Midsemester I test MIIM20001 Principles of Microbiology & Immunology

Describe Claviceps purpura:

-it parasitizes rye and other grasses -causes Ergot disease: toxin ingested with grass/grain -can be lethal -can cause psychotic delusion, nervous system problems, abortion

What are some symptoms of scabies

-itchy rash -skin bumps

What is an arthropod?

-largest, most successful group of animals -insects, spiders, crustaceans -live on humans, feed on humans

What is horizontal gene transfer?

-lateral gene transfer -the transfer of genes from one mature, independent organisms to another -it increases the ability of an organism to fit to its environment

Describe anti-fungals:

-limited range -unpleasant side effects -long treatment period -topical/ IV/ orally administered -targets essential components of fungal cell membrane (ergosterol)

How is scabies diagnosed?

-look for burrows in the skin -skin scrapings: looking for mites, eggs, faeces

Why is the cell wall so important?

-maintains cell shape -gives the cell strength -constrains turgor pressure exerted by the cytoplasm which prevents osmotic lysis

What is the spectrophotometry reading method?

-measure of TURBIDITY of a LIQUID culture as an indication of cell number -indicates total cells (living and dead)

How do you treat hookworms?

-mebendazole -pyrantel

Where are chromosomes found in eukarya?

-membrane bound organelle nucleus -more highly organized: histones, nucleosomes, chromatin

How do microbes communicate with each other?

-molecular signals in a density dependent manner

How do bacteria develop antibiotic resistance?

-mutations in key regions in the genome -acquisition of resistance genes from other bacteria via HGT mechanisms -resistance genes have moved from antibiotic produces to non producers

How do you diagnose candida albicans?

-no specific immunological based test yet -look at signs/symptoms/patient history -take a culture

What are spores? (fungi version)

-non motile -permit rapid dispersal by wind, water, animal vectors -survive long periods and harsh environments -useful for fungal identification

Do bacteria move aimlessly?

-nope -chemotaxis (towards attractants, away from toxic stuff)

Describe rolling circle conjugation:

-one strand of DNA is transferred down the pilus -A new complementary DNA stand is synthesized in the donor -synthesis of the new strand is presumably primed by the 3' end generated by a nick at the oriT -the transferred ssDNA strand is then replicated to dsDNA in the recipient

Describe specialized transduction:

-only carried out by temperate phages that have established lysogeny -a SPECIFIC piece of the bacterial genome is transferred -occurs when the prophage is excised incorrectly

What is a helminth?

-parasitic worm -multi-cellular organism

Who published the first drawings of microorgnaisms?

Robert Hooke in 1655

Is there more X-linking in the peptidoglycan in gram positive or in gram negative bacteria?

There is more X linking in gram POSITIVE. This is because gram positive is less porous

How do most bacteria grow?

binary fission

describe facultative anaerobes/facultative aerobes

can grow without oxygen but grow better with it

What is a batch culture?

closed culture vessel containing a single batch of fresh medium

Is bacterial growth faster in nature or in the lab

faster in the lab

What are 2 types of transduction?

generalized specialized

What are repressible genes?

genes whose expression (transcription) is turned OFF by stimulus -ex: trp operon

What are inducible genes?

genes whose expression (transcription) is turned ON by stimulus -ex: lac operon

What parasite causes giardia lamblia?

giardia lamblia (hehe)

What are some sources of carbon/energy in media?

glucose/carbohydrate peptones

What is a replisome?

group of proteins required for replication -it assembles at the origin

What causes histoplasmosis?

histoplasma capsulatum intracellular fungus

What is a subcutaneous mycoses?

involves dermis, muscle, fascia

What direction does replication of bacterial chromosome go?

it proceeds in both directions of the ori (circular chromosome)

What are the bacterial growth curve phases?

lag phase exponential log phase stationary phase death phase

What does LUCA stand for?

last universal common ancestor

What are 2 types of phage infections?

lytic lysogenic

What is the difference between resolution and magnification?

resolution is the ability to clearly determine 2 separate objects as singular, distinguishable entities magification is a microscope's ability to increase size, not clearity

What was the first technology used to make reads?

sanger sequencing

What parasite causes scabies?

sarcoptes scabei

What are 3 types of electron microscopes?

scanning EM (SEM) transmission EM (TEM) ccryotomography (CryoEM)

What causes mutations?

spontaneous -errors in DNA replication -mutagen: base analogues, DNA modifying agents, intercalating agents, UV radiataion

What is mycelium?

tangled mass of hyphae

What are the 3 main groups of helminths?

tapeworms flukes roundworms

how do you prevent hookworm infection?

-avoid contact with contaminated soil -improve hygiene and sanitation

What are the 5 major groups of anti-malarial drugs?

- 4 aminoquinilones: Chloroquine - 8 aminoquinilones: Quinine - Anti-folates: Pyrimethamine - Tetracyclines: Doxycycline - Sesquiterpenes: Artemisinin resistance is a major problem

What can parasitic disease be caused by?

-bacteria -viruses -fungi/algae -protozoa -helminths -arthropds

Describe simple transposition:

-also called cut and paste transposition -transposase catalyzed excision -cleavage of the target site, followed by ligation into site

What are degradative PBPs called?

autolysins

How do you prevent scabies?

avoid contact with infected people -dry clean, hot launder clothes

What are the 3 domains?

bacteria archaea eukarya

What are some basic characteristics of bacteria?

