DD+LOs+Unit+1

toc =Preamble= (from James Rose, the author of these notes) Monday, December 15, 2008

What follows is the original preamble (same as the notes from M2M). A few points on D+D: it’s a lot like M2M, with the unfortunate exception of actually being useful clinical information so you can’t tune it out. The block directors are well-meaning but it’s a sort of a hodgepodge course with a little of everything. Rest assured that by the time you hit ID you will likely remember about 3% of what you’re about to learn with regards to infection. That said, having a basic vocabulary to talk about common pathogens makes you look a little less like an idiot at your preceptor’s. And for the 3 or 4 people who really, desperately want to be dermatologists, the derm section will enable you to suck up to the derm staff with terrifying efficiency. So go to it, try and retain as much important info as you can, don’t kill yourself worrying about remembering pharmacokinetics, and enjoy. Trust me, first year is the time to really enjoy your classes. –jcr

=Pharmacodynamics and Drug Receptors=


 * Describe the drug-receptor concept and the types of bonds and receptor molecules involved in drug binding.
 * Drug binds specific target receptor; the act of binding changes the conformation of the receptor in forming the drug-receptor; this conformation transduces and amplifies a biological response.
 * Mechanisms of transduction/amplification (discussed in M2M, not a LO):
 * Ligand-gated ion channels
 * G-protein-coupled receptors
 * (serine/tyrosine) Kinase-linked receptors
 * Nuclear (hormone) receptors
 * Re selectivity of a given drug: weaker bond formation (ie H-bonds) is more important than covalent bond formation for selective drug-receptor binding. This is because the weaker bonds require a greater degree of conformational compatibility (which, in turn, is related to how specific a drug is to its target).
 * Types of receptors:
 * Proteins (can be highly specific to particular drugs thanks to 2o and 3o structure)
 * Nucleic acids (generally low specificity)
 * Membrane lipids (generally low specificity)
 * Further broken down into **specialized** receptors and **generalized** receptors:
 * Specialized receptors that are 'designed' to receive a particular signal and transduce a particular response.
 * Hormone receptors
 * Ion channel receptors
 * Neurotransmitters
 * Generalized receptors: essentially, any compounds that aren't specific receptors; any compound, doing any job in a cell, that can be targeted by a drug.
 * Enzymes
 * Transport proteins
 * Structural proteins
 * Note that it's easier to avoid widespread side effects with drugs targeting specialized receptors.
 * Explain the theoretical aspects and therapeutic consequences of the hyperbolic shape of the dose-response curve.
 * What he's talking about: The dose-response curve is asymptotic: it approaches a final degree of response (Emax), at first quickly but progressively more slowly.
 * Therapeutic (and theoretical, really) consequences:
 * At low doses, the effect responds in a roughly linear fashion to dose.
 * The region of the curve in which the dose and response are linearly related - where you get a proportional response for each dose of drug - is called the "**therapeutic dosage range** ".
 * At the high-concentration end of the curve, the response is more or less the same no matter what the dose is. This happens because all available receptors for that drug have complexed with drug molecules.
 * Notice this means you have a kind of diminishing-returns scenario with all drugs-- the more you give, past a certain point, the less additional response you get out of it.
 * Describe the advantages of the log dose-response curve versus the dose-response curve.
 * (So in a log-dose-response curve you've taken the base-10 logarithm of the dose of the drug (still on the x-axis) and plotted the response on the y-axis as its function.)
 * (Notice that this is another way of describing //exactly the same data// -- but it collapses the graph into a smaller frame and changes the shape of the curve from hyperbolic to sigmoidal (S-shaped).)
 * This allows a wide range of concentration values to be plotted in a small area.
 * This also allows the linear portion of the curve (the therapeutic dosage range) to be mapped out over a large portion of the x-axis.
 * Explain the following terminology:
 * The log dose response curve: Allows measurement of efficacy (what does it do) and potency (how strongly does it do it) of a given drug at various concentrations. Basically just plots response to a drug (y-axis) as a function of the concentration of that drug given (x-axis).
 * Potency: Defined as the dose of drug that gives 50% of the maximal molecular response (Emax).
 * Affinity/Kd/EC50:
 * These are terms related to potency.
 * EC50 (or ED50): Synonym for potency; ie, the __effective concentration__ (or dose) of the drug at which the effect is exactly 50% of the maximal effect (Emax).
 * *Notice the //__smaller__// the EC50, the //__more potent__// the drug.
 * Kd: Defined as the concentration of drug at which 50% of all available receptors are bound to the drug. Notice that this is often used interchangeably with EC50.
 * Notice that the potency information of a drug tells you nothing about what the maximal effect actually __is__- just how much a drug gets you to half that effect.
 * Thus: potency is used to figure out how much of a drug to deliver at a time.
 * Efficacy: A measure of the extent of the molecular response or effect __possible__ with a given drug.
 * **Notice** that this is a //pharmacological// term. You can give a drug at nowhere near the Emax of that drug (ie there are lots of available receptors not bound to drug) with a complete //clinical// effect (ie no more pain, remission of cancer, etc). Usually you don't want to give a drug at anywhere near its //pharmacological// efficacy level (Emax), because a much lower dose will achieve complete //clinical// efficacy and avoid additional side effects. Clinical efficacy relates to clinical effect.
 * Power/Emax: Other terms for pharmacological efficacy (in this context). Emax is the experimentally determined maximum molecular effect, or response, possible for a given drug. Power is sometimes used clinically to refer to what extent a drug produces a clinical outcome (ie analgesia).
 * Agonist: An agent that binds to a receptor to produce a biological response.
 * //Full agonists// : drugs that can achieve full Emax (all receptors occupied) at a certain dose.
 * //Partial Agonists// : Drugs that can't achieve full Emax at any dose.
 * For example: smoking cessation aids that deliver nicotine at a much lower possible maximal effect (enough to decrease symptoms of withdrawal but not enough to prolong addiction).
 * Few drugs are partial agonists; most are full.
 * Antagonist: A drug molecule that combines with a receptor compound but does not bring about a response-- effectively it prevents agonists from binding. See below for types and examples.
 * Explain the use of log dose-response curves to compare potency and efficacy of different drugs.
 * Can compare Emax and EC50 from different drugs on the same graph. See handout, p. 6. The maximal "height" of a drug's curve determines the Emax (efficacy) of that drug, how fast the drug gets to that height determines its potency (remember that potency is inversely related to EC50).
 * Notice that comparisons between full-agonist drugs are based on potency (how little can you use to have the same level of effect?).
 * Notice that these are concerned with comparing drugs that act on the //same receptors//.
 * (Not a LO: in clinical use, can also compare the clinical efficacy of drugs acting on different receptors-- measures different degrees of effect possible with different types of drugs, ie. 'power'.)
 * Distinguish between characteristics and provide examples of the different types of antagonism (pharmacological, physiological, chemical)
 * **Pharmacological antagonist** : binds to same receptor site as the agonist. Most antagonists are pharmacological.
 * Reversible vs irreversible: Classification of pharmacological antagonists based on whether or not the drug can become "unbound" from its receptor.
 * __Reversible antagonism__: This is another name for //competitive inhibition// . The antagonist competes for the active binding site of the receptor with the agonist. Note that it's generally not a winner-take-all situation; at any moment there's likely to be some receptor bound to agonist and some bound to antagonist. How much is which depends on the relative binding affinities of the receptor for the two of them and what their relative concentrations are (a sufficient quantity of agonist can overcome the antagonist activity).
 * Dose-response curve effect of reversible antagonists: they shift the curve to the __right__ (no effect on Emax, but EC50 gets higher, indicating you need a lot more agonist to have the same level of effect. Another way of saying this is that reversible antagonists decrease the __potency__ of a drug).
 * Note that most clinically used drugs are competitive agonists (you want a temporary, reversible effect that can be easily titrated to individual metabolisms).
 * __Irreversible antagonism__: This is another name for //noncompetitive inhibition// . The antagonist can bind either to the active binding site of the receptor or another location on it. It alters the receptor so as to destroy the receptor's affinity for the agonist. Notice that this effect can't be overcome by increasing the relative concentration of the agonist (it's not competing for the binding site with the agonist, it's changing the receptor so that the receptor no longer binds the agonist at all).
 * Dose-response curve effect of irreversible antagonists: they shift the curve __down__ (they lower Emax, but EC50 stays the same).
 * Note that there aren't many clinically used irreversible antagonists. One simple reason for this is that if you give too much of the drug, you can't back the dosage down-- you've effectively destroyed the patient's response to the agonist. This is a big problem for agonists that can be broadly useful at lower doses (which are most of them).
 * **Physiological antagonist** : one drug (the antagonist) produces an opposite effect to that of another drug (the agonist) by two separate pathways and receptor systems.
 * Example: histamine binds to histamine receptors to promote bronchoconstriction; epinephrine acts as its physiological antagonist during treatment for anaphylactic shock by binding to adrenergic receptors to promote bronchodilation.
 * Another example: norepinephrine binds to adrenergic receptors in heart tissue to increase heart rate. Acetylcholine can act as a physiological antagonist by binding to muscarinic receptors in heart tissue to decrease it again.
 * **Chemical antagonist** : one drug (the antagonist) binding to and antagonizing the effect of another drug (the agonist). Note that this does not involve the antagonist binding to a receptor (it binds to the agonist itself).
 * Example: excess stomach acid being neutralized by carbonate from calcium carbonate tablets.
 * Explain the use of population response curves to evaluate drug safety (Therapeutic Index and Standard Safety Margin) and the concept of "therapeutic window". This objective will be discussed in the Adverse Drug Effects lecture but is found in the "Pharmacodynamics and Drug Receptor" handouts on pages 11-14.
 * Waiting on this one til it's discussed.

=Bacterial Structure, Function, and Growth=


 * Describe the major structural features of bacteria and explain the principal function(s) of each feature.
 * Generally speaking, the following are present:
 * Rigid cell wall made up primarily of peptidoglycans (see below). Mainly important for resistance to antimicrobial agents and in order to contain the bacterial cell's internal osmotic pressure.
 * Peptidoglycans: lie directly above the cytoplasmic membrane.
 * Composed of a mesh of cross-linked hexose sugars.
 * Function both to influence shape and also to resist osmotic lysis.
 * Gram-positive bacteria (see below) have much more extensively cross-linked peptidoglycan layers and typically have much greater internal osmotic pressures.
 * Peptidoglycans are lots of fun pharmacologically because they're unique to bacteria-- thus a great target for antibiotics.
 * Cytoplasmic membrane underneath the cell wall/peptidoglycan layer:
 * Semipermeable lipid bilayer; impermeable to most hydrophilic compounds and all charged particles.
 * Electron transport chain to generate ATP is located in this membrane-- effectively uses proton gradient across the cytoplasmic membrane to drive ATP generation (very much like mitochondria in eukaryotes).
 * Membrane contains a variety of transporters to transport vital compounds.
 * Bacterial chromosome with no nuclear membrane:
 * The "nucleoid" is the region of the cytosol in which the chromosome is tightly packed- just a description of a cellular region, not a membrane-bound organelle.
 * Generally bacterial genomes are composed of a single, circular, double strand of DNA.
 * //Plasmids// : non-chromosomal, self-replicating DNA molecules (much smaller than entire bacterial chromosome). Generally contain specialized genes that are not necessary for survival of the bacteria-- these genes often contain virulence factors and resistance factors to antibiotics.
 * This is important. Plasmids are modular elements, interchangeable between bacteria, that confer drug resistance and virulent effects on the host. Sort of "plug and play" action here.
 * //Bacteriophages// : viruses that infect bacteria.
 * **Temperate** phages: integrate viral DNA into bacterial DNA (like retroviruses in eukaryotes).
 * **Phage conversion** : phage-mediated change in the phenotype (virulence, resistance, etc) of a bacterium.
 * Have ribosomes, but lack many membrane-bound organelles: ER, mitochondria, etc.
 * Bacteria are typically classified by shape: spheres are //Coccus//, cylinders are //Bacillus// , spirals are //Spirillum// , etc.
 * This can be important because the shape of bacteria are dependent on intracellular cytoskeletal elements (which are then potential targets for antibiotics):
 * //FtsZ// : prokaryotic analogue to eukaryotic tubulin. Aids in cell division.
 * //MreB// : analogue to actin. Influences elongation of Bacillus vs. Coccus.
 * //CreS// : analogue to intermediate filaments. Influences specific 'curving' of shape (ie spirillum vs. bacillus).
 * Sometimes present: the //capsule// . Effectively a "slime layer" (thank you, Dr. Holmes), generally made of polysaccharides, that hinders "engulfing" by macrophages in the host's immune system.
 * Can be negatively visualized by staining with India ink, which doesn't penetrate capsules.
 * Flagellae: organs of motility ("tails"). Allow swimming through liquid media. Used in //chemotaxis//, positive (movement towards a desired chemical) or negative (movement away from an undesirable chemical).
 * Notice that chemotaxis is predicated on a signal transduction system to detect the presence of chemicals.
 * Notice that there are two set "modes" of flagella, directed by rotation of the flagellae: rotated counterclockwise, promotes directed motion or swimming; rotated clockwise, promotes being more or less stationary ('tumbling').
 * //Pilli// : hair-like structures on the bacterial surface. Usually used in the context of adhesion (ligand sensor and adherent). Can also be used for junction with other bacteria (conjunction, see "Bacterial Gene Transfer").
 * Cytosol: notice that there are no compartmental barriers between bacterial DNA and ribosomes- thus the mRNA is transcribed and translated all in the same place without a transport mechanism between them.
 * Also, in prokaryotes, you find //polycistronic// mRNAs that contain multiple encoded genes (one mRNA makes a variety of different proteins), instead of the cap-dependent translation seen in eukaryotes.
 * Explain the importance of differences in cell wall structure among bacteria.
 * Bacteria are broadly classified into two types, based on the reactions of their cell walls to a particular stain (the Gram stain): **Gram-positive** and **Gram-negative**.
 * __Gram-negative__: have two layers of cell wall surrounding the cytoplasmic membrane, with a **periplasmic space** between them: one is called the **outer membrane**, the other is a peptidoglycan-rich layer.
 * Notice that the (thin, compared to Gram-positive) peptidoglycan layer is the inner of the two cell wall layers.
 * Gram-negative bacteria have **lipopolysaccharide** ( **LPS** ) chains coming off their outer cell wall layer- these cause toxic effects in the host.
 * They also have, in their outer layer, porin complexes that act as transmembrane channels.
 * __Gram-positive__: has only **one** (peptidoglycan-rich) cell wall layer surrounding the cytoplasmic membrane.
 * Gram-positive bacteria have, as mentioned, extensive cross-linking of their peptidoglycan layers-- this is mediated by **teichoic acids** and **lipoteichoic acids** which serve as scaffolds on which the cross-linking can occur. (teichoic acids are immersed in the peptidoglycan layer; lipoteichoic acids, as you might expect, are anchored in the lipid cytoplasmic membrane.)
 * Draw a typical bacterial growth curve and explain the characteristics of each growth phase.
 * Early phase: the //lag phase//, in which bacteria are adjusting to their new environment in media, shows no increase in the number of bacteria.
 * After this: the //exponential phase//, in which the number of bacteria increases by a rate of 2n each generation.
 * The doubling time (time it takes for each bacterium in a population to divide, thus doubling the bacterial population) varies by species.
 * When the bacteria reach a point at which the number of new bacteria equals the number of dying bacteria, the //stationary phase// has been reached, and the net viable bacterial population stays constant.
 * After this, it's possible for the number of dying bacteria to exceed the number of new bacteria (as, for example, when they run out of nutrients on their media)-- this is called the //death phase// . Notice that lots of dying bacteria means spreading around a lot of their now-released genetic material, which is a fertile environment for genetic change (see "Bacterial Gene Transfer").
 * Describe how bacteria are classified according to their nutritional requirements.
 * Sometimes divided on the basis of requirements for nutrients in the media:
 * //Heterotrophic// : require organic compounds in media for carbon source.
 * //Fastidious// : require growth factors (ions, nucleic acids, etc) in media.
 * //Autotrophic// : get their carbon from CO2 alone.
 * More commonly, divided on whether or not the bacteria uses oxygen to help generate energy:
 * //aerobes// survive (through oxidative metabolism) in the presence of oxygen and will die without it.
 * //anaerobes// survive (through anaerobic fermentation) in the absence of oxygen and will die in its presence.
 * Not needed but interesting: they die in the presence of oxygen because they lack the requisite enzymes for dealing with the inevitable production of reactive oxygen species (eg. H2O2).
 * //indifferent// bacteria does not use oxygen (always use anaerobic fermentation), but do not find O2 toxic.
 * //facultative// bacteria use oxygen, if present, with oxidative metabolism, but use anaerobic fermention in the absence of oxygen.
 * //microaerophilic// bacteria grow best at very low concentrations of oxygen, but can survive without it.
 * Define respiration and fermentation and explain how metabolic “energy currency” is generated.
 * Energy currency: ATP and "PMF" (proton motive force). ATP is energy stored in a molecule; PMF is energy stored as a proton gradient across the bacterial membrane. PMF is what drives flagellar rotation and some transport mechanisms.
 * Bacteria require reducing agents for electron transport (NADH, etc).
 * Fermentation: anaerobic.
 * Organic compounds serve as both the donators and acceptors of electrons. No net oxidation or reduction.
 * Respiration: aerobic.
 * Organic compounds donate electrons and are oxidized; oxygen (less commonly nitrate or nitrite) accepts electrons and are reduced.
 * [Sporulation:]
 * When a //Bacillus// bacterium encounters unfavorable biological conditions, the cytosol effectively divides into two parts, one of which is an arrested form of the bacterium: has the full bacterial chromosome, is metabolically inactive but still is viable, and has a specialized coat that helps it resist heat, dryness, radiation, etc. This is a spore: effectively a "suspended animation" for surviving adverse conditions. Once conditions are favorable again, this process can be reversed and the full bacterium form expressed.
 * Not all bacteria can sporulate.
 * Explain why unique bacterial components are important as potential targets for antimicrobial therapy.
 * This seems fairly self-explanatory. You want to target the bacteria and not the host cells-- therefore you look for bacterial cellular elements that aren't present in human cells to provide drug targets.
 * Identify the principal targets for the major groups of antibiotics used in human medicine.
 * As mentioned, peptidoglycans are a big one. Bacteria require these for resistance to osmotic pressure-- if peptidoglycan synthesis is interfered with, the bacterial cells will lyse ('explode') and die. This is the basis for a large class of antibiotics, including **beta-lactams**, **vancomycin** , and **cycloserine**.
 * Bacterial ribosomes (50S + 30S = 70S) are significantly different from eukaryotic ribosomes (60S + 40S = 80s)-- another good target. But notice that our mitochondrial ribosomes are very similar to bacterial ribosomes-- so have to make sure that the antibiotics don't target eukaryotic mitrochondrial protein synthesis. Include **aminoglycosides**, **tetracyclines** , **chloramphenicol** , **macrolides** ( **erythromycin** ), and **lincomycins** ( **clindamycin** ).
 * Can target bacteria-specific pathways in DNA replication and transcription (**quinolones, rifampicin** ) **,**
 * Can target metabolic pathways that are not duplicated in humans, like the pathway to produce folic acid (humans must consume it in their diet). Includes **sulfonamides** (folic-acid pathway), **trimethoprim**, **isoniazid** , and **metronidazole**.

