Wang Comprehensive questions

What are biomarkers? What are the three kinds?

Biomarkers are quantifiable molecules, biochemical processes or cellular alterations that are indicative of other biological states. The three biomarkers, as proposed in 1987, are biomarkers of exposure, effect and susceptibility

What do biomarkers of exposure, effect and susceptibility separately test for?

Biomarkers of exposure test for the presence of specific xenobiotics in the body; effect biomarkers test for the biological response to an exposure; susceptibility biomarkers quantify the ability of an organism to be susceptible to a xenobiotic

what is internal dose?

how much of an exposure was actually absorbed and retained in the body

what are the six steps to the “biomarker” theory? which steps apply to toxicokinetics and toxicodynamics?

exposure —> internal dose —> biologically effective dose —> early biological effect —> altered function —> disease

the first three steps represent toxicokinetics and the latter three represent toxicodynamics

what is toxicokinetics? toxicodynamics?

toxicokinetics is defined by how a xenobiotic is absorbed into the body, distributed, metabolized and excreted (ADME)

toxiodynamics is defined by how the xenobiotic mechanistically works at the site of action and how its downstream effects can lead to adverse effects

what is exposure?

the total amount of a toxicant or xenobiotic someone is exposed to

give multiple examples of biomarkers for internal dose?

• parent compounds or metabolites detected in urine (like heavy metals or a aflatoxin metabolite)

• hair can be a common place to detect addictive illicit drugs or even heavy metals

• ethanol on the breath

what is “effect” in toxicology?

an actual impairment or precursor of a disease cause by a toxin exposure

what is the early effect of exposure?

xenobiotic-induced changes at the intracellular level (DNA damage/gene mutation)

what does TH do in the production of dopamine? how does it achieve this?

help convert L-tyrosine into L-dopa via the hydroxylase adding an -OH group onto the L-tyrosine

what next two neurotransmitters does dopamine metabolize into? what do they do?

dopamine —> norepinephrine (raises alertness, blood pressure and heart rate) and epinephrine (similar things)

what are two broad examples of genotoxic biomarkers?

DNA damage markers and DNA adducts

what is the biologically effective dose (BED)?

the amount of a toxic carcinogen or ultimate toxicant that reacts at the site of the targeted effect

_________ indicates the level of sensitivity to the effects of a xenobiotic compound

susceptibility

what are some susceptibility factors in xenobiotic effect (think broadly)?

age, gender, lifestyle, concomitant therapy, nutritional status, overall health etc.

biomarker validation processes should include both ______ and _______ studies

human and animal studies

what six qualities should a validated biomarker have?

accuracy, biologically plausible, specificity, reproducibility, applications to population/database studies, high-throughput

why are accuracy and reproducibility both important for biomarkers?

to enhance the comparability of results between different in-lab experiments and experiments between external labs. Also, this helps to improve extrapolation to other un-tested models or population based studies with large number of samples.

in biomarkers, ________ analyzes the quality of the true positive rates while ________ analyzes the quality of the true negative rates

sensitivity - quality of true positive rates (think, a test HAS to be sensitive to correctly identify a positive)

specificity - quality of true negative rates

why is database structure important in biomarker studies?

to ensure that data can be effectively reevaluated by third parties and that old data can be effectively reviewed when new insights in the field appear

useful biomarkers for population-based studies should rely on _______ sampling. Give three examples

noninvasive sampling methods like blood, buccal swab (“buckle”, cheek swab) and urine samples to test for applicable biomarkers

what is a cross-sectional study? cohort? case-control?

• cross-sectional - retrieving data from a population at a single timepoint

• cohort - select participants based off of exposure and conduct follow ups at future timepoints to analyze outcomes

• case-control: match diseased and non-diseased subjects by confounding variables and analyze past exposures to uncover the root cause

what does GLP stand for in quality assurance? what does it mean?