- 1 to 5 micrometers in size -have a plasma membrane -the cell wall contains peptidoglycan -have 70S ribosomes -divide by binary fission

Describe transcription in Eukaryotes:

- 3 types of RNA polymerase -mRNA's have 5' caps and a long poly-A tail (protects from enzymatic attack and signals mRNA is ready for transport) -require several transcription factors -mRNA contains both exons and introns

What is to reference assembly?

-also called read mapping -when you have a reference genome -use a computer to line the reads up -easier to do -Need a reference -faster than de novo

How can you prevent malaria?

(kill all the mosquitos lol) -chemoprophylaxis -insect repellent -bed nets -protective clothing -mosquito control

Describe DNA polymerase III

- E. coli has 5 DNA polymerases -important in replication -assisted by DNA polymerase I - consists of 10 proteins -there are 3 core enzymes in each polymerase; each binds a strand of DNA and is responsible for catalyzing DNA synthesis and proofreading -also has a beta clamp and a Tau complex clamp loader

What does DNA polymerase require?

- a template: direct synthesis of complementary strand, read in 3 prime to 5 prime direction - a DNA/RNA primer -dNTPs

Describe the plasma membrane's lipid composition:

-amphipathic (hydrophobic and philic) -structurally asymmetric -lacks sterols (cholesterol) -many contain hopanoids

What is the definition of a parasite?

-an organism which lives upon or within another living organism at whose expense it obtains some advantage

What are some chronic symptoms of malaria?

-anaemia -spleno and hepatomegaly

who is at risk to get malaria?

- immunologically naive people -children under 5 -many Africans -pregnant women (especially during the first pregnancy) -non immune travellers

How do you obtain a pure culture?

-appropriate sterile culture medium in a sterile container -appropriate incubation conditions -good aseptic technique -a method for selecting a single cell

What is rolling circle replication?

- one strand is nicked -the 3' end serves as a primer -DNA polymerase synthesises a complementary strand from the 3' OH -intact strand serves as a template -displaces the original second strand -the displaced ssDNA molecule then serves as a template and is converted into a double strand circle

What is the leading strand?

- the 3' to 5' strand -this is the template and is read continuously

Describe a Gram positive cell envelope:

- the peptidoglycan is 20-80nm thick - doesn't have an outer membrane -has a small periplasmic space -Contains teichoic acids -Cells retain crystal violet dye during gram stain

How does the divisome form?

-anchoring proteins link the Z ring to the plasma membrane -synthesis of pqeptiodglyan and other cell wall components -constriction of the Z ring -invagination of the cell membrane and synthesis of the septum wall

What are some parasitic hookworms?

-ancylostoma duodenale -necator americanus

What was the Pasteur flask experiment?

-1861 -He took 2 swan neck flasks and put in a broth with microoransisms -He boiled both flasks until they were sterile -One flask's neck was broken. This allowed air and dust in. This flask showed microbial growth -The other flask's neck remained intact. The airbourne/dust particles remained trapped at the base. The broth remained sterile

What is the general approach to annotation of genomes?

-DNA genome sequence -Open reading frame identification -translate DNA sequence to amino acids -homology searches -annotation -woohoo

How is the Z ring assembled?

-FtsZ proteins polymerise to form filaments -portions are constantly being exchanged with the newly formed FtsZ polymers=dynamic assembly

What was Louis Pasteur's contribution to microbiology?

-He helped prove that spontaneous generation of living organisms form non living matter can't occur -He did this by filtering air through cotton wool. After doing so, he found microorganisms that he then was able to grow in a sterile medium

How did Semmelweiss support the germ theory?

-He noted increased incidence of death from puerperal fever in delivering women treated by students/physicians rather than midwives

What is transcription?

-RNA synthesis

What are some issues with adding oxygen?

-ROS is created -ROS can oxidize sulphydryl groups in proteins which denatures enzymes -ROS also damage lipids and nucleic acids

How can candida albicans by transmitted?

-STI -nosocomial infection

How does conjugation work with a mating pair?

-a donor cell produces a pilus -the pilus is encoded for in tra genes -the pilus contacts a recipient cell that doesn't contain the plamsid -retraction of the pilus brings the cells in close contact -formation of a mating pair signals for plasmid transfer to begin -a pore forms in the adjoining cell membranes -transfer occurs

What is a flagella and what does it do?

-a long, thin, hollow, rigid structure -important in motility

What is Oxford nanopore?

-a next generation sequencing technology -portable

What is a transconjugant?

-a recipient cell that has received DNA as a result of conjugation

Describe the streak dilution technique:

-a sample of cells picked up on a sterile wire loop -cells progressively wiped off by streaking along the surface of the agar -flaming of wire loop between sets of streaks -incubation -results in growth of well separated single colonies

What is a primer?

-a short strand of DNA or RNA that primes DNA synthesis -usually 20-25 nts in length -contains a region that is complementary to the target DNA sequence -can contain restriction enzymes sites at their 5' ends or mutant nucleotide sequences

What are some characteristics of a bacterial's plasma membrane?

