MMG 2010 Final Exam 🧫

empiric therapy

treatment begun on the bases of a clinical "educated guess" before specific causative agent is known

prophylaxis

process that prevents infection/disease in a person at risk

beta-lactamase role in resistance

enzyme that will hydrolyze (kill) beta-lactam drugs

PBP2A role in resistance

resistance gene, alternate form of PBP, all that produce this are beta-lactam resistant

CAT role in resistance

(enzymatic inactivation) acetylation of drugs

porins role in resistance

mutate to limit drug entry into cell

efflux pumps role in resistance

pumps a diverse class of drugs out of cell

person-person transmission

touching, saliva, sex, blood

zoonotic transmission

animal to human

vertical transmission

mother to infant/neonate

airborne transmission

airborne particles carry disease

droplet transmission

droplets expelled from mouth/nose

foodborne transmission

food and/or water carry pathogen (aka oral-fecal)

vector-borne transmission

insect/arthropod

exotoxins

protein made by G-/+, released from actively growing bacteria, MOA is cell toxicity, good vaccine target, sometimes fever inducing, can be neutralized by antibody, high toxicity level

endotoxins

lipid made by G-, release from cell wall when bacteria divide/die, MOA is systemic inflammation, not good vaccine target, fever inducing, cannot be neutralized by antibody, low toxicity level

toxin

molecules that generate adverse host effects

antitoxin

antibodies against specific endotoxins that provide immunity

toxoid

inactivated exotoxins used in vaccines

toxigenic

microbes that make toxins

toxemia

toxins in the bloodstream

intoxication

presence of toxin without microbial growth

innate immunity

rapid, nonspecific, no memory; involves barriers, phagocytes, cytokines, complement, inflammation, fever

adaptive immunity

slower, specific, memory-based; involves lymphocytes

3 immune cells that are phagocytes

dendritic cells, neutrophils, macrophage (all WBCs)

opsonin-independent (direct) recognition

phagocyte binds to PAMPs on microbe surface, pattern recognition receptors (PRRs) involved, no opsonins

opsonin-dependent (indirect) recognition

phagocyte binds to opsonins coating the pathogen, Fc receptors and antibody receptors involved, opsonins are antibodies and complement proteins

cardinal signs of inflammation

redness, heat, swelling, pain, loss of function

processes that lead to inflammation

cell damage and cytokines

presenting antigens: normal cells

MHC I-epitope complexes display self epitope

presenting antigens: infected cells

MHC II-epitope complexes display antigens

T cytotoxic cells (activation signal, differentiation, function, and elimination of antigen)

TCR binds specific MHC I-epitope, CD8 provides costimulation

-fxns: cause death of infected cell, release cytokines to attract NK cells and macrophages, release perforins and granzymes (apoptosis)

role of APCs in humoral immunity and 3 ex.

present antigens (MHCII) to T helper cells to initiate a response and provide co-stimulatory signals that help B cells differentiate into antibody-producing plasma cells

- ex. macrophages, B cells, dendritic cells

sequence of events for processing and presenting antigens from intracellular antigens

protein breakdown in the cytoplasm, transport into the ER, loading onto MHC class I molecules, and surface display

sequence of events for processing and presenting antigens from extracellular antigens

antigen uptake and processing, MHC II molecule prep, peptide loading, cell surface presentation

four ways antibodies help eliminate specific pathogens

neutralization, agglutination, opsonization, complement activation

how T helper cells activated

activated by MHC II + antigen on APC

how B cells activated

- T cell dependent: antigen binds BCR -> B cell internalizes and presents antigen -> helper T provides costim -> B cell proliferates

- T cell independent: BCR can bind free epitope -> B cell proliferates

cell-mediated vs. humoral immunity

cell mediated involves T cells and humoral involves B cells

microscopic morphology

- principle: identification based on cell shape, arrangement, and staining

- key techniques: Gram staining, acid-fast staining, KOH staining

- DA: rapid preliminary identification

- advantages: fast, cheap, informative

macroscopic morphology

- principle: microbial colonies show distinctive size, shape, color, texture, and hemolysis pattern

- key steps: inoculate -> incubate -> observe

- DA: differentiation of species, assess hemolysis patterns, recognition of fungal morph

- advantages: provides visible clues, allows selection of colonies for further testing

biochemical test methods

- principle: identify bacteria and other microbes based on metabolic activities/enzyme production