=PK- Absorption and Distribution=


 * I think it's important to clear up a few terms. **Absorption** has to do with getting the drug past membranes into the blood stream. This is more of a problem for enteric drugs and not at all a problem for intravenous drugs. **Distribution** has to do with getting the drug to its intended targets. How easy or not this is depends on the drug's structure and how hard it is to get to the targets in question (ie. for intravenous heparin, which acts on structures in the bloodstream, distribution is not really a problem, but for drugs that need to get to the brain or to specific intracellular compartment, it might be).
 * [Pharmacodynamics: related to drug effect, thus drug selection. Pharmacokinetics: related to drug concentration and plasma concentrations, thus drug dosing. This latter field works because __plasma concentrations are directly correlated to drug effect in most cases__.]
 * Describe the mechanisms by which drugs cross biological membranes (diffusion, transport, etc):
 * Passive diffusion: driven by concentration gradient.
 * Aqueous: have to go through channels or pores, which means they generally have to be really small.
 * Lipid: often pH dependent (nonionized lipid-soluble drugs diffuse much better than ionized lipid-solubles).
 * __Lipid passive diffusion__ is the major route of drug delivery.
 * Carrier-mediated diffusion (drugs must resemble endogenous compounds for this to work)
 * Facilitated diffusion (no energy requirement, driven by concentration gradient)
 * Active transport (energy requirement, can move against concentration gradient)
 * Endocytosis (minor)
 * Explain the influence of pH on the ionization of weak acid/weak base drugs.
 * It's explained below under "% ionized" and the H-H equation. Essentially, ionized drugs can't cross membranes well, and pH influences ionization status.
 * Notice that most weak acid drugs are weak acids due to a //carboxyl// (COOH-) group; most weak base drugs are weak bases due to an //amine// (NH3) group.
 * Use the Henderson-Hasselbeck equation to qualitatively predict the ratio of ionized to unionized species of a weak acid or weak base drug in various body compartments.
 * Recall: __pH = pKa + log ([A-/HA])__.
 * Quick and dirty: if pH is below pKa with an **acid** drug, it's predominantly __nonionized__. If pH is below pKa with a **basic** drug, it's __ionized__. And vice versa. Memorize or grok.
 * Notice that even though this means that weak acids are usually better suited for being absorbed in the stomach (which has an extremely low pH), they are in practice still better absorbed in the small intestine (which has a higher pH) because of the vastly increased surface area of the small intestine.
 * Another quick way to think of this: weak __acids__ are trapped (in the nonabsorbable, ionized form) in more __basic__ solutions; weak __bases__ are trapped in more __acidic__ solutions. Essentially drugs like to be absorbed on their 'home turf'-- acids absorb better in acid, bases absorb better in base.
 * Identify the factors that determine a given drug's ability to cross biological membranes.
 * //Size// : small drugs (200-500 g) cross membranes better.
 * //Lipid solubility// : membranes are lipids- therefore lipid-soluble drugs cross them better.
 * Notice that this is why the process of drug metabolism has to do with conjugating them with things that make them more water-soluble and less lipid-soluble.
 * Notice also that one route of metabolism, protein conjugation, depends on the concentrations of the appropriate proteins in the body.
 * However, if a drug's formulation is too lipid-soluble, it won't dissolve in the body's aqueous fluids (saliva, gastric fluids, blood) to deliver the drug effectively.
 * //% ionized// : Basically, ionized compounds do not cross membranes well (since charge is typically a polar characteristic). By contrast, nonionized drugs cross membranes better.
 * What this means is that at different pHs, different drugs can be either ionized or nonionized, which means at different pHs they are absorbed better or worse, respectively.
 * Notice that, if you want to keep a drug in a given fluid from crossing the membranes, you can make that fluid more or less acidic to trap the drug in its ionized form (ie can raise pH of urine to trap aspirin [acetylsalicylic acid] in overdose situations).
 * Notice that a drug needs to be both lipid-soluble and nonionized in order to absorb well through membranes.
 * Notice that all these criteria apply mainly to //per orem// administration-- another reason oral administration is a problem (see below for others).
 * Summarize the therapeutic advantages and disadvantages of the various routes of drug administration.
 * General types of routes:
 * __Enteral__ (oral/rectal): this blood always goes straight through the liver, which subjects it to first-pass metabolism and considerably lowers the effectively dose. Though it's easier, cheaper, safer, and usually more convenient, the bioavailability of enteral administration goes way down on account of the liver metabolism.
 * __Parenteral__ (every other systemic route): generally less easy, less cheap, more dangerous, but higher bioavailability and faster effect.
 * [minor] Localized/topical: administered directly to the tissue of action to avoid systemic effects.
 * Specific routes:
 * __Oral__: slow to moderate onset, bioavailability ranges from 0-100%.
 * Most common; most drugs are small, stable to low pH and digestive enzymes, and lipid-soluble.
 * Notice most oral drugs are absorbed in the small intestine-- this means that anything that slows gastric emptying is going to slow oral drug absorption, which is why you should eat something before binge drinking (you know who you are).
 * Notice also that the formulation of the drug - what the drug is encapsulated in - can be designed to break apart more quickly or more slowly to deliver a drug at particular rates.
 * **Enteric** coating: a coating for a drug that doesn't dissolve until it reaches higher-pH environment- this means it won't deliver the drugs until it reaches the small intestine. This can protect the stomach lining from the drug and the drug from the stomach's pH.
 * __Rectal__: slow onset, variable bioavailability. Usually used when patient is unconscious or vomiting.
 * __Sublingual__: Uptake into the caval venous system without going through the portal system (bypassing first-pass effect); don't need to use needles as per IV. High bioavailability and relatively rapid onset. Best with high-potency drugs.
 * __Intravenous__: Very rapid onset (5-10 minutes); bioavailability, by definition, is 100%.
 * __Intramuscular__: Slower, from slightly to much, onset than IV, depending on nature of drug. Close to 100% bioavailability.
 * IM drugs given as aqueous solution leads to near-immediate onset.
 * IM given as lipid solution can take days, weeks, or months to dissolve into the bloodstream. This gives a kind of timed, steady-release mechanism.
 * __Subcutaneous__: Similar to IM, often used to get steady-state administration. Examples: Depo-Provera shots and NPH insulin.
 * __Inhaled__: Can be topical (see below) or systemic. If the inhalant is a volatile gas, its effects will be systemic (can go to brain). If the inhalant is particles (ie. liquid droplets), its effects will be topical (throat and lungs only).
 * Notice that even topical inhalants are often, if fractionally, distributed systemically.
 * Notice also, not coincidentally, that most (close to 90%) of an inhaled drug is actually swallowed instead of inhaled.
 * Onset of systemic inhaled drugs is extremely rapid, even moreso than IV route.
 * __Topical__: Drug is put at its site of action and isn't dependent on circulation to have the desired effect. Eg.: local anesthetics.
 * You generally want to use compounds that are readily metabolized, to protect against accidental systemic effects from topical drugs.
 * __Transdermal__: Drug is put on skin; releases drug slowly into the systemic circulation (ie nicotine patches). Increases compliance (no missed doses).
 * Explain the therapeutic consequences of "barriers" to distribution and selective accumulation of drugs.
 * To get from bloodstream to tissues, there is some dependence on the structure of the capillaries of those tissues.
 * In the peripheral system, there are generally large gaps between adjacent endothelial cells which allow free drug to get into or out of the surrounding tissues (although not protein-bound drug-- it's too big).
 * In the brain, the endothelial cells are tightly sealed together (blood-brain barrier) so that this leakage is not possible.
 * At the placental border, there's some barrier action as well. Good rule of thumb is that if a drug can get into the bloodstream from oral administration (small, nonionized, lipid-soluble), it can get into both the brain and the fetus.
 * This is why you use heparin in pregnant women and not warfarin-- heparin is IV administered and won't affect the fetus, warfarin is orally administered and will.
 * Another barrier is in the kidneys-- after being taken up (filtered) by the glomerulus, to get back into the bloodstream it has to pass through the tubule membranes.
 * Explain the derivation and clinical relevance of the following pharmacokinetic parameters and their use in designing dosage regimens:
 * Bioavailability (F): what percentage of a given drug dose winds up in the blood. This depends on the absorption of the drug across membranes. By definition, IV administration of a drug has a bioavailability of 100%, and every other route of administration has a smaller bioavailability.
 * Notice that this means that bioavailability is the way to convert from oral to IV administration-- a 5 mg drug at 10% bioavailability orally equates to a .5 mg drug given intravenously. Important for avoiding overdose, etc.
 * Ie: dose at IV divided by bioavailability for a different route of administration = dose for that alternate route.
 * Note that bioavailability for a given drug for a given route of administration is calculated by comparing the plasma concentration-vs-time graph for that route vs. the IV route graph (defined as 100%). Essentially you divide the area under the curve of the route you're looking at by the area under the curve for IV administration.
 * Note also that F only measures __how much__ drug absorption takes place; the __rate__ at which absorption takes place is the time to the peak plasma concentration.
 * Adjustment of dose for oral vs parenteral administration: Drugs given orally have to pass through the liver to get to the bloodstream, which means they get hit by first-pass metabolism, which will oxidize and/or otherwise conjugate a significant fraction of the administered drug. What this means is that parenteral (non-oral) administration of drugs can have a smaller dose than //per orem// drugs because they're not subject to first-pass metabolism.
 * That is to say: if you're looking at your dosages and you've got a oral dose that's lower than your IV dose, you've screwed the pooch in there somewhere, so go back and check your figures.
 * Volume of Distribution (**Vd** ): The consideration of the volume of the tissues or fluids into which the drug is going to wind up. This is significant because the final concentration of drug at its site of action is dependent on it. Dr. French advises looking at this as a dilution factor-- it's the factor which, combined with the dose of the drug, is going to give the eventual plasma concentration, which in turn is going to give the clinical effect. Got it?
 * Notice here that the Vd parameter is usually only important with the loading dose; after this, the drug has been distributed to all the volume it's going to get to and no longer needs a dilution factor.
 * Measuring Vd:
 * Vd is measured in terms of L/kg.
 * After a given dose is administered by IV, the plasma concentration begins very high and initially drops precipitously: this is the **distribution phase**, in which the drug is being distributed to all the tissues and other fluids that it can get to.
 * After a bit, the concentration begins to drop at a steady, lower rate; this is the **elimination** phase, in which the drug is actively being excreted from the body but has finished distributing.
 * From the rate of elimination in the elimination phase, you can back-calculate the initial concentration (**Cpo** ) that would have been required to maintain that rate of excretion had there been no need to distribute into tissues; from this, can calculate the volume into which the drug has to distribute before the distribution phase was over (ie., Vd).
 * Vd = initial dose / Cpo
 * Some things to keep in mind: if the Cpo is much lower than the initially administered dose, then it had a large volume into which to go. And if a drug had a large volume into which it went, it's probably pretty lipid-soluble to be able to get out of the plasma into the tissues.
 * Dr. French sez: if a drug's Vd is about 40 L, that means it's in all the extra- and intra-cellular fluids in the body. If it's about 15 L, that means it's in all the extracellular fluids. If it's about 3 L, it's staying put in the plasma. If it's more than 40 L, it's getting into subcellular compartments of peripheral tissues.
 * Notice that volume of distribution can include just about everything: brain, mucus, muscle, whatever. It's limited only by the size of your body and the solubility of your drug.
 * Here's something else to think about that's easy to forget: //plasma itself has a volume of distribution// . There's roughly 3L of plasma in the average (nonexistent) human-- thus a volume of distribution of 3L indicates that a drug is trapped entirely in the plasma.
 * Selecting loading dose, implications of high or low values: This is mainly dependent on Vd-- you'd like to fill up the volume of distribution immediately so as to reach the steady-state plasma concentration that much quicker. High loading doses imply that there's a large volume of distribution to get through; low loading doses imply that the drug has a relatively restricted volume of distribution.
 * [Not anywhere in particular on LO's but important: your body has a plasma protein buffering system. Even if you can get drugs into your plasma, they often bind to plasma proteins, which means that they neither leave the plasma to their target nor get metabolized and excreted. This means you have a sort of reservoir of the drug in your plasma- which spreads out the time of action of the drug.]
 * This also means, if you're giving two drugs back to back, that this reservoir gets filled up with the first one and isn't available to buffer the second. For drugs with a narrow therapeutic range (that is, drugs whose plasma concentrations need to be tightly controlled) this can be problematic.