Good laboratory practices (GLP): guideline ensuring a labs practices and experimental designs align with standards of research and data quality

what does SOP stand for in quality assurance?

standard operating procedure (SOP): protocols outlining regular operations for studies or instrument usage/maintenance

what does GCP stand for in quality assurance?

good clinical practices (GCP): guideline to ensure clinical research will meet scientific rigor and ethical conduct in animal studies

what are the six criteria for selecting an analytical method for a biomarker?

selectivity, detection limit, precision, bias, sensitivity and concentration range

what is oxidative damage?

the accumulation of reactive oxygen species in a cell, outbalancing antioxidants resulting in cell/DNA damage

what is malondialdehyde (MDA)?

a biomarker of oxidative damage. it is a by product of lipid peroxidation that can form adducts on guanosines

what is oxo8dG?

8-oxo-dG is a very popular biomarker for oxidative damage to DNA, characterized by an adducted guanosine, which mismatches with an adenine

what is a transition in genetic mutations? transversions?

transition —> replaces a nucleotide with another of its class (purine to purine; pyrimidine to pyrimidine)

transversion —> replaces a nucleotide with a base from the opposite class (purine to pyrimidine; pyrimidine to purine)

what does LOAEL stand for and what does it indicate?

lowest observed adverse effect level - the lowest dose that induces an observable adverse effect

what are the two most important principles of toxicology? define them

dose-response principle: the magnitude of toxicological effect is directly related to the concentration of a xenobiotic

molecular target principle: the toxic action of a toxicant is a consequence of the chemical/physical interaction between the toxin and the target site

what are the four major components of risk assessment?

hazard identification: research identifying how the chemical can induce adverse effects

exposure assessment: characterizing the duration, amount and route of the exposure to the chemical

dose-response assessment: determine how much exposure of the toxin results in X amount of adverse effect

risk characterization: use all of the previous steps to characterize the risk of a chemical to cause illness, disease, cancer in exposed indivudals

toxicology is multidisciplinary, which subjects does it contain?

biology, chemistry, biochemistry, botany, physiology, pharamcology, ecology

place the following routes of exposure from most effective to least: dermal, intravenous, inhalation, oral, subcutaneous

most effective —> intravenous, inhalation, subcutaneous, oral and dermal

where are chemicals biotransformed at?

liver

what is the therapeutic index of a drug?

describes the toxic dose of a drug to the therapeutic dose of a drug

what organ is responsible for filtration, reabsorption and secretion of a toxin?

kidney

_________ - the biotransformation of a toxicant into a more toxic and reactive species

toxication

what is a nucleophile? electrophile? how to remember?

nucleophile - compound willing able to give up electrons to form a new covalent bond

electrophile - compound wanting an electron pair to form a new covalent bond (phile meaning “lover of”, lover of electrons)

how is phase I metabolism classified? phase II?

phase I - the addition of a polar group to a toxin by hydrolysis, reduction or oxidation

phase II - conjugation of molecules to more polar, excretable compounds

what is hydrolysis, reduction and oxidation?

hydrolysis - adding a water molecule to split up a parent compound

reduction - parent compound gains electrons (gains hydrogen atoms, loses oxygen atoms)

oxidation - parent compound loses electrons (gains oxygen atoms, loses hydrogen atoms)

what are some major enzymes in phase I metabolism?

cytochrome P450’s, reductases, oxidases

what are the main phase II metabolism conjugation enzymes?

glucuronidation (UGTs, UDP-glycosyltransferase) - transfers a glucuronic acid onto functional groups of toxic compound

sulfonation (SULTs, sulfonates) - adds sulfonic acid or a sulfonate to the parent compound

glutathione conjugation (GSTs, glutathione-S-transferases) - connects the parent compound to the thiol group on the glutathione compound

methylation (MTs, methyltransferases) - adds a methyl group to parent compound

acetylation (NATs, N-acetyltransferases) - adds an acetyl group to a parent compound

how do DNA adducts affect DNA?

prevent proper replication and translation

what is the function of IkB in cell cycle progression? how does NF-kB affect cell cycle progression?

