MBB11002 -Microbiology 1 Flashcards
What are microfossils?
microorganisms trapped in rocks which resemble modern species
-found in stromatolites/sediments
-photographic (rather than experimental) evidence
What are stromatolites?
sediments made from alternating layers of limestone and microbial mats (entrapped bacterial communities)
What are the 4 main theories to explain the origin of life?
-chemical origin (pre-biotic soup forming simple molecules abiotically)
-RNA world (RNA as the first macromolecule)
-apparition of cellular life (prebiotic chem leading to cellular life)
-panspermia (life on Earth originating from space) -Fred Hoyle and Chandra Wickramasinghe
What was Miller’s experiment for the chemical origin of life?
-most amino acids and nucleotides can be formed from simple molecules (H2, CH4, NH3) in conditions mimicking Earth primitive conditions
-in UV and presence of H2S, HCN can produce amino acid, lipid and nucleotide precursors
What are the limitations for Miller’s experiment for the chemical origin of life?
-no evidence of aas in sediments
-H2 required -based upon (controversial) hypothesis of a reducing atmosphere
Why might RNA have been the first macromolecule encoding complex information (the RNA world origin of life theory)?
-has 4 building blocks (rather than 20 for proteins)
-less energy to form and degrade compared to DNA
-early biochem pathways can form uracil
-ssDNA is used as genome by viruses
-can have catalytic activity (ribozymes)
What is the activity of ribozymes?
-cleavage/ligation of RNA (splicing)
-replication
-formation of peptide bonds
What is the theory of apparition of cellular life?
compartmentalisation occurs to give rise to last universal common ancestor
-compartmentalisation created by phospholipids
-aas and nucleotides trapped
Why is compartmentalisation needed?
-protection from environment
-selective barrier
-rate enhanced (conc of molecules for metabolism)
What are the two hypothesises for the apparition of cellular life?
-surface origin
-subsurface origin
What is the surface origin hypothesis for the apparition of cellular life?
-primitive cells formed spontaneously on surface of Earth from a prebiotic soup
-metabolic processes were optimised by natural selection
What is the subsurface origin hypothesis for the apparition of cellular life?
-life appeared in stable conditions on ocean floor in hypothermal mounds (geothermal heated water from a crack in floor and cool ocean water)
-H2 and H2S as source of e- to form organic molecules
-redox/pH gradients used as prebiotic proton motor force
What are microbes?
small, unicellular organisms
-wide range!
-10nm-1mm
What is genetic plasticity?
phenotypic variation due to genetic factors
-drives microbial diversity
Why are microorganisms more diverse?
-bacteria are haploid, meaning a mutation will def be passed on
-rapid divisions (binary fission) rather than reproduction
-horizontal gene transfer can occur (transformation, conjugation, transduction)
What ways can horizontal gene transfer occur in microbes?
-transformation (DNA is taken up from surrounding cells)
-conjugation (genetic material can be exchanged)
-transduction (bacterial cells can be infected by phages targeting them)
What is taxonomy?
the discipline dealing with classifications of organisms into taxonomic subdivisions
What is the taxonomic hierarchy?
domain
kingdom
phylum
class
order
family
genus
species
How is taxonomy defined?
-phenotypic analysis (morphology, differential sraining, phage typing, fatty acid profiles, mass spec, metabolism comparisons)
-genetic analysis (DNA hybridisation, FISH, rRNA sequencing, multi locus sequencing, whole genome sequencing)
How is taxonomy studied using phenotypical analysis?
-morphology and differential staining
-phage typing (resistance, etc studied in agar plates)
-fatty acid profiles (membrane compositions -both gram +ve and -ve bact)
-mass spec (using isolate of whole bact as sample)
-metabolism comparisons (spread on diff medias, metabolic galeries, etc)
How is taxonomy studied using genetic analysis?
-rRNA sequencing (most widely used with taxonomy!! -rRNA is v.specific to species)
-DNA hybridisation (compare 2 purified genomes)
-FISH
-multi locus sequencing (sequencing and comparing house keeping genes)
-whole genome sequencing
What is phylogeny?
study of evolutionary history of organisms
How is phylogeny defined?
-genetic info compared using molecular clocks (DNA/protein seqs)
-seqs compared
-% divergence calculated
-phylogenetic trees created
What are molecular clocks?
technique where the mutation rate of biomolecules is used to deduce the time in prehistory when two or more life forms diverged
How were organisms divided into the three domains bacteria, archae and eukarya?
by the phenotypic tree of life (comparing rRNA gene seqs)
by Carl Woese
What are the three domains?
-Bacteria
-Archae
-Eukarya
What are the major differences between eukaryotic and prokaryotic cells?
-size (eukaryotic ~1µm, prokaryotic ~0.5µm)
-presence/absence of nucleus
-compartmentalisation
What are the components of eukaryotic cells?
-nucleus
-endoplasmic reticulum
-golgi complex
-lysosomes
-peroxisomes
-mitochondria
-chloroplasts
-flagella/cilia
What is the structure of the nucleus in eukaryotic cells?
-contains chromatin (histones + DNA)
-euchromatin and heterochromatin
What is the function of the nucleus?
mRNA, tRNA and rRNA synthesis
What is the structure of the endoplasmic reticulum?
-extension of nuclear membrane
-rough has ribosomes, smooth doesn’t
What is the function of the rough endoplasmic reticulum?
-protein synthesis
-protein quality control
What is the function of the smooth endoplasmic reticulum?
-lipid synthesis
-metabolic activities (eg. toxin breakdown)
What is the structure of the golgi complex?
-network of membranes (cisternae)
-polarised -has cis and trans face (cis -entry, trans -exit)
What is the function of the golgi complex?
-carbohydrate synthesis (eg. cell walls, extracellular matrix)
-protein modification (for specific targeting)
-secretes proteins/incorporates proteins into membranes
What is the function of lysosomes?
-metabolic processes -hydrolysing macromolecules (contain digestive enzymes for this!)
What is the function of peroxisomes?
-incorporate lipids and proteins from the cytoskeleton
-lipid metabolism (oxidise alcohols and fatty acids)
What is the function of mitochondria?
-respiration, oxidative phosphorylation, Krebs cycle
What is the structure of chloroplasts?
-stacks of thylakoids, forming grana
-stroma (~matrix)
-own circular DNA
What is the function of chloroplasts?
-Calvin cycle (converts light to organic compounds)
What is the structure of flagella/cilia?
-bundle of 9 pairs of microtubules surrounding a central pair (axoneme)
-nexin molecules connect microtubules to adjacent microtubules
-dynein molecules (drive motion by ATP hydrolysis)
What are the components of prokaryotic cells?
-nucleoid
-cytoplasm
-envelope
-appendages (pilus, fimbriae, flagella)
What is the structure of a nucleoid?
-usually a single circular chromosome (<10Mbp)
-dsDNA complexed w/histone-like proteins
-also plasmids
What is the structure of cytoplasm in prokaryotes?
-contains proteins, tRNA, mRNA, ribosomes
-contains protein-bound inclusion bodies (carboxysomes, storage granules, gas residues)
-generally thought to have no organelles but some do (magnetosomes, photosynthetic membranes, internal membranes)
What is the structure of the envelope in prokaryotes?
inside…
cytoplasmic membrane
peptidoglycan
polymers cov bound to peptidoglycan
outer membrane
…outside
-varies depending on species
What appendages can prokaryotes have?
-pilus
-fimbriae
-flagella
What is a pilus?
prokaryotic appendage dedicated to conjugation (plasmid exchange)
-1 per cell
What is a fimbriae?
prokaryotic appendage involved in adherence to host cell surfaces
-antigenic structures
-made of 1 protein
What is a flagella?
(prokayotes)
appendage involved in motility
-moves via rotation
-have diff configurations -can have 1 or lots, diff ones exist, etc
-anchored in cytoplasmic membrane (varies in gram +ve/-ve)
-usually 1 protein in proks (diff to euks!)
What is the theory of the endosymbiotic origin of eukaryotes?
stable incorporation of endosymbiotic bacteria in formation of mitochondria and chloroplasts
-nucleus appears before mitochondria and chloroplasts by endosymbiosis
What properties of eukaryotes are in favour of the endosymbiotic origin of eukaryotes?
-mitochondria and chloroplasts have inner and outer membranes
-mitochondria and chloroplasts have specific ribosomes (called mitoribosomes and chlororibosomes) which are diff to eukaryotic ribosomes
-mitochondria and chloroplasts multiply by binary fission (like proks)
What are the issues with the endosymbiotic origin of eukaryotes?
-eukaryotes and prokaryotes have similar lipid compositions
What unicellular eukaryotes are there?
-fungi (obvs can be multicellular too!)
-unicellular algae (plant-like protists)
-protozoa (animal-like protists)
-slime moulds (protists)
What are the types of fungi?
-molds (filamentous fungi)
-yeast (unicellular fungi)
-basidiomycetes (mushrooms)
Why are fungi important?
-ecological role -act as decomposers in the carbon cycle
-economical benefits -biotech, plant pathogens, etc
-human health -fungal infections
What are the common properties of fungi?
-most form hyphae (multicellular filaments)
-most are pleomorphic (exist in various forms)
-have carbohydrate cells walls -often chitin, mannans and/or glucans
-have 2 phases in life cycle involving asexual and sexual reproduction (haploid and diploid forms) -can undergo transitions
What is the structure of moulds?
-have filament structures known as hyphae (which grow mycelium)
Whereabouts in moulds does growth and the absorption of nutrients occur?
tip of hyphae
What occurs in the lifecycle of moulds?
alternation between haploid and diploid phases
-fusion
-spores prod
How do basidiomycetes live in symbiosis with trees or algae?
-fungus supplies nutrients and minerals
-trees provides prods of photosynthesis
What occurs in the lifecycle of basidomycetes?
-primary mycelium (gametes) fuse to prod secondary mycelium
-secondary mycelium produces basidium
-basidium produces basidospores
Why are yeast important?
-ecologically -used in brewery and bakery
-human health -infections, some S.cerevisiae strains used as probiotics
-used as model organism
What is S.cerevisiae used as a model organism for?
