Microbiology Flashcards
What are stromatolites?
3.5 billion years ago -> sediments alternating layers of limestone and bacterial communities formed.
4 theories explaining the origin of life:
Chemical origin, RNA world, The apparition of a cellular life, Panspermia
RNA world hypothesis:
RNA could have been the first macromolecule encoding complex information.
RNA world hypothesis: Evidence
-4 building blocks
- Requires less energy than DNA to form and degrade
-Uracil formed in early biochemical pathways
-Some viruses use ssRNA
-Some RNA molecules have catalytic activities.
What are the activities of ribozymes?
-Cleavage/ligation of RNA molecules
-Replication
-Formation of peptide bonds to form RNA
Purpose of compartmentalisation:
-Protection from the environment
-Selective Barrier
-Controls concentrations for molecules.
How would compartmentalisation lead to the formation of LUCA?
The spontaneous formation of protocells by phospholipids would trap amino acids and nucleic acids being trapped. Either surface or sub surface origin
What is LUCA?
The last universal common ancestor
Surface origin of compartmentalisation:
Primitive cells formed spontaneously in prebiotic soup.
Sub-Surface origin of compartmentalisation:
Life originated in hydrothermal mounds.
H2 and H2S sued as source of electrons to form organic molecules. Redox and pH gradients used a prebiotic proton motive force to move synthesised components up the mound.
Panspermia:
Life comes from space -> waves of viruses from space drive evolution
Panspermia:
Life comes from space -> waves of viruses from space drive evolution
Microbes -> definition:
Generic term including all microorganisms.
Why are bacteria more susceptible to mutation?
They are haploid, and-so only have one copy of a gene.
What are the mechanisms by which bacteria transfer and acquire new DNA molecules?
Transformation, conjugation, transduction
What is taxonomy?
The study of the classification of organisms
What is the order of hierarchy of classification?
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
Binomial nomenclature:
Genus capital letter. species
What are the phenotypic analytical methods used to determine taxonomy?
-Morphology/ differential staining
-Metabolic Properties
-Phage typing
-Fatty acid profiles
-Mass spectrometry
Taxonomy: Metabolic Properties Analysis
Selective incubation tubes track growth of inoculation and pH using indicators. Results compared to a reference library.
Taxonomy: Phage typing
Unknown Bacteria exposed to known phages -> observe which it’s resistant to -> compare to reference library.
Taxonomy: Fatty acid profiles
Bacterial culture -> fatty acids extracted -> form methyl esters -> gas chromatography -> mass spec -> compare with database
-Compares membrane composition.
What are the genotypic analytical methods used to determine taxonomy?
-DNA/ DNA hybridisation
-Fluorescence In Situ Hybridisation (FISH)
-rDNA (16S) sequencing– Multi Locus Sequence Typing (MLST) / fingerprinting
-Genome sequencing
Taxonomy: DNA/ DNA hybridisation
2 genomes -> one labelled -> hydbridised -> amount of duplex genes observed
Taxonomy: Fluorescence in SItu Hybridisation
Fluorescent tags/probes attach to DNA -> allows for observation of the presence of specific sequences.
Requires heavy microscope usage.
Taxonomy: rDNA (16S) sequencing
Most organisms share rDNA (16S) -> variation can provide information on the closeness of relation between organisms.
Taxonomy: Multi Locus Sequence Typing (MLST) / fingerprinting
Establishes a “bar code” for loci of a sequence -> this is then compared to databases.
Taxonomy: Whole genome sequencing
-Most powerful technique but requires specialised equipment.
What is phylogeny?
The study of the evolutionary history of organisms.
How is phylogeny studied?
-Evolutionary relationships are measured by comparing DNA -> “molecular clocks” -> sequences encoding conserved proteins -> random + neutral mutations
What are the two types of cladograms? (Phylogenetic trees)
Rooted trees + unrooted tree.
Archaea:
-Prokaryotic
-Membrane composed of branched carbon chains
-Methionine start amino acid
-No antibiotic sensitivity
-Lacks rRNA loop
-Lacks common arm of tRNA
Eukarya:
-Eukaryotic
-Membrane composed of straight carbon chains
-Methionine start amino acid
-No antibiotic sensitivity
-No rRNA loop
-Common tRNA loop
Bacteria:
-Prokaryotic
-Membrane composed of straight carbon chains
-Formylmethionine start amino acid
- antibiotic sensitivity
- rRNA loop
-Common tRNA loop
Key components of a eukaryotic cell:
Nucleus, Endoplasmic Reticulum, Golgi complex, Lysosomes, mitochondria, chloroplasts. flagella/cilia
Key components of a prokaryotic cell:
Nucleoid, cytoplasm, envelope, appendages
Prokaryote: nucleoid
-Single, circular chromosome
-DNA complexed with histone-like proteins
-Genetic material also in plasmids
Prokaryotes: organelles
Some prokaryotes contain organelles -> photosynthetic bacteria.
Prokaryotes: Appendages
Pilus: extension used for conjunction
Fimbriae: involved in adhesion to surfaces
Flagella: Supramolecular assembly involved in motility (cell can have multiple) (anchored to cytoplasmic membrane) (rotate in response to ATP hydrolysis couple reaction)
What is endosymbiotic origin of eukaryote organelles?
-The stable incorporation of endosymbiotic bacteria resulted in the formation of mitochondria and chloroplasts.
When did the nucleus structure develop?
Before the acquisition of mitochondria and chloroplasts.
Evidence supporting endosymbiotic theory:
Mitochondria and chloroplasts contain their own DNA and ribosomes. They have a inner and outer membrane.
Problem with endosymbiosis theory:
Doesn’t account for the similar lipid composition of eukaryote and prokaryotes.
types of unicellular eukaryotes:
Fungi, Protozoa, Unicellular algae, slime moles
Which types of unicellular eukaryotes are protists?
Unicellular algae, protozoa, and slime molds.
Human impacts of fungi:
Ecological Role: Contribute to carbon cycle (decomposers)
Economic Role: 10-30% crops spoiled + key role in biotech
Human Health:>1.5mil deaths assosciated
Common properties of fungi:
Morphology: Form multicellular hyphae and are pleiomorphic
Cell Walls: Carbohydrates, chitin, mannans, or glucans
Life Cycle: 2 phases, asexual and sexual reproduction -> form spores -> alternate between diploid/haploid phases
Where does nutrient absorption and growth occur on a hyphae?
The tip
What are the 3 types of fungi?
Molds, Yeasts, and Basidiomycetes (mushrooms)
Symbiotic relationship between Basidiomycetes and plant roots?
Help plants obtain mineral nutrients from the soil in return for sugars produced by photosynthesis.
Human impact of Yeast:
Economic: S.cerevisiae used in brewery + bakery
Human Health: Some S.cerevisiae strains are probiotics + used to model cellular processes.
Cryptococcus and candida cause infections
Yeast cell lifecycle:
Alternate between haploid gametes and diploid cells. Both can replicate by mitosis.
What are the 3 types of unicellular algae?
Primary endosymbiotic algae, secondary endosymbiotic algae (diatoms), Predatory algae (dinoflagellates)
Secondary endosymbiosis:
A cell engulfs a primary endosymbiont (cell that has engulfed another cell)
Ecological importance of Algae:
-Compoonents of phytoplankton, produce half the atmosphere’s oxygen, key food item in ocean food web and aquaculture (zooplankton eat phytoplankton)
Key properties of algae;
-Photosynthetic organisms
-Have chloroplasts like plants but diatoms have a more diverse metabolism.
Primary endosymbiotic algae can be used to model what?
Photosynthesis, motility, cell cycle, and oxidative stress
What do primary endosymbiotic algae contain?
-Chloroplast (without phycoerythrin)
-Pyrenoid to stock bicarbonate (HCO3-) that can converted to Co2
-a contractile vacuole for osmoregulation
-A hydroxyproline-rich glycoprotein cell wall.