=PK: Drug Metabolism=


 * Describe the general principles and consequences of drug metabolism:
 * Essentially: the body interacts with drugs to modify (metabolize) and excrete them. The modification can change pretty much every thermodynamic characteristic of a given drug.
 * Notice that most drugs are metabolized in many different ways (oxidation, acetylation, etc). The pathway of metabolism that is the fastest tends to predominate.
 * If multiple drugs are taken, not only do you need to worry about the actions of one drug interacting with the actions of the other drug, but you have to worry about one drug affecting the __metabolism__ of the other drug (first drug can shut down or occupy enzymes which metabolize second drug or vice versa).
 * The liver is the primary site of drug metabolism. But notice that other tissues - kidneys, skin, etc - have enzymes that can metabolize drugs as well.
 * Most modifications of drugs occur in the smooth endoplasmic reticulum of tissue cells.
 * The smooth ER is also called the "microsomal fraction" of metabolism.
 * Oxidation is the most frequent drug metabolizing reaction.
 * Metabolic modifications tend to turn lipid-soluble compounds into more water-soluble compounds to facilitate excretion.
 * Notice that some drugs can stay active even after modification.
 * "__Prodrugs__": drugs, inactive when administered, that are activated only after being metabolized (ie codeine is inactive until metabolized to morphine).
 * Describe general characteristics of Phase I metabolism:
 * Phase I metabolism involves adding an oxygen atom to the drug, removing hydrogen atoms, or splitting the structure of the drug (ie hydrolysis), but doesn't involve any modifying agents larger than that.
 * Reactions: Oxidation [microsomal and nonmicrosomal], reduction, hydrolysis.
 * Main enzyme is cytochrome P450, which is an oxidizing enzyme. System involved with this is called the __mixed-function oxidation__ system (__MFO__ system). Almost 80% of all phase I metabolism is done with CYP (synonym for cytochrome P450).
 * About 30% of all CYP metabolism is done by the **CYP3A4** enzyme.
 * About 25% of all CYP metabolism is done by **CYP2D6** and **CYP2C9** enzymes.
 * Substrates of P450 drugs must be lipid-soluble.
 * CYP enzymes are mostly found in hepatic smooth endoplasmic reticulum (ie microsomal oxidation reactions, as opposed to those outside the smooth ER, which are nonmicrosomal).
 * Note that there are many in vivo ways to induce or inhibit CYP metabolism.
 * CYP cycle is __NADPH-dependent__-- which means its efficacy is dependent on NADPH levels in the body. It's also __iron-dependent__ (that's the "chrome").
 * Thing to watch out for in Phase I metabolism is mainly the addition of a hydroxyl or oxygen group to the drug. Notice that an exception is the dealkyation of amine groups, in which the oxygen is added to a part of the drug that breaks away. Four CYP reactions that we need to know about:
 * Hydroxylation of aromatic molecules
 * Hydroxylation of aliphatic molecules
 * Epoxification reactions
 * Dealkylation of amines
 * Notice that hydroxylation makes drugs less lipid-soluble.
 * It's called the "mixed-function oxidation" system because it uses the two oxygen atoms of O2 for different purposes: one goes to oxidize the drug compound, the other is incorporated into water.
 * Other (non-microsomal) phase I enzymes:
 * Oxidizers:
 * ADH or //alcohol dehydrogenase// : NADH-dependent. Replaces an alcohol group (OH) with a aldehyde group (COH). Reversible reaction.
 * ALDH or //aldehyde dehydrogenase//: NADH-dependent. Replaces an aldehyde group (COH) with a carboxyl group (COOH). Irreversible reaction.
 * MAO or //monoamine oxidase// : replaces a 1o amine group (NH2) with an aldehyde group (COH). Irreversible reaction.
 * For fun: notice that dopamine, serotonin, and melatonin (monoamine neurotransmitters) are metabolized by MAOs. Thus the antidepressant class of MAO inhibitors, or MAOIs, which prolong the circulation life of those neurotransmitters.
 * Reducers:
 * Nitro reductions (NO2 -> NH2)
 * Azo reductions (N=N -> NH2 + NH2)
 * Carbonyl reductions (C=O -> COH)
 * Hydrolyzers:
 * Mainly hydrolysis of esters and amides (amide hydrolysis is much slower, thus compounds containing amides have longer half-lives). Notice that esterases often convert prodrugs to their active forms.
 * Describe general characteristics of Phase II metabolism:
 * Phase II metabolism involves attaching larger endogenous biochemical units (not just oxygen) to the drug by way of cofactor enzymes. This process is referred to as **conjugation**.
 * The enzymes that make this possible are called **transferases**.
 * Something to watch out for is **enterohepatic recirculation** : the drug is conjugated in the liver but excreted in the __bile__, which gets passed back into the intestine. Once there, the intestinal enzymes can remove the conjugated compound from the drug, beginning the drug's action cycle over again (assuming the drug can get back into the plasma from the intestine)-- this can prolong the effective life of the drug.
 * Conjugation pathways, in particular, can easily become saturated (not a large enough store of the compound it's using to conjugate to keep up with the influx of drug).
 * Conjugation usually results in highly water-soluble compounds that are readily excreted- but note some exceptions (below).
 * Reactions (conjugations):
 * //Glucoronidation// : glucoruronide (large endogenous molecule) transferred onto drug.
 * Notice that conjugation does not always inactivate the drug; glucuronidated morphine, for example, stays pharmacologically active.
 * //Sulfation// : transfer of a sulfur group. This makes the drug highly charged and highly soluble; however, the compound from which the SO4 group is derived is found in very limited quantities-- thus sulfation is an easily saturable conjugation.
 * //Acetylation// : transfer of an acetyl (COCH3) group to the target group.
 * N-Acetylation: addition of acetyl group to an amine nitrogen.
 * Notice that acetylation can made the compound __less__, rather than __more__, soluble (this is the case with many N-acetylations).
 * A lot of genetic variability in quantity of N-acetylating enzymes (specifically N-acetyltransferase 2): divides into a bimodal distribution (rapid or slow metabolizers). This can impact metabolism of isoniazid and other amine-containing drugs.
 * //Methylation// : transfer of a methyl group to any target.
 * Note that this usually makes the compound less water-soluble.
 * //Glutathione// //conjugation// : not discussed, but note that g__lutathione metabolism is used to detoxify acetominophen derivatives__. When you drink a lot of alcohol, your glutathione levels are depressed, which is why drinking and Tylenol don't mix and result in hepatic and/or renal tubular necrosis.
 * Describe general characteristics of Phase I and Phase II reactions as they relate to:
 * 1) Inducibility: Phase I reactions can be induced or inhibited with relative ease (see below). Not so much Phase II.
 * 2) Relative ease of saturability: Phase II reactions usually saturate faster than Phase I reactions.
 * 3) Genetic polymorphism, developmental and age-related changes in activity:
 * Genetic variation: There's extensive genetic variability of CYP enzymes (phase I). There's extensive genetic variability of N-acetylation enzymes (phase II).
 * Age-related and developmental variability: some Phase II enzymes only show up at a certain age-- infants often lack the metabolizing enzymes that adults have (eg. glucuronidation enzymes). Also, depending on in what state your liver is in, it can be better or worse at both phases of metabolism.
 * Explain the therapeutic consequences of induction and inhibition of metabolism:
 * Essentially, some drugs can affect the transcription factors of CYP genes and either stimulate or repress the transcription of those genes.
 * This means that certain drugs can speed up or slow down the phase-I metabolism of other drugs.
 * This means you need to watch how the dosage requirements for a drug change in the presence of other drugs.
 * Notice that this also means that if a drug has a toxic metabolite (like acetominophen), then inducing its metabolism will make the accumulation of that toxic metabolite that much faster.
 * If you want an example of CYP inhibition, drink grapefruit juice, then chase it with espresso in about 10 minutes. You'll feel it a lot harder. In principle you could also reverse the order and subject yourself to any potentially toxic effects of grapefruit juice (don't hold your breath).
 * Seriously, grapefruit juice also causes problems with beta-blockers.
 * Notice also that drugs can induce the enzymes that metabolize __themselves__-- thus one basis for chemical __tolerance__. The dose must be increased after a regular application of drug because the drug has caused its own metabolism to kick into higher gear.
 * List the most common inducers and inhibitors of drug metabolism as below:
 * 1)Inducers:
 * Phenobarbitol [1A2, 2C8, 3A4];
 * Phenytoin [2C9, 3A4];
 * Carbamazepine [2C9, 3A4];
 * Rifampin [1A2, 2C9, 2C18, 3A4];
 * Ethanol [2E1];
 * St. John's Wort [3A4];
 * Tobacco smoke (not nicotine)[1A2]
 * 2) Inhibitors:
 * Cimetidine [2D6, 3A4, 1A2];
 * Erythromycin/Clarithromycin [1A2, 3A4];
 * Ketoconazole [3A4};
 * Fluoxetine (and other SSRIs) [2D6, 3A4];
 * HIV Protease Inhibitors [3A4];
 * Omeprazole [2C19]

=Bacterial Gene Transfer and Evolution of Virulence=


 * Describe the mechanisms that generate genetic diversity within a bacterial species and how these contribute to the evolution of virulence:
 * Note three different "bacterial genome" components:
 * Bacterial chromosome - large DNA molecule, usually circular, contains all genes necessary for growth under normal conditions.
 * Plasmids - small DNA molecules, usually circular, replicate independently from chromosome, encode genes for a variety of nonessential genes-- for example, those that make proteins that provide toxicity or antibiotic resistance.
 * Bacterial viruses - a bacteriophage chromosome incorporated into the bacterial chromosome; this can influence the phenotype of the bacterial cell (see below, "lysogenic conversion").
 * Example: diphtheria bacteria is only toxic if it stably acquires a particular viral gene.
 * Bacteria evolve both slowly, by standard-evolutionary genetic changes, and much more rapidly, by the acquisition of new genes by lateral transfer from other bacteria and viruses.
 * [Note that the printed LO's have the following addition: "Discuss how spontaneous mutation and selection can interact to determine the genetic composition of bacterial populations."]
 * Standard-evolutionary change methods: spontaneous mutations and recombination events that produce new genes. Notice that the process of host-immune-mediated selection can drive the latter process more quickly due to selection for recombination events that express different antigen patterns, etc.
 * Additionally, the environment (nutrients and minerals, temperature, etc) in which the bacteria are living can select for different patterns of gene expression.
 * Gene acquisition methods:
 * Transposable elements:
 * Insertion sequences: small pieces of DNA that can "jump around" within the genome to different location.
 * Composite transposons: DNA elements made up of several insertion sequences flanking a central region, usually containing an antibiotic or toxin-expressing gene. These elements are particularly important because once an antibiotic/toxic gene is surrounded by insertion sequences, that element effectively becomes a mobile element itself and can jump from one DNA molecule (or chromosome, or plasmid) to another.
 * Bacteriophage conversion (see lysogenesis and phage transduction)
 * Acquisition of plasmids (see conjugation, also plasmid-mediated transformation)
 * Acquisition of "pathogenicity islands" (still unclear, but seem to be large, foreign pieces of DNA that can alter the pathogenicity of the bacterium)-- this mechanism is responsible for the pathogenicity of //Salmonella//.
 * Virulence can be acquired through any of these mechanisms.
 * Distinguish between transformation, transduction and conjugation- identify the salient features of each:
 * __Transformation__: exchange of naked DNA fragments, which are released into the environment by one cell and taken up by another. The recipient bacterium engulfs and incorporates this free DNA into its own, exchanging its own homologous genes for the new genes by recombination.
 * Notice that transformation can also take place through plasmid mediation. Bacteria can pick up free-floating plasmids and keep them in their cytoplasm (notice that these aren't incorporated into the chromosome, as plasmids generally aren't).
 * __Transduction__: exchange of bacterial DNA between bacteria but mediated by viruses. During phage replication, when a virus is packing its genome into the newly produced capsids, occasionally the host's bacterial DNA is packed into the new phages instead. When that particular phage goes on to infect another bacterium, that new bacterium becomes infected with new bacterial DNA instead of viral DNA.
 * This means that this transduced bacterium can pick up homologous genes from the phage-encapsulated bacterial DNA by recombination or incorporation (if the phage-mediated bacterial DNA is plasmid).
 * __Conjugation__: exchange of DNA that requires cell-cell contact and passage of DNA from one to the other. Usually involves plasmids.
 * Conjugative plasmids: can initiate the conjugation process and mediate their own transfer between bacteria. Non-conjugative plasmids can't, but some ("mobilizable" plasmids) can be passively transferred during the transfer of other, conjugative plasmids.
 * Effectively a temporary conduit forms between bacteria; conjugative plasmids replicate into single-strand form and are transferred over to the new cell.
 * Describe how errors in bacteriophage development can lead to phage-mediated gene transfer:
 * See "transduction," above.
 * Define and give examples of lysogenic conversion. Distinguish lysogenic conversion and generalized transduction:
 * Diphtheria toxin (a toxic viral gene incorporated into normally innocuous bacteria through a lysogenic virus) is an example of lysogenic conversion. See "transduction," above; lysogenic conversion involves viral DNA, transduction involves bacterial DNA.
 * [Note that in the printed LO's, the following (mostly redundant) LO that was not online was present:]
 * Discuss the properties of bacterial viruses. Distinguish between the lytic and lysogenic state:
 * Carry their genomes in their heads, or capsids; inject this genome into bacterium, use cell machinery to replicate more virus, lyse host and spread.
 * Notice that some viruses incorporate their genome into the host genome (lysogenic), where it replicates with the genome (viral DNA in the host chromosome is called the prophage) but is largely not expressed (bacteriolytic genes are not expressed, though others can be - see lysogenic conversion).

=PK: Drug excretion and elimination kinetics=


 * Describe the general characteristics of drug excretion by the kidney (filtration, secretion, reabsorption, influence of pH and protein-binding).
 * Kidneys are the primary organ of elimination (excretion of unaltered drugs).
 * __Filtration__: get drugs into the urine from the blood.
 * Protein-bound drugs cannot be filtered (at least by a healthy kidney).
 * Can filter ionized or water-soluble drugs (notice these compounds can't cross membranes, important for reabsorption later).
 * Can filter pretty large drugs, although nothing the size of albumin.
 * __Secretion__: secrete acids or bases into the urine from the blood.
 * Only acts on ionized compounds. On them, this can speed up renal excretion considerably.
 * __Reabsorption__: reuptake of drugs out of the urine into the blood.
 * Specialized barrier: drugs have to go through membranes to return to the bloodstream (thus have to be nonpolar, uncharged).
 * Water-soluble, ionized, or large drugs (often conjugated or metabolized) can't be reabsorbed.
 * Remember that you can raise or lower the pH of urine to trap compounds in their ionized forms (keep pH low to increase urine retention of aspirin) and thus limit their reabsorption.
 * About the fastest renal excretion (filtration + secretion) rate is 600 mL/min (for ionized, large, water-soluble drugs); about the slowest (high reabsorption rate) is at the rate of urine excretion, about 1 mL/min (for nonpolar, small, lipid-soluble drugs).
 * Describe the therapeutic implications of enterohepatic recirculation of drugs.
 * Extend half-life of relatively large or charged drugs (excreted unchanged in bile to small intestine).
 * Note that gluconuridated drugs can be degluconuridated in the small intestine, which means they can be absorbed again (or, for drugs that have their action in the intestine, they can act on their targets multiple times).
 * Describe the factors influencing drug passage from plasma to breast milk.
 * Most drugs in the plasma will show up in some levels in the breast milk; but the level that makes it into the infant's __plasma__ will generally be less than 5%.
 * Drugs that pass well (ie, avoid these factors when giving drugs to nursing mothers): non-protein-bound drugs, weak basic drugs, more polar or charged drugs.
 * Explain the derivation and clinical relevance of these pharmacokinetic parameters and be able to use them in designing dosage regimens:
 * Notice he made a point of saying that most of this is more qualitative than quantitative. So don't get your head too far into the equations.
 * 1) Clearance (Cl): Selecting maintenance dose, dosage adjustments necessitated by alteration of kidney or liver function:
 * Clearance is, effectively, the metabolism of the drug plus the excretion of the non-metabolized drug.
 * Measured in volume over time (per kilogram body weight).
 * Clearance (L/hr) = ke * Vd.
 * 2) Half-life (t1/2): Time to steady state or removal from body, selecting dosage intervals, relation to fluctuations in plasma drug levels between drug doses (difference between Cp max and Cp min):
 * t1/2 = .693/ke.
 * Half-life implies time to reach steady-state: steady-state attained, with repeated administrations (not constant IV infusion), after **__four to five__** half-lives.
 * (Steady-state: drug administration rate at which the rate in equals the rate out (ie administration rate = clearance rate).
 * Another way of saying this is that __Dose/Interval = steady-state plasma concentration times clearance rate__.
 * Which means: higher clearance rate implies a need for lower dosing to keep steady-state plasma concentrations the same, and the inverse as well.
 * Also implies time to eliminate all effective drug from body if administration is stopped: also **__four to five__** half-lives.
 * Also can be used to determine the fluctuation in plasma concentrations between drug doses.
 * __Fluctuation = 2x, where x = the number of half-lives between doses__. What that means: the more half-lives between doses, the more fluctuation in plasma concentration.
 * 3) Elimination rate constant (ke): constant for any given drug; influences how fast the drug is eliminated (higher ke = faster elimination).
 * Again: Clearance (L/hr) = ke * Vd.
 * Again: t1/2 = .693/ke (ie it's inversely proportional to ke).
 * 4) First-order and zero-order kinetics: Implications for chronic dosing regimens.
 * First-order elimination kinetics: All drugs but three are eliminated by 1st-order kinetics.
 * The rate of elimination equals a constant times the present concentration remaining. dCp/dt = -keCp.
 * Thus rate of elimination starts high (with high plasma concentration) and slows down as there's less drug remaining in the plasma.
 * The reason that most drugs are first-order is that hepatic and renal excretion are first-order processes.
 * The reason that there's a couple of drugs that are zero-order is that they saturate the metabolism/excretion process.
 * Note that you can still calculate the half-life of first-order drugs-- effectively can always predict the time it takes to eliminate 50% of the drug given regardless of initial concentration.
 * Zero-order kinetics: The other three drugs, one of which is ethanol, another of which is aspirin at certain doses, are eliminated by zero-order kinetics.
 * The rate of elimination equals a constant. dCp/dt = ke.
 * No real half-life-- just a constant rate of elimination, since the rate doesn't depend on the concentration in the plasma.
 * As mentioned, these are only drugs that are given in such high doses that their receptors are saturated (process is going at roughly Vmax)

=Bacterial host-parasite interactions=


 * Define and describe “infection”, “infectious disease”, “pathogenicity” and “virulence”
 * Infection: 'the process of establishing a reaction, stable or transient, between microbe and host.' Notice that this does not always result in infectious disease (disease caused by the infectious microbe).
 * Pathogenicity is a measure of a microbe's ability to cause disease. Notice this is a spectrum rather than a binary; a microbe's pathogenicity has to be considered in the context of the immune system of the host.
 * **Frank pathogens** can cause disease in immunonormal hosts (anthrax, plague).
 * **Opportunistic pathogens** can cause disease in immunocompromised hosts but not usually in normal hosts (//Pseudomonas aeruginosa// ).
 * Notice that many normal human flora are opportunistic pathogens.
 * __Virulence__ is an inverse measure of how many bacteria are required to cause disease- if only a small amount of microbe causes disease, it is said to have high virulence. Another way of saying this is that virulence is a term for the pathogenicity of a microbe.
 * Notice that virulence is usually expressed in terms of "how many microorganisms are required to cause 50% of a population to get to the level of symptoms we define as disease"-- thus can depend on what the defined endpoint is.
 * Explain how a microbe is shown to be the cause of a specific disease. Describe typical stages in pathogenesis of an infectious disease and explain their importance.
 * (1) Must show that microbes are present in characteristic lesions of disease.
 * (2) Microbes must be isolated and grown in pure culture.
 * (3) Injection of isolated and grown microbes into undiseased animals must cause the original disease to appear.
 * (4) The same microbes must appear in the lesions on the new animal.
 * [Notice a couple of problems with this theory: one, you can't grow every disease-causing agent //in vitro// ; two, not every pathogen causes a characteristic lesion.]
 * Phases of infection:
 * Contact with host
 * Can be ingested, inhaled, skin contact, whatever.
 * Notice that most disease is spread by direct contact, not aerosolized droplets.
 * Entry into host
 * If the bacteria need to enter the body to cause disease, they need to cross some kind of membrane barrier.
 * Spread in host from entry site
 * Often aided by some kind of microbial activity-- secretion of enzymes to break down host tissue, ability to migrate to blood cells, etc.
 * Note that the body has enzymes that wall off infections with fibrous tissue to prevent spread.
 * Multiplication in host
 * Notice that multiplication in a friendly, nutrient-rich environment is very different from multiplication in a hostile one like the body.
 * Damage to host
 * Ie: microbial toxins //(// __aggressins__) //,// or __impedins__ that interfere with antimicrobial defenses of host
 * Outcome?
 * Microbe doesn't usually want to stay with you forever: it wants to further propagate once it's colonized you. Thus: how does it keep itself being transferred? TB is transferred in coughed droplets (and TB causes you to cough), cholera is transferred in feces (and cholera toxin causes you, to put it politely, to be in the powder room for a long time).
 * Notice that there are prophylactic steps able to be taken at any of these steps. Antibiotics are usually involved with inhibiting or delaying the multiplication stage. Antitoxins are usually involved with inhibiting the damage-to-host stage.
 * [Notice that where inhaled microbes wind up depend on their size-- large microbes get stuck on the sides of the nasal cavity, and only small microbes can get down the back of the throat. Also notice that one reason your lungs are kept clean is that the mucus in your lungs is constantly swept up and out by cilia; another is that you have specialized macrophages in the alveoli of your lungs that are very good at what they do.]