-lipid biology
-protein folding, quality control and degradation
-vesicular trafficking and fusion
-lysosomal and peroxisomal function
-apoptosis
-cell cycle
-mitochondrial and oxidative stress
What occurs in the lifecycle of yeast?
-cell division by budding and binary fission
-some form hyphae under specific conditions (dimorphic!)
What are the types of algae?
-primary endosymbiotic algae
-secondary endosymbiotic algae (diatoms)
-predatory algae (dinoflagellates)
What are primary endosymbiotic algae?
“true algae”
-green or red
-autotrophs
What are diatoms?
secondary endosymbiotic algae
-can be centric (have radial symmetry) or pennate (have non-radial symmetry)
What are dinoflagellates?
predatory algae
-very diff to endosymbiotic algae
What are mixotrophs?
organisms which can use a mix of energy sources
-dinoflagellates (predatory algae) -result from primary endosymbiotic algae being engulfed by a protist
What is the difference between primary and secondary endosymbiotic algae?
-primary have one membrane, whilst secondary have 2 membranes
-chloroplasts in primary endosymbiotic algae have a double membrane, while chloroplasts in secondary endosymbiotic algae have a triple membrane
Why are algae ecologically important?
-components of phytoplankton (produce lots of O2!)
-key food item in ocean web and aquaculture
What are the key properties of algae?
-photosynthetic organisms
-have chloroplasts
What are the properties of diatoms like?
-large biomass
-more complex chloroplasts than plants
-mobile (produces mucus to slide on -no appendages)
-have cell walls called frustule (made of silica)
What are the two types of diatoms?
-centric diatoms (radial symmetry)
-perinate diatoms (bilateral symmetry)
What are diatoms cell walls like?
frustules
-in two halves
-made of silicon dioxide crosslinked to form silica
-very rigid -makes life cycle more complicated
What happens in the life cycle of diatoms?
-each daughter cell inherits half of frustule, making it smaller than parents
-cells get smaller and smaller each generation, until they can’t divide anymore so undergo meiosis to form gametes
-gametes fuse, forming frustule same size as parents’
What are the cell walls of secondary endosymbiotic algae like?
frustules made of CaCO3 growing in multiple scales
What happens in the life cycle of primary endosymbiotic algae?
-colonial lifecycle
-asexual and sexual reproduction
What are the types of protozoa?
-ciliates (predatory protists)
-apicomplexans (parasites)
-dinoflagellates (predatory algae)
-metamonds
-trypanosomes
Which types of protozoa are alveolates?
-ciliates (predatory protists)
-apicomplexans (parasites)
-dinoflagellates (predatory algae)
What are the properties of alveolates?
-have alveoli (bags of fluid surrounded by lipid membrane)
-mobile (have cilia, can glide)
-mostly aquatic
What is the ecological importance of alveolates?
ciliates: food web (zooplankton)
apicomplexans: human health
dinoflagellates: involved in carbon cycle
What happens in the life cycle of ciliates?
-binary fission (asexual reprod.)
-conjugation (sexual reprod.)
What are the properties of paramecium (model ciliate)?
-alveoli under cytoplasmic membrane
-cilia and trichocyst
-oral groove (for food entry)
-contractile vacuole (for H2O reg)
-digestive vacuole
-3 nuclei (macronucleus, 2 micronucleus)
What’s the difference between macronuclei and micronuclei?
macronuclei
-transcriptionally active
-lots of copies of diff genomes
micronuclei
-transcriptionally inactive
-genetic recombination
What are the properties of apicomplexans?
-have flagella, cilia or pseudopods
-contain apical complex (aid entry into host)
-have apicoplast (degenerate chloroplast -no chlorophyll, no photosynthesis -involved in fatty acid metabolism)
What happens in the life cycle of apicomplexans?
-use a vector to infect host
-inside host, undergo morphological changes and multiplies, releasing merozoates, which differentiate into gametocytes
-in vector, gametes fuse, forming zygote which invades vector, producing sporozoites
What are the properties of dinoflagellates?
-mixotrophs (undergo photosynthesis and feed on bacteria, algae, etc)
-have 2 flagella
-have chloroplasts with complex membranes
-cell walls made of overlapping cellulose plates (theca)
-have extrusome (ejectable, membrane bound organelle which can discharge contents)
What happens in the life cycle of dinoflagellates?
-vegetative reproduction via binary fisson and sexual reproduction
-can exist in dormant forms (cysts)
What are the properties of slime moulds and amoebas?
-found in damp environments
-have complex life cycles involving the same developmental stage
How are amoebas mobile?
using pseudopod mobility
-actin polymerisation/disassembly
How do amoebas use pseudopod motility?
actin polymerisation/disassembly
What are amoebas?
parasitic unicellular eukaryotes
What happens in the lifecycle of cellular slime moulds?
-binary fission
-when stressed, release cAMP, which drives aggregation to form a “slug” (social motility!)
-release of spores (cysts) initiates new cycles
What happens when cellular slime moulds are stressed (eg. under starvation of nutrients)?
-release cAMP
-aggregation occurs, forming a slug (lots of cells together)
-slug differentiates into fruiting body (made of sporangium and stalk)
-fruiting body can form cysts
-cysts/spores released, initiating new cycle
What happens in the life cycle of a plasmodial slime mould?
-binary fission
-individual cells can aggregate to form a plasmodium (single cell with lots of nuclei)
-plasmodium differentiaes into fruiting body
-fruiting body can form cysts
-cysts/spores released, initiating new cycle
What are the general properties of viruses?
-needs host mechanism machinery to replicate (obligatory parasite)
-small
-made of nucleic acid genome surrounded by protein coat (capsid) and facultative lipid envelope
-can infect all living organisms
What is the general structure of viruses?
-nucleic acid genome
-capsid (protein coat made of capsomers, can contain polysaccharides)
-lipid envelope (lipid bilayer w/proteins from host)
What is the composition of a viral genome?
ss/ds DNA/RNA
What is the size of a viral genome?
2-20kb (small)
-minimal info needed (can get from host)
-only specific genes
-generally ds>ss and DNA>RNA
How is a viral genome generally organised?
as one molecule
-can be fragmented
What is the composition of a viral capsid?
1+ proteins called capsomers
What is the structure of a viral capsid?
-highly ordered
-self-assembly prods
What are the two types of viral capsids?
-icosahedral symmetry (spherical)
-helical symmetry (rod-shaped)
What is the structure of a nucleocapsid?
nucleic acid surrounded by capsomers
What is the composition of a viral envelope?
-lipid bilayer
-glycoproteins/proteins from host or viral encoded
What is the role of a viral envelope?
allows entry into host cell via fusion/endocytosis
What is the structure of a bacteriophage?
-mixture of icosahedral and filamentous structures
-head
-collar
-tail (ejects genetic info into host once strong connections are established)
-endplate
-tail fibres (recognise cell surface)
What are the issues with some nomenclatures for viral classification?
lots of diff systems going on
-names after disease
-named after place disease was first reported
-named after host/signs of disease
-named after shape of virus
-named after discoverer
-named after mechanism of transmission
How are viruses classified using the Baltimore classification?
into 7 classes
-separated by whether they are DNA or RNA viruses and how the genome is replicated and transcribed
What does the Baltimore classification take into account?
-the nature and type of genome (DNA/RNA, ss/ds)
-how genome is replicated
-how genome is transcribed
Which classes are DNA viruses?
1, 2 and 7
Which classes are RNA viruses?
3, 4, 5 and 6
Name an example of a class 1 virus
Papillomavirus
-dsDNA
Name an example of a class 2 virus
Adeno-associated virus
-ssDNA
Name an example of a class 3 virus
Reovirus
-dsDNA
Name an example of a class 4 virus
Foot-and-mouth disease virus
-ssRNA
Name an example of a class 5 virus
Influenza
-ssRNA
Name an example of a class 6 virus
HIV
-reverse RNA
Name an example of a class 7 virus
Hepatitis B
-reverse DNA
What are the major steps in the life cycle of a virus?
-attachment to host
-genome injection (entry)
-production of viral nucleic acids and proteins
-maturation (viral particles assembling)
-release of virus (exit)
What happens in the lifecycle of a bacteriophage?
lytic cycle
-attachment (using tail fibres) and genome injection
-cellularisation of phage DNA
-synthesis of phage DNA and proteins, assembled into virions
-cell lysis, releasing phage virions
lysogenic cycle (dormant)
-attachment and genome injection
-recombination of phage DNA into bacterial genome generates prophage
-cell divisions
-if prophage exists, goes into lytic cycle
What happens in the lifecycle of a DNA virus?
-attachment and entry
-viral DNA uncoated (capsids removed) and transferred to nucleus
-synthesis of viral DNA and proteins
-maturation (virions assemble)
What happens in the lifecycle of a RNA virus?
-attachment and entry
-depends on virus -mRNA transcription and translation
What happens in the lifecycle of a Retrovirus?
-entry via fusion
-viral DNA and enzymes reeased
-viral DNA copied to dsDNA by reverse transcriptase
-dsDNA transported into nucleus and integrated into host genome
-new genomes and RNA produced
-mature retrovirus buds out of host
How are viral particles packaged?
fragmented genomes: genome fragments in complex with proteins paired before encapsulation
dsDNA viruses: encapsulation coupled with replicative genome maturing
ssRNA viruses and Retroviruses: capsomers cooperatively assemble, promoted by electrostatic interactions between capsid proteins and RNA genome
How are viral fragmented genomes packaged?
genome fragments in complex with proteins paired before encapsulation
How are dsDNA viral particles packaged?
encapsulation coupled with replicative genome maturing
How are ssRNA viral and Retroviral particles packaged?
electrostatic interactions between capsid proteins and RNA genome promote the cooperative assembly of capsomers
What different morphologies of bacteria are there?
-cocci (round)
-rod-shaped
-curved
-spiral
-exotic
-morphologies can change during cell cycle
What are the advantages of bacteria having a large surface area to volume ratio?
-nutrient exchange and growth rates
-high intracellular nutrient conc
-rapid evolution (high selection rate of mutations)
What is bacterial colour due to?
the production of pigments
What is bacterial smell due to?
the production of secondary metabolites
-side prods from metabolism (mechanisms in growth and division)
In what ways are bacterial phenotypes diverse?
