Microbio Exam 2
Hfr cell
a cell with the F plasmid integrated into the chromosome
repression
- inhibition (turning off) of a gene expression
nucleic acid synthesis inhibition
- inhibits DNA or RNA synthesis - not very useful as it can affect host DNA/RNA - unique features of bacterial DNA synthesis are targeted - ex: rifamycin, quinolones, fluoroquinolones
what's the mode of action of ciprofloxacin?
- inhibits nucleic acid synthesis (inhibits DNA replication or repair) - used to treat UTIs
chemically defined media
exact chemical composition is known
genotype
genes of an organism
constitutive genes
genes that are expressed all the time
structural genes operon
genes that code for proteins
how does phosphorus affect growth?
it's required for synthesis of cellular material
how does sulfur affect growth?
it's required for synthesis of cellular material
how does nitrogen affect growth?
it's required for synthesis of cellular material (i.e. protein synthesis)
bactericidal
kills microorganisms
B-lactam ring in antibiotics
portion of the penicillin drug molecule that can break a bacterial cell wall
bacteriostatic
prevents microorganisms from growing
exon
a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence.
anticodon
a sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA.
mutagen
agent that causes mutations
genome
all the genetic material in a cell
antisepsis
destroying harmful microorganisms from living tissue
selective toxicity
drug that kills harmful microbes without damaging the host
aseptic
free from disease-causing microorganisms
tRNA
- transfer RNA - transfers AAs into peptide (translation of RNA into AAs/protein)
heavy metals
- Ag, Hg, Cu - oligodynamic action - denatures proteins - silver nitrate used to prevent ophthalmia neonatorum - mercuric chloride prevents mildew in paint - copper sulfate is an algicide - zinc chloride is found in mouthwash
DNA replication
- DNA is copied by DNA polymerase (enzyme) - in 5' to 3' direction (DNA polymerase only adds nucleotides to the 3' end of nucleic acid) - initiated by an RNA primer 1. enzymes unwind the parallel double helix 2. proteins stabilize the unbound parental DNA 3. leading strand is synthesized continuously by DNA polymerase 4. lagging strand is synthesized discontinuously - RNA polymerase synthesizes a short RNA primer, which is then extended by DNA polymerase 5. DNA polymerase digests RNA primer and replaces it w DNA 6. DNA ligase joins the discontinuous fragments of the lagging strand
transformation
- DNA is transferred as "naked" DNA in a solution - cells must be competent
conjugation
- DNA is transferred between bacteria that are in contact w each other - contact bw donor and recipient is made by a sex pilus or a conjugation pilus - DNA is transferred through a conjugation bridge bw donor and recipient cell (only one strand transfers) - mediated by a plasmid (F factor) aka conjugative plasmid - they carry genes for conjugation
transduction
- DNA is transferred by a bacterial virus (bacteriophage) - mediated by bacteriophage - DNA from donor is transferred to recipient via a phage particle - types: generalized and specialized
oxidizing agents
- O3, H2O2, peracetic acid
tryptophan operon model for tryptophan anabolism (repression)
- Tryptophan is produced by anabolic enzymes encoded by five structural genes; accumulation of tryptophan represses transcription of these genes, preventing further synthesis of tryptophan 1. operon consists of promoter and operator sites and structural genes that code for the protein; the operon is regulated by the product of the regulatory gene (I) 2. repressor inactive, operon on - repressor is inactive, and transcription and translation proceed, leading to synthesis of tryptophan 3. repressor active, operon off - when corepressor tryptophan binds to the repressor protein, the activated repressor binds w the operator, preventing transcription from the operon
asepsis
- absence of significant contamination
inhibition of cell wall synthesis
- affects actively growing cells - gram-positives are affected more than gram-negatives - no effect on eukaryotes - ex: penicillin, cephalosporins, carbapenems, bacitracin, vancomycin
cancidas
- antifungal - cell wall synthesis inhibition
what's the mode of action of polyenes?
