M2M Unit 3 Flashcards

Question

protein products of viral oncogenes- v-abl

Answer 1

codes for a protein kinase that phosphorylates tyrosine residues on other proteins. It is similar to the human gene c-ABL that is found on the BCR-ABL translocation in the Philadelphia chromosome and is overexpressed in BRC-ABL CML

Answer 2

Endogenous oncogenes are marked c-onc. Notice that c-onc genes are part of normal functioning of human cells, so therapy can only target overexpression, not all of c-onc Thus- it seems many oncogene products mimic hormones or growth stimulating factors either by resembling natural hormones or by affecting the structure of the cell surface receptors for these hormones. These altered receptors then send signals to the cell nucleus in an unregulated manner to affect growth

Answer 3

in the proto-oncogene: quantitative (too much protein) qualitative (overactive/unregulated protein)

Answer 4

level of oncogene expression tends to correlate w/ the rapidity of the progress of the cancer ex. N-myc gene expression used for neurobalstomas ex. increased HER2/neu gene expression correlates w/ poor breast cancer prognosis

Answer 5

oncogenes- promote cell proliferation tumor suppressor genes- inhibit cell proliferation if you have over-activation mutation in an oncogene and an inhibiting mutation in a tumor suppressor gene, then that will lead to cancer

Answer 6

can design either small molecs or antibodies as therapy targeting oncogenes: herceptin- drug antibody therapy against HER2/erb2 oncogene product small molecs- able to inhibit cancerous proteins, usually by binding to active sties ex. Gleevac (ATP analog- specific to binding pocket) inhibits ABL tyrosine kinase in patients w/ BRC-ABL translocation on philadelphia chr targeting tumor suppressor genes: inject RB directly into RB-negative tumors use drugs that kill only p53 deficient cells use drugs that correct mutant conformations of dominant-negative p53 proteins

Answer 7

rare inherited cancer susceptibility w/ large range of presentation must have more than 1 family member w/ cancer (autosomal dominant nature) usuallly assoc w/ p53 mutation (70%)

Answer 8

a proband w/ a sarcoma diagnosed before 45 AND a first degree relative w/ any cancer under 45 AND a first or second degree relative w/ any cancer under 45 or a sarcoma at any age

Answer 9

2 hits/mutations must accumulate in a tumor suppressor gene before progressing to cancer 1 inherited state/hit is premalignant ex. breast cancer= HER2, p53 lung cancer= EGFR, p53

Answer 10

p53 is required to protect from UV- a major carcinogen, by protecting skin- sensor of cell stress CHK1 and CHK2 bind to and activate p53 to act on target genes to help DNA repair and damage prevention DNA damage, cell cycle abnormalities, hypoxia --> activate p53 --> cell cycle arrest; DNA repair and cell cycle restart OR death/elimination of damaged cell --> cellular and genetic stability DNA damage can occur/accumulate w/o functioning p53; p53 is a common chemotherapy target and can have personally designed drugs to activate p53 w/o DNA damage

Answer 11

autosomal dominant; genetic testing can diagnose high penetrance by age 65 high variability in severity/onset characterized by formation of cystic and highly vascularized tumors in many organs major cause of death are metastatic RCC and CNS hemangioblastomas -cerebellar and spinal cord hemangioblastomas retinal hemangioblastomas bilateral kidney cysts clear cell renal carcinomas (RCC) pheochromocytomas- usually adrenal gland (night sweats; high bp; heart palpitations; panic attacks) pancreatic cysts and tumors endolymphatic sac (inner ear) tumors cystadenomas of genitourinary tract

Answer 12

based on presence or absence of pheochromocytoma and type of VHL mutation Type 1: hemangioblastoma + clear cell renal carcinoma (due to total/partial loos of VHL- impartial folding) Type 2: pheochromocytoma +/- hemangioblastoma +/- RCC different combos of Type 2 (due to VHL missence mutation)

Answer 13

VHL is a tumor suppressor gene located on 3p25-26 VHL protein is part of a complex that targets proteins for proteosomal degradation via ubiquitination VHL loss/inactivation leads to HIF accumulation, a high rate of aberrant aneuploidy, and disruption of primary cilia maintenance (leads to renal cysts and renal cell carcinoma)

Answer 14

interactions are dependent on oxygen conditions Normoxic conditions: HIF is hydroxylated. With WT VHL, HIF is ubiquitinated by VHL protein and undergoes degradation Hypoxic conditions: HIF doesn’t get hydroxylated and isn’t marked for degradation. HIF protein accumulates and the transcription of downstream genes that are involved in angiogenesis, metabolism, apoptosis, and other cancer-growth promoting processes and survival under low O2 conditions **Cells w/ mutated VHL act as if they’re hypoxic

Answer 15

Clear cell renal cell carcinoma (ccRCC) is the most common histologic subtype of RCC Majority of cases are sporadic (4% inherited) -VHL loss/mutation is responsible for almost 2/3 of sporadic cases Knudson’s TWO HIT theory is that the dev of VHL-related tumors requires inactivation of the 2 copies of the VHL gene VHL disease- patient already inherited 1 VHL gene mutation, so they only need one more hit for tumor Patients w/ VHL are at risk to develop up to 600 tumors on kidneys

