Module 4: Microbiology Flashcards
Microbes make up ____ the biomass on Earth
half
Where is the chromosome of a prokaryotic cell found
Nucleoid
What is the order of layers of a prokaryotic cell (inside to out)
Plasma membrane, cell wall, glycocalyx
What shapes can bacteria be
Cocci, rods, spirals
What is the function of a prokaryotic cell membrane
Cell regulation
What is the function of a prokaryotic cell wall
Cell integrity, shape, strength, prevent desiccation, osmotic lysis
What is the purpose of the glycocalyx
Extracellular: cell protection
Do archaea have peptidoglycan cell walls
No
Describe the bacterial genome and its location
One circular chromosome restricted to an area known as the nucleoid, and plasmids in the cytosol
What are plasmids
Small circular self replicating DNA molecules found in the cytosol
What are prokaryotes that lack cell walls called
Mycoplasmas (group of pathogenic bacteria)
Describe the structure of peptidoglycan
NAM-NAG sugar chains cross linked laterally by amino acid chains and vertically by amino acid side chains
What is the enzyme that cross links NAM-NAG sugar chains and amino acid chains
Transpeptidase
What are the most common gram stain reference bacteria
Staphylococcus aureus (gram positive) and escherichia coli (gram negative)
What colour are gram positive bacteria stained
Purple
What colour are gram negative bacteria stained
Red/pink
What are the four steps of the gram stain procedure
Application of crystal violet (purple dye), application of iodine (mordant), alcohol wash (decolourisation), application of safranin (counterstain)
Describe the structure of a gram positive bacterial cell wall
Thick peptidoglycan layer makes up the cell wall, plasma membrane underneath
Why do gram positive bacterial cells retain the crystal violet
Peptidoglycan traps violet, masks red
How thick is the peptidoglycan layer of gram positive bacteria
THICK: 20-80 nm
Describe the structure of a gram negative bacterial cell wall
Thin peptidoglycan layer and outer membrane make up the cell wall, plasma membrane underneath
Why do gram negative bacterial cells not retain the crystal violet
It is easily rinsed away, revealing red safranin dye
How thick is the peptidoglycan layer of gram negative bacteria
THIN: 5-10 nm (between two plasma membranes)
What does the gram negative bacterial outer membrane have that gram positive doesn’t
Carbohydrate portion: lipopolysaccharide
What are flagella made of
Flagellin protein
What is the diameter of flagella
10-20 nm
How many flagella per cell
5-10
How do flagella work
Act like propeller, cell rotates them to move through liquid medium
Chemotaxis
Bacteria move along a concentration gradient towards a chemical attractant (positive) or away from a chemical repellent (negative)
Function of fimbriae (can also be called adherence pili or adhesins)
Structures with adhesive properties that cause bacteria to stick/adhere to surfaces
What is the diameter of pili
2-8 nm
How long are pili
1µm
How many pili per cell
100-1000
Difference between fimbriae and pili
Fimbriae are for adhesion to surfaces, pili are for attachment to other bacteria
Purpose of a sex pilus
Horizontal gene transfer (conjugation)
What are the two forms of glycocalyx
Capsule (organised), slime layer (disorganised without cell shape, attached loosely to cell wall)
What is the glycocalyx
A gelatinous polysaccharide and/or polypeptide outer covering of a bacteria
Function of capsules
Virulence factors: evade immune system, protection from phagocytosis and engulfment by immune cells. Prevent cell from drying out (desiccation)
What is a bacterial endospore
Highly differentiated cells resistant to heat, harsh chemicals, antibiotics, disinfectants and radiation. Enable bacteria to stay dormant for a very long time
What cells have endospores
Some types of gram positive bacteria
Why do bacterial endospores form
Formed during unfavourable growth conditions to protect cells from stress, germinate under favourable conditions
Why are prokaryotes so dominant
Because they evolve so fast due to fast growth rate (exponential), have existed for so long so colonised most habitats resulting in extreme ecological and metabolic diversity
What does colonially pure mean
All cells identical
What is binary fission
The process of one cell becoming two (asexual)
Outline the process of binary fission
DNA replication (one origin of replication), two origins move to cell poles, two cells differentiate
What is a closed batch culture system