- antifungal - plasma membrane inhibition
azoles
- antifungal - inhibits fungal sterols (plasma membrane)
polyenes
- antifungal - inhibits fungal sterols (plasma membrane)
antifungal drugs (and mode of action)
- antifungals target several cell structures - plasma membrane: inhibits fungal sterols (azoles, polyenes) - cell wall synthesis inhibition (cancidas) - disruption of mitosis (inhibits microtubule formation - griseofulvin)
amantadine
- antiviral - inhibition of attachment or uncoating
interferons
- antivirals - prevent spread of viruses to new cells
purine and pyramidine analogs
- antivirals (nucleotide analogs)
antibiotics that are peptides
- bacitracin - vancomycin
nonsense mutation
- base change results in a stop codon (nonsense codon) instead of an AA - results in production of an incomplete protein - the protein is non-functional - ex: UAG (tyrosin) to UAA (stop codon)
silent mutation
- base change results in no change of the AA sequence of the translated protein - due to multiple codons coding for the same AA - no effect on phenotype, but change in genotype - ex: AGU and AGC both code for serine
missense mutation
- base change results in the change of an AA in the translated protein - ex: AAA (lysine) becomes AGA (arginine)
facultative anaerobes
- both aerobic and anaerobic growth - greater growth in presence of oxygen - able to continue growth without oxygen via fermentation or anaerobic respiration
broth dilution method
- can determine MIC and MBC of antimicrobial drug - determine MIC by making sequence of decreasing concentrations of the drug in a broth, which is then inoculated w the test bacteria - the wells that don't show growth (have a higher concentration than MIC) can be cultured in broth or plates free of the drug - if growth occurs in this broth, the drug was not bactericidal and the MBC can be determined
obligate anaerobes
- can't use oxygen for energy
osmotic pressure (as an agent of microbial control)
- causes plasmolysis
base substitution (point mutation)
- change in one base in DNA - can result in: silent mutations, missense mutations, nonsense mutations
deletion
- change to a chromosome in which a fragment of the chromosome is removed - may result in a frameshift mutation
biofilms
- communities of microorganisms (thin, slimy layer encasing bacteria that adheres to a surface) - bacteria communicate cell-to-cell via quorum sensing - bacteria secrete inducer (signaling chemicals) to attract other bacterial cells - share nutrients - sheltered from harmful factors
how are genes regulated based on an operon model?
- constitutive enzymes are expressed at a fixed rate all the time (not regulated) - aka "housekeeping genes" - other enzymes are expressed only as needed (regulation) two types of regulation: - induction (turning on of a gene expression - inducible genes) - repression (turning off of a gene expression - repressible genes)
reducing media
- contain ingredients that chemically combine with O2 and are heated to kill off O2 - used for growth of anaerobes
major modes of actions of antimicrobial agents
- damage to proteins (synthesis or function) - alteration of membrane permeability - damage to cell wall - damage to nucleic acids
standard plate counts
- direct counting method - pour plate or spread plate methods
filtration (as a counting method)
- direct counting method - used for dilute samples
disruption of plasma membrane
- disrupt plasma membrane and causes cytoplasm to leak - effective against gram-negative bacteria - ex: polymyxin B
phenol
- disrupt plasma membranes - ex: soap, lysol
what's the mode of action of polymixins?
- disruption of cell membrane
dessication
- drying prevents metabolism
feedback inhibition
- end-product inhibition - end product inhibits enzyme by binding to allosteric site
alcohols
- ethanol, isopropanol - denature proteins, dissolve lipids - no effect on endospores and nonenveloped viruses - require H2O - optimum concentration is 70%
inhibition of protein synthesis
- eukaryotic cells have 80S ribosomes, prokaryotic cells have 70S ribosomes - difference in ribosomal structure accounts for selective toxicity of antibiotics that affect protein synthesis - however, mitochondria also have 70S ribosomes, so antibiotics targeting 70S ribosomes can have adverse effects on cells of host - ex: tetracycline, erythromycin, streptomycin, chloramphenicol, gentamycin, neomycin
complex media
- exact chemical composition not known - made of extracts and digests of yeasts, meat, or plants
plasmids
- extra-chromosomal DNA - circular double stranded - much smaller than chromosome - self-replicating (don't rely on the main chromosome) - generally carry genes not essential for cell growth - can transfer from cell to cell
hyperthermophiles
- extreme thermophiles - optimum growth = above 80 degrees
aerotolerant anaerobes
- fermentative and can't use oxygen for growth but can tolerate it
culture of capnophiles
- for microbes that require high CO2 conditions - candle jars used to obtain high level of CO2 - cultures placed in jar containing lit candle that consumes O2 (candle stops burning when air has lowered concentration of O2 and an elevated level of CO2)
thermophiles
- heat-loving microbes - optimum growth temp = 50-60 degrees
rate of microbial death
- if death curve is plotted logarithmically, death rate is constant
gases
- inactivate proteins by cross-linking
metabolic activity
