Microbiology Flashcards

Question

When does disease occur?

Answer 1

10 hours unrestricted growth > 1 billion organisms Speed matters: Early defence response= no disease, Late response = disease

Answer 2

Causes Superficial ( e.g. skin and soft tissue) infections and Deep seated infections (bacteraemia, endocarditis, osteomyelitis). Community and hospital acquired infection. Leading cause of Surgical site infections, Leads to other hospital acquired infections e.g. bacteraemias, MRSA through acquisition of resistance genes. Virulence factors: Staphylococcal protein A - binds to immunoglobulins and reduces phagocytosis, Coagulase - activates host prothrombin to convert prothrombin to thrombin and promote clotting of host plasma/blood, Panton Valentin leukocidin (PVL) (some only) - skin abscesses and nectrotizing pneumonia, Biofilm - extracellular polysaccharide network allows persistence on prosthetic material, Clumping factor - mediates clumping and binding to fibrinogen, Toxic Shock Syndrome Toxin (TSST1/2) (some only) - superactivation of T-cells, Capsule - resists phagocytosis.

Answer 3

Colonisation in throat and nasopharynx -> Mucosal infection (Sinusitis, Otitis Media, Pneumonia) -> Invasive disease (Bacteraemia, Meningitis) Virulence factors: Capsule - Resists phagocytosis, Pneumolysin - damages epithelium and inhibits mucous-ciliary beating, Pili - binds to host epithelium, Hydrogen peroxide - cell damage and inhibits other bacteria, Neuraminidase - cleaves mucin, Cytokine production - promotes inflammation.

Answer 4

Ascending bacterial infection of the urinary system. Virulence factors: Fimbriae (type 1 and P) - Adhesion to host cell, Biofilm formation, Cytokine induction; Flagellum - motility; Lipopolysaccharide (LPS) - colonize bladder and induces cytokines; Outer membrane vesicles - bud off cell surface to deliver toxins to host; Capsule - inhibits phagocytosis; Siderophores - iron uptake system; Alpha-haemolysin - induces cell lysis.

Answer 5

Bacteria: Gram negative cocci, Carriage: nasopharynx of 5-10% population (Higher carriage rates in school-aged children and young adults), Transmission: Respiratory droplets, Diseases: Meningitis, Septicaemia (sepsis), Virulence factors: Pili - colonization of nasopharynx, Lipooligosaccharide (LOS) - mediates toxic effects, Capsule - inhibits phagocytosis. Mechanism: LOS > binds to cells in innate immune system > cytokine release > endothelial damage and capillary leakage

Answer 6

Hospitalized patients at great risk for new infections since greater opportunity for ‘opportunistic pathogens’. Host factors: breach in physical defences, loss of cellular immunity, prosthetic material, loss of microbiome. Pneumonia - S. pneumoniae initially but also Gram negative bacteria; Surgical site infections - S. aureus including MRSA but also other pathogens; Urinary tract infections - E. coli but also other pathogens (e.g. proteus…); C. difficile infections - loss of microbiome in bowel.

Answer 7

Humans evolved on a planet dominated by microbes. In the environment, microorganisms live in complex communities, with competitive and non- competitive interactions, dependencies, and adaptation to the habitat. Human commensals live in complex communities too: the human microbiome. Some areas of the body microbial organisms are not expected to occur under normal circumstances. Sterile sites: Major organs – Brain, heart, liver; Bone/bone marrow; Joints.

Answer 8

Commensals live within us but do not cause us disease (can be carriers), pathogens cause disease. In clinical practice distinguishing a commensal from a pathogen is complex. Any microorganism capable of causing disease is a pathogen; for many commensals disease causation is an accident because it is not required for their evolutionary survival. Obligate pathogens depend on disease causation for transmission and their evolutionary survival: Mycobacterium tuberculosis.

Answer 9

Commensals: live in humans but don’t cause harm, Obligate: depend on disease causation for transmission and their evolutionary survival (Mycobacterium tuberculosis), Zoonotic: microorganism that is a colonizer of pathogen in animals, transmitted to humans via direct vector or with direct contact with the animal or its products (Chlamydophila psittaci, Borrelia burgdorferi, Bacillus antracis), Environmental: microorganism able to cause disease transmitted to humans from an environmental source such as water or soil (Clostridium tetani, Clostridium botulinum)

Answer 10

Escape from the host or reservoir, Transport to the new host, Entry, Escape.

Answer 11

Entry, Niche establishment, Multiply, Spread, Exit the host. Entry via Adhesins Pili; leads to capsule formation; Detect changes in temp, O2, pH, metal concentrations; Quorum sensing; Small regulatory RNAs; Necrotic death means production of exudates that allows exit and transmission into a new host. Can spread through the body as blood, lymph + blood, nerves, cerebrospinal fluid. Portal of exit is the path used by the pathogen to leave the host. Usually corresponds to the site where the pathogen is located.

Answer 12

Time to infection with a microorganism to symptom development; Symptom onset reflects pathogen growth and invasion, excretion of toxins, initiation of host-defense mechanisms; Range between few hours (food poisoning) to decades (Tuberculosis), The infected host can be infectious. S. aureus food poisoning: 8-24 hours, Bacillus cereus food poisoning: within 24 hours, Salmonella: 6-48 hours, SARS-associated coronavirus: 3-10 days, Varicella-zoster: 10-21 days, Legionella pneumophila: 7-21 days, Treponema pallidum: 10-90 days, Hepatitis A virus: 14-50 days, HIV: <1 - >15 years

Answer 13

Concealment of antigens Intracellular persistence, Colonizing privileged sites, Concealment by taking up host membranes or molecules

Answer 14

Diabetes, Chronic renal disease, Chronic liver disease, Chronic obstructive pulmonary disease, Malignancy, Immunosuppression: Primary - congenital, Iatrogenic - Chemotherapy, Transplants (solid organ); Acquired - HIV.

Answer 15

E. Coli is most common cause of urinary tract infections: Lower urinary tract infection (bladder and urethra); Upper UTI (ascending to ureter/kidneys) - pyelonethritis, renal abscess; Prostatitis (form ascending or haematogenous infection). Other Enterobacteriaceae: Proteus mirabilis associated with renal calculi (urease protuction); Citrobacter spp., Enterobacter spp., Serratia spp. = associated with antibiotic resistance.

Answer 16

Direct: Direct contact, Droplet spread; Indirect: Airborne, Vehicle borne, Vector borne (mechanical or biologic).

Answer 17

Directed against the area in the infection chain most susceptible to intervention. Controlling or eliminating the agent at the source: Antimicrobial treatment, Isolating the infected patient, Soil might be covered; Mode of transmission: Water treatment, Hand washing, Decontamination of the environment, Modification of air pressure/quality – filters, Controlling vectors – mosquitoes; Portals of entry: Use of Personal protective equipment (PPE): masks, gloves, Bed nets in zones of malaria; Increasing host defenses: Vaccination, Prophylactic use of medication - antimalarials, Herd immunity.

Answer 18

Hand hygiene, PPE, Linen management, Equipment, Environment, Patient placement, Occupational Exposure, Respiratory & cough hygiene, Waste management, Blood & body fluid spillage

Answer 19

Clinician: Investigations, Antimicrobial treatment Infection control: Isolation in health care environment, Standard Infection Control precautions (SICPS), Outbreak detection Public health: Contact tracing, Containment in the community, Post-exposure prophylaxis Vaccination

Answer 20

Continuous and systematic collection and analysis of data and subsequent reporting of significant findings to effect change. Aim: Recognition and initial management of outbreaks. Examples: Influenza virus, Salmonella, E.coli 0157 outbreaks in food.

Answer 21

Primary: prevent occurrence of disease by preventing exposure to hazards that cause poor health (Prevention of smoking, Vaccination…) Secondary: Minimize impact of a poor health outcome that has already occurred (Screening tests at early stages fo disease - Hepatitis C…) Tertiary: Lessen the impact of a poor health outcome with lasting effects (Early antiretroviral therapy for HIV…)

Answer 22

Aim to contain the infected patient or deal with the source of infection in the community: Depend on the particular organism, Isolation of infected individual – exclusion from work during incubation or symptomatic periods, Environmental assessment, decontamination of sources, Post-exposure prophylaxis, Vaccination. Quaratine: Separating and restriciting movement of individuals exposed to a communicable disease. Isolation: Separating and restricting movement of individuals suspected or confirmed to be infected with a communicable disease.

Answer 23

Immunity is the ability of the body to protect itself from infectious disease. Can be innate or acquired. Acquired: specific to a single organism or a group to closely related organisms. Can be active or passive. Active - involves cellular and antibody responses, produced by patient’s own immune system, long lasting, can be acquired by natural disease or vaccination; Passive - protection by transfer of antibodies from immune individuals across the placenta or from transfusion of blood or blood products such as immunoglobulin.

Answer 24

Induce active immunity and provide immunological memory; Antibodies can be detected in blood or serum; Even in the absence of detectable antibodies, immunological memory may still be present. Types of vaccines: Inactivated organisms, Secreted products, Recombinant components – cell walls, mRNA

Answer 25

Establish a diagnosis: Clinical signs and symptoms, Relevant exposures – risk factors, Request appropriate investigations; Antimicrobial treatment, Source control, Infection control precautions to limit spread in the hospital environment, Public health interventions, Occupational health interventions

Answer 26

As part of infant immunisation programme; Routine older adult programme (>65 years); Clinical risk groups: Asplenia, Chronic respiratory disease, Chronic heart disease, Chronic kidney disease, Chronic liver disease, Diabetes, Immunosuppression, Individuals with cochlear implants, Individuals with cerebrospinal fluid leaks, Ocupational risk: exposure to metal fumes - welders

Answer 27

Urinary tract infection (UTI) commonly results from the presence and the multiplication of bacteria in one or more structures of the urinary tract with consequent tissue invasion. Can cause variety of clinical syndromes (acute uncomplicated cystitis, acute urethral syndrome, acute pyelonephritis, chronic pyelonephritis, perinephric abscess, renal abscesses, urethritis and prostatitis). Bacteriuria refers to the presence of bacteria in the urine sample. Significant bacteriuria is defined as >10^5 of colony-forming units (CFU) of a single species of bacteria per millilitre in a freshly voided midstream sample of urine. The presence of bacteriuria is NOT synonymous with UTI; the patient MUST have clinical symptoms of infection (dysuria and frequency, urgency of micturition, suprapubic discomfort, haematuria, pyrexia, loin pain and rigours). Asymptomatic bacteriuria is not a UTI and does not usually require antimicrobialtreatment (exception: pregnancy, renal transplant). Colony count and significance of the culture: >100,000 colonies/ml of one colony type - significant finding (from result using 1µl loop - plate shows >100 colonies of 1 type), 10,000-100,000 colonies/ml - indeterminate (from result using 1µl loop - plate shows 10-100 colonies of 2+ types), <10,000 colonies/ml - likely not a significant finding (from result using 1µl loop - plate shows <10 colonies).

Answer 28

If using 1µl loop: Plate shows <10 colonies - No significant growth, Plate shows 10-100 colonies of two or more types of colonies - Report as mixed organisms with colony count (10,000-100,000 cfu/ml), Plate shows >100 colonies of one colony type - Report the organism with colony count (>100,000 cfu/ml) and perform sensitivities, Plate shows >100 colonies of more than two types of colonies - Report as mixed organisms with the colony count (>100,000 cfu/ml), Add comment (for example “Doubtful significance. Please consult microbiologist if advice is required. Isolate(s) will be held for 7 days.”). Colony count and significance of the culture: >100,000 colonies/ml of one colony type - significant finding, 10,000-100,000 colonies/ml - indeterminate, <10,000 colonies/ml - likely not a significant finding. Culture media: MacConkey agar (pink) is a selective medium useful for the culture of coliforms, contains bile salts, lactose, and a pH indicator; The bile salts inhibit growth of non-intestinal bacteria, The pH indicator, neutral red, helps to distinguish the lactose-fermenting coliforms from the non-lactose fermenting organisms - some coliforms (for example E. coli) ferment lactose (catabolism), producing acid which acts on the neutral red pH indicator, causing a colour change, Lactose-fermenting colonies grown on MacConkey agar are therefore pink, Examples of non-lactose fermenters include Salmonella and dysentery groups.

Answer 29

Bacteraemia (bacteria in the bloodstream) and sepsis caused by Gram-negative bacteria are common problems in hospitalised patients. The cell wall of Gram-negative bacteria contains a component called endotoxin - this is responsible for much of the classical pathophysiology of septic shock; essentially, endotoxin causes immune cells to overproduce huge amounts of cytokines that result in increased vascular permeability and hypotension. The most encountered Gram-negative bacteria are members of the Enterobacteriaceae (also known as “coliforms”), including Escherichia coli. Other non-coliform Gram-negative species, such as Pseudomonas aeruginosa, are also important in hospitalised patients. Pseudomonas aeruginosa is resistant to many of the normally used antimicrobials (e.g. ampicillin) but is usually sensitive to other antimicrobials (including piperacillin-tazobactam, ciprofloxacin and gentamicin). In the laboratory, Pseudomonas aeruginosa is easily recognised - it often forms characteristic flat colonies with a metallic sheen on blood agar, does not ferment lactose on MacConkey agar, and is oxidase test positive. In hospitalised patients, common sources of Gram-negative bacteraemia include urinary tract infections (most common, particularly in those with a urinary catheter), abdominal infections and hospital-acquired pneumonia. Initial antimicrobial treatment should be chosen to cover the possible sources, considering previous microbiology results from the patient, your hospital’s antimicrobial prescribing policy, as well as any allergies your patient may have. It is also important to consider the source of the infection and remove it if possible (e.g. if the source is an abscess full of pus this will need surgical drainage, if the source is a urinary catheter - the catheter should be removed if possible or changed if still required.) Urinary catheters should NOT be used unless there is no alternative for the patient, as they are a definite risk factor for hospital-acquired infection.

Answer 30

Since the first widespread clinical use of penicillin in the mid-20th Century, bacteria have developed mechanisms to become resistant to antimicrobials. Although resistance in Gram positive bacteria, such as Staphylococci (e.g., Methicillin Resistant Staph. aureus - MRSA) is a worry, several new antimicrobials are available that have overcome this resistance - for now. More worrying at present is the rapid rise in resistance seen in Gram-negative bacteria (e.g. E. coli, Pseudomonas aeruginosa). In the UK, infections are still usually treatable with antimicrobials, but in some parts of the world infection with bacteria that are resistant to almost all antimicrobials have started to occur. The worry is that this resistance will spread to other parts of the world, including the UK. With few or no new antimicrobials that work against these resistant Gram-negative bacteria, we may be heading full circle back to an era when some bacterial infections are no longer treatable with antimicrobials.

Answer 31

Mandatory patient demographics on request form: 1. Patient Identifier Number (CHI/PAS) 2. Surname 3. Forename 4. Date of birth 5. Gender 6. Location (for hospital name of ward, clinic... For GP’s this must be the GP practice) NB. If the patient identifier is unavailable then the MDS includes: First line of patient address, Postcode. Mandatory information required on the sample: 1. Surname 2. Forename (preferably) or initial 3. Date of birth 4. Sample date/time Other information required: Consultant or GP, Specimen Type, Clinical details.

Answer 32

Septic arthritis is the inflammation of a joint, which is caused by microorganisms (mostly bacteria but also other organisms for example fungi). The signs and symptoms include pain, swelling, redness of the joint and fever. The organisms most frequently isolated are Staphylococcus aureus and Streptococci. Investigations must include aspiration of joint fluid and blood cultures prior to the initiation of antimicrobials. Methicillin-resistant Staphylococcus aureus (MRSA) can also cause septic arthritis. MRSA is resistant to beta-lactam antimicrobials e.g., flucloxacillin and standard antimicrobial treatment would fail if infection is caused by MRSA. It is very important to be aware of risk factors that should alert you towards this aetiology like previous history of MRSA colonisation/infection, recent surgery, admission to hospital or nursing home, previous exposure to antimicrobials, renal dialysis, permanent indwelling catheter, skin ulcers and some underlying diseases like diabetes mellitus. If MRSA is suspected, a glycopeptide antimicrobial (e.g. vancomycin) should be prescribed until identification and susceptibility testing results from the investigations are available.