Life cycle of primary endosymbiotic algae:
-Mostly found as haploid dividing by binary fission
-Haploid cells from opposite mating types fuse to form a zygote which loses flagella and grows protective coat.
-Zygote undergoes meiosis and regenerates haploid cells.
Example of unicellular primary endosymbiotic algae with a colonial lifestyle:
Volvox carteri
Which is more complex: the chloroplast structure in diatoms or plants?
The chloroplast structure in diatoms
Name of the cell wall surrounding diatoms?
Frustule
What are the three types of Secondary endosymbiotic algae?
Coccolithophores, Centric diatoms, and Pennate diatoms
Why do diatoms undergo an unusual form of cell division?
Their rigid frustules prevent ordinary division.
Centric Diatoms:
Diatoms with a frustule expressing radial symmetry.
Pennate diatoms:
Diatoms with a frustule expressing bilateral symmetry.
What are frustules made of?
Silica (Crosslinked silicon oxide)
Diatom reproduction:
Usual meiosis however:
Initially mitosis takes place and the Frustule is made of two valves and-so during first division one half is inherited and will synthesise a 2nd valve. This is followed by meiosis and and generation of gametes -> conjugation of a zygote -> formation of auxospore.
What is a household use for diatoms?
Natural treatment against fleas and red-mites
Coccolithophores:
Frustules of calcium carbonates -> growing multiple “scales” -> play key role in carbon cycle.
Why are protozoa classification controversial?
Protozoa are difficult so classify
What are the two major groups of Protozoa?
Alveolates and other parasitic protozoa.
What are the three types of alveolates?
Ciliates (predatory protists), Apicocomplexans (parasites), Dinoflagellates (Predatory algae)
What are the two types of “other parasitic protozoa”?
Metamonads (symbionts or parasites) and Trypanosomes (parasites)
Key properties of alveolates:
Contain alveoli - (Cytoplasmic fluid sacs unknown role)
Motile organisms - (Cilia)
Mostly aquatic
Ecological importance of Alveolates:
-Play a major role in food web (zooplankton)
-Apicomplexans (e.g malaria)
-Dinoflagellates key role in carbon cycle
Protozoa: Ciliate Structure
-Contain alveoli
-Cilia + trichocyst (protrusible filamets)
-Contractile vacuole
-Digestive vacuoles
-3 nuclei -(2 micro + 1 macro)
-Oral groove
Function of trichocysts:
Protrusible filament bags that “Sting” prey using toxins
Two types of ciliate reproduction:
Asexual binary fission or sexual reproduction (conjugation)
Ciliate binary fusion:
Micronuclei – diploid – transcriptionally inactive – germline – copy of genome to be passed on – aren’t used for transcription
Macronuclei – result from the duplication of micronuclei -> transcriptionally active – few hundreds-thousands copies of genome.
Ciliate conjugation:
Conjugation: requires an established physical contact -> macronuclei disintegrate and micronuclei duplicate -> two rounds of division -> 4 micronuclei -> undergo meiosis and become haploid -> exchange genetic material of the recombinants -> parent cells split -> undergo 3 successive nuclei divisions and then 2 mitotic divisions.
Apicocomplexans: Summary
-Spore-forming parasitic protozoans (without flagella, cilia, or pseudopods.
-Contains apicoplast (degenerate chloroplast carrying out fatty acid metabolism
-Obligate endoparasites
Examples of diseases caused by Apicocomplexans:
-malaria
-Crytosporidiosis
-Toxoplasmosis
Apicocomplex: life cycle
Infection sporozoites -> target cell -> multiply to form a schizont -> ruptures and releases merozoites -> invade cells before differentiate into gametes -> in host/vector gametes fuse to form resistant zygote -> meiosis to produce sporozoites
Dinoflagellates:
-Mobile predatory photosynthetic aquatic mixotrophs: use sources of energy that aren’t light or carbon sources
- involved in complex symbiotic or parasitic interactions.
What is meant by mixotroph?
mixotroph: use sources of energy that aren’t light or carbon sources
Dinoflagellate: Structure
-2 flagella (one wrapped around cell)
- Chloroplast with triple membrane
-“Cell wall” made of cellulose plates (thecae)
-Contain extrusomes
Dinoflagellates: life cycle
Very little known
Undergoes binary fission and sexual reproduction
Can form resistant “spore” (hypnozygote cyst)
“Other Parasitic Protozoa”:
-Mobile parasites causing common human disease
-Mostly harmful but sometimes symbionts (metamonds)
- Can be transmitted by vectors and direct contact
Three examples of metamondads:
Trypanosoma, Mixotricha paradoxa, and Giardia lamblia
Giardia Lamblia:
-Metamonad paraiste that causes diarrhea.
-Contains 2 nuclei
-Adheres to epithelial cells using ventral adhesive disk
-Divide by binary fission and form cysts when condition are unfavourable
Mixotricha paradoxa:
-Metamonad
-Found in gut of specific termite species
-Symbiont with other bacteria and the termite
-Important for metabolism
-Very large and can be seen with naked eye
Trypanosoma:
Parasitic Metamonad
-transmitted by fly vector
-2 successive phases of disease -> fever, headaches, inflammation -> invades CNS -> disrupts sleep
What do slime molds share morphology with?
Amoebas
Pseudopod mobility:
extensions formed by actin polymerisation/dissassembly which pushes the membrane and cell across a surface. These cna also be used during engulfment.
Are all amoeba shapeless?
No, some are shelled
What kind of diseases are amoeba often the cause of?
Water-borne diseases.
Example of a cellular sime mold:
Dictyostelium discoideum
Example of a plamsodial silme mold:
Physarum polycephalum
Dictyostelium discoideum:
-Cellular slime mold.
-Grows as an amoeboid unicellular organism that divides by binary fission
-Forms a “slug” through social mobility -> to move to favourable conditions.
-Slug forms fruiting body which releases cysts.
Physarum polycephalum:
-Grows and dives by binary fission as an amoeboid single cell.
-Lives as one large singular cell -> smaller amoeba like cells aggregate and fuse cytoplasm to form plasmodium. -> differentiates into fruiting body -> cysts released.
-
What are the two types of slime mold?
Plasmodial and cellular
Difference between cellular and plasmodial slime molds:
Plasmodial -> cytoplasms of smaller cells fuse to produce plasmodium
Cellular -> cells remain separate and move via social mobility.
What are the major components of viral particles
Nucleic acid genome, capsid, facultative lipid membrane.
What are the 5 stages of the viral life cycle?
Attachment, Genome injection, Production of nucleic acid and proteins, Maturation (assembly), release
What is the difference between lytic and temperate bacteriophages?
Temperate phages can enter the lysogenic cycle and can integrate with the host DNA and remain dormant -> replicating during cell divisions. This DNA can be excised from the host’s genome and initiate the lytic cycle.
What are viruses?
Oligatory parasites that hijack host metabolic machineries to replicates.
Size of virusal genome:
2-20kb
Viral genome fragmentation:
Genome can be split into multiple specialised fragments.
What proteins make up capsids?
Capsomers
What are the two types of symmetry capsids can expresss?
Icosahedral + helical symetry.
What is the role of the viral envelope?
To allow entry into a host cell via fusion/endocytosis
More complex viruses e.g bacteriophages contain multiple what?
Capsids -> e.g icosahedral head and helical tail fibres -> aids attachment to a cell by probing cell surface and form interactions -> allows injection of genome.
Example of a complex virus that effects humans?
Poxyviridae (small pox)
What does the balitmore classification of viruses consider?
-Nature of genome (DNA or RNA)
-The type of RNA/DNA (ds, ss, and polarity)
-The genome replication mechanism
Which groups of viruses are DNA viruses?
1,2, and 7
Which groups of viruses are RNA viruses?
3,4,5, and 6
Virus class 1,7: Genome replication
ds DNA viruses.
