Microbes and the immune system Flashcards
1
Q
What are the three types of symbiosis ?
A
- mutualism (A and B benefits) // 2. Commensalism (A benefits and B is unaffected) // 3. Parasitism (A benefits and B is harmed)
2
Q
What is meant by a microbiome?
A
a community of microorganisms within an area ~(microorganisms = bacteria/ virus…)
3
Q
Give an example of mutualism symbiosis.
A
Within the gut, microorganism produce over 50% of our Vitamin K (they gain a nutrient rich environemnt// human benefit by getting Vitamin K
4
Q
Give an example of commensalism symbiosis.
A
Staphylococcus epidermidis utilises dead skin cells without causing harm to us
5
Q
Give an example of parasitism
A
malaria/ tonge eating louse/ tapeworm
6
Q
What is zoonosis?
A
An infectious disease transmitted to humans from animals
7
Q
Give a brief evolution of the germ theory.
A
Ancient greeks posed miasma theory (get diseases from the air)// Van leeuwenhoek observed single celled organisms// Snow understood cholera was transmitted in water // Pateur discovered fermentation// lister started the use of disinfections in surgery // koch understood some major causes of bacterial infections
8
Q
What is pathogenicity ?
A
The ability to cause disease
9
Q
What is virulence
A
The degree of pathogenicity of an organism
10
Q
How is microarry technology carried out?
A
- insert single stranded DNA into a grid // 2. extract mRNA from samples and synthesis cDNA // 3. Combine samples together and add to microarray// 5. measure florescence and determine which genes are expressed in each populations
11
Q
What technologies are used for different biomolecules?
A
(BIOMOLECULE - TECHNOLOGY )
DNA- Genomics // RNA - transcriptomics // Protein - proteomics // metabolite - metabolomics //
12
Q
What are microbes?
A
Large mixed populations of microorganisms which coexist together under many circumstances
13
Q
What is Koch’s postulates (4 points)?
A
A set of 4 points which ensure a specific microorganisms is what causes a disease // 1. suspected pathogen must be absent in all individuals except all diseased hosts// 2. pathogen is isolated and grown in a pure culture // 3. Pathogen must cause the same disease when injected into a healthy individual// 4.pathogen must be re-isolated and identicle to the first pathogen which was isolated
14
Q
What are some limitations of modern technology used in Koch’s postulates?
A
Asymptomatic carriers (some pathogens are present in an individual without symptoms)// not all microorganism can be cultured// ethical issues
15
Q
What are basics of viral replication?
A
- Attachment- virus binds to specific receptors on the surface of host cells // 2.Penetration- virus enters the host cell // 3. Uncoating - viral genome is released // 4. Genome replication and transcription // 5.trasnlation and protein synthesis // 6. Assembly new synthesised viral genomes and proteins are assembled // 7. release - virion exit the host cell.
16
Q
What are the general properties of RNA viral genomes?
A
can be single or double stranded // if single can be positive stranded (encoding viral proteins) or negative stranded (antisense used as a template to produce positive/ sense strands) //
17
Q
What are the main differences between DNA and RNA viruses?
A
DNA is more intrinsically stable // DNA is usually larger so can acquire new functions // RNA is much more diverse - 1 mutation every cycle// RNA has a faster evolution capacity //
18
Q
What are the general properties of DNA viral genomes?
A
single stranded or double stranded// intrinsically stable // larger genome therefore can acquire new functions
19
Q
What is a quasispecies?
A
A group of closely related virus which arise within a single host due to high mutation rates variants which undergoes many mutations and is extremely genetic diverse// within viral infections quasispecies become drug resistant and are persistent to infection
20
Q
What is antigenic drift and why is it beneficial ?
A
Process in which antigens accumulate small mutations therefore changing antigens they present, as a result antibody’s and memory immune cells cannot act on them and the infection can continue
21
Q
How does recombination aid pathogenetic infections?
A
Major alternations acquisition of new or altered proteins become present through exchange of genetic material between viruses or with the host. Can create antigenic shift promoting infection
22
Q
What are 3 effects of mutation?