 * Describe the composition and physiologic importance of the normal flora of the human body.
 * Essentially, we have nonharmful //E. coli//, //Staphylococcus// , //Pseudomonas// , etc living in our various nooks and crannies. Some of these do good things for us: produce vitamins, degrade bilirubin, etc. You kind of want a gut full of harmless bacteria so that when you eat that five-day-old pizza, the nasty stuff on it doesn't have a lot of free space to land on.
 * Compare several disease paradigms that illustrate the selected mechanisms of pathogenesis.
 * Cholera: typical of non-invasive bacteria. It's ingested, it adheres to small intestine, and then it secretes toxins that case diarrhea. Notice that it's the toxin that damages cells, not the bacterium.
 * Pneumococcal pneumonia: typical of bacteria that multiply extracellularly. It replicates outside cells (and can get away with it because it has an anti-phagocytic capsule), it grows, and it eventually causes tissue damage in the lung. The host eventually produces antibodies that coat its capsule and cause it to be destroyed.
 * Tuberculosis: typical of bacteria that multiply intracellularly. Invades macrophages and replicates inside their vacuoles. The host defends itself by T-cell-mediated response, activating the affected macrophages to develop internal granules which kill microbes.
 * Rheumatic fever: typical of a pathology mediated by an immune response. Occurs after streptococcal infection-- the immune response to the strep infection is the thing that causes an autoimmune fever to sprout up a couple of weeks later. Here, the microbe is not directly (although indirectly) responsible for the fever.
 * Compare mechanisms of innate and acquired host defense against infections
 * Innate: defends against immediate infection.
 * Acquired: defends against future recurrences of infection. Also helps the innate system when it's being overwhelmed.

=Bacterial toxins=


 * Define and describe the term “microbial toxin”.
 * Microbial toxins: macromolecular products of microbes that harm the host by altering cellular structure or function.
 * Notice that microbial toxins can be unbelievably potent- 0.000025 micrograms (0.000000000025 grams) of botulinum toxin will kill a mouse. A teaspoon of purified botulinum toxin has the potential to kill about 11 million people. Also notice that botulinum toxin can be inhaled and still be active. Lots of fun, you bet. No, calm down, not really.
 * Notice also that three preventable toxin-mediated diseases - diphtheria, pertussis, tetanus - kill millions of children every year between them.
 * Explain how microbial toxin is implicated in pathogenesis of an infectious disease
 * If you can purify the toxin and show that it reproduces the disease upon its injection into a healthy volunteer, that's proof.
 * If you can show that upon delivery of an active antitoxin, the disease stops working, that proves it pretty well.
 * If you can show that there's a correlation between virulence of bacteria and the amount of toxin they produce, that's another good argument.
 * If you can show that mutant bacteria that cannot produce toxins are nonvirulent, that's a fourth way.
 * Here you should show not only that you can knock out virulence by knocking out a given gene, but that upon restoration of that gene, virulence is restored.
 * Compare the properties of microbial toxins that have different mechanisms of action:
 * Lipopolysaccharides: called "endotoxins" since they're an intrinsic part of the outer membrane of Gram-negative bacteria. Can interact with a large number of components of the body to cause pathogenesis (principal cause of Gram-negative septic shock). We're not going to worry about these too much at the moment.
 * Bacterial protein toxins: heat-labile, immunogenic; called "exotoxins" since they're released from the bacterial cells. Types:
 * Toxins that facilitate spread of microbes: these mainly break down extracellular matrices (like collagen or elastin) to allow bacteria to spread extracellularly.
 * Toxins that damage cell membranes: also called __cytolysins__. Often work by inserting into membranes and forming pores in them.
 * One subset of these are __hemolysins__: break down red cell membranes.
 * Toxins that induce the production of excessive amounts of cytokines: also called __superantigens__. Binds antigen-presenting cells artificially to T cells, causing massive overactivation of T cells, which triggers a cytokine storm. The inflammation is what causes the disease pathology.
 * Examples: //Staph// toxic shock syndrome toxin, //Staph// enterotoxins (food poisoning), pyrogenic toxins.
 * Notice the difference between //Staph// toxic shock and //Staph// enterotoxin: in the latter, you ingest a single dose of the toxin in the food, and thus you're generally okay; in the former, toxin is actively being produced in your body, which is a much more serious problem and can kill you.
 * Toxins that interfere with protein synthesis pathways: these, usually, kill cells.
 * Examples: diphtheria and //Pseudomonas aeruginosa// both interfere with elongation factor 2.
 * Toxins that modify signal transduction pathways in cells:
 * Many toxins go after adenylate or guanylate cyclase pathways:
 * Cholera toxin / heat-labile enterotoxin of //E. coli// - cause massive, watery diarrhea and dehydration. They do this by increasing cAMP production in the small intestine epithelia (cAMP opens chloride channels, water efflux follows) by continuously activating the Gs pathway.
 * Pertussis toxin acts on respiratory epithelial cells- also increases cAMP production, but by inhibiting the Gi pathway.
 * Heat-stable enterotoxin of //E. coli// activates cGMP production instead of cAMP to cause diarrhea.
 * Other toxins mimic endogenous adenylate cyclase themselves (anthrax edema factor and adenylate cyclase toxin): these are usually dependent on calmodulin and calcium levels to become activated (thus are inactive in bacteria, but when released into host cells rich in calcium they become active). Anthrax edema cAMP activity causes water efflux, leading to edema.
 * Anthrax lethal factor acts as a peptidase that cleaves MAP kinase kinase proteins and leads to cell death.
 * Other toxins alter the cytoskeleton of cells //(C. difficile// ) //:// in large intestinal epithelia, this causes diarrhea.
 * Toxins that inhibit the release of neurotransmitters:
 * Botulinum toxin: flaccid muscle paralysis (including muscles of respiration) by inhibiting ACh release at neuromuscular junctions.
 * Tetanus: sustained, involuntary muscular contractions by inhibiting NT release from inhibiting interneurons in spinal cord.
 * Both botulinum and tetanus toxin work by inactivating SNARE membrane fusion proteins that allow stored neurotransmitters to be released into the synapse.
 * Notice that bacterial protein toxins that need to get inside cells usually have two parts: an "A" fragment that contains the active, disease-causing portion of the toxin, and a "B" fragment that is responsible for transporting the toxin inside the cell.
 * Explain the principles of immunization against toxin-mediated diseases.
 * Antitoxin: antibodies against a toxin (prevent toxic action before it binds to target cells).
 * Many toxins can be converted to //toxoids// : toxins that no longer have toxic effect but can be recognized by the immune system so as to make antibodies against the active form.
 * Immediate remedy: administer antitoxin.
 * Lasting prophylactic: give toxoids to develop own antibodies.
 * Explain the principles for developing novel therapeutic agents based on toxins.
 * Effectively you can make use of the "A" (active) part of the toxin by coupling it to an antibody that's specific to a type of cell that you want to destroy (tumors, etc). Then you have a little tame toxin that can go kill specific cells for you.
 * Ongoing theme: we tend to use certain biological pathways that we find in microorganisms for therapeutic uses (ie antibiotics).

=Host responses to bacterial infection=

[Nice guy but uneven presentation. This is my best guess about what he wants us to know.]


 * Define the main function of the immune system:
 * As outlined here, to differentiate between self and non-self and defend self from non-self by triggering defense mechanisms ('effector functions').
 * [Notice that the native flora of the gut are not living in a happy peaceful world-- they're constantly fighting each other for nutrients and space. Thus ingested bacteria have to deal with our native bacteria in addition to all the other barriers we present.]
 * Identify and describe the basic principles by which the innate immune system differentiates between self and invading pathogens.
 * Pattern recognition receptors (ie mainly Toll-like receptors) are the basic innate mechanism to recognize self vs non-self, by recognizing set molecular patterns that are common on microorganism surfaces. (Recall that these patterns are called PAMPs or Pathogen-Associated-Molecular-Patterns.)
 * Notice that while the adaptive immune system relies on variability to bind to antigens, the innate immune system relies on constancy: it looks for certain very specific binding motifs that are common to many microorganisms.
 * Understand the mechanisms by which the recognition of non-self by “pattern recognition receptors” activates innate effector functions.
 * [What's missing to really answer this question is a good overview of this process: what's activated first, what second, and so on, to get an idea of its cascade-like nature. At the moment, that's not available, so the following is an attempt at piecemeal.]
 * When the PRRs of phagocytic cells (and, potentially, other cells: epithelia, other leukocytes, dendritic cells, etc) are activated, the phagocytes engulf the pathogens and activate nearby T cells as well as signaling for inflammatory cascade through cytokines and chemokines.
 * Recall that in an inflammatory response, chemotaxis-promoting enzymes cause leukocytes to be pulled out of the bloodstream and into the infection site (this process is called //extravasation// ).
 * Complement system: another, hitherto largely undiscussed, aspect of the innate immune system.
 * Able to distinguish between self and non-self in much the same way as PRRs, by looking for motifs that don't belong on the surfaces of human cells; specifically, look for bound, activated antibodies and certain bacterial sugars.
 * Trigger effector responses in a number of ways:
 * Classical pathway: complement response as mediated by antibodies.
 * Lectin pathway: lectins binds certain sugars that are usually only present on the surface of microorganisms (recall that LPS is made up of sugars), and triggers complement.
 * Alternative pathway: Dr. Cohen sez that alternative complement involves protein complexes that form on the surfaces of antigen, and trigger complement, because the microbes lack special proteins to disassemble them. Our cells, by contrast, have lots of those proteins.
 * Complement effector (defense) functions:
 * __Membrane attack complexes__: form on surface of pathogens. Bore holes in pathogen membranes and lyse them.
 * __Opsonins__: also form on surface of pathogens. These bind to antigen to enhance its phagocytosis.
 * __Anaphylatoxins__: secreted proinflammatory compounds that attract and activate phagocytic cells.
 * Activation of B cells with complement-antigen fragments.
 * What can we learn from the inherited primary immuno-deficiencies about the role that the immune system plays in resistance to microbial pathogens? How do these basic principles translate to clinical disease?
 * Primary immunodeficiencies in essential immune enzymes are very rare in the population; they're rare because they usually result in death. Assuming they live long enough and are cool with being poked and prodded, we can study people who have these immunodeficiencies to get an idea of what that particular immune enzyme was so important for.
 * I think what he's getting at is the idea that our innate immune systems are constantly kicking the crap out of various uppity microorganisms. Without certain key enzymes in that process, we're killed pretty quickly by all the pathogens flying around and the ones we normally keep under control in our flora.
 * I'm not sure how these basic principles apply to clinical practice, other than to develop a healthy respect for the immune system and to be wary of immunosuppressant drugs.
 * Discuss the various roles of phagocytic cells in innate and acquired immunity.
 * Can trigger inflammatory response
 * Can stimulate T cells by __costimulatory molecules__
 * Can stimulate lymphocyte differentiation (evidently other lymphocytes than T cells).
 * Can directly kill pathogens:
 * __Respiratory burst oxidase__: enzyme complex activated on contact with pathogen, which produces superoxide (very reactive, toxic oxygen species) that kills the pathogen.
 * Alternatively, can also use reactive-nitrogen species (nitric oxide).
 * Can take engulfed organisms to lysosomes to be degraded by lysosomal enzymes (I think this is what he means).

=Mechanisms of Resistance to Antimicrobial Agents=


 * Discuss the issues associated with an increased use of antimicrobial agents in the past several decades both in terms of human medicine and agriculture.
 * The obvious one: we're breeding antibiotic-resistant microorganisms. The more we give antibiotics, especially prophylactic antibiotics, the faster this happens.
 * Resistant bacteria are defined here as __being able to live and multiply in the presence of therapeutic levels of antibiotic__. In principle you could kill them in a petri dish with massive quantities of antibiotic, but //in vivo// that would toast the host.
 * Note that the practice of prescribing antibiotics for viral infections doesn't help this: this selects for resistance in normal, commensal bacteria (gut //E. coli//, for example) that can then be transferred to pathogens.
 * Development of antibiotic resistance is inevitable, unless you can completely destroy all instances of a microorganism (good luck unless you have a vaccine). What you can control is how fast the resistance evolves, by limiting your prescription of antibiotics and ensuring that patients finish their antibody regimens when you do prescribe them.
 * Antibiotic resistance means higher mortality/morbidity rates, higher health care costs (have to use new, patented drugs), and longer hospitalizations. It also promotes a kind of 'kitchen-sink' approach to treatment where you throw every antibiotic you have at a microorganism to try and kill it.
 * However, before you get too excited about how you're going to change the world by prescribing antibiotics responsibly, notice that the primary use of antibiotics is in livestock-- and that largely to increase meat production rather than to treat illness. As much as 70-80% of antibiotics used in the US are given to animals; not primarily Fluffy, but animals that we kill and eat.
 * Disclaimer: I'm not a vegetarian but I freely recognize that, were I a better person, I would be. The fact that the breeding, drug-injecting, and mass killing of animals under appalling conditions is resulting in proliferating drug-resistant strains is just another argument towards that point. But it kind of sucks that people in Africa get diseases that are resistant to even the few medications they can afford just because we can't do without our hamburgers.
 * Note that I don't call them "agricultural animals" or even "food animals" because it obscures the point. Might as well call a spade a spade; they're animals that we breed to kill and eat.
 * [Another fun fact: the number of new antibiotics under research has steadily decreased for the last twenty years because it's not a money-maker-- the inevitable specter of resistant bacteria evidently smothers investor enthusiasm.]
 * What are the major selective pressures that drive the emergence of antimicrobial resistance?
 * This one seems pretty obvious. If you kill everyone with brown eyes, you're going to find that a much larger proportion of the population is going to start cropping up with blue eyes. We drive resistant-strain evolution by killing everything else but allowing the resistant strains to survive and take over the entire niche.
 * What are the major reservoirs of resistant organisms?
 * Animals that we kill and eat, followed by hospitalized patients and humans in the community at large.
 * What are the indicators that antimicrobial resistance is a global issue and not merely related to the increased usage of antibiotics in doctors’ offices and hospitals in developed countries?
 * //Salmonella DT104//, a strain resistant to five common antibiotics, was first noticed in England in the 80's but is currently all over the US and Europe. It's not hard to see how someone can get on a plane carrying a resistant strain of bacteria and spread it to anywhere they want to go.
 * Describe the essential components of:
 * __Resistance transfer factors__ (RTFs): plasmids that can self-replicate and transfer themselves to nearby bacteria (ie __conjugation__). Notice that the target bacteria don't have to be the same species or genera as the bacterium of origin. RTFs, despite the name, may or may not encode antibacterial resistance-- the point is that they can transfer genetic material between highly dissimilar bacteria.
 * Integrons: DNA sequences that allow the capture and integration of genes from external DNA sources.
 * Insertion elements (IS elements): Mentioned earlier in "Bacterial Gene Transfer;" these are small DNA sequences that can 'hop' from one DNA source to another (plasmid, chromosome, etc). They cannot replicate by themselves (need to be located in a replicating DNA unit).
 * Transposons: one or more genes (which can convey antimicrobial resistance) flanked by insertion sequences. This means that the entire IS-gene-IS complex can jump between DNA sources. They cannot replicate by themselves either.
 * Conjugative transposons: Still can't replicate by themselves, but these are transposons whose genes encode the RTF-like ability to jump from microorganism to microorganism.
 * (it seems to me like RTFs are just conjugative, self-replicating transposons.)
 * Describe the genetic mechanisms associated with antimicrobial resistance.
 * As far as I'm concerned, I just did (for more details, read "Bacterial Gene Transfer"). Bacteria are smart little one-celled bastards and they swap DNA - both between plasmids and chromosomes and between individual bacteria - all the damn time. It's like trying to stop gossip on a kindergarten playground.
 * What are the differences between resistance from mutation versus those resulting from acquisition of new genetic information? Are both forms highly transmissible between different genera or different species?
 * Mutation:
 * Resistance from mutation occurs because of a random genetic event in a particular microorganism strain that confers resistance. Notice that even if a mutation isn't on a mobile element, the strain can still be spread worldwide by human contact with other humans.
 * Acquisition:
 * Conjugation: two bacteria transfer pieces of DNA, generally plasmids, between each other. In class he said that usually the two species have to be the same or highly similar, but given the RTFs discussed above, that doesn't seem to be the case.
 * Note that resistance genes in a bacterium's chromosome tend to be more stable, and more stably transmissible to the next generation, than the same genes in a bacterium's plasmids.
 * Acquired DNA-mediated resistance is, obviously, highly transmissible (otherwise how was it acquired?). Mutant DNA can be highly transmissible or not depending on where the mutation occurred (in a bacterial chromosome without a lot of IS elements- not so much. In a transposable region of a conjugative plasmid- very.).
 * Discuss the several major biochemical and physiological mechanisms by which bacteria become resistant to antimicrobial agents. Which of these mechanisms are responsible for clinically significant resistance?
 * (1) Innate resistance: many bacteria produce __biofilms__-- a matrix coating the bacteria that keeps it mainly in a quiescent (nondividing) state. Since most antibiotics work only on actively dividing bacteria, this matrix provides some resistance. Notice that bacteria don't have to divide to secrete toxin.
 * (2) Mutational alteration of the antibiotic target: for example, a tandem repeat region expansion of the transpeptidase where beta-lactam binds can reduce or eliminate penicillin efficacy. This mechanism is less likely to be clinically significant, but there are exceptions (eg. //M. tuberculosis// ).
 * (3) Enzymatic alteration of the antibiotic target: can develop enzymes that alter the target to make it unrecognizable (particularly the targets of erthyromycin and vancomycin).
 * (4) Enzymatic alteration of the antibiotic itself before the antibiotic can have effect: often associated with mobile genetic elements. Ie: beta-lactamase, aminoglycoside-modifying enzymes.
 * (5) Transport of the antibiotic out of the cell: some bacteria can actively pump antibiotic out of themselves (especially //Pseudomonas aeruginosa// ). Example cited is tetracycline resistance. These mechanisms are called __efflux pumps__.
 * (6) Alteration in the expression of normal genes which antibiotic action relies on: eg. if an antibiotic relies on a porin protein to be taken up by the bacterium, if the bacterium stops making that porin, the antibiotic no longer works.
 * (7) Alternative metabolic pathways around a drug target: if a sulfonamide antibiotic inhibits an enzyme leading to folate synthesis, bacteria can develop alternative enzymes for that same pathway, or simply massively overproduce that enzyme and overload the drug.
 * [Intrinsic resistance: Gram-negative bacteria are intrinsically penicillin-resistant due to outer membrane buffer. As opposed to acquired resistance, in which mutation or acquired DNA produces resistance.]