-about 5-10nm thick -selectively permeable (nutrients/waster) -location of many metabolic processes -encompasses the cytoplasm -has a phospholipid bilayer

What is occurring in the log phase?

-adaptation to the environment is complete -growth is occurring in a constant exponential rate -cells are doubling in number at a regular interval -doubling time is used as a measure of growth rate

What is aspergillus sp?

-aerobic filamentous fungus -found in organic debris

How are hookworms transmitted?

-begins and ends in the small intestine -eggs hatch into larvae in the soil -larvae penetrate the skin often by bare feet -if swallowed, it goes from mouth, lungs, small intestine -larvae develop into half-inch long worms and attach to the intestinal wall and suck blood -adult worms produce eggs that are passed in the stool and contaminate the soil

How does DNA replicate in Bacteria?

-begins at a single point (origin of replication ori) -synthesis occurs at the replication fork -proceeds in a bi-directional manner from the ori -stops at the ter: which is directly opposite the ori

What are some sources of growth factors in media?

-blood -serum -vitamins -they are usually heat labile substances

What is the thallus?

-body or vegetative structure of the fungus -devoid of root, stem, or leaf -varies in complexity and size -in moulds, it is composed of hyphae

What does saprophytic mean?

-breaks down dead organic material via secreted enzymes and then uptake these dissolved nutrients by absorption (osmotrophic)

Why can fungi be bad?

-can cause disease -bio deteriorate foods/wood/organic material -mycotoxin

Describe anaerobes:

-can't use oxygen -obligate (strict) anaerobes are killed by oxygen

What fungus causes Candidiasis?

-candida albicans -aerobic fungus

What does DNA polymerase do?

-catalyse synthesis of DNA

What is occurring in the death phase?

-cells lose the ability to divide and die -total viable cell number decreases exponentially -conditions aren't as supportive of cell division

What is the plasmid structure?

-circular -dsDNA molecules -usually supercoiled -replicate independently of the chromosome -there are variable copes per cell

What does the DNA look like in archaea?

-circular chromosomes -have histones that form nucleosomes (like eukarya) -chromosome is found in the nucleoid -most have a single ori (some have multiple) -it has replisome proteins like eukarya

What do Type II and III restriction enzymes do?

-cleave DNA at specific DNA sequences -usually 4-6 bp long -ex: EcoRI, HindIII

What does the chromosome look like in bacteria?

-closed, circular, supercoiled, double stranded molecule -not membrane bound -found in the nucleoid

What are 2 common bacterial cell shapes?

-coccus (plural=cocci) -bacillus (plural=bacillli)

How are fungi ID?

-colony characteristics, media, colour, texture -presence/arrangement of fruiting or sporing bodies

How did John Snow support the germ theory?

-correlated incidence of cholera with living/drinking water from certain sources

What is the viable count method?

-count colonies produced on a SOLID media as an indication of cell number -indicates total viable cells

What is a cutaneous mycoses?

-cutaneous: involves skin epidermidis -ex: tinea, ringworm -caused by Epidermophyton sp. , microsporum sp. , trichophyton sp. -diagnosed by skin biopsy/scrappings cultured on SAB

Describe roundworms:

-cylindrical bodies -lack specialised attachment organisms

Why are fungi good?

-decomposers -fermenters (bread, wine, beer, soy sauce) -producers (cheese, antibiotics) -research tools

What are some arthropod based diseases?

-dengue fever -yellow fever -plague -relapsing fever -lyme disease -malaria -leishmaniasis

What did Antony van leeuwenhoek do/his importance?

-developed a better/stronger microscope -observed and drew bacteria

What are some symptoms of Giardiasis?

-diarrhoea (leads to weight loss and dehydration -stomach aches -greasy stools (float) -nausea these occur 1-2 weeks after infection they last 2-6 weeks

Describe Slime (outer layer from cell wall)

-diffuse unorganised polysaccharide material -easily washed off -not easy to visualize -facilitates motility -commonly produced by gliding bacteria

what type of growth pattern does histoplasma capsulatum grow in?

-dimorphic: 37C grows in as small budding yeast cells 25C grows as mould producing microconidia

How do you diagnosis Aspergillus?

-direct examination of specimens: hyphae or sporing bodies -culture -immunological based test to detect aspergillus sp. antigens

What are 2 ways peptidoglycan helices join?

-direct linkages -peptide interbridges

How is scabies transmitted?

-direct or prolonged skin to skin contact with an infected person -sharing infected clothing, linens, bedding -crowded conditions

Describe Algae:

-diverse eukaryotic organism -cells can be spherical or filamentous -they photosynthesise using chlorophyll -found in freshwater and marine environments

What are some symptoms of aspergillus in healthy individuals?

-doesn't typically produce disease -allergic responses -if contaminated via food: liver disease and cancer

What are the taxonomy groups?

-domain -kingdom -phylum -class -order -family -genus -species Dear King Phillip Came Over For Good Spices

How do you treat giardia lamblia?

-drink fluids to prevent dehydration -Meronidazole or tinidazole

What is chocolate agar? (CHA)

-enriched medium -7% blood added to sterile NA and held at 80C, then cooled and plates poured -used for very fastidious bacteria -often incubated in CO2

What is the pathogenesis of Giardia lamblia?

