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Fundamental Biology 2X > Microbes and the immune system > Flashcards

Microbes and the immune system Flashcards

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1
Q

What are the three types of symbiosis ?

A
  1. mutualism (A and B benefits) // 2. Commensalism (A benefits and B is unaffected) // 3. Parasitism (A benefits and B is harmed)
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2
Q

What is meant by a microbiome?

A

a community of microorganisms within an area ~(microorganisms = bacteria/ virus…)

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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

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4
Q

Give an example of commensalism symbiosis.

A

Staphylococcus epidermidis utilises dead skin cells without causing harm to us

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5
Q

Give an example of parasitism

A

malaria

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6
Q

What is zoonosis?

A

An infectious disease transmitted to humans from animals

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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

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8
Q

What is pathogenicity ?

A

The ability to cause disease

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9
Q

What is virulence

A

The degree of pathogenicity of an organism

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10
Q

How is microarry technology carried out?

A
  1. 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
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11
Q

What technologies are used for different biomolecules?

A

(BIOMOLECULE - TECHNOLOGY )
DNA- Genomics // RNA - transcriptomics // Protein - proteomics // metabolite - metabolomics //

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12
Q

What are microbes?

A

Large mixed populations of microorganisms which coexist together under many circumstances

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13
Q

What is Koch’s postulates?

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

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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

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15
Q

What are basics of viral replication?

A
  1. 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.
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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) //

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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 //

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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

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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

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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

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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

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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 )

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23
Q

What is horizontal genetic transfer?

A

acquiring new genetic traits in bacteria// rapid growth ensures spread within the population

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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.)

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25
Q

What is a relaxasome?

A

A molecular structure DNA passes through (strains in which plasmids integrate into chromosomes)

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26
Q

What are the two life cycles of transduction?

A

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

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27
Q

What is quorum sensing

A

bacteria sense their population size and coordinate behaviour in response

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28
Q

What is a photoautotroph? Give an example of one.

A

Organism which uses sunlight and carbon dioxide as its primary sources of carbon to produce organic compounds // plants, algae, cyanobacteria.

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29
Q

What is a photoheterotroph? Give an example of one.

A

An organism which uses sunlight and pre-formed organic -compounds as its primary source of carbon// purple/ green non-sulphur bacteria

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30
Q

What is a chemoautotroph? Give an example of one.

A

An organism which uses chemical oxidation(breaking down organic or inorganic compounds through chemical reactions) and carbon dioxide as its carbon sources.// extremophiles

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31
Q

What is a chemoheterotroph? Give an example of one.

A

An organism which uses chemical oxidisation of pre-formed organic compounds // humans and animals

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32
Q

What is the optimal temperature for growth of a mesophile?

A

Body temperature e.g. human pathogen

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33
Q

What is the optimal growth for psychrophiles ?

A

<15 degrees C e.g. listeria monocytogenes (a pathogenic bacteria found in most environments )

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34
Q

What is the optimal temperature for growth of hyperthermophiles?

A

> 70 degrees C e.g. Thermus aquatic

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35
Q

What type of saturated fats do psychrophiles have in there membrane and why?

A

unsaturated fats // ensure membrane is fluid as they are found in low temperatures unsaturated fats are liquid at lower temperatures making them more suitable

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36
Q

Should a membrane be solid or liquid and why ?

A

More liquid consistency as this allows movement of compounds between cells.

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37
Q

What type of saturated fats do hyperthermophiles have in there membrane and why?

A

Saturated fat , ensures the membrane maintains structure at high temperatures.

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38
Q

What is the role of Synchronous?

A

To fixate 50% of marine carbon

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39
Q

Compare the neritic and oceanic zone.

A

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

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40
Q

What is biodegradation?

A

Physical or chemical change of material by microorganism (bacteria/ fungi)

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41
Q

What is the aerobic breakdown of plastic?

A

Plastic + oxygen -> CO2 + H20+ residual carbon

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42
Q

What is the anaerobic breakdown of plastic?

