Microbiology Flashcards

Question

How do we do phenotypic analyses?

Answer 1

For taxonomy - morphology/differential staining - can do in hospital - metabolic properties - biochemical tests and unknown bacteria are mixed - results show what organism it is - phage typing - fatty acid profiles - use extracts to form methyl esters then do gas chromatography - mass spectrometry - last 4 are with pure isolates

Answer 2

For taxonomy - DNA/DNA hybridisation: 75% - same species, 25-50 - same genus - Fluorescent In Situ Hybridisation (FISH) - rDNA (16s) sequencing - Multi locus sequence typing/fingerprinting - Whole genome sequencing

Answer 3

Study of evolutionary history of organisms - evolution Measured by comparing genetic information - uses sequences called molecular clocks - line them up and see similarities. These encode for conserved proteins with similar functions and are undergoing random and neutral mutations.

Answer 4

Through cladograms (phylogenetic trees) - rooted - unrooted

Answer 5

Eukarya Archaea Bacteria

Answer 6

Archaea: prokaryotic, no peptidoglycan, mem lipid are branched carbon chains attached to glycerol by ether linkage, first aa is methionine, no antibiotic sensitivity, no rRNA loop, no tRNA arm Eukarya: membrane lipids are straight carbon chains attached to glycerol by ester linkage, first aa is methionine, no antibiotic sensitivity, no rRNA loop, there is a common arm of tRNA Bacteria: same membrane lipids as eukarya, first aa is formylmethionine, there is antibiotic sensitivity, there is a rRNA loop and there is a common arm in rRNA. Sometimes eukarya and bacteria are similar, sometimes eukarya and archaea is - shows how analysing different things show different results

Answer 7

History of animals - Aristotle in 400 BC Enquiry into plants - Theophrastus in 200 BC

Answer 8

Nucleus vs no nucleus - compartmentalisation Size Membrane bound organelles in eukaryotes

Answer 9

- Contains chromatin = DNA with histones - histones only found in eukaryotes - Site of mRNA, tRNA and rRNA synthesis - Has euchromatin and heterochromatin (denser)

Answer 10

RER: membrane network with ribosomes, site of proteinsynthesis, signals allow import into RER SER: no proteinsynthesis, lipid synthesis, steroids and toxin breakdown - important for protein trafficking

Answer 11

- Carbohydrate synthesis (plasma synthesis) - Modify proteins for specific targeting - receive vesicles from the RER

Answer 12

Lysosomes: originate from golgi, contain digestive enzymes Peroxisomes: from ER, encorporate lipids and proteins from cytoplasm, oxidise alcohol and fatty acids

Answer 13

- Respiration/ox phos/kreb cycle --> ATP and reducing power Has own genome (15kB and 37 genes) - multiply by division Transcription can occur here

Answer 14

Made of thylakoids - form grana in stroma Converts light into organic compounds Similar to mitochondria - own DNA (150 kB) and multiply by division Transcription can occur here

Answer 15

- Bundles of 9 pairs of microtubules surrounding central pair - axoneme. - Microtubules attached together by nexin molecules. - ATP is used and motion is carried out by dynein. - Slide past eachother - whiplike.

Answer 16

Usually one circular chromosomes - ds DNA - less that 10 Mbp Has histone like proteins - but not HISTONES Can have plasmids

Answer 17

Some contain organelles (compartment enclosed with membrane with dedicated physiological function) e.g. magnetosomes (have magnetite - Fe3O4), photosynthetic membranes, internal membranes (planctomycetes) Contains proteins, tRNA, mRNA and ribosomes. Can contain inclusion bodies (protein bound): carboxysomes (CO2 reduction), storage granules (S, PO4, N2), gas vesicles

Answer 18

Cytoplasmic membrane (no carbohydrates or sterols) --> peptidoglycan --> polymers covalently bound to peptidoglycan --> outer membrane (not always got outer membrane) Pg + polymers = cell wall

Answer 19

Pilus: appendage dedicated to conjugation (plasmid exchange) - long Fimbriae (pili): involved in adhering to host cells/surfaces - antigenic structures are made of 1 major protein Flagella: supramolecular assembly involved in motility

Answer 20

Monotrichous - 1 flagella Lophotrichous - many on one side Amphitrichous - one on each side Peritrichous - loads on all sides

Answer 21

Simple - two protein subunits, in eukaryotes: complex microtubules Driven by ATP hydrolysis like eukaryotes

Answer 22

Eu: mitosis except for mitochondria and chloroplasts - binary fission Pro: binary fission

Answer 23

Eu: 80s except for mitochondria and ribosomes - 70s Pro: 70s

Answer 24

All cells from LUCA Incorporation of bacteria led to mitochondria and chloroplasts. Nucleus appeared before both. Chloroplasts came after mitochondria Doesn't account for the fact that prokaryotic and eukaryotic cells have similar lipid composition.

Answer 25

Both mitochondria and chloroplasts have inner and outer membranes with some signatures of prokaryotes - cardiolipin/peptidoglycan. They contain mitoribosomes and chlororibosomes - not identical to bacterial ribosomes. Semi autonomous organelles that can do binary fission.

Answer 26

Mitochondria originated from engulfment of a H2 producing bacterium by a H2 consuming archaea Genes for lipid synthesis were transferred to host - gave rise to nucleus Chloroplasts were acquired later by endosymbiosis - first phototropic eukaryotes

Answer 27

Invagination of the cell membrane

Answer 28

Fungi (can be multi) Protists: Algae - plant-like Protozoa - animal like Slime molds

Answer 29

Animalia Fungi Plantae Protista

Answer 30

Molds - filamentous Yeasts - unicellular Basidiomycetes - mushrooms

Answer 31

Ecological role: decomposers in carbon cycle Economical role: key in biotechnology and can be plant pathogens Human health: >1.5 million deaths from fungal infections

Answer 32

Morphology: most form multicellular filaments (hyphae) and are pleiomorphic (can have different forms) Cell walls: carbohydrates - often chitin, mannans or glucans Life cycle: 2 phases involving asexual/sexual reproduction to form spores - undergo transitions between uni/multicellular forms

Answer 33

Molds: bread mold, aspergillus, morel Vegetative form = hyphae - not all form it Mycelium (body) is a section with nuclei, cell wall, pore and septum (branched) - some have just nuclei and cell wall - coenocytic hyphae - unseptated Absorption of nutrient and growth occur at tip of hyphae Can have wide range of morphologies due to complex life cycle - doesn't have to be the same for each species

Answer 34

Alternate diploid/haploid phases - can form spores which help fungi survive harsh conditions Can spend most of life cycle as haploid or diploid - different between species

Answer 35

Mushrooms: death cap, starfish stinkhorn, magic mushroom, enoki mushroom, oyster mushroom, spiny puffball Ectomycorrhizal basidomycetes are found near tree roots - help plants obtain minerals and in return receive sugars

Answer 36

They grow a mycelium from spores during vegetative growth - the cytoplasm of gametes fuse (plasmogamy) which forms fruiting bodies (mushrooms) - nuclear fusion will form basidium (true zygote)

Answer 37

Single cell fungi: saccharomyces (baker's yeast), crytococcus, candida Economic: S.cerevisiae used in brewery, baking Health: cryptococcus and candida cause infection, some used as probiotics Used as a model organism

Answer 38

Protein folding Lipid biology Vesicular trafficking and fusion Lysosomal/peroxisomal function Apoptosis Cell cycle Mitochondria

Answer 39

Cell division by budding/binary fission Some form hyphae under specific conditions (dimorphic) Can be haploid or diploid Haploid (mitosis) -> mate -> cell fusion -> nuclear fusion -> Diploid -> make ascus by meiosis -> ascospores (haploid) -> germination

Answer 40

Primary endosymbiotic: green and red from ancestral endosymbiosis (autotrophs) - 2 MEMBRANES Secondary endosymbiotic (diatoms): centric (circular) and pennate (long). From protists that engulfed primary - mixotrophs - 3/4 MEMBRANES Predatory algae - dinoflagellates - secondary - From protists that engulfed primary - mixotrophs - 3/4 MEMBRANES

Answer 41

Ecological importance: component of phytoplankton - produce half of atmosphere's O2 and is a key food item (zooplankton eats phytoplankton) Algae are photosynthetic organisms and have chloroplasts - diatoms are more diverse metabolism

Answer 42

Primary endosymbiotic - Chlamydomonas reinhardtii Model for photosynthesis, motility, cell cycle - doubling time is 6-8 hours at 25 degrees

Answer 43

Swims with 2 flagella (breast stroke) Contains: - a huge chloroplasts (2 membranes) with chlorophyll a and b - no phycoerythrin - a pyrenoid to stock bicarb which can be converted to CO2 - a contractile vacuole for osmoregulation - cell wall made of hydroxyproline rich glycoproteins - NO CELLULOSE

Answer 44

Mostly found as haploid dividing by binary fission (asexual) Haploid cells from opposite mating types can fuse to form a zygote - loses flagella and grows protective coat The zygote undergoes meiosis to regenerate haploid Some primary endosymbiotic algae have colonial lifestyle: Volvox carteri made of generative or somatic cells - generative cells make colonies

Answer 45

Diatoms Most abundant organisms in phytoplankton - produces 20% of O2 Mobile but no appendages - use actin and myosin on mucus they produce Used in toothpaste Same biomass as rainforests Large morphology diversity and unusual division mechanism

Answer 46

Much more complex Has a pyrenoid, encircling lamellae, periplastid reticulum, osmiophilic globules, multiple membranes

Answer 47

Cell wall called frustule made of silica Two types of diatoms: Radical symmetry: centric Bilateral symmetry: pennate Between 1-2000 micrometres Frustules sediment at bottom of ocean - have usual division due to rigid cell wall Large range of morphologies

Answer 48

Frustules are made of two valves - one overlaps the other like a petri dish Each daughter cell inherits one half of frustule - smaller than parental When size is reached - undergoes meiosis to form gametes After gamete fusion - zygote forms a frustule same size as parental

Answer 49

Treatment against fleas/red mites - dries them out Diatomaceous earth

Answer 50

Secondary endosymbiotic algae Frustules made of calcium carbonate - key role in carbon cycle

Answer 51

Alveolates: Ciliates - predatory protists Apicomplexans - parasites Dinoflagellates - predatory protists Parasitic protozoa: Metamonads - symbionts/parasites Trypanosomes - parasites

Answer 52

- contain alveoli (cytoplasmic sacs of fluid surrounded by lipid membrane - unknown role) - motile (cilia/gliding) - mostly aquatic Ecological importance: - ciliates play a role in food web (zooplankton) - apicomplexans impact health (malaria) - dinoflagellates are key in carbon cycle