Answer 33

Slide agglutination test for Identification of Staphylococcus aureus: (You can use the positive and negative control if result is difficult to interpret.) 1. Shake the latex to obtain an even suspension and dispense a drop into a circle on the reaction card for each culture to be tested. 2. Take a loop and pick up some of the culture by touching it with the flat end of the loop. As a guide, an amount of growth roughly equivalent to 1-2 average-sized colonies should be picked. 3. Emulsify the sample of culture in a drop of latex by rubbing with the flat end of the loop. Rub thoroughly, but not too vigorously or the surface of the card may be damaged. Some strains, particularly of species other than S. aureus remain difficult to emulsify and this should be noted, since lumps of unemulsified culture can make the latex appear ‘rough’ or ‘stringy’ on reading. Spread the latex over approximately half the area of the circle. Discard the mixing stick for safe disposal. 4. Rotate the card gently and examine for agglutination for approximately 20 seconds, holding the card at normal reading distance (25-35 cm) from the eyes. Do not use a magnifying lens. The patterns obtained are clear-cut and can be recognised under any normal lighting conditions. A Positive test is indicated by agglutination within 20 seconds. A Negative test shows no agglutination. NB An uninterpretable result shows agglutination in the negative control.

Answer 34

Complete set of genetic informationin an organism, Provides all the information an organism requires to function, Genome is stored in long molecules of DNA packaged in chromatin andformed into chromosomes, In eukaryotic cells, the genome is contained within the nucleus.

Answer 35

The nucleotide: 5-Carbon sugar - 2-deoxyribose, Phosphate, Base - nitrogen containing ring - either pyrimidines (cytosine/thymine {- all got Ys}) or purines (adenine/guanine) Base pairs: A pairs with T, G pairs with C (Just the base + sugar is called a nucleoside)

Answer 36

DNA is a polynucleotide chain. Sugars are joined by a phosphodiester linkage - linkage is via the 5’ and 3’ groups on the sugar. Chain has distinct directionality or polarity. The free 5’ phosphate is the 5’ end of the chain (the start), The free 3’ OH is the 3’ end of the chain (the end)

Answer 37

DNA is packed into chromosomes by first packing into nucleosomes (beads on a string arrangement). DNA is associated with proteins: histones & other nonhistone chromosomal proteins, known as chromatin, First and most fundamental ‘level’ of chromatin packing is the nucleosome, Histones are DNA-binding proteins (small positively charged proteins). Two each of: H2A, H2B, H3 & H4 (octamer), Histone tails are significant (+ charge, provide driving force for folding by mediating favorable internucleosomal interactions and screening DNA repulsion), Histones are highly conserved in evolution - only 2 differences in amino acid sequence between pea and cow (histone H4). Highly-ordered: Short region of DNA double helix (2nm), "Beads-on-a-string" form of chromatin (11nm), Chromatin fiber of packed nucleosomes (30nm), Chromatin fiber folded into loops (700nm), Entire mitotic chromosome (1400nm), Net result: each DNA molecule has been packaged into a mitotic chromosome that is 10,000-fold shorter than its fully extended length.

Answer 38

Histones are DNA-binding proteins (small positively charged proteins). Two each of: H2A, H2B, H3 & H4 (octamer), Histone tails are significant (+ charge, provide driving force for folding by mediating favorable internucleosomal interactions and screening DNA repulsion), Histones are highly conserved in evolution - only 2 differences in amino acid sequence between pea and cow (histone H4)

Answer 39

23 chromosomes; 46 chromosomes in diploid cells; 3 billion nucleotide (base) pairs; 22 autosomes; 1 pair sex chromosomes; Average chromosome = 4.8 cm length, 140 million nucleotides per strand = a lot of DNA in a very small space.

Answer 40

Each strand of a DNA molecule can act as a template for the synthesis of its complementary strand. Base-pairing enables DNA replication. DNA replication is semiconservative (original strand remains intact through many rounds of replication). Strands must be separated before replication can begin; Initiator proteins recognise replication origins & open up the helix locally; Provides single-stranded templates ready for DNA synthesis. ~10,000 replication origins in human genome DNA synthesis occurs at replication forks, two forks form at each origin; Replication proceeds bidirectionally, unzipping the DNA strands as it goes; Most important enzyme in DNA replication is DNA polymerase. DNA is synthesised in the 5’ to 3’ direction; DNA polymerase adds deoxyribonucleotides to the 3’ end of the growing chain; Added as deoxyribonucleotide triphosphates (dNTPs); Base-pairing dictates which nucleotide is added; Energy required for synthesis reaction comes from hydrolysis of the dNTP’s high-energy phosphate bond. At a replication fork, the two newly synthesised DNA strands are of opposite polarities - this creates a problem for DNA polymerase, which can only synthesise DNA in a 5’-3’ direction; Solution: Semidiscontinuous replication; Leading strand synthesised continuosly, Lagging strand synthesised discontinuosly - short sections (Okazaki fragments) are subsequently joined together by enzyme DNA ligase. DNA polymerase can only continue an existing strand, not initiate new ones; An RNA polymerase known as primase makes RNA primer first (~10 bases long); DNA polymerase can then extend the RNA chain; Only one RNA primer needed for leading strand, but lagging strand has continuous requirement; RNA later removed by nuclease activity. DNA synthesis is carried out by a group of proteins that act together as a DNA synthesis machine: Single stranded binding proteins keep the helix unwound, DNA helicase helps unwind the double helix. DNA polymerase proofreads its own work: Replication must be very, very accurate (although mutations must arise at some frequency, or evolution couldn’t occur); Consequences of errors can be fatal; Allowing for proofreading, DNA polymerase makes around 1 error in 10^7 bases.

Answer 41

DNA mismatch repair: Mismatch repair corrects ~99% of errors made by DNA polymerase; Mutations in mismatch repair genes predispose to cancer; Must repair new strand.

Answer 42

Replication errors, UV light, Chemicals, Radiation, Cellular metabolism all lead to DNA damage, so need DNA repair mechanisms. DNA continuously suffers damage in cells - spontaneous intracellular chemical reactions (eg depurination, deamination), exposure to ultraviolet light can form thymine dimers.

Answer 43

Many different repair pathways exist, each recognising and correcting a specific type of damage. Most often, information in the undamaged strand is used to correct the damaged strand; Repair relies on the redundancy of information, if one strand is damaged, the encoded information is not lost.

Answer 44

Genetic defect: Affected individuals cannot repair thymine dimers, Leads to severe skin lesions, including skin cancer.

Answer 45

Mitochondrial: Circular, 16,569 base pairs, 37 genes - 2 rRNAs, 22 tRNAs and 13 core subunits of the cellular respiratory chain that drives oxidative phosphorylation (ATP), Genome is not enveloped and not packaged into chromatin, Inheritance is strictly maternal, Replication via DNA polymerase γ Nuclear: Linear, 3.3 billion base pairs, ~21,000 genes, Genome is enveloped and packaged into chromatin, Inheritance equal from both parents.

Answer 46

Genes contain information to make proteins; Proteins: Serve as building blocks for cell structures, Form enzymes to catalyze the cells chemical reactions, Regulate activity of genes, Enable the cells to move and communicate with each other.

Answer 47

DNA: Very long - many genes (250 million nucleotides), Double stranded, ‘Simple’ 3-D structure (double helix), Chemically stable, Contains deoxyribose, Contains thymine RNA: Short - copy of a single gene (500-2000 nucleotides), Single stranded, Complex 3-D structure (more like protein), Less stable, Contains ribose, Contains uracil in place of thymine

Answer 48

Transcription produces an RNA copy of the coding strand of DNA (except that it contains U, not T)

Answer 49

DNA has a coding (sense) strand and noncoding (template, antisense) strand. The non-coding strand of DNA provides the template for mRNA synthesis.

Answer 50

DNA has a coding (sense) strand and noncoding (template, antisense) strand. The non-coding strand of DNA provides the template for mRNA synthesis. Transcription is carried out by RNA polymerase. Three types; mRNA is made by RNA polymerase II: Makes an RNA copy of one DNA strand (= mRNA), Requires a DNA template and activated precursors (nucleoside triphosphates - ATP, GTP, UTP and CTP), Synthesises in 5’ - 3’ direction, Does not require a primer, Error rate ~1 in 10^4, Many RNA polymerases can transcribe a gene at the same time

Answer 51

Although all cells in a human contain the same set of genes, each different cell type expresses a different complement of genes. Genes may be either on (expressed) or off in a given cell - not all genes are expressed in all tissues at all times - gene expression is highly controlled. Genes may be expressed in a: tissue-specific pattern; developmentally regulated pattern; combination of these; “on” all the time, in all tissues (constitutive - e.g. housekeeping genes).

Answer 52

There are 6 possible control arenas to modulate/control gene expression: Control of the activation of gene structure (open chromatin/euchromatin) - promoters, Control of the initiation of transcription and transcriptional elongation - enhancers, Processing the RNA transcript, Transport of mRNA to the cytoplasm from the nucleus, Translation of mRNA, Degradation and turnover of RNA. Promoters and enhancers: A promoter is made up of the sequence elements found immediately 5’ to the gene that interact with RNA polymerase & other components of the transcription machinery; Enhancers increase transcription from a nearby gene but can operate over considerable distances; Promoters and enhancers contain sequences to which transcription factors specifically bind.

Answer 53

Transcription factors are proteins which bind to specific DNA sequences (upstream/downstream to RNA polymerase complex) within the promoter or enhancers so as to increase or decrease gene expression

Answer 54

One gene may encode more than one product Expression of a single gene can be controlled at various levels to give different products: • alternative promoters • alternative splicing • alternative polyadenylation

Answer 55

Most eukaryotic genes are discontinuous, being split into exons and introns - exons contain coding sequences; introns (‘intervening sequences’) are found between exons. Introns are removed from the primary transcript by splicing to give a functional RNA molecule. Alternative splicing means can express >1 product from one single gene (e.g. the alpha-tropomyosin gene can be spliced in many different ways)

Answer 56

Transcription occurs in the nucleus; Translation occurs in cytosol. Before RNA can be exported from the nucleus it must go through RNA processing steps: • Slicing • Capping • Polyadenylation

Answer 57

Modifies the 5’ end of a RNA transcript. The RNA cap includes an atypical nucleotide: a guanine nucleotide that has a methyl group attached to the 5’ end of the RNA in an unusual way.

Answer 58

A polyA tail is a string of adenylate residues added to the 3’ end of an mRNA. Not found on rRNAs or tRNAs; Transcription proceeds past polyA site, transcript is cleaved, the polyadenylated (i.e. termination of transcription is distinct from polyadenylation).

Answer 59

5’ untranslated (5’UTR) is the region of an mRNA that is found upstream of the translated region; Function of 5’UTRs is mostly unclear, may affect translational control. 3’ untranslated (3’UTR) is the region of an mRNA that is found downstream of the translated region; 3’UTRs can determine the stability of the mRNA.

Answer 60

mRNA: messenger RNA, encodes proteins tRNA: transfer RNA, adaptor molecules rRNA: ribosomal RNA, component of ribosome Three major classes of RNA, all 3 encoded by DNA, not all RNAs encode proteins.

Answer 61

Majority of genes specify amino acid sequences; Final products of other genes is the RNA itself: non-coding RNAs. mRNA (messenger RNA) encodes proteins, rRNA (ribosomal RNA) form core of ribosome structure and catalyse protein synthesis, miRNAs (micro RNAs) regulate gene expression, tRNA (transfer RNA) serve as adaptors between mRNA and amino acids during protein synthesis, Other noncoding RNAs are used in RNA splicing, gene regulation, telomere regulation…

Answer 62

Class of RNA molecules with closed loops, High stability, Abundantly expressed in eukaryotic organisms.

Answer 63

Based on DNA replication, in vitro. Applications include genotyping– e.g. to detect mutations in the DNA of patients affected by a genetic disorder. Get region of double stranded DNA to be amplified, then heat to separate strands, cool to anneal primers (+ pair of primers), allow for DNA synthesis (+ DNA polymerase + dATP + dGTP + dCTP + dTTP). And you will get the products of the first cycle. Products of first cycle is 2 double-stranded DNA molecules, Products of second cycle is 4 double-stranded DNA molecules, Products of third cycle is 8 double-stranded DNA molecules…

Answer 64

Deoxyribonucleic acid is a nucleic acid polymer, formed by two polynucleotide chain strands usually arranged in adouble-helix, The nucleotides are joined to one another by a covalent (phosphodiester) bond; The individual bases of the two separate polynucleotide strands are associated with each other according to the rules ofcomplementary base pairing (a pyrimidine always binds to a purine): adenine with thymine via two hydrogen bonds and cytosine with guanine via three hydrogen bonds to form double stranded DNA; Both strands of double-stranded DNA store information that is complementary. It has a direction: the phosphodiester bonds form between the third and the fifth carbon of adjacent deoxyribose sugar molecules. Therefore, any DNA strand normally has one end (the 5’ end) where there is a terminal phosphate group attached to the 5′ carbon of a ribose (the 5′ phosphoryl); while at the other end of the chain (the 3’ end), there is a free hydroxyl group attached to the 3′ carbon of a ribose (the 3′ hydroxyl). The 3’-hydroxyl is one of the most important groups in all biology: in a DNA double helix, the two complementary strands of DNA run in opposite directions to each other (anti-parallel); each complementary strand runs from 5’ to 3’ but in opposite directions in the helix.

Answer 65

Interphase (most time spent here): The cell grows and copies its DNA; G1 - Cell growth, S: DNA synthesis, G2: More growth, preparation for mitosis Mitosis: The cell divides its DNA and cytoplasm, forming two new cells; Prophase, Metaphase, Anaphase, Telophase G0: Resting state where the cell performs its functions and is not preparing to divide (kinda like a pause G1 stage) Checkpoints: G1 checkpoint (restriction) - at end of first growth phase of interphase, G2 checkpoint - at end of second cell growth phase in interphase, M checkpoint - just after metaphase in mitosis Control: Cyclin D CDK4 - start of G1, Cyclin E CDK2 - middle/end of G1, Cyclin A CDK2 - during S, Cyclin B CDK1 - between G2 and Mitosis

Answer 66

DNA replication occurs in S phase of cell cycle; Before DNA replication can begin the super-coiled DNA in the chromosome must be relaxed, this occurs in segments and begins at multiple origin of replication sequences (and requires the action of topoisomerase) to transiently separate the two strands of the parental DNA to create a ‘replication bubble’. The enzymes that can synthesise the new DNA strand from a template are called DNA polymerases (and in all eukaryotes and prokaryotes, different DNA polymerases share the same fundamental type of synthetic activity (anti-parallel synthesis in the 5’ to 3’ direction). DNA polymerases can only elongate a DNA strand, not initiate synthesis, so a primer (providing the critical 3’OH group) is needed to initiate DNA synthesis; This function is provided by a special RNA polymerase (called a primase) which synthesis a short complementary RNA chain that provides the 3’OH priming end from the DNA template (both the lagging strand and the leading strands require primers).

Answer 67

In semi-conservative replication, each parental strand of DNA serves as the template for the synthesis of a new strand so that, eventually, the old parental duplex is replaced by two parental duplexes (each formed by one parental strand and one newly-synthesised strand). The enzymes that can synthesise the new DNA strand from a template are called DNA polymerases (and in all eukaryotes and prokaryotes, different DNA polymerases share the same fundamental type of synthetic activity (anti-parallel synthesis in the 5’ to 3’ direction).

Answer 68

Most important enzymes in DNA replication are the DNA polymerases (nuclear DNA replication in eukaryotes requires multiple proteins including three DNA polymerases: α {alpha}, δ {delta}, ε {epsilon}); Two forks form at each origin; replication proceeds bi-directionally, unzipping the DNA strands as it goes

Answer 69

DNA is synthesised in the 5’ to 3’ direction. DNA polymerase (as part of a large multi-protein ‘holo-enzyme’ complex adds deoxyribonucleotides to the 3’ end of the growing chain); Added as deoxyribonucleotide triphosphates (dNTPs). Base-pairing dictates which nucleotide is added; the energy required for the synthesis reaction comes from hydrolysis of the dNTP's high-energy phosphate bond. But the fork exposing more 5’ creates a problem for DNA polymerase, which can only synthesise DNA in the 5’ to 3 direction - solution is semi-discontinuous replication.