=Common Bacterial Pathogens=


 * For each of the organisms listed below, know and understand the following:
 * (1) Morphology and Gram reaction
 * (2) Characteristics that influence appropriate and successful antimicrobial use (e.g. peculiar structure, enzymes etc);
 * (3) Association with each of the representative diseases discussed in class;
 * (4) Virulence factors (as discussed in class);
 * (5) Reservoir of the bacterium and means of acquisition by patients
 * [Note the following definitions: __catalase__ is an enzyme that catalyzes the conversion of hydrogen peroxide to water (H2O2 -> H2O). __Coagulase__ is an enzyme made principally by //Staph aureus// that catalyzes the formation of fibrin around the bacterium.]
 * [Note also that (1) some information fits under more than one category, so take all categories with a grain of salt, and (2) Dr. Gill was fairly vague about some of this info (particularly acquisition and virulence information), so this is a little uneven. Emailed requests for clarification have thus far produced no results.]
 * [Finally, the following - while it is more or less what he mentioned in class - is not what I would call a well-organized way to approach the information. I would suggest finding another way of assembling all of this to study with.]
 * //Staphylococcus aureus// :
 * __Physical characteristics__: Gram-positive coccus clusters (when cells divide, cell walls remain attached to each other); coagulase-positive, catalase-positive.
 * __Antimicrobial data__: Certain strains are resistant to penicillin (beta-lactamase), methicillin (altered drug target), emerging vancomycin.
 * __Diseases__:
 * Cutaneous infection
 * Causes boil on wound as infection site is walled off in a fibrin capsule
 * Can spread to different organ systems, eg. to cause endocarditis and bone infections.
 * Some strains are toxigenic:
 * Enterotoxin: can cause food poisoning
 * Toxic shock syndrome toxin: can cause systemic toxic shock syndrome
 * Pneumonia
 * Particularly in immunocompromised patients
 * High mortality rate (50%) for staphylococcal pneumonia.
 * __Virulence__: Note 30% of the healthy population are asymptomatic carriers (ie. //Staph aureus// is part of their normal flora). Note that disease can progress from opportunistic endogenous bacteria or from exogenous bacteria touched, inhaled, or ingested.
 * __Acquisition__: Endogenous or exogenous; reservoir in normal flora. Notice that MRSA (methicillin-resistant staph aureus) is no longer restricted to hospitals and can be acquired in the community.
 * //Staphylococcus epidermidis// (SSNA/CNS):
 * [SSNA: **S** taph **S** pecies **N** ot **A** ureus; CNS is an obsolete term for the same group, standing for **C** oagulase **-N** egative **S** taphylococcus.]
 * __Physical characteristics__: Gram-positive, catalase-positive, coagulase-negative, coccus clusters. Adheres tightly to foreign bodies (catheters, heart valves, etc) by means of a sticky extracellular matrix ('slime') that promotes spread of bacteria.
 * __Antimicrobial data__: Difficult to treat, both because of resistance to antibiotics and the fact that antibiotics don't penetrate well into the calyx (slime).
 * __Diseases__: Mainly medical prosthesis contamination-- ie pericarditis from infected heart valves.
 * __Virulence__: A small amount is hard to get rid of on devices; large amounts on skin are normal and avirulent.
 * __Acquisition__: Reservoir on normal skin flora.
 * //Streptococcus pyogenes// (also called 'Group A strep' for its distinctive surface antigen):
 * __Physical characteristics__: Gram-positive cocci, more often in chains than clumps, catalase-negative, coagulase-negative.
 * __Antimicrobial data__: As opposed to //Staph aureus//, these bacteria produce enzymes that break down fibrin containing walls, as well as anti-phagocytic enzymes (M proteins) that help prevent it from being engulfed. (After antibody-mediated opsonization of the bacteria, phagocytosis can proceed.)
 * Note that there are lots of different antigenic types of M proteins--thus acquired immunity doesn't work well here. Repeated infection is possible.
 * __Diseases__:
 * Skin wound infections: produce spreading lesions (they break down the fibrin barrier)
 * Causes strep throat
 * [Side fact: Strep pyogenes is the most common cause of necrotizing fasciitis.]
 * Some strains are toxigenic: cause scarlet fever
 * Some post-infection autoimmune disease association:
 * Glomerulonephritis: self-limiting inflammation caused by immune complexes stuck in the kidneys.
 * Rheumatic fever: antibody cross-reaction with heart valve tissue, very dangerous, only seen after certain strep throat infections.
 * __Virulence__: Opportunistic pathogen
 * __Acquisition__: Carried as normal pharyngeal flora in 15-20% of the healthy population.
 * //Streptococcus pneumoniae// :
 * __Physical characteristics__: Catalase-negative; seen as __pairs__ of Gram-positive cocci stuck together (diplococci). Forms thick, viscous colonies.
 * __Antimicrobial data__: Strep pneumoniae produces a polysaccharide capsule that slows or prevents phagocytosis. Antibody-mediated opsonization of the capsule is the normal, effective immune response.
 * Similar to the M proteins, there are over 84 different capsule types, which can result in repeat infections.
 * __Diseases__:
 * Pneumonia (possibly the major cause of bacterial pneumonia)
 * Sinus or middle ear infections, bronchitis, meningitis
 * __Virulence__: Primarily affects very young or elderly (populations with decreased ability to make anti-polysaccharide antibodies), alcoholics (have defect in ability of cilia to clear mucus from lungs), those who are already sick with respiratory viral infections (ie. rhinovirus). Seems to be a problem when it gets into places it isn't normally found and isn't cleared out promptly (Eustachian tubes, lungs, etc).
 * __Acquisition__: Carried as normal flora in pharynx in up to 40% of population.
 * //Enterococccus faecalis// :
 * __Physical characteristics__: Gram-positive, chain-linked cocci, catalase-negative; facultative anaerobes (can use oxygen).
 * __Antimicrobial data__: Resistant to cephalosporins and strains are resistant to a wide other range of antibiotics.
 * __Diseases__:
 * Frequent cause of nosocomial infections; treatment with cephalosporin tends to wipe out a lot of the rest of the normal GI flora and allows //E. faecalis// to flourish.
 * Infects urinary tract (common), surgical wounds (colon leaking into peritoneum), biliary tract.
 * __Virulence__: Seems to mainly be a problem under conditions of broad antibiotic use or colon perforation.
 * __Acquisition__: Normal flora in some healthy individuals' GI tracts.
 * //Clostridium difficile// :
 * __Physical characteristics__: Gram-positive rods (bacilli). Strict anaerobes (cannot grow in oxygen), but form resilient spores that are very hard to get rid of.
 * __Antimicrobial data__: Resistant strains exist for virtually every antibiotic. Generally //C. difficile// infections flourish in conditions in which antibiotics have been administered, allowing it to flourish in the gut. Metronidazole is an effective antibiotic (at the moment) if other antibiotics are stopped.
 * __Diseases__:
 * Toxin-producing.
 * //Clostridium// organisms (not specifically //difficile// ) can cause tetanus, botulism, gangrene, and other tissue infections
 * //C. difficile// typically causes nosocomial infections that result in diarrhea and/or pseudomembranous colitis (diarrhea, intestinal pain, fever).
 * __Virulence__: Again, flourishes in conditions of broad antibiotic use (ie hospitals).
 * __Acquisition__: Normal flora; found in anaerobic environments: frequently at the gumline in the mouth and in the colon.
 * //Escherichia coli// :
 * __Physical characteristics__: Gram-negative rods; many different strains.
 * __Antimicrobial data__: Antibiotic use may or may not be indicated; diseases such as traveler's diarrhea go away on their own in a few days.
 * __Diseases__:
 * Toxin-mediated; generally diarrhea by bacteria (1) adhering to intestinal epithelia and (2) producing toxin similar to cholera toxin.
 * Note that some //E. coli// can also cause urinary tract infections; these are caused by strains capable of adhering to bladder epithelium and frequently show hemolytic activity.
 * According to Wiki, //E. coli// is by far the most common cause of UTIs, mostly caused by fecal contamination of the urethra and bacterial spread up into the bladder.
 * Also often involved in abdominal infections from a perforated colon. Can form abscesses in tandem with anaerobic microorganisms.
 * __Virulence__: Many different strains; virulence varies.
 * __Acquisition__: Normal flora in colon; can be acquired endogenously or exogenously (latter mainly from ingestion- don't drink the water).
 * //Pseudomonas aeruginosa// :
 * __Physical characteristics__: Gram-negative rods.
 * __Antimicrobial data__: innately resistant to most antibiotics; very difficult to treat. Protected from phagocytosis by a secreted biofilm.
 * __Diseases__:
 * Mostly toxin-mediated: can damage tissue, particularly in lungs.
 * Generally trauma, surgical wounds, and burns are vulnerable to //Pseu. aer.// infection.
 * Can also show up as a lung infection in cystic fibrosis patients. Nearly all CF patients chronically infected by 15-20. Frequent cause of death.
 * __Virulence__: Opportunistic pathogen; most people are highly resistant under normal conditions.
 * __Acquisition__: Extremely common bacteria; can acquire just about anywhere.
 * //Neisseria gonorrhoeae// :
 * __Physical characteristics__: Gram-negative diplococci (cocci found in joined pairs, like //Streptococcus pneumoniae// ).
 * __Antimicrobial data__: Notice that antigenic variation of this bacterium's pillus (a primary antigen site) means that repeated infection by different strains is possible.
 * __Diseases__:
 * Cause infections by __pilli__, which are the key to its adherence and antiphagocytic activity.
 * Causes gonorrhea, as well as conjunctivitis and blindness in infants born to gonorrheal mothers.
 * Males: urethritis
 * Females: infection of cervix, urethra- can result in fibrosis and infertility.
 * Both genders can be asymptomatic. Look for pus discharge from urethral membranes.
 * [Treat newborn gonorrheal conjunctivitis with silver nitrate.]
 * [Random fact: //N. gonorrhoeae// is found only in humans, possibly because it is reliant on binding human iron transporting proteins.]
 * __Virulence__: Online microbiology text says it's a 'relatively fragile organism' which needs a lot of ambient nutrients to survive.
 * __Acquisition__: Reservoir in asymptomatic patients. Usually transmitted by sexual contact or childbirth only.
 * //Bacteroides fragilis// :
 * __Physical characteristics__: Gram-negative bacillus. Obligate anaerobe.
 * __Antimicrobial data__: Metronidazole, carbapenems, and penicillins with penicillinase inhibitors work well.
 * __Diseases__:
 * Found in many anaerobic abscesses in the abdomen
 * Generally found after colon perforation by surgery or tumorigenesis.
 * Makes enzymes that destroy tissue and allow spread, as well as enzymes that produce an anti-phagocytic capsule.
 * Notice that //B. fragilis// actually tolerates oxygen better than most obligate anaerobes; it produces superoxide dismutase to allow it to get by at low levels of O2.
 * __Virulence__: Opportunistic pathogen; generally harmless unless taken out of the colon.
 * __Acquisition__: Common colonic flora.
 * //Chlamydia trachomatis// :
 * __Physical characteristics__: Gram-negative, intracellular bacteria. Grows only inside eukaryotic cells.
 * __Antimicrobial data__: Aminoglycosides work poorly; need antibiotics that get into cells to kill bacteria-- azithromycin/erythromycin (macrosides), doxy/tetracycline (tetracyclines).
 * __Diseases__:
 * Chronic conjunctivitis (__trachoma__): leads to scarring and blindness. Endemic in Asia and Africa, spread by poor hygiene
 * Genital infections: non-gonococcal urethritis, and cervicitis and pelvic inflammatory disease in women (often spread along with gonorrhea, common practice to treat both of them at once)
 * Neonatal conjunctivitis and pneumonia if mother is infected
 * __Virulence__: Majority of cases are asymptomatic carriers.
 * __Acquisition__: As gonorrhea, major reservoir in asymptomatic population. Transmitted through sexual contact or childbirth.
 * //Mycoplasma pneumoniae// :
 * __Physical characteristics__: Bacteria without cell walls; can live inside or outside eukaryotic cells.
 * __Antimicrobial data__: Penicillins are useless- no cell walls to impact. Have to select antibiotic based on whether or not it's inside cells. Wiki says you often use erythromycin/azithromycin or doxycycline (notice that these are treatments for intracellular microorganisms like //Chlamydia trachomatis// ).
 * __Diseases__:
 * Can cause pneumonia.
 * __Virulence__: Wiki says disease is 'mild to moderate.'
 * __Acquisition__: Spread through respiratory droplets.

Types of //Staph// : aureus, epidermidis

Gram-positive: Staphylococcus x 2 Streptococcus x 2 Enterococcus x 1 Clostridium x 1 (bacillus)

Gram-negative: Escherichia x 1 Pseudomonas x 1 Neisseria x 1 Bacteroides x 1 Chlamydia x 1

Unknown: Mycoplasma x 1

Types of //Strep// : pyogenes, pneumoniae

=Antimicrobial Agents=

Dr. Churchill has laid this out pretty well. Go look at those notes.

Drugs targets and drugs discussed this year:
 * 1) Cell wall synthesis (don't enter bacterial cells, wide application)
 * 2) beta-lactams- bacteriocidal
 * 3) vancomycin- bacteriocidal
 * 4) Protein synthesis, particularly ribosome (enter bacterial cells, wide application, cross-rxn with euk. mitochondria)
 * 5) aminoglycosides- bacteriocidal; all the rest are bacteriostatic.
 * 6) macrolides
 * 7) lincosamides
 * 8) streptogramns
 * 9) amphenicols
 * 10) tetracyclines
 * 11) oxazolidinones

Remember that bacteriostatic drugs aren't going to work in immunocompromised patients or in situations in which waiting for the infection to resolve isn't an option.

Types of bacterial resistance:
 * 1) Natural: there's no drug target present in the bacteria.
 * 2) Ie. no cell wall, as per mycoplasma, for penicillins.
 * 3) Escape: although the bacteria are susceptible, the drug can't effectively act on them.
 * 4) Ie. if the bacteria are in a folate-rich environment, inhibiting their folate synthesis isn't going to work well.
 * 5) Notice that anaerobic pus environments, or abscesses, can be protective in this way.
 * 6) Acquired: bacteria have a specific mechanism for avoiding an antibiotic, acquired through selective pressure.
 * 7) See "Mechanisms of Resistance to Antimicrobial Agents."

Post-antibiotic kill effect: bacteriocidal drugs are often effective even when they're not in the plasma at appreciable concentrations because they're irreversibly bound to bacteria. This means that there's a 'post-kill' effect of bateriocidal drugs (which is an exception to the usual rule that drug effect is proportional to plasma concentration).

Cell Wall Synthesis Inhibitors:

· Notice that beta-lactamases hydrolyze (open) the beta-lactam ring; some act only on penicillins (penicillinases), some only on cephalosporins (cephalosporinases), some on both. · Notice that beta-lactamases are naturally produced by many //Staph// species. · Notice that, as acidic molecules, penicillins have a hard time getting through the outer membranes of Gram-negative bacteria; cephalosporins do it better. Notice also that Gram-negative bacteria can keep a reservoir of beta-lactamases in the periplasmic space between their plasma and outer membranes, thus have the potential to break down beta-lactams very efficiently. · Beta-lactams mimic D-Ala-D-Ala (peptide chain in bacterial cell wall) and bind irreversibly to the enzyme catalyzing the cross-linking of peptidoglycans in the cell wall.