-it lives in teh mucosa of the small intestine -it binds to host cell receptor via mechanical sucker -impairs small bowel function/absorption

What are fungi? Describe them:

-eukaryotic organism -cell wall is made of chitin -can't photosynthesize -they require external source of organic compounds (heterotrophic) -they are saprophytic -reproduce by sexual spores (or asexual means) -there are 6 major groups -can be divided into moulds and yeasts (molds=filamentous, yeasts=unicellular)

What are plasmids?

-extrachromosomal, self-replicating DNA molecules -add genetic flexibility -not essential for basic cellular processes

How do you diagnosis for hookworms?

-faecal analysis -there are eggs in the faecal smear

What are some acute symptoms of malaria?

-fever (last 6-8 hours recurring every 2-3 days) -anaemia due to destruction of RBCs -headache -diarrhoea -vomiting

What are 3 types of bacterial motility?

-flagellar motility (propeller like) -twitching -gliding

What are two component signal transduction systems (TCSTS)?

-found in all 3 domains -2 proteins govern this pathway -sensor kinase (transmembrane protein): senses metabolite -response regulator protein: activated by the sensor kinase. Once phosphorylated it binds to DNA sequence that it regulates

How do you prevent giardia lamblia?

-good hygiene practices -avoid contaminated water sources -contaminated water can be boiled or filtered but chlorine treatment won't work

why are reads important?

-he length is important -we need to know how many reads it takes to determine the whole genome sequence -EX: if the genome is 3 million bps and your machine does 100 reads of 300 bps in length then you only read 30,000bps which doesn't cover the entire genome

What are the components of a bacteriophage?

-head (capsid), collar, sheath, base plate, tail fibres, and tail pins

What are some other cloning methods used?

-homologous recombination -Gibson cloning -SLIC, LIC, TAR

What is HBA?

-horse blood agar -its an enriched medium -5% blood added after sterile NA cooled to 50C -used for fastidious bacteria -indicator of haemolysis

How do you treat candida albicans

-if topical: anti fungal creams, Lozenges -if systemic: Ketocanazole, flucanzole -in general: azoles -no vaccines

Who shows symptoms from candida albicans?

-immunocompromised individuals -disrupted normal flora individuals

How can transduction occur?

-imperfect excision of the prophage from the host genome in lysogenic infections -some bacterial DNA may accidentally be included in the forming phage particles during packaging

How do genomes vary?

-in size -in DNA content -richness in AT -number of genes -types of genes

Where is histoplasma capsulatum found?

-in soil rich in bird/bat shit (guano)

What is the life cycle of Giardia?

-ingest comtaminated water -cyst phase: dormant, infectious -trophozoite: actively growing, causes disease -once infected, the parasite lives in the intestines and is passed in faeces

How is aspergillus sp transmitted?

-inhalation of fungal spores -ingestion of contaminated food/water

How is histoplasma capsulatum transmitted?

-inhalation of spores

What is the lagging strand?

-is replicated discontinuously -there is no free 3' OH -it requires multiple RNA primers -DNA polymerase III copies in opposite direction to replication fork movement: from one primer to the next (Okazaki fragment) -DNA pol I fills in the gaps between fragments and removes the primers -Ligase joins fragments together by forming phosphodiester bonds

Describe aspergillus flavus

-it contaminates fungi -fungi -heat stable aflatoxins are produced and ingested with food -causes liver disease and cancer

Why is HGT so important?

-it explains why there are large degrees of phenotypic diversity in bacterial species that have little diversity in the 16s rRNA genes -provides organisms with important mechanisms to acquire new genes= enhanced ability to respond to the environment

Describe RNA polymerase

-it is a DNA dependent RNA polymerase -complex of many proteins -produces a 5'-3' mRNA from a 3'-5' template

What is giardia lamblia?

-it is a diarrhoeal disease -most common waterbourne disease -causes Giardiasis

What is a basal media?

-it is a general purpose base media -used to grow non-fastidious microbes

What is MacConkey agar? (MAC)

-it is a selective indicator medium -contains bile salts, lactose, neutral red -used in isolation and enumeration of coliforms and intestinal bacterial pathogens

Where is candida albicans found?

-it is normal flora in GIT, RT, vaginal area, and mouth -worldwide

Describe cerebral malaria:

-it is responsible for almost all deaths from malaria -caused by P. falciparum -infected RBCs adhere to vascular epithelial cells

What is a promoter?

-it is the RNA polymerase recognition/binding site -it orients the RNA polymerase to the correct location ready for transcription -located upstream the coding region -it isn't transcribed or translated -Sigma factors and RNA polymerase bind the Pribnow box sequences -variations in promoter sequence allows for variation in expression

What is used today to classify microorganisms?

-small subunit rRNA molecules

Describe the process of binary fission:

-parent cell enlarges and duplicates chromosome -septum growth starts -chromosome and cytosolic components move to opposite ends -septum and new wal synthesis completes -daughter cells divides (in some species they remain attached)

What are some mechanisms of uptake of nutrients by bacteria?

-passive diffusion -facilitated diffusion -active transport -siderophores (iron uptake) most are taken up against a concentration gradient most must cross a selectively permeable plasma membrane

How do you diagnosis malaria?

