Exam 1 Flashcards
Define Taxonomy
a system that is applied to all living organisms to classify them based on their phenotype or genotype
Define Epigenetic
variations in gene expression not caused by nucleic acid sequence similarities or differences, using chemotaxonomic methods
Define Classification
a method for organizing microorganisms into groups or taxa based on similar morphologic, physiologic and genetic traits
chemotaxonomic
proteins, lipids, cell wall, and biochemical analysis
What is the Gold standard for classifying bacteria?
The “gold standard” for classification of bacterial species has historically been based on deoxyribonucleic acid (DNA) using 16S rRNA (ribosomal subunit is unique to organisms down to species)
Name the hierarchy of Taxonomic classification
Domains (Bacteria, Archaea, and Eukarya) Kingdom Phylum Class Order Family Genus Species
- Which of the following is not a correct use of the binomial nomenclature (two named) system? (Select all that apply.)
a. Staphylococcus Aureus
b. S. aureus
c. Staphylococcus aureus (is in italics)
A
What spectrometry method is useful for ID of bacteria
MALDI-TOF
What is virulence
what tools the pathogen has to colonize and destroy cells
What makes bacteria more efficient than us?
They can have transcription and translation occurring at the same time
What is the disadvantage bacteria have in their cell structure
They do not have organelles so they need to balance their resources carefully
What do bacteria have instead of a nucleus
a nucleoid-DNA bunched up together
Where is it possible to find genes in a bacteria
can be in chromosomes or on plasmids and transposable elements
What is different about the extrachromosomal elements in bacteria
they can incorporate into the host genome or replicate independently, refers to chromosomes outside of nucleoid
What structure do bacteria have in their extrachromosomal DNA
double-stranded, closed and circular
What are transposable elements in bacteria
pieces of DNA that can move from one genetic element to another like from plasmid to chromosome. they cannot replicate independently
What type of transposable elements are present in bacteria?
simple- insertion sequence
composite- complex transposon
How do bacteria multiply
binary fission
What is special about bacterial mRNA
it is polycistronic-one transcript of mRNA can be used to make many genes
What products come from bacterial transcription?
mRNA, tRNA, rRNA, ncRNA (regulatory non coding)
What kind of ribosome do bacteria have?
16S
bacteria have anabolic enzymes that _____ genes, which are ____ when the gene’s final product is ___, turning off the pathway to continue to produce that product
they have anabolic enzymes that repress genes, which are increased when the gene’s final product is abundant, turning off the pathway to continue to produce that product
when the degraded substrate of a catabolic enzyme is present, these enzymes are _____.
If the substrate is ____- they are repressed
they are ______ enzymes that beak things down
when the degraded substrate of a catabolic enzyme is present, these enzymes are induced.
If the substrate is absent- they are repressed
they are degradative enzymes that beak things down
Describe bacterial replication
bidirectional, circular, origin and 2 replication forks
What are the 3 types of bacterial horizontal transfer
transformation, transduction, conjugation
What is the difference between horizontal gene transfer and vertical gene transfer
horizontal-friends and neighbors
vertical-offspring
What is transformation gene transfer
a cell takes up free (naked) DNA from a dead bacterial cell
What is transductional gene transfer
transfer of genetic info through viruses (bacteriophages) that inject DNA from one into the other bacteria
What is conjugation gene transfer
transfer of genetic info through sex pili of a plasmid or a chromosome
The lac operon is an example of what kind of enzyme system?
Catabolic
How is polycistronic mRNA regulated in bacteria?
an operon based promoter
At what stages does gene regulation occur in bacteria?
all 3 transcriptional, translational and post translational
What type of transfer is occurring if an F+ donor cell gives genetic info to an F- recipient cell
conjugation
What is the most common way bacteria transport things across their membranes
active transport-moving things against the concentration gradient
What is the “best” method of ATP production for bacteria
substrate level phosphorylation because the energy is derived exothermically with O2
What are the two general mechanisms for ATP production in bacteria
substrate level phosphorylation
oxidative phosphorylation
Briefly describe substrate level phosphorylation
exothermic metabolism- energy made by production of high energy phosphate bonds produced by the energy pathways
What is the initial substrate in the substrate level phosphorylation pathway
pyruvate
What method do bacteria use to produce ATP when in non-oxygen environments
fermentative metabolism, also produce alcohols, acids, CO2 and H
Briefly describe oxidative phosphorylation
the ETC produces oxidation-reduction reactions to generate ATP
When is oxidative phosphorylation an anaerobic process? When is it aerobic?
anaerobic- when O2 is the terminal electron acceptor in the ETC
aerobic- When some other mol is used as the final electron acceptor, no O2
Explain
Strictly aerobic-
facultative anaerobic-
strictly anaerobic-
Strictly aerobic- must have O2
facultative anaerobic- with out without O2
strictly anaerobic- O2 kills them
What type of respiration do most of the illness causing bacteria use
facultative anaerobic
What are the differences between the cell walls of eukaryotes vs prokaryotes
eukaryote- cytoskeleton
prokaryotes-peptidoglycan
What color is the gram negative stain? the gram positive?