-morphologically (diff shapes: cocci, rod, curved, spiral)
-size
-colour
-smell
How is the gram stain carried out?
-stain with crystal violet
-fix with iodine (mordant)
-wash with alcohol
-counter stain with safranin
What is the gram stain used for?
bacteria diagnostics
-can be used with complicated (rather than isolated) populations
What bacteria is stained purple by the gram stain?
gram positive
What are the properties of gram positive bacteria?
-no outer membrane
-thick cell wall
What bacteria is stained pink by the gram stain?
gram negative
Why is gram positive bacteria stained purple in the gram stain?
-crystal violet penetrates into peptidoglycan and gets trapped when the mordant is added
Why is gram negative bacteria stained pink in the gram stain?
-crystal violet sits on top of envelope and gets washed away
-safranin stains the outer membrane pink
What are the properties of gram negative bacteria?
-outer membrane
-thin cell wall
What is the structure of a S-layer in bacteria?
-made of proteinaceous crystalline arrays (self-assembled proteins)
-non-covalently bound to cell surface (in gram +ve, directly bound to peptidoglycan, in gram -ve, anchored to lipid membrane)
How are S-layers bound to the cell surface differently in gram positive and negative bacteria?
gram +ve: are directly bound to peptidoglycan/anything on peptidoglycan
gram -ve: anchored to lipid membrane
What is the structure of capsules in bacteria?
-made of polysaccharides or amino acids
-covalently bound to cell wall/outer membrane (anchored)
What do capsules do?
-gives resistance to host’s phagocytes/bacteriophages
-keeps environment hydrated (because polysaccharides are hydrophilic)
What is the structure of exopolysaccharides in bacteria?
-complex repeating units containing 2-20 sugars (variable!)
-non-covalently bound to cell surface
-homo or hetero -polysaccharides
-encase biofilms (thin layer of community of microorganisms protecting cells from environment)
How are exopolysaccharides important in biotechnology?
xanthan gum in toothpaste, ice cream, salad dressing, etc
What is the structure of the outer membrane in bacteria?
-asymmetric lipid bilayer (diff to inner membrane, w/symmetric bilayer)
-contains phospholipids, proteins (porins), lipoproteins, lipopolysaccharide (LPS)
What is LPS?
lipopolysaccharide
-contains lipid anchor, core polysaccharide, O-specifc polysaccharide)
-found in bacterial outer membranes
What was the structure of peptidoglycan (murein) in bacteria originally thought to be like vs what we know now?
originally…
-rigid exoskeleton (protective role)
now…
-flexible, elastic, dynamic
-composed of alternating N-acetylglucosamine (G) and N-acetylmuramic acid (M) substituted by short polypeptides (L and D amino acids)
How has better understanding of the structure of peptidoglycan in bacteria come about?
atomic force microscopy
-gives info on shape, height, elasticity, etc based upon deflection
What are the roles of peptidoglycan in bacteria?
-cell shape
-exoskeleton (resistance to osmotic stress)
-scaffold for displaying polymers and proteins (covalently and non-covalently anchors them)
What is the highly conserved structure of peptidoglycan?
alternating N-acetylglucosamine (G) and N-acetylmuramic acid (M)
-from M, pentapeptides (L and D amino acids) -sometimes w/a lateral chain
How is the alternating sequence of N-acetylglucosamine and N-acetylmuramic acid in peptidoglycan assembled?
by D,D-transpeptidases
-bifunctional enzymes (aa transfer, bind to penicillin)
What is the structure of the cytoplasmic membrane like in bacteria?
-phospholipids
-hopanoids (like steroids)
-proteins
What are chromosomes like in bacteria?
-always dsDNA
-usually singular circular chromosome
-varies in size (0.5-14Mbp)
-organised as nucleoid (supercoiling, histone-like proteins)
What are plasmids like in bacteria?
-always dsDNA
-usually circular
-varies in copy number (1-100s)
-varies in size (2-600kbp)
-can be transferable (self or non-self) via horizontal transfer
-can carry resistance genes
How is bacterial gene organised in regards to expression (What is its gene structure like)?
-genes made of continuous coding sequence known as open reading frame
-no introns
-organised in operons
-genes relatively small (compared to eukaryotes)
What happens in transcription initiation in bacteria?
-RNAP scans DNA, forming a loose complex
-sigma factor binds to 2 specific sequences upstream from the start codon, forming a closed complex
-RNAP is recruited, increasing its affinity for DNA
-DNA unwinds, forming an open complex and sigma factor is released
What happens in transcription termination in bacteria?
-palindromic GC-rich region (upstream of AT-rich region) is needed for termination
-once GC-rich region is transcribed, a hairpin structure forms
-this makes RNAP dissociate (helped by there being less H-bonds in AT-rich region)
or
-Rho proteins bind to 72 res GC-rich
-RNA downstream wraps around itself, when it reaches RNAP Rho proteins unwind the RNA-DNA duplex, releasing RNAP
What are the differences between bacterial and eukaryotic transcription?
-transcription site (bact-cytoplasm, euks-nucleus)
-1 RNAP in proks, 3 in euks
-euk termination involves mRNA cleavage using AAUAAA seq
-euks modify mRNA (capping, polyadenylation, splicing)
What are the differences between bacterial and eukaryotic translation?
-proks have 70S ribosomes, euks have 80S ribosomes (80S ribosomes can bind mRNA in tRNA absence)
-in pros translation is coupled to transcription
-translation is specifically inhibited by cyclohexamine in euks but not proks
What are the requirements for bacterial growth?
-temperature
-pH
-osmotic pressure
-nutrients
-oxygen
What are cardinal temperatures?
the specific temperature range a bacteria can survive
-minimum, optimum and maximum temperatures
-diff cardinal temps for diff organisms
What is happening in bacteria at the minimum temperature for growth?
-membrane gelling
-transport processes so slow that growth can’t occur
What is happening in bacteria at the optimum temperature for growth?
-enzymic rxns occurring at max possible rate
What is happening in bacteria at the maximum temperature for growth?
-protein denaturation
-cytoplasmic membrane collapse
-thermal lysis
What are the cardinal temps for psychrophiles?
0-20°C
What are the cardinal temps for mesophiles?
10-45°C
What are the cardinal temps for thermophiles?
40-80°C
What are the cardinal temps for extreme thermophiles?
60-120°C
What are the adaptions of psychrophiles to cold temperatures?
-increased membrane fluidity (high content of unsaturated and methyl-branched fatty acids and shorter acyl-chains -to limit membrane cohesion and homogenity)
-production of anti-freeze proteins
-production of cryoprotectants (trehalose, exopolysaccharides)
-production of cold-adapted enzymes (higher proportion of helices, less weak bonds and interdomain interactions)
Why do psychrophiles have increased membrane fluidity?
-limits membrane cohesion and homogenity
What do anti-freeze proteins do?
bind to small ice crystals which inhibits their growth/formation (as the proteins cover their water accessible surfaces)
What are the properties of cold-adapted enzymes (produced by psychrophiles)?
-have a higher proportion of helices
-have less weak bonds and interdomain interactions
-increased flexibility
What are the adaptions of thermophiles to high temperatures?
-genome protection (stabilisation by DNA binding proteins, high GC%, supercoils)
-modification of membrane composition (ester-linked phospholipids, single lipid layer)
-production of thermostable proteins
-existence of thermostable chaperones
How are the genomes of thermophiles protected to be adapted to high temperatures?
-DNA-binding proteins stabilise the DNA
-supercoils (introduced by reverse DNA gyrases) make it harder for strands to be untwisted and denatured (higher temps required to do so)
-high G-C% makes DNA more resistant to denaturation
How is the membrane composition modified in thermophiles?
-phospholipids are linked by ether bonds rather than phosphodiester bonds
-single lipid later (glycerol tetraethers)
What are the properties of thermostable proteins (produced by thermophiles)?
-higher proportion of ionic interactions and hydrophobic interactions
What are the different types of micro-organisms adapted to specific pHs?
-acidophiles (pH 0-6)
-neutrophiles (pH 6-8)
-alkaliphiles (pH 8-14)
What are the metabolic adaptions of acidophiles?
-respiratory chains pump H+
-H+/Na+ antiporters used to maintain internal pH below external pH
-membrane impermeability/stability
-reverse membrane potential
-H+ motor force drives flagellar motor, ATP synthesis and substrate symport
-H+/K+ antiporters excrete H+
SUMMARY: MOSTLY USE H+ TO POWER PROCESSES TO MAINTAIN HIGHER [H+] OUTSIDE CELL
What are the metabolic adaptions of alkaliphiles?
-respiratory chains pump Na+
-H+/Na+ antiporters used to maintain internal pH above external pH (take in H+)
-Na+ driven ATPases export Na+
-Na+ motor force drives flagellar motor, ATP synthesis and substrate symport
-Na+ secreted by decarboxylases
SUMMARY: MOSTLY USE NA+ TO POWER PROCESSES TO MAINTAIN HIGHER [H+] INSIDE CELL
∴ live in salty places
What are the different types of micro-organisms adapted to different osmotic pressures?
-non-halophiles (not salty conditions)
-halotolerants
-halophiles (salty conditions)
-extreme halophiles
How are micro-organisms adapted to respond to osmotic stress?
-regulate water movement (by passive diffusion and aquaporins)
-produce compatible solutes
-release solutes by mechano-sensitive channels
How are halophiles adapted in terms of their salt requirement?
-stabilisation of S layer glycoprotein by Na+
-accumulate K+ as compatible solute
What nutrients do microorganisms require?
-nitrogen
-sulphur
-phosphorus
-some vitamins
-cofactors -K+, Ca2+, Mg2+
-trace factors -Fe, Cu, Zn
What do phototrophs use as their source of electrons carbon?
light
organic compounds
What do chemotrophs use as their source of electrons and carbon?
inorganic compounds
What are reactive oxygen species?
toxic forms of oxygen
-superoxide (O2 -)
-hydrogen peroxide (H2O2)
-hydroxy radical (OH*)
Which enzymes can detoxify reactive oxygen species?