IkB (IkB kinase) is a NF-kB inhibitor and NF-kB translocates to the nucleus and promotes transcription of cyclin D1, which promotes cell cycle progression

how does elevation of calcium intake into the cytoplasm ruin normal ATP production?

it dysregulates the electrochemical gradient needed to keep normal ATP production functioning

the release of cytochrome c into the cytoplasm is an important step in _________ inititation

cytoplasmic cytochrome c is important in apoptosis initiation

loss of cytochrome c from the inner mitochondrial membrane results in what?

an accumulation of reactive oxygen species

what is the main difference in base excision repair and nucleotide excision repair? what two proteins are needed in both?

base excision repair replaces the one incorrect base while nucleotide excision repair removes a chunk of nucleotides around and including the incorrect one. Both are reliant on DNA ligase and DNA polymerase

what is the difference between DNA ligase and DNA polymerase?

DNA ligase connects the new nucleotide with the surrounding nucleotides whereas DNA polymerase brings in the correct nucleotide to bind to the strand

__________ repair requires a sister strand to serve as a template to fill in missing nucleotides

recombinant repair!

mutations, Ras activation, apoptosis inhibition and DNA repair failure all can lead to what?

cancer/carcinogenesis

the possibility of an adverse outcome is defined as a _____

risk

_____ _______: the systemic characterization of adverse effects from human exposure to a hazardous chemical

risk assessment

what are some features of standard cancer bioassays?

more than one species, both sexes, lifetime exposure, approximately 50 animals per dose group

which epidemiological study is always retrospective?

case-control, disease and non-diseased are matched and looked back upon to find the exposures

_______: the dose below which no additional increase in response is observed

threshold

______ is the highest non-statistically significant dose tested

NOAEL

What is a benchmark dose?

a dose that is representative of producing a predetermined low-level change

what is the difference between exposure and dose?

exposure regards the presentation of the chemical to the host whereas dose refers to the amount of chemical that is absorbed in the body and reaches the target molecule

______________: the quantitative study that analyzes how a chemical is absorbed in the body, distributed, metabolized and subsequently excreted

toxiockinetics

what are five factors that affect a chemicals ability to be transported?

• size and shape of chemical

• polarity or lipid solubility

• membrane composition/permeability

• membrane thickness

rate of distribution depend on which two things?

duration and concentration

name some excretion methods

urinary/fecal excretion, milk, saliva, sweat, exhalation

tubular reabsorption (increases/decreases) renal elimination

decreases

what is the difference between first and zero order kinetics?

zero order: drug is eliminated from the body at a constant rate over time

first order: drug is eliminated from the body depending on the concentration of the chemical and how saturated a metabolic process is

when elimination of a toxicant from the body occurs in exponential fashion, is signifies a (zero/first/second)-order process

FIRST

what does the volume of distribution? what unit is it?

the volume of distribution is defined as the proportion of total toxicant in the body to the amount of toxicant in the bloodstream, typically signified by L/kg of body weight

what is the main difference between classical and physiological compartmental models for distribution?

classical models assume a constant distribution rate whereas a physiological model fluxuates the distribution rates (order kinetics) based on tissue and organ parameters

what are the four parameters of a physiological model and what constitutes them?

• anatomical - indicates the physical size of the compartments

• physiological - quantifies the biological processes and mechanisms in organs

• thermodynamics - relates total concentration of chemical in a tissue to total chemical in a tissue

• transport - how a chemical transports through biological barriers. what channels does it travel through, electrochemical gradient, how much energy is needed

what is one of the best illustrations for PBPK (physiological models)?

the ability to extrapolate kinetic behavior from animal studies to humans

which conjugation enzyme plays the largest role in phase II metabolism?

UDP-GT - UDP-glucuronosyltransferases

where are UGTs and P450s located in the cell?

smooth endoplasmic reticulum

ACh metabolism by AChE will ______ muscles and ________ synaptic transmission between neurons

relax muscles and terminate synaptic transmission

which P450 metabolizes ethanol? antidepressants?