Defined (limited) supply of nutrients provided, once used cells cannot proliferate
What are the 4 stages of microbial growth in a closed batch system
Lag, exponential, stationary, death
Describe the lag phase
Time taken to get biosynthetic reactions running
Describe the log phase
Cells are actively dividing and nothing is limiting for growth. Population is doubling in a constant time interval under ideal conditions
Describe the stationary phase
Cells stop growing and cryptic growth is observed, equilibrium between growing and dying cells
What is cryptic growth
When organisms survive by consuming lysed cell constituents of other dead cells within the culture
Describe the death phase
Equilibrium between growing and dying cells is skewed toward death
What do batch culture assays measure
The average behaviour of cells
What do prokaryotes need to multiply
Carbon source, energy source (electrons to power anabolic and catabolic reactions), reducing power (carriers of electrons (NAD+, NADP+))
Catabolism
Breakdown: energy generation
Anabolism
Build up: energy consumption
Photoautotroph (plants, algae, cyanobacteria, green and purple sulfur bacteria)
Light energy source, inorganic carbon source
Photoheterotroph (green and purple non sulfur bacteria)
Light energy source, organic carbon source
Chemoautotroph (hydrogen, sulfur and nitrifying bacteria)
Chemical energy source, inorganic carbon source
Chemoheterotroph (animals, fungi, protozoa)
Chemical energy source, organic carbon source
What is a wild type strain
Bacteria with all essential genes, can grow by itself and be isolated in pure culture
What is an auxotroph (98% of microorganisms sequenced lack essential pathways for synthesis of amino acids)
Bacteria lacking or defective in one or more essential genes, cannot grow unless missing factor supplied
What is cross feeding (also known as syntrophy)
When one species gains metabolic products of another species. Can benefit one or both species
Microbiome definition
The complete collection of microorganisms and their genes within a particular environment
Microbiota definition
Individual microbial species in a biome- bacteria, fungi, archaea and viruses
Opposite of being dependent on others
Autonomy
Culture dependent methods pros
Access to phenotype, can study one organism at a time, can manipulate conditions to see response of organism
Culture dependent methods cons
Not all organisms can be cultured, too many species to grow them all, culturing requires precise conditions to match microbes needs, doesn’t match real world conditions
Culture independent methods pros
Allows access to genotype, can study many organisms at a time, shows communities as they are in nature, can target non-culturable organisms, provides access to unknown information/species
Culture independent methods cons
No pure culture so no ability to manipulate, expensive and complex
What is a culture dependent method
Culturing of microbes in lab, uses pure cultures or simple (reduced diversity) enrichments
What is a culture independent method
Relies on nucleic acid based methods, uses sequencing or metabolic profiling to study all microbes in a sample
What is microbial ecology
The field of study focused on the relationship between microbes and their environment (interrelationships among organisms and their environment)
What is a microbial population
Individual microbial cells of a species proliferated
What is a microbial community
Interaction of populations of microbes
Anabolism and catabolism must be
Coupled (harvesting of building blocks = harvesting of energy)
For every oxidation reaction in the body there must be
An equal and opposite reduction
What are the electron carriers in the body
NAD+ and NADP+ (NADH and NADPH when they have electrons)
Facilitate redox reactions without being consumed
Photoautotroph
Light energy source, inorganic carbon source
e.g plants
Chemoautotroph
Chemical energy source, inorganic carbon source
e.g hydrogen, sulfur and nitrifying bacteria
Photoheterotroph
Light energy source, organic carbon source
e.g green and purple non sulfur bacteria
Chemoheterotroph
Chemical energy source, organic carbon source
e.g animals, fungi, protozoa
Decomposers are
Heterotrophs (reliant on primary producers)
Primary producers are
Autotrophs (fix CO2)
Chemical energy source examples
Glucose: organic, H2S: inorganic
How can so many different microbes share the same metabolisms?
Evolve to require very specific resources (e.g absorption of wavelength of light)
How can a microbe live in an anoxic place if it requires oxygen to live?
