E3 Helicobacter pylori Flashcards
where are bacteria located in the GIT and in what amounts?
- tongue / mouth
- saliva (millions of bacteria per ml)
- oesophagus / stomach (very few bacteria)
- lower part of small intestine / colon (trillions of bacteria)
what percent of faeces is bacteria?
bacteria constitute 40% of dry weight of faeces
state some examples of bacteria in the stomach that cause nausea, vomiting and diarrhoes
- camplylobacter jejuni
- salmonella spp
- shigella spp
- escherichia coli
- vibrio cholerae
describe the bacteria in the stomach that cause nausea, vomiting and diarrhoea
- short term survival (unpleasant side effects but body will clear this within a couple of days)
- unable to colonise
bacteria that cause gastric ulceration
Helicobacter pylori
describe the bacteria in the stomach that cause gastric ulceration
- long term survival
- not readily eradicated
- able to colonise mucus cells lining the stomach and break down mucus layer
- causes a permanent infection that can also be asymptomatic
what symptoms can helicobacter pylori cause?
inflammation
gastric ulcer
duodenal ulcer
increased acid secretion
is helicobacter pylori infection common? describe the infection
- very common, usually during childhood
- infects lower part of stomach (antrum)
- infects around 40% of people in the UK
- asymptomatic in 80-90% of infected people
what does helicobacter pylori increase the risk of?
stomach cancer
asymptomatic infections of helicobacter pylori are not well understood. what are some reasons there could be for this?
- individuals characteristics of immune systems
- varying strains of H. pylori
- other unknown environmental factors
4 requirements for colonisation of the stomach by H. pylori
- acid neutralising system
- adhesion molecules
- movement
- degradation of mucus
what does H. pylori colonisation of the stomach cause?
- damage to the mucus layer
- epithelial cells are no longer protected against gastric acid
describe the requirement for H. pylori colonisation of the stomach: acid neutralising system
- urease enzyme (converts urea into ammonia)
- transporter proteins (proton-gated urea channel)
describe the requirement for H. pylori colonisation of the stomach: adhesion molecules
- present on outer membrane
- bind sugar molecules on surface of stomach
describe the requirement for H. pylori colonisation of the stomach: movement
flagella
describe the requirement for H. pylori colonisation of the stomach: degradation of mucus
enzymes:
- lipases
- proteases
why is a proton-gated urea channel required for H. pylori to neutralise stomach pH?
urea needs to get into the cell so it can be converted into ammonia by urease enzyme
describe the acid neutralising activity of Helicobacter pylori in detail
- urea is converted into ammonia and carbon dioxide (carbon dioxide leaves the cell)
- ammonia accepts protons in the inter membrane space that are readily available from the stomach and removes protons from free state
- this increases the pH and makes the stomach less acidic
describe the structure of the urease enzyme
2 amino acid chains
alpha chain: 238 amino acids
beta chain: 569 amino acids
describe the structure of the proton-gated urea channel
- single amino acid chain of 195 amino acids
- ring-like structure with pores to permit urea transport
- ‘proton-gated’ = pH sensitive
what pHs is the proton-gated urea channel fully open and closed?
pH < 5 = channel fully open
pH > 7 = channel closed
non-invasive diagnostic tests for H. pylori
- breath test
- stool antigen test
- blood test
invasive diagnostic test for H. pylori, give an advantage of it too
- gastroscopy and take biopsy for culture
advantage: high sensitivity testing
- patients with reduced antibiotic choice (hypersensitivity, previous use of antibiotics)
- can tell you the specific strain of H. pylori so a specific antibiotic can be chosen
who are the invasive H. pylori diagnostic tests used on?
patients who received eradication therapy, but remain Helicobacter positive
what is sensitivity in terms of a diagnostic test?
the ability of a test to correctly identify those with the disease
what is specificity in terms of a diagnostic test?
the ability of the test to correctly identify those without the disease
how many people are correctly identified in a test with 95% sensitivity and 95% specificity if there are 1000 patients with 100 true positive cases?
- 95% sensitivity = 95 out of 100 cases correctly identified correctly (5 false negatives in this sample)
- 95% specificity = 855 out of 900 negatives correctly identified (45 false positives in this sample)
how does the urea breath test work?
- detection based on urease enzyme activity (urea -> ammonia + carbon dioxide)
- based on detection of heavy isotopes (given urea drink with carbon labelled so it can be tracked throughout the body, urease will notice urea drink if H.pylori is present in the stomach)
how is carbon labelled for the urea breath test?