A
Alter efficacy of antibiotic by alteration of target site // alter receptor recognition (of tissue) // alter recognition by the host (immunity )
23
Q
What is horizontal genetic transfer?
A
acquiring new genetic traits in bacteria// rapid growth ensures spread within the population
24
Q
What are the different ways horizontal genetic transfer occures?
A
1.Natural transformation (and incorporation of DNA) // 2.conjunction (bacterial sex, genetic material is transferred)// 3. transduction ( a phage is released from one phage-infected donor and the phage’s nucleic acid is inserted into the other cell.)
25
What is a relaxasome?
A molecular structure DNA passes through (strains in which plasmids integrate into chromosomes)
26
What are the two life cycles of transduction?
LYSOGENIC - integration of bacteriophage DNA into bacterial chromosome // LYTIC - bacteriophage actively replicates within the host bacterial cell causing the cell to burst and release a phage partcile
27
What is quorum sensing
bacteria sense their population size and coordinate behaviour in response
28
What is a photoautotroph? Give an example of one.
Organism which uses sunlight and carbon dioxide as its primary sources of carbon to produce organic compounds // plants, algae, cyanobacteria.
29
What is a photoheterotroph? Give an example of one.
An organism which uses sunlight and pre-formed organic -compounds as its primary source of carbon// purple/ green non-sulphur bacteria
30
What is a chemoautotroph? Give an example of one.
An organism which uses chemical oxidation(breaking down organic or inorganic compounds through chemical reactions) and carbon dioxide as its carbon sources.// extremophiles
31
What is a chemoheterotroph? Give an example of one.
An organism which uses chemical oxidisation of pre-formed organic compounds // humans and animals
32
What is the optimal temperature for growth of a mesophile?
Body temperature e.g. human pathogen
33
What is the optimal growth for psychrophiles ?
<15 degrees C e.g. listeria monocytogenes (a pathogenic bacteria found in most environments )
34
What is the optimal temperature for growth of hyperthermophiles?
>70 degrees C e.g. Thermus aquatic
35
What type of saturated fats do psychrophiles have in there membrane and why?
unsaturated fats // ensure membrane is fluid as they are found in low temperatures unsaturated fats are liquid at lower temperatures making them more suitable
36
Should a membrane be solid or liquid and why ?
More liquid consistency as this allows movement of compounds between cells.
37
What type of saturated fats do hyperthermophiles have in there membrane and why?
Saturated fat , ensures the membrane maintains structure at high temperatures.
38
What is the role of Synchronous?
To fixate 50% of marine carbon
39
Compare the neritic and oceanic zone.
Neritic has mild temperature, low pressure and is nutrient rich (contains many photosynthetic organisms and diverse marine life)// oceanic has an increased pressure with depth, not a stable environemnt and is home to single celled organism and chemotrophs
40
What is biodegradation?
Physical or chemical change of material by microorganism (bacteria/ fungi)
41
What is the aerobic breakdown of plastic?
Plastic + oxygen -> CO2 + H20+ residual carbon
42
What is the anaerobic breakdown of plastic?
Plastic -> methane + CO2 + residual carbon
43
What is the difference between anaerobic and aerobic breakdown of plastic?
Anaerobic also produces methane .
44
What is the role of CRISPR- Cas9 ?
Clustered regulated short tandem repeats// it is a genome-modifying tool which can be used in industries to for gene therapy . developing specific traits in crops
45
What are the 3 stages in recombination vaccines ?
1. Scientists take genes from virus spike protein and inject it in an individuals // 2.vaccine enters cell and produces spike protein and the body's immune system makes specific T cells // 3. if a patient later gets the virus, these antibodies created through vaccine are activated.
46
What microbes are associated with what types of cancer?
Cervical cancer -> human papillomavirus // gastric cancer - > helicobacter pylori // bladder cancer -> schistosoma haematobium
47
What is a actinomycetes?
A gram positive bacteria which has high GC levels
48
What is the microbiota ?
the system of microorganisms within an individuals body (mainly in colon but also lings , skin , teeth
49
What is 16S sequencing?