Answer 53

Alveolates - predatory protists - alveoli under cytoplasmic membrane - cilia and trichocyst (protrusible filaments) - use cilia for motility and to catch prey - enclosed in phagocytic vacuole and dissolved by enzymes - contractile vacuole to regulate water exchanges - digestive vacuoles - 3 nuclei: 2 micro, 1 macro Goes through binary fission and/or conjugation (starts with fusion of 2 micronuclei) - sexual and asexual

Answer 54

Alveolates - parasites Spore-forming parasitic protozoan - no flagella/cilia/pseudopods Contain an apical complex involved in entry into host cell Contains an organelle called apicoplast - degenerate chloroplast (no chlorophyll) which carries out fatty acid metabolism All are endoparasites causing diseases: malaria (Plasmodium falciparum), cryptosporidiosis (Crytosporidium parvum), toxoplasmosis (Toxoplasma gondii)

Answer 55

Sporozoite is infectious form Multiply in a structure called schizont which ruptures to release merozoites The merozoites can differentiate into male and female gametocytes that are transmitted to mosquito In mosquito host - gametes fuse - form zygote and invade vector cells to produce sporozoites Diploid in mosquito, haploid in human

Answer 56

Alveolates - predatory algae Photosynthetic organisms Mixotrophs - use non light/carbon sources except CO2 Responsible for algal blooms which can be toxic Mobile - feed on bacteria, algae, small dinoflagellates, diatoms, ciliates and other dinoflagellates Involved in complex symbiotic/parasitic interactions Life cycle is unknown but mostly vegetative reproduction and can exist as dormant (cysts)

Answer 57

2 flagella - 1 wrapped around cell Contain a chloroplast with complex membranes Cell walls made of cellulose plates called thecae Contain an organelle called extrusome - all ciliates have this

Answer 58

Parasitic protozoa Mobile parasites that cause disease (diarrhea, sleeping sickness, chagas disease) Mostly harmful but sometimes symbionts (metamonads) Can be transmitted via a vector or direct contact

Answer 59

Parasitic protozoa Mixotrichia: Found in gut of specific termites, lives in symbiosis with other bacteria: 1 endosymbiotic bacteria which degrades cellulose, 3 ectosymbiotic bacteria (short/long spirochetes and bacteriodes) providing motility, possess 4 non-functional flagella Giardia lamblia: Human parasite - diarrhea 2 nuclei Adhere to epithelial cells using ventral adhesive disk Divide by binary fission and forms cysts when conditions are unfavourable

Answer 60

Through fly (vector) Sleeping disease 2 phases: Acute) fever, headaches, lymph node inflammation Chronic) if not treated - invades CNS and disrupts sleep cycle

Answer 61

Slime molds (pleiomorphic) and amoeba (parasite) - Common predatory organisms in damp environments - Both have similar morphology and share a developmental stage - Differentiate to multicellular reproductive stage when food supply is low - Amoebas are responsible for human diseases

Answer 62

Shape is variable Mobility is conferred by pseudopods created by actin polymerisation/disassembly - actin pushes the membrane to form pseudopods Same mechanism as human phagocytes

Answer 63

Dictyostelium discoideum - cellular slime mold Grows as amoeboid unicellular organism that divides by binary fission Under starvation - produces cAMP - forms slug by plasmogamy - undergoes differentiation into a fruiting body (sporangium and stalk) Spores (cysts) are released to initiate a new cycle

Answer 64

Plasmodial slime mold Grows and divides by binary fission as an amoeboid single cell Individual cells can aggregate to form plasmodium - single cell Plasmodium undergoes differentiation into fruiting body (sporangium) Spores (cysts) are released to initiate a new cycle Slime mold cell walls are not made of cellulose

Answer 65

Morphology Size Colour Smell

Answer 66

Cocci e.g. staphylococcus aureus and streptococcus pneumoniae (circular) Rods e.g. escherichia coli (round cylinder like a pill) Curved e.g. vibrio cholerae (like a boomerang) Spiral e.g. titanospirillium velox and borellia burgdorferi (like a hair curl) Exotic e.g. stella humosa (like 2 stars attached together) and aloquadratum walsbyi (square)

Answer 67

Yes! - during the cell cycle e.g. Caulobacter crescentus - unequally divides into a swarmer and stalked

Answer 68

Yes! Thiomargata magnifica - 1cm Mycoplasma pneumoniae - 0.2 micrometres Means a large SA:V - nutrient exchange and growth rate, higher intracellular nutrient conc, rapid evolution due to a high selection rate of mutations

Answer 69

Yes! - produce pigments Serratia marcescens: pigment = prodigiosin - pink -> immunosuppressant Staphylococcus aureus: pigment = staphyloxanthin - yellow -> antitoxin and detoxify ROS Chromobacterium violaceum: pigment = violacein - purple -> antitoxin and detoxify ROS Pseudomonas aeruginosa: pigment = pyocyanin - green/blue -> cytotoxicity, neutrophil apoptosis, ciliary dysmotility, proinflammatory

Answer 70

Yes! e.g. degrade apocrine secretions - human odors. Leucine -> isovaleric acid (short FA) by staph, propanoic production by propionibacteria e.g. decarboxylation of amino acids to produce polyamines - putrescine, spermidine, cadaverine - role in bacterial physiology - ROS scavenger and signalling

Answer 71

Stain: Crystal violet Fix: Iodine Wash: alcohol Counter stain: Safranin Can show differences in gram positive vs negative

Answer 72

Positive - no outer membrane, thick cell wall thin, really thick Negative - outer membrane, thin cell wall - thin, thick, thin Some exceptions e.g. mycobacteria

Answer 73

Facultative structures (not in most model organisms) Non-covalently bound to cell surface Proteinaceous crystalline arrays: self assembly

Answer 74

Most are made of polysaccharides Some made of AA's (poly-y-D-glutamate) Covalently bound to cell wall or outer membrane Confer resistance to host phagocytes/bacteriophages and keep environment hydrated Can be seen with indian ink stain - halo

Answer 75

Homo/hetero polysaccharides - non covalently attached to cell surface Important for biofilm formation, some economically important e.g. xanthan gum - ice cream, toothpaste, salad dressing

Answer 76

Asymmetric membrane Made of: - phospholipids - proteins e.g. porin - lipoproteins (Lpos/braun lipoprotein) covalently linked to peptidoglycan - LPS (endotoxin) - activates immune system (septic shock) LPS - O-specific polysaccharide, core polysaccharide and lipid A

Answer 77

Makes the cell wall - also has teichoic acid and lipoteichoic acid Roles: exoskeleton (resistance to osmotic stress), cell shape and scaffold for display of polymers and proteins Protective role and acts as a sieve to regulate exchanges - not rigid (elastic)

Answer 78

Glycan chains of alternating N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) - bound to pentapeptide stem This is substituted by short peptides (L and D aas) - contains high proportion of proteins Involves glycosyl transferase and transpeptidase activity Not found in fungi Composition doesn't change Multiple layers in gram positive Assemble via peptide bonds

Answer 79

Key components: - phospholipids - hopanoids (equivalent to sterols in eukaryotes) - protein (transporters/signals - for ion, protein and nutrient transport - selective permeability)

Answer 80

Polar head (alcohol and phosphate) -- glycerol derivative -- fatty acid Phosphatidyl ethanolamine Phosphatidyl choline Unsaturated fatty acids modulate fluidity and permeability

Answer 81

Pentacyclic lipids in bacterial cytoplasmic membrane which modulate membrane fluidity and permeability Equivalent to cholesterol in eukaryotes

Answer 82

ALWAYS dsDNA Single circular chromosomes in most bacteria - can be 0.5 Mbp -14.8 Mbp Can have more than one Can be linear Organised as a nucleoid (histone-like protein - supercoiling)

Answer 83

Always dsDNA - usually circular but can be linear Variable copy number (1 to hundreds) - number of copies in a cell Between 2 kbp - 600 kbp Can be self-transferable (horizontal transfer) - conjugation Carry resistance genes

Answer 84

NO! Continuous coding sequence = open reading frame (ORF)

Answer 85

One promotor - multiple open reading frames

Answer 86

Yes! E.g. human dystrophin = 2.2 Mbp -3500 residues, E.coli Ihr = 4.6 kbp - 1538 residues

Answer 87

1) RNA polymerase haloenzyme scans DNA forming loose complex 2) The sigma factor binds to 2 specific sequences upstream from start codon - closed complex 3) The DNA is unwinded - allows formation of open complex - transcription starts and sigma factor released 4) Termination requires either: Rho independant - palindromic GC rich region upstream from AT rich sequence - one GC rich region is transcribed, forms hairpin that makes RNA polymerase fall apart - helped by AT rich region - few H bonds Or: Rho proteins (275 kDa hexamer) recognises and binds 72 residues GC rich It has RNA dependent ATPase activity - wraps the RNA around itself - one it reaches polymerase, Rho unwinds RNA-DNA duplex in the polymerase and releases RNA polymerase

Answer 88

Similar to eukaryotes but the ribosomes are different. Prokaryotes (70s) = 50s (31 proteins) + 30s (21 proteins) Eukaryotes (80s) = 60s (50 proteins) + 40s (33 proteins) 80s - mRNA bind in absence of tRNA, 40s subunit is guided by 5' cap 70s - interact better with mRNA in presence of tRNA, 30s recognises shine-delgarno sequence Transcription and translation are coupled in prokaryotes Translation is inhibited by cycloheximide in eukaryotes

Answer 89

Eukaryotes - in nucleus, prokaryotes - in cytoplasm Eukaryotes - 3 RNA pol, Prokaryotes - 1 Eukaryotes termination involves AAUAAA (mRNA cleavage) mRNA is modified in eukaryotes

Answer 90

Energy source + source of electron + carbon source Energy = light/ preformed molecules Electrons = organic (oxidise organic molecules), inorganic (oxidise inorganic e.g. Fe2+ (ferrous iron) --> Fe3+ (ferric iron), NO2- (nitrite) --> NO3 (nitrate), S (sulfur) --> SO42- (sulfate)) Carbon = organic (aas, carbohydrates), inorganic (CO2)

Answer 91

Energy source: Light (photo), preformed molecules (chemo) Electrons: organic (organo), inorganic (litho) Carbon: organic (heterotroph), inorganic (autotroph)

Answer 92

Counting cells or measuring cell biomass. More conveniently - monitoring the turbidity/optical density (we can use a spectrophotometer - cells scatter the light, more cells = more scattering = increases optical density)

Answer 93

Disc diffusion assay Etest Minimal inhibitory concentration assay Antimicrobial assay

Answer 94

Bacteria spread on plate - form a lawn of cell On lawn - place thin paper disks with antibiotics If cells are susceptible - zone of inhibition - diameter can be measured

Answer 95

Spread bacteria on agar = lawn of cells Place a strip with gradient of antibiotic concentrations on surface The minimum inhibitory conc can then be read

Answer 96

Time consuming and uses liquid culture. A growth media with various conc of antibiotics is inoculated with 5 x 10^5 colony forming units per ml. Growth is then monitored for 24/48 hours.