Class 1 - classical semi conservative
Class 7 - transcription followd by reverse transcription
Virus class 2: Genome replication
ssDNA (+) virus
Classical semiconservative -> discard -ve strand. forms dsDNA intermediate before transcription of -ve strand.
Virus class 3: Genome replication
dsRNA virus
Makes ssRNA (+) from dsRNA -> transcribed to give ssRNA(-) which is then translated
Virus class 4:Genome replication
ssRNA (+) virus:
makes ssRNA (-) and transcribes from this to give ssRNA(+) genome.
Virus class 5: Genome replication
ssRNA (-) virus:
makes ssRNA (+) and transcribes from this to give ssRNA(-) genome.
Virus Class 6:Genome replication
ssRNA (+) Retrovirus:
Makes ssRNA (+) genome by transcription of (-) strand of dsDNA (synthesised from rev.transription)
Papilomavirus:
dsDNA class 1 virus: HPV16
No envelope.
5.3-8.kb
19 million new cancer cases (2020)
Causes 2% of cancers in UK
90% of cervical, 85-90% of vulvar, 95% vaginal HPV related cancer in women, 90% HPV related anal cancers in men and women.
Adeno-associated virus
Harmless ssDNA class 2 virus
Reovirus:
dsRNA class 3 virus:
rarely fatal but associated with economic burden.
Rotavirus vaccine protects against 90% of strains.
Foot-and-mouth disease virus:
(+) ssRNA class 4 virus:
2001 outbreak -> 2000 cases across UK -> 4-10mil sheep and cattle killed.
-Cost >3bn to public sector and >5bn to private sector.
Influenza virus:
(-) ssRNA class 5 virus:
infected 500mil people across the world and killed 3-5% of the world’s population (1918-1920)
HIV:
class 6 retrovirus (RNA):
-Associated with cancer
-Causes AIDS - progressive failure of immune system
-Following loss of immunity body becomes susceptible to opportunistic viruses
-78miilion people infected, 39mil have died, 37mil living with HIV
Hepatitis B virus:
reverse DNA class 7 virus:
-Causes cirrhosis and liver cancer
What is cirrhosis:
Live damage (degeneration) and scarring
Are all viruses enveloped?
No.
Advantages of the small size of bacteria:
Largers SA:V -> nutrient exchange and grow rate, > Intracellular nutrient conc, rapid evolution due to high selection of mutations.
Bacteria-specific genetic properties: (transcription)
-Transcription occurs in cytoplasm.
-1 RNA pol in prokaryotes (3 in eukaryotes)
-No splicing
-Eukaryotes terminate at AAUAAA seq rather than GC dense region.
What are the most common morphology types for bacteria?
cocci, rods, curved, spiral, and exotic.
Can morphology change during a bacterial cell cycle?
Yes
Phenotypic diversity of bacteria:
Size, Pigmentation, Smell
Bacteria smell example:
-contribute to human odour -> degradation of apocrine secretion products
Gram stain method:
Stained with crystal violet -> this is then fixed to positive bacteria by iodine -> the culture is washed (alcohol) and then a safranin counterstain is used + attaches to gram -ve bacteria.
Gram +ve bacteria;
Have no outer membrane and a thick cell wall
Gram -ve bacteria:
Have an outer membrane and a thin cell wall.
Do exceptions to gram+ve/-ve staining exist?
Yes, e.g mycobacteria
What is the bacteria s-layer?
Layer of facultative structures non covalently bound to the cell wall (Gram +) or surface membrane (Gram -). Made from proteinaceous crystalline arrays;
Bacterial capsules:
Most made from polysaccharides.
Some are made from amino-acids.
Covalently bound onto the cell wall or outer membrane.
-confer resistance to phagocytes and bacteriophages.
Bacterial exoploysaccharides:
homo/heteropolysaccharides. -> non covalently attached to cell surface. -> important for biofilm formations, some are used commercially in toothpaste, ice creams etc.
Key components of gram - membranes:
Phospholipids, proteins, lipoproteins, bacterial liposaccharides (LPS).
Outer membrane interacts with peptidoglycan cell wall.
Integrity provided by anchor proteins.
Bacterial anatomy: peptidoglycan (murein)
Elastic 3D network part of a subcellular compartment. Dynamically regulates exchange with the environment. Forms cell wall (heterogenous structure like a sponge)
Determines cell shape and acts as a scaffold for polymers and proteins.
Composition of peptidoglycan:
Glycan chains alternating N-acetylglucosamine (G) and N-acetylmuramic-acid (M), substituted by short peptides (L- and D-amino acids)
Key components of the cytoplasmic membrane of a bacteria cell:
-Phospholipids, hopanoids (equiv. sterols in eukaryotes), proteins (transporters, sensors, etc.)
Role of hopanoids in bacteria cytoplasmic membrane:
Modulate membrane fluidity and permeability. (similar to cholesterol)
Bacterial chromosome:
-Always made of dsDNA
-Singular circular chromosome
-Variable size 0.5-14.8Mbp
-chromosome organised as a nucleoid -> supercoiled around histone-like proteins
Bacterial Plasmid DNA:
-ds DNA, usually circular
-2-600kbp
-can transfer between bacteria
-carry resistance genes
-can have multiple copies within one cell.
Bacterial gene structure:
-No introns -> continuous open reading frame -> don’t req. splicing
-Use operons to control transcription
Gene expression of Bacteria: transcription initiation
-The RNA polymerase (a2bb’sw) scans
DNA forming a loose complex
- sigma factor binds to a two specific
sequences upstream of start codon
-DNA is unwound, allowing for the formation of an “open complex” -> transcription starts -> sigma factor released.
Gene expression of Bacteria: transcription termination (rho independent)
-Palindromic GC-rich region upstream of an AT-rich sequence.
-Once G-C rich region is transcribed -> hairpin structure forms -> causes RNA poly. to fall apart.
Gene expression of Bacteria: transcription termination (rho dependent)
-Rho proteins recognise and bind to 72 residues GC-rich
-RNA-dependent ATPase activity of Rho protein -> wraps around downstream RNA -> once reaches the polymerase Rho unwinds the RNA-DNA duplex and releases RNA polymerase.
What is translation in prokaryotes coupled with?
Transcription
Bacteria-specific genetic properties: (translation)
-Prokaryotes have 70S ribosomes (Eu have 80S), and bind more productively to mRNA in presence of tRNA.
-40S subunit guided by 5’ mRNA cap
-30S subunit recognise Shine-Dalgarno sequence.
(Eukaryotic translation is inhibited by cycloheximide)
What is the shine-Dalgarno sequence?
AGGAGG -> only in prokaryotes -> helps ribosome bind to mRNA -> initiate protein synthesis
What are the two types of energy sources for bacteria?
Sunlight (photo) or preformed molecules (chemo)
What are the two types of electron sources for bacteria?
Organic (organo), inorganic (Litho)
What are the two types of carbon sources for bacteria?
Organic compound (Heterotroph), Inorganic compounds (Autotroph)
What are the 5 parameters important for bacterial growth?
Temperature, pH, Osmotic temperature, Nutrients, Oxygen requirements
What are the different methods used to measure bacterial growyh?
What are the different classes of microorganisms (Classed by temp. required for optimum growth):
Psychrophiles, Mesophile, Thermophile, Extreme Thermophile
Psychrophiles: Membranes
Microorganisms adapted to cold temperatures -> have a higher content of unsaturated, polyunsaturated, methyl-branched fatty acids -> increase membrane fluidity.
Psychrophiles: Synthesis
Synthesise anti-freeze proteins, cryoprotectants, and cold adapted enzymes (more alpha helices + less weak bonds -> more flexible).
Thermophiles: Genome protection
-Stabilise DNA using DNA binding proteins.
-Introduce supercoils using reverse DNA gyrases
-High G-C% -> increased res to denaturation
Thermophiles: Membrane
Esther-linked phospholipids (less prone to reactions and alterations) and single lipid layer (glycerol tetraethers bind leaflets)
Thermophiles: Synthesis
-Production of thermostable proteins, with increase hydrophobic and ionic interactions.