-patient history -symtoms -blood smears: peripheral blood is collected and the smears are prepared and stained with Giemsa stain

What are some sources of nitrogen in media?

-peptones -protein hydrolysates

What are the 3 phases in the bacterial cell cycle?

-period of cell growth -DNA replication and partitioning -cytokinesis

How is scabies treated?

-permethrin cream -ivermectin in severe cases

What are some sources of inorganic elements in media?

-phosphates -sulphates -usually don't have to be added because they are normally present as contaminants

What does the bacterial cell envelope include?

-plasma membrane -cell wall -some have: outer membrane, capsule, slime layer, S-layer

What are contributors to horizontal gene transfer

-plasmids -phages -transposons

What are miasmas?

-poisonous vapours -This is what people believed caused/spread disease

What does PCR require?

-primers (forward and reverse) -DNA polymerase -dNTPs -template -co factors -specific sequence of temperatures (thermal cycling)

What is translation?

-process of turning mRNA sequence into protein sequence -ribosomes bind mRNA at the Shine Dalgarno sequence located slightly upstream from the start codon of the coding region -once bound, the ribosome forms peptide bonds between amino acids donated by tRNAs -sequence is read off the mRNA ini sets of 3 bases

What is genome annotation?

-process that locates genes in the genome map -preformed by a computer -identifies each open reading frame within the genome

What is conjugation?

-process whereby certain plasmids can transfer themselves and other DNA elements, from one cell to another -DNA moves from the bacterial cells containing the plasmid through a pilus -DNA moves from the donor to the recipient cell

What is cytokinesis?

-processes that apportion the cytoplasm and organelles, synthesize a septum, and divide a cell into 2 daughter cells

how do you prevent histoplasma capsulatum?

-protective clothing/masks -soil decontamination

What are some symptoms of aspergillus sp. in immunocompromised individuals?

-pulmonary infection -leads to dissemination to brain, kidney, liver, etc

What are some symptoms from hookworms?

-rash, itch at site of infection -mild diarrhoea and cramps -anaemia, abdominal pain, loss of appetite and weight loss -in heavy, chronic infection: stunted growth and mental development

what is a trailer?

-region immediately following the stop codon -it is transcribed -signals the end of protein during translation: stops the ribosome

What is a leader?

-region of DNA located between the promoter and the coding region -it is transcribed -it isn't translated -directs the ribosome to bind -contains the transcription start site and the shine-dalgarno sequence

What is the coding region?

-region of DNA that is transcribed and translated -bounded by start and stop codons

Describe S-layers (outer layer from cell wall)

-regular arrays of protein or glycoprotein -found in GP, GN, archaea -protects against the environment -helps in cell shape, rigidity, adhesion

What are types of global regulatory systems?

-regulatory proteins -alternative sigma factors -2 component signal transduction systems -phosphorelay systsems

What is parasitism?

-relationship between 2 organisms: one is the parasite, the other is the host

Describe the cell wall:

-rigid -just outside the plasma membrane -strength is due to peptidoglycan -is one of the main differences between gram positive and gram negative

What are some arthropod infections

-scabies -head lice -pubic lice (crabs)

What is the CRISPER region?

-sets of repeated nucleotide sequences separated by short spacers -associated with cas genes -stands for clustered regularly interspersed short palindromic repeats

What is fimbriae (pili) and what does it do?

-short, fine, hair-like appendages -they are used to attach to surfaces -type IV is used for motility and uptake of DNA in transformation -mostly found on GN

What was Koch's significance?

-showed specific microorganisms caused particular diseases -showed bacillus anthracis caused anthrax in 1876 in cattle -perfected methods for sterilization, disinfection, and filtration -discovered causative agents in tuberculosis and cholera -established postulates to link a particular microorganism with a particular disease

What are some characteristics of archaea?

-similar shapes to bacteria -often 1-10um -cell wall is made of glycoprotein, not peptidoglycan -L amino acids used in X-links -membrane lipids are ether linked, not ester linked= more stable in extreme pH and heat -many are extremophiles: thermophiles, halophiles

What are 2 mechanisms of transpositions?

-simple -replicative

What are some bacterial cell arrangements?

-single cells -chains -clusters

What are the best generally lab conditions for growing fungi?

-slightly acidic, low moisture -SAB or MEA -aerobic -25-27C

What was wrong with Koch's original postulates?

-some pathogens are part of the normal microbiota -some pathogens can't be grown/cultured -some pathogens are only found/cause disease in humans -in some diseases more than one pathogen is the cause

Where does the replication of bacterial chromosome start and end?

-starts at the origin of replication (ori) at a single point -ends directly opposite the origin (terminus ter)

How do you diagnose Giardia lamblia?

-stool samples

What are 2 ways to select a single cell?

-streak dilution -limiting dilution followed by spread/pour plate -goal is to progressively dilute the cells of a sample until there is one cell per unit volume

What are some symptoms of histoplasma capsulatum?

-takes about 10 days -fever, cough -head and muscle aches -MOST often assymptomatic -infects lung macrophages but rarely disseminates

What effects growth rate?