+ purple
- red
Which Gram bacteria have the thicker cell wall? which ones have the thinner one?
gram + thicker
gram - thinner
Which gram bacteria have a periplasmic space?
gram negative
Which gram bacteria have an inner and outer membrane?`
thin
Which gram bacteria have lipopolysaccharide porins (lipid A) in their cell walls?
gram -
What is the purpose of an outer and inner membrane?
for controlling permeability
What is the purpose of porins in a bacterial cell wall?
allow nutrients and solutes to pass through the outer membrane
this includes being able to take up antibiotics
What is the purpose of the peptidoglycan in the bacterial cell wall
gives it shape, strength ability to withstand osmotic pressure
What is the main target in antimicrobial agents and drugs
peptidoglycan because it is essential for the survival of bacteria
Describe what peptidoglycan is made of?
NAG- N acetylglucosamine
NAM-N acetylmuramic acid
linked together by 4 AAs that end in Ala
What other materials could bacteria have in their cell wall? What are these types of bacteria called/
no cell wall- mycoplasma or ureaplasma
mycolic acid-mycobacteria
What molecules are in gram positive cell walls and not in gram negative?
teichoic acids and lipoteichoic acids
What virulence advantages do mycobacteria have?
the mycolic acids in their cell wall refract toxic substances like acids, they are much harder to stain and grow in vitro
What is the really important bacteria that belongs to the mycobacteria group?
tuberculosis
Put the following structures in order for gram ____ bacteria
- inner membrane
- outer membrane
- periplasmic space
- inside of bacteria
- outside of bacteria
- lipopolysaccharide porins
- capsule
- murein layer
outside of bacteria capsule outer membrane- lipopolysaccharide porins periplasmic space-murein layer inner membrane inside of bacteria
Gram negative
What is murein?
a layer in the periplasmic space that helps take in nutrients
Which gram bacteria tends to be more resistant to antibiotics? Why?
Gram negative because they can control what fluids and proteins enter and exit their cell wall, they can pump antibiotics right back out with all of their extra fancy channels
What other name does the inner membrane have? Which gram bacteria has it?
cytoplasmic- both
What are the functions of the cytoplasmic membrane
transport of solutes
enzymes that help with synthesis of wall, membrane and assemple secretion substances
generation of ATP
cell motility
Which parts of the plasma membrane are hydrophobic? which ones are hydrophilic? polar? non polar?
polar-hydrophilic- outside
non polar-hydrophobic-inside
Where is the capsule in gram positive bacteria? gram negative?
gram + right before the murein layer
gram- right before the outer membrane
Put the following structures in order for gram ____ bacteria
cytoplasmic membrane murein layer capsule inside of bacteria outside of bacteria
outside of bacteria capsule murein layer cytoplasmic membrane inside of bacteria
Gram positive
What are bacterial capsules made of
high molecular weight polysaccharides
What is the purpose of a bacterial capsule, what doesn’t it do?
Does
increases pathogenicity
protects bacteria from immune sys
Does not
increase strength
help with` permeability
What is a slime layer/ biofilm?
a type of capsule made of a biochemical matrix that stabilizes, and protects against biocides and the immune system
What type of bacterial groups have slime layers?
monomicrobic or polymicrobic
What bacteria have sex pili?
only the ones that produce a protein call F factor
What are flagella made of?
flagellin
Ideally, most specimens should be transported to the lab within how many hours of collection?
2 hrs
During what phase of a patient’s illness should a specimen be colleced?
during the acute phase-
2 to 3 days for viruses
before any antimicrobial, antiviral or antifungal medication is used
What is the best choice for specimen collection, put in order from best to worst
cotton swaps
needle aspirates
wooden swabs
needle aspirates-best
cotton swab
wooden swab-worst
What organism is susceptible to changes in temperature
Neisseria meningitidis
What organism is susceptible to changes in pH
Shigella
What preservatives are used for
urine
stool
urine-boric acid
stool- PVA and buffered formalin
What type of preservatives are used as anticoagulants for organisms like Neisseria and anaerobic bacteria?
sodium polyanethol sulfonate- SPS 0.025%
in blood cultures
What kind of preservative is used as an anticoagulant for viral cultures
Heparin
What kind of preservative CANNOT be used as an anticoagulant
EDTA
What temperature should urine, stool, viral specimen, sputa, swabs and foreign devices like catheters be stored at?
