Test 3

chemotherapy

use of drugs to treat a disease

antimicrobial drugs

interfere with the growth of microbes within a host

antibiotic

a substance produced by a microbe that, in small amounts, inhibits another microbe

selective toxicity

a drug that kills harmful microbes without damaging host cells

in 1940 who performed first clinical trials of penicillin

Howard Florey and Ernst Chain

True or false: almost all antibiotic-producing microbes sporulate

true

broad spectrum

wide range of bacteria against which drug is useful (useful when you do not know the pathogen’s ID)

narrow spectrum

small range of microbes against which drug is useful (useful when you know that pathogen’s ID)

Superinfection (2 meanings)

1. killing normal microbiota along with pathogens, leaving room for opportunistic pathogens to flourish (secondary infection)

2. killing drug-sensitive pathogen cells, but not killing drug-resistant cells (“superbugs” he doesn’t like this)

inhibition of cell wall synthesis

particularly effective against gram-positive cells, less effective against gram-negative cells, harmless to animal cells. Examples: penicillin and its derivatives, bacitracin

inhibition of protein synthesis

generally equally effective against gram positive and negative cells. Because all ribosomes are similar, very selective against Eukaryotes or prokaryotes (ribosomes are different between Pro and Euk). Examples: tetracycline, chloramphenicol, erythromycin, streptomycin, kanamycin

inhibition of cytoplasmic membrane (CM)

change permeability of CM, metabolites could be blacked from cell, some can have adverse effects on humans. Examples: ketoconazole, Amphotericin B, Miconazole, Tolnaftate

inhibition of DNA synthesis

can interfere with humans. Examples: Naladixic acid (inhibits DNA gyrase)

inhibition of synthesis of essential metabolites

effect could be indirect. Examples: sulfonamides (inhibit formation of para-amino benzoic acid (PABA)), a precursor to the vitamin folic acid (which is used to make purine and pyrimidine bases of DNA)

Cell wall synthesis inhibitors- b-lactams (penicillins)

prevents cross-linkages of PG

b-lectams subclasses

1. natural (direct from nature, intramuscular injection, excreted quickly)

2. semisynthetic (tweak structure a bit)

3. extended-spectrum (chemically engineered, better against gram-negatives than before)

cell wall synthesis inhibitors- Glycopeptide antibiotics

Vancomycin, was considered the “last line of defense” against MRSA infections, considered a very serious medical emergency

cell wall synthesis inhibitors- mycobacterium (special case)

Isoniazid and Ethambutol used now, prevent mycolic acids from being produced, no longer acid-fast cells - leaves them as just gram-positive cells, usually administered with other antibiotics

Protein synthesis inhibitors- Aminoglycosides

changes shape of 30s subunits

Protein synthesis inhibitors- Tetracyclines

blocks tRNA binding to A-site, broad spectrum

Protein synthesis inhibitors - Macrolides

somehow binds to 50s subunit, have huge lactone ring, newer generation have broader spectrum

injury to cytoplasmic membrane- lipopeptides

best against gram-positive cells, binds selectively to bacterial membranes, forms a pore in membrane

nucleic acid synthesis inhibitors - quinolones and fluoroquinolones

inhibits DNA gyrase, relatively non-toxic (maybe too non-toxic, build up resistance to it quickly)

inhibition of metabolism- sulfonamides

long term nucleotide synthesis, inhibits formation of acids that then inhibits biosynthesis of purine and pyrimidine bases

antifungal drugs

ergosterol synthesis is a common target (important part of fungal cell’s CM), hard because it can have adverse side effects on humans because we are eukaryotic too

Antifungal drugs- fungal cell walls

cell walls have b-glucans, drugs weaken the cell wall and causes lysis

Antifungal drugs- nucleic acid biosynthesis

flucytosine is an analog of cytosine, inhibits protein synthesis and disrupts translation, toxic to kidneys and bone marrow

antiviral drugs

useful drugs are nucleoside/nucleotide analogs

what can be tricked into producing false nucleotides

viral thymidine kinase

HIV

is a retrovirus, so reverse transcriptase is used. Can use nucleotide analogs, proteases, fusion inhibitors, to teat it (won’t cure it but keeps you alive).

testing drug effectiveness

1. Kirby-Bauer method (disk-diffusion test), helps to find the minimum inhibitory concentration

2. E-test, uses a strip with antibiotic gradient (epsilometer)

3. broth dilution test

how does a bacterium become resistant to an antibiotic?