Answer 97

Semi quantitative - not used in hospitals. Bacteria are serially diluted - each dilution is spotted on the surface of agar containing an antimicrobial compound at a given conc

Answer 98

Heat Irradiation Filtration

Answer 99

Moist heat (boiling water/autoclave) - 15 minutes at 121 degrees under pressure is required for spores Dry heat (oven) - direct flaming, incineration, - 150 degrees for 2 hours Pasteurization (mild heat/HTST/UHT) - Can't kill spores - temperature below 100 degrees to avoid casein aggregates, HTST = 72 degrees for 15 seconds - kills 99.999% of microorganisms in milk, UHT = 140 degrees, 2-5 seconds

Answer 100

Thermal death point - minimum temperature where all organisms are killed in 10 minutes

Answer 101

Minimal time required to kill all bacteria in a liquid at a given temperature

Answer 102

Ionizing radiations (x rays and gamma rays) - food industry/ medical and lab equipment - destroys DNA via double strand breaks + ROS Non ionizing radiations (UV) - surface decontamination, DNA damage (breaks/dimers) Energy is inversely proportionate to wavelength

Answer 103

Used to sterilize gases or liquids that can be damaged by heat The porosity of filters can be chosen for specific applications (1mm - 0.01um) e.g. nucleopore, membrane filter

Answer 104

Bacteriostatic - stops cells from reproducing Bacteriocidal - kill bacteria - number of cells stay the same Bacteriolytic - kill bacteria - both number of cells and viable cell count decrease

Answer 105

Destroy on objects Sterilants: completely destroy all forms of microorganism, including spores. e.g. ethylene oxide Disinfectants: kill microorganisms but not endospores e.g. alcohol Destroy on living tissue: Antiseptics/germicides: inhibit/kill microorganisms e.g. handwash

Answer 106

Disc diffusion technique: Inocculate plate with liquid culture - discs containing antimicrobial agents are placed on surface - shows susceptability if there are zones of inhibition or can do etest Spot assays: Bacteria are serially diluted - each dilution is spotted on the surface of agar containing an antimicrobial compound at a given conc Minimum inhibitory concentration: Lowest conc of a drug inhibiting the visible growth of a test organism after overnight incubation - use liquid cultures and add different conc of agent - see which is clear Minimum bactericidal concentration: Lowest conc of a drug killing >99.9% of a test organism after overnight - better indicator

Answer 107

Minimum inhibitory concentration: Lowest conc of a drug inhibiting the visible growth of a test organism after overnight incubation - MEASURES GROWTH INHIBITION Minimum bactericidal concentration: Lowest conc of a drug killing >99.9% of a test organism after overnight incubation - MEASURES DEATH - better indicator

Answer 108

Phenolic: can be local anaesthetic at low concs, high conc - antimicrobial - disrupts cytoplasmic membrane and denatures proteins e.g. chlorhexidine (mouthwash), triclosan Alcohols: denature proteins, lipid solvent, disrupts membrane - active conc = 60-85% Aldehydes: alkylating agents which modify proteins and DNA - cell death e.g. formalin/formaldehyde, glutaraldehyde Quaternary ammonium compounds 'quat': interact with phospholipids of cytoplasmic membrane Halogen releasing agents: can be chlorine/iodine releasing

Answer 109

YES Temperature: cardinal temperatures - minimum (enzymatic reactions at increasing rate - low = membrane gelling), optimum, maximum (protein denaturing) Different classes have different cardinal temps: psychrophile (4 degrees), mesophile (E.coli 37 degrees), thermophile (TAQ 70 degrees), extreme thermophile (P.fumarii - 106 degrees)

Answer 110

- Increased membrane fluidity - high amount of unsaturated/polyunsaturated and methyl branched fatty acids - shorter acyl-chain length - Production of Anti-Freeze proteins (AFPs) - these bind to small ice crystals to inhibit their growth by covering water accessible surfaces of ice - Produce cyroprotectants - trehalose and exopolysaccharides - Produce cold adapted enzymes - more a helices, less weak bonds and interdomain interactions - greater flexibility

Answer 111

Polaromonas vacuolata in Lake Bonney, Antarctica

Answer 112

- Protects genome: stabilises DNA by DNA-binding proteins, DNA gyrases introduce supercoils, have high GC% - resistant to denaturation - Membrane composition: ether linked phospholipids, single lipid layer (glycerol tetraethers) - Produces thermostable proteins: increases ionic interactions and hydrophobic interactions - Thermostable chaperonins: thermosome in Pyrodictium abyssi

Answer 113

Thermus aquaticus in Yellowstone

Answer 114

Yes! Can be a neutrophile, acidophile (volcanoes, fruit, gastric juices) or alkaliphile (limes, seawater, ammonia)

Answer 115

Membrane is impermeable - tetraether lipids There is a H+ motive force which powers motility, substrate symport and ATP synthesis H+/Na+ antiporters help maintain pH lower than external K+/H+ antiporters excrete H+ Respiratory chains pump H+ Reverse membrane potential

Answer 116

Na+ motive force drives motility, ATP synthesis and substrate symport Decarboxylases secrete Na+ Respiratory chains pump Na+ Na+ driven ATPases export Na+ H+/Na+ antiporters scavenge proteins

Answer 117

Yes! Extreme halophile (2M<) e.g. Halobacterium salinarum - high salt conc Halophiles (0-2.5 M - optimum is 1) e.g. Aliivibrio fischeri - requires high salt concentrations and thrive in salt lakes Halotolerant (high at 0 - decreases to 2.1M) e.g. Staphylococus aureus - can survive in salty environments but don't need salt to grow Nonhalophile e.g. E.coli

Answer 118

Response to osmotic stress: - regulate water movement by passive transport and aquaporins - produce compatible solutes (proline, glutamic acid) - release solutes by mechano-sensitive channels Salt requirement in halophiles - needed for stabilization of S-layer glycoprotein by Na+, accumulation of k+ as a compatible solute (>4M in cell)

Answer 119

Yes! Needs: nitrogen, sulfur, phosphorus, vitamins, K+/Ca2+/Mg2+ (cofactors), trace elements (Fe/Cu/Zn)

Answer 120

Yes! - for metabolism There are toxic forms of ROS that may form: superoxide (O2-), Hydrogen peroxide and hydroxyl radical Catalase/peroxidase: convert H2O2 into H2O Superoxide dismutase/reductase + catalase: convert O2- into H2O2 then H2O

Answer 121

Obligate aerobes - use exclusively O2 - need catalase and superoxide dismutase Facultative aerobes (E.Coli) - can use O2 - need catalase and superoxide dismutase Microaerophiles - require O2 Anaerobes aerotolerant - no O2 - need superoxide dismutase Obligate anaerobes - die if used oxygen

Answer 122

Direct measuring: microscopic counting, viable counting (serial dilution so can count), flow cytometry (light scattering - cell density - can distinguish between living and dead) Indirect: optical density (measures unscattered light - needs high cell densities, doesn't distinguish live vs dead cells, OD differs between organisms, doesn't work with molds and filamentous bacteria), dry weight, metabolic activity Bacterial growth curve: exponential growth

Answer 123

1) Lag phase - metabolism starts but NO DIVISION 2) Log phase - exponential increase in population 3) Stationary phase - microbial death balances new cells 4) Death phase - population decreases

Answer 124

Two types: Chlorine releasing agents - sodium hypochlorite (bleach) - forms chlorinated bases in DNA and oxidises proteins. Hypochlorite ion OCl- is in equilibrium with hypochlorite acid HOCl. Iodine releasing agents - very powerful but stain, targets DNA and proteins

Answer 125

Black plague - 1328-1350 - killed 30%-50% of the population in europe 1918 flu pandemic - killed 3-5% of world population (50-100 million) 2020 COVID pandemic - 400 million cases, 6 million death

Answer 126

Antibiotics (infections) and vaccinations

Answer 127

Louis Pasteur in the 1860s - the concept of antibiotics emerged

Answer 128

He established that relationship with microbes and disease - 1890. 1) The microorganism must be found in all suffering organisms - not in healthy. 2) Must be isolated from diseased organism and grown in pure culture. 3) This should cause disease when introduced in healthy organism. 4) The microorganism should be reisolated and identified as being identical to original.

Answer 129

1888: Emmerich and Low - Pyocyanase showed antibacterial activity - unstable, toxic. 1910: Ehrlich: Salvarsan (dye linked to arsenic - magic bullet) - treated syphilis - very painful and toxic side effects 1928: Fleming - penicillin formed from fungi. 1932: Domagk - protosil red

Answer 130

Can effect cell wall synthesis, folic acid metabolism, DNA gyrase, RNA elongation, Proteinsynthesis (30s/50s subunits), lipid biosynthesis

Answer 131

- Drug inactivation - Target modification - Efflux/impermeability - Bypass

Answer 132

Yes! 1.4 million died with TB in 2019 700,000 deaths a year from resistant bugs - by 2050 ~ 10 million a year - cost economy £75 trillion

Answer 133

European Centre for Disease Prevention and Control (2015 - 2019) - 670,000 infections due to antibiotic resistant bacteria - 33,000 deaths - annual loss of £1 billion US WHO data 2019 - 3 million infections due to antibiotic resistant bacteria - 50,000 deaths (700,000 worldwide) from drug-resistance pathogens

Answer 134

Some have some really soon, some takes years but always has a resistant bacteria eventually

Answer 135

1) Antibiotic misuse in human therapeutics 2) Farming: started in the 40's, animals are fed with antibiotics - 4 x more than humans, the dose required has increased by 10-20x 3) Agriculture: treatment of diseases in trees and plants (oxytetracycline/streptomycin) 4) Aquaculture: 2g/ton (Norway) to 150g/ton (Canada) 5) Pets

Answer 136

1) Target - selective toxicity and must inhibit an essential process/inhibit virulence 2) Stability and effectiveness - pharmacokinetics - what does the body do to the antibiotics, pharmacodynamics - what does the antibiotic do to the body 3) Cost

Answer 137

Inhibit peptidoglycan polymerisation mediated by D,D-transpeptidases (penicillin binding proteins) Cheap, target both gram +/-

Answer 138

Structural analogs of D-Ala-D-Ala C-terminal residues in the peptide stem They are used by Penicillin binding proteins as substrates and inactivate these enzymes irreversibly - form covalent complex penicillin-PBP

Answer 139

1) Drug inactivation - B-lactamases 2) Target modification - low affinity PBP/overexpression of PBP targeted by B-lactams (so not all are inhibited and peptidoglycan can still be formed) 3) Efflux - efflux systems (Gram negative) 4) Bypass - alternative pathway