-catalase/peroxidase (convert hydrogen peroxide to water)
-superoxide dismutase and catalase/superoxide reductase and catalase (convert superoxide to hydrogen peroxide to water)
What are the different types of microorganisms adapted to different oxygen availabilities?
-obligate aerobes (only use oxygen for respiration)
-facultative aerobes (can use oxygen for respiration)
-microaerophiles (require an exact amount of oxygen for respiration)
-aerotolerant anaerobes (don’t use oxygen for respiration but can survive in the presence of oxygen)
-obligate anaerobes (don’t use oxygen for respiration and can’t grow in the presence of oxygen)
What are obligate anaerobes?
organisms which can only use oxygen for respiration
-have catalase and superoxide dismutase enzymes
eg. Pseudomonas aeruginosa
What are facultative aerobes?
organisms that can use oxygen for respiration
-have catalase and superoxide dismutase enzymes
eg. Escherichia coli
What are microerophiles?
microorganisms that require oxygen in exact amounts for respiration
eg. Campylobacter jejuni
What are aerotolerant anaerobes?
organisms that do not use oxygen for respiration but can still grow in the presence of oxygen
-have superoxide dismutase enzymes (but not catalase)
eg. Streptococcus mutans
What are obligate anaerobes?
organisms that do not use oxygen for respiration and can not grow in the presence of oxygen
eg. Clostridium difficile
How can bacterial growth be measured?
direct measurements
-microscopic counts (spreading suspense on cell counter and counting)
-viable counting (spreading serial dilutions on agar plates and counting colonies)
-flow cytrometry (pumping suspension through capillary and measuring how much light scatters)
indirect measurements
-optical density
-dry weight
-metabolic activity
How can bacterial growth be measured directly?
-microscopic counts (spreading suspense on cell counter and counting) -don’t know if cells are dead or alive
-viable counting (spreading serial dilutions on agar plates and counting colonies) -doesn’t directly tell us the number of cells
-flow cytrometry (pumping suspension through capillary and measuring how much light scatters) -gives idea of cell density, can distinguish between dead and alive cells
How can bacterial growth be measured indirectly?
-optical density
-dry weight
-metabolic activity
What are the limitations of using optical density to indirectly measure bacterial growth?
-requires high cell densities
-doesn’t distinguish between dead and living cells
-OD values differ depending on organisms
-doesn’t work on mounds or filamentous bacteria
What are the phases of a typical bacterial growth curve?
-lag phase
-log phase
-stationary phase
-death phase
What happens in the lag phase of a typical bacterial growth curve?
constant no. cells
-metabolism starts
-no divisions
What happens in the log phase of a typical bacterial growth curve?
no. cells increases exponentially
-divisions
What happens in the stationary phase of a typical bacterial growth curve?
no. deaths = no. new cells
-nutrients exhausted
-inhibition
What happens in the death phase of a typical bacterial growth curve?
no. cells decrease
-depends on bacteria -not all undergo lysis
How can bacterial growth be physically controlled?
-using heat (moist heat, dry heat or pasteurisation)
-using irradiation (ionizing or non-ionizing)
-using filtration (nucleopore, membrane or depth filters)
How can bacterial growth be physically controlled using heat?
-moist heat (boiling heat/autoclave)
-dry heat (direct flaming, incineration or exposure to high temp for long time)
-pasteurisation (mild heat, HTST or UHT)
How can bacterial growth be physically controlled using irradiation?
-ionizing radiation (electron beams, gamma rays, x-rays) -used in food industry, for lab equipment and medical use (destroys DNA by creating breaks in double strand and using reactive oxidative species so more sterile)
-non-ionizing radiation (UV) -used for surface decontamination (less sterile)
How can bacterial growth be physically controlled using filtration?
-sterilises gases or liquids that can be damaged by heat
-porosity of filter chosen for specific applications:
nucleopore filters (membranes w/defined holes) -v. precise control of sizes
membrane filters -quick and easy, can use for things you don’t want to heat, less specific than nucleopore filters
depth filters -recycle air, less specific than nucleopore filters
What are the types of chemical antimicrobial agents?
-bacteriostatic
-bactericidal
-bacteriolytic
What are bacteriostatic agents?
compounds which inhibits bacterial growth
-bacteria stay alive but stop growing
-viable cell count stays constant after
-rare
What are bactericidal agents?
compounds which kill bacteria
-viable cell count decreases after
-most common antibmicrobial agents
What are bacteriolytic agents?
compounds which kill bacteria (are bactericidal) by causing cell lysis
-number of cells and viable cell count decreases after
What are the differences between different classes of chemical antimicrobial agents?
-sterilants -applied on objects, kill microorganisms but not spores
-disinfectants -applied on objects, completely kill all forms of microorganism including spores
-antiseptics and germicides -applied on living tissue, inhibit growth of/kill microorganism
How can antimicrobial activity be measured experimentally?
-disc diffusion plates (discs containing antibiotics placed on surface of agar plates spread with microorganism)
-E-test (strip containing varying concentration of antibiotic placed on surface of agar plates spread with microorganism)
-minimum inhibitory concentration (MIC) assays
-minimum bactericidal concentration (MBC) assays
What is a minimum inhibitory concentration (MIC)?
lowest concentration of antibiotic that inhibits the viable growth of a microorganism after overnight incubation
What is a minimum bactericidal concentration (MBC)?
lowest concentration of antibiotic that kills 99.9% or microorganism after overnight incubation
What chemicals are used for antimicrobial control?
-phenolic compounds (aromatic derivatives)
-alcohols
-aldehydes
-quaternary ammonium compounds (quarts)
-halogen releasing agents (chlorine-releasing or iodine-releasing)
Why are phenolic compounds used as chemicals for antimicrobial control?
-local anaesthetics at low concs, antibacterial at high concs
-denature proteins and disrupt membranes
eg. phenols in TCP, chlorohexidine in mouthwashes, triclosan in soap and toothpaste
Why are alcohols used as chemicals for antimicrobial control?
-denature proteins, dissolve lipids and disrupt membranes
eg. hand sanitiser
Why are aldehydes used as chemicals for antimicrobial control?
-are alkylating agents -modify proteins and DNA, causing cell death
eg. preserving tissues, microscopy
Why are quaternary ammonium compounds (quarts) used as chemicals for antimicrobial control?
-disrupt phospholipids in cytoplasmic membranes
Why are quaternary ammonium compounds (quarts) used as chemicals for antimicrobial control?
-disrupt phospholipids in cytoplasmic membranes
Why are halogen releasing agents used as chemicals for antimicrobial control?
-chlorine-releasing agents chlorinate bases in DNA and aid oxidation of proteins
eg. household bleach
-iodine-releasing agents target DNA and proteins
eg. iodine, iodophores
What are the two major therapeutic strategies?
-antibiotics
-vaccinations
Who discovered penicillin?
Alexander Fleming
What do the major classes of antibiotics target?
-cell wall synthesis
-DNA gyrase
-RNA elongation
-DNA-directed RNA polymerase
-protein synthesis (50S, 30S or tRNA inhibition)
-lipid biosynthesis
-cytoplasmic membranes
-fatty acid metabolism
What are the modes of action of antibiotic resistance?
-drug inactivation
-target modification
-efflux/impermeability
-bypass
What causes antibiotic resistance?
misuse in human therapeutics
-farming (excessive use of antibiotics)
-agriculture
-aquaculture
-pets
What are the properties of an ideal antibiotic?
-target is selectively toxic (kills microorganism, not hosts)
-target must inhibit essential processes or virulence
-stable
-effective
-cost
What is pharmacokinetics?
study of how body interacts with antibiotics
What is pharmacodynamics?
study of how antibiotics work and what they do to the body
What is the mode of action of β-lactams (type of antibiotic eg. penicillin)?
inhibition of peptidoglycan polymerisation, mediated by D,D-transpeptidases (aka penicillin binding proteins)
Why do D,D-transpeptidases (aka penicillin binding proteins) act on β-lactams?
-β-lactams are structural analogues of D-Ala-D-Ala C-terminal residues in peptide stems
-D,D-transpeptidases (aka PBPs) use them as substrates and irreversibly inactivate them
What are the modes of action of resistance to β-lactams?
-drug inactivation by β-lactamase
-target modification by overexpression or low affinity penicillin binding proteins
-efflux systems (gram -ve bacteria)
-bypass with alternative pathways
What happens in the mechanism of resistance to β-lactams via inactivation by β-lactamase?
-catalytic Ser undergoes nucleophilic attack (towards C=O)
- β-lactam ring opens, forming covalent complex penicillin-β-lactamase
-hydrolysis of penicillin, splitting OH-Ser-β-lactamase off from rest of compound
-opening of β-lactam ring makes drug inactive
What happens in the mechanism of resistance to β-lactams via mutation of target enzymes?
-conformation altered so that penicillin binding proteins have lower affinity for β-lactams
-overexpression of penicillin binding proteins targeted by β-lactams lowers efficiency of drug
What happens in the mechanism of resistance to β-lactams via secretion of antibiotics?
-overproduction of system leads to resistance
What are Archaea?
prokaryotes representing 1 domain in the tree of life
What are the 2 major phyla of Archaea?
-euryarcheota
-crenarchaeote
What are extremophiles?
organisms whose growth is dependent on extreme conditions, which are generally inhospitable to most forms of life
Why is it still under debate whether there are 2 or 3 domains?
-euryarchaea could have evolved from Asgards (branch of Archaea)
-Asgards contain genes with equivalents in eukaryotes but no equivalents in bacteria
-diversity of microorganisms is underestimated
Are S layers present in Archaea?
yes
-v common
What are Archaea cell walls made from?
pseudomeurin
(occasionaly found in bact, never in euks)
What is the structure of pseudomeurin?
-heteropolymer
-N-Acetylglucosamine and N-Acetyltalosaminurmonic
What are Archaea cell walls resistant to?
-lysozymes
-most antibiotics which target bacterial peptidoglycan synthesis
Why can pseudomeurin not be studied in the same ways peptidoglycan can be?