Answer 70

DNA polymerase a/primase binds to the initiation complex at the origin of replication and synthesizes a short strand (of approximately 10 bases of RNA followed by 20 to 30 bases of DNA) - forming a different primer on both the leading strand and the lagging strand. DNA polymerase a/primase is then replaced by a different DNA polymerase which will extend the DNA chain from the 3’-OH - DNA polymerase e on the leading strand and DNA polymerase d on the lagging strand (polymerase-switch). The leading strand at each replication fork is synthesised continuously (requiresonly one primer) while the lagging strand of each replication fork requires a series of initiation events/primers and is synthesised discontinuously (requiring multiple primers) (But the replication fork moves)

Answer 71

Fragments formed by semi-discontinuous replication on the lagging strand of the DNA fork. 1000-2000 bases in length; Synthesis of the next upstream Okazaki fragment displaces the original RNA primer, An enzyme (flap endonuclease 1, FEN1) cleaves the RNA primer, All of the fragments are joined together by the enzyme DNA ligase.

Answer 72

‘Hereditary non-polyposis colorectal cancer’ syndrome. Most colo-rectal cancers are sporadic but inherited cancer syndromes account for 5-10%, most commonof these is Lynch syndrome: The individual has an 80% life-time risk of colo-rectal cancer and a 60% risk, if female, of endometrial cancer; There is also an increased risk of malignancy at other sites (e.g. stomach, ovary, small intestine). Lynch syndrome is due to a germline mutation in one of 4 mismatch repair genes: MLH1, MSH6, PMS2 and MSH2, These proteins are necessary for repairing incorrectly-paired nucleotide bases during DNA replication; Individuals with Lynch syndrome have one function alallele and one non-functional allele of the pertinent DNA repair gene; Their risk of cancer increases when the previously functional allele acquires a mutation that inactivates its function; Lynch syndrome can be inherited as autosomal dominant; But acquired mutations can also occur sporadically, in both alleles of the pertinent genes, in individuals without an inherited pre-disposition.

Answer 73

Tightly-regulated process of cell death (‘programmed cell death’) in multi-cellular organisms, Almost all of the genes involved in its regulation are alternatively spliced: the different forms can exhibit opposite functions: pro-apoptosis vs anti-apoptosis. It can be initiated via two pathways: Intrinsic pathway - due to intrinsic cell stress, including DNA damage, and Extrinsic pathway - because of signals from other cells; Both pathways, eventually, induce cell death by activating proteases called caspases (initiator and execution caspases) that lead to cell death by indiscriminate protein degradation.

Answer 74

Defective apoptosis is associated with pathological processes as the death of a cell with too high a DNA-damage burden may not occur. Mutations in certain apoptosis-associated genes can be seen in neoplastic cells… e.g. BCL2 (an anti-apoptotic gene): if over-expressed (follicular lymphoma) it leads to a shift in the sensitivity of the cell to apoptotic stimuli (apoptosis evasion), e.g. p53 (a transcription factor that influences the regulation of >900 genes in many processes, including apoptosis): has a complex role in both the intrinsic and extrinsic apoptotic pathways. If the gene encoding p53 (TP53) is damaged, tumour suppression is severely compromised; individuals who inherit only one functional copy of the TP53 gene have a high risk of neoplasia in early adulthood (Li-Fraumeni syndrome).

Answer 75

For DNA-based organisms, a gene could be considered to be the part of a DNA nucleotide sequence which is copied (transcribed) into a corresponding RNA nucleotide sequence that either encodes a functional protein (if the transcript is mRNA) or a functional structural RNA (eg. tRNA or rRNA). The sequence of a particular gene can differ between individuals of the same species. These variants are known as alleles and can be associated with different phenotypic traits (because they can encode slightly different proteins).

Answer 76

A variant in the sequence of nucleotides, at a particular location (locus), in a DNA molecule. Alleles can differ at a single position through a single nucleotide polymorphism (SNP) or through larger insertions or deletions. Different alleles often result in little or no change in function of the gene product encoded but sometimes they can result in a different phenotype. In diploid organisms, every cell in an individual has two full sets of somatic chromosomes, meaning that there are two alleles for any gene (one is inherited from each parent); If these two alleles are the same = homozygous, If these two alleles are different = heterozygous.

Answer 77

Genotype is the complete set of genetic material; Phenotype is the observable traits and characteristics of an organism/individual. The genotype contributes to, and can significantly determine, the phenotype but the environment is also influential in the phenotype. Some alleles are ‘dominant’ over others and, therefore, in certain scenarios, it is possible to have a different genotype but the same phenotype.

Answer 78

DNA sequences vary considerably between individuals: these variations are sometimes described as mutations and sometimes as polymorphisms. A mutation is any change in a DNA sequence different to ‘normal’ - this implies that there is a normal allele (wild-type) that is prevalent in the population and that the mutation changes this to a rare and abnormal variant. A polymorphism is a DNA-sequence variation that is, in contrast, ‘common’ in the population (and, in this case, may be no single allele is regarded as the standard ‘normal’ sequence). The arbitrary cut-off-point between a mutation and apolymorphism is 1% (i.e. to be classed as a polymorphism, the least common allele must have a frequency of 1% per or more in the population); if that frequency is lower than this, then that allele is regarded to represent a mutation. However, a rare disease allele in one population can become a polymorphism in another if it confers a selective advantage and, as a consequence, increases in frequency in that population. E.g. sickle-cell disease occurs when codon 6 of the beta globin gene is changed from GAG to GTG, causing a Glutmate to Valine substitution (E6V); the haemoglobin produced is referred to as Haemoglobin S. In Caucasian populations this is a rare sequence variant of the beta-globin gene but in certain parts of Africa (etc.), the same allele is polymorphic because it is much more common, as it confers some resistance to blood-borne malaria parasites.

Answer 79

DNA is packaged in chromatin; chromatin has a compact organisation in which most DNA sequences are structurally-inaccessible and functionally-inactive. The fundamental subunit of chromatin has the same type of design in all eukaryotes: The nucleosome is formed by a core histone octamer - there are two copies of each of the small basic histone proteins H2A, H2B, H3 & H4 organised as an H3 2 - H4 2 octamer and two H2A-H2B dimers; These are associated with about 145-147 bp of DNA wrapped around the outside of the octamer, This is further packaged.

Answer 80

Gene expression is mainly controlled at the level of the initiation of transcription; this is associated with the opening of chromatin (open chromatin = euchromatin), histone H3 & H4 acetylation and CpG-island demethylation. Active or potentially-active (‘poised’) genes are normally found in open chromatin. In contrast, heterochromatin is usually associated with inactive genes, where there is methylation of lysine residues on histone H3 and methylation of CpG islands in the upstream DNA-regulatory sequences of the gene.

Answer 81

RNA polymerases have about 12 subunits. No RNA polymerase recognises a promoter directly - first, the chromatin must be ‘opened’. An RNA polymerase II promoter consists of a variety of short sequence elements in the region of the transcriptional start site; Each of these elements is bound by one or more transcription factors including multiple ‘basal’ transcription factors (which include members of the TFII family); These forma pre-initiation complex, assemble at the promoter and provide a target for RNA polymerase II. A unifying principle is that transcription factors have primary responsibility for recognising and binding many of the characteristic regulatory sequences in a promoter and they, in turn, serve to bind RNA polymerase II and position it correctly at the transcriptional start point.

Answer 82

RNA is the central player in gene expression; all RNAs require processing of the primary transcript to become functional and mature. The 5’ end of eukaryotic mRNA is capped, during transcription, by the addition of G residue, by guanylyl transferase; this is subsequently methylated. The cap has an influences: mRNA stability, mRNA splicing, mRNA transport and mRNA translation. A typical gene has many introns and these are removed from the RNA transcript by splicing (RNA splicing). Most introns are associated with a GU...AG consensus. The mRNA is spliced by the spliceosome (which has over 100 proteins). The transcription and splicing machinery are physically and functionally-integrated, therefore, transcription and RNA processing are highly coordinated in multi-cellular eukaryotes. 3’ end processing: the addition of a poly A tail (poly-adenylation) influences mRNA stability by protecting against 3’ to 5’ exonuclease degradation, signals the termination of RNA polymerase II transcription, and also influences translation efficiency.

Answer 83

Alternative splicing results in the production of mRNAs with different sequences (even although they have been generated from the same RNA transcript); when these are translated different proteins (or variations on the same protein) can be produced. Multiple gene products can therefore be produced from the same locus (structural diversity) and possibly more than 90% of genes in mammals are differentially spliced.

Answer 84

An mRNA transcript carries a sequence that can be divided into groups of 3 (each group of 3 is a codon and specifies a specific amino acid in a polypeptide). The codons interact with the anti-codons on the tRNA component of an amino-acyl tRNA. There are 64 possible codons (4^3); 61/64 codons specify for one of the 20 amino acids; 3/64 are STOP codons (terminate translation); The 61 amino acid-specifying codons are each recognised by a specific aminoacyl-tRNA with an anti-codon complementary to the codon and carry the amino acid specified by that codon. The order of the codons in the mRNA determines the order of amino acids incorporated into a polypeptide chain. Almost all amino acids are coded for by more than one codon except methionine (MET, M) and tryptophan (TRP, W); As a consequence, there is intrinsic redundancy to the genetic code; In contrast to the 61 codons specifying an amino acid, the 3 termination codons are each recognised by protein release factors.

Answer 85

AUG = start (Met, M), UAA = stop (ochre), UGA = stop (opal), UAG = stop (amber)

Answer 86

Code is read from 5’-3’, An mRNA can be translated in three different reading frames, Critical that translation starts at the correct point and in the correct reading-frame.

Answer 87

Most mRNAs need a 5’cap to be translated efficiently (there are some exceptions e.g. polio virus RNAs are uncapped). Translation occurs in three stages (and different sets of multiple accessory proteins are required to assist the ribosome at each of these stages). Initiation: Prior to the start of translation, the pre-initiation complex (PIC) scans the mRNA for the translational start site; The PIC consists of the 40S ribosome bound to elongation initiation factor 2 (eiF2), GTP and the initiator MET-tRNA; Multiple other proteins bind the PIC and aid in its binding to the m7G 5’ cap; This protein complex scans the mRNA until it reaches the AUG initiation codon (this is usually the first AUG but it is also part of a longer specialised sequence); To eukaryotes, the Kozak (Consensus) sequence usually functions as the site of mRNA translation initiation - the AUG codon is recognised, and bound by, the the anti-codon of the aminoacyl-initiator-tRNA (MET-tRNA); This binding leads to a structural re-arrangement that results in the PIC binding the large 60S ribosome (to form the ribosomal complex, 80S); Once the 80S ribosomal complex is formed the elongation phase of translation begins.

Answer 88

Elongation: all the reactions involved from the formation of the first peptide bond to the addition of the last amino acid; amino acids are added one-at-a-time and in the order specified by the mRNA sequence. tRNAs (transfer RNAs) are the key adaptors required for protein synthesis.

Answer 89

tRNAs (transfer RNAs) are the key adaptors required for protein synthesis. Anti-codon forms base-pairs with the complementary sequence in mRNA; the first base in the anti-codon pairs with the 3rd base of the codon; Some tRNAs require accurate base-pairing at only the 1st two nucleotides; This ‘wobble’ may account for the finding that many alternative codons for a particular amino acid differ only in their 3rd nucleotide. In order to attach the correct amino acid to the tRNA, aminoacyl tRNA synthetases are required; A high energy bond then holds the amino acid in place once linked to tRNA.

Answer 90

Chemically-similar amino acids are often represented by related codons; This can potentially reduce the probability of a random base change mutation having an impact on the encoded protein sequence (and its structure and function). e.g. if a mutation changed a codon from CUC to CUG, the translated polypeptide is unchanged as both codons direct the addition of leucine (LEU, L). e.g. if a mutation changed a codon from CUU to AUU, this would replace LEU with the chemically-similar Isoleucine (Ile, I) (both are hydrophobic and more likely to play a similar role).

Answer 91

RibosomeS are complex migrating factories made of RNA (rRNAs) & proteins; Structure is highly conserved during evolution and provides the environment to control the specific interaction between aminoacyl-tRNAs and mRNA (and all other activities required for all steps of translation). Composed of a large and small subunit: Large subunit catalyses formation of peptide bonds that covalently link a.a., Small subunit matches aminoacyl tRNAs to mRNA codons. They moves along the mRNA transcript, from 5’ to 3’, bringing in the correct amino acids (on aminoacyl-tRNAs) and engages in rapid cycles of peptide-bond synthesis (catalysed by the large subunit of the ribosome) to build a polypeptide.

Answer 92

A site: Aminoacyl tRNA site, P site: Peptidyl tRNA site, E site: Exit site

Answer 93

Step 1: ‘charged’-tRNA binds the vacant A-site (elongation factor Tu loads the specific amino-acyl-tRNA into the A-site), base-pairing with the mRNA codon determines which tRNA binds. Step 2: a new peptide bond forms between amino acids on tRNAs in P & A sites; for a ribosome to form a peptide bond, peptidyl-tRNA must be in the P-site and the sequence-specified amino-acyl tRNA in the A-site; peptide bond formation occurs when the polypeptide carried by the peptidyl-tRNA is transferred to the amino acid carried by the aminoacyl tRNA - this is catalysed by the large subunit of the ribosome. Transfer of the polypeptide results in the P-site now being occupied by a deacetylated tRNA (lacking any attached amino acids) and a new, extended, peptidyl-tRNA in the A-site (the peptide on this peptidyl-tRNA is one amino acid residue longer than the one that was initially joined to the tRNA that had been in the P-site). Step 3: the ribosome moves one triplet (three bases) along the mRNA (translocation); shifts the new peptidyl-tRNA into the P-site and the deacetylated tRNA into the E-site which then exits the ribosome complex. Step 4: the ribosome is now ‘reset' with a vacant A-site and is ready to start another synthetic cycle. mRNA is associated with the small ribosome subunit and about 35 bases (approximately 12 codons) are bound by a single ribosome. In essence, for each ribosome, only two aminoacyl-tRNAs are involved in active translation at any moment, therefore, polypeptide synthesis involves reactions at just 2 of the 11 codons associated with the ribosome.

Answer 94

Termination: the processes involved in release of the completed polypeptide chain and ribosomal dissociation from the mRNA elongation. Translation terminates at one of three STOP codons - UAA, UAG and UGA. These are not recognised by aminoacyl-tRNAs but, instead, all three are recognised by a single class 1 release factor protein (eRF) which transfers a hydroxyl group from water to hydrolyse the polypeptide-tRNA linkage and, thereby, leads to release of the polypeptide chain from the last tRNA. The post-termination reaction involves release of the tRNA and mRNA and dissociation of the ribosome into its subunits (a process that requires multiple proteins: ribosome recycling factor (RRF) and EF-G in a reaction that uses GTP).

Answer 95

Tetracycline - inhibits binding tRNA, Streptomycin - inhibits the initiation complex, Chloramphenicol - inhibits peptidyl transferase, Erythromycin - inhibits translocation, Puromycin - inhibits premature release.

Answer 96

Mitochondrial DNA is transcribed as near-genome-length transcripts; In general, the mitochondrial genes lack introns; The RNA transcripts are predominantly regulated post-transcriptionally by nuclear-encoded proteins; The mature mitochondrial mRNA is translated on mitochondrial ribosomes; Most of the genetic information is on the heavy (H) strand; Replication and transcription of the H and L strands is initiated from a non-coding control area called the displacement loop (D loop); Mutations in mitochondrial genes are the most common genetic cause of metabolic disorders (about 1/5000 individuals).

Answer 97

Human genome contains ~30,000 genes; Typical human cell contains ~5,000-15,000 protein types; Some proteins found in most cell types (for shared essential cell function) – ‘housekeeping’; Some are specific to particular cell types (luxury functions) – ion channel in neurons, muscle myosin in muscle cells, liver enzymes in hepatocytes, keratin in skin epidermal cells, haemoglobin in RBCs… Genetic information is not lost when cells differentiate - all cells in a multicellular organism have full gene complement; Cells are specialised because of differences in gene activity (not gene content).

Answer 98

Transcription factors - analagous networks regulate selective gene expression in other differentiated cells. Switched genes on and off. E.g. MyoD (Myogenic Differentiation gene) is a switch to a muscle cell fate and induce expression of muscle-specific genes; MyoD – DNA binding protein (a transcription factor) binds the enhancer of muscle specific genes and activates them; Feedback – differentiated state is very stable.