1. destroy drug enzymatically

2. prevent the drug from penetrating

3. alter drug’s target site (rRNA seqs)

4. eject drug from cell (efflux pumps, multi-drug efflux pumps)

taxonomy

the science of categorizing organisms

why is taxonomy important

provides universal names for all biological organisms, provides a reference for identification, allows for international communication

systematics (phylogeny)

study of evolutionary history of organisms

what does systematics demonstrates

relatedness (relationships) among organisms, evolutionary history of organisms

Carolus Linnaeus

Swedish botanist, proposed the formal system of naming

What three things do we use to group species together

1. anatomy of extant cells (still alive cells)

2. fossilized remains of cells (morphology)

3. rRNA gene sequences

Domain Archaea

• cell type: prokaryotic

• cell wall: varies in composition; contains no peptidoglycan'

• membrane lipids: composed of branched carbon chains attached to glycerol by ether linkage

• First amino acid in protein synthesis: methionine

• Antibiotic sensitivity: no

Domain Bacteria:

• cell type: prokaryotic

• cell wall: contains peptidoglycan

• membrane lipids: composed of straight carbon chains attached to glycerol by ester linkage

• First amino acid in protein synthesis: formylmethionine

• Antibiotic sensitivity: yes

Domain Eukarya

• cell type: Eukaryotic

• cell wall: varies in composition; contains carbohydrates

• membrane lipids: composed of straight carbon chains attached to glycerol by ester linkage

• First amino acid in protein synthesis: methionine

• Antibiotic sensitivity: no

why do bacterial and archaeal cells not make good fossils

too soft

binomial nomenclature

always in latin, genus is always capitalized, specific epithet is always lowercase

animalia

multicellular, no cell walls, chemoheterotrophic

plantae

multicellular, cellulose cell walls; usually photoautotrophic

fungi

chemoheterotrophic; unicellular or multicellular; cell walls of chitin; develop from spores or hyphal fragments

protista

a catchall kingdom for eukaryotic organisms that do not fit other kingdoms- default category

viral species

population of viruses with similar characteristics that occupies a particular ecological niche- similar host cells, very vague

prokaryotic species

a population of cells with similar characteristics

eukaryotic species

a group of closely related organisms that breed among themselves and offspring are viable

what strains can be named

only cultivated, pure (axenic) cultures

strain

genetically different cells within a clone

what do you need to be named as a species

about 1400 base pairs of rRNA gene sequenced

what were the historical methods of identifying a bacterium

morphology, differential staining, biochemical testing

what are the “modern” methods of identifying a bacterium

mostly same methods but faster, high-throughout biochemical testing, antibody-antigen reactions (agglutination), DNA sequencing (usually rRNA gene)

High-throughput biochemical testing

API strips by Bio Merieux, BIOLOG 96-well carbon utilization tests

Antigen-antibody tests

usually used for very specific pathogens (fast tests- results in about 10 min), mix in cells with antibodies for specific antigens

antigens

cell surface markers

upside of antigen-antibody tests

dirt cheap, very fast, extremely specific and sensitive

downside of antigen-antibody tests

only test for one thing, will only know yes or no on one thing

ELISA (enzyme-linked immunosorbent assay) Antigen-antibody tests

antibody linked covalently to enzyme, substrate for enzyme added, if bacterium is present, color changes. Can do pretty much anything with these

antigen

what is being detected

DNA sequencing

almost always rRNA genes, in small subunit of ribosome; first used by Carl Woese for bacterial evolution, very useful for identification and quantification

PCR

16 s rRNA gene, about 1500 basepairs long, certain regions are more variable than others, PCR primers can be made for all bacteria or certain species, almost the whole thing is amplified

Pelagibacter ubique

gram negative, a marine microbe, most common species on earth, 20% of prokaryotes in oceans are this species, small genome, heterotrophic

Caulobacter

Gram negative. Have prosthecae, is found in soils and water- stalked and swarming cells (can’t move once stalk is formed),

hyphomicrobium

gram negative, commonly found in lakes- budding cells, not symmetrical when dividing

Bartonella

causes cat-scratch disease

rickettsia

gram negative, intracellular parasites, are arthropod-borne and case spotted fevers

Enrlichia

gram negative, intracellular parasites

Brucella

gram negative, intracellular parasites

Domain bacteria, phylum pseudomonadota (all are gram negative) - Wolbachia

live inside insects and other animals, many are beneficial to the host, responsible for parthenogenesis?