- indirect counting method - amount of metabolic byproducts is proportional to the bacterial population
dry weight
- indirect method - for microorganisms that don't form distinct colonies or are filamentous
sanitization
- intended to lower microbial counts to safe public health levels and minimize chances of disease transmission
antimicrobial drugs
- interfere with the growth of microbes within a host
halogens
- iodine, chlorine - oxidizing agents - iodine: impairs protein synthesis and alters membranes - chlorine: oxidizing agents - shut down cellular enzyme systems (bleach)
dry heat
- kills by oxidation - flaming, incineration, hot-air sterilization (oven) - hot air - 170 degrees for 2 hours
boiling
- kills by protein coagulation or denaturation
germicide
- kills microorganisms
lac operon model of E. coli for lactose catabolism (induction)
- lactose-digesting enzymes are produced in the presence of lactose; in E. coli, the genes for the three enzymes are in the lac operon; B-galactosidase is encoded by lacZ; the lacY gene encodes the lac permease, and lacA encodes transacetylase 1. operon consists of promoter and operator sites and structural genes that code for the protein; the operon is regulated by the product of the regulatory gene (I) 2. repressor active, operon off - repressor protein binds w the operator, preventing transcription from the operon 3. repressor inactive, operon on - when the inducer allolactose binds to the repressor protein, the inactivated repressor can no longer block transcription; the structural genes are transcribed, ultimately resulting in production of enzymes needed for lactose catabolism
typical bacterial growth curve (lag, log, stationary, and decline/death phases)
- lag phase: intense activity preparing for population growth, but no increase in population - log phase: logarithmic (exponential) increase in population - stationary phase: period of equilibrium; microbial deaths balance production of new cells - death phase: population is decreasing at logarithmic rate
lagging strand
- lagging strand is synthesized discontinuously - Okazaki fragments are lagging strand segments - RNA primers are removed and Okazaki fragments joined by a DNA polymerase and DNA ligase
leading strand
- leading strand is synthesized continuously
freezing
- low temp inhibits microbial growth - deep freezing = -20 degrees
refrigeration
- low temp inhibits microbial growth - refrigeration = 2-8 degrees
thermal death point (TDP)
- lowest temp at which all microorganisms in a particular liquid suspension will be killed in 10 minutes
freeze-drying
- lyophilization (freezing and drying method)
translation
- mRNA is translated in codons (three nucleotides) - translation of mRNA begins at start codon (AUG) - translation ends at stop codon (UAA, UAG, UGA)
differential media
- make it easy to distinguish colonies of different microbes
mRNA
- messenger RNA - contains info to make protein
how does osmotic pressure affect growth?
- microorganisms obtain nutrients from water and require water for growth - when osmotic pressure is too high, necessary water is removed from cell (hypertonic environments cause dehydration and plasmolysis)
MBC
- minimal bactericidal concentration
MIC
- minimal inhibitory concentration
thermal death time (TDT)
- minimal length of time for all bacteria in a particular liquid culture to be killed at a given temperature
mesophiles
- moderate-temperature loving microbes - optimum growth temp = 25-40 degrees
MPN
- most probable number - multiple tube MPN test (count positive tubes, compare w statistical table) - useful for dilute samples
ionizing radiation
- mutagen that causes formation of highly reactive ions that can react w nucleotides and the deoxyribose-phosphate backbone - x-rays, gamma rays, electron beams - short wavelength - ionizes water to release OH - damages DNA - used to sterilize medical supplies, plastic, hospital food
frameshift mutation
- mutagen that causes insertions - one or a few nucleotide pairs are deleted or inserted in the DNA - this mutation can shift the codons - almost always results in long stretch of altered AAs and production of an inactive protein from the mutated gene - in most cases, a nonsense codon will eventually be encountered and thereby terminate translation
non-ionizing radiation
- mutagen that causes the formation of pyrimidine dimers (causes adjacent thymines to dimerize) - UV, 260 nm - longer wavelength - damages DNA by dimerizing adjacent pyrimidines - sterilizes surfaces - can't penetrate solid/opaque surfaces
insertion
- mutation involving the addition of one or more nucleotide pairs to a gene - may result in a frameshift mutation
antiviral drugs (and mode of action)
- nucleotide analogs (DNA/RNA synthesis inhibition) - inhibition of attachment or uncoating (amantidine/oseltamivir) - inhibition of enzymes (reverse transcriptase) - interferones/immunoenhancers (prevent spread of viruses to new cells)
factors that influence effectiveness of antimicrobial agent
- number of microbes - environment (temp, pH, biofilms) - time of exposure - concentration of agent - microbial characteristics - interfering agents (solvent, debris, blood, saliva, feces)
chemical food preservatives
- organic acids (inhibit metabolism) - nitrites and nitrates (prevents endospore germination) - antibiotics (prevent spoilage of cheese) - sulfur dioxide prevents wine spoilage
what's the mode of action of semisynthetic penicillin?