-thermostable chaperonins restore fold to damaged enzymes.
What are the metabolic adaptations of acidophiles?
Respiratory chain pumps h+ out of cell. Use H+ symports to let in solutes. K+/H+ antiporters excrete protons.
-Metabolism mostly reliant on proton gradient.
What are the metabolic adaptations of alkaliphiles?
Most transport reactions don’t utilise protons but instead use metal ions (sodium)
ATP is synthesised using Na+ rather than protons.
Alkaline environments often have high salt content -> hence intake of salt to maintain osmotic grad.
The classifications of microorganisms (when classified by resistance to osmotic pressure)
Nonhalophile, Halotolerant, Halophile, Extreme Halophile
Example of a non-halophile:
E.coli
Why do halophiles require salt?
Stabilization of the S-layer glyco-protein by Na+ ions
Accumulation of K+ as a compatible solute (>4M in the cell!)
-> Maintain the integrity of the cell surface membrane -> use counter salt to balance wp balance.
How do microorganisms that have adequately adapted respond to osmotic stress?
They regulate water movements by passive diffusion and aquaporins.
What are the the toxic forms of oxygen known as?
Reactive Oxygen Species
What are the different reactive oxygen species?
Superoxide, Hydrogen Peroxide Hydroxyl Radical
What enzyme breaks down hydrogen peroxide?
Catalase/peroxidase (breaks down H2O2 into H2O)
What combinations of enzymes can be used to detoxify superoxide:
Superoxide dismutase/reductase + catalase
What are the classification of microorganisms (When classified by oxygen requirements):
Obligate aerobes, Facultative aerobes, Microaerophiles, Anaerobes aerotolerant, obligate anaerobes.
Obligate aerobes:
Use O2 exclusively for respiration
Have catalase and SOD enzymes
Facultative aerobes:
Can use O2 to respire.
Have catalase and SOD enzymes
Microaerophiles:
Require O2 for respiration
Anaerobes aerotolerant:
Do not use O2 for respiration
Only has SOD enzymes
What are the two ways to measure bacterial growth?
Direct and indirect measurements.
What are the direct ways to measure bacterial growth?
Microscopic counts, Flow cytometry and viable counting.
Microscopic counts:
Microscopic counts – count the number of cells and compare to the number in the original suspension. (Petroff-hauser cell counter)
Viable counting:
Viable counting - Start with a cell suspension and use serial dilution -> doesn’t demonstrate number of cellular entities but rather identical colonies.
Flow cytometry:
Flow cytometry – Capillary with suspension in – laser used to count number of cells by the effect of density on light scattering.
What are the indirect methods of measuring bacterial growth?
Optical density, dry weight, and metabolic activity
Optical density (as a means of measuring bacterial growth):
-Measures light not scattered by cells
-Optical density values vary by organism
-Doesn’t work with filamentous bacteria
-Requires high cell densities (>10^7 cell/ml)
What are the 4 phase of the bacterial growth curve?
Lag phase, log phase, stationary phase, deathn phase.
What are the 2 major phyla of archaea:
Euryarcheota + Crenarcheaota
What microorganism classification are most archaea part of?
Extremeophiles
Components of Archaeal ultrastructure:
S-layer,
Cell wall (pseudomurein),
Unusual cell envelope structures, Cytoplasmic membrane
Archaeal Cell wall:
-not always present
-Made from pseudomurein (similar to bacterial peptidoglycan)
-Heteropolymer (disaccharide-peptides)
-Resistant to lysozymes and most antibiotics
Archaeal Cytoplasmic membrane:
-Phospholipids contain no fatty acid -> contain isoprenes
-Phospholipids ether linked (not ester linked)
-More stable -> as present as mixture of mono and bilayers,
Notable unusual Archaeal cell envelope structures:
Archaellum, cannulae, and hooks
Chromosome organisation and replication of Archaeal cells:
-Circular chromosome (+plasmids)
-Circular chromosome wrapped around histones
-Has multiple origins of replication
-Encodes polymerases B (Found in eukarya) and D (Specific to Archea)
Transcription and RNA processing of Archaeal cells:
-> has a single RNA polymerase -> similar to eukaryotic RNA polymerase 2
-DNA has introns
-Genes organised within operons
Translation in Archaeal cells:
-Coupled to transcription (Like prokaryotes)
-Involves translation factors (like eukarya)
-Ribosomes are 70S (Like prokaryotes)
Hyperthermothiles:
Two groups: Crenarchaeota and Euyarchaeota
-High growth temp 80-120’c
-Require elemental sulfur for growth
-Often acidophiles
Ex. Acidanus infenus:
Crenarchaeota (hyperthermophile):
Facultative aerobe
-optimal growth 75’C pH 2.5-3
Industry role of sulfate-reducing archaea:
They have a negative impact on the oild industry -> increase sulfur emissions, cost of refining oil, and attak metal in well casings and pipelines.
Where are halophiles often found?
Evaporating ponds, dead sea, great salt lake
Methanogens:
Type of Euyarcheaota
-Found in anaerobic env.
-Use acetate as electron acceptor in respiration.
Chemoorganotrophy:
Reduced organic molecules (e.g sugars) are broken down and used as an energy source
Chemolithotrophy:
Reduced inorganic molecules (geological compounds) are broken down and used as an energy source.
Phototrophy:
Sunlight is used as an energy source.
What are used as electron donors by chemoorganotrophic, chemolithotrophic, and phototrophic microorgansims?
Organic molecules, inorganic molecules, and light energy (used to reduce compounds which then act as electron donors)
Free energy change of electron movement:
Delta Gibbs = -1 x number of e- transferred x Faraday constant x Redox potentail change
Metabolic diversity in prokaryotes: electron transfer systems:
NADH, NADHPH, and FADH2 electron acceptors/donors -> pump H+ out of cell -> create PMF to drive synthesis of ATP
What are teh 3 metabolic types undergone by Chemoorganotrophs?
-Oxygenic respiration
-Anaerobic respiration
-Fermentation
Chemoorganotrophs: Oxygenic respiration
Glycolysis -> link reaction -> TCA cycle -> Electron transfer chain -> ATP synthesis
Chemoorganotrophs: Anaerobic respiration
-Wide range of inorganic compounds can be used as electron acceptors
-ETC occurs by cytochromes, quinones, and iron-sulfur proteins
-Depending on redox potential of acceptor -> distinct amounts of energy generated.
Anoxygenic respiration:
Method using oxygen to expolit wide range of ecological niches.
Two key types of chemoorganotrophic anaerobic respiration:
Denitrification + methanogenesis (can also be used by chemolithotrophs)
Difference between anaerobic respiration and fermentation:
Anaerobic uses any molecules (Except O2) as terminal electron acceptors via membran bound resp. chain.
-ATP produced by oxidative phos. via PMF
Fermentation uses organic molecules as electron acceptors -> no resp chain -> ATP produced by substrate-level phos. in the cytoplasm.
Major Types of lithotrophy:
Hydrogenotrophy, (Sulfate reudction + Methanogenesis), Iron oxidation, Ammonia oxidation, Nitrification, Anammox, Sulfide oxidisation and sulfur oxidation.
Important properties of chemolithotrophs:
-most use CO2 as carbon source to produce organic molecules
-Can also use complex molecules like acetate
-Use NADH to “fix carbon” -> requires H+ to reverse electron flow process.
Iron oxidisation: Chemolithotrophy
Reduced Fe2+ can be oxidised into Fe3+ at low pH -> can form insoluble Fe3+ ferrix hydroxide at even lower pH.
Use of acid-producing microbes in biomining:
Acidothibacillus ferroxidans -> oxidise sulfide of Fe and Cu -> oxidisation of Cu+ and acid production dissolves the metal from the rocks.
What are the two types of Phototrophy?