-diff compositions
-at the moment, no commercial enzymes can hydrolyse pseudomeurin
-pseudomeurin isn’t affected by β-lactases
What unusual structures exist in Archae?
-Archaellum (sim. to flagella)
-Cannulae (tubes connecting cells)
-Hooks
What are Archaellum?
structures present in Archaea made from lots of proteins, which move via rotation
-like flagella
What are Cannulae?
tubes present between cells in Archaea, which establish physical contact between cells
-connected to S layer
What is the structure of the cytoplasmic membrane like in Archaea?
-phospholipids contain isoprenes, rather than fatty acids
∴ ether links not ester links
How is the genome organised in Archaea?
-circular chromosome (and plasmids)
-histones present
-have multiple replication origins
Which DNA polymerases are encoded in Archaea?
polymerase B (also present in Eukarya) and polymerase D (exclusive to Archaea)
How many RNA polymerases do Archaea have?
one
-very similar structure to Eukarya’s RNAP
Are introns present in Archaea?
yes
How are genes organised in Archaea?
in operons
Which ribosomes are present in Archaea?
70S
What is translation like in Archaea?
-coupled to transcription
-involves several translation factors
-uses 70S ribosomes
In what ways are Archaea very diverse?
-in terms of habitats -hot springs, Antartica, volcanic environments, etc
-in terms of metabolism -phototrophs and chemotrophs, can use organic or inorganic carbon sources and can use organic or inorganic reducing equivalent sources
What are the three major types of Archaea?
-(hyper)thermophiles
-halophiles
-methanogens
Describe (hyper)thermophile Archaea
-high growth temps
-often acidophiles
-most require sulphur for growth
eg. Acidianus infernus
-found in hot springs
-used in biotech
-grows anaerobically or aerobically
eg. Thermococcus barcosi
-found in hydrothermal vents
-requires S
-grows anaerobically
Describe halophile Archaea
-mostly Euryarchaeota
-found in evaporated ponds, salt lakes, the Dead sea
-require up to 5M NaCl for growth
eg. Halobacterium
-found in the Great Salt Lake (4M NaCl)
-uses light as energy source to secrete H+
Describe methanogen Archaea
-Euryarchaeota
-found in anaerobic environments (gut, marine sediments, etc)
-use acetate, fumarate, CO2, etc as e- transporters
eg. Methanopyrus kandleri
-found in deep-ocean hydrothermal vents
eg. Methanobrevibacter smithii
-found in human gut
-removes bacterial end products of fermentation
How are metabolic types names?
-chemo (molecules as energy source) or photo (light as energy source)
-organo (organic molecules as e- source) or litho (inorganic molecules as e- source)
-heterotroph (organic compounds as C source) or autotroph (inorganic compounds as C source)
What organisms are chemoheterotrophs?
-animals
-fungi
What organisms are chemoautotrophs?
-extremophiles
What organisms are photoheterotrophs?
-purple and green non-sulphur bacteria
What organisms are photoautotrophs?
-plants
-algae
-cyanobacteria
ΔG =
(Gibbs free energy)
-nFΔE
where
n = no. e-s transferred
F = Faraday’s constant
ΔE = redox potential change
What value of proton motor force (Δp) must the redox potential change (ΔE) exceed to be coupled to electron transfer and H+ translocation?
180mV
What are the key energetic currencies used by chemoorganotrophs?
ATP
NADH and H+, FADH2
What are the major metabolic types within chemoorganotrophy?
-aerobic respiration
-anaerobic respiration
-fermentation
How are chemoorganotrophs metabolically diverse?
-use range of organic compounds as e- sources (carbs, lipids, peptides, aromatic comps)
-can produce acetyl-coA and pyruvate
-use ATP or NADH or FADH2 as energy currencies
-can use aerobic or anaerobic respiration or fermentation
What are the differences between anaerobic respiration and fermentation?
anaerobic resp:
-resp chain and ox phos
-e- transport via cytochromes, quinones and iron-sulphur proteins
-can use many inorganic compounds
fermentation:
-no resp chain
-substrate-level phos to prod ATP (no ATP synthases)
-low yields
What are the types of chemolithotrophy?
-hydrogenotrophy (incl sulphate reduction and methanogenesis)
-iron oxidation
-nitrogen oxidation (incl nitrification and anammox)
-sulfide oxidation
-sulphur oxidation
What does chemo mean in terms of metabolic types?
use molecules as energy source
What does photo mean in terms of metabolic types?
use light as energy source
What does heterotroph mean in terms of metabolic types?
use organic compounds as carbon source
What does autotroph mean in terms of metabolic types?
use inorganic compounds as carbon source
What does organo mean in terms of metabolic types?
use organic compounds as electron source
What does litho mean in terms of metabolic types?
use inorganic compounds as electron source
What can chemolithotrophs use as electron donors?
-hydrogen
-iron
-ammonia
-nitrates
What do hydrogenotrophs use as electron donors?
H2
What do hydrogenotrophs use as electron acceptors?
O2
SO4 2-
CO2 (methanogenesis)
chlorinated compounds (dehalorespiration)
What do chemolithotrophs which use iron oxidation use as electron donors?
Fe
What do chemolithotrophs which use nitrogen oxidation use as electron donors?
ammonia (NH3)
nitrates (NO2 -)
What is anammox?
anaerobic ammonia oxidation
NH4 + + NO2 - -> N2 + 2H2O
-Planctomycetes
What is nitrification?
aerobic ammonia oxidation
NH4 + + NH2OH -> NO2 - -> NO3 -
-Nitrosomas and Nitrosobacter
What do chemolithotrophs which use sulphur oxidation use as electron donors?
sulphur derivatives
-elemental sulphur (S)
-hydrogen sulphide (H2S)
-thiosulfate (S2O3 2-)
-ferrous sulphate (F2S2)
What is biomining?
-using acid-producing microbes to dissolve metals from rocks as an alternative to commercial mining
-less hazardous waste
eg. using Acidothiobacillus ferroxidans
What are the types of phototrophy?
-oxygenic
-anoxygenic
What is oxygenic photosynthesis?
-carried out by plants and cyanobacteria
-uses photosystems PSI and PSII
What is anoxygenic photosynthesis?
-carried out by bacteriorhodopsin, green sulphur bacteria and purple bacteria
-uses photosystems BR, PSI and PSII
What is bacteriorhodopsin?
primitive photosynthetic system
-very abundant light-driven H+ pump in archeal membrane
-contains pigment retinal (undergoes conformational change when excited by light)
-produces ATP using movement of H+
What happens when bacteriorhodopsin undergo anoxygenic photosynthesis?
-retinol is excited by light, causing it to undergo a conformational change (from trans to cis)
-conformational change triggers transfer of H+ to Asp85
-deprotonated retinol pushes against helix, opening channel on cytoplasmic side, inducing retinol to be deprotonated from Asp96
-Asp96 is reprotonated
-Asp85 transfers H+ outside through H-bonding, resetting retinol to trans state
How does oxygenic photosynthesis vary between plants and cyanobacteria?
-occurs in chloroplasts in plants
-cyanobacteria don’t have chloroplasts -their photosynthetic apparatus varies greatly but most are made from thylakoids
What happens in anoxygenic photosynthesis in green sulphur bacteria (eg. Chlorobium)?
-light captured by antenna complexes in chlorosomes and photon energy is transferred to PSI rxn centre
-PSI donates e- to ETC
-e- transport pumps H+ outside cell and reduces NADP via ferredoxin
-ATP generated by H+ gradient
PSI receives e- from inorganic sulphur derivatives
What happens in anoxygenic photosynthesis in purple bacteria?
-light captured by antenna complexes in chromatophores and photon energy is transferred to PSII rxn centre
-PSII donates e- to cyclic ETC
-e- transport pumps H+ outside cell
ATP generated by H+ gradient (cyclic phosphorylation)
-inorganic compounds used as e- donors to produce NADPH (reverse e- flow)
N/B: NADH can’t be produced -there aren’t any transporter with an electronegative enough reducing potential
What happens in oxygenic photosynthesis in cyanobacteria?
-2 distinct PSs are excited by light, which provides energy to take e- from H2O to produce H+
-e- transport pumps H+ outside cell and reduces NADP
-ATP generated by H+ gradient
-CO2 is fixed by NADPH and ATP, making glucose
What is the name of the organelle which captures light in green sulphur bacteria during anoxygenic photosynthesis?
chlorosomes
What is the name of the organelle which captures light in purplebacteria during anoxygenic photosynthesis?
chromatophores
What is symbiosis?
intimate relationship between different organisms
What are the three types of symbiosis?
-mutualism
-commensalism
-parasitism/predation/competition
What is mutualism?
symbiosis where both organisms benefit from the interaction
eg. microbe using host’s nutrients to grow and produces vitamins host can use
What is commensalism?
symbiosis where microbe benefits from the interaction, without impacting the host
eg. bacteria living on skin/in gut
What is parasitism/predation/competition?
symbiosis where the microbe benefits from the interaction at the expense of the host
eg. obligate parasites
What are the limitations of categorising the three types of symbiosis?
-symbiosis isn’t set in stone -can change as conditions change
-hard to tell if microbe can ever really not effect the host in any way
What is endosymbiosis?
symbiosis where the parasites lives inside the host
What is ectosymbiosis?
symbiosis where the parasites lives on the surface of the host
What are bacteriocytes?
specialised structures in insects which contain bacteria, involved in endosymbiosis
-can aggregate to form organs called bacteriomes
What are bacteriomes?
specialised organ in insects which hosts endosymbiotic bacteria
Why do plants require nodulation?
-plants can’t use atmospheric N2
-some legumes (beans, peas) can fix N2 via a symbiotic interaction with bacteria in soil (Rhizobia) -form structures known as nodules
What is Rhizobia?
-gram -ve bacteria (an alphaproteobacteria)
-part of rhizosphere (root microbiome -area of soil surrounding roots)
-have complex genome
What is nodulation?
the formation of nodules (structures in roots containing symbiotic bacteria) in legumes
What happens in the process of nodulation?