- part of penicillin is produced by the mold and other part is added synthetically - inhibit cell wall synthesis
inhibition of essential metabolites/enzymatic activity (as antimetabolites)
- pathways that are exclusive to bacteria - competitively inhibits bacterial enzymes - imitates normal metabolites - ex: sulfonamides
which antimicrobial drugs inhibit cell wall synthesis?
- penicillin - bacitracin - cephalosporin - vancomycin
Kirby Bauer test (disk diffusion method)
- petri dish seeded uniformly over entire surface w standardized amount of test organism - filter paper disks impregnated w known concentrations of chemotherapeutic agents are placed on agar surface - during incubation, chemotherapeutic agents diffuse from disks into the agar - the farther the agent diffuses from the disk, the lower its concentration (of bacteria)
repairs of mutation
- photolyases separate thymine dimers (light repair) - nucleotide excision repair (dark repair)
DNA polymerase
- polymerizes nucleotides (deoxyribose) - can add nucleotides to the 3' end of existing strand only - proofreads - repairs DNA
quats (quaternary ammonium compounds)
- positively charged portion functions - more effective against gram-positive than gram-negative - also fungicidal, amoebicidal, and virucidal (enveloped virus) - don't kill endospores and mycobacteria
chemical mutagens
- reacts directly w nitrogenous base and alters the base - intercalate between base pairs causing insertion or deletion
competence (in gene transformation)
- recipient cell must be in a physiological state in which it can take up DNA - competence = alterations in the bacterial cell wall that make it permeable to large DNA molecules - some bacteria, which are not naturally competent, can be made so in lab (w CaCl2 or other methods)
pasteurization
- reduces spoilage organisms and pathogens - 63 degrees for 30 min - thermoduric organisms survive - prevents transmission of milk-borne diseases
anaerobic techniques
- reducing media - anaerobic chamber
promoter
- region of a gene where RNA polymerase can bind and begin transcription (transcription begins when RNA polymerase binds to promoter sequence)
repressors
- regulatory proteins that inhibit (turn off) gene expression by blocking RNA polymerase from initiating transcription - genes that are by default "on" until they are repressed - usually anabolic genes
filtration (as an agent of microbial control)
- removes microbes and spores from liquids and air - perforated membrane - filter pore size varies (0.2 - 0.45 micrometers) - 0.01 micrometers will block all viruses and bacteria - applied for liquids that are sensitive to heat (serum, vaccine, media)
microaerophiles
- require oxygen concentration lower than air - in test tube of solid medium, they grow only at depth where small amounts of oxygen have diffused into the medium (they don't grow near oxygen-rich surface or below the narrow zone of adequate oxygen)
how do plasmids affect drug resistance
- resistance genes can be plasmid-borne
rRNA
- ribosomal RNA - structural part of ribosome
which antimicrobial drugs inhibit nucleic acid synthesis?
- rifamycin - quinolones (ciprofloxacin) - metronidazole
structure of RNA
- single strand of nucleotides - nucleic acids = polymers of nucleotides - each nucleotide has three components: nitrogenous base (A, C, G, U), 5-carbon sugar (ribose), phosphate group
toxic forms of oxygen
- singlet oxygen - superoxide free radicals - peroxide anion - hydroxyl radical
operator
- site for binding of a repressor protein
surfactants
- soaps and detergents
terminator
- special sequence of nucleotides in DNA that marks the end of a gene - It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene (transcription stops when it reaches terminator sequence)
causes of mutations
- spontaneous - chemical mutagens - radiation (ionizing and non-ionizing)
direct measurements of microbial growth
- standard plate counts - filtration - MPN (most probable number) - direct microscopic count
steam sterilization
- steam must contact item's surface
autoclaving
- steam under pressure - effectively destroys spores - sterilizes inanimate objects - 121 degrees for 15 min
nonsense codon
- stop codons - one of the three mRNA codons that specifies termination of translation
genetics
- study of what genes are, how they carry info, how info is expressed, and how genes are replicated
inducer
- substance which acts to induce transcription of a gene - often on the substrate of the enzyme - inducible genes are by default "off" and are not transcribed until they are induced - usually catabolic genes
selective media
- suppress unwanted microbes and encourage desired microbes
transcription
- synthesis of complementary RNA strand from a DNA template - DNA is transcribed to make RNA - enzyme that carries out transcription = RNA polymerase 1. RNA polymerase binds to promoter, and DNA unwinds at the beginning of a gene 2. RNA is synthesized by complimentary base pairing of free nucleotides w the nucleotide bases on the template strand of DNA 3. site of synthesis moves along DNA; DNA that has been transcribed rewinds 4. transcription reaches the terminator 5. RNA and RNA polymerase are released, and the DNA helix re-forms
psychrotrophs
- temp optimum = 20-30 degrees
which antimicrobial drugs inhibit protein synthesis?