Answer 99

Regulate the cell by switching genes on and off. E.g. the tryptophan repressor switches genes OFF; When tryptophan is low the genes are switched ON, When tryptophan is abundant the genes are switched OFF; Regulatory sequence in the operon’s promotor recognized by a transcription factor – the tryptophan repressor, Tryptophan repressor blocks access to RNA polymerase so the repressor can bind DNA only when bound to tryptophan; Simple device to switch genes ON/OFF according to availability of tryptophan (end product of the pathway). E.g. E.coli Lac operon encodes b-galactosidase – converts lactose into galactose and glucose; Transcriptional activator – CAP, which binds DNA in presence of cAMP (cAMP elevated in cells deprived of glucose); No glucose - cAMP produced, activates CAP to switch ON b-galactosidase; No lactose - Lac repressor shuts OFF operon; Allows the integration of 2 signals - glucose absent and lactose present (similar to logic operation in a computer).

Answer 100

RNA polymerase is directed to gene transcription start sites within a gene’s promoter by a number of ’helper’ proteins. E.g. the TATA box is a DNA signal sequence to which the general transcription factor ‘TATA binding protein’ TFIID binds. TFIID controls the position where all protein coding genes start but not when the gene is transcribed. Nearby are other DNA sequences (5-10 nucleotides) in a regions called ‘enhancers’; Enhancers are recognized by proteins called transcription factors – if the transcription factor is in the cell it binds to it’s enhancer and this can activate or repress RNA polymerase function; There are many different enhancers, which are recognized by different transcription factors; The gene is switched ‘ON’ or switched ‘OFF’ for transcription.

Answer 101

Transcription factors can attract: 1. histone modification enzymes, 2. ATP-dependent chromatin remodelling complexes, 3. histone chaperones. These alter chromatin structure of promoters, Facilitate assembly of general transcription machinery to promoter, Alterations to chromatin structure can be rapidly reversed, or can be maintained for greater periods of time.

Answer 102

Differentiated cells generally remain differentiated; Their progeny will inherit their identity – e.g. fibroblasts, smooth muscle, liver cells (n.b. some differentiated cells never divide, e.g. neurons, skeletal muscle); Patterns of gene expression required for identity must be ‘memorized’. This ‘memory’ must be passed on to daughter cells - it does this via the positive feedback loop. Positive feedback loop: TF (transcription factor) activates its own gene, TF is distributed to both daughters, Continues to stimulate positive feedback loop - ‘self sustaining’ circuit of gene expression, e.g. MyoD.

Answer 103

Histone modification: Histone tails can be (reversibly) chemically modified to make the chromatin more or less accessible – e.g. to increase or decrease gene expression, Patterns of histone modification can be long-term – reinforce cell memory. DNA methylation: DNA methylation regulates gene expression; It can occur on cytosine in the sequence CpG; Patterns of DNA methylation propagated through DNA replication, Efficient form of gene repression, Direct action to inhibit binding of general transcriptional machinery/transcription factors, indirect by recruiting histone modifying enzymes.

Answer 104

Females are XX and males are XY. Mammals have evolved a dosage compensation mechanism to equalize the dosage of X-chromosome gene products; Transcriptional inactivation of one X-chromosome in female somatic cells – X-inactivation – by chromatin condensation; X-inactivation is random, therefore every female is a mosaic of clonal groups of cells with one or other X-chromosome active.

Answer 105

Cell lineage (history), and Environment (interaction between cells). Cell fate decisions are made progressively. Cell lineage: All cells contain the same genetic information - progenitor cell divides and differentiates into specialised cell types with different patterns of gene expression - additional information tells what type of cell to be. Additional information comes from two sources: From inside - asymmetric distribution (inheritance) of factors as cells divide during early development, and From outside - cells signal to each other, to ‘induce’ behaviour of neighbours.

Answer 106

Blood contains many different cell types; Blood cells have limited lifespans (so are produced throughout the lifetime); All blood cells are generated from a common multipotent stem cell (in the bone marrow) – the haematopoietic stem cell. Differentiation is a stepwise process; Commitment is regulated by activity of specific transcription factors; E.g. GATA1 - transcription factor that binds to specific DNA sequences; targets a-globin & b-globin genes, haem biosynthesis enzymes, erythropoietin receptor; mutation of mouse Gata1 gene - anaemia due to death of erythroid precursor cells; end product is RBC (cell structure – disc shaped with reduced organelles including no nucleus, expression of a-globin & b-globin {adult haemoglobin}). Stromal cell signals regulate stem cell differentiation. Haematopoesis is also regulated by ‘outside’ signals - chemical signals elsewhere in the body; E.g. Erythropoietin (hormone produced by the kidney in response to lack of O2/shortage of erythrocytes) acts on erythropoietin precursor cells to increase their proliferation/survival. E.g. Neutrophils and macrophages production selectively increases in response to infection; Signals (colony-stimulating factors, CSFs) are released by various cell types (endothelial cells, fibroblasts, macrophages, lymphocytes) in response to tissue infection; CSFs act on precursor cells in the bone marrow to promote the production of neutrophil and macrophage.

Answer 107

Haematopoietic stem cells depend on signals from their ‘niche’ within the bone marrow. Bone marrow stromal cells (specialised connective tissue) signal to them; Contact between stem cells & stromal cells maintains ‘stemness’; Contact-dependent interaction between receptor on stem cell and ligand in stromal cell; When a stem cell divides one daughter will lose contact with the stromal cell – and will differentiate. Haematopoesis is also regulated by ‘outside’ signals. Chemical signals produced elsewhere in the body act on blood cell lineage to influence selective blood cell production: Erythrocytes need to be replaced - limited lifespan (~120 days in humans, with 10^11 senescent erythrocytes removed per day); Erythrocyte production selectively increased in response to anemia (lack of haemoglobin) due to blood loss/acclimatization at high altitude; Erythropoietin is a hormone produced by the kidney in response to lack of O2/shortage of erythrocytes; Erythropoietin acts on erythropoietin precursor cells to increase their proliferation/survival; The erythropoietin receptor was one target of GATA1. Neutrophils and macrophages production selectively increases in response to infection. Signals (colony-stimulating factors, CSFs) are released by various cell types (endothelial cells, fibroblasts, macrophages, lymphocytes) in response to tissue infection. CSFs act on precursor cells in the bone marrow to promote the production of neutrophil and macrophages.

Answer 108

The body is not static – it is a structure in dynamic equilibrium, where new cells are continually being born, differentiating and dying. Maintained by: Growth control, Control of cell proliferation, and Cell death.

Answer 109

Growth of paired body parts (like arms) stay ‘in-sync’ with each other despite the fact they originated on opposite sides of the body and grew independently during their development. Size is dependent on total cell mass, which is influenced by cell growth, cell divisions, and cell death; These factors are controlled by intracellular programmes which are influenced by external signals: Mitogens – stimulate cell division by triggering a wave of G1/S-Cdk activity that relieves intracellular negative controls blocking the cell cycle. E.g. platelet-derived growth factor (PDGF), epidermal growth factor (EGF), erythropoietin. Growth factors – extracellular signal proteins which stimulate cell growth (an increase in cell mass) promoting the synthesis of proteins and other macromolecules & by inhibiting their degradation. There are also factors that inhibit growth e.g. Myostatin – signal specifically inhibits the growth (& proliferation) of myoblasts (muscle precursors). Survival/death factors – promote cell survival or death by suppressing or inducing apoptosis (a type of cell suicide). Many breast cancers depend on oestrogen as a survival signal; Tamoxifen = powerful inhibitor of oestrogen and is used as a very effective drug against breast tumours. Survival is dependent on co-ordination between tissues. Misrouted cells (i.e. lost cells) will die.

Answer 110

Stem cells are cells that are specialised to provide a fresh supply of differentiated cells where these need to be continually replaced, or when the are required in great numbers for the purposes of repair and regeneration. Defining characteristics of a stem cell: 1. A stem cell is not terminally differentiated, 2. It can divide without limit, 3. Upon division each daughter has a choice - stem cell or terminal differentiation.

Answer 111

Can be asymmetric division (e.g. neuroblast) - localised determinant is only inherited by one of the two daughter cells so one stays as a stem cell and the other becomes terminally differentiated, OR Independent choice (e.g small intestine epithelium) - each daughter cells’ environmental factors help determine its fate.

Answer 112

Between villus are the crypts of the small intestine. At the bottom of the crypts are multipotent stem cells, as well as non-dividing differentiated Paneth cells. Each daughter stem cell has independent choice of whether to differentiate or divide; This is determined by its intestinal stem cell niche - Stem cells fate induced by signals from Paneth cells & connective tissue surrounding crypt; The Paneth cell secretes WNT (secreted signalling molecule), WNT signal is received by a WNT receptor on receiving Stem cells, Absence of WNT – Apc degrades b-catenin, Presence of WNT – Apc is inhibited, Apc is an inhibitory component of the WNT pathway, b-catenin translocates to nucleus – transcriptional regulator to drive proliferation and stem cell state.

Answer 113

Self renewing tissues – breeding ground for great majority of human cancers, e.g. epidermis, intestine, reproductive tract & bone marrow. Example: colorectal cancer – affects epithelium of colon (large intestine) and rectum; common (about 10% deaths from cancer); develop from benign tumor or adenoma ‘polyp’; renewal in large intestine is similar to small intestine - stem cells that lie in crypts, similar signals maintain stem cells and control renewal. Familial adenomatous polyposis coli (FAP) – rare hereditary condition predisposition to colorectal cancer, FAP individuals have a deletion or inactivation of one copy of the Apc gene, if the other (normal) copy of Apc becomes inactivated during the patients lifetime – leads to the tumour. Most patients with colorectal cancer do not have the hereditary condition, but in 80% of cases their cancer cells inactivated both copies of Apc through mutation acquired through the patients lifetime.

Answer 114

Lack of oxygen, Physical agents (temperature, pressure, electricity, radiation), Chemicals and drugs, Infectious agents, Immune reactions, Genetic defects, Nutrition (deficiency, imbalance).

Answer 115

Rapid changes, Swelling due to loss of ion/fluid homeostasis, Fat accumulation (steatosis), Irreversible if persistent injury, "Point of no return" not defined.

Answer 116

Type of irreversible cell injury: "Dropping off" of petals or leaves, Programmed cell death - cell suicide, Ordered, regulated process, Physiological, Pathological.

Answer 117

Pathway: DNA damage due to injury (radiation, toxins, free radicles) or withdrawal of growth factors/hormones causes p53 to signal to mitochondria and executioner caspases, Mitochondria releases pro-apoptotic molecules (e.g. cytochrome c), Pro-apoptotic molecules signal initiator caspases which signal to executioner caspases, Executioner caspases cause endonuclease activation and cytoskeleton breakdown, This leaves a cytoplasmic bud which becomes an apoptotic body, which gains ligands for phagocytic cell receptors, It is then engulfed by a phagocyte. Regulation: Cytokine deprivation, intracellular damage and oncogenes signal to BH3-only proteins; BH3-only proteins inhibit pro-survival BCL-2 proteins and activate the BAX-BAK complex, Pro-survival BCL-2 proteins normally inhibit the BAX-BAK complex but they are now inactivated; BAX-BAK complex signals to mitochondria to release cytochrome c and SMAC, Cytochrome c activates APAF1 which activates caspase 9, SMAC inhibits XIAP which normally inhibits caspase 9 and effector caspases; Caspase 9 activates effector caspases to bring about apoptosis.

Answer 118

Receptor-ligand interactions (FAS, TNF receptors) or cytotoxic T lymphocytes signal for cell death, The receptor-ligand interactions signal via adapter proteins which activate initiator caspases, which go on to activate executioner caspases, The cytotoxic T lymphocytes signal for Granzyme B to activate the executioner caspases; Executioner caspases cause endonuclease activation and cytoskeleton breakdown, This leaves a cytoplasmic bud which becomes an apoptotic body, which gains ligands for phagocytic cell receptors, It is then engulfed by a phagocyte. Regulation: Death-receptor ligand binds to the death receptor, coupled to TRADD and FADD intracellularly; They activate caspase 8 which activate tBID and also activate effector caspases directly; tBID inhibits the pro-survival BCL-2 proteins and activates BAX-BAK complex, Pro-survival BCL-2 proteins normally inhibit the BAX-BAK complex but they are now inactivated; BAX-BAK complex signals to mitochondria to release cytochrome c and SMAC, Cytochrome c activates APAF1 which activates caspase 9, SMAC inhibits XIAP which normally inhibits caspase 9 and effector caspases; Caspase 9 activates effector caspases to bring about apoptosis.

Answer 119

Coagulative - cell proteins denature ("ghost" outlines), cells lose nuclei and stain more deeply, e.g. heart muscle ischaemia causing coagulative necrosis leading to infarction; Liquefactive - cell protein digested, loss of tissue architecture, infiltration by inflammatory cells (neutrophils) [pus], secondary infection by bacteria [wet gangrene], normally lipid rich tissue e.g. cerebral infarction; Caseous - end result of granulomatous inflammation (granulomas - large aggregates of macrophages; epithelioid & giant cells), macrophage - phagocyte, e.g. autoimmune conditions/foreign body/mycobacterial infection (M.tuberculosis); Gangrenous (dry) - coagulative necrosis of extremity due to slowly developing vascular occlusion, e.g. diabetic foot; Fat necrosis - degradation of fatty tissue by lipases, forming chalky deposits, e.g. in acute pancreatitis/trauma to fatty tissues.

Answer 120

(Apoptosis = A, Necrosis = N) Morphology: Earliest changes = A. Cell shrinking, N. Cell swelling; Membrane = A. Remains intact (blebbing), N. Loss of integrity; Chromatin = A. Aggregation at nuclear membrane, N. No change; Vesicles = A. Formation of membrane enclosed vesicles (apoptotic bodies), N. No vesicle formation but lysis; Termination = A. Continued fragmentation into smaller bodies, N. Complete lysis. Biochemistry: Regulation = A. Tightly controlled, N. Loss of homeostatic regulation; Energy requirement = A. Energy dependent, N. Passive; DNA = A. Non-random fragmentation prior to apoptotic body formation, N. Random fragmentation after cell lysis; Effector mechanisms = A. Caspase cascade, N. None. Consequences: Extent = A. Localised - individual cells, N. Groups of cells - indiscriminate; Cause = A. Triggered - withdrawal of survival factor or pro-apoptotic stimulus, N. Evoked by significant non-physiological disturbance; Elicited response = A. No inflammatory response and bystander damage, N. Significant inflammatory response and bystander damage.

Answer 121

Molecules, cells and tissues that mediate immune responses. Molecules: Complement - system of soluble serum proteins, Cytokines - immune messenger hormones, Chemokines (cytokines which specialise in making cells move), Antibodies - secreted molecules which bind pathogens. Cells: Leukocytes = all immune cells (innate and adaptive) Literally “white blood cell”, Innate cells (Macrophages, dendritic cells, neutrophils, eosinophils, basophils and mast cells), Adaptive cells (T cells, B cells) (lymphocytes). Tissues: lymphatics, lymph nodes, spleen, thymus and bone marrow. Systems: Lymphatic system, Blood, Interaction of immune organs; Organs: Lymph node, Spleen, Bone marrow, Thymus; Cells: Dendritic cell, T cell, Macrophage, Eosinophil, B cell, NK cell and more...; Molecules: Antibody, Complement, Cytokines/Chemokines.

Answer 122

Immune cells are made in the bone marrow and thymus. Adaptive immune cells spend most of their time in lymph nodes and spleen. The lymphatics provide drainage for the periphery. Lymph nodes at lymphatic junctions. Lymphatics drain into the blood (subclavian veins) via the thoracic duct. Lymphatics are required for drainage of the periphery - ideal for immune system “scanning” for anything dangerous in the body. Lymph nodes are highly organised accumulations of immune cells at lymphatic junctions. Swell during infection - lymphadenopathy. Primary lymphoid organs are where immune cells are made - bone marrow and thymus; Immune cells are made in the bone marrow; T cells mature in the thymus. Secondary lymphoid organs are where immune responses are initiated; Where T and B cells live, most of the time (lymphocytes); Most important are lymph nodes and spleen; Other secondary lymphoid organs include the tonsils, appendix, Peyer’s patches (gut).

