penicilium fungus made an antibiotic , penicillin that killed S
...
g
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Use harmless virus to carry missing or new gene into certain host cells, where the
gene is picked up and inserted into the appropriate chromosome (use for SCID, ADA)
...
Bacteria and fungi can produce a variety of proteins including vaccines and enzymes through this

Genetically modi ed organisms often use bacterial genetic components to protect crops from
insects, chemicals and freezing

temp, ph , and presence or absence of chemical cmpds determine if microbiota stay

Transient microbiota

Antibiotics used to treat bacterial infections but have NO impact on viruses and other microbes

When looking at unicellular life, rapid progress made in genetics


microbial genetics - mechanisms by which microorganisms inherit traits


molecular biology - looks at how genetic info is carried in molecules of DNA


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Sewage treatment - uses microbes to recycle water

Bioremediation - uses microbes to clean up pollutants


Insect pest control by microorganisms

Resistance - ability to ward o disease

Bio lm - microbial community that forms as a slimy layer on the surface


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Antibiotic resistance


MRSA and less sensitivity to vancomycin —> vancomycin resistant S
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4 and 13

2
...
2

Prokaryotic cells —- BACTERIA

-avg size: 0
...
0 micro meters x 2-8 micro meters

-monomporphics shapes: all cells have constant shape


-coccus = round


-bacillus = rod shape
...
g
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3

Prokaryotic Structures:

Always require: cytoplasm, plasma membrane, 70S Ribosomes, nucleoid containing DNA

^Glycocalyx
...
Paired cocci within capsule

^Flagella —Use for movement


-Outside cell wall


-Made of chains of agellin


-Attached to a protein hook


-Anchored to the wall and membrane by the basal body


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Motic Cells


-Rotate agella to run or tumble




-CCW: swimming motion, CW: bacterial cell change direction


-Move toward or away from stimuli (chemotaxis)


-Flagella proteins are H antigens
...
g
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- agella w/in cell, wrapped around body of cell beneath plasma membrane


-Endo agella


-in spirochetes


-anchored at one end of a cell


-rotation causes cell to move

Fimbriae and Pili
...
Allow attachment



-Gliding motility



-Twitching motility


-Pili - used to transfer DNA from one cell to another

2
...
— UNIQUE TO PROKARYOTIC CELLS

-Prevents osmotic lysis

-made of peptidoglycan (in bacteria) - around plasma membrane


-Peptid
...
Cell wall


-thick peptidoglycan layer (located on exterior surface of the cell)


-Teichoic acids

-Gram neg
...
— all cells take up crystal violet stain and

become purple


2) add alcohol


-Gram pos
...
__PINK OR RED



-Alcohol dissolves outer membrane and leaves holes in peptidoglycan



-CV-I, washes out (bc degrades LPS layer and purple color leaves so cells are
clear, then colored red or pink by stain saccharin)


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Atypical cell walls


-Acid fast cell walls



-Like gram pos cell walls



-Waxy lipid (mycolic acid) bound to peptidoglycan








-Mycobacterium (tuberculosis)


—Use acid fast stain for this unique cell wall


Damage to cell wall


-Lysozyme digests disaccharide in peptidoglycan


-Penicillin (many antiobiotics) inhibits peptide bridges in peptidoglycan


-Protoplast - wall-less cell


-Spehroplast - partially wall-less cell



-Protoplasts and Spheroplasts are susceptible to osmotic lysis


-L Forms - wall-less cells that swell into irregular shapes

2
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6 inside the cell

-Nuclear area w/ DNA (nucleoid) -[not enclosed in membrane bc prokaryote]



-Bacterial cell can have chromosome and plasmids (smaller circular DNA, contain
genes that have nothing to do w/ basic fn of cells but control external processes: antibiotic resistance)

-Ribosomes for protein synthesis


-70S (composed of over 30 proteins and rRNA)


-S = svedburg units (centrifuge sedimentation)



-50S (large subunit) + 30S (small subunit) subunits = 70S

[Eukaryotic 80S (60S and 40S)]

-Cytoplasm is the substance inside the plasma membrane

-No nucleus so transcription (conversion of DNA to RNA) and translation (ribosomes read RNA
for protein) can be coupled/occur in tandem

-Inclusions/Deposits found in some bacteria [these substances become insoluble at high concentration]
...
——therefore, much more di cult to ght o bacteria that can create
spores bc if unfavorable envt then can become dormant

-Metabolically inactive (still alive)

-resistant to desication, heat and chemicals

-sporulation occurs during stress (unfavorable envt)

-Bacillus, Clostridium —— these species will create spores

-Sporulation: Endospore formation

-Germination: return to vegetative state (occurs when spore nd a favorable envt)

2
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— CAN CAUSE DISEASE


-Molds



-the fungal thallus (growth) consists of hyphae ; a mass of hyphae is mycelium


-Yeast
...
- classi ed by site of infection rather than by the organism


-Systemic mycoses - deep within the body


-subcutaneous mycoses - beneath the skin


-cutaneous mycoses - a ect hair, skin , nails


-super cial mycoses - localized ie hair shafts



-opportunistic mycoses - caused by normal microbiota or fungi that are usually not
pathogenic




