WEEK 1-7 OBJs Flashcards
Necrosis
o Non-programmed cell death
o Caused by accidental damage of a cell – does not follow a specific cellular program
• Membrane integrity is lost - cell body swells
• Eventually, cell bursts open
• Cellular contents are released as the cell bursts
• This can cause an inflammatory response
Apoptosis
o Programmed cell death
o Enables individual cells to commit suicide when they are dysfunctional
o During apoptosis, the dying cells fragment into membrane-bound apoptotic bodies
o Cellular contents are not released so cannot affect neighbouring cells
What are the three primary causes of necrosis?
- ATP depletion
- Excitotoxicity
- Oxidative stress
- What are the four key mechanisms by which ATP can be depleted?
1- Inhibition of electron transport
e.g. cyanide inhibits cytochrome oxidase phosphorylation
2- Inhibition of oxygen delivery
e.g. cocaine, carbon monoxide
3- Inhibition of ADP
e.g. DDT
4- Damage to mitochondria
e.g. chronic ethanol abuse
What is the role of ion gradients in necrosis?
- A key consequence of ATP depletion is the loss of control of ion gradients
- This is a positive feedback loop: as more Na+ and Ca2+ enter the cell, more voltage-gated channels open and more ions enter
- This causes loss of volume control: water influx, cell swelling
- Eventually, the cell lyses: necrosis
Why are the levels of calcium ions tightly regulated within a cell?
- Calcium is toxic to the cell if present at high levels in the cytoplasm
- Consequence of increased intracellular Ca2+ is excitotoxicity
What are four consequences of excitotoxicity? (Calcium)
- Depletion of ATP
- Mitochondrial ATP production is decreased; activation of Ca2+ ATPase uses ATP - Activation of Ca2+-dependent hydrolytic enzymes
- Leads to disintegration of membranes, proteins etc. - Production of reaction oxygen and nitrogen species
- Leads to disintegration of membranes, proteins etc. - Microfilament dysfunction
- Disrupted morphology and function, impaired motility
Define the term ‘oxidative stress’. What causes oxidative stress? How can it be avoided within a cell?
- Oxidative stress occurs when the balance between free radicals and antioxidants is disrupted, meaning that more oxidants are present
- Oxidative stress is caused by reactive oxygen (ROS) and nitrogen (RNS) species
- Having enough antioxidants in diet
What are the cellular consequences of ROS production? List at least six.
- ROS directly oxidise proteins affecting their function
- ROS can also mutate DNA causing cellular dysfunction
- Lipid peroxidation
- Cell swelling
- Cell lysis
- Inactivate Ca2+ ATPase, increasing intracellular Ca2+
Define the terms toxicodynamics and toxicokinetics.
Toxicodynamics refers to the signs and symptoms a toxic agent causes.
Toxicokinetics refers to how the body metabolizes and eliminates the agent.
Define the terms ED50 and LD50. How can these values be derived?
- ED50 (median effective dose): The dose of a substance that produces the desired effect in 50% of the population that takes it
- LD50 (median lethal dose): The dose of a substance that is required to kill 50% of the population that takes it
- Dose-effect relationship
What is meant by the therapeutic index of a drug?
- The therapeutic index of a drug is a quantitative measurement of the relative safety of a substance. Therapeutic index = LD50/ED50
What is first-pass metabolism and how can it be avoided?
- The first-pass metabolism or the first-pass effect or presystemic metabolism is the phenomenon which occurs whenever the drug is administered orally, enters the liver, and suffers extensive biotransformation to such an extent that the bioavailability is drastically reduced, thus showing subtherapeutic action - determines the concentration of drug (active metabolite that will act on the target site and in systemic circulation)
- One effect of this process is the liver can make drugs inactive (biotransform) before they arrive at their site of action.
- First pass metabolism is why pain control is hard to achieve by oral means only
- It is the fraction of lost drug during the process of absorption which is generally related to the liver and gut wall.