Answer 123

Epithelial surfaces represent an entry point for pathogens. Barriers to prevent entry of extracellular pathogens: Physical - skin (dead), gut epithelium (rapid turnover); Chemical - low pH of skin, vagina, stomach; Flushing - tears, sweat, mucus (constant flushing keeps pathogen numbers low); Antimicrobial peptides - present in many secretions; Competitive - commensal (friendly) bacteria out-compete dangerous bacteria in the gut. If these passive mechanisms fail, then the immune system steps in.

Answer 124

Virally-infected cells release IFNα and IFNβ; IFNα and IFNβ induce an antiviral state in neighbouring cells, Upregulate antiviral proteins (including more IFNs), and antigen presentation, Downregulate everything else by degrading mRNA and inhibiting protein translation factors (suppress viral proliferation); Synthetic IFNα administration is highly effective in Hepatitis B virus infection.

Answer 125

Danger = signals indicating there is harm to the body, and/or that infectious agents are present; Recognised by innate immune response. Self/non-self = The immune system can recognise your own proteins (= self) and knows not to attack; Anything it doesn't recognise (= non-self) it will kill; Recognised by adaptive immune response. Need both Danger & Non-self to get an adaptive immune response.

Answer 126

2 types of danger signals: PAMPs = Pathogen Associated Molecular Patterns; Types of molecules only produced by infectious agents and not host tissue - critical for survival/virulence; E.g. bacterial cell wall constituents (lipopolysaccharide - LPS). DAMPs = Damage Associated Molecular Patterns; Molecules released from injured cells; E.g. DNA, RNA, ATP, breakdown products of extracellular matrix.

Answer 127

Recognise Pathogen Associated Molecular Patterns (PAMPs) and Damage Associated Molecular Patterns (DAMPs); Examples of PRRs - Toll-like Receptors (family - TLR1-10): TLR3 binds double-stranded RNA (viruses), TLR4 binds LPS (bacterial cell wall), TLR5 binds flagellin (flagellated bacteria).

Answer 128

During development, the adaptive immune system samples everything in its environment, and decides thats “self”; Can react to anything new (non-self), but not your own molecules (self), through the process of “negative selection”.

Answer 129

Innate immune system = neutrophils, macrophages, dendritic cells, natural killer (NK) cells, eosinophil, basophil and mast cells, complement… Detects danger, brings about rapid generic response, communicates danger to adaptive immune system. Adaptive immune system = T cells (CD4 + T helper cell; CD8 + cytotoxic T lymphocyte); B cells + antibodies… Differentiates between self and non-self, slow highly specific response, has “memory” to antigens it has seen before.

Answer 130

Susceptibility - poor immune response, Immunity - appropriate immune response, Immunopathology - over active immune response. Interactions between innate and adaptive immunity are there to ensure that the immune system only attacks when necessary. Example - Influenza infection: Most people clear virus due to effective immune response; Old and young can die of influenza due to poor immune responses leading to overwhelming infection; Aggressive strains (e.g. 1918 Spanish flu) and overactive immune response leads to “cytokine storm” - mostly killed people in their prime. Infection with Sars-cov-2 causes COVID-19; Treatment with dexamethasone reduces mortality of hospitalised patients with acute respiratory failure; Treatment with Tocilizumab (arthritis drug), an antibody that blocks binding of the cytokine Interleukin 6, improves ‘outcomes’.

Answer 131

Allergies and Autoimmunity. Like a harmless environmental molecule (allergy) or “self” (autoimmunity); Can be fatal (anaphylactic shock) and/or very hard to treat (multiple sclerosis, rheumatoid arthritis). Need to maintain control of the immune response; Hence integration of innate (senses danger) and adaptive (senses non-self) - without both these signals there should not be an immune response; However, system clearly not perfect.

Answer 132

When you are first exposed to a pathogen, you get sick (e.g. chicken pox), but then you usually never get it again: The adaptive immune system has memory - remembers what it has seen and how to kill it. Takes around a week to get a good primary immune response (in the meantime innate immunity tries to deal with the infection); Much quicker in secondary immune response. Response also tailored to type of infection; Different mechanisms required to control viral vs bacterial vs parasitic infection.

Answer 133

Vaccination is a method for inducing a big immune response to a pathogen. Does away with the need for a primary infection; Get effective secondary response to infection - immunity. Use inactivated pathogen, or a subunit of the pathogen - no infection.

Answer 134

Blood contains <1% white blood cells (leukocytes) - it’s mostly red blood cells. Of leukocytes: More than half are neutrophils (>60%), About a quarter are lymphocytes (B and T cells), About 5% monocytes (Macrophage precursor), <5% eosinophils and basophils.

Answer 135

Adaptive: Recent evolutionarily development - developed 500 million years ago in cartilaginous fish (sharks), Responds to specific (non-self) antigens and gives a response tailored to the infection, Slow, highly specific. Innate: Evolutionarily ancient - all multicellular animals have some form of innate immune system, Responds to danger and gives a generic response, Rapid, non-specific.

Answer 136

Part of the innate immune system that enhances the ability of antibodies and phagocytic cells to clear microbes and damaged cells from an organism, promote inflammation, and attack the pathogen's cell membrane. They are a series of soluble proteins in the blood, called C1, C2, C3… to C9. It is a triggered enzyme cascade. Pathogens lead to the activation of complement by one or more of three pathways: Classical pathway, Mannose-binding lectin pathway, Alternative pathway. Their activation can cause: Anaphylotoxins (inflammation), Opsonisation, or Membrane Attack Complex (Lysis).

Answer 137

Only occurs when there are antibodies present specific to a foreign antigen (e.g. on a bacteria, or soluble). The antibody complexes are bound by complement component C1q which activates subsequent complement components.

Answer 138

Activation through mannose-binding lectin which binds mannose (or similar carbohydrates) on bacteria. Mannose is not present on surface of host cells. The binded mannose-binding lectin activates the subsequent complement components.

Answer 139

Complement component C3 spontaneously activates and binds to nearby membranes; Host cells have control proteins on their surface to prevent further complement activation; Bacterial cells do not - activates complement.

Answer 140

Membrane Attack Complex (MAC) forms in membrane of bacteria - barrel-like structure formed from multiple late complement components (C6-C9). Water rushes in, ions rush out, bacteria swells and bursts. Can also happen to host/foreign cells marked for killing.

Answer 141

Soluble complement components are released on complement activation: ‘Anaphylotoxins’ (toxins that can cause anaphylaxis). Their release results in blood vessels becoming leaky (oedema), resulting in infiltration of plasma proteins and recruitment of immune cells (e.g. neutrophils) and activation of mast cells.

Answer 142

Membrane-bound complement components also opsonise pathogens; They bind to the surface of bacteria, Phagocytes have Complement Receptors which bind membrane-bound complement and encourage phagocytosis and killing.

Answer 143

Phagocytes - Neutrophils, macrophages and dendritic cells; Phagocytes eat pathogens (phago = eating, cyte = cell); Neutrophils: Recruited rapidly to the scene (30-80% of white blood cells), Good at killing - many preformed granules, Very short-lived (a few days), Chief constituent of pus; Macrophages (macro = big, phage = eaters): Good at killing if activated, Also involved in tissue healing, clearance of dead cells, metabolism..., Reside in tissue (and supplemented by monocytes); Dendritic cells: Poor at killing, Rare, Reside in tissues, Initiate adaptive immune responses - take a “message” to T cells. Eosinophil, Basophil, and Mast cell are all involved in allergic and anti-parasite responses. Natural Killer (NK) cells kill virally infected/sick cells.

Answer 144

Type of phagocyte, Recruited rapidly to the scene (30-80% of white blood cells), Good at killing - many preformed granules, Very short-lived (a few days), Chief constituent of pus.

Answer 145

Macrophages (macro = big, phage = eaters): Type of phagocyte, Good at killing if activated, Also involved in tissue healing, clearance of dead cells, metabolism..., Reside in tissue (and supplemented by monocytes).

Answer 146

Type of phagocyte, Poor at killing, Rare, Reside in tissues, Initiate adaptive immune responses - take a “message” to T cells.

Answer 147

Neutrophils need to get from the circulation to the site of inflammation - this is the process of extravasation. Endothelium of blood vessel are altered by inflammatory cytokines, Neutrophil starts to roll along endothelium, then firmly adheres, and exits between endothelial cells (diapedesis), Follows chemokine gradient to site of inflammation.

Answer 148

Phago = eat, cyte = cell. Phagocyte (Monocytes, macrophages, dendritic cells, neutrophils) detects pathogen and engulfs it - forms phagosome, Lysosome fuses with phagosome - lysosome contains toxic products to kill/degrade pathogen, Now called phagolysosome. Phagolysosome “matures” as more lysosomes fuse with it and H+ ions are pumped in (acid), Lots of other nasties inside - proteases, oxygen radicals, nitric oxide, pore-forming proteins…, Neutrophils also make HOCl (hypochlorite = bleach).

Answer 149

Macrophages must be activated before they can effectively phagocytose and kill bacteria. Activation can come from danger signalling or cytokines, especially IFNγ, IFNγ from other cells - NK cells, other activated macrophages, but in an established immune response, from helper T cells.

Answer 150

Neutrophil Extracellular Traps. Neutrophils can extrude their DNA, acting like a net which traps pathogens. This causes “Netosis” (vs apoptosis and necrosis), Primarily seen in extracellular fungal infections.

Answer 151

Adaptive immune cells are randomly generated to express a unique receptor which recognises a specific antigen (termed antigen-specificity). Antigens are molecules that are recognised by the adaptive immune system, Can be self-antigens or non-self antigens (eg pathogen or environmental).

Answer 152

When dendritic cells in the periphery they are constantly taking up antigen. If they sense danger they ‘mature’: Get better at antigen presentation, and upregulate different chemokine receptors; This results in their migration to the lymphatics, and into the draining lymph node, where they will present antigen to T cells.

Answer 153

Have multiple afferent lymphatic vessels going into the node and one efferent lymphatic vessel coming out, accompanied by the blood supply (with high endothelial venule). They have T cell areas with a B cell follicle at the centre of it.

Answer 154

The B cell receptor (BcR) can recognise soluble antigen in its normal form. The T cell receptor (TcR) has to have antigen “presented” to it on Major Histocompatibility Complex (MHC) molecules on another cell (dendritic cells). Antigens must be chopped up into peptides, then “loaded” onto MHC molecules and presented on the surface of a cell. There must be two signals: 1. Specific antigen (MCH + antigen), 2. Danger (co-stimulation, B7-CD28). PAMPs/DAMPs signal danger due to a pathogen/damage respectively. This is picked up but immature DC in periphery which matures and in the lymph nodes lead to activation. The immature DC in periphery can also sense environmental Antigen and apoptotic cells and in the lymph nodes when immature/semi-mature, activate T cells to cause anergy/death without the need for the second signal.

Answer 155

Steady state (constitutive innate immunity): Pre-empts inflammation so homeostasis is uninterrupted, Barriers maintained, Anti-microbial molecules mop up danger, Contribute more from at the beginning of the infection and act quick, Have a constant medium amplitude of response. Inducible immunity: Alert response to mounting danger disrupts & damages tissue; Two main pathways: Pattern recognition receptors (germline-encoded) over a threshold, trigger inflammation (induced innate immunity), Antigen-specific receptors (genes rearranged) after antigen encounter trigger adaptive immunity, Contribute more once the microbial load has increased, Take more time to be activated, Amplitude of response corresponds to microbial load - low normally but high peak infection.

Answer 156

Intact barriers – cilia, gastric acid, intestinal mucus, keratinocyte sloughing; Antimicrobial molecules (basal type I IFN) – reduce pathogen replication/integrity (cytoplasmic nucleases, nutrient depletion, RNA interference, lysozyme, defensins) and increase cellular recycling (e.g. proteosome degradation {virus capsid}, autophagy {TB, HSV}, phagocytosis); Healthy microbiota – moderates immune reactivity, maintains barriers, out-competes pathogens; Sleep quality – antiviral (type I IFN) vs. pro-inflammatory state (IL1, TNF); Active skeletal muscle – anti-inflammatory/immune protective cytokines (myokines); Adipose – Lean (subcutaneous) adipose is anti-inflammatory. Disturbance can increase susceptibility to infections or conversely, trigger unnecessary sterile inflammation.

Answer 157

Contracting skeletal muscle: Major source of cytokines (myokines), Mobilises NK cells, T cells (exercise lymphocytosis) which then enter tissues (surveillance) and mobilises senescent T cells for deletion, Inactive, sarcopenic muscle impairs immune regulation - <10% over-65s get 150 min aerobic exercise per week. Myokines: Support immunity & surveillance, suppress inflammation; Innate (NK sentinel, macrophage function), Adaptive (replenish T cells) (IL15, IL7), response to new and recall antigens in elderly (extends influenza vaccine protection). Prehabilitation: Physical therapy as immune adjuvant (booster) before cancer treatment to improve outcome (inpatient stay, complications, toxicity).

Answer 158

Most healthy tissues contain resident macrophages imprinted for vital tissue-tailored homeostatic functions. Tissue-resident sentinel cells: Mast cells, macrophages, T and dendritic cells; Monitor near surfaces like skin, GI mucosa, alveoli. Sentinel cells line or patrol inside blood vessels: Monocytes, NK cells, resident liver macrophages. Non-inflammatory: Macrophages maintain cardiac myocyte and brown adipocyte and erythroblast health by clearing damaged mitochondria; Macrophages in skeletal muscle cloak trivial damage (prevents inflammation); Synovial macrophage layer protects the joint against inflammation; Spleen macrophages clear old & damaged red cells from blood.

Answer 159

The global decline of specific immunity as we age. Ageing reduces: Lymphocyte diversity – Thymus & Marrow atrophy, Lymphocyte effector responses – Reduced mitochondrial bioenergetics, Memory cell generation – Global DNA hypo-methylation reduces survival factor production. Infection history: Chronic antigen stimulation by persistent infection (CMV, parasites) – exhausted (unresponsive) and senescent T cells (inflammatory, less specific, inhibit other T cells), smaller pool of competent naïve and mature T cells (less diversity), exercise helps eliminate senescent T cells, Epigenetic ‘scars’ from severe infection (sepsis, measles) – suppress immunity (months-lifelong) . Clinical consequences: Reduced response to new antigen – susceptible to bacterial and viral infection, reduced vaccine efficacy, Reduced immune surveillance of self (Tc, NK) – re-emergence of latent viruses (e.g. shingles [Varicella Zoster]), increased cancers.

Answer 160

The Global increase of mild inflammation (‘inflammaging’). Chronic low grade inflammation – contributes to age-related multi-system morbidity (e.g. atheroma). Accumulating danger signals stimulate innate immunity: Self – cell debris (garbaging) (e.g. circulating mitochondrial DNA, misfolded/oxidised/non-degradable proteins), senescent cell secretions (inflammatory cytokines, proteases); Quasi-self – nutrient volume/quality, remodelled microbiota (pathobionts); Non-self – chronic virus (CMV), periodontitis (P gingivalis activates PRR, C5a to feed on tissue breakdown).

Answer 161

Visceral adiposity (not subcutaneous) – omentum, peri-renal, retroperitoneal, mesentery. Nutrient stress (volume/quality): Mitochondrial dysfunction (‘gridlock’), Also affects liver, pancreas, brain; Stressed adipocytes release inflammatory cytokines, causing influx of inflammatory monocytes and T cells, senescent immune cells accumulate (proteases, cytokines), insulin resistance in skeletal muscle (poor glucose control); Gut dysbiosis is pro-inflammatory. Calorie balance & exercise attenuate inflammatory signals: Remove danger signals [e.g. mitochondrial stress peptides, senescent cells (apoptosis), improves microbiota], Restore muscle insulin sensitivity (better glucose control) & myokine release (immunoregulatory). The concept of ‘biological age’ refers to modifiable factors affecting healthy vs unhealthy metabolic aging. Your ‘immunobiography’ and ‘inflammaging phenotype’ is affected by your metabolic & infection history.