13C (non-radioactive)
is the urea breath test a common test for H. pylori?
it is the most commonly used test
state 4 ingredients in the urea drink used for the breath test
- citric acid
- sugar
- labelled urea
- flavour compounds
explain the use of citric acid in the urea drink used in the urea breath test for H. pylori
- low pH
- ensure proton-gated urea channel is open due to low pH
- enhances the low pH environment
explain the use of sugar in the urea drink used in the urea breath test for H. pylori
- mannitol, high calorie
- ensure parietal cell is actively secreting
- palatable
- makes sure cells have sugar so they can function
explain the use of labelled urea in the urea drink used in the urea breath test for H. pylori
substrate for urease enzyme
explain the use of flavour compounds in the urea drink used in the urea breath test for H. pylori
makes the test agreeable for the patient
describe the use of antibodies in the antigen test for H. pylori
- antibodies are key components of the immune system
- able to bind antigen
- used in the test to detect antigen
what methods do the antigen test for H. pylori use?
- capillary action
- lateral flow
from left to right, what do these results from the antigen test mean?
negative
positive
invalid
what happens at the reaction and test zone in the antigen test for H. pylori?
- polystyrene bead (dye) is bound to the antibodies at the reaction zone then they move up the test strip
- bound antibodies (complementary to H. pylori antigens) bind to the antigens and dye beads form a line at test zone
- only shows a line for positive results
what happens at the control zone in the antigen test for H. pylori?
bound antibodies bind to dye-labelled antibodies regardless of whether antigen is bound (shows line for positive or negative results)
describe the blood test for H. pylori
- lab-based
- quantitative
- ELISA
- multiple tests can be carried out in parallel
describe the steps of the ELISA test for H. pylori
how can the colour change in the blood test for H. pylori be measured?
visually or with colorimeter
how can acidity / basicity be predicted in drug molecules?
- look for functional groups able to donate or accept protons
- become familiar with the range of pKa values typical of organic function groups
- explore the role of structure (particularly inductive and resonance effects) on the stability of the conjugate acid / base pair
what does a low pKa mean for an acid?
low pKa means strong acid because the hydrogen is weakly attracted
what does a larger pKa mean for bases?
pKa is larger in conjugate acid if base is stronger
when does acidity increase in relation to A-?
- acidity, and hence Ka, will increase if A- is stabilised (and hence its concentration increased) relative to HA
- increase in A- increases the numerator so it makes the Ka, and therefore acidity, greater
what structure-related aspects can determine / affect acidity?
bond energies
electronegativity
inductive effects
hybridisation
resonance / delocalisation
how can bond energies determine / affect acidity?
- control the ease and extent to which the proton can be lost from the acid (I.e. the strength of the acid)
how does bond strength change in groups of the periodic table?
bond strength weakens on descending groups in the periodic table
describe and explain the changes in acidity of ‘hydro-halogens’
increasing order of acidity:
H-F, H-Cl, H-Br, H-I
- pKa values decrease with increasing acidity
- HI is the strongest acid as the bond is the weakest (proton dissociates more easily)
how does electronegativity change across a period / row of the periodic table?
- electronegativity increases across a row in the periodic table (from left to right)
- C, N, O, F
what is electronegativity?
the ability of an atom to attract a pair of electrons
what is an inductive effect?
- the ability of a ligand to change electron density at a nearby atom via sigma bonds
- can be transmitted through a series of sigma bonds
- image shows negative inductive effect of X
what is the difference between inductive effects and resonance effects?
- ligands changing the electron density at a nearby atom through sigma bonds is an inductive effect
- ligands changing the electron density at a nearby atom through pi bonds is a resonance effect
what are the 2 types of inductive effects and what are their effects on acidity and stability of anions?
electron-withdrawing inductive effect:
- stabilises anion
- enhances acidity
- negative inductive effect
electron-donating inductive effect:
- destabilises anion
- reduces acidity
- positive inductive effect
do electron-attracting ligands provide a positive or negative inductive effect?
- negative
- X is the attracting group and the electrons are attracted towards it so the electron density is higher closer to X
do electron-releasing ligands provide a positive or negative inductive effect?
- positive
- electron density moves towards carbon away from Y because Y is electron-releasing
how does hybridisation contribute in determining / affecting acidity?
- the more s character of an orbital, the closer the electrons are to the nucleus
- this is comparable to increased electronegativity of the atom
what is the order of effective electronegativity in carbon based on hybridisation states?
sp > sp2 > sp3
how do you see how resonance determines / affects acidity of molecules?
- draw resonance structures for the acid and the conjugate base
- assess which is more stabilised
- if A- is more stabilised, Ka is larger so acidity is greater
- if HA is more stabilised, Ka is smaller so acidity is less
describe and explain the series of resonance structures in the image in terms of acidity
- in the series in the image, resonance structures increasingly stabilise the conjugate base more than the acid
- therefore, acidity increases across the series
what does this image show about basicity and hence Kb?
- basicity, and hence Kb, will increase if BH+ is stabilised relative to B
- hence its concentration increased
describe the 2 types of inductive effects relating to basicity
electron-donating
- stabilises cation
- enhances basicity
electron-withdrawing
- destabilises cation
- reduces basicity
how can inductive effects in bases also be considered?
electron-donating groups enhance electron density at the basic centre (B), hence encouraging protonation to occur