4C
What temperature should serum and tissues be stored at
frozen at 20C
What extra information might be listed on a micro specimen label or requisition?
nature and source of specimen
any current antimicrobial therapy
True or False: Preparation may vary of the sample comes from a superficial, vs deep part of an abcess
True- if superficial, normal microbiota must be accounted for
What are blood culture sets like? Colors?
they come in a set of two bottles
blue-aerobic
purple-anaerobic
When do samples get a direct gram stain?
positive blood cultures, also need to call in results
Sterile body fluids
When is a specimen NEVER a direct gram stain
urine or stool, throat, nasopharyngeal specimen because there would be too much normal microbiota
Describe what nutritive media is for
grows a wide range of non-fastidious organisms, non selective
Describe what Blood agar is for
nutritive and
differential based on hemolysis
fastidious organisms cannot grow here
What are the possible results of a blood agar culture and what do they mean
alpha- visible hemolysis- green
beta-cells are destroyed entirely, can see through the plate, clear
gamma- hemolytic (still red from plate, no hemolysis)
Describe what MacConkey Agar is for
selective- inhibits gram positive
Allows gram negative to grow
differential-lactose fermentation
positive for fermentation-pink
negative for fermentation-clear
Describe what chocolate agar is for
Enrichment media for fastidious organisms
What organisms can grow on chocolate agar
haemophilus species, good for organisms in sterile body sites
Explain what backup broth is for
supplemental or enrichment broth, allows a low number of organisms to grow
good for anaerobes
damaged organisms
What are the 3 common backup broths
thio
BHIB
TSB
Explain what specialty agars and media are for
colorful special medias usually for yeast or bacteria with special plasmids or for antibiotic resistant bacteria
What are the 2 big antibiotically resistant bacteria
MRSA- methicillin resistant staph aureus
VRE- Vancomycin resistant enterococci
What organisms are lactose fermenters
E. coli, Klebsiella, enterobacter, citrobacter
What organisms are non lactose fermenters
pseudomonas
What is homogenization
grinding of bone, mincing of tissue, into a solution that can be plated
What is centrifugation
concentrating a sample with high volume
How is streaking for isolation used to quantify results?
can be 1+ to 4+, depending on which quadrant was the last to show growth,
What % of O2 do aerobes need? what else do they need?
21% O2
0.03% CO2
What % O2 do obligate anaerobes need? what other things do they need?
0% O2
some H
5-10% CO2
80-90% Nitrogen
What O2% do capnophlies need? what else do they need?
5-10% CO2
15% O2
What O2% do microaerophiles need? What else do they need?
O2 5-10%
CO2-8-10%
How are bioterrorist agents classified?
Category A, B and C,
A are highest risk
What category is an organism that: Easily disseminated or transmitted from person to person with high mortality rates, and may cause widespread public panic
Category A
What category organisms: are moderately easy to disseminate and have moderate to low mortality rates, and less likely to cause public panic
Category B
What category organisms contain emerging pathogens that could be engineered for mass spread in the future
Category C
What are the 6 category A organisms
Anthrax- bacillus anthracis botulism-clostridium botulinum plague- yersinia pestis tularemia viral hemorrhagic fever
Brucellosis, Glanders, Typhus fever and food or water safety threats are examples of bioterrorist agents in what category
B
Emerging infectious diseases like Nipah virus and hentavirus are from what bioterrorist category
C
All of the following are differential media except:
a. Blood agar
b. Chocolate agar
c. MacConkey’s agar
d. Eosin methylene blue agar
b. Chocolate agar
Selective media contains…
Contain dyes or antibiotics to suppress the growth of some organisms
- Specimens may include all of the following except:
a. Sputum
b. Tissue biopsy
c. Vacutainer needle
d. Rectal swab
c. Vacutainer needle
True or False: Nutritive media supports the growth of all organisms.
False
True or False-A requisition should include the patient’s name, hospital ID, birth date, specimen source, and collection date/time.
True
True or False: EDTA is commonly used to collect blood for specimens in the microbiology laboratory.
False
True or False The majority of microbiologic specimens should be set up within 2 hours of collection.
True
T or F Serum samples may be stored frozen for up to 1 week.
True
SPS is…
a blood culture system
fastidious organisms require…
enrichment
MacConkey Agar is…
Selective
Differential
Non selective
Selective
A gram negative broth
chocolate agar
a positive CSF is
a critical value
Blood agar is…
Selective
Differential
non selective
differential
Phenotypic or Genotypic? Color of growth on artificial media
phenotypic
phenotypic (P) or a genotypic (G) The presence of an antibiotic-resistance via DNA sequences
Genotypic
Phenotypic or genotypicThe shape of the bacterial cell
Phenotypic
Phenotypic or genotypic: The arrangement of the bacterial cells on a microscope slide
Phenotypic
The ability of the organism to ferment lactose on MAC. Phenotypic or genotypic
phenotypic
Mass spectrometry is a technique used to separate and identify the spectrum of proteins and peptides that are expressed by microorganisms after the colony morphology and phenotypical characteristics of the bacteria have been evaluated. This method is considered a ________method for the characterization and classification of organisms
chemotaxonomic
- The periplasmic space is required for:
b. Collection and enzymatic degradation of nutrients in gram-negative bacteria