-temperature -ion composition -ion concentration -amount of oxygen -nutrient concentrations -restraints (predation, antibiosis) -energy available -amount of nitrogen -pH -water and solutes -pressure -radiation

Describe biofilms:

-the are attached microbes in complex, slime-encased communities -ubiquitous in nature -dynamic and heterogeneous in composition

What is occurring during the lag phase

-the cells are metabolically active but not increasing in number -cells are adapting to the new environment -synthesis of enzymes, ribosomes, etc -large production of energy

Describe how Horizontal gene transfer works:

-the donor DNA is exposed to the recipient cell -conjugation/transformation/or transduction occurs -there is now a partially diploid recipient cell -then the cell can undergo 4 fates: integration of donor DNA, donor dNA self replicates and is a plasmid, the donor DNA can't self replicate or integrate, or restriction or CRISPR/Cas degradation of donor DNA occurs -there are 2 end results: population of stable recombinants, or no stable recombinants

Why is iron uptake difficult

-the ferric iron (Fe3+) is extremely insoluble -iron is often a limiting nutrient -almost all microbes require iron -many bacteria/fungi secrete siderophores

What were Koch's original postulates?

-the microorganism must be present in every case of disease but absent in healthy organisms -the suspected microorganism must be isolated and grown in pure culture -the sam disease must result when the isolated microorganism is inoculated into a healthy host -the same microorganism must be isolated again from the diseased host

Describe a Gram negative cell envelope:

-the peptidoglycan is 2-7nm thick (smaller than GP) -there IS an outer membrane -the periplasmic space is large -Contains LPS -cells don't retain crystal violet dry during gram stain

What is host range?

-the range of bacterial species of bacteria in which the plasmid can repliate -broad=replicate many species -narrow=restricted to a single species

How are DNA and RNA similar?

-the sugars are both linked together by phosphodiester bonds

What is occurring during the stationary phase?

-the total number of living cells remains constant -new cells are made at the same rate as old cells die -nutrients become more limited, wastes accumulate, etc -critical cell population is reached

describe replicative transposition:

-there are 2 genes coding for enzymes: transposase and resolvase -the original transposon REMAINS at parental site in DNA -the copy is inserted into the target DNA

What is the lifecycle of malaria?

-there are 2 hosts: mosquito and a vertebrate -it is spread by female mosquitoes (Anopheles genus) -There is 2 life cycles, in the liver and the blood

How is a new cell wall made during binary fission without compromising the cell's integrity?

-there is a balance between degradation and synthesis/insertion of peptidogylcan

What does a high turbidity mean?

-there is a higher cell number -there is a lower transmittance of light through the culture -the higher the absorbance of light (less light reaches sensor), the higher the cell number

What is next generation sequencing?

-these are just new technologies that sequence genomes -they are cheaper, take less time, and have a larger data output than Sanger sequencing

What are insertion sequences?

-these are the simplest transposable elements -IS elements -only encode the genes for transposase

What are restriction enzymes?

-they are bacterial enzymes that protect against an attack from incoming foreign DNA -they restrict (digest) the foreign DNA within a cell -usually cuts in a palindromic sequence

Describe tapeworms and flukes:

-they are platyhelminths -they have flattened bodies -muscular suckers or hooks for attachment -generally large with a complex body organisation

What are antisense RNAs?

-they bind to the mRNA leader sequence making a dsRNA molecule -this inhibits ribosome attachment and translation

Why do people use enriched cultures?

-they chemically inhibit other bacteria -they nutritionally favour the desired bacterium -its a manipulated environment to suit the desired bacterium

What are transposons (Tn)?

-they exist in all organisms -discovered in corn by Barbara woohoo -A transposable element is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size.

How do bacteria protect themselves against ROS?

-they possess enzymes and pigments that detoxify ROS -many anaerobes don't have these mechanisms, so they can only live where there isn't oxygen

What are some features of transposons?

-they range in size (1-5kb to 38kb) -all contain inverted repeats -during transposition, the target site is duplicated at either end to produce direct repeats -are found in plasmids, phages, and conjugative

What is a lysogenic infection?

-this is a temperate phage -ex: lambda -have lytic cycles -the phage genome integrates into the host genome (prophage) -the phages genome replicates with the host's DNA (inherited in bacteria's offspring) -the prophage can excise itself from the host's DNA via induction and then revert to the lytic cycle

What is a lytic infection?

-this is a virulent phage -ex: T4 -these phages lyse their bacterial host cells

What is copy number?

-this is the average number of single plasmid type per cell -it is well regulated -small plasmids have higher copy numbers

What does WalKR control?

-this protein controls cell wall synthesis

Describe operons:

-transcribed from a single promoter -can encode for more than one gene product

What is transduction?

-transferring bacterial DNA between bacterial cells

What are composite transposons?

-transposable elements which contain additional genes (other than those used for transposition) -encode for antibiotic resistance, resistance to heavy metals, virulence factors

Where are hookworms most common?

-tropical and subtropical countries -it causes serious health problems for newborns, children, pregnant women, malnourished people

How do you treat histoplasma capsulatum?

-typically resolves spontaneously -anti fungal drugs

What is metagenomics?