Cables (shuttle electrons from anoxic to oxic zone: oxygen terminal electron acceptor) (gram negative: 2 membranes)
What is metabolism
2 linked but different process (anabolism and catabolism)
What was the aim of the human microbiome project? (2008)
Characterise microbial communities found at multiple human body sites and look for correlations between changes in the microbiome and human health
How was the human microbiome project undertaken
Culture-independent methods of microbial community characterisation as well as whole genome sequencing of individual bacterial species
What parts of the body did the human microbiome project put emphasis on
Oral, skin, vaginal, gut, nasal/lung
How many microbial species are in the the human microbiome
10000
How many microbial species are in the human gut
500-1000
What were the goals of the HMP
Develop a reference set of microbial genome sequences and perform preliminary characterisation of the human microbiome. Explore the relationship between disease and changes in the human microbiome. Develop new technologies and tools for computational analysis, establish a resource repository, study the legal, ethical and social implications of human microbiome research
Is there diversity within and among individual microbiomes
Yes
How much more genetic diversity does an individual’s gut bacteria have compared to the human genome
50 times
Why might the HMP not be representative of all people
Most information came from healthy Western people
Everyone’s microbiome has around ___ species
160, 57 very common
A person’s microbiome community can change, but its _____ will not much
Function
What are the functions of the human microbiome
Prevent pathogens from being successful, block colonisation niches, competing for nutrients, modifying environment to change virulence factor expression, making environment actively hostile, lowering pH, cause host to thicken mucus layer, cause host to upregulate antimicrobial peptides (defensin, IgA), primes host neutrophils and macrophages
What do microbes produce to make an environment actively hostile
Bacteriocins (antimicrobial) and short chain fatty acids (SCFAs)
How many phylum groups dominate human microbial communities
4 (firmicutes, bacterioidetes, actinobacteria, proteobacteria)
What percent of human associated microbes are thought to have eluded cultivation so far
20-80%
The human microbiome is undiverse in _____ but very diverse in ______
Phyla, species, strains (can be as unique as a fingerprint)
What is the purpose of SCFAs that gut microbiota produce
Modulate our metabolisms and affects our defence against pathogens
What vitamins can the human microbiome synthesise
Many B vitamins and vitamin K
What is a functional food
A food claimed to have a health promoting or disease preventing property beyond the basic function of providing nutrients
What are probiotics
Live microorganisms (most commonly lactic acid bacteria (LAB) and bifidobacteria)
What are prebiotics
An ingredient that beneficially nourishes the good bacteria already in the large bowel or colon (e.g body doesn’t digest some plant fibres (oligosaccharides) but they promote growth of bacteria)
What is the problem with broad spectrum antibiotics
If you clear out all your commensal microbes you may be colonised by pathogenic microbes
What does C.difficile do to the gut
Heterotroph that uses sialic acids from mucins (main structural component of mucus layer in gut) as carbon/energy source, speed of growth and presence of accessory genes make it pathogenic: cause damage to cells and inflammation and fluid build up. Flushed out by diarrhea
What is the purpose of faecal matter transplants
Provide healthy bacteria to outcompete pathogenic. Highly successful in mutliple recurrences of C.difficile
What are the 4 groups of bacteria that dominate the human microbiome
Firmicutes, bacteroidetes, actinobacteria, proteobacteria
What host processes do the microbiome affect
Digestion, immune system, pathogen susceptibility, neurology
What is the genetically most diverse biological entity on earth
Viruses
What are viruses
Acellular organisms with no metabolic abilities of their own (rely entirely on biosynthetic machinery of host to multiply)
What is the most abundant biological entity on eath
Viruses
How do viruses vary in size
10-400 nm
What is a capsid
Protein coat made of capsomers
What is an envelope
Envelope of lipids surrounding capsid when outside cell
What is the function of the capsid
Protect viral genome
What are the three types of capsid symmetry
Helical, icosahedral (20 faced polyhedron, each face an equilateral triangle), complex
How do nucleic acids vary between viruses
Can be RNA or DNA, linear or circular, segmented or not, and single or double stranded. Can be 4000 to >1 million nucleotides
How are viruses classified?