Answer 140

Nucleophilic attack by catalytic serine on B lactamase This forms a covalent complex penicillin-B-lactamase Water is added - penicillin hydrolysis

Answer 141

E.g. P.aeruginosa Overproduction of MexAB-OprM system - carbapenam resistance Overproduction of MexEF-OprN system - imipenem resistance

Answer 142

L,D-transpeptidation is B-lactam insensitive - no D-ala-D-ala 3- crosslink and not 3-4 crosslink This causes resistance

Answer 143

Diffusion disk assay In a hospital - tests antibiotics on patients blood

Answer 144

Energy: Preformed molecules (redox) - chemo Sunlight - photo Carbon: Organic (aas/carbohydrates) - heterotroph Inorganic (CO2 - NO C-C/C-H bonds) - autotroph

Answer 145

Chemoheterotroph - animals and fungi Chemoautotroph - extremophiles Photoheterotrophs - purple and green non-sulphur bacteria Photoautotrophs - plants, algae, cyanobacteria

Answer 146

Organo: Organic - e.g. CH2O - have C-H/C-C bonds Litho: Inorganic - e.g. Fe2+ (ferrous ion) -> Fe3+ (ferric ion) NO2- (nitrite) -> NO3- (nitrate) S (sulfur) -> SO42- (sulphate) 2H20 -> 4H+ + 4e + O2

Answer 147

- Chemoorganoheterotroph = animals - Chemoorganoautotroph = some archaea - Chemolithoheterotroph = sulfur bacteria - Chemolithoautotroph = bradyrhizobiaceae - Photoorganoheterotroph = heliobacteriaceae - Photoorganoautotroph = x - Photolithoheterotroph = rhodobacteraceae - Photolithoautotroph = algae and plants - often shortened to photoautotroph

Answer 148

Chemoorganotrophy (reduced organic molecules) Chemolithotrophy (reduced inorganic) Phototrophy (sunlight) These are broken down - catabolism and form ATP This is coupled to anabolism - long term energy storage, biosynthesis, C/N2/H2O

Answer 149

Co2 + H2O -> O2 + sugars -> H2O + CO2

Answer 150

Chemoorganotrophy: organic Chemolithotrophy: inorganic Phototrophy: use light energy to reduce compounds, then use these as an electron donor

Answer 151

Respiration: inorganic or organic molecules Fermentation: organic molecules

Answer 152

NADH donates electron to cytochrome C - this conserves energy (E) in the form of a transmembrane PMF used for ATP synthesis From low to high redox potential O2 is the electron acceptor

Answer 153

From -340 mV - 800 mV Delta g = -nF x change in energy n = number of e F = faraday constant The PMF is 180 mV

Answer 154

Reducing power (NADH/NADPH/FADH2) ATP

Answer 155

Used: organic compounds e.g. carbohydrates, lipids, peptides, aromatic compounds 2 metabolites produced: Acetyl-CoA and pyruvate Distinct pathways (Glycolysis, Entner-Doudoroff, Pentose Phosphate Pathway) lead to key metabolites and energy currencies: ATP/NADH/FADH2 Example of glucose metabolism

Answer 156

Both have no oxygen Anaerobic is where there's an alternative inorganic electron acceptor or organic via a membrane bound respiratory chain. ATP produced by oxphos via PMF Fermentation is where there's an organic acceptor but NO RESPIRATORY CHAIN - ATP is produced by substrate level phosphorylation in cytoplasm

Answer 157

- oxygenic respiration - anaerobic respiration - fermentation

Answer 158

High energetic output Glycolysis Link reaction Kreb cycle Oxidative phosphorylation

Answer 159

A wide range of inorganic compounds used as electron acceptors E transport occurs via cytochromes, quinones and iron-sulfur proteins Bacteria usually use anaerobic when no O2 is available Depending on redox potential of acceptor - different amounts of energy are generated

Answer 160

To exploit a wide range of ecological niches e.g. aquatic water quality Use different electron acceptors at different points in the ocean

Answer 161

Respiration: Nitrate -> nitrite -> nitric oxide -> nitrous oxide -> N2

Answer 162

Acetate CH3-COO + H+ -> CH4 + CO2 Methanol 4CH3OH -> 3CH4 + CO2 + 2H2O

Answer 163

Under anaerobic conditions when no electron acceptor is available ATP produced by SLP - not oxphos Energy yields are low - cells grow more slowly

Answer 164

H2 - hydrogenotrophy, sulfate reduction, methanogenesis Fe2+ - iron oxidation NH3 - anammox, ammonia oxidation NO2 - nitrification HS - sulfide oxidation S - sulfur oxidation

Answer 165

Use CO2 as a carbon source to produce organic molecules via calvin cycle Also produce more complex molecules - acetate To fix carbon they require NADH, this needs the consumption of H+ for a reverse electron flow process

Answer 166

Colony forming unit Number of viable microorganisms

Answer 167

Oxygenic respiration and fermentation

Answer 168

Yes - hydrogenotrophy H2 is a great electron donor that uses a wide range of acceptors O2 as acceptor: H2 + 1/2O2 --> H2O SO42- as acceptor: 4H2 + SO42- + H+ --> HS- + 4H2O CO2 as acceptor (methanogenesis): 4H2 + CO2 --> CH4 + 2H2O Chlorinated compounds as acceptors (dehalorespiration): Dehalobacter (tetrachloroethene -> trichloroethene -> dichloro ethene) to Dehalococcoides (dichloroethene -> vinyl chloride -> ethene) Formate and acetate can also be used - yields CO2 and CH4

Answer 169

Yes! Fe2+ can be oxidised to Fe3+ at a low pH 2Fe2+ + 1/2O2 + 2H+ --> 2Fe3+H2O Ferric ions (Fe3+) can form insoluble ferric hydroxide as pH gets lower: Fe3+ + 3H2O --> Fe(OH)3 + 3H+ Acceptors other than Oxygen can be used e.g. nitrates to nitrites

Answer 170

Some sulfur derivatives can be used as electron donors to form sulfuric acid. H2S (hydrogen sulfide) -> S (elemental sulfur) -> S2O32- (thiosulfate) -> H2SO4 Acid producing microbes can be used in biomining e.g. Acidothiobacillus ferrooxidans - oxidise iron and copper - Cu+ and acid dissolves the metal from rocks

Answer 171

Yes! Ammonia and nitrites can be used as electron donors to produce nitrates Nitrification: NH4+ -> NH2OH (this bit by nitrosomonas) -> NO2- -> NO3- (nitrosbacter) Occurs in aerobic conditions Anammox: NH4+ + NO2- -> N2 + 2H2O (planctomycetes) Occurs in anaerobic conditions

Answer 172

Oxygenic: cyanobacteria and plants - PSI + PSII Anoxygenic: bacteriorhodopsin, green sulfur bacteria, purple bacteria - BR, PSI (green), PSII (purple)

Answer 173

A primitive photosynthetic system Very abundant light-driven proton pump in archaeal membrane Contains a pigment (retinal) that undergoes conformational change when excited by light The movement of H+ generates gradient used to produce ATP

Answer 174

Excitation of retinal induces conformational change: trans -> cis This triggers transfer of proton to Asp85 Deprotonated retinal pushes against helix F - opens cytoplasmic channel - induces reprotonation of retinal from Asp96 Asp96 is reprotonated Asp 85 transfers H+ outside through hydrogen bonding with water

Answer 175

Oxygenic photosynthesis No chloroplasts - are primitive chloroplasts Often made of thylakoids - sometimes does not

Answer 176

Light is captured by light harvesting complexes (contain chlorophyll, carotenoids, bilins) - channel energy to reaction centre 'Z pathway' - 2 distinct photosystems are excited by light - light provides energy to strip e from H20 - forms H+ - electron flow is used to pump H+ outside to form NADPH - H+ gradient forms ATP - NADPH + ATP are used to fix CO2

Answer 177

Anoxygenic photosynthesis - light captures by antenna complexes in organelles called chlorosomes - photon energy is transferred to PSI - PSI donates e to ETC - electron transport pumps H+ outside the cell and reduce NADP+ via ferredoxin - H+ gradient forms ATP -PSI receives electrons from inorganic sulfur derivatives (H2, H2S)

Answer 178

Anoxygenic photosynthesis - light captured by antenna complexes called chromatophores - photon energy is transferred to PSII reaction centre - PSII donates e to a cyclic ETC - e transport pumps H+ outside cell - generates ATP - cyclic phosphorylation - NADH is produced by reverse electron flow - this is where e is transferred from reduced components with higher redox potential - not energetically favourable - needs energy - e transferred to NAD by ETC - replenished by inorganic/organic compounds (H2S/succinate)

Answer 179

Euryarcheota Crenarcheaota (part of the TACK superphyla) Most are adapted to extreme conditions - extremophiles

Answer 180

S layer Pseudomurein cell wall (not always) Other unusual cell envelope structure/organisation Cytoplasmic membrane

Answer 181

Cell shape - Can be glycosylated

Answer 182

In archaea cell wall - not always present Heteropolymer - disaccharide-peptides - has N-acetyltalosaminuronic acid Similar to bacteria peptidoglycan Resistant to: - lysosomes - most antibiotics targeting peptidoglycan synthesis (penicillin)

Answer 183

Sulfolobus -> Archaellum - like a flagellum Pyrodictium abyssi -> Cannulae Altiarcheum hamiconexum -> Hooks The organisation of s layer and pseudomurein can be different - some don't have pseudomurein, some have pseudomurein above/below s layer

Answer 184

Phospholipids contain no fatty acids - instead have isoprenes These are ether-linked - NOT ESTER They are more stable than bacterial cytoplasmic membranes Some contain diglycerol tetraether lipids Can be present as mono and/or bilayers - always present

Answer 185

- circular chromosome and plasmids - histones - multiple replication origins - encode polymerase B (eukarya) and polymerase D (specific to archaea)

Answer 186

Polymerase B - eukarya Polymerase B & D - archaea Polymerase C - bacteria

Answer 187

Has a single RNA polymerase - similar to eukaryotic RNA pol II Has introns Genes are organised in operons - polycistronic (multiple proteins from one mRNA)

Answer 188

Coupled to transcription Involved several translation factors like eukarya Ribosomes are 70 S particles

Answer 189

Lots of habitats - Antarctica, volcanoes. hot springs, hydrothermal vents

Answer 190

Include Crenarchaeota and Euryarchaeota High growth temp (80-120) Most require elemental sulfur for growth Often acidophiles (pH 1-3)

Answer 191

Hyperthermophile - crenarchaeota Isolated in geothermic hot spring - optimal growth at 75 and pH 2.5-3 Grows anaerobically (produces H2S) or aerobically (produces H2SO4)

Answer 192

Produces H2S which is highly soluble in oil. Increases sulfur emissions when oil is burned and the cost of refining oil. Sulfur also attacks metal in pipelines - causes leaks and corrosion.