- Notable drugs that experience a significant first-pass effect are imipramine, morphine, propranolol, buprenorphine, diazepam, midazolam, demerol, cimetidine, and lidocaine.
- Avoided by subcutaneous administration/ injection
What is bioavailability when applied to a substance?
- Bioavailability (F) refers to the fraction of a substance that reaches the systemic circulation
- When given intravenously, the bioavailability is 100%
- Administration by other routes is typically lower, and is compared to the intravenous bioavailability
- Many substances have the lowest bioavailability after oral administration, due to first-pass metabolism
- Bioavailability is determined by plotting the plasma concentrations of the substance administration, and calculating the area under the curve
Describe the four components of ADME.
- Absorption: The process of the substance being taken up into the circulation
- Distribution: The transfer of the substance from the bloodstream to the tissues
- Metabolism: The conversion of the substance by enzymes into metabolites, which can either activate or deactivate the substance
- Elimination: Removal of the substance from the body by the kidneys, gut, lungs or skin
What is the volume of distribution of a substance?
- The volume of distribution (VD) is a theoretical volume that represents the degree to which the substance is taken up by the tissues rather than staying in the plasma
What is the function of phase I, II and III metabolism?
Phase I metabolism:
- The first stage of metabolism, whereby the substance is converted to a more polar metabolite by adding or changing a functional group
- This phase includes reactions such as oxidation, reduction and hydrolysis
o Often involves the cytochrome P450 enzyme system
- If sufficiently polar, the metabolite may be eliminated at this point without undergoing further metabolism
- This phase activates or deactivates the original substance
Phase II metabolism:
- In this phase, the metabolite is conjugated with a charged compound such as glutathione
- This increases the molecular weight and the hydrophilicity
o Deactivates the substance if Phase I did not
- Phase II reactions are catalysed by a family of nonspecific transferases
o These require endogenous co-factors in order for the reaction to proceed
Phase III metabolism:
- This phase further processes metabolites that could not be eliminated after Phase I and II
- Further modifications may be made to conjugates, such as acetylation
o Products of Phase II and III metabolism are removed from the cell by various transporter proteins, where they can be eliminated
What are the two components that make ICP-MS a hyphenated technique?
- An ionisation source: inductively-coupled plasma
- A detector: mass spectrometer
- Explain how the ICP ionization source allows elements to be analysed.
- An ICP-MS instrument uses a plasma (ICP) to ionize the elements in a sample and then measures the ions using a mass spectrometer (MS)
How are samples typically prepared for ICP-MS analysis?
- Due to the nature of the instrument, samples must be either liquids or solids that are fully dissolved
- This is usually achieved using acid, most commonly nitric acid (HNO3) – to break it down an analyse its molecular or elemental composition
- For complex solid samples, a period of digestion in acid (often at high temperature) may be required – often overnight
- Other digestion methods are available, e.g. microwave
What are the two phases involved in any chromatographic technique? Explain how HPLC uses these two phases.
- The mixture is dissolved in fluid, the ‘mobile phase’
- It is passed through a solid material, ‘the stationary phase’
- Different components of the mixture will separate based on partitioning between the stationary and mobile phases
- Solid phase extraction most commonly used
For what types of sample is HPLC analysis most suited?
- Liquid state
Explain the difference between reversed-phase and normal-phase chromatography.
Reversed-phase chromatography:
- The most popular type of HPLC
- Non-polar stationary phase and moderately-polar (aqueous) mobile phase
- Hydrophobic (non polar) molecules will be retained by the stationary phase and eluted when the mobile phase gradient changes
Normal-phase chromatography:
- Polar stationary phase and non-polar mobile phase
- Hydrophilic molecules will be retained by the stationary phase and eluted when the mobile phase gradient changes
- Aqueous normal-phase (ANP) allows the use of the same solvents as for reversed-phase chromatography
o Hydrophilic interaction (HILIC) is another variant of NP that is widely used
What is solid phase extraction, and how is it related to HPLC?