Oxygenic photosynthesis (cyanobacteria and plants) + Anoxygenic photosynthesis (bacteriorhodopsin, Green sulfur bacteria, purple bacteria)
What photosystems are used by oxygenic photosynthesis?
PS1 and 2
What photosystems are used by anoxygenic photosynthesis?
BR, PS1, PS2
What is Bacteriorhodopsin?
-Abundant light-driven proton pump in archaeal membranes
-Contains a retinal pigment that undergoes conformation (trans->cis) change once excited by light
-The movement of protons generated PMF for ATP synthesis.
Mechanism of BR (bacteriorhodopsin):
Retinal pigment excited -> (cis -> trans) -> transfeer of proton to Asp85 -> deprotonates retinal pushes against helix F, opening a channel -> induced deprotonation of retinal from Asp96 -> Asp96 is reprotonated -> Asp85 transfer proton outside through H-bonding via water.
Do cyanobacteria have chloroplasts?
No they are primitive chloroplasts.
-Either no thylakoids or they are organised with wide range of architecture
What are the pigments used by cyanobacteria?
Chlorophylls, carotenoids, bilins
Oxygenic photosynthesis of cyanobacteria:
-Both photosytems excited by light -> energy used to strip e- from H2O -> protons pumped outside cell -> PMF ATP synthesis -> NADPH and ATP fix CO2 -> glucogenesis
How are electrons excited in photosystem 1? (green sulfur bacteria)
Light is captured by antenna complexes (chlorosomes) and photon energy is directed at the PS1 reaction centre.
Anoxygenic photosynthesis: (Green sulfur bacteria)
PS1 donates e- to ETC -> ETC pumps protons + reduce NADP+ via ferredoxin -> PMF used to generate ATP -> PS1 recieves electrons from sulfur derivatives.
How are electrons excited in photosystem 2? (purple sulfur bacteria)
Light is captured by antenna complexes (chromatophores) and photon energy is directed to the PS2 reaction centre.
Anoxygenic photosynthesis: (Purple bacteria)
-PS2 donates electront to cyclic ETC
-ETC proton pumps establish PMF
-NADH cannot be produced -> lack of transporter with reducing potential
-Inorganic compounds used as electron donors to produce NDAPH
Mutualism:
Both organisms benefit from the interaction
Commensalism:
The microbes benefit from the interaction but with no impact on the host
Parasitism/Predation/Competition
The microbes benefits from the interaction at the expense of the host
Ectosymbiosis:
Symbiont living on the surface of host cells, e.g Mixotricha Paradoxa
Endosymbiosis:
Symbiont living inside host cells, e.g associations in Hemiptern insects -> bacteriocytes which can aggregate to form bacteriosomes
Parasites: intracellular bacteria: example
Legionella pneumophila -> found in fresh water -> parasite of amoeba that can also replicate within alveolar macrophages
Parasites: bacterial predators: example
Bdellovibrio bacteriovorus: attacks gram - bacteria -> invades perisplasm (cell wall) -> feeds on host cell
Plant nodulation as an example of symbiosis:
Nodulation, legumes, and Rhizobia
Rhizobia:
-Alphaproteobacteria (gram -) -> soil dwelling bacteria part of the “rhizosphere” -> induce nodulation
Nodulation:
Rhizobia induce the formation of root nodules that allow plants to fix atmospheric N2
Difference between an organelle and an endosymbiont?
Organelles are usually widely conserved accross a range of organisms.
What are the 3 physical methods that can be used to eradicate bacteria?
Heat, Irradiation, Filtration.
What is the difference between bactericidal and bacteriostatic agents?
Bacteriostatic control prevents further growth in the number of cells and viable cells, whereas bactericidal control maintains the number of cells but DECREASES the viable cell count.
Using heat as a physical antimicrobial control:
-Autoclave (15min 121’C), dry heat (oven >150’C 2hours), pasteurization (Mild heat/ HTST 72’C 15s/ UHT140’c 2-5s)
Using irradiation as a physical antimicrobial control:
ionising (food industry + lab equip) and non-ionsing (surface decontamination) (DNA damage, oxidative stress)
Using filtration as physical antimicrobial control:
Use of specific pore sizes to exclude microorganisms.
Thermal death point:
Minimal temp. at which all organisms are killed in 10min in a particular liquid
Thermal death time:
Minimal time required to kill all bacteria in a particular liquid at a given temperature.
Sterilants:
Completely eliminate or destroy all forms of microorganisms (including spores) - e.g ethylene oxide
Disenfectants:
Kill microorganisms, but not necessarily endospores -> e.g alcohols (dentatures proteins + is a lipid solvent disrupting cytoplasmic membranes)
Antiseptics + germicides:
Inhibit growth or kill microorganisms -> e.g handwash
The 3 methods for measuring antimicrobial activity:
Disc diffusion technique, Minimum inihibtory Concentration (MIC), Minimum bactericidal concentration (MBC)
What is the Minimum Bactericidal concentration?
The lowest concentration of a drug killing 99.9< of a test organism after overnight incubation
What is the Minimum inhibitory concentration?
The lowest concentration of a drug inhibitng the visible growth of a test organism after overnight incubation.
Disc diffusion technique:
Add microbial disks to culture of test organism -> incubate for 24-28 hours -> test organism shows susceptibility to some agents -> areas of inhibition.
Phenolic compounds (1867):
Aromatic derivatives -> can be used as local anesthetic at low conc. -> antibacterial (but toxic) at high conc. -> disrupts cytoplasmic membranes and denatures proteins.
Aldehydes:
Alkylating agents: modify proteins and DNA -> causing cell death
Quaternary ammonium compounds:
Interact with phospholipids of the cytoplasmic membrane (cationic detergents)
Halogen releasing agents:
2 types: chlorine/iodine-releasing.
Chlorine: Na hypochlorite (bleach) -> forms chlorinates bases in DNA
Iodine: target DNA and proteins.
Louis Pasteur (1822-1895)
Formally demonstrated the theory of germs
Robert Kock (1843-1910):
Establihes relationship between microbe and disease
Alexander Flemming (1928):
Discovered Penicillin produced by fungus.
What are the two major therapeutic strategies?
Antibiotics and vaccination.
What are the 4 major classes of antibiotics based on modes of action?
-Drug inactivation
-Target modification
-efflux/impermeability
-Bypass
What causes antibiotic resistance?
Overuse of antibiotics and misuse in human therapeutics, farming, agriculture + aquaculture
What are the properties of the ideal antibiotic?
-Display selective toxicity towards bacteria (selective of essential process or inhibit its virulence)
-Stable in host and active at low concentrations
-Cheap
beta-lactam: function
inhibit peptidoglycan polymerisation mediated by D,D-transpeptidases.
-Resist against penicillin
What are beta-lactams?
Structural analogs of D-Ala-D-Ala C-terminal residues in the peptide stem. Used by penicillin binding proteins as substrates and inactivate the enzymes irreversibly.
Mechanism 1: inactivation by beta-lactamases
Nucleophilic attack by catalytic serine -> form a covalent complex penicillin-beta-lactamase -> penicillin hydrolysis.
Mechanism 2: Beta-lactam mutation of target enzyme
Reduction of PBP affinity for beta-lactams + the overexpression of PBP targeted bt Beta-lactams
Mechanism 3: secretion of antibiotics (gram - bacteria)
e.g P. aeruginosa
-Overproduction of MexAB-OprM system -> carbapenem resistance
Overproduction of the MexEF-OprN system -> imipenem resistance
Mechanism 4: Modification of the synthetica pathway targeted by beta-lactams
Modification of pathway causes beta-lactams to become ineffective on target.
Difference between parasites and pathogens?
Pathogens aren’t visible to naked eye.
What type of microorganisms doesn’t adopt pathogenesis?
Archaea
What “non-living” particles can be pathogenic?
Viruses and proteins (prions)
Criteria of a successful pathogen:
-Gain access to host
-Locate nutritionally compatible niche
-Avoid, subvert, or circumvent hist innate and adaptive immune responses.