-bacteria attracted by root via secretion of root exudates, causing bacteria to migrate towards root and establish contact
-nodulation genes are activated and Nod factors are produced and secreted
-Nod factors trigger differentiation growth of root, causing root to curl, entrapping bacteria on surface
-bacteria move from outside to inside of root, forming infection thread
-bacteria bud off from infection thread and invade cortical cells
-bacteria differentiate into bacteroids, which is controlled by plant producing NCR-peptides, forming determinate or indeterminate nodules
What distinguishes obligate symbionts, parasites and organelles?
-organelles are essential and conserved across wide range of organisms
-parasites are harmful to organism they have infected
-symbionts are beneficial to organism that live in association with that organism
What has metagenomics allowed?
-bacteria to be studied (genomes sequenced) in their environment
-allows bacteria that can’t survive in lab conditions to be studied
Name some examples of unusual symbiotic bacteria
In Mycoplasma genitalium…
-Candidatus Sulcia muelleri
-Candidatus Zinderia insecticola
-Candidatus Carsonella rudii
-Candidatus Hodgkinia cicadicola
-Candidatus Tremblaya princeps
Why do symbionts often have a small/incomplete genome?
-genome size is a result of gene loss
-don’t have an independent origin
Name an example of complex symbiosis
nested symbiosis in Mealybugs
-Mealybugs have organelles called bacteriocytes containing the bacteria Tremblaya and Tremblaya contain bacteria Moranella
-amino acid biosynthesis is underpinned by a mosaic biosynthetic pathway
-insect’s genes contribute to bacteria’s peptidoglycan synthesis
What is a pathogen?
any agent that causes disease
What is the difference between a pathogen and a parasite?
-parasites are visible to the human eye, whilst pathogens are not
What is pathogenesis?
when an organism uses another organism’s resources in a way which is not beneficial to the host
What types of organisms can be pathogens?
-bacteria
-viruses
-fungi
-protozoa
-prions
-NOT Archaea
What are prions?
infectious proteins
-considered pathogens
What makes a pathogen successful?
-able to gain access to host
-can locate a nutritionally compatible niche
-can avoid host’s innate and adaptive immune responses
-able to access host’s resources and replicate
-can exit and spread to new host (transmission)
What is an innate immune response?
-rapid
-non-specific
What is an adaptive immune response?
-highly-specific
-slow
What types of transmission are there?
-air-borne
-water
-food
-mechanical/vector
What is the difference between mechanical transmission and transmission using a vector?
mechanical: pathogen doesn’t interact with the other’s biology -just uses it as a mean of transportation
vector: pathogen interacts with other’s biology -to survive in it
How can the success of a pathogen be measured?
-if it’s still here, must be successful
quantitatively… -virulence (mortality, morbidity, infectious dose)
What is virulence?
the measurement of the severity of a disease
What is mortality?
the number of deaths from a disease
What is morbidity?
the number of cases of a disease in a population
What is infectious dose?
the number of individual cells/particles required for an infection
How can virulence be measured?
-mortality
-morbidity
-infectious dose
What are virulence factors?
factors which enable pathogen to colonise host
-intention is for survival, not for causing disease, however disease is often caused in the process
eg. toxins, capsules
What virulence factors are there?
-adhesins
-capsules/S-layers
-digestive enzymes
-toxins
-stealth mode/reductive evolution
How do adhesins act a virulence factors?
find niche and colonise host
How do capsules/S-layers act a virulence factors?
immune evasion/survival in host
How do digestive enzymes act a virulence factors?
find niche, colonise, find host’s resources
How do toxins act a virulence factors?
reprogram host’s biology to benefit the pathogen
How does stealth mode act as virulence factors?
immune evasion (via absence of outer-surface structures)
What sources are there for reliable information on pathogens?
-WHO
-UK Health and Security Agency (humans) and DEFRA (animals/plants)
-CDC (humans) and USDA (animals/plants)
What is Germ Theory?
microorganisms (pathogens) cause disease
What are Koch’s postulates?
-microbe is found in all cases of disease and absent in healthy individuals
-microbe can be isolated from diseased host and be grown in pure culture
-when a pure culture is introduced into a healthy, susceptible host, the same disease occurs
-same strain or microbe can then be obtained from the newly diseased host
How did Koch establish a scientific method to link microbes and diseases?
came up with Koch’s postulates, a set of criteria a microorganism must fulfil to prove a specific pathogen causes a specific disease
-by studying Bacillus anthracis (gram +ve bact causing anthrax)
What do treatments need to be able to do?
block pathogen’s steps to infection, such as…
-entry to host
-avoidance of host’s immune responses
-access to host’s reserves and replicate
-exit and spread to new host
What treatments prevent a pathogen’s entry to host?
sanitation and antiseptics
What treatments prevent a pathogen from avoiding its host’s immune responses?
vaccination
What treatments prevent a pathogen from accessing its host’s resources?
antimicrobials
What advancements have aided the combat of disease?
-better diet
-clean drinking water
-improved sanitation
-less overcrowding
-better living conditions
What are vaccines?
chemical agents which prime the adaptive immune system to repel a pathogen
-tricks immune system into going through primary immune response 1
How was smallpox treated as the first form of vaccination?
-puss from smallpox directly put into patient’s open vein
-got smallpox but not so badly
Why are antibiotics the last therapeutic option?
-conditions for killing pathogens could also harm patient
What is the magic bullet idea?
pathogenic infections need to be controlled without harming the patient
What are antibiotics?
chemicals produced by bacteria or fungi which inhibit or kill other microorganisms
eg. penicillin
How are antibiotics organised?
into classes and families
How was Penicillin discovered?
-Fleming’s Staphylococcus plate was contaminated by Penicillin
-Staphylococcus didn’t grow around the penicillin -mold was producing compound killing bacteria
-Florey and Chain modified penicillin into a usable drug
What is a sympton?
a change in body function that is felt by the patient as a result of a disease
eg. feeling tired
What is a sign?
a change in body that can be objectively measured or observed as a result of a disease
eg. high temperature
What is a syndrome?
a specific group of signs and symptoms that accompany a disease
eg. pneumonia
In which scenarios do Koch’s postulates not work?
-when a pathogen causes multiple diseases
-when a disease can be caused by multiple pathogens
What are the benefits of having a microbiota?
-helps digestion
-helps metabolism
-aids immune function
-benefits mood and behaviour
What types of relationship can there be between a human and microbe?
-commensalism (organism benefits and doesn’t affect the other)
-mutualism (both organisms benefit)
-parasitism/pathogenesis (organism benefits at other’s expense)
What is a diseased state?
product of relationship change/conflict between host and pathogen
What disease does Clostridium difficle cause?
Clostridium difficle infection
What are the symptoms of Clostridium difficle infection?
-diarrhoea
-colonisation and inflammation of colon (large intestine)
What is the virulence of Clostridium difficle?
mortality ≈ 9%
What are opportunistic pathogens?
microorganisms which are not normally pathogenic but can cause an infection or disease on a “compromised” host
What is a hospital aquired infection?
an infection acquired as a result of a hospital stay not linked to the reason for the patient’s hospitalisation
-patient is their own source of infection
eg. C.difficile
How has urbanisation affected pathogens?
higher population densities drive many potential routes of transmission
What disease does Vibrio cholerae cause?
Cholera
What are the symptoms of Cholera?
large amounts of watery diarrhoea (aka rice water stool)
How is Cholera transmitted?
via the faecal-oral route
What is the virulence of Vibrio cholerae like?
death through severe dehydration
if treated rapidly mortality can be as low as 1%
How is Cholera treated?
oral rehydration
What are the virulence factors of Vibrio cholerae?
cholera toxin
What is epidemiology?
study of when and where diseases occur to control the spread of disease
What are the principles of epidemiology?
-identify first person to have the disease (person zero)
-identify anyone who has been in contact with that person
-identify reservoir for pathogen
-block/contain its reservoir
What are the difficulties with the principles of epidemiology?
-disease needs to be recognised first, by which point the disease will have already infected many individuals
What is an epidemic disease?
when a disease is acquired by many hosts in a given area in a short time
What is an endemic disease?
when a disease is constantly present in a population
What is a pandemic disease?
when a disease is acquired by many hosts worldwide in a short time
What disease does Salmonella typhi cause?
typhoid fever
What are the symptoms of typhoid fever?
rose spots (rash)
How is Salmonella typhi transmitted?
-human carriers (colonised gall bladder)
-faecal-oral route
What is the virulence of Salmonella typhi?
without treatment mortality ≈ 30%
with treatment mortality ≈ 1%
What disease does Polio virus cause?
Polio (poliomyelitis)
What are the symptons of polio?
-irreversible paralysis
-muscle weakness
-atrophy
-deformities
-twisted feet/legs
normally very mild symptoms
How is polio transmitted?
-faecal-oral route
-contaminated water source
How is polio treated?
vaccine (attenuated virus)
-but in rare cases vaccine does make healthy carriers :(
What disease does Yersinia pestis cause?
Bubonic plague
Pneumonic plague
What are the symptoms of bubonic/pneumonic plague?
-buboes (swollen lymph glands)
-pneumonia
How is bubonic/pneumonic plague transmitted?
-rodents, prairie dogs and fleas
-human respiratory aerosol
What is the virulence of Yersinia pestis like?
if untreated
bubonic mortality ≈ 50%
pneumonic mortality ≈ 90-100%
treatable under 24hrs
What is a zoonotic disease?
an infectious disease which is transferred between humans and other organisms
What disease does Phytophthora infestans cause?
potato blight
late blight
What is the virulence of Phytophthora infestans like?
nearly 100% with crops
How is potato/late blight treated?
fungicides
copper sulphate
What is an issue with potato blight in the UK?
-pathogens have similar geographic distributions to hosts and co-evolve with them
-few varieties of potatoes came to UK (genetic bottleneck)
-monoculture potatoes will all die when diseased and leave soil full of spores
What disease does Influenza virus cause?
Influenza
flu
What is the virulence of Influenza like?
very varied mortality (0.01-50%) due to different strains
What disease does Zika cause?
Zika virus disease
What is the virulence of Zika like?
very low (most no symptoms)
associated with birth defects (microcephaly, Guillon-Barré syndrome)
How is Zika transmitted?
sexually
-men 6mnths, women 8wks
What are the issues with epidemiological surveillance?