-understanding complexities of a mixed genomic population -DNA from environmental samples -this is important because 99% of all bacteria can't be cultivated

Describe protozoa:

-unicellular eukaryotic organism -least evolved of the Eukarya -very diverse -usually motile -extensive use of vacuoles -obtain food by ingesting other organisms or organic material -mostly free living, some are parasites -can be transmitted by insect, ingestion fo infective stages, or STI

Describe yeasts:

-unicellular fungi -reproduce asexually by budding/fission or sexually by spores -generally larger than bacteria

What are 3 plasmid replication schemes?

-unidirectional -bidirectional -rolling circle

What is theta replication?

-unidirectional and bidirectional replication -most common -basically the same mechanism as chromosome replication -1 or 2 replication forks

what is transformation (DNA uptake definition)?

-uptake of naked DNA by bacteria -more random -any free DNA in the environment can be taken up -bacteria that do this are called competent -cells can be naturally competent or be made competent

what is an enriched media?

-used for the fastidious microbes

How did Lister support the germ theory?

-used heat sterilization and phenol to reduce incidence of surgical infections

Why are plasmids useful?

-useful for cloning genes -can use then as structures/vectors to move genes between bacterial cells

Describe electron microscopy:

-uses beams of electrons -x100,000 better magnification than light microscopes -wavelength is waaayyy smaller than that of visable light which makes the resolution much better -the cells are dead and stained with chemicals

Describe Moulds:

-usually multicellular -produce filamentous or branched hyphae -can produce macroscopic fruiting bodies -reproduce sexually by fusion or hyphae or asexually by spores

What is the hyphae?

-vegetative organ of the fungi -grow when fungal spores germinate -long, branched, thread-like filaments

What is a bacteriophage?

-viruses that use bacteria as their host -possess one type of nucleic acid as their genome -usually dsDNA (mainly linear) -only reproduce inside host cells -have no independent metaolism

How do you treat aspergillus?

-voriconazole -itraconazole -depends on treating the underlying disease to increase host resistance -no vaccines

Describe capsules:

-well organised polysaccharide material -not easily washed off -aids in cell adhesion -protects against dehydration, phagocytosis, bacteriophage attack, toxic stuff -can be seen in negative staining

Describe generalized transduction"

-when any part of the bacterial genome is transferred -occurs primarily during the lytic cycle of virulent phages -during phage assembly, fragments of host DNA is mistakenly packed into phage head

What are riboswitchs?

-when mRNA leader sequence directly binds metabolite. this causes the mRNA to fold differently -this impedes access to ribosome binding site= impeded translation

What is transposition?

-when segments of DNA can move about the genome

What is an intermediate host?

-when the host serves as a temporary but essential environment for development of a parasite and completion of its lifestyle

What is comparative genomics?

-when you compare whole genome sequences within populations of bacteria -allows you to trace evolution: drug resistance, antigen variation -allows tracing transmission and spread of resistance bacteria in populations

What does the ori determine?

-where replication starts -host range -copy number

What is de novo assembly?

-you have a bunch of reads -they overlap by at least 4 bps -you line up the sequences -the overlapping regions allow you to line them up -there is NO reference to align against

How many genomes does genomic analysis look at?

1

What are the steps of the CRISPER/Cas system?

1) CRISPR adaptation: integration of foreign DNA fragments into CRISPR array as spacers -this is then transcibed into a long pre-crRNA which encodes the repeats and spaces and form the CRISPR array 2)CRISPR RNA biogenesis: processing the pre-crRNA into crRNAs 3) CRISPR interference: foreign DNA degradation

What are the stages of transcription?

1) Sigma factor interacts with the RNA poly core enzyme and directs it to a promoter, by interacting with the -35 sequence of the promoter 2) RNA poly unwinds a short stretch of DNA in the -10 region of the promoter, forming an open complex. Sigma interacts with this single stranded region stabilising the open complex 3)RNA poly core begins synthesizing RNA. After about 12 ribonucleotides have been linked together, the sigma factor dissociates from the core RNA poly, and transcription enters the elongation phase 4)Elongation continues until a terminator is encountered. RNA poly ceases transcription and the RNA is released

How do you sequence a genome?

1) generate DNA sequence reads -extract DNA from target -put this in a sequencing machine -the machine outputs reads 2) assemble -assemble the reads into one continuous DNA sequence 3)Annotate -identify the genes and features

Describe Sanger sequencing:

1)isolate unknown DNA fragment 2)Denature the DNA to produce a single template strand 3)Add a labelled specific primer molecule to hybridize the DNA strand 4) in 4 different tubes: add DNA polymerase, dATP, dCTP, dGTP, dTTP (these are in different tubes) with the foreign DNA. These nucleotides are labelled with a tracer 5)the newly replicated strands are terminated at the point of addition of a dd nucleotide 6)load these onto a gel and electrophorese them to see how they line up by size

List the biofilm formation steps:

1-substratum precondition by ambient molecules 2-cell deposition 3-cell absorption 4-desorption 5-cell to cell signalling and onset of exopolymer production 6-convective and diffusive transport of O2 and nutrients 7-replication and growth 8-secretion of polysaccharide matrix 9-detachment, erosion, and sloughing

How often do errors occur in replication?

10^-8 errors per base pair

What direction does DNA polymerase add in?

5 prime to 3 prime

What direction does DNA synthesis occur?

5 prime to 3 prime direction -needs a free 3 prime OH at the end of the growing strand

how many possible reading frames are there?