Answer 193

Archaeal hyperthermophile Isolated from a hydrothermal vent - optimal growth at 82 and pH 2.5-3 Grows anaerobically - requires sulfur

Answer 194

Mostly Euryarchaeota Found in evaporating ponds, dead sea, great salt lake. Require up to 5M NaCl for growth

Answer 195

Archaeal Halophile Prevalent species in Great Black Lake (4M salt) Optimal growth at 75/pH 2.5-3 Uses light as energy source to make H+ gradient - make ATP Other transporters (halorhodopsin) ensure ion transport

Answer 196

Archaeal Euryarchaeota Found in anaerobic environments Use acetate/formiate/CO2 as electron acceptor e.g. CO2 + 4H2 --> CH4 + H2O

Answer 197

Methanopyrus kandleri - isolated in deep ocean on hydrothermal vent - optimal growth at 105-115 - growth conditions = high pressure. We can use OD/production of methane to see growth Methanobrevibacter smithii - prevalent species in human gut, contributes to removal of bacteria end products of fermentation.

Answer 198

Eukarya Some studies say eukarya evolved from them

Answer 199

Marine sediment - may be over one million Seawater - may be ~ 5000 types Human gut - may be over 1000

Answer 200

- Viruses are obligatory particles: need to hijack host metabolic machineries to replicate - Small - Made of a nucleic acid genome surrounded by a protein coat (capsid) and facultative lipid membrane (envelope) - Viruses exist which infect all living organisms: archaea, bacteria (bacteriophages), animals, plants, fungi, protists, viruses (virophages)

Answer 201

Genome composition: DNA - ss or ds, RNA - ss(+/-) or ds Size: usually between 2-20kb (1.2Mb for megaviruses) - minimal info required - only specific genes needed for hijacking. DS>SS, DNA>RNA Organisation: usually 1 molecule - can be fragmented

Answer 202

Surrounds nucleic acid (both together = nucleocapsid) Composition: made of proteins (1 or more) called capsomers Structure: self assembly products - highly ordered - can be - icosahedral symmetry (spherical viruses like mastdenovirus) - helical symmetry (rod shaped viruses like ebola)

Answer 203

Surrounds the nucleocapsid Composition: made of lipid bilayer with glycoproteins from host or virus encoded Role: allows entry into host cell (fusion/endocytosis) E.g. SARS-Cov2 spike protein binds to ACE-2 - modulates angiotensin II activity - increases BP and inflammation

Answer 204

Virus Contains a mixture of icosahedral/filamentous structures Head Collar Tail Tail pins Endplate Tail fibers

Answer 205

Virus Lots of different morphologies

Answer 206

Complex virus e.g. poxyviridae (smallpox)

Answer 207

Named in lots of different ways - After disease: measles - After place reported: ebola - After host/signs: tobacco mosaic - After shape: coronaviridae (crown) - After discover: Epstein-Barr - After supposed transmission: Influenza - influence of bad air - Combination of above

Answer 208

Group I, II and VII - DNA viruses Group III, IV, V, VI - RNA viruses Takes into account: nature of genome RNA/DNA, type of RNA/DNA (ds/ss/polarity), genome replication mechanism By Baltimore, Dulbecco and Temin

Answer 209

Needs host to replicate I - classical semiconservative - transcribes minus strand to form (+) mRNA II - classical semiconservative, discard negative strand (make itself ds then transcribe to make a + mRNA) VII - transcribed into RNA - forms mRNA (+) - followed by reverse transcription III - make ssRNA (+) then transcribe from this to give ssRNA (-) partner - forms (+) mRNA IV - use ssRNA+ directly as mRNA (+) - make ssRNA (-) and transcribe from this to give ssRNA genome (+) V - make ssRNA (+) and transcribe from this to give ssRNA (-) genome VI - reverse transcribe into dsDNA then make ssRNA (+) genome by transcribing (-) strand of dsDNA ALL FORM mRNA (+)

Answer 210

I - Herpesvirus, HBV, Poxviruses, Adenoviruses, Papillomaviruses II - Parvovirus B19 III - Rotavirus IV - HCV, Poliovirus, Rhinovirus, Coronavirus, West-Nile-Virus V - Influenzavirus, Rabies Virus, Measles Virus, Respiratory Synctial Virus VI - HIV, Human T-cell Leukemia Virus VII - Hepatitis B Virus

Answer 211

7 classes: 1 ssDNA, 2 dsDNA, 2 ssRNA(+), 1 ssRNA, 1 dsRNA

Answer 212

A positive strand of RNA

Answer 213

dsDNA - no envelope - 5.3-8 kb Papillomavirus - warts and cervical cancer 19 million new cancer cases, 9.9 million deaths (2020) - 15% due to infectious agents ~ 600,000 cases of cervical cancer in 2020 - 95% due to HPV - 342,000 deaths Vaccination campaign in the UK (9-14 year old girls) - offered to Y8 boys in 2019 - 4 vaccines

Answer 214

ssDNA - no envelope - 5 kb Adeno-associated virus - harmless

Answer 215

dsRNA - no envelope - 18-31 kb Reovirus - causes rotavirus (severe gastroenteritis) 2 million hospitalization (1986-2000), 530,000 deaths in 2000, 215,000 deaths in 2013 In the UK - rarely fatal but has economic burden There is a vaccine - protects against 90% of strains - 1st dose before 8 weeks - 2nd dose 1 month later

Answer 216

(+) ssRNA Foot and mouth (no envelope - 7.5kb) - blisters in cloven hoofed animals - aphtovirus 2001 outbreak - 2000 cases - 4 million cattle died - EU imposed worldwide ban on british exports of lifestock - Cost >3 billion to public sector, >5 billion to private Coronavirus (has an envelope - 26-32kb)

Answer 217

(-) ssRNA - has an envelope and 12 - 15 kb Influenza - killed 20-100 million in 1918 - killed 3-5% of the world 3-5 million cases a year

Answer 218

reverse RNA - has an envelope - 9.7 kb HIV - can cause AIDS (progressive failure of immune system) - body more susceptible to opportunistic infections HIV has a tropism for immune cells: macrophages, dendritic cells, CD4+ T cells 78 million deaths to date In 2016 - 38 million living with it, 1.5 million contaminations and 0.5 million deaths

Answer 219

reverse DNA - has an envelope - 3.1 kb Hepatitis B - cirrhosis and liver cancer

Answer 220

I - dsDNA II - ssDNA (+) VII - dsDNA III - dsRNA IV - ssRNA + V - ssRNA - VI - ssRNA +

Answer 221

YES! There are lots of different forms Bacteriophages - different sizes, dsDNA Animal/plant - nonenveloped, enveloped

Answer 222

1) Attachment 2) Genome injection (entry) 3) Production of nucleic acid and protein 4) Maturation (assembly of viral particles) 5) Release

Answer 223

1) Attachment 2) Genome injection 3) Phage DNA circulates - could enter lysogenic 4) Phage DNA and proteins are synthesised and assembled into virions. 5) Cell lyses - releases phage virions Lytic cycle - infectious

Answer 224

1) Attachment 2) Genome injection (entry) 3) Phage DNA circulates 4) Phage DNA integrates within the bacterial chromosome by recombination = prophage 5) Cell division 6) The prophage may excise from the chromosome initiating a lytic cycle. Lysogenic cycle

Answer 225

1) Attachment (virion attaches to host) 2) Entry (virion enters cell, DNA is uncoated) 3) Viral DNA is transferred to nucleus and the DNA is replicated - viral proteins are produced 4) Maturation - Virions assemble 5) Release - virions are released

Answer 226

1) Attachment 2) Entry 3) Maturation: - group IV - make proteins directly from ssRNA (+), make genome via ssRNA (-), - group V - make ssRNA (+) first and use this to produce proteins and ssRNA (-) genome, - group III - make ssRNA (+) and use it to make proteins and ssRNA (-) genome 4) Maturation - capsid forms 5) Release

Answer 227

1) Retrovirus enters by fusion between attachment spikes and host receptors 2) Viral RNA genome and 3 viral enzymes are released: reverse transcriptase, integrase, protease. 3) Reverse transcriptase copies viral RNA to dsDNA in the cytoplasm 4) dsDNA is transported to nucleus and integrated into host genome by integrase - the provirus is replicated when host replicates 5) Transcription of the provirus produces new genomes and RNA encoding capsid, enzymes and envelope proteins 6) Viral proteins are processed by viral proteases - some go to plasma membrane 7) Mature retrovirus buds out of host cell with envelope and attachment spikes

Answer 228

dsDNA viruses: encapsidation is coupled with maturation of replicative genome ssRNA virus (inc. retroviruses): electrostatic interactions between basic capsid proteins and RNA genome (acidic), promote cooperative assembly of capsomers Fragmented genomes: genetic fragments in complex with proteins are paired before encapsidation

Answer 229

Any agent that can cause disease

Answer 230

Survival strategy One organism using resources of another in a way which is not beneficial to the host Tick on a dog = parasite Common cold = virus = pathogen

Answer 231

No - there is none that cause disease to any pathogen

Answer 232

Bacterial - yersinia pestis - plague Viral - polio virus - polio Fungal - cryptococcus - meningitis Protozoa ('eukaryotic) - plasmodium falciparum - malaria Prions (infectious proteins) -vCJD - human 'mad cow' disease NO ARCHAEA

Answer 233

1) gain access to host 2) locate a nutritionally compatible niche 3) avoid/subvert/circumvent the host innate and adaptive immune responses 4) access host's resources and replicate (THIS IS WHERE INFECTION HAS OCCURED - not all exposure results in disease) 5) exit and spread to new host - transmission - air (droplets), water, food, vector

Answer 234

Innate: - non-specific - rapid Adaptive: - highly specific - slower

Answer 235

Measure of disease severity Mortality - number of deaths from a disease Morbidity - number of cases of a disease Ebola (EBOV strain) - ~ 90% mortality Plague (pneumonic), rabies (preventable) and vCJD have mortality rates near 100%

Answer 236

See if the pathogen is still there

Answer 237

Number of individual particles/cells required for infection High virulence: e.g. Shingella dysenteriae - diarrhoeal disease - 10 cells Low virulence: e.g. salmonella - food poisoning - 1,000,000 cells

Answer 238

These enable a pathogen to colonise the host - DO NOT CAUSE DISEASE Adhesins 'anchors' - find niche and colonise Capsules/s-layers 'armour' - immune evasion and survival in host Digestive enzymes - finding niche, colonising and finding host resources Toxins - reprogram host biology to benefit pathogen Stealth mode - absence of outer surface structures - immune evasion

Answer 239

You can see a parasite with the naked eye

Answer 240

World: WHO UK: UK health security agency (humans), DEFRA (animals/plants) USA: CDC (humans), USDA (animals/plants)

Answer 241

26% lower resp - 2.2 million in 2019 diarrhoeal diseases - 1.5 million TB - 1.2 million HIV/AIDS - 700,000 Heart disease, stroke, COPD, resp infections, child birth, lung cancer, dementia, diarrhoeal diseases, diabetes, kidney disease = 55% of all deaths worldwide

Answer 242

Founding principle States many diseases are caused by microbes

Answer 243

Established a scientific basis linking microbes and disease. Used pure cultures to understand infectious diseases. Used the bacterium Bacillus anthracis (Anthrax). He studied this disease because it would kill sheep and cattle.