Penicillins: · Tend to distribute well in fluids, but don't reach tissues well unless there's a lot of inflammation. · Not generally metabolized; excreted by the kidneys, and fairly quickly. · Extended-spectrum penicillins can get through the porins in the outer layer of Gram-negative organisms because they have amino groups added to them to neutralize their charge (these are thus called aminopenicillins). · Notice that beta-lactamase inhibitors bind to beta-lactamases; they have no intrinsic antibacterial activity. · Note that in milder allergic reactions to penicillin, you may still be able to give cephalosporins. · Note that the half-life of simple penicillins is pretty short-- they're both filtered and secreted by the kidney.

Cephalosporins: · Have two R groups (one one either side of the beta-lactam ring). · Generational differences: § 1st generation: Similar to aminopenicillins: Gram+, some Gram-, don't act on //Pseudomonas//, don't cross into CSF. § 2nd generation: Less Gram+, more Gram-, don't act on //Pseudomonas//, don't generally cross into CSF. § 3rd generation: Even less Gram+, way more Gram-, some anaerobic, some act on //Pseudomonas// (Ceftazidime), cross into CSF. Generally reserved for sepsis and CSF-contained microorganisms.

Carbapenems: · Good distribution; will all reach CSF; renally excreted. Very broad-spectrum; generally can target anything with a cell wall (Gram +/-. aerobes, anaerobes, whatever). Thus used only when really needed. · Note that carbapenems are resistant to beta-lactamases.

Monobactams: · Slightly different beta-lactam ring. Has a very narrow effective spectrum of Gram- organisms. · Can also reach the CSF; used mainly for Gram-negative meningeal infections.

Vancomycin: · Not a beta-lactam. Large molecule that binds to D-Ala-D-Ala chains in cell walls, limiting peptidoglycan elongation. Note that some microbes use different amino sequences instead of D-Ala-D-Ala, rendering them resistant to vancomycin. Overall, resistance is still rare at the moment. Used to treat methicillin-resistant staph aureus and, orally, to treat some clostridium difficile. · Distributes well to fluids, generally no po admin (except to treat gut c. difficile).

Protein Synthesis Inhibitors:

· Note that ribosomal 'decoding' of mRNA occurs in the 30S ribosomal subunit; the peptide bonds form in and the polypeptide exits from the 50S subunit. · Note that all these drugs except the aminoglycosides bind reversibly-- that is, when there's no more drug, protein synthesis can continue; thus drugs are bacteriostatic. Aminoglycosides bind irreversibly and are bacteriocidal.

· Aminoglycosides: · Bind directly to the decoding sites on the 30S subunit and alters the proteins that are made, causing cell death. · Target aerobic Gram- bacteria (streptomycin used as second-line to target TB). · Notice there are a number of sites can be modified on aminoglycosides to inactivate them; later generations of aminoglycosides have fewer potential sites for resistance development. · These are basic; thus must be actively transported (which is why they only target __aerobic Gram- species__). But notice that with synergy with cell wall synthesis inhibitors (see below) they are able to target some Gram+ species as well. · Not well absorbed po · Have a very narrow therapeutic index- the concentration at which they're useful is very close to the concentration at which they're toxic. And they are very toxic. A lot of potential for renal and ear damage; these occur in up to 25% of patients. Renal toxicity is reversible; ototoxicity and hearing loss is not. · Note that these can be given once a day due to post-antibiotic killing effect, decreasing the amount of time the patient is exposed to · Tobramycin is effective against pseudomonas aeruginosa, sometimes as an inhalant. · Can use thecal injections (into CSF) to treat certain meningeal infections. · Note that there is synergy with cell wall synthesis inhibitors (cell wall synthesis inhibitors help aminoglycosides to get into the cell) like penicillin. But notice can't administer at same time (penicillin inactivates aminoglycosides).

· Tetracyclines: · Four-ringed structure that binds to 30S subunit and prevents tRNA from binding. Bacteriostatic. · Because of aromatic character, can pass/be transported into cells fairly easily; thus a broad spectrum of activity (intracellular pathogens). · Lots of resistant strains, mainly by cellular efflux (pumped out of bacteria). · Used for many intracellular organisms (chlamydia, mycoplasma, etc) and as a possible penicillin alternative. · Notice that these accumulate in places with lots of divalent metal ions, like bone (which also makes them good to treat bone infections). · Orally available with very good distribution, but absorption impaired by milk, aluminum, calcium, magnesium, and iron salts. · Should not be prescribed for pregnant women or children-- accumulates in teeth and bone and interfere with development. · Tendency to cause __superinfections__-- as I understand it, these are infections that follow the primary infection due to either the emergence of a drug-resistant strain or a population of opportunistic microbes, naturally resistant to the antibiotic, which can expand and get out of control now that the antibiotic has killed off all their competition (C. difficile is a good example). I don't think 'superinfection' is 'super' in the same way as 'Superman,' but in the sense of 'on top of'-- it's an infection on top of an infection. Notice that she didn't actually go into this much, so this is supposition and hearsay from Wiki. · When outdated ('expired'), tetracyclines are very toxic.

· Macrolides: · Bind to 50S subunit; mainly bacteriostatic. · Access Gram+ organisms better than Gram-; used as penicillin alternative and for pertussis and mycoplasma. · Resistance largely arises from altered binding sites and efflux to the cell. · Absorbed well, particularly at alkaline pH (thus often enterically coated for duodenal absorption). Good distribution: azithromycin better than clarithromycin better than erythromycin (first two enter mammalian cells). · Note that erythromycin and clarithromycin inhibit CYP 3A4 in first-pass metabolism.

· Chloramphenicol: · Hydrophobic drug, binds to 50S subunit. · Broad-spectrum antibiotic. · Absorbed and distributed very well, but is highly toxic (enters into mitochondria, can cause aplastic anemic and superinfections). Not generally given in this country except for really bad infections (certain Gram- or anaerobes) · Hepatic metabolism; not well metabolized in babies- can accumulate and be particularly toxic.

· Lincosamides (Clindamycin): · Similar mechanism of action- binds to 50S subunit. · Hepatic metabolism. · Narrow-spectrum; used for anaerobic infections, or when penicillin can't be used. · When used, often results in C. difficile superinfection in the gut

· Streptogramins and oxazolidinones: · Bind 50S subunit; newer drug reserved for life-threatening infections · Streptogramins: hepatically metabolized; inhibit a very common CYP enzyme (3A4)

· Drug interactions: certain drugs are preferentially metabolized by CYP enzymes in the liver. If several of them are administered, their effective duration may change due to saturating microsomal oxidation processes. · Mnemonic: · **C** hloramphenicol/Clindamycin · **R** (ifampin) · **I(** soniazid) · **M(** etronidazole) · **E** rythromycin · **S** treptogramins/(Sulfonamides) § (In parentheses are drugs we won't cover til next year.)

=Clinical Principles of Antibiotic Usage=


 * Define antimicrobial susceptibility, MIC, MBC. Describe the laboratory tests used to determine measures of antimicrobial susceptibility.
 * MIC: Minimal inhibitory concentration. The concentration at which the bacterial infection stops growing.
 * MBC: Minimal bacteriocidal concentration. The concentration at which the bacterial infection is completely eliminated. Notice that only certain drugs actually do this.
 * You measure these by putting increasing concentrations of the antibiotics in test tubes containing a certain steady amount of bacteria and look for concentrations at which the bacteria doesn't make the solution cloudy (MIC). Then you streak out the solutions that are inhibited and figure out at what antibiotic concentration nothing is growing on your plates anymore (MBC).
 * Can also test (as in our labs) by looking at the zone of inhibition around disks of antibiotic or strips containing various levels of antibiotic.
 * Antimicrobial susceptibility: Means that the microbes are vulnerable to levels of antibiotics that can be attained **__in the blood__**, presumably without killing the patient.
 * Recall that susceptibility at the level of antibiotics possible in the blood is not the same as susceptibility at the level of antibiotics possible in the tissues (partic. hard-to-get-into tissues like the meninges). The tissue site can also be at a different pH or other physiological conditions; the concentration of microbe can also vary considerably from site to site. Thus organisms that are 'susceptible' to levels of antibiotic in the blood can still, in practice, be impervious to the levels of antibiotic that can get to the infection site.
 * In a similar vein, the levels of antibiotic at the site of infection (as in the urinary tract) can be highly concentrated relative the what is possible in the blood-- thus 'resistant' organisms at levels that can be achieved in the blood may still be susceptible at the levels that can be achieved in the urine.
 * Discuss the variables that affect clinical outcome of antimicrobial use:
 * Well, antibacterial resistance is a good one to start with.
 * Also: even really broad-spectrum antibiotics have holes in their spectrum, which can give rise to one or two species of normal flora that happen to be resistant growing out of hand.
 * Also need to consider side effects.
 * Knowing what microbe you're up against is one of the best things you can do.
 * What I think he actually wants us to know for this one:
 * Organism concentration at the focal site of the infection (may differ from levels in blood)
 * pH at focal site of infection (may change antibiotic dynamic)
 * Antibiotic penetration (can antibiotic effectively get to infection?)
 * Host defenses (is that patient's immune system effective enough to deal with any stragglers left over after antibiotic administration?)
 * Discuss clinical and economic considerations for parenteral vs oral administration of antimicrobials:
 * Oral is cheaper, easier, has less risk of administration, and can be administered at home. But once the patient's at home, you can't watch the disease progression or regression any more.
 * What I think he's getting at: in an inpatient setting, you want to figure out what the cause of the infection is while they're on IV antibiotics before you send the patient home with oral agents. Effectively you want to identify the disease pretty clearly before you release the patient to somewhere they aren't being monitored.
 * Discuss the patterns and sources of the development of antimicrobial resistance
 * See "Mechanisms of Resistance to Antimicrobial Agents."
 * Discuss the strategies to deal with emerging antimicrobial resistance:
 * Mainly, the strategies involve only using antibiotics in particular, targeted ways.
 * On the other hand, you have to use your clinical judgment in making a 'first-guess' as to what organism it likely is and how to treat it.

=Viral Structure and Function=


 * [Helpful term: a **virion** is an infectious, mature viral particle, as opposed to the crappy little half-assembled things that are its precursors.]
 * Define 'virus' and understand the strategy viruses use for survival.
 * Submicroscopic, obligate intracellular parasites. They are defined here variously as molecular parasites or chemicals, but not as alive. As you all presumably know, they can't replicate on their own, but depend on their host's replication machinery to make proteins and replicate their own genetic material.
 * More formally, they don't encode information for energy production, ribosomes, lipid membrane synthesis, or (mostly) tRNAs.
 * Allow me to emphasize that you can't see viruses - with a few notable exceptions - with a microscope. Need electron microscopy.
 * Note that this is more of a spectrum than an absolute category-- some viruses have genomes larger than bacteria, have genes for protein translation, DNA repair, etc.
 * Three-part strategy:
 * Build small structures to contain genetic material.
 * Have in their genome all the information needed to initiate and complete an infectious cycle.
 * Establish a relationship in hosts (can be benign, neutral, or hostile).
 * Identify the main structural characteristics of the types of virus particles.
 * Really, they're a capsid, a genome, and maybe an envelope. Details follow.
 * Capsid, also called coat: protective layer that surrounds and protects the viral genome.
 * Functions both as protection and delivery device.
 * Two mechanisms for packaging genomes into capsids: helical capsids and "icosahedral" (wiki: "a convex regular polyhedron composed of twenty triangular faces") capsids.
 * Helical: effectively you wind up the capsid proteins like a solenoid around a cylinder. Often the ends of the solenoid aren't sealed off but remain open (thus a kind of 'hollow' solenoid?).
 * Notice that **all helical-packaged capsules in animal viruses always have envelopes** to the best of our knowledge. The genome is always RNA, and is never DNA.
 * Icosahedral: form roughly spherical structures (ie geodesic dome structure). Notice that, given its triangular faces, it has a lot of different symmetries.
 * The triangular faces can be made up of a number of interlocking viral proteins.
 * This makes a lot of space to accommodate large genomes.
 * Capsomere: "knobs" or "clusters" on capsid (ill-defined in notes).
 * Core: nucleic acids and associated proteins. Stuff that's packaged in the capsid.
 * Nucleocapsid: capsid + core.
 * Envelope: derived largely from host cell genes; a lipid bilayer, containing protruding viral spike proteins, that surround the viral particle (virion).
 * Serve a variety of protective and insertion uses.
 * Note that envelope viruses usually leave their host cell by budding through the membrane; non-enveloped viruses usually have to lyse the cell to leave it. Thus enveloped viruses don't always have to kill the host cell (though many do anyway).
 * Recognize the possible structures and compositions of viral genomes:
 * Note that viral genomes are very compact-- not a lot of wasted, untranslated space.
 * Convention: **viral mRNA that's ready to translate into protein is defined as** " **positive strand** " (+). Its complementary sequence is called negative (-).
 * Viral genomes: DNA or RNA:
 * DNA: linear or circular, single stranded or double stranded.
 * RNA: strictly linear, but can be single- or double-stranded. Single-stranded RNA can be either + or - strands.
 * Can be a single piece of RNA or in multiple genome segments.
 * Describe several representative virus genomes.
 * I don't exactly understand what she means. Maybe "give a couple examples of how X virus has Y genome"-- but that didn't seem to be the emphasis of her talk or her notes, really. Go look at the notes and see if you can figure it out.
 * Describe a typical, generalized replication cycle of a virus.
 * Couple of notes: viruses do not grow at a steady, exponential rate (as bacteria do); they're released in 'bursts' of fully-formed virions.
 * Note that you have a latent period after infection during which the virus is doing the following:
 * (1) **Attachment** (also called 'adsorption' for some reason) of virus to cell.
 * Generally this happens via a protein on the envelope or capsid of the virus. The protein binds specifically to a viral-attachment protein on the target cell membrane (generally the targets are common proteins or carbohydrates found on target cell surfaces).
 * This is pretty much catch-as-catch-can; any virus will attach to anything it can attach to. Different viruses can attach to the same receptors; viruses of the same families will attach to different receptors. Some viruses will attach to a variety of different receptors, or use multiple receptors to bind.
 * HIV: Uses CD4 on T helper cells.
 * Influenza: Uses particular sialic acid linkages on target surfaces.
 * (2) **Penetration** of virus into the cell.
 * __Generally energy-dependent__.
 * Rare strategy: translocation of entire genome across lipid bilayer (a la bacteriophage).
 * More common: endocytosis of virus into intracellular vesicles
 * Once endocytosed, the virus can split open the endocytosing vesicle and get into the cytoplasm.
 * Some enveloped viruses fuse their envelope with cell membranes.
 * Note that this can occur after endocytosis and can be pH dependent; that is, the cell can endocytose the virus and take it to a very acidic environment, at which point the viral membrane is triggered to fuse with the endocytic vesicle, and the virion is let out into the cell (ie influenza).
 * Notice this is also a common strategy in HIV and Ebola.
 * (3) **Uncoating** : virus capsid is disassembled and the viral genome is exposed.
 * Enveloped viruses, as mentioned, can fuse with viral membrane and the capsid dissociates on the spot to release genome into the cytoplasm.
 * Capsid can dissociate upon viral escape from the endocytic vesicle.
 * Capsid can also uncoat upon docking with the nuclear membrane.
 * Note poliovirus particles can bind to target cell surface membrane and form a pore into which to directly pour viral genome (again, a la bacteriophage).
 * (4) **Viral gene expression** : generally, the virus expresses genes before replicating because viral proteins are needed to promote viral replication.
 * DNA viruses: must transcribe RNA using the - strand of the DNA genome as a template. They generally need the host's RNA Pol II to do this.
 * Notice poxviruses encode their own RNA polymerase and can make protein in the cytoplasm.
 * RNA viruses:
 * + stranded: can either duplicate to a - strand or go directly to ribosomes and be translated.
 * Note retroviruses can integrate into host genome instead.
 * - stranded: can't be translated directly by host ribosomes; need to recruit enzymes to create their complement strand before that strand can be translated.
 * Retroviruses: reverse transcribed (by an enzyme that is packaged with the virus's genetic material-- host doesn't have it) into viral DNA from the original RNA; this DNA is taken to the host's nucleus and integrated by another protein that comes with the virus.
 * (5) Viral genome replication:
 * Double-stranded DNA viruses either replicate exclusively in the cytoplasm (generally viruses that have a lot of their own replication machinery) or replicate exclusively in the nucleus.
 * Single-stranded DNA viruses: replication occurs in the nucleus; double-stranded intermediate formed.
 * Most RNA viruses replicate in the cytoplasm.
 * Double-strand RNA: positive strand serves to make protein; negative strand serves to replicate.
 * Single-strand RNA: similar to double-strand, they use their - strands to replicate and + strands to translate. Obviously, they need enough - strands to get going, but once they have a good base of - strands they start just cranking out + strands for all they're worth.
 * (6) Assembly of new viruses and egress from cell:
 * **For icosahedral capsids: generally seem to feed the entire assembled viral genome into a fully assembled capsid.**
 * **For helical viruses, on the other hand, the genomic nucleic acid is coated with capsid as it's synthesized.**
 * Notice that capsid proteins are produced in high abundance in infected cells; cause "inclusions" (extranuclear bodies) in cells sometimes visible by light microscopy.
 * Egress:
 * **"naked" or non-enveloped viruses are released by lysis, inevitably resulting in cell death.**
 * Enveloped viruses can acquire their envelope either by budding off from their host's cell membrane or by budding off membrane-bound organelles (like Golgi) in cell and leaving cell with their envelope fully formed.
 * Kind of cool, actually. Herpes virus picks up two layers of membrane on its trip through the Golgi; the outer one it uses to merge with the outer membrane, the inner one it keeps as its envelope.
 * Describe classification strategies of viruses.
 * __Classical system: use shared, visible properties to classify__:
 * Nature of genetic material (DNA vs RNA)
 * Symmetry of capsid
 * Naked (non-enveloped) or enveloped
 * Dimensions of virion and capsid
 * __Baltimore classification system: use the mechanism of mRNA production to classify__:
 * Double-stranded DNA viruses can be directly transcribed by host machinery (eg. herpes viruses)
 * Single-stranded DNAs need to go through a double-stranded intermediate
 * Retroviruses need to get put into the host DNA
 * Single-strand RNAs can be directly translated by host