A method used for identifying and comparing bacteria samples dependent on the 16S RNA gene which encodes for a subunit within a ribosome.
50
Compare 16S sequencing and Whole genome sequencing.
16s is much cheaper and can usually identify the bacteria type// WGS is much more expansive but also more accurate and specific identification of bacteria.
51
Give some examples of ways the microbiota is developed in humans.
vaginal or caesarean delivery / milk consumption / diet / antibiotics/ environemnt/ pets
52
How does gut bacteria promote a healthy human?
metabolises carbohydrates into short chain fatty acids // synthesises key micronutrients alike vitamin B3 / B5/ B6 / B12 //
53
Why is it beneficial for carbohydrates to be broken down into short chain fatty acids?
can be absorbed and transported in blood to reach all somatic cells / main energy source for epithelial cells (needed to prevent pathogenic bacteria causing issues)// reduces inflammatory response
54
What is inflammatory bowel disease?
ulcerative colitis// it is infiltration of bacteria which drives inflammation // lesions are generated by the immune response against disease
55
What is clostridium difficile infection ?
usually found in colonel bacteria/ a hospital bound disease / enters the body and multiple in the gastrointestinal tract / pseudomembrane formation within the colon/ c difficile releases toxins which damage the colon and lead to pseudomembrane formation
56
What are different methods of curing the microbiota ?
Faecal microbiota transplantation// full spectrum of microbial components // much less success for other conditions
57
How do microbiota limit disease?
Limit disease as pathogenic microorganisms must compete with gut biota in order to survive and infect the individual
58
What different microbial substances activate innate immune cells ?
pathogen-specific molecules (on the surface of microbes)/ double stranded - RNA / complement (blood proteins which distribute the membrane )
59
What receptors do immune cells use to respond to microbial products and the damage they cause?
pattern recognition receptors- PRR ( on innate cells to recognise pathogenic molecular patterns - PAMS)//MHC proteins , determine if the cell is 'friendly' or not, triggering immune response// Complement proteins - blood proteins which punch holes in pathogens creating leaks leading to cell death
60
What are 4 main resistance mechanisms used by bacteria?
reduce uptake of antibiotics // modify target if antibiotic reducing affinity// inactivate drug through producing enzymes// Efflux, bacteria pump the antibiotic out of the cell
61
What is the difference between intrinsic and acquired resistance?
intrinsic is present before treatment but acquired is created during or after treatment
62
What are the two types of substances and give examples.
Foreign and dangerous (viral and bacteria ) // innocuous or self (pollen and self epithelial cells)
63
Give a brief overview of a initial response to infection or trauma.
1. activation of local innate immune cells/ 2. increased permeability of local blood vessel / 3. migration int tissues of more immune cells and plasma proteins
64
What did Charles Janeway predict and when?
1989 - the presence of host receptors which recognise conserved pattern on pathogenic molecules
65
What is a PAMPs?
pathogenic associated molecule pattern , a high conserved molecule which is expressed by foreign cells e.g. glycoproteins on virus
66
Give an example of a PAMP for a virus, bacteria, fungi and protozoa.
Virus = glycoprotein // Bacteria= cell wall component // Fungi = Polysaccharides // Protozoa = Glycolipids
67
What is a DAMPs?
A damage associated molecular pattern , evidence of damage resulting from an infection which is further developed from a PAMP
68
Where do DAMPs come from?
They are released from dying cells acting as a signal to immune cells
69
Give some examples of immune cells and their function
Dendritic cells - engulf pathogens to activate adaptive immune cells // macrophage- engulf and destroy pathogens// neutrophils - release toxic molecules or engulf and destroy pathogens // eosinophils and mast cells - release toxic molecules to kill pathogens
70
What is a complement within the immune response?
A series of plasma proteins that act in an enzymatic cascade.
71
What is the difference between gram positive and gram negative bacteria?
CELL WALL STRUCTURE AFFECTING THE STAINING - gram +ve have thick peptidoglycan layer and becomes purple // gram -ve have a thin peptidoglycan layer staining red or pink
72
Give some examples of Pattern recognition receptors.