-time consuming
-can be inaccurate
-correlation based data (not cause and effect)
What is epidemiological surveillance?
collection, analysis and dissemination of public health data
What disease does Ebola virus cause?
Ebola virus disease
Ebola haemorrhagic fever
What are the symptoms of Ebola?
-bleeding
(-headache and muscle ache
-fever
-sore throat)
What is the virulence of Ebola like?
very high
mortality = 40-90%
death from shock, nerve damage and seizures
What is the reservoir for Ebola?
unknown
maybe zoonotic (bats)
How is Ebola treated?
currently no treatment
-antibody therapies and vaccinations under development
What would be the issues with modern medicine without antbiotics?
-minor infections become life threatening
-surgery becomes too dangerous
-increased risks in child birth
-chemotherapy
-infectious diseases
Why is antimicrobial resistance so complicated?
-antibiotics all have diff targets
-pathogens all have diff virulences and survival strategies
-resistance mechanisms are varied and not yet well understoogd
What is immunology?
study of the immune system
What is the immune system?
molecules/cells across the body which defend the body against disease (by reacting against infectious pathogens)
Why is immunology medically important?
-can be used to manipulate the immune system medically -vaccines
-needed to understand malfunctions in the immune system eg. immunodeficiencies, allergies
What malfunctions in the immune system are there?
-immunodeficiency (immune system has decreased ability to fight disease)
-allergies (immune system inappropriately reacts to a substance)
-autoimmune disease (immune system reacts against own tissues)
-graft rejection (immune system rejects and destroys transplanted tissue/organ)
What are immunological techniques?
techniques which use components of the immune system eg. antibodies
-used in research, diagnostics (eg. pregnancy tests) and therapeutics
What are the properties of the innate immune system?
-broad specificity
-no memory (doesn’t improve with repeat infection)
-rapid response (hours)
Which leucocytes are involved in the innate immune system?
Lots!
-phagocytes
-natural killer cells
Which soluble factors are involved in the innate immune system?
Lots!
-lysozymes
-complement
-integerons
What are the properties of the adaptive immune system?
-highly specific
-has memory (improves with repeat infection)
-slower response than innate (days)
Which leukocytes are involved in the adaptive immune system?
B and T lymphocytes
Which soluble factors are involved in the adaptive immune system?
antibodies
What are the two lineages leukocytes give rise to?
-myeloid cells
-lymphoid cells
What are leukocytes derived from?
pluripotent stem cells in bone marrow
What external barriers to infection does the body have?
-keratinized skin (diff for bact to digest/penetrate)
-secretions (sebums, fatty acids, lactic acid, lysozymes)
-mucous
-low pH (stomach)
-commensals (organisms present on surface of skin)
What is the role of phagocytes?
to take up and digest pathogens/dying cells
What are the main types of phagocytes?
-neutrophils
-mononuclear phagocytes (monocytes and macrophages)
What are neutrophils like?
-nucleus has multiple forms
-has granules (release enzymes, etc)
-short lived
-fast moving
-main lymphocyte in blood
What are the two types of mononuclear phagocytes?
monocyte -in blood
macrophages -in tissues
What are mononuclear phagocytes like?
-long lived
-carry out phagocytosis and help initiate adaptive responses
-some of the first cells to respond to infections in tissues
What do natural killer cells do?
-non-specifically kill virally infected cells
-(might) kill cancer cells
-self and non-self (or infected and non-infected self) recognition
How do phagocytes recognise pathogens?
have pathogen-recognition receptors (PRRs) which recognise microbe-associated molecular patterns (MAMPs)
How do natural killer cells recognise pathogens?
recognise self proteins (MHC) so if they are not present, they will kill the cells
What soluble factors does the immune system have?
-complement (proteins involved in bact cell lysis)
-defensins (+ve charged protein that disrupt bact membrs)
-interferons (made by virally-infected cells to protect other cells by activating macrophaes and natural killer cells)
-cytokines (small proteins involved in cell-cell communication)
-inflammatory mediators (eg. histamine)
What is inflammation?
localised immune response to infection/damage causing heat, redness, swelling and pain
-inflammatory mediators (eg. histamine) are released when there is infectiondamage
What causes heat and redness in inflammation?
dilation of blood vessels
What causes swelling in inflammation?
increased permeability of capillaries
-cells linking capillaries become leaky and release fluid into tissue
What causes pain in inflammation?
stimulation of nerve endings
Why does a fever (temp response) come about during infection?
macrophages release cytokines which…
-act on hypothalamus, raising temp
-stimulate phagocytosis
-decrease iron levels in blood
Where do B lymphocytes mature?
-in bone marrow (antibody receptor)
-then in primary lymphoid tissue (antigen independent differentiation)
-develop further when encounters antigens
Where do T lymphocytes mature?
-in thymus (T cell receptor)
-then in primary lymphoid tissue (antigen independent differentiation)
-develop further when encounters antigens
What are antibodies?
anti-foreign bodies produced in response to antigens (antibody generating material)
What is the clonal selection hypothesis?
-B cell with correct receptor binds to antigens on surface by chance + undergoes clonal selection
-B cell divides, giving lots of clones
-cells differentiate into plasma cells (prod antibodies) and memory cells (long-lived, after infection)
How is lymphoid tissue organised?
-primary lymphoid tissue (thymus and bone marrow) -where lymphocytes reach matureity and aquire specific receptors
-secondary lymphoid tissue (lymph nodes, vessels, etc) -where mature lymphocytes are stimulared by antigen
What is primary lymphoid tissue?
where lymphocytes reach maturity and acquire specific receptors
-thymus and bone marrow
What is secondary lymphoid tissue?
lymphoid tissue where mature lymphocytes are stimulated by antigen
-lymph nodes, vessels, spleen, etc
What is the structure of an antibody like?
-Y-shaped
-has 2 Fab (fragment antigen binding) regions and a Fc (fragment crystallisable) region
-has 2 heavy chains and 2 light chains (IgG)
-compact globular domains (2 in each light chain, 4 in each heavy chain)
What do the Fab regions of an antibody do?
bind specifically to antigens
-are very variable in aa seq
What does the Fc region of an antibody do?
bind to complement, Fc receptors on phagocytes/NK cells, etc
-constant aa seq
What did the reduction of intra-chain disulphides experiment show about antibody structure?
presence of light and heavy chains (and ratios)
light chains: 25kDa
heavy chains: 50kDa
IgG: 150kDa ∴ L2H2
What did the protein cleavage experiment show about antibody structure?
cleaved into 2:1 ratio
∴ 2 Fab arms and 1 Fc region
What did crystallography show about antibody structure?
hinge region is highly flexible
What experimental evidence is there for antibody structure?
-intra-chain disulphide reduction shows presence of light and heavy chains
-protein cleavage shows 2:1 ratio of Fab:Fc regions
-crystallography shows flexibility of hinge region
What are the 5 classes of immunoglobulins?
-IgG (γ)
-IgM (μ)
-IgA (α)
-IgD (δ)
-IgE (ε)
How are immunoglobulins classified?
-by heavy chain amino acid sequence (IgG, IgM, IgA, IgD, IgE)
-by type of light chain (kappa or lambda)
What is IgG involved in?
secondary memory responses
What is IgM involved in?
primary responses
What is IgA involved in?
protection of mucosal surfaces
What is IgD involved in?
unknown function
What is IgE involved in?
allergic responses
protection from parasites
Where is IgG found?
in serum
(N/B: crosses placenta from mother to foetus)
Where is IgA found?
in serum and secretions (tears, saliva, breast milk, etc)
Which immunoglobulins exist as monomers?
IgG
IgD
IgE
IgA (can also exist as dimer)
Which immunoglobulins exist as dimers?
IgA (can also exist as monomer)
Which immunoglobulins exist as pentamers?
IgM
What is the constant region of an antibody?
region which is the same for antibodies of a given H and L chain class
What is the variable region of an antibody?
region which differs between antibodies with different specificities found at N-terminal of heavy and light chains
-recombination and mutations of variable region exons in genome during B cell differentiation can give different antibody specificities
How do antibodies protect against infection?
using specific binding
-neutralise (toxins)
-immobilise mobile microbes
-prevent binding to (and ∴ infection of) host cells
-form complexes
using effector functions
-activate complement
-bind Fc receptors
Which classes of antibodies neutralise toxins?
IgG
IgA
Which classes of antibodies immobilise mobile microorganisms?
IgM
Which classes of antibodies activate complement?
IgG
IgM
Which classes of antibodies bind to Fc receptors on phagocytes?
IgG
IgA
Which classes of antibodies bind to Fc receptors on mast cells?
IgE
Which classes of antibodies bind to Fc receptors on natural killer cells?
IgG
What is complement?
series of around 20 proteins in the blood/serum which are normally inert but are activated as part of the immune defence against bacteria (and viruses) and induce inflammation
-activated by an enzyme cascade
Which protein component of the classic complement pathway is most abundant?
C3
Which protein component of the classic complement pathway is first in the pathway?
C1
What activity do most components of the classical complement pathway have?
protease activity
-generates fragments with biological activity
What does the classical complement pathway require?
1 antigen
2 antibodies
What happens at the start of the classical complement pathway?
-C1 is activated by interacting with 2 Fc regions
-once C1, C4 and C2 are activated, C3 convertase is generated
-C5 convertase is made by C3b joining to C3 convertase
How is C1 activated?
by interacting with two Fc regions
What are the three major biological activities of complement?
-activation (C5a, C3a)
-opsonisation (C3b)
-cell lysis (C5-9)
What does complement act as in order to undergo activation?
-as chemoattractants (induces cell movement along conc gradient)
-as anaphylatoxins (cause allergic response -mast cells release histamine, inflammation)
Which components of complement are involved in activation?
C5a
C3a
Which components of complement are involved in opsonisation?
C3b
Which components of complement are involved in cell lysis?
C5-9
What happens in opsonisation?
increased binding and phagocytosis
How does complement cause cell lysis?
-whole cascade is activated
-membrane attack complex (hollow cylinder) forms
-complex forms pores in bacterial membranes
Why can complement only cause cell lysis in gram negative bacteria?