6 -there are 3 forward -there are 3 backward -mRNA is translated by reading codons which consist of 3 nucleotides so each mRNA has 3 possible reading frames

What is one of the most common mycoses in humans?

Aspergillus

What causes Aspergillosis?

Aspergillus sp.

How are DNA and RNA different? (nucleotide...)

DNA -Cytosine, Guanine Adenine, THYMINE RNA -Cytoine, Guanine, Adenine, URACIL

What is a missense mutation?

DNA change alters a single amino acid within a polypeptide sequence

What is a nonsense mutation?

DNA change creates a premature stop codon which truncates the amino acid sequence

What is a silent mutation?

DNA change doesn't alter the amino acid squence

What is the basis flow of info to get gene expression?

DNA to RNA to protein

What is the size difference between eukaryotic ribosomes and bacterial ribosomes?

bacterial: 70S (50S and 30S)

What malaria parasite causes the most malignant infections?

P. falciparum

How is peptidoglycan synthesised?

PBPs are involved: -they link strands of peptidoglycan together -it controls degradation of the peptidoglycan layer to allow insertion of new units It grows due to the FtsZ placement

What 2 scientists proved the germ theory?

Pasteur and Koch

Who first used a microscope to view microorganisms?

Stelluti in 1625-1630

What are some polymerases that are commonly used?

Taq Pfu

What are Koch's molecular postulates?

Virulence gene (VG) -VG must be found in pathogenic strains -V must be expressed during infection/disease -mutation/deletion of the VG decreases pathogenicity -replacement/restoration of the VG mutation/deletion restores pathogenicity

What is a transformant?

a bacterial cell that has taken up DNA

What is a divisome?

a collection of proteins that aggregate at the region in a dividing cell where a septum will form

What is a mycoses?

a disease caused by infection with a fungus, such as ringworm or thrush.

What is a transmission vector?

a living organisms that transfers an infective agent between hosts

What is a frameshift mutation?

addition or removal of a base alters the reading frame of the gene

What is the terminator?

arnold schwarzenegger (lol no) -signals RNA polymerase to stop transcription

Where are fungi found?

mainly terrestrial organisms -usually aerobic -dark, moist environments

What is the dominant life form on earth?

microoragnisms

how many genomes does comparative genomics look at?

multiple

Are there any vaccines for giardia lambia?

no

Are there any vaccines for malaria?

no

Are there any vaccines for scabies?

no

Do all conjugation systems involve a pilus in mating pair formation?

no

are there vaccines for hookworm infections?

no

What makes up the bacterial genome?

nucleoid: single chromosome of closed circular dsDNA Plasmids: -there may be more than one -they replicate independently of the chromosome

What is growth rate?

number of generations per unit of time

What is nutrient agar called when made without agar?

nutrient broth

What is the centre of a phylogenetic tree called?

origin

does oxygen diffuse faster in air or in water?

oxygen diffusion is 10^4 greater in air than in water -it can take years for it to diffuse in water depending on how deep it is

What was the first way microbials were classified?

phenetic system -based on phenotypic characteristics

What is a promiscuous plasmid?

plasmids that can move DNA between unrelated species

What is an incompatibility group?

plasmids with similar mechanisms of replication are incompatible -one will be preferentially replicated over another

What parasite causes malaria?

plasmodium spp (single celled protozoan parasite)

What does PCR stand for?

polymerase chain reaction

What are genes?

polynucleotide sequences that code for a functional product

How can you ensure that you are working with just one microbe?

prepare a pure culture

what is septation?

process of forming a cross-wall (spetum) between 2 daughter cells

What is cloning?

process that allows us to make many copies of a specific gene -this is generally done via PCR

How does a flagella work (motion)?

propeller like manner

How often does transposition occur?

rarely 1:10^-3 to 10^-8 -similar to other mutation rates -it is tightly regulated

What is an example of bacteria that has similar gene sequenes, but due to plasmids have very different phenotypes?

the Bacillus spp. B. anthracis: toxic against mammals B. thuringiensis: toxic to insects B. cereus: causes food poisoning they are all closely related by 16s gene sequences but the presence/absence of plasmids encode these different factors

what is a host?

the host is where the sexual reproduction (or sexual lifecycle) of the parasite occurs

In HIGH temperatures are there more saturated fatty acids or unsaturated fatty acids in bacterial PMs?

there are more SATURATED

In LOW temperatures are there more unsaturated fatty acids or saturated fatty acids in bacterial PMs?

there are more UNsaturated

What is the purpose of inclusions in bacteria?

they are mainly used for storage -they are aggregates of organic and inorganic material

What is the importance of ribosomes?

they are the site of protein synthesis: translation

describe microaerophiles:

they need oxygen, but at lower than atmospheric concentration

Describe obligate aerobes

they require oxygen

When is nutrient agar used?

to culture/store non fastidous bacteria

What is FtsZ?

tubulin like protein

When do you use a selective media?

when you want to encourage the growth of some microbes but suppress the growth of others

When do you use an indicator/differential media?

when you want to see a change when the microbe grows -there is usually a component that causes an observable change

Can plasmodium spp. parasites infect other animals?

yes

Are mutations heritable?

yes -add a level of variability into genes

Who is most susceptible of Giardia lamblia?

young children and pregnant women