A

Plastic -> methane + CO2 + residual carbon

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43
Q

What is the difference between anaerobic and aerobic breakdown of carbon?

A

Anaerobic also produces methane .

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44
Q

What is the role of CRISPR- Cas9 ?

A

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

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45
Q

What are the 3 stages in recombination vaccines ?

A
  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
Q

What microbes are associated with what types of cancer?

A

Cervical cancer -> human papillomavirus // gastric cancer - > helicobacter pylori // bladder cancer -> schistosoma haematobium

47
Q

What is a actinomycetes?

A

A gram positive bacteria which has high GC levels

48
Q

What is the microbiota ?

A

the system of microorganisms within an individuals body (mainly in colon but also lings , skin , teeth

49
Q

What is 16S sequencing?

A

A method used for identifying and comparing bacteria samples dependent on the 16S RNA gene which encodes for a subunit within a ribosome.

50
Q

Compare 16S sequencing and Whole genome sequencing.

A

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
Q

Give some examples of ways the microbiota is developed in humans.

A

vaginal or caesarean delivery / milk consumption / diet / antibiotics/ environemnt/ pets

52
Q

How does gut bacteria promote a healthy human?

A

metabolises carbohydrates into short chain fatty acids // synthesises key micronutrients alike vitamin B3 / B5/ B6 / B12 //

53
Q

Why is it beneficial for carbohydrates to be broken down into short chain fatty acids?

A

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
Q

What is healthy inflammatory bowel disease?

A

ulcerative colitis// it is infiltration of bacteria which drives inflammation // lesions are generated by the immune response against disease

55
Q

What is clostridium difficile infection ?

A

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
Q

What are different methods of curing the microbiota ?

A

Faecal microbiota transplantation// full spectrum of microbial components // much less success for other conditions

57
Q

How do microbiota contribute to disease?

A

Limit disease as pathogenic microorganisms must compete with gut biota in order to survive and infect the individual

58
Q

What different microbial substances activate innate immune cells ?

A

pathogen-specific molecules (on the surface of microbes)/ double stranded - RNA / complement (blood proteins which distribute the membrane )

59
Q

What receptors do immune cells use to respond to microbial products and the damage they cause?

A

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
Q

What are 4 main resistance mechanisms used by bacteria?

A

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
Q

What is the difference between intrinsic and acquired resistance?

A

intrinsic is present before treatment but acquired is created during or after treatment

62
Q

What are the two types of substances and give examples.

A

Foreign and dangerous (viral and bacteria ) // innocuous or self (pollen and self epithelial cells)

63
Q

Give a brief overview of a initial response to infection or trauma.

A
  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
Q

What did Charles Janeway predict and when?

A

1989 - the presence of host receptors which recognise conserved pattern on pathogenic molecules

65
Q

What is a PAMPs?

A

pathogenic associated molecule pattern , a high conserved molecule which is expressed by foreign cells e.g. glycoproteins on virus

66
Q

Give an example of a PAMP for a virus, bacteria, fungi and protozoa.

A

Virus = glycoprotein // Bacteria= cell wall component // Fungi = Polysaccharides // Protozoa = Glycolipids

67
Q

What is a DAMPs?

A

A damage associated molecular pattern , evidence of damage resulting from an infection which is further developed from a PAMP

68
Q

What happens to PAMPs ?

A

They are released from dying cells acting as a signal to immune cells

69
Q

Give some examples of immune cells and their function

A

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
Q

What is a complement within the immune response?

A

A series of plasma proteins that act in an enzymatic cascade.

71
Q

What is the difference between gram positive and gram negative bacteria?

A

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
Q

Give some examples of Pattern recognition receptors.

A

Toll like receptors/ nucleotides -binding oligomerization domain -like recpetors / Retioic acid -inducible gene i like recpetors/ C-type lectin -Like Receptors ..

73
Q

Why do we need so many receptor types?

A

To prevent mutations against receptors.