- tetracycline - erythromycin - streptomycin - gentamycin - neomycin - chloramphenicol
decimal reduction time (DRT)
- time (in minutes) it takes to kill 90% of bacteria population at a given temp
singlet oxygen
- toxic - oxygen that has been boosted into a higher-energy state and is extremely reactive
effects of antibiotics on a host
- toxicity - allergy - disruption of normal microbiota
directionality of DNA
- transcription occurs in 5' to 3' direction 1' = attached to base 2' = attached to OH in RNA and to H in DNA 3' = attached to OH group 4' = attached to 5' 5' = attached to phosphate group
how is eukaryotic transcription different from prokaryotic transcription?
- transcription occurs in nucleus - eukaryotic genes are composed of exons and introns - exons = regions of DNA that code for proteins - introns = regions of DNA that don't code for proteins - snRNPs: remove introns and splice exons together
types of gene transfer that occur in bacteria
- transformation - conjugation - transduction
indirect measurements of microbial growth
- turbidity - metabolic activity - dry weight
induction
- turning on transcription/expression of a gene
structures of DNA
- two polynucleotide strands h-bonded to each other (h-bonds are between A and T and C and G) - strands are complementary and antiparallel - nucleic acids = polymers of nucleotides - each nucleotide has three components: nitrogenous base (A, C, G, T), 5-carbon sugar (ribose), phosphate group
how do humans contribute to the problem of antibiotic resistance?
- using outdated or weakened antibiotics - using antibiotics for the common cold and other innapropriate conditions - use of antibiotics in animal feed - failure to complete prescribed regimen - using someone else's leftover prescription
binary fission
1. cell elongates and DNA is replicated 2. cell wall and plasma membrane begin to constrict 3. cross-wall forms, completely separating the two DNA copies 4. cells separate
how can a microorganism develop resistance towards an antibiotic?
1. lots of germs - a few are drug resistant 2. antibiotics kill bacteria causing the illness, as well as good bacteria protecting the body from infection 3. the drug-resistant bacteria are now allowed to grow and takeover 4. some bacteria give their drug-resistance to other bacteria, causing more problems
generalized transduction
1. phage infects donor bacterial cell 2. phage DNA and proteins are made, and the bacterial chromosome is broken into pieces 3. occasionally during phage assembly, pieces of bacterial DNA are packaged in a phage capsid; then the donor cell lyses, and releases phage particles containing bacterial DNA 4. a phage carrying bacterial DNA infects a new host cell (the recipient cell) 5. recombination can occur, producing a recombinant cell w a genotype different from both the donor and recipient cells
recombination
1. recipient cell takes up donor DNA 2. donor DNA aligns w complementary bases 3. recombination occurs between donor DNA and recipient DNA
F+ cell
Bacterial cells that possess a plasmid called the F factor, which includes a gene for a sex pilus.
peroxidase
an enzyme that destroys hydrogen peroxide
catalase
breaks down hydrogen peroxide
superoxide dismutase
catalyzes conversion of superoxide radicals to hydrogen peroxide (neutralizes them)
psychrophiles
cold-loving microbes
sterilization
complete destruction of microbial life
RNA polymerase
enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template
phenotype
expression of the genes
superoxide radicals
form during incomplete reduction of oxygen in aerobic and anaerobic respiration
what's the mode of action of sulfonamides?
inhibition of folic acid metabolism
what's the mode of action of ethambutol?
inhibits incorporation of mycolic acid
what's the mode of action of isoniazid?
inhibits mycolic acid synthesis
degerming
mechanical removal of microbes from a limited area
nucleoside analog
mutagen that is incorporated into DNA in place of a normal base
spectrum of activity
narrow or broad
genetic recombination
new combination of genes produced by crossing over and independent assortment
calculate number of bacteria at end of a given number of generation
number of cells at the end = number at the beginning x 2^n n = generation number
F- cell
recipient cell
gene
segment of DNA that encodes a functional product, usually a protein
intron
sequence of DNA that is not involved in coding for a protein
genetic code
set of rules that determines how a nucleotide sequence is converted into the AA sequence of a protein
chromosome
structure containing DNA
antibiotics
substance produced by a microbe that, in small amounts, inhibits another microbe
disinfection
targeted removal of all pathogens, not necessarily all microorganisms
chemotherapy
the use of drugs to treat a disease
how do the trace elements affect growth?
they are necessary for the functions of certain enzymes
codon
three-nucleotide sequence on messenger RNA that codes for a single amino acid