Innate immune system:
Not specific and rapid. Not improved by repeat infection
Adaptive immune system:
Highly-specific + slower (esp. on first exposure)
Improved by repeat infection (memory)
What are the portals of entry for pathogens into a human?
Conjunctival route (eyes), Aural route (ears), Oral route, Respiratory route (nose), abrasions, wounds, puncture of skin (by insects), injections, Genital tract, Animal bites, Transcutaneous channel
When does infection upon exposure to the pathogen?
Once the host has been exposed to the pathogen past a threshold.
Modes of pathogenic transmission:
Air(droplets), Water, Food, Mechanical/vector
Difference between mechanical and vector?
A vector will have its biology effected by the disease and integral to the life cycle of the pathogen -> a mechanical (fomite) will not have its biology effected
What values determine virulence:
Mortality + Morbidity + infectious Dose
Morbidity:
The number of case of a disease in the population
Mortality:
The number of deaths from notifiable diseases
Why is high virulence not good for pathogens?
High mortality rates reduce spread.
Infectious Dose:
Number of individual particles/cells required for infection
What are virulence factors?
Factors that enable a pathogen to colonise the host -> however don’t cause the disease.
Virulence Factors: Adhesins
Find a niche and colonise host
Virulence Factors: S-layers
Immune evasion/ survival in host
Virulence Factors: Digestive enzymes
Help find a niche, colonising it, and finding host resources. e.g collegenases to breakdown and reach deep into tissues
Virulence Factors: Toxins
Reprogram the host biology to benefit the pathogen
Virulence Factors: “stealth mode”
Absence of outer-surface structures -> immune evasion -> this is an example of reductive evolution.
Worldwide how many deaths is pathogenesis responsible for?
26%
How many deaths were caused by lower respiratory infections in 2019?
2.2million deaths
How many deaths were caused by Diarrhoeal diseases?
1.5 million deaths
How many deaths were caused by Tuberculosis?
1.2millions
How many deaths were caused by HIV/AIDS in 2019?
700,000 people
Robert Kock:
Established link between diseases and microbes.
Pioneered use of pure cultures to understand infectious diseases. (using Bacillus anthracis - Anthrax)
What is Koch’s postulates?
Host + pathogen = Death
What have the main advances in public health been caused by?
Improved sanitation (clean drinking water + waste disposal), less overcrowding, better living conditions, and better diet
What is immunity?
Upon second exposure to the disease’s antigens the subject doesn’t develop the disease.
Small pox vaccination example:
1717 Lady Montagu -> innoculated people using pus of small pox into open vein
1796: Edward jenner innoculated person with cowpox -> protected them from small pox.
What is the term used for when immunity to a pathogen protects the host from a very similar pathogen?
Cross-protection
Who developed the first “antibiotics” of penicillin?
Florey and Chain
What process do penicillins target?
The cell wall synthesis of the pathogen.
What is a symptom?
A change in body function that is felt by the patient as a result of disease.
What is a syndrome?
A specific group of signs and symptoms that accompany a disease.
Some diseases are caused by multiple pathogens: example
Pneumonia -> can be bacterial, viral, and fungal
What is disease state determined by?
The reaction to a pathogen rather than the pathogen itself -> the product of a relationship change/conflict between the host and pathogen
Why are general antibiotics often administered for diseases?
Many different pathogen can be responsible for the disease, and-so general antibiotics will be administered until a pathogen sample is taken,
What is our microbiota?
The range of microorganisms that may be commensal or symbiotic found in and on us.
What effect do our microbiota have on us?
-Aid digestion
-Healthy metabolism
-immune function
-mood and behaviour
-obesity, heart disease + diabetes
C.difficile:
Clostridium difficile -> causes diarrhoea, colonisation and inflammation -> 9% mortality rate
Opportunistic pathogens:
Microbes that aren’t ordinarily pathogenic but can cause infection or disease in a compromised host.
“hospital aquired “ infections:
Infections aquired as a result of hospital stays. E.g C.diff and MRSA
Vibrio Cholerae:
Disease: Cholera
Symptoms: Diarrhoea, pain + vomiting
Virulence: death through dehydration, 1.3-4mill cases + 21-143 thousand deaths
Classification:Gram - bacteria
Major Virulence factors: Cholera toxin
Transmission: Faecal-oral route (via contaminated water)
Treatment: Oral Rehydration + anitbiotics
Vibrio cholerae: Broadstreet pump
1854 cholerqa outbreak -> first historical case of a disease outbreak being methodically investigated.
Principles of epidemiology:
-Identify first patient “patient 0”
-Identify people in contact
-Identify the reservoir for the pathogen
Blocking/containing the pathogen
Epidemic disease:
Disease aquired by many hosts in a given area in a short time
Endemic disease:
Disease constantly present in a population
Pandemic disease:
Worldwide epidemic
Salmonella enterica serovar Typhi:
Disease: Typhoid fever
Symptoms: Rash + others extremely variable
Virulence: 30% mortality rate
Classification: gram -
Major Virulence factors: toxins
Transmission: Faecal-oral route. Human colonised gall bladder
Treatment: Antibiotics or vaccine
Polio Virus:
Disease:Polio
Symptoms: 95% mild
or irreversible paralysis, muscle weakness + deformities
Virulence: 15% symptomatic cases death occurs when breathing muscles immobilised
Classification: - strand RNA virus
Transmission:Faecal-oral route (via water contamination)
Treatment: Vaccine - (attenuated)
Issue with polio vaccine:
In extremely rare cases immunocompromised individuals can become “healthy carriers” and spread disease.
Yersinia pestis:
Disease: Bubonic and Pneumonic plague
Symptoms: Buboes (swollen lymph glands), fever, sepsis, pneumonia
Virulence: Bubonic = 50%
Pneumonic = 90-100% mortality rate
Classification: Gram - bacteria
Major Virulence factors: toxins, V, W, YopB, Yop D (avoid phagocytosis), F1 (makes fleas hungry)
Transmission: Rodents, prairie dogs (rodent fleas) + human respiratory aerosol
Treatment: Antibiotics + vaccine
Zoonotic pathogens:
Pathogens that affects both animals and humans
Why is epizootics important?
Epidemics in animals can be warning signs of potential epidemics.
2017 Madagascar:
Madagascar - Pneumonic plague outbreak -> epizootics used -> reservoir identified -> killed fleas + rodents -> care workes wore PPE + antibiotics -> 8.6% mortality rate
Phytophthora infestans:
Disease: “potato blight”
Symptoms: white mycelium growth over surface of leaves and tubers
Virulence: near 100% of crops
Classification: Spore forming oomycete (water mold)
Transmission: Spores
Treatment: Fungicides = CuSO4
Influenza virus:
Disease: Influenza (flu)
Symptoms: Fever etc.
Virulence: 0.01%-50% -> newer strains have higher case fatality rates
Classification: - ssRNA orthomyxoviridae
Transmission: Droplets
Treatment: Antiviral drugs + vaccine
What are the key enzymes found on the surface of influenza virus?
Hemagglutinin and Neuraminidase.
How can new viruses arise?
The reassortment of two virus strains within a host cell, e.g bird flu + human flu -> swine flu
How many H1N1 death worldwide?
50-100million -> maybe more than black death
10-20% mortality rate.
Zika virus:
Disease: Zika virus disease
Symptoms: mild fever, rash
Virulence: Extremely low (birth defects: microcephaly + Guillain-Barre syndrome)
Classification: + ssRNA virus
Transmission: Vector by Aedes mosquito + STD (by semen)
Treatment:
Microcephaly:
Skull doesn’t grow correctly -> brain doesn’t correctly develop - Medical conditions + disease
Zika Virus Response:
Very fast, epidemiological surveillance took place at the same time as containment.