2
...
— very speci c, only infect 1 kind of plant or animal and then only
infect 1 cell type within that organism

-evolve quickly

-Capsid - the protein shell that encloses the viral genome


-build from proteins called Capsomeres (glycoproteins)

-Some viruses also have lipid membranes


-Viral envelope — don’t necessarily need this



-contains capsid - protein cap



-aids entry to cell

**All have genetic material and capsid

*all viruses constructed same way but can con gure selves di erently


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Prions - proteins that cause brain diseases in mammals [not viruses]

-infectious proteins that build up in nervous tissue - proteins misfold and clump together, nonliving , contain no genome (RNA, DNA)

-propagate by converting normal proteins into the prion version —- cause degradation of nervous system

-Creuzfeldt Jakob disease - acquired (vCJD) or inherited

-PRNP gene —> PrP normal protein

-Scrapie; Mad cow Disease (BSE)


Module 3 - read chs 5-6

3
...
5, molds and yeast grow between pH 5 &
6, acidophiles grow in acidic envts


-Osmotic pressure



-hypertonic envts - increase salt or sugar, cause plasmolysis [plasma membrane
pulls away from cell wall]; honey -very much sugar, high osmotic pressure for any bacteria in
that substance = inhospitable to bacteria so honey very rarely spoil



-extreme or obligate halophiles require high osmotic pressure



-facultative halophiles tolerate high osmotic pressure

3
...
—candle produces extra CO2


-CO2 - packet — gas generator


3
...
— use CFU (colony forming units)

-bacteria mainly undergoes binary ssion - single cell to 2 cells 1-> 2-> 4 -> 8

—1 bacteria could create a colony in less than a day but cannot grow forever

-Growth plots are linear on a log scale (y-axis = log of binary ssion events of cells; x-axis =
generations) —- log gives better indication of the trend - see exponential growth


-Log Phases:



-Lag Phase
...
Bc # of organisms w/in a culture can be
very high
...
Find best plate = most statistically signi cant plate - the plate comes from ex
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4 Bio lms

-microbial communities; forming along solid surfaces ; in natural or industrial settings

-form slime or hydrogels(if excessively hydrated w/water-] [composed by macromolecules:
polysaccharides, proteins etc]


-bacteria communicate by chemicals via quorum sensing — get community of bacteria
to work in unison

-share nutrients

-bio lms allow sheltered from harmful factors


-environmental waste products, antibiotics


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3
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6 Enzymes

-Activation energy
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Collision energy required for chemical rxn to occur


-collision theory states that chemical rxns can occur when atoms, ions and molecules
collide
...
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7 Enzymatic activity —inside cell = endo-enzymes

-enzymes can be denatured by temp and pH (protein shape will change) — prevent enzyme
from working properly and that part of metabolism will also stop - can lead to death of cell


-In uenced by temp, pH, substrate concentration (-saturation)—bc enzymes can only
work so fast



-Competitive inhibition - competitive inhibitor t into substrate site where it
binds



-(Allosteric inhibition )noncompetitive inhibition - inhibitor select portion of enzyme that’s not location where substrate binds — protein/enzyme changes shape a bit and this
shape change prevents substrate from binding at its location



-Feedback inhibition/ end product inhibition - nal product of metabolic pathway
can act as inhibitor at early step by binding to early on enzyme - this is normal mechanism of
cellular control ; when enough product is made = metabolic pathway can stop to conserve energy and resources
...
8 Energy


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-metabolic pathway - sequence of enzymatically catalyzed chemical reactions in a cell; determined by enzymes


-enzymes are encoded by genes


-breakdown of carbs to release energy : Respiration (aerobic)
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1 into to genetics

Genetics - study of what genes are, how they carry info, how info is expressed, and how genes
are replicated

Gene - segment of DNA that encodes a functional product, usually a protein

Genome - all of genetic material in a cell


1st fully sequenced organism was a bacterium in 1995 [since have very small genome
size]

Genomics - molecular study of genomes

Genotype - genes of an organism

Allele - variant of a gene

Phenotype - expression of the genes

DNA

-polymer of nucleotides: adenine, thymine, cytosine, guanine

-double helix associated w/proteins

-backbone is deoxyribose-phosphate


-sugar phosphate

-2 strands held together by hydrogen bonds between AT and CG

-strands are antiparallel


-5’ (free phosphate group) and 3’ (free hydroxyl group) at opposite ends

*nucleotides: phosphate group, carbohydrate, nitrogenous base (A,T,C,G)

4
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New strand used to create new DNA
strands [each new dNA molecule is identical to the original one]

- Semiconservative - ea
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3 microbial genetics

-How genes expressed and regulated in Prokaryotic cells

-Plasmids — independent from bacterial chromosome [but also circular, but smaller]



-conjugative plasmid - carries genes for sex pili and transfer of the plasmid


-Dissimilation plasmids - encode enzymes for catabolism [break down carbs/nutrients]
of unusual compounds


-R factors - encode antibiotic resistance

-Flow of genetic info options:


-Vertical gene transfer - how genetic info/dna transferred parent to o spring



-pairs up w/process of replication previously discussed


-horizontal gene transfer - transfer dna to unrelated organisms that exist in the same
generation [Recombination- exchange of DNA and incorporation of that DNA into the host
genome/chromosome]


-cell reading coded message in own genes and make expected products

-DNA is transcribed to make RNA (mRNA, tRNA, rRNA)
...
[ribosome attach to mRNA at speci c sequences] to create protein


-one such sequence is shine dalgarno sequence



-Each codon corresponds to one amino acid




-Amino acids form long chain to make protein

*prokaryotes = no nucleus in bacterial cells SO can have transcription and translation occurring
in tandem w/one another; nearly no processing of mRNA molecule

Regulation of bacterial gene expression

-constitutive enzymes/proteins are expressed at a xed rate

-other enzymes are expressed ONLY as needed


-Repressible enzymes


-Inducible enzymes —- Lać operon {lactose operon} - genes transcribed here required
for lactose breakdown ; allolactose binds repressor/operator (trigger conformational change;
protein no longer binds to operator so…
...
4 genetic Mutations


-change in the genetic material

-DNA polymerase delity - the ability to make an exact copy of the chromosome

-Mutations can be neutral, bene cial or harmful

-Mutagen - agent that causes mutations

-Spontaneous mutations - occur in absence of a mutagen

-spontaneous mutation rate: 1 in 10^9 replicated base pairs of 1 in 10^6 replicated genes


-Mutagens increase this rate to 1 in 10^5 or 1 in 10^3 per replicated gene

-STOP codons: UAA, UGA, UAG


-redundancy built into system but product/protein could be changed



-change codon but still get same amino acid

-START codon: AUG (a
...
=Met)

-Mutation — point mutations:


-Base substitution (point mutation) - change in 1 nitrogenous base/nucleotide


-Silent mutation - no amino acid change


-Missense mutation - change codon such that result in change in amino acid



-nonsense mutation - results in a nonsense codon [stop codon] - don’t get full protein
being created


—Frameshift mutation: - insertion or deletion of 1 or more nucleotide pairs



—-catastrophic disruption of protein


—Ionizing Radiation (x rays and gamma rays) - causes the formation of ions that can
react w/nucelotides and the deoxyribose phosphate backbone
...
— spot chemical mutagens/carcinogens

*experimental tube (take mutated bacteria usually salmonella - can’t produce a
...
histodine)
and control tube


-mutate DNA such that gene that disrupted to initially make it a mutant, and revert that
bacteria back to its original state


—Take these tubes of His- salmonella and put on medium lacking histamine and if see
colony growing from experimental group, means the mutagen that you chose worked to make
it His+

4
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Even though plasmid integrated
can still be transferred, part of HFR can give part of DNA to recipient cell [recipient cell still recombinant cell even if got only partial or full genes from donor cells]

-Transduction - Use Virus as means to transfer DNA from 1 cell to another cell (need infection
process) —- bacteriophage (viruses target only bacteria) - delivers own genetic material into
cell, codes for protein, breaks chromosome down - -if virus brings broken down chromosome
to new cell then that cell becomes recipient cell/make recombinant cell

-Transformation - some bacteria have RECEPTORS for DNA incorporation/incorporate exogenous dna (naked DNA) - Competent bacteria; holes in the cell membrane can allow the DNA to
enter


-in lab: use heat, electrical shock, chemicals i
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salt to create holes in membrane

Transposons aka jumping genes


-segment of DNA that can move from one region of DNA to another - movement mediated through enzyme: transposase - cut DNA and allow for incorporation of DNA into new region ie insert antibiotic resistance gene


-contain insertion sequences for cutting and resealing DNA (transposase)


-complex transposons carry other genes


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Plasmids, viruses, transposons [ie insert gene of interest into plasmid - make recombinant DNA molecule] - mimics natural process/that process in nature

-Clone: population of cells arising from 1 cell; each carries the new gene


-genetically identical cells (puri ed colonies considered clonal or clones)

*some bacteria changed/manipulated to clean up toxic waste ETC

AND sometimes gene grown in bacteria to then be extracted and transferred to other organisms - give to something that wouldn’t make product normally

AND sometimes just want new protein - harvest the protein [ex
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1 – control terminology

--how better control mirobial growth

Sepsis – microbial contamination

Asepsis – absence of signi cant contamination

Aseptic surgery techniques – prevent microbial contamination of wounds

Sterilization – removal of ALL microbial life


-commercial sterilization – remove endspores too [applied to can foods to prevent food
poisoning]

Disinfection – removal of pathogens from inanimate objects

Antispesis – removal of pathogens from living tissue {disinfection of living tissues}

Degerming – mechanical removal of microbes from a limited area via washing or chemical antispetic

Sanitization – lower microbial counts - to safe level for public health (clean public restroom/
utensils at a restaurant)

Biocide/Germicide – kills microbes [su x -cide]

Bacteriostasis – inhibiting, not killing, microbes


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E ectiveness of antimicrobial tx depends on:

-Bacterial populations die at a constant logari

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