74
Q

Give an example of a pathogen which has adapted to overcome Pattern recognition receptor

A

Helicobacter pylori - reduces recognition by TLR5 // polio virus ‘steals’ RNA host 5’ caps mimicking the hosts genome, hiding from NLRs

75
Q

What are some responses of Protein Recognition Receptors

A

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
Q

What are some uses of antibiotics?

A

Reduce infection during surgery / treat bacterial infections / used during chemotherapy and other cancer treatments /

77
Q

What are some causes of antibiotic resistance ?

A

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
Q

What are some mechanisms of antibiotics?

A

Targets synthesis of : RNA / DNA / nucleic acids / ribosomal functions making pathogenic proteins/ cell wall synthesise // also inhibits cell metabolism and growth

79
Q

What antibiotic can be used to combat penicillin , how does it work?

A

B-LACTAM -> binding to penicillin-binding proteins within bacteria preventing the cross-linkage of peptidoglycan layer of bacterial wall

80
Q

How is antibiotic resistance developed?

A
  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
Q

What are some current methods of tackling antibiotic resistance?

A

Developing new drugs/ vaccines // develop rapid diagnosis reducing the number of inappropriate antibiotic prescriptions// infrastructure preventing infection (e.g. better sanity…)

82
Q

What is antigen variaton?

A

Microbes sequentially express different surface antigens to the immune system making it harder for the immune system to specifically defend against these pathogens

83
Q

Why are memory cells better than naïve B lymphocytes

A

Longer life/ increased frequency / rapid proliferation/ produce more Antibodies / Have class switching - changing an isotype to the better functioning IgM from IgG

84
Q

How do parasites evade the mammalian immune system?

A
85
Q

Give an example and explain a disease which uses antigen variation.

A

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
Q

What are helminths?

A

A parasitic worm which cause infections on individuals

87
Q

How do helminths subvert the immune response by enhancing networks

A

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
Q

Describe the IgE response to parasitic helminth

A
  1. IgE binds to a specific helminth// 2.recruiting eosinophils 3. eosinophils release proteins, histamine and other immune cells to attack the helminth
89
Q

How do parasites carry out antigen variation?

A

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
Q

Using polio vaccine explain how vaccines are made.

A
  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
Q

What is the hygiene hypothesis?

A

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
Q

What is meant by adjuvant

A

An agent which acts non-specifically to increase the specific immune response or responses to an antigen

93
Q

How are killed vaccines produced?

A

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
Q

How are subunit vaccines produced?

A

Toxoids (chemically inactivated toxins) are used, so only toxiods are within the vaccine, to trigger an immune response

95
Q

How are recombinant subunit vaccines produced?

A
  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
Q

How are live attenuated vaccines produced?

A

synthesis of attenuated pathogen using cultures are injected

97
Q

Outline the design process for SARS-Co-V-2

A
  1. antigen is identified (spike protein for COVID)// 2. vaccine delivery // 3. immune actiavtion
98
Q

What is the process that activates Tells?

A

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
Q

What is the function of CD4 cells?

A

HELPER CELLS (activated by MHC Class II ) enhance innate T cells // enhances mucous response //activates neutrophils and produces antimicrobial molecules

100
Q

What is the function of CD8 cells?

A

Killer molecules (activated by MHC Class I) release inflammatory cytokines // release toxic granules which create holed in cells and enzymes triggering apoptosis.

101
Q

How does the antibody response mature during primary immune response ?

A

Through class switching- different antibodies being present on the cell

102
Q

What is the process that activates B cells?

A

BCR binds to antigen activating B cells

103
Q

What is the responses of T cells to infection?

A

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
Q

Outline the process of dendritic cells processing antigens and activating T cells.

A
  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
Q

What is apoptosis?

A

cell death

106
Q

What is the response of B cells?

A
  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
Q

What are the 4 main antibody types and what does this mean?

A

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
Q

What is virus latency?

A

Ability of the virus to lie dormant within a cell (DNA virus are most stable and create more persistent infections through latency

109
Q

How do bacteria sense and respond to environmental changes?

A
  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
Q

What is comparative transcriptomics?

A
  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

Fundamental Biology 2X (7 decks)

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