- key steps: inoculate onto differential media -> detect metabolic end products -> compare results

- DA: identify unknown bacterial/fungal isolates in clinical specimen

- advantages: simple, cheap, provide functional and phenotype info

NAAT/PCR

- principle: amplifies specific DNA sequences using template DNA, primers, nucleotides, and Taq polymerase

- key steps: denaturation -> annealing -> extension -> exponential amplification

- DA: detects pathogen DNA/RNA, identifies genetic mutation/drug resistance genes, used in forensic testing + research diagnostics

- advantages: highly specific + sensitive, real-time PCR

DNA microarray

- principle: uses a chip w/1000s of DNA probes that hybridize to cDNA/RNA sequences to detect gene expression patterns/presence of specific sequences

- key steps: extract mRNA/DNA -> convert to fluorescently labeled cDNA -> hybridize -> fluorescent signal

- DA: identify pathogen species/strains, detect gene expression changes, used in pharmacogenomics + personalized med

- advantages: can test 1000s of genes simultaneously, provides broad genomic info, useful for comparing gene activity

precipitation test

- principle: Ag + soluble Ab -> visible precipitate

- key steps: mix Ag w Ab in liquid/gel medium

- DA: radial immunodiffusion and ouchterlony double diffusion

- advantages: simple, inexpensive, visual, high specificity

agglutination test

- principle: Ag on cells/particles + specific Ab -> clumping

- key steps: mix sample w known Ab/Ag, allow binding (clumping = +), reaction may be direct/indirect

- DA: blood typing, latex agglutination tests, widal test

- advantages: rapid, easy to interpret

neutralization test

-principle: Ab can neutralize activity of Ag

- key steps: mix pt serum w known virus/toxin, incubate, add susceptible cells/test animals, if no CPE/toxicity -> positive

- DA: virus and toxin neutralization tests

- advantages: high specificity, indicates immunity/past infection, vaccine efficacy

complement-fixation

- principle: detects Ag-Ab complexes by measuring the consumption of complement

- key steps: pt serum heated, mix w known Ag and source of complement, add indicatory system, observe hemolysis

- DA: detects Abs in pt serum rather than pathogen itself

- advantages: useful when direct pathogen detection is difficult

EIA/ELISA

-principle: detects presence of Ag/Ab using an enzyme-labeled Ab -> color change when substrate added

- key steps: Ab immobilized on surface, pt sample added, Ab added to detect binding, substrate added -> enzyme converts substrate -> colored product

- DA: detection of HIV, hepatitis, hormones, drugs, allergens; basis for rapid dx kits

- advantages: high-through put, quantitative

ICAs

- principle: uses capillary flow of a liquid sample across a porous strip coated w/Ab -> Ab-Ag binding

- key components: nitrocellulose membrane and labeled Abs w colored particles create visible lines

- DA: pregnancy tests, rapid COVID/flu/strep tests

- advantages: fast, simple, useful for point-of-care dx

Western Blotting

- principle: detects specific Ag/Ab in a sample using Ab-Ag binding after gel electrophoresis and transfer to a membrane

- key steps: protein separation, transfer, blocking, Ab detection, visualization

- DA: confirms HIV and Lyme, detects specific viral/bacterial proteins that indicate infection

- advantages: high specificity

live attenuated vaccines

contain microbes that can multiply in host but are too weak to cause disease

- benefits: best immune response, closely mimics natural infection

- drawbacks: need fridge, may not be safe for immunocompromised, possible mutation to infectious form

recombinant vector vaccines

genes from pathogen and encoding Ag packed into a vector

- benefits: good immune response, very safe, harmless virus

- drawbacks: need fridge, may require boosters

whole-agent vaccines

consists of whole killed/inactivated pathogens

- benefits: good immune response, safe for immunocompromised, stable at room temp

- drawbacks: boosters required

subunit vaccines

consists of purified Ag, require adjuvants

- benefits: good immune response, safe, stable at room temp

- drawbacks: may need booster, public wary of adjuvants

DNA/RNA vaccines

identify the Ag that are most immunogenic and isolate the genes for those Ag

- benefits: good immune response, very safe, host cell makes viral Ag, results in humoral and cell immune response