Nucleic acid -> capsid symmetry -> naked or enveloped -> genome architecture
What do viruses infect
All cell types and all forms of life
What are bacteriophages
Viruses that infect and replicate in bacteria
What is a lytic (virulent) cycle
Using a host cell to manufacture more viruses and results in destruction of the host cell
What are the 5 stages of the lytic cycle of bacteriophages (takes 20-30 minutes)
Attach, penetrate, uncoat (expose genetic material), genome replication and gene expression, assembly, release (likely destruction of cell)
What are the 6 stages of viral infection
Attachment, penetration, uncoating to expose genetic material, gene expression and genome replication, assembly, release
Describe the SARS-CoV-2 virus
Enveloped ssRNA linear non segmented virus with spikes and nucleocapsid protein
How are virus variants generated
D/RNA polymerase making errors
What is the purpose of a virus spike (vaccines target the spike)
Bind to a receptor protein to infect a cell (ACE2 for SARS-CoV-2)
What are the 6 stages of the SARS-CoV-2 replication cycle
- Spike binding to ACE2 receptor
2/3. Cell entry/fusion - Genome translation replication module only
Viral RNA synthesis
Viral mRNAs and genome
Translation - Assembly
- Exocytosis
Describe the HIV virus
RNA enveloped retrovirus that causes AIDS
What are the 6 stages of the HIV replication cycle
1/2/3. HIV fuses with cell membrane and digestion of capsid
4. Reverse transcriptase converts ssRNA to dsDNA (mistakes), incorporated into host genome. DNA replicated and viral proteins and glycoproteins synthesised (sent to membrane in vesicles)
5. Assembly (enveloped as exocytosed)
6. Release (with viral envelope glycoproteins)
What are two important attributes transferred by horizontal gene transfer
Virulence and drug resistant factors
What is horizontal gene transfer
The ability of one mature organism to pass its DNA directly to another mature organism
What is vertical gene transfer
Passing DNA from a parent to an offspring
Why did heat treated cells and harmless cells result in the death of the mouse
Horizontal gene transfer of pathogenic genes by transformation
What are virulence factors
Attributes that help bacteria survive in the host, sometimes at a cost to the host (e.g capsules which prevent phagocytosis). May help with adherence, invasion, proliferation, survival and disease causing
What is antibiotic resistance
Attributes of bacteria that reduce the effectiveness of antibiotics (e.g beta lactamase enzyme which inactivates penicillin)
What is transformation
Form of horizontal gene transfer involving the uptake of short fragments of naked DNA by naturally transformable bacteria (dead or dying release genetic material)
What is transduction
Form of horizontal gene transfer from one bacterium to another via bacteriophages (accidentally will package plasmid from within bacteria and form new type of phage, instead of killing next bacteria will form new type of phage)
What is conjugation
Form of horizontal gene transfer involving a sexual pilus (cell to cell contact) Doesn’t have to be between same bacteria
What is a sex pilus
Long tube through which unwound plasmids are transferred
What are the features of a bacteriophage
Icosahedral head, helical tail, sheath, base plate, tail fibres with very specific ligands to attach to specific bacterial cell membrane
What is phage therapy
The therapeutic use of bacteriophages to treat pathogenic bacterial infections
Are fungi pro or eukaryotic
Eukaryotic
Are protozoa pro or eukaryotic
Eukaryotic
Are helminths pro or eukaryotic
Eukaryotic
Are bacteria pro or eukaryotic
Prokaryotic
What are Koch’s postulates
Guidelines used to demonstrate that a specific pathogen causes specific disease symptoms
Outline Koch’s postulates
Pathogen must be present in every individual with the disease, sample of microorganism taken from diseased host can be grown in pure culture, sample of pure culture causes same disease when injected into healthy host, microorganism can be recovered from experimentally infected host
What are the exceptions to Koch’s postulates
Microbes that can’t be cultured, pathogens that can also be found in healthy subjects
What are the 4 stages of microbial pathogenesis
- Adherence to host cells
- Invasion of host tissues
- Replication within host tissues
- Disease causing damage to host tissues (pathology)
What is a virulence factor
Something that enables a microbe to be pathogenic, protect bacteria from phagocytosis and engulfment by immune cells, prevent cell from drying out (desiccation)
What is the virulence factor associated with the adherence stage of microbial pathogenesis
Fimbriae
What are the virulence factors associated with the invasion stage of microbial pathogenesis
Flagella, internalin-related proteins
What are the virulence factors associated with the replication stage of microbial pathogenesis
Siderophores, capsules
What are siderophores
Scavenge iron from blood by solubilising and binding, and taking back to bacteria
What are the virulence factors associated with the pathology stage of microbial pathogenesis
Exotoxins and endotoxins (toxic virulence factors)
What are endotoxins
Lipopolysaccharides (LPS) components found in the outer membrane of gram negative bacteria, and elicit strong immune responses
What effect do endotoxins have
Inflammation (, fever, blood clotting, shock) I.e causes our immune system to be overworked, immune system causes the pathology, not LPS itself