=Mechanisms of Viral Pathogenesis=


 * [He seems really interested in going into slight detail on lots of things that have nothing to do with his posted LO's, and there's not a coherent thread or theme to hang onto here-- so I'm not really sure what to do with these. This is my best guess. Note that under "Review session for exam II" he talked a little about it again.]
 * I'm not sure how much he thought we knew, but this is important to know before you get into this:
 * **Primary viremia** refers to the initial spread of systemic virus in the blood from the first site of infection.
 * **Secondary viremia** occurs when primary viremia has resulted in infection of additional tissues through the bloodstream, and that secondary infection has re-entered the bloodstream to infect more (tertiary) sites.
 * By definition, local acute viral infections do not show viremia.
 * But notice that even local infections can cause systemic symptoms from a systemic immune response (inflammation, fever, etc).
 * Consider cytokines (interferons, TNF-alpha). When infected with flu, even if only locally in the respiratory tract, the inflammation can be systemic due to widespread cytokine release.
 * Also keep in mind that host immune responses can be hard to distinguish from virus-mediated symptoms.
 * **Viral shedding** I'm not sure about. Wiki says it's just the production of virions and their egress from the cell to infect other cells. Other sites seem to imply that it has more of a role in person-to-person contact infection. How he's using it here is hard to pin down, since I don't think he mentioned it but once, and in passing, in his lecture.
 * Most viral infections occur first at the epithelium.
 * [Note that secreted IgA and serum antibodies (mainly IgG) play a preventative role against re-infection; killer T cells and natural killer cells, macrophages, etc, have the job of clearing the virus once it's established.]
 * Explain how tissue tropism, virulence and host responses determine the characteristics of a viral disease.
 * I'm not sure what he's getting at here. The topology of the tissue that the virus comes in contact with obviously affects how the disease is contracted because it determines what the virus needs to interact with and how it can get into the bloodstream if it's a systemic virus. If a virus is particularly virulent, it will cause severe symptoms.
 * Compare and contrast the events during the incubation periods of acute local viral diseases and acute systemic viral diseases. Compare the period of virus shedding, the immune responses and susceptibility to reinfection.
 * [__Acute local infections__: colds, diarrhea. __Acute systemic infections__: smallpox, measles. __Chronic__: rubella in neonate. __Latent__: varicella zoster in nerves/herpesviruses. __Slow__: AIDS, HPV.]
 * Acute local: tend to have very quick incubation periods.
 * Acute systemic: tend to have longer incubation periods.
 * Evidently, as a general rule, the more complex the virus, the longer the incubation period.
 * __Local__: the virus is absorbed from one side of the cell and released on the same side; thus if absorbed through epithelial cell on the apical side, it's released also on the apical side (doesn't go into circulation). Mainly targeted by IgA antibodies. __The duration of adaptive immunity to the virus is pretty short because the adaptive system doesn't really have a chance to get into it__ (IgA-only exposure since it's only on the epithelium, no IgG involvement since it's not in the blood, short duration of infection). This means the possibility of re-infection is higher.
 * Note that local viruses can still spread to other local areas-- oropharyngeal infections can spread to the bronchi or the lungs, for example. They just don't get into the blood (viremia).
 * __Systemic__: the virus is absorbed from the apical side of the epithelium but released from the basolateral surface, usually into the blood, where it can spread to secondary sites of infection. Primary site of replication is the epithelium, mainly the upper respiratory tract. Secondary sites of infection tend to be the spleen, the lung, and the liver (also lymph nodes). Tertiary sites are often on the skin (pox in smallpox, rash in measles) Shows both primary and secondary viremia. __Infection can result in lifelong immunity if the adaptive immune system has a chance to get involved__ (IgG antibodies hang around for a long, long time). This means the possibility of re-infection is low. The primary sites are targeted by IgA; internal (secondary) sites are mainly targeted by IgG.
 * I don't think he mentioned much about viral shedding.
 * Explain determinants of viruses or host responses that favor persistent infection.
 * **Lots of different serotypes**, by which is meant the surface antigens on a virus. Obviously if there's a lot of variation in these, you have to raise antibodies to every serotype as you get infected by them, which is not a great strategy to beat a virus. Notice this also means that it's very difficult to develop vaccines for these viruses.
 * Host responses I'm not sure about. Immunosuppression, I guess.
 * Compare persistent and latent viral infections. What viral gene products are present in each type of infection? What events lead to reactivation of a chronic or latent infection?
 * Two ways of doing persistent/latent infections; they both involve a period of latency to avoid detection by the immune system.
 * One: Be a retrovirus (integrate into host DNA, just get replicated along with the cell).
 * Two: Have quiescent viral DNA that just sort of hangs out in the cell without actively making proteins (a la //Mall Rats// : "They're not there to shed. They're not there to lyse. They're just there.").
 * Reactivation: it seems to depend on conditions in which the immune system is suppressed (which makes sense for the virus-- it wants to come out when it can't be effectively combated).
 * [Recall that shingles is an excruciatingly painful disease along particular dermatomes resulting from reactivation of latent varicella zoster virus in dorsal root ganglia.]
 * Describe how symptoms of a viral disease, period of virus shedding, and amount of virus shed may be quite different in an immunosuppressed patient and an immuno-competent person.
 * It's all worse when you're immunosuppressed, pretty much. No surprises there.
 * T cell deficient: pretty bad. Can be life-threatening.
 * B cell deficiency: not as bad, but still bad. Can't make antibodies, which means it takes a lot of time to clear infections.
 * Consider whether or not it is possible to **predict** whether a virus in a novel host will cause a highly virulent disease, mild disease, or no disease at all.
 * Again, I'm not sure what he's getting at. Many viruses are no trouble at all for an immunocompetent host, and don't cause symptoms, either because they're relatively benign or because the immune system destroys them pretty easily. He calls this the "Iceberg Concept" of infection-- the viruses you see (symptomatic) are a small subset of the total infectious viruses, most of which don't do much that you can see.

=Host Responses to Viral Infection=


 * [Note that it's not generally in the interest of the virus to kill its host- balance its survival with the host's.]
 * List the effects of viruses on infected cells: CPE, syncytia, growth, apoptosis
 * "__Cytopathic effect__" (CPE): damage to cells.
 * Indirect cell damage:
 * Integration of viral genome
 * Induction of mutations in host genome
 * Inflammation + other innate (or adaptive) host immune responses (including antibody cross-reactions with normal tissue)
 * Direct cell damage:
 * Generally lyse a whole bunch of cells, that's pretty direct.
 * **Syncytia** : virus-mediated fusion of cells.
 * Growth: Viruses can turn cells into replicating fiends (viral oncogenes).
 * Apoptosis: Viruses can inhibit apoptotic pathways.
 * Other stuff:
 * Nuclear alteration (shrinkage, membrane alteration)
 * Chromosomal breakage (mainly viruses that replicate in nucleus)
 * Inclusion bodies: usually big concentrations of viral protein or RNA in the cell, often visible under a light microscope
 * Notice that the cell isn't stupid about all this. When the cell is infected, frequently they figure it out, and release interferons, apoptose, or what have you.
 * "Intracellular restriction factors": factors produced by a cell to defend itself against viruses that have already invaded it; to date, mainly these have been discovered against retroviruses.
 * The example that she gave (APOBEC3G) integrates with HIV particles and damages its genome. Note, no surprise, that HIV has a protein (Vif) that blocks its action.
 * Explain IFN response and "anti-viral state"
 * **Interferons** (IFNs): cytokines; the single most important anti-viral soluble agent. Once a cell is infected, it releases interferon to signal the cells around it to resist infection.
 * Type I IFNs (alpha and beta) produced and secreted by most infected cells (just about every cell can make them).
 * Type II IFNs (gamma) are only produced by T cells and natural killer cells. Recall that these attract macrophages and activate them like crazy. These are not made in response to infection but in response to finding an antigen (viral or otherwise, see Blood and Lymph on T cells).
 * We're mainly talking about type I interferons here.
 * IFNs (mainly Type I) can affect cells that aren't infected yet (hence their value as signaling agents of viral infection).
 * __Anti-viral state__ refers to a series of cellular responses to type I interferons. The idea is that they've been signaled that active viruses are nearby ("the zosters are coming! The zosters are coming!") and they're getting ready to repel boarders (or at least make it harder for the boarders to spread from them).
 * Specifically, it alters its gene transcription patterns:
 * **Blocks cell proliferation**
 * Protein called PKR **decreases protein translation** ; OASa **degrades mRNA** in cell.
 * **Reduces cellular metabolism**
 * Makes **more type I IFNs**
 * **Presents more surface antigen fragments** via MHC-type I proteins
 * Can apoptose
 * Etc.
 * In uninfected neighboring cells, many of the more drastic pathways are 'set up' by interferon signaling but don't actually activate until infection of those cells occurs. Don't want to destroy your own cells until you have to.
 * IFN type I can be triggered by double-stranded RNA (never found in normal human cells, only in viruses) or massive, abnormal replication of nucleic acid in places it doesn't belong.
 * Note that type I IFNs increases/induces NK (natural killer) cells activity and, through them, type II IFN response.
 * Distinguish between innate and adaptive anti-viral responses
 * Innate: immediate and non-specific defense.
 * 'Immediate' here means "within hours of infection."
 * Recall that the innate response directs the adaptive response later on.
 * One innate response: **TLRs (toll-like receptors) often pick up double-stranded RNA, viral nucleic acid patterns, etc.**
 * Share many similar signaling pathways with interferons.
 * Note that TLRs are frequently located on the //insides// of cells to detect viral infection, as well as on surface membranes.
 * Note some treatments involve artificially signaling TLRs in the area of the infection (topical cream for HPV, freezing/burning them affected areas (triggers similar pathways).
 * Generally, the innate response seems to be pretty much the same as discussed previously.
 * Adaptive: acquired over time, attuned to specific viruses.
 * Notice that IgG can be opsonizing for phagocytosis, and, once bound, can also prevent a virus from binding to its host cell target or expressing its genome effectively. This doesn't always work, particular with enveloped viruses (not binding to virion itself).
 * Antibodies which serve this function are called "**neutralizing antibodies** ."
 * Antibodies which can bind epitopes shared by all or most of a virus group are called "**group specific** ;" antibodies that can only bind to a couple of viruses in a virus group are called " **type specific** ." Obviously group specific antibodies are good for both vaccines and prevented recurrent infections.
 * Recall that B cells can see virions as antigens directly (whereas T cells look for them on the surfaces of cells-- though since B cells can display engulfed virion fragments to activate T cells, it's sort of a false dichotomy).
 * Note that you need Th1 activation to really kick off the antibody response. If the infection's in a place where you haven't got a lot of B cells and the macrophages haven't shown up yet, you're relying on dendritic cells. Remember that dendritic cells are the only cells that can activate both helper and killer T cells (MHC types I and II) with the same antigen.
 * In the context of viruses, Th1s are particularly important-- need to flood the area with interferon gamma and activate lots of killer cells to immediately contain the infection. Th2s are activated a little later to start up antibody production by the B cells.
 * That's how it works in principle. But, for example, in the hepatitis C virus, it can replicate and spread faster than your killer cell response can react. In the context of this never-ending infection, the collateral damage from chronic inflammation causes a lot of organ trouble.
 * There's also a middle ground in which your immune system can contain the virus but not completely destroy it. I would imagine this frequently involves viruses that are partially latent (like varicella).
 * Note that innate response - interferons, NK cells, chemokines, inflammation - often plays the "containment" role until your adaptive immune system can get into gear and destroy it.
 * Compare antibodies produced in primary and secondary responses
 * Primary responses: tend to be lower-affinity, largely IgM (immature response).
 * Secondary responses: tend to be higher-affinity, largely IgG or IgA (mature response after somatic hypermutation of activated B cells).
 * List and describe major cell types involved in anti-viral responses
 * Macrophages, neutrophils, dendritic cells, NK cells. You know about most of these already, except NK cells, which target and destroy virus-infected cells.
 * Compare the effectiveness of antibody versus cell-mediated immunity in the anti-viral response
 * Antibody: target virions outside the cell
 * Cell-mediated: target viruses inside the cell.
 * Explain the means by which viruses evade the host defenses
 * Popular option is to infect the immune system (T/B cells, dendritic cells, macrophages, etc).
 * They can vary their surface antigens (often used by small or uncomplicated viruses that don't have space to encode complicated proteins to inhibit host pathways).
 * Can inhibit IFN pathways (secretion, reception, transduction). This is another very popular pathway and most viruses do it.
 * Can avoid antibodies by shedding "decoys"
 * Can inhibit apoptosis/cell cycle control
 * Can mimic endogenous cells/proteins
 * Can infect sites where the immune system doesn't go (ie brain or spinal cord)
 * Can down-regulate cell MHC presentation proteins
 * etc, etc.
 * List and describe the major soluble mediators involved in anti-viral responses
 * Interferons are the big one (type I, the 'alert' type, is given off by all infected cells; type II, the 'over here' type, is given off only by NK cells and T cells). Also TNF-alpha (inflammatory mediators) which are given off by macrophages.