CDC set up Zika Birth defect surveillance -> found small chance of zika effecting birth. (p = 0.009)
Ebola Virus:
Disease: Ebola Viruse disease + Ebola hemorrhagic fever
Symptoms: fever, headaches, muscle pain, bleeding
Virulence: 40-90% mortality
Classification: - ssRNA filovirus
Transmission: direct contact + maybe sex -> no known reservoir
Treatment: Currently “untreatable”
Ebola 70-70-60 rule:
60 days: 70% of patients in isolation and “treatment” + 70% “safe” burials
What is the biggest challenge in global health?
Antimicrobial resistant (AMR) -> could lead to absence of antibiotics in modern medicine -> increasing dangers of infection
What 3 things make antimicrobial resistance complex?
Antibiotics: each have different target
Bacterial pathogens: Different virulence characteristics and survival strategies
Resistance Mechanisms: Varied and not well understood.
What is immunology?
The study of the immune system
What is the immune system?
Integrated system of cells and molecules that defends against disease.
Leucocytes part of the innate immune system:
Phagocytes, natural killer cells
Leucocytes part of the adaptive immune system:
B and T lymphocytes
Soluble factors involved in the innate immune system:
Lysozymes, complement, inferons
Soluble factors involved in the adaptive immune system:
antibodies
What are leucocytes?
White blood cells
Which stem cell do all blood cells derive from?
Haematopoietic stem cell in bone marrow
Which stem cell do leukocytes part of the innate immune system derive from?
Myeloid stem cell
Which stem cell do leukocytes part of the adaptive immune system derive from?
lymphoid stem cell
External barriers to infection:
Keratinised skin, Secretions, Mucous (cilia), low pH of stomach (2.5), Commensals
What external secretions help prevent infection?
Sebum, fatty acids, lactic acid, and lysozymes.
Why is prevention of infection more beneficial than cure of infection?
Prevention requires less nutrients and has less impact on the human -> no symptoms of disease -> increased chance at survival
Neutrophils:
Type of phagocyte.
-Main phagocyte in the blood
-Short-lived, fast-moving
-Lysosomes release H2O2
-Multi-lobed nucleus
Mononuclear phagocytes:
-Long lived (months)
-Help initiate adaptive responses.
-Monocytes develop into macrophages in tissue.
-Macrophages ingest hundreds of bacteria.
What are phagocytes more effective than macrophages at treating?
Bacterial and fungal infection.
Natural Killer Cells:
type of lymphocyte:
-Kill virally infected cell non-specifically
- important in self/non-self recognition
-May kill cancer cells
-Have prominent granules
Pathogen recognition by NK cells:
Kill targets unless they recognise self-proteins (major histocompatability complex) that are present on all nucleated cells
Pathogen recognition by Phagocytes:
-Have general pathogen-recognition receptors (PRRs) that recognise microbe-associated molecular patterns (MAMPS) - shared by microbes.
Example of Phagocyte recognising pathogen:
Toll-like receptor 4 (TLR4) recognises lipopolysaccharide
Defensins:
Similar to antibodies -> +ve peptides ->synthesised by neutrophils -> disrupt bacterial membranes
Interferons:
Produced by virally infected cells -> protect uninfected cells -> interfere with viral replication -> activate macrophage + NK cells
What is the complement system?
~20 proteins in blood, activated enzyme cascade triggered by infection -> trigger bacterial cell lysis
-Can induce inflammation
Cytokines:
Produced by innate immune system cells -> small secreted proteins that bind to cell and regulate the immune response e.g interleukins
-Act locally
-Act by binding to spec. receptors on target cells
Inflammatory Mediators:
Cause conditions (and symptoms of allergy) that inhibit/reduce the action of infection. e.g histamine, prostaglandins.
What are the symptoms of inflammation?
Heat, redness, swelling, pain
What induces the release of inflammatory mediators?
Infection or damage + the production of cytokines.
Inflammation:
-Localised response to infection/damage -> dilation of blood vessels -> increased capillary permeability -> phagocytes migrate to effected tissue
integrated responses to infection example: fever
On infection, macrophages release cytokines e.g interleukin 1. -> acts on hypothalamus -> raises body temp (fever) -> stimulates phagocytosis + B/T lymphocytes + reduces Fe levels of blood
Where do B lymphocytes mature?
In bone marrow -> develop antibody receptors
Where do T lymphocytes mature?
The thymus -> develop T cell receptors
What component of the adaptive immune system recognises antigens?
Specific Receptors on T and B lymphocytes
What is the response of B lymphocytes?
secretion of antibodies
What kind of immunity is the response of B lymphocytes?
Humoral
What is the response of T lymphocytes?
Kill infected host cell, make cytokines
What kind of immunity is the response of T lymphocytes?
cell-mediated
What kind of infections are T lymphocytes effective against?
Viral, intracellular bacterial, and intracellular parasitic infections
What kind of infections are B lymphocytes effective against?
extracellular bacterial, and secondary viral infections
Clonal selection hypothesis: Burnett 1958
Lyphocytes that recognise “self” (healthy cells) are deleted early in development -> to prevent damage to host’s tissues
Primary lymphoid tissue:
Where lymphocytes reach maturity and aquire specific receptors
Secondary Lymphoid tissue:
Where mature lymphocytes are stimulated by antigemn
What can B cells differentiate into upon antigen binding induced mitosis?
Plasma cells and Memory cells.
What occurs at the spleen?
Location at which antigens in the blood are filtered out.
Anitbody shape:
Y shape made of 4 polypeptide chains -> two light chains (25kD) and two heavy chains (50kD)
Other name for antibodies:
immunoglobulins
What joins the chains of antibodies?
Disulphide bridges and non-covalent interactions
What is the name of the arm regions of the antibody:
FAB arms
FAB arms:
variable regions of the antibody -> specific to different antigens depending on antibody
Role of antibodies:
Agglutination and regulation and antigen elimination
What is antigen elimination?
The process of antibodies “marking” infected cells by the FC region binding to FC receptors on NK cells -> leading to lysis of infected cell.
What does FAB stand for?
Fragment antigen binding (arms of antibody)
What does FC stand for?
Fragment crystallizable (tail of antibody)
What are the 5 classes of immunoglobulins?
IgG, IgM, IgA , IgD, IgE
IgG:
Immunoglobulin -> Gamma heavy chain -> most abundant in serum and tissues -> can cross placenta -> provides newborns with immune memory from mother
IgM:
Immunoglobulin -> Mu heavy chain -> first antibody produced upon primary inection-> pentamer shape
IgA:
Immunoglobulin -> Alpha heavy chain -> in serum and secretions -> protects mucosal surfaces (gut infections)-> either monomer or dimer
IgD:
Immunoglobulin -> heavy delta chain -> unknown function -> might work against respiratory infection
IgE:
Immunoglobulin -> Epsilon heavy chain -> present at low levels in serum -> protective against extracellular parasites
What is Serum?
Blood without cells and clotting factors.
What are the two different types of immunoglobulin light chains?
kappa and lambda -> not class restricted -> promotes diversity.
Primary response to infection in terms of antibodies:
-Slower recognition and lower production of IgG -> lag of IgG production after IgM
Secondary response to infection in terms of antibodies:
-Faster recognition and greater production of IgG = production of IgM.
Why do maternal antibodies last a long time?
Maternal antibodies are IgG -> which have a higher half life -> can alst 6 months
Are variable and constant regions of antibodies coded together?
No they are coded by separate exons.
What mechanism is used by B+T cells to combat the mutation and variation of viruses and pathogens?
Variable region exons can recombine and mutate during the differentiation of B+T cells -> leading to increased variation in the variable regions of antibodies.
Which antibodies neutralise toxins?
IgG and IgA
Which antibodies immobilise motile microbes?
IgM
What do all antibodies do as a result of their specific binding/multivalency:
-Prevent binding to, and infection of, host cells.
-Form complexes
What are the effector functions of antibodies?
Activate complement (IgG, igM)
Bind Fc receptors: phagocytes (IgG, IgM), mast cells(IgM), NK cells (IgG)
What are the two methods by which complement can be activated?