Answer 162

Steady state immunity varies between tissues: brain, retina, intestine, testis, ovary, foetus, skin… Although they remain connected: CNS nerves increase colon inflammation; colitis increases liver inflammation… Tolerant immune environment is usually: Physical barriers reduce access e.g. from blood vessels (endothelium), surfaces (epithelium), tight junctions between cells (e.g. blood-brain barrier & choroid plexus epithelium) Local ecosystem maintained by resident immune & structural cells: e.g. liver Kupffer cells; intestinal Treg cells (release IL10 and TGFβ); skull bone marrow, meningeal sentinel lymphocytes & CNS microglia; Dysfunction is associated with leucocyte invasion and disease. Healthy microbiota help maintain mucosal barriers: e.g. short chain fatty acids (enhance Treg differentiation, energy source for epithelium). E.g. brain has its own immune system - Neuronal circuits affect inflammation elsewhere, Circulating cytokines affect CNS function. E.g. intestinal barriers - Mucosal immunity: A healthy intestinal ecosystem preserves the healthy microbiota but minimises microbe entry. It maintains immunity but tolerates incoming antigens from the healthy microbiome & food. There is an epithelial barrier and vascular barrier within the mucosa. In health, mucosa houses 75% lymphocytes and most antibody production.

Answer 163

Keep microbes away from epithelium: Goblet cell mucus (gel of glycoprotein + water), Acts as a physical barrier, Holds antimicrobial peptides (epithelium, Paneth cells) and immunoglobulin (IgA). IgA (intestinal plasmacells) transcytosed across epithelium – coats microbes and toxins, shapes the microbiome by selective targeting & supports some symbionts. Steady state low level neutrophil emigration to luminal surface – kill approaching microbes. Prevent penetrant organisms accumulating: Resident macrophages (lamina propria) kill without inducing inflammation (anergic) – liver-resident macrophages (Kupffer cells) are a backstop if organisms get into the circulation.

Answer 164

The intestinal barrier (mucosal firewall) gets disrupted - dysfunctional barrier, dysbiosis and inflammation. Genetic factors and environmental factors cause pathobiont accumulation and penetration, so pathogens get passed barriers leading to inflammation. This can lead to decreased microbial diversity, loss of beneficial symbiosis and pathobiont expansion, and penetration of the pathobiont passes the epithelium into the mucosa. Genetic predisposition for altered intestinal ecosystem: Intestinal permeability (tight junction function), Innate anti-bacterial immunity, T cell signalling & effector function. Mucosal barrier homeostasis breaks down: Dysbiosis (altered gut microbiota including bacteria, fungi, yeasts, viruses) - reduced diversity with accumulation of pathobionts (symbionts which cause disease under changed conditions, including bacteria, fungi, viruses), Microbes accumulate near epithelium, penetrate into lamina propria promoting inflammation, Cycles of inflammatory damage, barrier breakdown, further dysbiosis - other tissue problems common (joints, skin, eye, hepatobiliary), CNS (stress) influences colitis (cortisol on enteric glia promotes inflammation).

Answer 165

Sense of environmental quality; Whole organism – hypothalamus (via blood & brain), Single cells – sense locality (nutrients, energy status, oxygen, stress) & organism (endocrine). Unfavourable factors would be low resources (nutrients), normal for stable differentiated cells competing for limited growth factors, fitness impact (pathogen, toxin, trauma, cold...). Optimally allocate resource budget (metabolic flexibility): Between growth, reproduction and survival, Substrate switching. Metabolic resources are carbon for energy or biomass – anabolic vs catabolic programs, Catabolic is default for many stable mature/quiescent cells, Dysregulation fuels inflammatory, autoimmune, metabolic diseases and cancer growth.

Answer 166

In the absence of growth factors binding to its receptor, glutamine and glucose won’t enter cell and undergo hydrolysis or go through TCA cycle, allowing for growth. Instead lipids and amino acids will be catabolise and used in TCA cycle instead. Immunometabolism is resource allocation to defence and survival – resources diverted from movement, growth & reproduction (e.g. sickness behaviours). Cell metabolic programs: Dormancy is catabolic: Cells not directly involved in defence (muscle, adipose, naïve/quiescent immune cells), Resource light - sustenance-energy not biosynthesis, basal nutrient uptake, Recycling (autophagy), alternative fuels (fatty acids, ketones), Maximise energy yield (ATP) from carbon resources – oxidative phosphorylation (TCA cycle) and fatty acid oxidation, Stress-resistant, tolerant (anti-inflammatory), progenitor self-renewal not proliferation. Growth is anabolic: Activated immune & repair cells, Resource demanding, biosynthesis over energy - high nutrient uptake, Glucose & glutamine fuels - excess carbon secreted as lactate for Cori cycle, Proliferation, differentiation, pathogen clearance. Mitochondria reprogram from catabolic to anabolic: Metabolic reprogramming is signalled by oncogene proteins, TCA cycle intermediates exported as carbon source for biomass - Citrate for fatty acids, cholesterol, epigenetic change (acetyl CoA in histone acetylation)], Transamination (⍺-ketoglutarate, oxaloacetate) for amino acids, nucleotides.

Answer 167

Anabolic reprogramming in T cell activation means instead of being at metabolic quiescence during steady state (basal nutrient uptake, basal glycolytic rate, minimal biosynthesis, no net growth), glycolysis is greater than oxidative phosphorylation. This leads to metabolic activation, increasing nutrient uptake, glycolytic rate, protein/lipid/nucleic acid synthesis, causing cell growth and proliferation. Once immune challenge starts to decrease and oxidative phosphorylation is greater than glycolysis once again, the T cell return to basal nutrient uptake but has greater mitochondrial mass so is metabolically primed but returns to steady state.

Answer 168

In scarce quiescence (scarce nutrients): If fasting, stable differentiated cells in homeostasis, passive immune defence, stress resistance (dormancy), naive/quiescent/exhausted immune cells…, Then the cell components are the primary substrate and burn, Produces a catabolic process, The output is Mitochondria extracting the maximum energy from limited carbon input, alternative fuels, autophagy & proteosome degradation feed lipolysis & glycolysis with oxidative phosphorylation of carbon for energy. Growth-associated (fed state): If need cell differentiation & replenishment, immune cell activation, inflammation, autoimmunity, autoinflammation cancer growth…, Then the environmental nutrients are the primary substrate and build, Process is anabolic, Creates biomass and defence/attack molecules, The output is Mitochondria reprogrammed for biosynthesis from high carbon input, Glycolysis maintains ATP; most carbon forwarded for biosynthesis & epigenetic modification.

Answer 169

The reaction of living, vascularised tissue to injury (danger above a threshold). Inflammation delivers concentrated, activated defensive materials in fluid: Phagocytes (monocytes, macrophages, neutrophils, dendritic cells), and Plasma proteins (opsonins, complement). Delivered cells, proteins, fluid = exudate. Delivery + battle = inflammation. Examples of inflammation: Infection - cold sore, pneumonia…, Irritation/obstruction - gallstone cholecystitis…, Trauma - burn, surgery, fracture…, Around dead tissue - stroke, myocardial infarct…; Can be acute or chronic. Inflammation is recognised by swelling, heat, painful, redder, loss of function. The signs differ depending on the setting but are driven by active changes in the microvasculature which delivers the exudate.

Answer 170

Inflammation starts within minutes Mildly hydrated hyaluronan becomes a Hydrated hyaluronan matrix because Arterioles dilate and vessels leak. In the beginning, small blood vessels and extracellular matrix respond to danger signals which include: Damaged matrix (hyaluronan fragments, liberated cytokines), Stressed/dying tissue cells, Mast cells (degranulate), Histamine – a vasoactive amine (mast cells, nettles, wine...) – short-lived response, Pathogens. As a result of the danger signals: Blood fills the capillary and venular bed (redder, warmth), Exudate fluid leaves capillaries/venules, Interstitial matrix actively hydrates (local swelling), Venous outflow becomes sluggish (stasis, congestion). Sustained by cytokines in substantive injury: Perivascular mast cells degranulate and release cytokines through projections into vessels, Incoming leucocytes take over.

Answer 171

Exudate leak and tissue swelling are active. Local swelling: Water uptake (hydration) into connective tissue matrix (hyaluronan), This relaxes compression - collagen detachment & unfolding, fibroblasts relax, Major factor especially burns/freeze injury. Vascular leak: Junction breaks between endothelial cells (cytokines & autacoids: VEGF, BK, His), Capillary filtration pressure (arteriole dilation, increased cardiac output), The clot protein Fibrinogen is small enough to escape with the fluid. ‘Passive’ leak from microvessels is usually less important: Endothelial cell loss, until it regenerates - direct injury from uv light in sunburn, During angiogenesis - new capillaries are leaky.

Answer 172

Leucocytes and platelets entering venules are pushed toward the walls by the haemodynamics of normal blood flow. Useful to screen for problems. But normal endothelium has a thick glycocalyx ’blanket’ (0.2-2u) that blocks inflammatory cells from sticking firmly onto endothelium. If the endothelium is injured, this blanket is damaged to neutrophils stick to it.

Answer 173

Contact, capture and rolling: DAMP and cytokines (TNF, IL-1) cause endothelium to shed glycocalyx within minutes, exposing surface adhesion molecules like selectins, These enhance neutrophil and platelet rolling. Firm adhesion, spreading, and crawling: Cytokines increase endothelial adhesion molecules (integrin ligand) that bind neutrophils, which spread and crawl, Platelets boost endothelial activation - fibrin strands form on the endothelium, recruiting more platelets. Transmigration: When crawling neutrophils encounter platelets bound to endothelium, they move to the endothelial junction to exit, using proteases.

Answer 174

Pericytes guide out transmigrating neutrophils, helping them cross the basement membrane into the tissue, Extravasated neutrophils emerge and screen the perivascular tissue, Rigidity of inflamed tissue further activates traversing neutrophils, Platelets seal the transmigration site behind the neutrophil. Chemotaxis is directed migration up a concentration gradient. Phagocytes need a matrix to crawl over, thus fibrin is present to allow them to do chemotaxis. Things that attract neutrophils: Self - Coagulation products, Complement C5a/C3a, IL-8. Non-self - Bacterial endotoxin, f-met-leu-phe peptides. Minor damage can be cloaked by resident macrophages, so concealed from scanning neutrophils. Activation increases neutrophil lifespan.

Answer 175

Minor damage can be cloaked by resident macrophages, so concealed from scanning neutrophils.

Answer 176

Neutrophils soon accompany the escaping fluid to enter the injury site. They leave a ‘breadcrumb’ trail of their granule proteins, Monocytes/macrophages follow to surround neutrophil swarms.

Answer 177

Pus - Neutrophil and enzyme-rich, Fibrinous - fibrin>>cells causing greyish sticky fibrin coating, Serous - fluid>>cells, looks serum-like, lacking fibrinogen and platelets, like in burn blister/allergic polyp, Haemorrhagic - Vascular destruction.

Answer 178

In inflammation, draining lymph carries immune cells, inflammatory cytokines, extracellular vesicles, matrix fragments, etc. from the injury site to local lymph nodes. This is the adaptive immune responses. Tissue swelling opens up lymphatics. Lymphangitis is inflammation triggered by cytokines draining up the lymphatic.

Answer 179

Not all pain is explained by local pathology - pain perception is heavily influenced by other cognitive input/stresses. Not all inflammation is painful - indirect pain from adjacent structures (liver capsular stretch, parietal pleura over lung infarct…) Visceral pain - poorly localised, complex, autonomic activation (pale, sweaty, heartrate, BP). Sensory nerve endings (Aẟ, C): Dying cells - H+, ATP, K+; Mediators - lipid, bradykinin, ATP, inflammatory cell cytokines (IL1β, TNF, NGF). Aberrant pain: Pain sensitisation (hyperalgesia) - resident macrophage cytokines, Pain to innocuous stimuli (allodynia), Direct nerve injury (neuropathic pain). Inhibition: Neuroinflammatory reflex (vagus via brainstem) attenuates pain & inflammatory cytokine release (shock), Immune cell opioids.

Answer 180

Cytokine effects distant to the injury: IL-1β, TNF, IL-6, chemokines. Liver: Acute phase proteins (mostly from liver, also adipose/macrophages), Fibrinogen, C-reactive protein, serum amyloid A, haptoglobin (IL6, IL1). Bone marrow: Accelerated WBC release from marrow (especially neutrophilia). CNS: Fever - alters PG in hypothalamus; Sickness behaviours - neurotransmitter availability (monoamines: serotonin, dopamine, Nor) and autonomic dysfunction, Sleep, listlessness, decreased appetite, irritability and social withdrawal, heightened pain sensitivity, anhedonia; Effort preference impaired - cortical integration of motor effort against malaise; Cognitive impairment (‘brain fog’) (chronic inflammation), maybe microglial neurotoxicity in white matter; Cytokine-induced depression (chronic inflammation or immunotherapy). Skeletal muscle: Fatigue - ER stress protein WASF3 (endotoxin, virus) disrupts mitochondrial respiration (supercomplexes).

Answer 181

Resolution, organisation, dissemination, chronic inflammation.

Answer 182

Elimination of the cause of injury is essential. Danger signals wane: Pro-inflammatory mediators are catabolised, Extravasation diminishes, Neutrophil apoptosis. Anti-inflammatory signals predominate: Macrophages engulf apoptotic neutrophils (efferocytosis) - metabolic switch - scavenging, anti-inflammatory (IL-10, TGFβ); Soluble mediators promote clearance - pro-resolving lipids (lipoxins, resolvins & protectins), complement and cytokine inhibitors; Neuroendocrine - cortisol, anti-inflammatory cytokines (IL10, IGF-1) attenuate sickness behaviours. Removal of exudate and debris, Recovery of tissue architecture (damage must be limited, short-lived and regeneration possible, e.g. lobar pneumonia), Chromatin modification (epigenetic) - changes future innate responses in tissue (Boosted or Suppressed, Lasts months-years).

Answer 183

Exudate is replaced with granulation tissue that remains to form a collagen scar, Typical settings are extensive necrosis, leftover fibrin, poor regenerative capacity. Scar tissue is stiffer to traverse (dense collagen, cross linked hyaluronan), Promotes leucocyte activation, favouring disease progression. Organisation of sticky fibrin adhesions binds surfaces together: Adjacent bowel loops, Adhesion over an entire serosal surface (symphysis), e.g.pericardium, The omentum is designed to wrap around inflamed intestine, to protect from rupture (appendicitis).

Answer 184

Regeneration – renewal or compensatory growth to replace damaged tissues. Repair – fibrous scar production (fibrosis) to patch damaged tissues.

Answer 185

Labile cells – dividing in homeostasis; rapid regeneration (skin, GI tract), constant proliferation and apoptosis. Stable cells – non-proliferative in homeostasis; capable of regenerating after injury (Liver - regeneration after significant damage to liver, proliferation of remaining cells and progenitor cells, rapid restitution after 70% PHx; Kidney - Renal tubular epithelial cells regenerate after injury like ischaemic/toxic). Permanent cells – unable to regenerate (neurons, cardiac myocytes).

Answer 186

Cell number tightly controlled; balanced growth and loss. Unbalanced growth (↑growth or ↓loss) leads to neoplasia. Signals: Soluble growth factors – autocrine, paracrine, endocrine – bind to receptors, trigger intracellular cascade to change behaviour; Physical stimuli – cell-cell and cell-matrix interactions – cell-matrix interactions mediated by integrins, triggering similar cascades.

Answer 187

1. Bleeding; 2. Clot formation; 3. Acute → chronic inflammation; 4. Fibroblast infiltration, neomatrix, granulation tissue; 5. Angiogenesis, fibrillar collagen; 6. Scar maturation

Answer 188

Forms rapidly ~1 day into the process of tissue healing by scarring; Grainy/shiny wound base; Early new vessels, acute inflammation - neutrophils, neomatrix. It is new connective tissue with Fibroblasts, vessels, lymphatics, Hyaluronan-matrix (dynamic turnover); Collagen scar eventually (myofibroblasts), high tension increases inflammation and scarring. Surrounds dead tissue, pus or irritants, isolates cause; Retains inflammatory cells (restricts motility), Delivers more exudate.

Answer 189

Blood vessel formation in adulthood. Wound healing; physiological (e.g. endometrium); pathological (e.g. neoplasia).

Answer 190

Fibroblast migration and proliferation: Resident mesenchymal cells, Source of connective tissue, Migration/proliferation triggered by growth factors, e.g. TGF-β produces fibroblast migration & proliferation, ECM↑ production and↓ degradation, PDGF produces proliferation. Extracellular matrix deposition: Produced by fibroblasts, Collagens – fibrillar type I/III, basement membrane type IV, Elastin, proteoglycans, glycoproteins, Net fibrillar collagen accumulation - ↑ production and ↓degradation. Tissue remodelling: Remodelling of granulation tissue ECM requires degradation by MMPs, Matrix metalloproteinases (MMPs) produced by many cell types, All ECM components as substrate, Regulated – production and activity (TIMPs), Mediate long term scar maturation and degradation. These processes coexist and co-ordinate.