=Cell and Tissue Injury=


 * Understand major causes (etiologies) of cell injury
 * [Most cellular injuries are involved with epithelia - the skin and the linings of body cavities/organs - and endothelia in vascular vessels.]
 * (1) Physical agents: trauma, heat, cold, etc.
 * Specific notes on burns: outcomes depend on total surface area burned, depth of burn injury, lung injury, age, and prompt treatment.
 * Depth- has burn damaged the dermis/basal lamina/underlying connective tissue or only the epidermis? Partly this is a basal laminal regeneration thing, partly it's a stem cell preservation issue.
 * Burns also lead to neurogenic shock, anemia, hypermetabolism, and especially infections (pseudomonas aeruginosa, staph aureus).
 * Heat stroke: classically, respiratory alkalosis (from hyperventilation trying to cool off) and hypotension.
 * Hypothermia:
 * Cells freeze: salts precipitate out, damaging cells.
 * Poor perfusion of tissues.
 * Metabolism in brain is inadequate.
 * Electric shock: tissue damage from heat, tetanic contractions of heart or disruption of cardiac conduction, etc. Household AC current is sufficient.
 * (2) Chemical/drug agents: toxins, poisons, etc.
 * (3) Infection: bacteria, viruses, etc.
 * (4) Immune response: anaphylaxis, collateral damage, autoimmunity, etc.
 * (5) Genetic abnormalities: cystic fibrosis, etc.
 * (6) Nutritional imbalance: deficiencies (eg. folate), overabundance (eg. iron), etc.
 * (7) Hypoxia: too little oxygen received. Causes:
 * Inadequate blood supply
 * Lung disease
 * Heart failure
 * Shock
 * Understand how cell injury contributes to the pathogenesis of disease
 * Disease is, here, effectively defined as cell injury (direct or by alteration of normal pathways leading to suboptimal performance). Injuries to specific cells tend to have specific symptoms associated with them-- pretty basic idea. Knock out cell type X, look for disease symptoms in whatever system type X cells usually supports.
 * Be able to describe major mechanisms of cell injury
 * [Note that one differentiation between acute and chronic cellular injuries is the presence of certain types of inflammatory cells found at the injury site.]
 * If mainly PMNs are present, it's acute (occurs quickly)
 * If mainly lymphocytes and macrophages are present, it's chronic (ongoing injury).
 * [Note that many forms of cellular damage can be fixed- membrane lipids can be replaced, denatured proteins can be refolded by chaperone proteins, etc.]
 * Classic examples of cell injury (reversible):
 * Cell swelling (membrane damage)-- see below.
 * Increase in extracellular metabolite (such as glucose in diabetes) leads to massive overproduction of intracellular molecules (such as glycogen).
 * Fatty change in hepatocytes-- fat vacuoles accumulate under conditions of high fat metabolism (such as in starvation conditions or excessive, chronic alcohol consumption, which shuts down some parts of glucose metabolism).
 * Ischemic cell injury (without oxygen):
 * Neurons can only go 3-5 minutes without oxygen until irreversible damage.
 * Cardiac myocytes can go about twenty minutes; liver and renal epithelium up to 2 hours.
 * Cells of soft tissue (skin, skeletal muscle) can go up to several hours.
 * How can the study of morphologic change caused by cell injury explain the whys and wherefores of signs and symptoms of disease
 * Again- think small to large. Changes in this structure in this type of cells must be due to such-and-such a condition and leads to this other type of cellular dysfunction, which causes a problem with X system, which leads to Y symptoms/signs.
 * Example here is hepatocytes: with particular cellular changes (swollen hepatocytes, ropy, eosinophilic aggregates within hepatocytes) you can diagnose specific diseases that we know show up with those cellular symptoms (in this case alcoholic hepatitis).
 * What are free radicals, how do they arise, and how do they produce cell injury
 * Free radicals: molecules with a free, unpaired electron. These are frequently the results of thermodynamic breakdown or alteration of O2. Hydrogen peroxide (H2O2) is a compound that really easily breaks down to two free radical OH molecules. Superoxide (O2-) is also a free radical species, often generated from the interaction of O2 with the endoplasmic reticulum.
 * The problem with free radicals is that they react with everything under the sun, which basically means you have random oxygen atoms oxidizing (pulling electrons) from a variety of cells (think Fe2+ to Fe3+: there goes methemoglobinemia). An example of cellular injury from this is peroxidation of lipids on artery walls, leading to atherosclerosis.
 * Generally you have antioxidants that keep this process under control. But under conditions in which you have a lot of free radicals or a lesser production of antioxidants, you're in trouble.
 * Understand how ischemia/hypoxia creates a setting where free radical damage becomes an important cause of cell injury
 * Mitochondria are deprived of oxygen; acute drop in ATP level, ATP mobilized from creatine phosphate and glycolysis- glycolysis leads to drop in cellular pH due to accumulation of lactic acid. Ion pumps stop working; cell swelling ensues. Protein synthesis decreases.
 * Up to this point it's reversible. (frequent exam question)
 * After this point, if the pH drops to about 4.5, the lysosomes burst, and their proteases and nucleases are released. Alternatively, if cellular levels of calcium accumulate to a certain point, they activate a whole bunch of lipases and proteases. The end result is to degrade nuclear chromatin and essential cellular proteins.
 * (The calcium in question can come from extracellular sources or from intracellular sinks in endoplasmic reticula or mitochondria.)
 * The other problem is in reperfusion (giving hypoxic tissues oxygen)-- if you treat hypoxic patients with lots of oxygen, they accumulate free radicals like crazy. Hypoxic tissue + reperfusing oxygen = free radicals. One theory about this is that you have high infiltration in hypoxic tissues of PMNs, which produce free oxygen species from ambient oxygen. If you give 100% O2, this combination can be very bad.
 * What are examples of free radicals and how does the body get rid of them
 * As mentioned, superoxide or hydroxyl radical molecules. The body uses particular antioxidant enzymes (eg. superoxide dismutase) to convert them.
 * One enzyme he mentioned in particular is glutathione peroxidase-- uses reduced glutathione to be oxidized, harmlessly, by the oxygen free radicals.
 * Note that oxygen free radicals are often called reactive oxygen species or ROS.
 * Ie: O2- + superoxide dismutase leads to H2O2, which is further converted by catalase to water and O2. A deficiency in either superoxide dismutase or catalase can lead to ROS.
 * Understand how necrosis differs from apoptosis
 * Effectively, necrosis is 'unplanned death' and tends to occur in clumps of cells.
 * DNA from necrotic cells is cut up more or less at random (lots of released, unspecific endonucleases).
 * Apoptosis is 'planned death' (the cell committing suicide) and tends to occur in isolated cells that have received particular apoptotic signals.
 * DNA from apoptosis is chopped up into discrete segments by particular enzymes that cut at particular sites.
 * Understand the four major types of necrosis seen in human disease:
 * __Coagulative (hypoxic) necrosis__- the dead cell remains intact but resembles a hollowed remnant of its former cell (example is myocytes in heart: dead myocytes have their old shape but lack a nucleus).
 * Can be caused by hypoxia/reperfusion injury. In shock, for example, you get inadequate blood/oxygen supply to peripheral tissues, leading to coagulative necrosis.
 * Particular signs: nucleus shrinks, then fragments, then disappears completely.
 * __Liquefactive necrosis__- the dead cell just dissolves away. Classically seen in brain and spleen, and/or with acute infection.
 * This happens because lysosomal enzymes in the cell are released, pretty much eating away the entire cell (what remains, remains as pus).
 * __Caseous necrosis__- only seen in tuberculosis. Cells turn a kind of grayish-white and get very soft, sort of milky (thus casein-caseous). Particularly found in lymph nodes.
 * __Fat necrosis__- typically seen in acute pancreatitis or some trauma (car accidents). Lipases of dying cell leak out into extracellular space, reacting with extracellular lipids to make gray-white "calcium soaps."
 * Understand how chronic injury leads to adaptation
 * Four general types of adaptive responses.
 * __Atrophy__: Cell decreases size and function.
 * __Hypertrophy__: Cell increases size, organelle complement, and function (eg. left ventricle enlarges to compensate for overload in chronic hypertension).
 * __Metaplasia__: One type of cell is replaced by another. Classic example of this is the replacement of columnar epithelia in the bronchus by squamous epithelia in response to cellular (thermal) damage from cigarette smoke. Notice that this is a frequent cause of oncogenesis.
 * __Hyperplasia__: One cell type proliferates in a particular location. Example: with a endocrine tumor that produces adrenocorticotropic hormone (ACTH), the adrenal cortex cells multiply like crazy.
 * Be able to describe the major alterations in the cell membrane, mitochondrion and nucleus that occur during cell injury
 * Membrane: Mainly due to either a physical break in the membrane or inactivated ion pumps (controlling osmotic pressure). Recall that ion pumps require ATP, so if ATP supplies are diminished, this can be a problem. Cellular swelling in damaged cells due to osmotic imbalance is very common (accumulation of ions inside cells). Physical breakdown of the membrane often results from oxidation of the lipids inside it.
 * Mitochondria: Largely due to swelling of the mitochondria due to disruption of oxygen supply (interrupts ATP production, which interrupts ion pumps in mitochondrial surface). Note that interference with mitochondrial function can also impact ATP-dependent processes (like ion pumps).
 * [Endoplasmic retic: Due to distortion of cisternae and detachment of ribosomes from rough ER (inhibits lipid-soluble protein synthesis).]
 * Nucleus: basically, notes say "who knows," but the nucleus looks wonky during/after cellular damage (presumably decreasing RNA synthesis).
 * Know which morphologic and biochemical alterations during hypoxic injury are reversible and which are irreversible
 * See above under "how ischemia creates a setting where free radical damage (etc)".
 * Main point: release of calcium stores or a severe drop in pH (< 4.5) lead to irreversible cellular damage.

=Review session for exam I=

Drug selection: based on benefit/risk estimates Dose selection: based on dose-response curves (gives you info on the amount of dose that makes it into the plasma). Remember that plasma concentration is proportional to clinical response. Recall that, given the volume of distribution and the Cp, should be able to figure out original (loading) dose. (More on this below.) Some questions about what small vs large Vds mean-- small means it stays mainly in the plasma, don't need a high loading dose; large means it gets out into the tissues, so may need a high loading dose to get plasma concentrations up to what you want them to be. May need to calculate a loading dose given a patient's weight. Equation sheet will be given out with exam; shouldn't particularly need it, though. Clearance, hepatic or renal, varies considerably from patient to patient. Steady-state: rate in (dosing at intervals) equals the rate out (clearance).

__Absorption__: determined by bioavailability (fraction of drug that gets into Vd). Be able to calculate dosage changes from oreal to parenteral (remember that dosage should always go down from oral to parenteral). __Distribution__: determined by Vd-- a measure of how well it gets through barriers (cross GI membrane, into CSF, through placenta, out of kidney tubule for reabsorption). __Dosing Interval__ (for steady-state): determined by elimination characteristics (excretion by kidney, metabolism by liver). If there's renal damage (less excretion) or liver altered function (increased or decreased metabolism), the dosing interval will change correspondingly.

Note that Dr. French writes the questions on pharmacodynamics, pharmacokinetics, drug metabolism, and antibiotics.

No questions on bonding forces in drug receptors. At most clinical doses, the response is more or less linearly related to the dose. Look at sigmoidal shape of log dose-response curve and hyperbolic shape of non-log curve and know why the response gets smaller at high concentrations. Know comparisons of efficacy with Emax; know comparisons of potency with EC50. Remember that EC50 is 50% of max response __for that drug__. High EC50 = low potency. Generally drugs that can't reach the maximal response possible in the system (highest Emax of drugs affecting that system) aren't used.

Difference between pharmacological/physiological/chemical antagonists. Pharm reversible antagonists: EC50 increases, apparent potency decreases, Emax is unchanged (shifts dose-response curve to the right). Most antagonists are in this class. Pharm irreversible antagonists: EC50 is often unchanged, Emax decreases, efficacy decreases.

Ways to get through membranes: diffuse through (lipid drugs), go through pores (small hydrophilic drugs), passively or actively transported (drugs that resemble endogenous compound, or are transported into the kidney tubules by secretion). Most drugs are small, lipid-soluble, and uncharged at physiologic pH.

Metabolism: usually involves making a drug more water-soluble (Phase I reactions) or larger/more charged (Phase II reactions) Most drugs = weak acids or weak bases. H-H equation: weak acids are nonionized more at acidic pHs (acids can be absorbed through membranes from acids), weak bases are nonionized more at basic pHs (bases can be absorbed through membranes from bases). Weak acids are trapped in basic solution; weak bases are trapped in acidic solution. Remember that the pKa is the pH at which the number of ionized and nonionized molecules are equal. Essentially: given two pHs on either side of a membrane and the pKa of a drug, which side has more drug trapped on it? Routes of admin: oral most common, IV results in the most reliable dose (for narrow therapeutic drugs). Essentially you're comparing bioavailability and rate on drug effect's onset between routes. IVs are fastest, except maybe for inhaled gases (inhaled particles tend to get caught by epithelia, which is why they're used for topical application). Remember difference between topical (local, doesn't get through membranes to blood) and transdermal (depot effect: slow absorption into bloodstream through skin membranes).

Drug metabolism: make sure you know if a given drug is hepatically (biliary) or renally (tubule excretion) cleared. The more you're water-soluble, the less you need hepatic reactions to change you into something that can be excreted by kidney or thrown out into the bile. Rate of urine formation: 1 mL/min; rate of renal filtration: 120 mL/min; rate of renal secretion + filtration: 600 mL/min. Lipid-soluble drugs get reabsorbed back across the tubule membrane pretty quickly (thus reduce effective filtration rates). Phase I metabolism reactions: __oxidation__, __reduction__, __hydrolysis__. Oxidation reactions: can be non-CYP (alcohol/aldehyde dehydrogenases) or CYP450's. CYP450's metabolize about half the drugs that go through first-pass metabolism. Important targets for inducers/inhibitors. __Don't need to know specific targets of inducers or inhibitors__ (but need to know list of inducers/inhibitors). Polymorphisms found in CYP2D6 and CYP2C19 that produce significant variation in drug metabolism. Notice that CYP reactions are not really saturable (not going to run out of oxygen atoms to attach to things). Reduction reactions: not much detail. Hydrolysis: esterases and amidases (amidases are slower).

Inhibitors/inducers of CYP metabolism on drug list: DQ CRIMES: Doxycycline/streptogramins (DQ), chloramphenicol/clindamycin (C), erythromycin/macrolides (E) (for macrolides: **A** zithromycin is **A** -ok; **C** larithromycin and **E** rythromycin **C** ause **E** ffects in CYP metabolism.)

Drug list of CYP inducers and inhibitors we need to know: [Warning: the hokey mnemonics that follow are really, truly, hokey.] Inducers: Phenobarbitol, Phenytoin, Carbamazepine, Rifampin, Ethanol, St. John's Wort, Tobacco smoke Hokey mnemonic: PEPR-CST (pepper-cyst; pepper induces sneezing); alternatively, "St. John has Barbed Toenails, and Smokes and Drinks while Riffing on Carbs." Inhibitors: Cimetidine, Erythromycin/Clarithromycin, Ketoconazole, Fluoxetine, Grapefruit juice, HIV protease inhibitors, Omeprazole Hokey mnemonic: "Om, Er, Hi, can you Clarify Flux through Simulated Grapefruit Ketones?"

Phase II metabolism reactions: saturable because you run through your stores of conjugation molecules (sulfate, acetyls, etc) fairly quickly. Also, in neonates, can have undeveloped production pathways of conjugation molecules (thus can't conjugate with those molecules-- lack of glucuronic acid causes gray baby syndrome on administration of chloramphenicol in neonates).

Drug excretion and elimination kinetics: filtration, secretion, and reabsorption take place in kidney can change pH of urine to increased ionized drug trapped there (aspirin) protein-bound drugs aren't filtered or metabolized-- extends half-life enterohepatic recirculation concept Plasma to milk: same as any membrane barrier (not protein bound, lipid soluble, small). Notice that milk has a higher pH than plasma. Half-life: time to 50% of initial plasma concentration of a given drug. 1st order elimination kinetics: rate of excretion depends on the concentration of the drug (half-life stays the same for all concentrations or doses of drug) Uses of half-lives: can use to get time to steady-state (four to five half-lives, without a loading dose) can use to get time to more or less complete elimination (four to five half-lives) The number of half-lives in the dosing interval (x) predicts fluctuations in plasma concentrations (fluctuations proportional to 2x). If there's two half-lives in the dosing interval, there's a four-fold fluctuation between doses (if initial dosage is 100, it'll be at 25 before you give another dose). To calculate the initial dose of a drug given its plasma concentration at first-order kinetic levels (after distribution to tissues) and body weight: Assume 3.64 g/L plasma concentration of ethanol; body weight of 5.5 kg. Volume of distribution of ethanol is to total body water (in an infant, 0.6 L/kg =, here, 3.3L). __Initial dose = Cp * Vd__ Initial dose = plasma concentration at first-order kinetics (3.64 g/L) times Vd (3.3 L) = about 12 g of ethanol.

Divided by the specific gravity of ethanol = about 15 mL; divided by the concentration of vodka (40%) = about 38 mL (1.3 ounces, or one generous shot) of vodka.

[I don't think he's actually going to have us figure any of this out past the part where we get the gram weight of the initial dose. The important thing to remember is that the Cp after the distribution phase, times the volume of distribution, equals the initial dose.]

Antibiotics (10-11 questions on exam): most questions have both the therapeutic class as well as drug name, so not to worry too much about specific drugs. Mechanism of action: particularly, know the target (protein synthesis vs cell wall synthesis) Target gives you mechanism of selective toxicity; also gives mechanism of antibiotic resistance in bacteria Recall that bacteriostatic drugs are less good in immunosuppressed patients and that bacteriocidals drugs bind irreversibly to targets, thus have post-antibiotic killing effect. Bacteriocidal mechanisms: decreased cell wall synthesis Bacteriostatic mechanisms: decreased protein synthesis (note aminoglycoside exception) Pharmacokinetics: Absorption (is it available per orem, or is it given IV? Note cephalosporins are ok for PO.) Distribution (does it cross into CSF? Especially 3o cephalosporins) Elimination (is it renal or hepatic?) Renal: Aminoglycosides, penicillins, cephalosporins Hepatic: Doxycycline, macrolides, clindamycin, chloramphenicol __Not a lot of emphasis on spectrum and usage__ due to small exposure to microbiology thus far. Cell wall synthesis inhibitors: Penicillin G: good for Gram+ cocci.

Methicillin/Oxacillin: good against penicillinase-producing //Staph aureus//. __MRSA: resistant due to change to penicillin-binding protein (target of penicillin), not due to penicillinase__

Vancomycin: good against methicillin-resistant //Staph aureus// because it inhibits a different binding protein (inhibits stage II, not stage III, cell wall peptidoglycan formation) than all the other cell-wall-synthesis inhibitors. For the moment, consider using vancomycin for all MRSA. In reality, note that community-acquired MRSA is treated with different drugs (tetracyclines and sulfa drugs).

Pipericillin: __good against Pseudomonas__.

Aminopenicillins (amox and amp): get into cells better: more Gram- targets. Remember than aminopencillins will be targeted by penicillinases unless you add beta-lactamase inhibitors with them. [Penicillins: Type III rashes most common reaction; Type I anaphylaxis what you worry about.]

Note that by combining amoxicillin with clavulonate can get around penicillinases. Note that it __still doesn't target MRSA__ (MRSA has an altered binding target; need vancomycin). Or can use Piperacillin with tazobactam to get around penicillinases in Pseudomonas.

Cephalosporins: 1st gen: similar to amoxicillin. 2nd gen: increased Gram-, less Gram+. Good anaerobic activity. 3rd gen: very good Gram-, even less Gram+. __Good against Pseudomonas__. Good CSF distribution.

Protein synthesis inhibitors: Macrolides: similar to Penicillin V-- good if patient has Type I allergy to penicillin. Not bacteriocidal, though. Common side effect is GI upset, erythromycin in particular. Dosing: Azithro = 1 time a day (longest half-life) ; clarith = 2 times a day; eryth = 4 times a day.

Clindamycin: gram+, effective against anaerobes __except C. difficile__. Can result in diarrhea or pseudomembranous colitis due to C. diff expansion and toxicity.

Aminoglycosides: good against Gram- aerobes; good against Gram+ when used in conjunction with penicillins. Toxicities: ototoxic, renal toxicity. Have to routinely monitor plasma levels (narrow therapeutic index).

Tetracyclines: broad spectrum. Can deposit in bone/teeth (developmental concern in children < 8 yo). Another concern is fungal superinfection after killing off all competition.

He expressly said not to worry about streptogramins, linezolid, chloramphenicol. He didn't mention monobactams or carbapenems one way or the other.

Briefly: [my gloss from here on out] PO-ok drugs: Pen V, Amp/Amox (with or without b-lactamase inhibitors), oxacillin, cephs, tetracyclines, macrolides, clindamycin, vancomycin to treat C. diff, chloramphenicol No-PO drugs: Pen G, methacillin, piperacillin, aminoglycosides, vancomycin to treat MRSA

Renal clearance: all cell-wall synthesis inhibitors, aminoglycosides Hepatic clearance: doxycycline (other tetras are mixed), macrolides, chloramphenicol, clindamycin

[recall that aminoglycosides are strongly basic and don't go through cell membranes well.] [macrolides tend to accumulate, beneficially, in lung tissues]

Read his pharmacology questions closely on the test. They can be tricksy, precious.