Answer 244

He proved that a specific pathogen causes a specific disease. 1) The microbe is found in all cases of disease and absent from healthy individuals. 2) The microbe is isolated from the diseased host and grown in pure culture. 3) When the microbe is introduced into a healthy susceptible host, the same disease occurs. 4) The same strain of microbe is obtained from the newly diseased host. Host + pathogen = disease

Answer 245

In the last 200 years - better diet and clean drinking water. Improved sanitation and less overcrowding in urban areas and better living conditions.

Answer 246

Chemical agents which prime the adaptive immune system to repel a pathogen. After vaccination, if the subject can be exposed to the pathogen and does not develop the disease - they are now IMMUNE

Answer 247

Very common disease in 1800's with mortality rate of 30%. Between 1900-1979, 300-500 million died of smallpox. Lady Montagu (1717) introduced an early form of vaccination by directly adding pus from smallpox into the open vein of the patient. Edward Jenner (1796) inoculated a person with cowpox virus (less virulent than smallpox) - they were then protected against smallpox - cross protection

Answer 248

Yes! As the smallpox vaccine worked - smallpox is extinct from 1979.

Answer 249

It varies for disease Chickenpox - attenuated strain Hepatitis A - inactivated virus Hepatitis B - viral antigen Influenza - inactivated virus MMR - attenuated viruses Polio - inactivated Rabies - inactivated Yellow fever - attenuated virus

Answer 250

NO - but work well with viruses

Answer 251

Chemicals produced by bacteria and fungi that inhibit or kill other microbes Last therapeutic options. Compound which controls pathogen infections without harming patient - magic bullet

Answer 252

Penicillin - the first - Alexander Fleming noticed that the penicillium mold was killing staphylococcus Penicillium mold

Answer 253

Florey and Chain's challenges: - purification - production - prove penicillin was non-toxic - 'first' human and animal tests Saved millions of lives - 80-200

Answer 254

Classes or family e.g. penicillins Injection - Penicillin G Orally - Amoxycillin Narrow spectrum - Oxacillin Broad spectrum - Ampicillin Extended spectrum - Carbenicillin Resistant to B-lactamase enzymes - Methicillin

Answer 255

Fundamental processes in a bacterial cell - not human Cell wall synthesis - penicillins Proteinsynthesis Cell membrane integrity Nucleic acid function Intermediary metabolism

Answer 256

Symptom: a change in body function felt by a patient as result of disease e.g. feeling tired Sign: a change in a body which can be measured or observed as a result of disease e.g. high temp Syndrome: a specific group of signs and symptoms that accompany a disease

Answer 257

Yes! Streptococcus pneumoniae (gram positive bacteria) - pneumonia - sepsis - meningitis

Answer 258

920,136 children under 5 in 2015 died - accounts for 16% of deaths for under 5 The most common cause of infection-related deaths in UK and USA

Answer 259

YES Pneumonia: Bacterial - Streptococcus pneumoniae, Haemophilus influenzae Viral - respiratory syncytial virus Fungi - Cryptococcus neoformans (usually in immunocompromised individuals) The symptoms and signs are identical

Answer 260

A reaction of the body to colonisation or damage to the airways

Answer 261

It benefits our health and wellbeing: - helps with digestion - healthy metabolism - immune function - mood and behaviour - obesity/diabetes/heart disease

Answer 262

Relationship between bacteria and organisms One organism benefits, the other is unaffected - friendly colonisers e.g. Staphylococcus epidermidis on the skin

Answer 263

Both organisms benefit e.g. E.coli in large intestine - makes vitamin K12 - blood clotting

Answer 264

One organism benefits at the expense of the other Human viruses

Answer 265

Clostridium difficile - spore-forming gram positive bacteria Causes Clostridium difficile infection: diarrhoea colonisation and inflammation of the colon, abdominal pain, fever

Answer 266

Faecal-oral route Mortality = 9% In USA - 500,000 infections, 29,000 deaths Virulence factors = TcdA and TcdB, S-layer armour The spores allow them to survive penicillin - allows c.diff to colonise (is it a pathogen or a survivor?) Treatment: antibiotics, infection control, faecal transplantation

Answer 267

Microbes which aren't normally pathogenic but can cause infection/disease in a compromised host Sepsis - treatment requires total annihilation of the organism

Answer 268

Infections acquired as a result of a hospital stay Usually the patient themselves which are the source of their own infections e.g. C.diff and MRSA

Answer 269

Urban areas 2007 - >50% of the world's population live in urban areas - Africa and Asia expect to rise Drives potential routes of transmission

Answer 270

Causes Cholera Gram negative bacteria

Answer 271

By Vibrio cholerae Symptoms: large amounts of watery diarrhoea (rice-water stool), abdominal pain, vomiting Virulence: death through severe dehydration - 1.3/4 million cases and 21,000 - 143,000 deaths - mortality can be 1% if treated rapidly Virulence factors: cholera toxin

Answer 272

Transmitted: faecal-oral route (water/food) Treatment: oral rehydration and antibiotics

Answer 273

Investigated the 1854 cholera outbreak - the broad street pump

Answer 274

Study of where and when diseases occur to control spread of disease

Answer 275

- identify first person to have disease 'patient zero' - identify anyone who had contact with that person - identify reservoir for pathogen - blocking or containing it (difficult for new pathogen, disease must first be recognised, many already infected by then)

Answer 276

Yes! 'Tracking and surveillance of disease patterns is an essential tool to control disease' - WHO

Answer 277

Epidemic: disease acquired by many hosts in a given area in a short time Endemic: disease constantly present e.g. common cold Pandemic: worldwide epidemic e.g. HIV

Answer 278

Gram negative bacteria Causes Typhoid fever

Answer 279

Caused by Salmonella enterica serovar Typhi Symptoms/signs: rash (rose spots), malaise (feeling ill), delirium, fever, pain , high BP, diarrhoea Symptoms are non-specific and extremely variable e.g. rose spots only in 50% of cases

Answer 280

Mortality rate - 30% with no treatment, 1% with treatment Virulence factors: toxins, capsule

Answer 281

Transmission/reservoir: human carriers (colonised gall bladder), 1-3% of exposed will permanently carry disease, faecal oral route Treatment: antibiotics, vaccine (doesn't offer full protection)

Answer 282

Caused by polio virus (+) strand RNA virus picornavirus

Answer 283

95% have mild symptoms 1/200 - irreversible paralysis Muscle weakness Atrophy Deformities Twisted feet/legs Virulence: 15% of symptomatic cases = death as breathing muscles become immobilised

Answer 284

Transmitted: humans (some chimps), faecal oral route usually by contaminated water source Treatment: vaccine - attenuated(weakened) virus, few treatment options

Answer 285

Uses attenuated version (weakened) In rare cases the virus can revert to a form which causes disease and infects others In extremely rare cases some immunocompromised individuals become healthy carriers - excrete large amounts of active polio for long amount of time - OPV paradox

Answer 286

Individuals capable of transmitting disease to others but so not have signs of symptoms of infection e.g. Typhoid mary, Birmingham man (excreted polio for the last 31 years)

Answer 287

A gram negative bacteria causing bubonic and pneumonic plague Virulence factors: many toxins. V, W, YopB, YopD - avoid phagocytosis, F1 - makes flea hungry

Answer 288

Symptoms: buboes (swollen lymph glands), flu symptoms (chills, fever), sepsis, pneumonia Virulence: very high mortality if untreated - bubonic = 50%, pneumonic = 90-100%, treatable if <24 hours since first symptoms

Answer 289

Transmitted: rodents/prairie dogs - rodent fleas, human respiratory aerosol (pneumonic) Treatment: antibiotics and vaccine

Answer 290

Yes! It can be equally as devastating to rodent Epizootics - animal equivalent of epidemic - have animal reservoir

Answer 291

Spore forming oomycete (water mold) which causes potato blight

Answer 292

Symptoms/signs: white mycelium growth over surface of leaves and tubers (potatoes) Virulence: approaching 100% of crops - especially if soil is pre-contaminated and the potato variety is susceptible

Answer 293

Transmitted: very stable spore structures Treated: fungicides (limited use), copper sulphate (could cause heavy metal toxicity)

Answer 294

Yes! They usually co-evolve with them Tight population bottleneck reduced genetic diversity in potatoes - greater disease

Answer 295

Caused by influenza virus - Orthomyxoviridae (- ssRNA) Virulence factors: changed in the H (hemagglutinin) and N (neuraminidse) proteins

Answer 296

Symptoms: fever, chills, cough, chest pain, sore throat, muscle pain Virulence: 0.01-50% mortality - newer strains have higher fatality

Answer 297

Transmission: human reservoir, respiratory droplets, can infect other animals Treatment: antiviral drugs, vaccine - varied efficacy due to differing strain types

Answer 298

Re-assortment of genetic material E.g. bird virus + human virus -> swine (pig) cell - makes a new reassortant virus - this can infect humans

Answer 299

Economic changes Social changes Scientific changes

Answer 300

Identified in 1947 and named after the Zika forest in Uganda Symptoms: mild fever, rash, muscle and joint pain, headache, symptoms last for 2-7 days Virulence: extremely low, most people won't have symptoms at all - associated with birth defects - microcephaly, Guillain-Barre syndrome Transmitted: Aedes species mosquito, sexually transmitted - men can infect for 6 months, women = 8 weeks Treatment = control of mosquito population, condoms

Answer 301

A disease is first identified as a geographically clustered pattern of symptoms and signs

Answer 302

August 2015 - Dr van der Linden noticed an increase in microcephaly in newborns in Brazil October 2015 - She alerted the state health secretary At the same time and location - outbreak of mosquito associated diseases 2016 - link between Zika and microcephaly was established by 'scientific consensus'

Answer 303

Vector for more than one pathogen Dengue virus - high virulence Zika virus - low virulence

Answer 304

Collection, analysis and dissemination of public health data - takes time - can be inaccurate - correlation does not mean causation

Answer 305

Brain abnormalities Microcephaly Eye defects Hearing loss Damage to: nerves, muscles and bones

Answer 306

Reported cases in south and north america, south asia, some africa and france Zika is no longer strictly limited to areas where mosquitos are found