Answer 191

Continued injury → progressive scarring → irreversible. E.g. Liver cirrhosis, end stage kidney disease.

Answer 192

An inflammatory syndrome after infection. “Life-threatening organ dysfunction caused by a dysregulated host response to infection” - lung; abdominal; urinary tract [sepsis-3 consensus 2016]. Hyperinflammation and ‘recoil’ immunosuppression - responses and restraints out of kilter, causing inflammatory tissue and circulatory damage, susceptibility to secondary infection (1/3 ICU patients - especially pneumonia when ventilator acquired - high mortality. Medical emergency: Early antimicrobials and organ support, (immune therapy), Mortality unchanged for a decade ~50,000 UK deaths/yr, 15% mortality (40% for septic shock).

Answer 193

When collateral damage from inflammation exceeds benefit of pathogen clearance: Pathogen (load, virulence, PAMP), Host (comorbidity, genetic, therapy). Cytokine storm: TNF + IL-18, Ifn-𝛾, IL1-β, (others), causing: Endothelial damage: Fluid leak syndromes (++litres) - soft tissues, muscles, lungs, mucosae, mesentery; Coagulopathy - glycocalyx degradation activates coagulation and platelet deposition depletes clotting factors/platelets causing haemorrhage and intravascular thrombosis, Intravascular inflammation (danger + cytokines): NETosis, Platelet pyroptosis (escalates NETosis, depletes platelets), Complement activation, Tissue necrosis and inflammation: Perpetuates danger signals, Sequential organ failure (lung, cardiovascular, CNS, renal, marrow, liver), Septic shock: High serum lactate and hypotension needing vasopressors (refractory to fluid resuscitation) - 40% mortality.

Answer 194

Dominant inflammation or immunosuppression (‘immune paralysis’) - different treatment priorities. Varies between patients (and over time), Clinically similar pictures conceal different underlying immune pathologies, Biomarkers e.g. raised serum ferritin vs low monocyte MHCII. Immunosuppression: Secondary infections (opportunistic, viral reactivation), Lymphocytes and/or myeloid cells suppressed so can’t activate innate immune surveillance/adaptive immunity; anti-inflammatory cytokines; T cell exhaustion/apoptosis; metabolic paralysis - reduced glycolysis, ATP, NAD+ content, epigenetic reprogramming.

Answer 195

WCC plunges, platelet count rises; Cognitive & physical impairment (multifactorial): PTSD/depression/anxiety, Fatigue - e.g. ER stress protein WASF3 (endotoxin, virus) disrupts muscle mitochondrial respiration; Increased readmission: Sepsis survivors have lingering immune suppression - epigenetic restraint on immune cell hyper-activation, increased bacterial infections and mortality.

Answer 196

Repeated or persisting injury/irritant - infection (e.g. TB), foreign body, obstruction; Undegradable foreign body undermines phagocytosis: Decoy foreign body (suture), Slippery prey (Pneumococcus capsule), Frustrated by slime, Intracellular organisms evade (tuberculosis). Inflammation can be the disease that needs treatment - atheroma, inflammatory bowel diseases.

Answer 197

Monocyte-macrophage tissue infiltrates in chronic inflammation. Mostly from circulating monocytes (differentiation to a macrophage which enlarges, lysosomes, mitochondria, E.R.). In the steady state they do sentinel patrol in vessels to survey and support endothelium, and migrate into tissue. In inflammation, enhanced monocyte migration, activation, proliferation; acquire APC ability, secrete TNF (anti-microbial). Some become macrophages, pro-inflammatory then restorative, macrophages and myofibroblasts nurture each other; exit by lymphatics or cell death.

Answer 198

Resolving vs organising repair, Focal scarring can protect - e.g. chronic ulcer, abscess; Widespread scarring destroys - e.g. cirrhosis, chronic pyelonephritis, chronic ischaemic heart disease; Persistence promotes cancer - e.g. osteomyelitis, cirrhosis.

Answer 199

They intensify and prolong inflammation. Importance: Defense against pathogens, Chronic inflammatory diseases (Atheroma, Alcohol liver disease). Formation: PRR detect danger, Filamentous complexes and particulate ‘specks’ of active caspase 1 enzyme. Effects: Inflammatory cytokines IL-1β and IL-18, Pyroptosis (regulated lytic cell death) - leaky corpse liberates cytokines and inflammasomes. Inflammasomes persist and circulate: Uptake by monocytes incites more inflammasomes.

Answer 200

Dysfunction from scarring and barrier damage: Tissue cell stress signals, Mechano-transduction (stiffer tissue is pro-inflammatory), Stable fibrosis state. Enhanced response to more injury (trained immunity): Epigenetic modification in tissue cells/progenitors - anabolic metabolism (acetyl CoA: acetylation), Evolved for benefit against infections, Lasts months-longer, but not specific - BCG protects against non-TB neonatal infections (heterologous protection) and adult recurrent bladder cancer.

Answer 201

Abnormal tract in an epithelial surface lined by granulation tissue. Blind ending (sinus) or linking two epithelial surfaces (fistula).

Answer 202

A localised, full thickness defect in an epithelial surface, caused by the sloughing of inflammatory, necrotic tissue.

Answer 203

Pus in newly formed cavity, granulation tissue surrounds it. Outcomes: Persists, Scars, Discharges (sinus, fistula).

Answer 204

Organised clusters of mature activated macrophages, in response to persistent stimuli. Larger cells, more organelles (multinucleate macrophages…) Low turnover (foreign body) - inert indigestible material, long lived stable macrophage population. High turnover (immune): Toxic agent (if known), Short-lived mobile macrophages with continual replenishment, T cells and other immune cells admixed, Can be infectious - TB, leprosy, schistosomiasis, protozoa, some fungi; or “Non-infectious” - sarcoid, Crohn

Answer 205

Manipulates mφ responses: Uses mφ and renders them insensitive to T cell help, Inhaled bacteria are imported into lung tissue within mφ, Promotes its own phagocytosis (avoiding lysosomes) and phagocytosis of infected apoptotic mφ. Granulomas form and spread the infection unrestricted: Phagocytosis of apoptotic infected mφ infects the arriving mφ, Migration of infected mφ initiates secondary granulomas, mφ necrosis permits exuberant extracellular proliferation - soft ‘caseous’ necrosis. Specific T cells are required to arrest infection: TNF and Ifn-γ increase microbicidal capacity, Contribute to lung destruction (cavitation) and so transmission, Bacterial population stabilises, Some proliferate, others go dormant until immunity dips.

Answer 206

Extracellular accumulation of insoluble fibrils made from a misfolded polypeptide (plus amyloid P protein). Many causes: different disease proteins; some local, others multiorgan, E.g. amyloid AA (serum amyloid A) in chronic inflammatory disease. The misfolded proteins self-associate: Either aggregation-prone mutant or over production of normal protein (+/- defective degradation).

Answer 207

It’s specific - Pathogens are diverse, occupy different compartments and have different life styles. It has memory so second exposure to antigen is larger and faster than primary immune response. Pros: fight infections, immunity to reinfection (vaccination possible), kill mutated/tumour cells. Cons: tolerance (allergy, autoimmunity), transplant rejection.

Answer 208

T cells and B cells - both are types of lymphocytes: Predominant cells found in the lymph, Spend most of their time in the secondary lymphoid organs (e.g. spleen and lymph nodes), Recirculate via the lymph and blood, then back to secondary lymphoid organs. Every cell has a unique receptor which binds a specific antigen (immunological term = antigen specificity), If they never been activated, called naive T/B cells, Once specific cells have been activated (e.g. after vaccination), the are called effector T/B cells and some become memory T/B cells.

Answer 209

Antibody-producing cells, Once activated, become plasma cells (aka effector B cells). Plasma cells produce antibodies which bind to a specific antigen. Antibodies are Y-shaped, soluble, secreted molecules that circulate in the blood/body fluids, Bind to pathogens and kill them/mark them to be eaten/neutralise them.

Answer 210

2 main types of T cells: CD8+ Cytotoxic T Lymphocyte (CTL): Kills infected/mutated ‘self’ cells. CD4+ T helper cell (Th cell): Organise immune responses - produce different cytokines, Can differentiate into different types - Th1, Th2, Th17, Treg.

Answer 211

T and B cells express receptors of random specificity. Each naïve T or B cell bears receptors of a single specificity; When the T/B cell binds its specific antigen, it activates and proliferates; Daughter cells express identical receptor to parent (hence clonal); Expanded population mediates immune response; Some daughter cells become memory cells- these are maintained at higher frequency and are primed to respond rapidly in future.

Answer 212

1. Variable regions are encoded by Variable (V), Diversity (D) and Joining (J) gene segments. 2. Complete functional genes that encode a variable region are generated by somatic recombination of separate VDJ segments (E.g. 5.8x10^6 VDJ combinations in TcR). 3. Multiple contiguous copies of V D & J gene segments are present in BcR/TcR gene loci - these are randomly selected during somatic recombination. Diversity of BcR and TcR: Imprecise and random events occur when DNA breaks and rejoined allowing nucleotides to be lost or new ones to be inserted (E.g. 2x10^11 variations in TcR). Very wasteful process as can cause frame shift mutations and coding nonsense. There is Combinatorial Diversity: Different V-D-J combinations, Different Heavy/Light chain (BcR) combinations, Different alpha/beta chain(TcR) combinations; and Junctional Diversity: Extra/fewer nucleotides at V-D-J junctions.

Answer 213

B cell receptors (BcR) and T cell receptors (TcR) contain: Variable regions - bind antigen and are different between receptor on different cells, and Constant regions - do not vary and important for function and signalling. The BcR is a membrane bound version of antibody with identical specificity.

Answer 214

The B cell receptor (BcR) and antibody recognise soluble antigen in its normal (native) form. Antigen can be sugar, lipid, or protein. The T cell receptor (TcR) has to have antigen “presented” to it on Major Histocompatibility Complex (MHC) molecules on another cell. Antigens are proteins and must be chopped up into peptides, then “loaded” onto MHC molecules and presented on the surface of a cell.

Answer 215

There are Class I and Class II Major Histocompatibility Complex (MHC). CD8+ CTLs only bind antigen on class I MHC (MCHI). CD4+ T helper cells only bind antigen on class II MHC (MCHII). MHCI: On all nucleated cells (not red blood cells), apart from neurons (do not want to kill these), Presents only endogenous antigens = proteins from within the cell, Self proteins, mutated proteins (e.g. in cancer) and intracellular pathogen proteins (e.g. viral, intracellular bacteria). MHCII: Only on specialised Antigen Presenting Cells (APC), The most important of these are dendritic cells, Presents exogenous antigens = proteins from outside of the cell, Extracellular pathogens, environmental proteins, food proteins, self proteins, etc.

Answer 216

Both classes have 4 units and a peptide-binding cleft. MHCI (binds CD8) has 3 alpha helices (a1, a2, a3) and one beta sheet (b2- = microglobulin), made of 8-10 amino acids; MCHII (binds CD4) has 2 alpha helices and 2 beta sheets (a1, a2, b1, b2),made of 13-25 amino acids. Each MHC molecule presents a restricted range of peptides: Peptides bind anchor pockets in MHC via ‘anchor’ amino acids, Anchor pockets interact with only a limited range of biochemically similar ‘anchor’ amino acids, A single MHC molecule presents peptides with a shared sequence or MOTIF.

Answer 217

Just as our pool of T cells can theoretically recognise any protein peptide, we need the MHC to present as many different peptides as possible. Polymorphism, polygeny and co-expression allow presentation of diverse antigens Polygeny - multiple independent genes for each MHC type. Co-expression: alleles inherited from mother and father. Polymorphisms - multiple variants of each gene within the human population (most polymorphic of all genes - mainly in the peptide binding domain). MHC mismatch is the major cause of transplant rejection: Very rare for 2 unrelated individuals to express the same combination of MHC variants; Polymorphisms cause MHC to be seen as ‘non-self’ upon transplant; MHC - Major Histocompatibility Complex; HLA - Human Leukocyte Antigen; 1 in100,000 chance of matching an unrelated donor.

Answer 218

Prevention of unnecessary and harmful responses to self and environmental antigens. Central Tolerance: Deletion of self reactive T cells in the thymus, Deletion of self reactive B cells in the bone marrow. Peripheral Tolerance: Activation of lymphocytes requires recognition of Danger, Recognition of antigen in the absence of danger causes lymphocytes to become anergic or die.

Answer 219

The process of T cell selection in the thymus = eliminate the harmful and reject the useless. T cell are selected in the thymus on 2 criteria: Ability to bind MHC - signalling allows survival - called positive selection; Strength of binding to MHC presenting self-peptide - strong signalling causes death - called negative selection. Hugely wasteful - 95% of developing T cells deleted. Clones with low TCR affinity for MHC/peptide fail selection and die by neglect, Clones with high affinity are negatively selected and deleted, Only clones with intermediate affinity are positively selected and survive.

Answer 220

Peripheral tolerance through anergy: Dendritic cell (class II MHC) needs to present antigens (peptide) to CD4+ T helper cell (has TcR), The activation of naive T-cells requires 2 signals, Signal 1 is the peptide bound to MHCII presented to TcR, Signal 2 is a costimulation signal with B7 on the DC and CD28 on the CD4+ T helper cell. Signal 1 with signal 2 = activation Signal 1 without Signal 2 = anergy/death. Activation of T cells require DC to sense danger (PAMPs/DAMPs - pathogen/damage). This is communicated through signal 2. Without danger, DC don’t become fully mature in the lymph nodes where they meet the T cells.

Answer 221

B cells & Antibody: Basic functions of antibody, Class switching, Functional specialisation of different antibody classes, Fc receptors CD4+ T helper cell functions: Costimulation to B cells - affinity maturation, Cytokine production & costimulation drive antibody class switching, Cytokine production drives activation innate immune cells CD8+ cells: Cytotoxic killing of infected cells NK cells: Prevent evasion of killing by virally infected cell

Answer 222

DC can present antigen to either a naive CD4 T cell via MHCII or a naive CD8 T cell vis MHCI; Naive CD8 T cell will be activated into CD8+ ‘cytotoxic T lymphocyte’ (CTL) and undergo cytotoxic lysis of infected cells, killing intracellular pathogens and tumour cells; Naive CD4 T cells will be activated into CD4+ T 'helper' cells which will help B cells and innate cells, indirectly killing extracellular and intracellular pathogens and tumour cells; Naive B cells can be activated by a native antigen or a CD4+ T 'helper' cell, Leads to plasma and cell antibody production, which bind extracellular pathogens and infected cells, so killing extracellular and intracellular pathogens.

Answer 223

Antibody = immunoglobulin = Ig 5 forms of antibody: IgM (complement activation), IgG (complement activation), IgA (antibody neutralisation), IgE (mobilisation of inflammatory mediators), IgD Overall, they have roles in antibody neutralisation, compliment activation, opsonisation, ADCC (Antibody-dependent cell cytotoxicity), and mobilisation of inflammatory mediators.

Answer 224

In enveloped viruses (a heat-sensitive virus cell that is inside a lipid membrane), neutralising antibodies block the attachment of a virus to the cell as well as its entry into the cell, so a neutralising antibody will block binding of toxins to cell surface receptors, e.g. vaccination to tetanus, diphtheria and cholera toxins. Example: Seasonal flu vaccine to Haemagglutinin & Neuraminidase: anti-influenza virus IgA antibodies will mean the virus cannot infect the cells.

Answer 225

IgM and IgG can activate the classical complement pathway. Complement: 1. Directly lyses bacteria, 2. Opsonises cells for uptake by phagocytes, 3. Activates the immune response. Pentameric ('planar' form) IgM molecules bind to antigens on the bacterial surface and adopt the 'staple' form of IgM, This causes C1q to bind to one bound IgM molecule; IgG molecules bind to antigens on bacterial surface, One C1q binds to at least two IgG molecules together; Binding of C1q to Ig activates C1r which cleaves and activates the serine protease C1s.