Gram positive bacteria have a thick peptidoglycan coat so are resistant to the membrane attack complex forming pores in its membranes
What do Fc receptors on phagocytes do?
enhance recognition of microbes
What do Fc receptors on natural killer cells do?
mediate antibody dependent cell-mediated cytotoxicity (ADCC) by secreting perforin, which acts as a channel to discharge enzymes into target cell to induce apoptosis
What do Fc receptors on mast cells do?
-mediate allergic response
-defence against large parasites
-sensitises mast cell and degranulation (release of inflammatory mediators)
What are antisera?
blood serum containing antibodies against specific antigens injected as treatment
-generates a memory response
-conventionally use polyclonal antisera
What is an epitope?
the shape an antibody binds to
What are the issues with antisera containing a mixture of antibodies to different epitopes?
-difficult to standardise (antiserums vary in composition)
-may lack specificity
How is antisera produced?
-sample of blood is taken from animal and allowed to clot (forming serum)
-serum is checked to see if antibodies are present
What are monoclonal antibodies?
antibodies derived from a single B lymphocyte which have one single specificity (to one epitope)
How are monoclonal antibodies produced?
-fusion of B cell (from animal immunised to antigen) and tumour cell (which divides indefinitely) to produce a hybrid cell
-hybrid cell divides indefinitely and produces specific antigen
How are antibodies used in research, diagnostics and therapy?
-to identify and label molecules in complex mixtures
-to identify pathogens
-to characterise cell surface proteins and identify cell types
-in therapy as “humanised” antibodies
What are the two types of T cells?
-T helper cells
-T cytotoxic cells
What protein do T helper cells have on their cell surface?
CD4 +ve
What protein do T cytotoxic cells have on their cell surface?
CD8 +ve
What are the functions of T helper cells?
-help B cells to make antibodies
-activate macrophages and natural killer cells
-aid the development of T cytotoxic cells
What are the functions of T cytotoxic cells?
-recognise and kill infected host cells
What is the structure of a T cell receptor like?
-α and β chains each with a variable domain and a constant domain
-disulphide bridge
-anchored in cell membrane
When can B cells recognise an antigen?
when it is soluble, free and native
When can T cells recognise an antigen?
when it is cell-associated and processed (broken down into smaller peptides)
How do infected host cells display foreign proteins on their surface (for T cells to detect them)?
using major histocompatibility protein complex (MHC)
What is the role of major histocompatibility protein complex (MHC)?
-initiates T cell responses
-involved in graft rejection
What is the major histocompatibility protein complex (MHC) encoded by?
major histocompatibility gene complex on chromosome 6
What are the two major histocompatibility proteins (MHC)?
MHCI and MHCII
Where is MHCI expressed?
in all nucleated cells
Where is MHCII expressed?
in macrophages, dendritic cells (in skin, lymphatic systems), B cells
What does MHCI do?
displays antigen to cytotoxic T cells (with CD8 +ve receptor)
What does MHCII do?
displays antigen to T helper cells (with CD4 +ve receptor)
How does MHCI help cytotoxic T cells to recognise an antigen?
-viral proteins are broken down in cytosol by proteosome
-peptides are transported to ER
-at ER, MHCI binds to peptides
-MHCI moves to cell surface and displays foreign peptides on the cell surface
-T cytotoxic cells detect foreign peptides displayed by MHCI and are activated
-once activated, they kill the infected cell by inducing apoptosis
How does MHCII help T helper cells to recognise an antigen?
-macrophage/dendritic cell/B cell internalises and breaks down foreign material
-peptides bind to MHCII in endosomes
-endosomes transport MHCII to cell surface, where MHCII displays the peptides
-once activated, T helper cells help B cells to make antibodies, produce cytokines, activate other leukocytes
What happens to T cells in the thymus?
-they acquire T cell receptors and are educated
-selection occurs, where only the cells which recognise self-MHC but not self peptides survive (majority do not pass test and must undergo apoptosis)
What are cytokines?
small (5-20kDa) secreted proteins involved in cell communication in the immune response
-produced and act locally (unlike hormones, otherwise sim)
-bind to specific receptors (cytokine receptors) on target cell surfaces
-produced by T helper cells and macrophages
What are the biological effects of cytokines on the target cell?
-changes in cell behaviour
-changes in gene expression
What are the main groups of cytokines?
-interleukins
-interferons
-chemokines
-tumour necrosis factor
-colony stimulating factors
What are interferons involved in?
-viral infections (IFNα, IFNβ)
-cell activation (IFNγ)
What are chemokines involved in?
-cell movement/chemotaxis (IL-8 aka CXCL8)
What are tumour necrosis factors involved in?
-pro-inflammatory
-can kill some cells
What are colony stimulating factors involved in?
-leukocyte production (M-CSF)
What did Edward Jenner do in terms of vaccination?
-showed infection with cowpox was protective against small pox (now know bc antigens are very similar)
What are the different types of vaccines?
-attenuated strains of pathogen
-killed pathogen
-subunit of pathogen (toxoid, virus spike protein, etc)
-engineered virus
-RNA
What type of virus is HIV?
a retrovirus (ssRNA, undergoes reverse transcription)
a tumour virus (associated with cancers)
a lentivirus (causes infection slowly)
What is a retrovirus?
a virus which reverses the normal flow of genetic information (uses reverse transcription)
-have ssRNA
What is the genetic information of HIV like?
ssRNA
What is a lentivirus?
a retrovirus with a long incubation period
eg. HIV
What is the structure of the HIV virion like?
-nucleocapsid containing ssRNA genome and enzymes (reverse transcriptase, integrase, protease)
-lipid bilayer (obtained from host)
-gp120 embedded in lipid bilayer (binds to host)
What happens in the lifecycle of a retrovirus?
-virus binds to host cell receptor
-viral envelope fuses with host cell, so that nucleocapsid enters cytoplasm of host
-reverse transcription occurs to produce dsDNA (from viral RNA)
-viral DNA is transported into the host nucleus and integrated into the host genome (producing a provirus)
-provirus is transcribed to produce viral genomic RNA and mRNA, which are transported into the cytoplasm
-viral mRNA is used to translate viral proteins
-new nucleocapsids form and virus buds from the cell, acquiring a lipid envelope from host
What are the types of retroviral infection?
-latent (dormant in host)
-permissive (doesn’t kill host but produces new viruses)
-lytic (host overwhelmed and undergoes lysis)
What type of cells are susceptible to HIV infection?
CD4 +ve cells
-mainly T helper cells
-some monocytes, macrophages and dendritic cells
What happens in HIV infection?
-T helper cells initially destroy virus however T helper cells are susceptible to infection so number of infected cells increase
-T cell stimulation activates transcription of the HIV provirus
-causes T cell lysis
-number of T cells infected increases with each round of viral replication
What happens in the HIV infection of dendritic cells?
-dendritic cells present antigen to T cells in lymphoid tissue
-infection is permissive -dendritic cells act as a reservoir of virus
What happens in the HIV infection of monocytes?
-monocytes can cross the blood/brain barrier so carry infection into the brain
-CNS involvement
Why is CD4 expression not sufficient for HIV infection?
co-receptor for virus needed
CCR5 (chemokine receptor)
-required for virus to fuse with host cell
What is CCR5 required for in HIV infection?
fusion of virus to host cell
What does the depletion of T helper cells lead to?
AIDS (acquired immune deficiency syndrome)
What causes the depletion of T helper cells (in HIV infection; leading to AIDS)?
-direct lysis of T helper cells by virus -syncytium formation
-T helper cells killed by cytotoxic T cells/other immune mechanisms
-apoptosis of T helper cells
What is the blood count of CD4 +ve cells less than to lead to AIDS?
200cells/mm3
Where are the infected T helper cells during HIV infection?
lymphoid tissue
What symptoms are associated with AIDS?
-opportunistic infections (pathogens which usually have little affect are more threatening, due to compromised immune system)
-reactivation of latent viruses (eg. Herpes)
-rare cancers
-CNS involvement can lead to blindness, paralysis, dementia, etc
What is the origin of HIV-1?
Central Africa
What is the likely source of HIV-1?
related virus affecting chimpanzees
-cross-species transmission 1910-1930ish
What is the origin of HIV-2?
West Africa
(probs predates HIV-1)
-less virulent, less easily transmitted ∴ not really left West Africa
What is the likely source of HIV-2?
related virus affecting sooty mangabeys
How is HIV transmitted?
-unprotected sex
-blood/blood products (drug use, sharing needles)
-breast-feeding
-mother to foetus
What are the problems with vaccines for HIV?
-virus has high mutation rate
-humoral immunity may not be protective, so vaccine needs to be able to induce cytotoxic T cells
How can HIV be treated?
-drug therapy
(combination therapy! -mixture of drugs)
future…
-stem cell therapy (bone marrow cells w/o CCR5)
-kick and kill (reactivating latent virus and immunotherapy)
-passive immunisation (human monoclonal antibodies or engineered T cells)
-potentially CRISPR-Cas9 gene editing
What are the problems with drug therapy for treating HIV?
-virus has high mutation rate
-toxicity of drugs (could effect our cells as well as the virus’ cells)
-viral latency (remaining dormant in host)
-high cost (issue in poorer countries)
What is combination therapy?
mixture of drugs directed at different viral targets
-used for treating HIV
What drugs are included in combination therapy for HIV?
-azidothymidine (AZT -a nucleoside analogue)
-other reverse transcriptase inhibitors
-HIV protease inhibitors
-fusion inhibitors
-capsid inhibitors
What is a symbiosome?
membrane-bound vesicles (in host cell) that contains endosymbiont (eg. rhizobium cells)
What is a thermosome?
Archaeal group 2 chaperonin protein which increases tolerance to heat
What are osmolites?
low molecular weight compounds which influence fluidity
-accumulated by halophiles
Is a more negative or more positive reduction potential a better electron donor?
more negative
What is a mesosome?
a folded invagination in bacterial membrane
-aids DNA rep and protein synth
What is seroconversion?
the point where antibodies become present in the blood
-antibodies are specific to protein (eg. antibodies for HIV core protein and HIV envelope protein)