- drawbacks: need fridge and booster

obligate aerobes

only aerobic growth; O2 required

obligate anaerobes

only anaerobic growth; growth ceases in O2 presence

aerotolerant anaerobes

only anaerobic growth; growth continues in O2 presence

facultative anaerobe

both aerobic and anaerobic growth; > growth in O2 presence

microaerophile

only aerobic growth; O2 required in LOW concentration

what is biofilm

cells enmeshed in a polysaccharide matrix attached to the surface of smth

- polymicrobial communities

steps for biofilm formation

1. attachment

2. colonization

3. development

4. dispersal

- reversable + can rinse and repeat

indirect methods of measuring cell growth

spectrophotometry -> measures optical density (OD)

chemotroph

organism that generates ATP from chemicals in its environment

chemoorganotroph

use of organic molecules to make energy

- glycolysis (can be) followed by aerobic/anaerobic respiration or fermentation

phototroph

organism that generates ATP from light

- oxygenic/anoxygenic photosynthesis

autotroph

organism that produces their own food via chemotrophy/phototrophy

heterotroph

an organism deriving its nutritional requirements from complex organic substances

chemolithanotrophy

use of inorganic molecules to make energy

- aerobic/anaerobic

3 mechanisms for generating ATP

1. substrate-level phosphorylation

2. oxidative phosphorylation

3. photophosphorylation

substrate-level phosphorylation

direct transfer of phosphate from an organic compound to ADP (-> ATP)

oxidative phosphorylation

proton motive force (electrochemical gradient)

photophosphorylation

light used to form proton motive force

vertical gene transfer

transfer of genes from an organism to its offspring via normal repro

horizontal gene transfer

transfer of genes between cells of the same generation

3 mechanisms of HGT in bacteria

1. transduction

2. conjugation

3. transformation

transduction

DNA transferred from a donor cell to a recipient via bacteriophage

conjugation

plasmid transferred from one bacterium to another through cell-cell contact

- sex pilus or mating bridge

transformation

uptake of naked DNA from external environment (in nature and in lab)

3 possible fates of DNA fragments during HGT

- destroyed by recipient cell

- becomes an extrachromosomal element

- recombines into recipient chromosome

2-component regulatory systems

how prokaryotes regulate metabolism in response to environment

1. sensor kinase

2. response regulator

sensor kinase

in cytoplasmic membrane; detects environmental signal and autophosphorylates at a specific histidine residue

response regulator

in cytoplasm; DNA- binding protein that regulates transcription, receives phosphate from sensor kinase

quorum-sensing

regulatory mechanism using AI by which bacteria and archaea assess their population density

- also in microbial eukaryotes

blue-white screen results

white cells = cells w/rDNA (YAY)

blue cells = cells w/just plasmid (boooo)

beta-galactosidase

reporter gene lacZ encodes for this enzyme

- ONPG -> yellow/white cells

- Xgal -> blue cells

PCR steps

1. add primers, nucleotides, and DNA pol

2. incubate at 94 degC for 1 min

3. incubate at 60 degC for 1 min

4. incubate at 72 degC for 1 min

5. repeat cycle of heating/cooling to make two more copies of target DNA

Sanger sequencing

uses bacterial DNA pol to replicate DNA with chain-terminating nucleotides that give every possible nucleotide length

- gel electrophoresis

sterilization

removing/destroying all microbial life

disinfection

destroying harmful microbes on inanimate surfaces

sanitization

lowering microbial counts on eating utensils to safe levels

bacteriostasis

inhibiting, not killing, microbes

endospore levels

controlled by autoclaving, hydrogen peroxide vapor, ethylene oxide, chlorine dioxide, sporocides

prion levels

controlled by chemical treatments and autoclaving

virus levels

controlled by heat, drying, detergents

- naked virus -> use chlorine-based agents

protozoan levels

controlled by filtration, CO2, UV, ozone

- diff stages can resist certain methods

major characteristics of bacteria

prokaryotes, unicellular, PG cell wall, asexual repro, chemotrophs and phototrophs, sometimes motile, pathogenic

major characteristics of fungi

eukaryotes, uni/multicellular, chitin cell walls, asexual and sexual repro, chemotrophs, not motile, pathogenic

major characteristics of viruses

no domain, acellular, no cell wall, obligate intracellular parasites (repro + metabolism), no motility, pathogenic