Toll like receptors/ nucleotides -binding oligomerization domain -like recpetors / Retioic acid -inducible gene i like recpetors/ C-type lectin -Like Receptors ..
73
Why do we need so many receptor types?
To prevent mutations against receptors.
74
Give an example of a pathogen which has adapted to overcome Pattern recognition receptor
Helicobacter pylori - reduces recognition by TLR5 // polio virus 'steals' RNA host 5' caps mimicking the hosts genome, hiding from NLRs
75
What are some responses of Protein Recognition Receptors
inform neighbouring cells -> Make inflammatory cytokines// tell adaptive immune cells -> phagocytose microbe and transport it to lymph node to be drained// limit microbe replication -> controlling pathogen
76
What are some uses of antibiotics?
Reduce infection during surgery / treat bacterial infections / used during chemotherapy and other cancer treatments /
77
What are some causes of antibiotic resistance ?
Over prescribing antibiotic -increases bacteria exposure to antibiotics // patients not finishing prescriptions- bacteria then multiply and gain more mutations// Over-use in live stock
78
What are some mechanisms of antibiotics?
Targets synthesis of : RNA / DNA / nucleic acids / ribosomal functions making pathogenic proteins/ cell wall synthesise // also inhibits cell metabolism and growth
79
What antibiotic can be used to combat penicillin , how does it work?
B-LACTAM -> binding to penicillin-binding proteins within bacteria preventing the cross-linkage of peptidoglycan layer of bacterial wall
80
How is antibiotic resistance developed?
1. Reduced drug uptake // 2. enzyme deactivates reducing antibiotic potency // 3. Target modification - reducing affinity // 4. increased drug efflux - increasing expression of drug efflux pumps
81
What are some current methods of tackling antibiotic resistance?
Developing new drugs/ vaccines // develop rapid diagnosis reducing the number of inappropriate antibiotic prescriptions// infrastructure preventing infection (e.g. better sanity...)
82
What is antigen variaton?
Microbes sequentially express different surface antigens to the immune system making it harder for the immune system to specifically defend against these pathogens
83
Why are memory cells better than naïve B lymphocytes
Longer life/ increased frequency / rapid proliferation/ produce more Antibodies / Have class switching - changing an isotype to the better functioning IgM from IgG
84
How do parasites evade the mammalian immune system?
angenic variation/ antigen mimicry/ immunosupression/ intraceullar processes/ cysts
85
Give an example and explain a disease which uses antigen variation.
African trypanosomes- parasite transmitted through taxi flies which is transported in the blood stream enters the CNS making an individual loose control of sleep patterns// This parasite has 1,000+ genes which encode for different versions of the protein coat
86
What are helminths?
A parasitic worm which cause infections on individuals
87
How do helminths subvert the immune response by enhancing networks
Being large, the immune system cannot destroy them via macrophages therefore complement proteins must be used to lysis or a specific immune response e.g. IgE.
88
Describe the IgE response to parasitic helminth
1. IgE binds to a specific helminth// 2.recruiting eosinophils 3. eosinophils release proteins, histamine and other immune cells to attack the helminth
89
How do parasites carry out antigen variation?
Have many genes which encode for different protein coats , genes become duplicated then the gene moves into the expression site body in order to be expressed
90
Using polio vaccine explain how vaccines are made.
1. pathogenic virus is isolated and cultured on a host// 2. Virus is incubated on cells from another host// 3. virus spontaneously mutates and grows on monkey cells // 4. virus can be used as a vaccine as it cannot grow on human cells
91
What is the hygiene hypothesis?
Helminths produce secreted molecules which trigger immunosuppression in the host (calm down the immune response) therefore it was thought that a lack of worm infections as reducing the regulation of T cell network therefore making the population more vulnerable to allergies
92
What is meant by adjuvant
An agent which acts non-specifically to increase the specific immune response or responses to an antigen
93
How are killed vaccines produced?
Using chemicals or heat the organism is killed making it ineffective, however these organism are still useful as they trigger an immune response without affecting an individual
94
How are subunit vaccines produced?
Toxoids (chemically inactivated toxins) are used, so only toxiods are within the vaccine, to trigger an immune response
95
How are recombinant subunit vaccines produced?