Activated specifically by antigen/antibody complexes or non-specifically by bacteria
What are the main proteins of the classical complement pathway?
C1, 4, 2 , 3, 5, 6, 7, 8, 9
What property do the main proteins of the classical complement share?
They have enzymic (protease) activity + generate fragments with biological activity
What occurs during the initiation of the classical pathway of complement activation?
1 antigen bound to 2 antibodies. C1 interacts with the 2 Fc regions to activate them. Activation of C1, C4, and C2 -> generates C3 convertase.
Which antibody is the most efficient activator of complement?
IgM -> because it’s a pentamer with the most Fc tails -> therefore most regions for C1 interaction.
Role of C5-C9:
Hollow cylinders form “membrane attack complex” -> create pores in bacterial membranes. -> leading to cell lysis
Role of C3 convertase:
Breakdown of C3 into C3a and C3b.
What is the role of C3b?
The activation of C5 convertase and opsonisation ->increase binding of phagocytes -> increase rate of phagocytosis.
Role of C5a and C3a:
recruitment of phagocytes + induce inflammation.
-Act as chemoattractants and anaphylaxans
Which type of bacteria aren’t susceptible to the “membrane attack complex”?
Gram + (because peptidoglycan shields the cytoplasmic membrane)
Which classes of antibodies can also act as opsonins?
IgG, IgA
What are opsonins?
Antibodies that enhance the recognition of microbes by binding to Fc receptors on the phagocyte surface.
What do NK cells secrete?
Perforin ->target cells undergo apoptosis.
What antibody binds to NK cells?
IgG
What do mast cells protect against?
Mediate allergy + defence against large parasites
By what mechanism do mast cells cause local inflammation?
Degranulation (exocytosis) releases inflammatory mediators.
What antibody is present on mast cells?
IgE
Polyclonal b cell response to antigen:
-Lacks fine specificity -> more flexibility
-Antibodies bind to different shapes “epitopes” on the antigen -> produces mixture of antibodies
Monoclonal antibodies:
- Have single specifity
-Derived from single B lymphocytes
How are antibodies produced industrially?
The fusion of B cells from an immunised animal and a Tumour cell line -> hybrid cell that secretes antibody and divide indefinitely.
OKT3:
-Specific to CD3 -> used to treat graft rejection
Herceptin:
-Specific to Her-2 - treats Breast cancer
Rituximab:
-Specific to CD20 -> treats B cell leukaemia
Remicade:
-Specific to TNF -> treats Crohn’s diease + rheumatoid arthiritis
Tocilizuman:
-Specific to interleukin 6 receptor -> treats COVID and arithitis
Sotrovimab:
-Specific to SARS-COV-2- spike protein -> treats severe covid
T helper cells (CD4 +):
-Help B cells make antibodies
-Activate macrophages and NK cells
-Help development of cytotoxic T cells
T cytotoxic cells (CD8 +):
-Recognise and kill infected host cells
-Similar to NK cells however are more specific.
T cell receptor structure:
-T lymphocyte receptor (TCR) similar to antibody -> has beta and alpha chain, hinge region, disulphide bonds, variable and constant regions.
What type of antigens do T cells recognise?
“cell-associated”, processed antigens, which have been broken down into smaller peptides
Which types of infection are T cells most effective with treating?
Viral, intracellular bacteria, and intracellular parasitic infections.
What proteins bring foreign proteins to the surface to form an MHC?
MHC proteins
Variation of MHC proteins:
MHC proteins express great variation -> because they’re the most polymorphic proteins in a human
MHC 1:
Found on all nucleated cells -> (not on RBC’s) -> display antigen to CD8 +ve T cells
MHC 2:
expressed by macrophages, dendritic cells, and B cells -> displays antigens to CD4 + T cells
T cytotoxic cell recognition of antigen:
Proteosome breaks down viral proteins -> peptides transported to the ER and bind to MHC1 -> transported to cell surface -> CD8 + T cells recognise peptide bound to MHC -> kill effected cell by induced apoptosis.
T Helper Cell recognition:
Macrophage/ dendritic cell/ b cell internalises and breaks down foreign material in endosomes -> peptides bind to MHC2 and transported to cell surface -> Activated T helper cell then helps B cells make antibodies, or produce cytokine that activate/regulate of leucocytes
What are the main groups of cytokines?
interleukins (IL1 -> IL38), interferons (treat viral infections), chemokines (Control cell movement or chemotaxis)
Tumour Necrosis Factor (TNF):
pro-inflammatory, toxic factor responsible for the symptoms of sepsis. -> Can kill some tumour cells
Colony stimulating factors (CSFs):
Stimulate the production of leucocyte colonies in bone marrow.
Activation of adaptive immunity in the draining lymph node:
Tissues are supplied by lymphatic vessels -> drain to lymph nodes containing B and T cells -> dendritic cells will activate naive T cells via MHC expression.
Activation of adaptive immunity in the draining lymph node:
Tissues are supplied by lymphatic vessels -> drain to lymph nodes containing B and T cells -> dendritic cells will activate naive T cells via MHC expression.
Why are the adaptive and innate immune system interlinked?
Both have co-evolved.
Vaccination:
attenuated form of pathogen -> Evokes a primary response -> a booster evokes a secondary response -> forms an immune memory in event of exposure to disease.
What are the different types of vaccine:
Attenuate strains, Killed pathogen, subunits, Engineered virus, or RNA
What is a risk of the use of attenuated viruses in vaccines?
They may revert and become pathogenic.
What significant diseases are there with no effective vaccine?
Malaria, Schistosomiasis, TB, and HIV/AID (although trials)
What is the viral HIV receptor that binds to the surface of host cells?
GP 120
Steps of HIV integration into DNA:
GP 120 binds to cell receptors -> viral envelope fuses with plasma membrane -> nucleocapsid enters cytoplasm -> Viral RNA reverse transcribed into ds DNA -> transported to nucleus and integrates in DNA -> forms provirus
What cells are GP120 (HIV receptors) specific to?
CD4 receptors on T helper cells.
Upon initial infection of HIV what occurs?
The virus is “cleared”, however the pool/reservoir of infected cells gradually increases due to proviruses not being identified.
What in addition to CD4 expression is required for HIV infection of a cell?
co-receptor. e.g CCR5 -> required for virus fusion with host cell
Effect of HIV infection of monocytes?
Monocytes can traverse blood/brain barrier -> impact CNS
Effect of HIV infection of dendritic cells:
Spread infection to multiple T-cells. Dendritic cells experience a permissive infection and-so act as a reservoir of the virus.
Why is there a rise in HIV virus in plasma years after infection?
The virus will mutate to avoid immune detection.
What leads to AIDS?
T helper cell depletion caused by: direct lysis by viral infection, killed by cytotoxic T cells, apoptosis
What is the tissue effects by AIDS?
Lymphoid tissue
What is the Blood count threshold of CD4+ T cells for aids?
<200/mm^3
Symptoms of AIDS:
-Opportunistic infections
-Reactivation of latent viruses
-Rare cancers
-CNS (dementia, paralysis, blindness)
Transmission of HIV:
-Sexual intercourse 70%
-Blood 28%
-Breast-feeding
-Mother-foetus
What are the 3 key ways to deal with aids?
Change to behaviour, vaccination, and drug treatment
Prevention of HIV infection: Changes in behaviour
Blood testing, “safe sex”, decrease i.v drug use treat HIV + pregnant women
Drug therapy of HIV/AIDS: problems
-Virus has high mutation rate
-Toxicity of drugs
-Viral latency
-Cost
Combination therapy:
cocktail of drugs directed at different viral targets
How many licensed drugs block HIV replication?
> 25
Future treatments of HIV/AIDS:
Stem cell therapy, “Kick and kIll” (reactivation of virus + immunotherapy), “passive immunisation) (monoclonal antibodies), Gene editing with CRISPR/Cas9