- SPE is essentially a form of chromatography that is used to purify or concentrate samples before we analyse them
- The sample in fluid (mobile phase) is passed through a stationary phase to achieve separation – same as HPLC
What chromatographic parameter do we commonly use in analysis of HPLC data?
- The column contains the stationary phase, of which many chemistries are available
- Other important parameters:
1. Internal diameter (ID): determines sensitivity and analyte loading
o Most common: 2.1 mm, 4.6 mm
2. Particle size: the size of the stationary phase beads
o Smaller = more surface area but higher pressure
3. Pore size: porosity increases surface area for separation
Explain how GC uses the two phases of chromatography.
- The ‘mobile phase’ is a carrier gas such as helium or hydrogen
- The ‘stationary phase’ is a layer of liquid or polymer contained within a column made of glass or metal
- Separation occurs primarily on the basis of differences in boiling point
For what types of sample is GC analysis most suited?
- Liquid or gas state
What is the function of the inlet of the GC?
- The inlet is used to introduce the sample into the gas flow
What factor is most important in selection of a column for GC analysis?
- Polarity of the sample
What factor is most important in sample preparation for GC analysis? How does derivatisation allow this to be achieved?
- Sample must be in liquid or gas state
- Separation occurs on basis of different boiling points
- Derivatisation is used to chemically transform a compound into a derivative with different physical properties
- For GC, this is done to reduce the boiling point of the molecule
- It is achieved by adding non-polar groups
- Derivatisation allows us to use GC on molecules that would otherwise not be possible
Explain how the three basic components of a mass spectrometer allow this type of analysis to be achieved.
- Components are ion source, mass analyser and detector
- The sample (solid, liquid or gas) must first be ionised in an ion source
- The ions are then separated in an electromagnetic field (deflection directly related to mass) - This is known as the mass analyser
- The ions must then be detected (detector)
Explain the concept of the mass-to-charge ratio (m/z).
- Mass spectro measure the mass-to-charge ratio or m/z
- An ion of mass 100 with 1 charge will have a m/z of 100
- An ion of mass 100 with 2 charges will have a m/z of 50
- Particles with the same m/z will behave the same when subjected to electromagnetic fields
Explain the key differences between the electron and electrospray ionization sources.
- Electron ionisation (EI) is where gas-phase molecules interact with electrons to produce ions
- Electrospray ionisation (ESI) applies a high voltage to a liquid to create an aerosol containing ions
Explain the terms ‘resolution’ and ‘accuracy’ as related to mass analysers.
- Resolution: the ability to distinguish two peaks of similar m/z - e.g. 50.1 and 50.2, or 50.005 and 50.006
- Accuracy: the ratio of the measurement error to the true m/z • Usually measured in ppm
Briefly explain how quadrupole, triple quadrupole and time of flight mass analysers function.
- Quadrupole systems consist of four rods that are electrically connected
- Oscillating electric fields are applied to the rods, allowing specific masses to be transmitted
- By varying the voltage applied to the quadrupole, the entire mass range can be scanned continuously
- Triple quadrupole systems have three quadrupoles connected in series for tandem MS analysis
- The first quadrupole is used to select the mass(es) of interest
- The second quadrupole is a collision cell, where ions are fragmented by collision with a gas (e.g. argon)
- The third quadrupole is used to scan for specific product masses of the mass of interest
- QQQs are very fast instruments, so hundreds of pairs of ions can be scanned (multiple reaction monitoring, MRM)
- Time-of-flight instruments accelerate ions in an electric field
- Ions then move through the mass analyser at a velocity defined by the m/z (smaller = faster)
What are the two types of data generated by MS analysis? How does this differ between hard and soft ionization techniques?
- Mass chromatogram
o x-axis is time, y-axis is signal intensity
o Mass information is not visualised - Mass spectrum
o x-axis is m/z, y-axis is signal intensity/abundance
o The most abundance m/z is the base peak
- Hard ionisation techniques (e.g. EI) will fragment the molecule
- Soft ionisation techniques (e.g. ESI) will not fragment the molecule to the same extent