1. Nucleic acids from virus are isolated // 2. transferred into yeast cells // 3. virus -like particles generated and then purified and injected into an individual
96
How are live attenuated vaccines produced?
synthesis of attenuated pathogen using cultures are injected
97
Outline the design process for SARS-Co-V-2
1. antigen is identified (spike protein for COVID)// 2. vaccine delivery // 3. immune actiavtion
98
What is the process that activates Tells?
T cells recognise processed antigens present on MHC molecules on the surface of the antigen presenting cells (CD4 T cells see longer peptides on MHC Class II molecules and CD8 cells see short peptides on MHC Class I molecules.)
99
What is the function of CD4 cells?
HELPER CELLS (activated by MHC Class II ) enhance innate T cells // enhances mucous response //activates neutrophils and produces antimicrobial molecules
100
What is the function of CD8 cells?
Killer molecules (activated by MHC Class I) release inflammatory cytokines // release toxic granules which create holed in cells and enzymes triggering apoptosis.
101
How does the antibody response mature during primary immune response ?
Through class switching- different antibodies being present on the cell
102
What is the process that activates B cells?
BCR binds to antigen activating B cells
103
What is the responses of T cells to infection?
T cells are activated by Dendritic cells / 2. T cells proliferate// 3. T cells migrate out of lymph node// 4. T cells migrate to infected tissue and clear infection// 5. some T cells are destroyed and some remain as memory cells
104
Outline the process of dendritic cells processing antigens and activating T cells.
1. Pattern Receptor Recognition triggers enhanced phagocytosis // 2. Bacteria are digested within endosomes // 3. MHC molecules inside endosome meets pathogen// 4. MHC molecule contains peptides from pathogen and presents these on the cell surface // 5. PRR triggers dendritic cells to migrate from tissue into draining lymph node // 6. DC expresses MHC class I and II activating CD4 and CD8 T cells
105
What is apoptosis?
cell death
106
What is the response of B cells?
1. Activated by CD4 cells or BCRs(B cell receptors)// 2. Class switching // 3. B cells move to follicle forming germinal centre// 4. B cells proliferate and undergo somatic hypermutation changing the nucleotide in their receptor // 5. B cells compete for antigens -> B cells get help from CD4 T cells and differentiate into plasma cells
107
What are the 4 main antibody types and what does this mean?
IgM (Low affinity but lots of them ) // I gG (most abundant , activates complement pathway) // IgE(involved in anti-worm response)// IgA (found at mucosal site providing immediate protection)
108
What is virus latency?
Ability of the virus to lie dormant within a cell (DNA virus are most stable and create more persistent infections through latency
109
How do bacteria sense and respond to environmental changes?
1. SENSE KINASE detect conditions outside the cell// 2. AUTOPHOSPHORYLATION is trigged by signals// 3. PHOSPHATE BCEOMES A RESPONSE REGULATOR //4. RESPONSE REGULATOR BINDS TO DNA stimulating or repressing the target gene
110
What is comparative transcriptomics?
1. mRNA recovered from bacteria grown conventionally// 2. mRNA recovered from bacteria recovered from infected cell vitro// 3/ sequencing of nucleic acid// 4. identification can occur
111
Give some examples of when microbes are used in technology.
Taq DNA (used in PCR) //Biodegrading of plastics (anaerobic conditions = production of methane)// Restriction enzymes // Gene editing (CRISP-Cas-9)
112
What are the responses of some innate immune cells microbial products and what damage do these cause?
DENDRITIC CELLS - engulf pathogen + activate active immune // MAST CELLS + EOSIPHINS - release toxic molecules// MACROPHAGES - engulf and destroy// NEUTROPHILLIS- releases toxins
113
What are the four resistant mechanisms used by bacteria?
Reduced drug uptake// enzymatic degradation / target modification / increased drug efflux
114
What do antibiotics target and affect?
BACTERIA
Nucleic acid synthesis - targets machinery// ribosomal function- altering protein production // cell wall manufacturing // cell membrane- inhibiting cell metabolism and growth
115