Answer 307

In the USA - the Zika Birth Defects Surveillance system monitors birth defects potentially due to Zika virus infection e.g. 2,394 births, 116 with defects, 9 died due to defects The correlation between Zika virus infection during pregnancy and birth defects has a mild effect size - 2 to 2.4 cases per 1000 births

Answer 308

Zika-associated birth defect rate = 5% Any pregnancy having a birth defect = 3%

Answer 309

Filovirus - (-) ssRNA Causes Ebola virus disease and Ebola hemorrhagic fever Named after the Ebola river in the democratic republic of congo

Answer 310

Symptoms: fever, sore throat, muscle pain, headaches, bleeding (vomiting blood, eyes, nose, mouth, anus) Virulence: highly - 40-90% mortality rate

Answer 311

Transmission: by direct contact, sexual transmission (unclear), reservoir not known but believed to be fruit bats - zoonotic Treatment: currently untreatable - isolation, potential antibody therapies, vaccine under development

Answer 312

Antimicrobial resistance - superbugs

Answer 313

Modern medicine relies on antibiotics Without them: minor infections become life threatening, surgery, child birth, chemotherapy (immunocompromised), infectious diseases would claim more lives

Answer 314

Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes - but these bacteria can fight back 1943 penicillin: - 1940 Penicillin-R Staphylococcus - 1965 - Penicillin-R pneumococcus 1950 tetracycline - 1959 tetracycline-R Shingella The rate of drug discovery has sharply declined - continued use of antibiotics has driven selection for resistant strains

Answer 315

Yes - we estimate it to kill 10 million in 2050 Now - 700,000

Answer 316

Penicillin - clostridium difficile Tetracycline - staphylococcus aureus Erythromycin - streptococcus pneumoniae Vancomycin - neisseria gonorrhoeae Chloramphenicol - mycobacterium tuberculosis Polymyxin - salmonella serotype typhi Trimethoprim - shingella

Answer 317

Chemical modification of antibiotic Biochemical changes in target protein Multidrug resistance pumps

Answer 318

Mutualism: both benefit e.g. E.coli in the intestine produce vitamins beneficial for the host, in return they use nutrients to sustain growth Commensalism: microbe benefits from the interaction, no impact to host e.g. bacteria on the skin - can be sometimes beneficial to host Parasitism/predation/competition: microbe benefits at the expense of the host e.g. some intracellular pathogens - chlamydiae, apicomplexans

Answer 319

Ecto - lives on the surface of another species Endo - one organism inside another Not mutually exclusive

Answer 320

Found in the gut of specific microbes Lives in symbiosis with other bacteria: - 2 endosymbiotic bacteria which degrade cellulose - replace mitochondria - 3 ectosymbiotic bacteria (outside the mixotrichia) (short spirochetes, long spirochetes and bacteroides) which provide motility - possess 4 non functioning flagella

Answer 321

Several bacterial species are found: intracellular (A and B) and extracellular (C and D) These are found in specialised structures called bacteriocytes which can aggregate to form organs called bacteriomes

Answer 322

Parasite of amoebae than can replicate within alveolar macrophages Found in freshwater

Answer 323

Parasite which attacks gram-negative bacteria Invades the periplasm and feeds on the host - multiply then release

Answer 324

Plants can't use atmospheric N2 (can only use ammonium or NO3) Some legumes (Fabaceae) can fix N2 via a symbiotic interaction with soil bacteria - Rhizobia This is nodulation - increases growth rate

Answer 325

Alphaproteobacteria (gram negative) Soil dwelling bacteria part of rhizosphere Complex genome - 5-10Mbp, several plasmids Help some legumes

Answer 326

1) Bacterial attraction: flavonoids (root exsudates) attract bacteria Acidic: Rhizobium has glucomannan which touches Lectin on a root hair, cellulose then traps lots of others Basic: They bind with Rhicadhesin Form biofilm Lectin act as plant surface receptors

Answer 327

2) Nodulation genes are activated in the Rhizobium - Nod factors produced Nod factors are short oligosaccharides

Answer 328

3) Root curls around rhizobium

Answer 329

4) Formation of infection threads - like tunnels where rhizobium can enter the root hair Symbiosomes (membrane vesicles) contain rhizobium cells

Answer 330

5) Bacterial differentiation into bacteroids - NCR transforms them They invade cortical cells in symbiosomes Viable = determinate nodules Dead = indeterminate nodules

Answer 331

6) N2 fixing

Answer 332

Allow us to identify bacterial species which can't be grown in lab conditions Axenic = independently of any other living organism

Answer 333

Its genome is 580 kbp - within the circle there are 5 organisms genetic material The five are likely to be due to endosymbiosis - have at least half the size of genome

Answer 334

Phylogenetic studies indicate that these organism do not have an independent origin Genome size is a result of gene loss

Answer 335

Can grow them on potatoes In symbiosis with Moranella and Trembaya organisms - nested symbiosis This is where an organism has an endosymbiosis relationship with a bacteria (Trembaya) which itself has an endosymbiosis relationship with another bacteria (Moranella)

Answer 336

Underpins amino acid biosynthesis The mealybug combines genes from all three organisms - this symbiotic relationship has been selected as all three organisms contribute to the biosynthetic pathway of some amino acids The mealybug also contributes specific components and genes for peptidoglycan synthesis in Moranella

Answer 337

Yes some do Some can also eat bacteria

Answer 338

Product of a relationship change/conflict between host and pathogen

Answer 339

Study of the immune system - integrated system of cells and molecules that defend against disease Reacts against infectious diseases

Answer 340

Immunodeficiency Allergy Autoimmune disease Graft rejection

Answer 341

Research Diagnostics and therapeutics

Answer 342

- Broad specificity - Not improved by repeat infections - no memory - Rapid (hours) - First form of immunity to evolve - Helps initiate and mediate adaptive immune responses

Answer 343

Leucocytes: phagocytes, natural killer cells (NK) Soluble factors: lysozymes, complement, interferons

Answer 344

- Highly specific - Improved by repeat infection (memory) - Slower response (days) - Foreign material (antigen) is recognised by specific receptors on T and B lymphocytes - Immune system is tolerant of own body's cells and molecules

Answer 345

Leucocytes: B and T lymphocytes Soluble factors: antibodies

Answer 346

Derived from pluripotent stem cells in bone marrow. Gives rise to two main lineages: one for myeloid (polymorphonuclear leukocytes from myeloblast - neutro/eosino/basophils, monoblasts - macrophages, monocytes dendritic) cells, one for lymphoid (lymphocytes - natural killer cells, B/T) cells

Answer 347

Keratinised skin - keratin Secretions: sebum, FAs, lactic acid, lysozyme Mucous - cilia in resp tract Low pH - stomach pH is 2.5 Commensals

Answer 348

Elie Metchnikoff 1883 saw them firstly Neutrophils: main phagocyte, short-lived, fast-moving, lysosomes release enzymes, H2O2 ect. Mononuclear phagocytes: long lived (months), help initiate adaptive responses Monocyte (blood) --> macrophage (tissues)

Answer 349

Type of lymphocyte - kill virally infected cells non-specifically - important in self/non-self recognition - may kill cancer cells

Answer 350

Have general pathogen-recognition receptors (PRRs) that recognise microbe-associated molecular patterns (MAMPs) which are shared by many microbes and essential e.g. Toll-like receptor 4 (TLR4) recognises lipopolysaccharide

Answer 351

Kill targets unless they recognise self-proteins (MHC) which are present on all nucleated cells

Answer 352

Complement system: ~ 20 in blood which are activated during infection - bacterial cell lysis Defensins: positively charged peptides made by neutrophils, disrupt bacterial membranes Interferons: produced by virally infected cells - protect uninfected cells and activate macrophages and NK cells

Answer 353

Cytokines: small, secreted proteins that bind to cells and regulate immune response e.g. interleukins - produced by cells of innate and adaptive IS Inflammatory mediators: histamine, prostaglandins

Answer 354

Heat, redness, swelling, pain Localised response to infection/damage Dilation of BV, increased capillary permeability, phagocytes migrate into tissues Infection/damage induces release of inflammatory mediators (PG, histamine) and production of cytokines

Answer 355

Macrophages may release cytokines when there's infection e.g. interleukin 1 This acts on hypothalamus --> raise temp --> stims phagocytosis --> reduces level of iron in blood (as bacteria use the iron to grow)

Answer 356

Vaccination

Answer 357

Bacteria (1-5 micrometres) - Staphylococcus aureus (MRSA) = Boils, septicaemia Viruses (20-400 nm) - HIV = AIDS, influenza = flu Fungi (2-20 micrometres) - Candida albicans = thrush, Epidermophyton flocosum = ringworm Parasites (1 micrometres - 10m) - Schistosoma mansoni = schistosomiasis, Typanasome brucei = sleeping sickness

Answer 358

T - mature in thymus, has a T cell receptor B - mature in bone marrow , has an antibody Primary lymphoid tissue - antigen independent differentiation

Answer 359

Antigen dependent differentiation B and T lymphocytes go to lymph nodes and spleen Causes humoral and cell mediated immunity Humoral - B cells - secrete antibody, for extracellular bacteria and secondary viruses Cell mediated - T cells - kill infected host cells and make cytokines, for viral, intracellular bacteria and intracellular parasite

Answer 360

Produces in response to antigen (antibody generating material)

Answer 361

Macfarlane Burnett Those B cells with the antigen are chosen for division- form plasma cells to produce antibodies and form memory cells Lymphocytes that recognise 'self' are deleted early in development

Answer 362

Only antigen bound to host cells

Answer 363

T cells Clonal expansion --> differentiation --> memory

Answer 364

Primary: lymphocytes reach maturity and acquire their specific receptors Secondary: mature lymphocytes are stimulated by antigen

Answer 365

Primary: thymus and bone marrow Secondary: Tonsils, adenoids, lymph nodes, spleen, peyer's patches, appendix, lymphatic vessels

Answer 366

Belong to class of soluble glycoproteins known as immunoglobulins - act as labels for infectious material Dual role Fab regions - variable and binds different antigens specifically - antigen recognition FC region: constant in sequence, binds to complement, Fc receptors on phagocytes, NK cells ect. - antigen elimination

Answer 367

Light chain: 25kD Heavy chain: 50kD L2H2 = 150kD Bound together by disulphide bridges

Answer 368

Fab = fragment antigen binding Fc = fragment crystallizable Fab are two arms, Fc is bottom Papain cleavage cuts the hinge region - 2 Fab, 1 Fc

Answer 369

IgG = γ - main class in serum (blood without cells and clotting factors) and tissues important in secondary responses - can cross placenta IgM - µ - important in primary responses IgA - α - in serum and secretions, protects mucosal surfaces IgD - δ - ? IgE - ε - low levels in serum, involved in allergy, protective against extracellular parasites Also two light chain types - kappa (κ) and lambda (λ) - not class restricted - e.g. can have IgGλ antibodies