CYP2E1 metabolizes ethanol and CYP1A2 metabolizes antidepressants

what are the two forms of radiation and what is the difference between the two?

ionizing - has the ability to knock electrons off of atoms

nonionizing - does not have this ability

what are the three main versions of ionizing radiation and what are the differences in travel speed?

alpha - travels slow, cytotoxic inside the body

beta - travels quick, cytotoxic outside the body

gamma - travels very fast, cytotoxic outside the body

what radiation exposure has the highest natural exposure rates? what kind of radiation does it emit?

radon emits alpha waves

how is radiation used in medicine and how is it used in research?

radiation is used in medicine via the treatment of cancers whereas it is used for X-rays in research

what are the three main types of genetic alterations?

DNA damage (single/double strand breaks, adducts, etc.)

DNA mutations (missense, nonsense)

chromosomal aberrations

what are the five main types of DNA repair?

base excision, nucleotide excision, recombinational repair, DNA mismatch repair, O6-methyguanine-DNA-methyltransferase repair

what are the four stages of carcinogenesis?

initiation —> promotion —> progression —> metastasis

what broadly happens during the initiation step of carcinogenesis? promotion?

initiation - the chemical is metabolized, potentially activated into an ultimate carcinogen, forms an adduct or results in a gene mutation. This mutation escapes DNA repair/apoptosis in just one cell

promotion - is a reversible stage that induces the proliferation of cell growth by promoting chemicals (non-tumorigenic by themselves)

what broadly happens during the progression step of carcinogenesis? metastasis?

progression - cells begin to grow at an uncontrollable rate and causes karyotypic instability which can cause more copied mutations

metastasis - uncontrolled cell growth spreads to other tissues and is likely caused by more mutations

what is the main difference in primary vs secondary cancer prevention methods? what are some examples of secondary?

primary - focused on minimizing known exposure routes and improving lifestyle changes

secondary - conducting an early diagnosis and stopping the cancer in its tracks, preventing it from progressing and metastasizing

• surgery

• chemotherapy

• radiotherapy

what is tertiary prevention for cancer?

after the cancer is removed, additional therapies are conducted to prevent relapse

list six toxic metals

lead (Pb), cadmium (Cd), Nickel (Ni), Arsenic (As), Mercury (Hg) and Chromium (Cr)

how can metals be toxin intracellularly?

they can mimic essential metals and prevent the essnetial metals from healthily binding to receptors. they can catalyze redox reactions and promote lipid peroxidation, protein denaturation, DNA damage and organelle dysfunction. modulate gene expression

which route of solvent contamination is a significant health concern?

evaporation. solvents enter the environment evaporating as volatile organic compounds (VOCs). prevalent in urban areas and can seep in soil and groundwater, contaminating food/water supply as well as direct inhalation through occupational exposure

what are the six primary pollutants?

• carbon monoxide

• sulfur dioxide

• nitrous oxides

• volatile organic compounds (VOCs)

• lead

• particulate matter

what are the four most dangerous indoor air pollutants in the developed countries?

tobacco smoke, aldehydes, radon and particulate matter

what are the 3 R’s of toxicology?

reduction, refinement and replacement

what are the three air pollution management strategies?

reduction (reducing the amount of air pollution to below tolerable levels), elimination (completely getting rid of air pollution) and conversion (converting air pollution into a new usable resource)

what was the clean air act?

a law passed in 1963 that set standards for acceptable limits of common air pollutions and gave credits to companies that used pollution control devices

what are four common sources for DNA damage?

UV light, x-rays, electrophilic chemicals and ionizing radiation

what two kinds of DNA repair mechanisms are likely to introduce mutations into the genetic composition? why?

non-homologous end-joining and homologous recombination, because they work to repair double strand breaks

what is the ames test and how does it work?

it tests the mutagenicity of a select compound. If the compound causes DNA damage, reverse repairing will occur and cause a lot of revertant colonies to grow in the absence of food (which would not normally happen)

when in the cell cycle is chromosomal aberration tested for?

S-phase

what are examples of dietary carcinogens?

excess caloric/alcohol intake, AFB1 contamination and nitrites