Burkholderia

gram negative, are ubiquitous in nature, can grow in disinfectants, nosocomial (hospital acquired) infections are common

Neisseria

gram negative, common pathogens, STI’s (gonorrhea, bacterial meningitis)

Bordetella

gram negative, causes whooping cough

Order Pseudomonadales

gram negative, Pseudomonas is a very large genus, important ecologically in N-cycle, opportunistic pathogens in burn wounds and cystic fibrosis, also plant and mushroom pathogens

Order Legionellales- gram negative

• Legionella causes legionellosis, first identified in a convention in Philadelphia, difficult to grow- needs a charcoal-based medium, can live inside amoebae, can be found in ventilation ducts, pneumatic tools

• Coxiella causes Q fever, obligate parasites of mammals (farm animals), have an endospore-like body that forms (leathery not as tough as endospores), usually get infections from bad milk

Order Vibrionales

Gram negative, Vibrio are common pathogens, commonly found in coastal water, can cause choler, gasterocenteritis from contaminated shellfish, Vibrio is responsible for bioluminescence is the bobtail squid.

Order Enterobacteriales

gram negative, Many are human pathogens, facultative anaerobic, Bacilli, straight rods (no curved, club-shaped, etc)

Order Enterobacteriales, (9 genera)- all gram negative

1. Escherichia

2. Salmonella

3. Shigella

4. Enterobacter

5. Klebsiella

6. Serratia

7. Proteus

8. Yersinia & plague

9. Erwinia

Order Enterobacteriales, (9 genera) -Escherichia

gram negative, Most common intestinal organism in mammals, most species are NOT pathogens, even benign strains can cause UTI’s- most common cause, E. coli are foodborne pathogens

Order Enterobacteriales, (9 genera)- Salmonella

Normal in birds and reptiles intestines, serious foodborne pathogens from poultry, salmonellosis

Order Enterobacteriales, (9 genera)- Shigella

Very serious intestinal pathogen in humans, very difficult to distinguish from Escherichia, even with molecular methods (probably the same thing… more serous case of Escherichia)

Order Enterobacteriales, (9 genera)- Enterobacter

Water, sewage, soil, UTI’s, Nosocomial infections

Order Enterobacteriales, (9 genera)- Klebsiella

Common in soil or water, occasionally causes pneumonia in humans

Order Enterobacteriales, (9 genera)- Serratia

Can contaminate indwelling medical devices, opportunistic pathogen, tested by military

Order Enterobacteriales, (9 genera)- Proteus

Highly motile, swarming colonies on a plate, UTI’s

Order Enterobacteriales, (9 genera)- Yersinia and Plague

Killed >100 million people in Roman Empire, might even be responsible for the renaissance, spread by fleas on infected mice and prairie dogs, can be aerosolized- bioterrorism agent

Order Enterobacteriales, (9 genera)- Erwinia

plant pathogens, can break down pectin in plant cell walls (pectinase- what makes potatoes and fruits firm), cause “soft rots”, not known as human pathogens

Order Haemophilus

Haemophilus: all over human body, require blood (or heme) in their medium, require nicotinamide adenine dinucleotide (NAD+ or NADP+) in medium, some might be involved in sinus infections

Myxococcus

gliding motility, have external fruiting bodies (sporangioles) that produce myxospores- for reproduction

Camplyobacter

microaerophilic, causes foodborne illnesses (poultry carries this)

Helicobacter

H. pylori is thought to cause most ulcers, cancer?

Phylum Cyanobacteria

gram negative, oxygenic photoautotrophic bacteria, once called blue-green algae

Phylum Chlorobiota

gram negative, green sulfur bacteria, photoautotrophic, but anoxygenic

Bacteroides

anaerobic, gram negative, most common bacterium in human intestine, each mammal has different species, can be used to track contamination

Fusobacterium

anaerobic, fusiform (spindle-shaped), found in mouth and gut of mammals, contribute to dental diseases,

Domain bacteria, Gram-positive ones: overview

major division is due to G+C % of genome

phylum Bacillota, Mycoplasmatota

Have low GC content

phylum Actinomycetota

Has high GC content