What are the tree types of exotoxins
Cytotoxins, neurotoxins and enterotoxins
What are exotoxins
Proteins produced within living bacteria and then released into the surrounding medium
What do cytotoxins do
Destroy cells (e.g beta haemolysis)
What do neurotoxins do
Destroy the brain (e.g cause paralysis)
What do enterotoxins do
Harm the digestive system (e.g cause dysentery)
What is selective toxicity
Finding a way to kill pathogenic cells and not host cells
How did the idea of selective toxicity originate
Methylene blue stained microbes better than host cells
How was penicillin discovered
A fungi that prevented bacterial growth (zone of inhibition created)
How does penicillin work
Interferes with the formation of the host cell wall by inhibiting the formation of peptidoglycan cross links
What bacterial cell components can antibiotics target
Cell wall synthesis, protein synthesis, cytoplasmic membrane, general metabolic pathway, inhibition of DNA or RNA synthesis, inhibition of pathogen’s attachment or entry into host cell
What is the most important cause of genetic diversity in microbial populations
Mutation
What is the enzyme produced by penicillin resistant bacteria called
Beta lactamase
How does beta lactamase work
Breaks a bond in the beta lactam ring of penicillin to disable the molecule
What gene causes the production of beta lactamase on penicillin resistant bacteria
blaZ gene
How can we reduce the development of antibiotic resistance
Decrease antibiotic utilisation, improve diagnostics, identify new targets, combination therapies
What are antibiotic combination therapies
Traditional antibiotics combined with molecules that block resistance mechanisms
What are the five stages of an infectious disease
Incubation period, prodromal period, illness, decline, convalescence
What characterises the incubation period
Infected but no signs and symptoms
What characterises the prodromal period
Vague, general symptoms
What characterises the illness period
Most severe signs and symptoms, most amount of microbe so most infectious
What characterises the decline period
Declining signs and symptoms
What characterises the convalescence period
No signs or symptoms
What is epidemiology
The study of disease transmission
What are the six parts of the chain of infection
- Causative agent: pathogenic organism
- Reservoir/source (human, animal, water, etc)
- Means of exit: way out of the body
- Mode of transmission: method of spread
- Portal of entry: way into the body
- Person at risk (elderly, young, immunocompromised)
How can the causative agent stage of the chain of infection be disrupted
Rapid detection and treatment
How can the reservoir/source stage of the chain of infection be disrupted
Good hygiene/sterilisation/disinfection
How can the means of exit stage of the chain of infection be disrupted
Waste removal/disinfection
How can the mode of transmission stage of the chain of infection be disrupted
Airflow control/ bed spacing
How can the portal of entry stage of the chain of infection be disrupted
Aseptic technique catheter/wound care
How can the person at risk stage of the chain of infection be disrupted
Identifying at risk and targeting them for special care, vaccination and education
What is mortality
The incidence of death in a population
What is morbidity
The incidence of cases in a population, fatal and non fatal
What is the incidence of a disease
The number of new cases of the disease in a given time
What is the prevalence of a disease
The total number of new and existing cases in a population in a given time
What does endemic mean
The amount of a disease that is usually present in a community
What does sporadic mean
A disease that occurs infrequently and irregularly
What does epidemic mean
An increase, often sudden, in the number of cases of a disease above what is normally expected in that population in that area
What does pandemic mean
An epidemic that has spread over several countries or continents, usually affecting a large number of people
Describe the HIV virus
A lentivirus (RNA genome) that causes AIDS, infection through bodily fluids (blood products before recognition), infects and causes failure of the immune system
What does sequencing a virus mean
Using PCR isolate viral genomes from infected patients
What was the key finding of the tree of HIV sequences
More variation between patients than within
What were the two possible explanations for why there is more HIV variation between patients than within
Infections from multiple viruses, viruses are changing
What does proximate mean
By what mechanism is the change occurring
What does ultimate mean
What is causing the change
Why does HIV change as it proliferates
Reverse transcription of RNA genome by reverse transcriptase enzyme which has no proof reading mechanism, resulting in errors
Why is HIV mutation classed as evolutionary
All variants found encode active working viruses because HIV has variation, inheritance, selection and time
What selects for or against HIV variants
The immune system, drug regimen, changes in the receptor, tropism in tissues
How do we know that HIV evolves (testing)
Viruses evolve differently if patient is put on antiretroviral drugs
Approximately how many HIV variants could be in a person
5x10^10
What is a retrovirus
A virus that synthesises DNA from its RNA genome (reverse transcription)