Answer 370

IgG and IgM in primary (IgM first) and secondary - IgG higher in secondary IgA and IgE in secondary depending on type of pathogen and site of infection

Answer 371

Variable - bind to antigen - differ between antibodies Constant - same for antibodies of a given H or L chain type Encoded by different exons Multiple V region exons in genome can recombine and mutate giving B cell differentiation to give different specificities

Answer 372

Amino acid sequence of heavy chain

Answer 373

IgA - can be monomer (serum) or dimer (secretions) IgM - pentamer

Answer 374

Specific binding/multivalency (FAB): - Neutralise - IgG, IgA - Immobilise motile microbes - IgM - Prevent binding to, and infection of, host cells - Form complexes Effector functions (Fc): - Activate complement - IgG, IgM - Bind Fc receptors - phagocytes (IgG, IgA), NK cells (IgG), mast cells (IgE)

Answer 375

Immune defence against bacteria (viruses) and inducer of inflammation - can cause pathology ~ 20 serum proteins activated via enzyme cascade e.g. proenzyme 1 makes enzyme 1 which makes proenzymes 2 ect. Activated specifically by antigen/antibody complexes (CLASSICAL pathway) or non-specifically e.g. by certain bacteria (MB-LECTIN or ALTERNATIVE pathway)

Answer 376

C1, 4, 2, 3, 5, 6, 7, 8, 9 Many components have enzymatic (protease) activity - generate fragments with biological activity e.g. C3 --> C3a + C3b

Answer 377

C1, C2, C4 Require 1 antigen and 2 antibodies C1 must interact with 2 Fc regions to be activated IgM is more potent activator of complement as it's a pentamer

Answer 378

Leads to generation of C3 convertase C3b joins C3 convertase to make C5 convertase

Answer 379

1) Activation (phagocyte recruitment and induce inflammation) - C5a (C3a), chemoattractants and anaphylatoxins 2) Opsonification - C3b, increased binding and phagocytosis 3) Cell lysis - Membrane Attack Complex: C5-9 - hollow cylinders which form 'pores' in bacterial membranes

Answer 380

Gram positive

Answer 381

IgG and IgA Fc receptors bind to Fc region - help phagocytes engulf using pseudopods Pseudopods then fuse - phagosome - lysosomes fuse with phagosome - phagolysosome - enzymes (lysozymes), competitors (lactoferrin), reactive oxygen species (H2O2) - bacteria killed

Answer 382

Yes! Mediate antibody dependent cell-mediated cytotoxicity (ADCC) IgG Secretion (perforin) - Target then undergoes apoptosis

Answer 383

Yes! Mediate allergy/defence against large parasites IgE Degranulation releases inflammatory mediators e.g. histamine - local inflammation - beneficial in response to parasites

Answer 384

Producing antisera (ready made immunity from animals/humans already exposed) - gives antibodies directly Conventional antisera = polyclonal antisera (mix of antibodies targeting same antigen at different sites (epitome))

Answer 385

Mixture of antibodies to different epitome (shape antibody binds to) May lack fine specificity and difficult to standardise

Answer 386

Single specificity derived from single B lymphocytes B cell from animal immunized with antigen A + Tumour cell line (divides indefinitely) = hybrid cells making anti-A antibody and divide indefinitely

Answer 387

1) identify and label molecules in complex mixtures 2) identify pathogens 3) characterise cell surface proteins, identify cell types 4) humanised antibodies are used in therapy

Answer 388

T helper cells (CD4 +ve): - help B cells make antibodies - activate macrophages and NK cells - help development of cytotoxic T cells - do all this using cytokines T cytotoxic cells (CD8 +ve) - recognises and kills infected host cells

Answer 389

Has an alpha and beta chain which both have control and variable regions Chains help by disulphide bridges TCR structure is similar to Fab arm of antibody

Answer 390

B cells - 'soluble', free, native antigens T cells - 'cell-associated' processed antigens on MHC molecules

Answer 391

Major histocompatibility proteins On body cells - can tell immune cells that the cell is infected

Answer 392

Encoded by Major Histocompatibility gene Complex on chromosome 6 Important in graft rejection Very polymorphic - lots of different alleles Major role in initiating T cell responses

Answer 393

MHC I - expressed by all nucleated cells - display antigen to CD8+ve T cells (cytotoxic) MHC II - expressed by macrophages, dendritic cells and B cells - display antigen to CD4+ve T cells (helper)

Answer 394

Recognises peptide bound to MHCI Virus infected cell --> viral proteins broken down in cytosol (proteosomes) --> peptides transported to ER and bind MHCI --> cell surface Activated cytotoxic T cells kill infected cell (perforins) by inducing apoptosis

Answer 395

Macrophage/dendritic/B cell internalises and breaks down foreign material ---> peptides bind to MHCII in endosomes --> cell surface T helper cells bind and help BB cells make antibodies and produce cytokines that activate/regulate other leucocytes

Answer 396

T cells acquire their receptors and are 'educated' in thymus Only T cells that recognise self-MHC and not self-peptides survive 5% go to peripheral lymphoid tissue

Answer 397

'Hormones' of immune response Small (5-20 kD) secreted proteins involved in the communication between cells of immune response Usually produced and act locally Act by binding to specific receptors on the surface of target cells (cytokine receptors) Biological effects: changes in cell behaviour e.g. movement, secretion, changes in gene expression

Answer 398

Interleukins (IL-1, IL38?) -often made by T cells Interferons - viral infections e.g. IFNalpha, IFNbeta; cell activation (IFNgamma) Chemokines - cell movement or chemotaxis e.g. IL-8 (CXCL8) Tumour necrosis factor - proinflammatory, can kill some cells Colony stimulating factors - leukocyte production e.g. M-CSF

Answer 399

In lymphatic vessel: Lymph draining from infected tissue --> dendritic cell with bacterial antigen --> T cells activated --> plasma cells and antibodies made --> effector T cells Naive T cells in blood

Answer 400

Co-evolved Innate initiate adaptive Adaptive augment innate

Answer 401

1796 Showed that infection with cowpox was protective against smallpox This is because they share antigens Smallpox is eradicated (1979)

Answer 402

Attenuated strains e.g. polio Killed pathogen e.g. polio Subunit e.g. toxoid (from toxin), virus spike protein Engineered virus e.g. Astrazeneca SARS CoV-2 RNA e.g. Moderna CoV-2; melanoma vaccine mRNA-4157

Answer 403

Malaria Schistosomiasis TB HIV/AIDS

Answer 404

1981 The HIV virus was identified in 1983

Answer 405

Retrovirus - tumour virus (association with cancer shown in 1911 by Peyton Rous) Lentivirus - "slow virus"

Answer 406

2 copies of + ssRNA

Answer 407

It's RNA (can act as mRNA) is converted to DNA by reverse transcriptase The DNA then can be transcribed to RNA then protein Life cycle of retroviruses determined in 1973

Answer 408

Has viral receptors - gp120 which is bound to the gp41 in the membrane Nucleocapsid - has reverse transcriptase, protease, integrase, RNA

Answer 409

1) virus binds to cell receptor 2) envelope fuses with plasma membrane 3) nucleocapsid enters cytoplasm 4) viral RNA reverse transcribed into dsDNA 5) viral DNA is transported to nucleus and integrates into host genome = provirus 6) new viral genome RNA and mRNA --> cytoplasm 7) viral mRNA --> viral protein 8) new nucleocapsids form and virus buds from cell - acquires lipid envelope

Answer 410

Latent Permissive Lytic

Answer 411

CD4 +ve cells (T helper) susceptible to infection by Gp120 T helper cells - virus initially cleared but pool of infected cells gradually increase Latent ----> activated - caused by T cell stimulation activating HIV provirus transcription Number of T cells infected increases with each round of viral replication

Answer 412

Dendritic cells present antigen to T cells in lymphoid tissue Infection is 'permissive' - acts as reservoir of virus Monocytes may cross the blood brain barrier - CNS involvement

Answer 413

Co-receptors required - identified in 1996 Co-receptors are chemokine receptors e.g. CCR5 - required for virus fusion with host cell May influence susceptibility to infection/disease progression

Answer 414

Initially high levels of virus in the blood are cleared Antibodies to HIV may not be detected for 3 months (seroconversion) Immune system mounts a strong response - CD8 +ve cytotoxic cells are important BUT virus mutates to avoid immune detection

Answer 415

AIDS - direct lysis by virus - syncytium formation - killed by cytotoxic T cells or other immune mechanism - apoptosis Infected cells are in lymphoid tissue

Answer 416

Blood count CD4+ve T cells < 200/mm3 = AIDS

Answer 417

- memory T cells lost - all adaptive immune responses are compromised - opportunistic - reactivation of latent viruses - rare cancers - CNS involvement - Dementia

Answer 418

HIV-1 - central Africa Likely source - related virus infecting chimpanzees Phylogenetic studies suggest cross-species transmission 1910-1930 HIV-2 - west Africa - pre-dates HIV-1 Likely source - related virus affecting sooty mangabees Less virulent and less easily transmitted

Answer 419

Claimed over 32.7 million lives so far ~ 38 million people currently living with it New infections decreasing by 1 million over last 10 years

Answer 420

Unprotected Sexual intercourse ~ 70% Blood/blood products ~ 28% Breast feeding Mother to foetus

Answer 421

Change behaviour: blood testing, safe sex, less needle sharing, treat HIV+ve pregnant women

Answer 422

Currently focus on: vaccines inducing 'broadly neutralising antibodies' - self-assembling nanoparticles and mRNA. Also engineered virus vaccines which induce cytotoxic T cells Problems: high mutation rate (60x higher than flu), 'humoral' immunity may not be protective, need to induce cytotoxic T cells 9 vaccine trials to date - only one (RV144) showed protection (31%) - a combination of two vaccines that didn't work

Answer 423

Combination therapy: - cocktail of drugs directed at different viral targets e.g. AZT (nucleoside analogue), inhibitors of reverse transcriptase, HIV protease inhibitors, fusion inhibitors, capsid inhibitors. > 25 licenced drugs which block HIV replication Preventative drugs: twice yearly injections of Lenecapavir (multistage HIV-1 capsid inhibitor with long half-life)

Answer 424

- high mutation rate - toxicity - viral latency - cost

Answer 425

At end of 2019: 67% of HIV +ve people had antiretroviral therapy and 59% had suppression of virus 2020 - drop in new people starting treatment e.g. due to COVID 2025 - US cuts funding to science and aid

Answer 426

Stem cell therapy (bone marrow cells lacking CCR5) "Kick and kill - reactivate latent virus and immunotherapy Passive immunisation - using monoclonal antibodies or engineered T cells Gene editing with CRISPR/Cas9 Engineered T cell receptors recognising reservoirs of infected CD4+ve T cells

Microbiology Flashcards

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