Answer 226

Phagocytes have receptors on their surface for antibodies (Fc receptors) and complement (e.g. CR1), If a pathogen has antibody and/or complement deposited on its surface it is opsonised (phagocytes can now see it) - antibodies engage Fc receptors and drives phagocytosis, Tells the phagocyte that this is something that should be eaten/destroyed.

Answer 227

Infected cells can have pathogen molecules on their surface, Antibodies bind and mark them for killing, NK cells and neutrophils recognise antibodies (since they have Fc receptors) and tell the cells to apoptosis via release of cytotoxic granules, E.g. via release of perforin/granzyme or cytokine TNFa.

Answer 228

Mast cells and basophils active in anti-worm/allergy responses (allergen = allergy-inducing antigen), Have Fc ε receptors that binds free IgE, Binding antigen leads to cross-linking of IgE receptors and rapid release of inflammatory compounds (e.g. histamine), Is the reason we get a rapid response after seeing an allergen. Systemic mast cell degranulation = anaphylactic shock.

Answer 229

Due to B cell activation. Antibody function is determined by Fc region - termed isotypes, Naive B cells express IgM (& IgD): early response dominated by IgM, Activated B cells can class switch to make IgG, IgA and IgE.

Answer 230

Distinct Fc receptors for each isotype: Fcɣ receptor for IgG, Fcε receptor for IgE, Fcɑ receptor for IgA, Fcμ receptor for IgM. Expression of receptors differs between different immune cells, e.g. Fcε receptor 1 only on Mast cells and basophils. Different functions of isotypes partly due to the restricted expression pattern of Fc receptors.

Answer 231

IgM: First isotype to be produced, Multimer - great for trapping and neutralising lots of antigen, Very good at activating complement, Poor at opsonising and ADCC. IgA: Dimeric, Found in mucosa - gut and lung, Good for neutralising intestinal pathogens and ensuring they are flushed out, Poor at activating complement, opsonising and ADCC. IgG: Monomeric, Action depends on subclass, but can opsonise, neutralise, activate complement and ADCC. IgE: Monomeric, Best for activating basophils, mast cells and eosinophils, In allergy and parasite infection.

Answer 232

Activated B cells undergo somatic hypermutation - point mutations in variable regions of receptor/antibody. Leads to generation of antibodies with stronger or weaker binding to antigen. Those with stronger binding are selected by affinity maturation - important for monomeric antibodies like IgG.

Answer 233

DC and other cells determine the quality of T cell response (gives out signal 3 - signal 1 is antigen + MHC, signal 2 is costimulation danger signal). The Signal 3 that naive CD4+ T helper cell gives is by releasing either Th1, Th2, Th17, Treg... Th1 produces the prototypic cytokine IFN-γ, which fights intracellular bacteria and viruses but can cause autoimmunity and IBD; Th2 produces the prototypic cytokine IL-4, which fights parasitic worms but can cause allergy. Th17 produces the prototypic cytokine IL-17, which fights extracellular bacteria and fungi, but can cause autoimmunity and IBD. Treg produces the prototypic cytokine IL-10 which suppresses the immune response.

Answer 234

1) provide co-stimulation to B cells 2) drive affinity maturation of B cells 3) drive class-switching of B cells 4) Activate innate immune cells

Answer 235

B cells also require both signal 1 and signal 2 for activation, Signal 1 (antigen) provided by binding of native antigen to B cell receptor, Signal 2 (co-stimulation) provided by activated CD4+ T cells. CD4+ T cells provide signal 2 only when B cells present them with peptide/MHCII that they recognise. B cells only present MHCII-peptide complexes when antigen is taken up via the B cell Receptor. Thus, CD4+ T cells effectively only provide help to B cells that recognise the same antigen as they do - called ‘linked recognition’. Linked recognition prevents CD4+ T cells helping B cells that recognise self/environmental antigens.

Answer 236

Following somatic hypermutation, linked recognition by CD4+ T cells allows selection of those B cells expressing receptors/antibodies that bind antigen most strongly. Hence, the requirement for help from CD4+ T cells is essential to drive affinity maturation of B cells.

Answer 237

Class-switching requires co-stimulation by CD4+ T cells, Cytokines from CD4+ T cells select class of antibody.

Answer 238

CD4+ T cells are a peptide + MHC. TH1 cells bind to macrophages (IFN-y receptors) to stimulate them to kill intracellular bacteria. TH2 cells release IL-4, IL-5, IL-13 which stimluates eosinophils, mast cells, IgE to bind to plasma cells. TH17 cells release IL-17 which stimulates fibroblasts/epithelial cells to release chemokines which attracts neutrophils. Treg cells inhibit immature DC so cause lack of T cell activation.

Answer 239

CD8+ CTLs recognise non-self peptides on class IMHC, All nucleated cells express class I MHC (except neurons), Class I MHC presents “endogenous antigens” (i.e. those from inside the cell), Kill the infected cell. Initial activation: MHCI/peptide on Dendritic cells, termed cross-presentation, leads to activation. Subsequent activation: MHCI/peptide on infected cells - leads to killing. CD8+ CTL kill through FAS ligation and perforin and granzyme release. FAS ligation directly signals to induce apoptosis, Perforin forms pore allowing granzyme to enter, Granzyme activates caspases, DNAase activation and mitochondrial break down.

Answer 240

Pathogen sensed by sentinel cell PRR in epithelium, resident macrophages, mast cells, dendritic cells; different pathogen types elicit particular cytokine alert patterns. Within minutes, innate lymphoid cells respond to alert patterns with rapid cytokines and chemokines that amplify and tailor innate response (cells activated & recruited) to initialise specific immunity (via dendritic and naïve cells). Within hours, local inflammation brings innate effectors onsite, which buys time for adaptive response. Then by a week, specific immunity targets pathogen and boosts innate killing; T-helper cells organise immune response (Th1/2/17 cytokines); CTL kills Ag+ target cells; Ab specific opsonin, activates phagocytes (FcR), NK cell killing (ADCC), classical complement. After pathogen elimination, clearance of effector cells, debris and healing; most effector lymphocytes die (clonal contraction). Ready for re-challenge with specific protective immunity primed for a disease-preventing secondary response - long-lived plasma cells (months-years), small populations of memory B & T cells (years); tissue acquire trained immunity.

Answer 241

Innate lymphoid cells shape the immune response. They are enriched at surface barriers (gut, lung, skin) and lymphoid tissue; promote tolerance and barrier stability in homeostasis; induce Treg, induce effector T cell death. Rapid early cytokine response to alert signals from barrier sensor cells (not antigen-specific), shapes and intensifies innate cell infiltrate, initialise pattern of specific immunity - polarises DC and naïve T cell maturation (‘signal 3’).

Answer 242

Type 1: Intracellular pathogens: NK, ILC1, Th1 (with help from CTL and IgG) signal macrophages via Ifn-y. Type 2: Large parasites: ILC2, Th2 signal basophils and mast cells (with IgE receptors) and eosinophils via IL-5, IL-13. Type 3: Extracellular fungi, bacteria: ILC3, Th17 signal neutrophils via IL-17, IL-22.

Answer 243

Harmful immune reactions: Hypersensitivity (allergy) - to inherently harmless environmental antigens (‘allergens’), Autoimmunity - failure to tolerate self antigens drives tissue damage. Immunodeficiencies.

Answer 244

Neo-antigen: self Ag can become modified and immunogenic; Molecular mimicry: microbe Ag can resemble self; Hidden antigens (sequestered): revealed by tissue damage - dying neutrophils release many autoantigens; Persisting weakly self-reactive lymphocytes: adults rely mostly on peripheral tolerance, but this can leak - e.g. inhibition via surface PD1 (T/B cell), CTLA4 (active T cell) - inflammation breaks anergy, stimulates bystander lymphocytes. Predispositions and triggers (infection, tissue damage) leads to self-reactive T and B lymphocytes activated, leading to chronic inflammation and epitope spreading (other epitopes on the autoantigen, other self-antigens revealed by damage).

Answer 245

Failure to tolerate self antigens drives tissue damage. 1 in 25 worldwide, 80% autoimmune diagnoses are in women. Progressive often - wax & wane: Infections can trigger, Perpetuated by target abundance, tissue damage and innate immunity, Neutrophils often involved in autoimmune disease flares (SLE, RA, vasculitis), as are ROS, cytokines, NET, autoantigens (DNA, histones, citrullinated peptides, MPO, proteinase 3). Can be single organ or multisystem depending on antigen targets. Can have multiple autoimmune diseases since shared risk factors (e.g. Type 1 diabetes with coeliac disease, autoimmune hypothyroidism). Serum autoantibodies alone don’t mean disease - low level autoantibodies are common with age, ≠ autoimmune disease, and some autoantibodies produced after tissue damage may help clearance.

Answer 246

Inactivated X chromosome in women = Xi. Why autoimmunity is more common in women. Xi-chromosome is immune stimulatory, risking autoimmunity; XIST (non-coding RNA) coats the Xi chromosome in the Barr body, which is a danger signal (ssRNA) revealed to immune system after cell death by phagocytosis, activates PRR (TLR7) - type I IFN response (plasmacytoid DC) (as in SLE). X-linked immune gene dosage: Incomplete/part-reversal of epigenetic 2nd X-chromosome inactivation (Xi), affects XX, X-aneuploid (Klinefelter XXY, triple X) individuals; Activated or aging lymphocytes cause greater X-linked inflammatory gene expression, TLR7 (ssRNA receptor) signalling in B cells (SLE) so better pathogen response, but more precarious self-tolerance.

Answer 247

Oestrogen: Autoantibodies (B cell reactions, reduced central tolerance), Low normal = pro-inflammatory, High normal (ovulation, pregnancy) = anti-inflammatory. Progesterone: Opposes oestrogen (reduced autoantibodies and anti-inflammatory), but Th2, eosinophil degranulation (atopy). Testosterone: Immunosuppression, central tolerance. Transitions: Pregnancy (placental oestriol: Treg) - RA, MS flares improved (Th1) but SLE flares worsen (autoantibody). Post-partum - SLE & RA flares worsen. Menopause - SLE flares improve, RA flares worsen. Inflamed tissue: TNF stimulates aromatase to convert ++ androgens to oestrogen (pro-inflammatory), TNF inhibitors benefit men relatively more.

Answer 248

Immune reaction to innocuous foreign material - no infection, no benefit, only damage. Can be food, pollen, drug, chemicals, harmless animal/fungal antigens, venom. >20,000 UK hospital admissions (2013-14; primary diagnosis), 20% as emergency for suspected anaphylactic reaction. Note: Food allergy ≠ Food intolerance (non-immune e.g. enzyme deficiency).

Answer 249

Atopy: predisposition to become IgE-sensitised to innocuous environmental Ag (allergen) - environmental and genetic factors; Often multiple sensitivities, e.g. atopic dermatitis and food allergy; allergic rhinoconjunctivitis and asthma; ‘Atopic march’ is age progression of atopic dermatitis-allergic rhinitis-allergic asthma. Allergy in non-atopic people is usually isolated (bee venom, drug), any age. Allergens are protein (often protease, has peptides that themselves/modified bind MHC); small, soluble (diffuse in mucus); stable (desiccate; resist stomach pepsin); Pollen - seasonal; Food - Peanuts, Tree nut, Shellfish; Drug - b-Lactam antibiotics; Insect - Bee/wasp venom, House dust mite faeces; Pet - Cat dander (=skin+saliva).

Answer 250

Unwanted anti-parasite immune response to innocuous antigen, 1st exposure to antigen in skin/mucosa causes ILC2 to react: Dendritic cells migrate & present antigen in node; Naïve T cells polarise to TH2 cells that induce B cells to switch to IgE production & mature; Mature IgE plasma cell; Released IgE gathered on mucosal mast cells/circulating basophils (on IgE Fc receptors). Re-exposure causes IgE-bearing mast cells/basophils to rapidly trigger an allergic reaction: Local reactions - urticaria, hay fever (allergic rhinitis), allergic asthma, food allergy; Systemic anaphylaxis - life threatening.

Answer 251

Rapid life-threatening IgE-mediated hypersensitivity: vasodilation + vascular leak due to mast cell products. Breathing/circulation problems: Difficulty breathing (pharyngeal/laryngeal oedema, bronchospasm), Vascular shock (low BP, tachycardia), Skin has evolving redness, itch, swelling (weals, angioedema), Mucosal oedema (lips, tongue, palate), gut spasm (colic, vomiting, diarrhoea). Setting: food (peanut, cow milk, shellfish), bee/wasp venom, drug (penicillin/cephalosporin); may not have a history of allergy; when fatal, death often occurs within minutes (food 35mins; sting 20mins; ivi <5mins). Treatment: remove cause; early i.m. adrenaline (+ oxygen, antihistamine, corticosteroid). Non-allergic causes of mast cell degranulation (anaphylactoid reaction): Radiocontrast medium (osmolar), opiates (opiate R), NSAID (COX-1), anaphylotoxins (C3a, C5a), physical (heat/cold/vibration), bradykinin activation.

Answer 252

After persistent allergen exposure and Th2 reaction, chronic inflammation and wound healing leading to: Persistent oedema (airway narrowing), and Airway remodelling: goblet cell metaplasia (mucus hypersecretion; mucus plugs), sub-epithelial collagen fibrosis, bronchial smooth muscle hypertrophy and hyperplasia, chronic inflammation (eosinophils+) and tertiary lymphoid tissue. Airway hyper-reactivity to other challenges cause acute exacerbations to epithelial damage: Rhinovirus, irritants (perfumes, pollutants), NSAID intolerance (reduced PGE2 worsens bronchoconstriction).

Answer 253

Reaction purpose is to opsonise extracellular microbes for better phagocytosis; here it is misdirected to our cells. Type II hypersensitivity. This leads to: Destruction of opsonised target cells - removal by phagocytes (Fc receptor), complement activation, lysis by Ab-dependent cell cytotoxicity (NK cells); Autoantibody binds cell surface receptor, Graves’ disease - stimulates TSH receptor causing hyperthyroidism, Myasthenia gravis - blocks Ach receptor causing neuromuscular weakness.

Answer 254

Reaction purpose: opsonise extracellular virus; but here as capacity expands insoluble inflammatory deposits occur. Type III hypersensitivity. Large insoluble complexes deposit: In skin, vessels, joints, glomeruli, elsewhere, leading to complement & inflammation; IgG with high levels of allergen - C3 usually breaks up large complexes to easily phagocytosed small soluble ones, but this depletes; Resolves if free antigen levels decline. Acute antigen exposure: Hypersensitivity (unsensitised) causes inflammation after several days due to foreign protein infusion - antivenom (horse serum), mouse/chimaeric monoclonal Ab; Primary Immune response from IgM, IgG causes ‘serum sickness’ (itchy rash, urticaria, fever, arthritis, vasculitis, glomerulonephritis); Hypersensitivity (sensitised) is inflammation in several hours; Acute farmer’s lung (hypersensitivity pneumonitis) causing breathless, fevers, neutrophil alveolitis. Chronic antigen exposure: Autoimmunity - SLE is nuclear autoantigens from dying cells; Chronic infection - infectious endocarditis (not hypersensitivity or autoimmunity).

Answer 255

Reaction purpose: clear infected cells (intracellular pathogen), but here its fake infection. Type IV hypersensitivity reaction. Autoimmunity: type 1 diabetes - CTL kill pancreatic islet β cells (target insulin-related peptides); Hypersensitivity: coeliac disease - sentinel intraepithelial CD8 T cells kill intestinal epithelium stressed by cytokines from Th1 cells sensitised to modified dietary gliadin; Hypersensitivity: allergic contact dermatitis - manifests 2-4 days after re-exposure (‘delayed hypersensitivity’); causes red plaques, vesicles, oedema (acute), evolving to dry, scaly skin; effector memory T cell reaction to neoantigen - keratinocyte protein haptenized to Ni, Co, Cr, topical drug; sensitised cytotoxic T cells kill keratinocytes.

Answer 256

Type I hypersensitivity: IgE (Mast cell reaction) = antibody driven hypersensitivity. Type II hypersensitivity: Cell-bound IgG/IgM = antibody driven hypersensitivity & autoimmunity. Type III hypersensitivity: Extracellular IgG/IgM = antibody driven hypersensitivity & autoimmunity. Type IV hypersensitivity: T cell cytotoxicity, or immune granuloma = T cell driven hypersensitivity & autoimmunity.

Microbiology Flashcards

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