Answer 16

Management of local renal cell carcinoma typically involves surgical resection w/ either partial or radical nephrectomy Management for metastatic renal cell carcinoma involves systemic therapy --vascular endothelial GFR (VEGF-R) tyrosine kinase inhibitors, MTOR inhibitors, and immunotherapies localized RCC- ongoing surveillance- 20-30% will relapse metastatic RCC- surgery, radiotherapy, systemic therapy

Answer 17

lipid bilayers composed of lipids, cholesterol, and proteins ~5nm thick serve as barriers to most water-soluble molecs dynamic and fluid (depends on composition and temp) membrane proteins mediate most of membrane func

Answer 18

the degree to which lateral motion is possible among adj phospholipids on a given side of the bilayer. Some lipids are anchored, some are free-floating within a given membrane. different compartments of a membrane have different degrees of fluidity. ex. acyl chains unsaturated makes the membrane more fluid ex. Cholesterol, when intercalated in membranes, stiffens the membrane and makes it less fluid (Thickens the membrane by straightening out non-polar, hydrophobic groups inside the bilayer) ex. Membrane composition also determines curvature (size of polar heads and temp)

Answer 19

Phosphoglycerides: have a glycerol-3-phosphate backbone with 2 fatty acyl chains (either saturated or mono- or polyunsaturated) at one end and a polar head group at the other end. Head group determines which phosphatidylglycerol it is Sphingolipids: have a 'sphingosine' (long acyl unit) with either of two polar head groups (which one it is distinguishes which type of sphingolipid it is) and an attached fatty acid chain. ex. Sphingomyelin: phosphocholine head group. These are started to be made in the ER and finished in the Golgi apparatus. Cholesterol: have a characteristic hydroxylated ring structure at one end, and a fatty acid chain on the other.

Answer 20

particular phospholipids don't flip from one side to another w/o enzyme activity, but lots of lateral diffusion occurs Phosphatidylserine, phosphatidylthanolamine, and phosphatiddyinositol are more abundant on internal surface PC, sphingomyelin, and glycolipids are more abundant on external surface Cholesterol is thought to be distributed evenly across both membranes

Answer 21

Integral proteins (fully or partially embedded in membrane)- have multiple transmembrane domains (can go back and forth through the membrane) Peripheral membrane proteins- covalently interacting with proteins bound in the membrane, but not themselves embedded in the membrane

Answer 22

via ingestion and uptake or synthesis by the liver. Uptake depends on Low-density lipoprotein receptor LDLR -Negative feedback loop- sufficient cholesterol in the diet decreases synthesis and vice versa -Sterol regulatory element binding protein (SREBP) regulates both uptake and synthesis of cholesterol (SREBP- A protein containing a transcription factor that regulates both LDLR and all 30 synthesis proteins)

Answer 23

depends on approx 30 enzymes First and rate-limiting enzyme is HMGCoA reductase - Statins block this step and are used to lower cholesterol - Low cholesterol- transcription factor is cleaved by SREBP to go to nucleus to activate genes - -Sensor is in ER membrane, where cholesterol is lowest and changes are easiest to detect - -Held in ER until cholesterol becomes low, then SREBP moves to Golgi to get cleaved 3 protein complex - SREBP - SCAP (SREBP cleavage activating protein) binds both SREBP and sterols like cholesterol - Insig- binds SCAP when cholesterol is high, blocks SCAP’s signaling - -SCAP signal domain is recognized by a coat protein COPII for vesicles to move from ER to Golgi - -As cholesterol conc drops, Insig doesn’t bind SCAP, so SCAP/SREBP moves to Golgi in vesicles

Answer 24

``` 45 L total plasma- 3 ICF- 27 ECF- 13 + 5 for third space (incl interstitial fluid, plasma, lymph) ```

Answer 25

Na+ 14 ICF; 140 ECF; (-) K+ 145 ICF; 5 ECF; + Cl- 5 ICF; 145 ECF; + proteins- 126 ICF; ~0 ECF; - water ~55,000 ICF = ECF; +

Answer 26

Lipid- “impermeable to charge” and strong polarity Electrically strong; membrane potential -50mV across 5 nm membrane = -100,000 V/cm Ion channels and transporter proteins Channels- ions and water -Selective -Gated- temperature; mech; chem; electrical Transporters -Big molecules -Pump (move against gradient with an E source- ATP)

Answer 27

Diffusion- passive movement; small and neutral charged Channels- selective and gated Transporters- big molecules, sometimes via pumps

Answer 28

temp mechanical chemical electrical

Answer 29

according to conc gradient high to low

Answer 30

look at osmotic pressure in and outside of cell inside the cell: high osM= cell swells low osM= cell shrinks assume ECF is constant and only water can change cell volume; ignore permeable substances

Answer 31

Make a cell impermeable to water Build a strong wall around the cell to keep it from swelling by brute force Balance osmotic force osmotically

Answer 32

Pi= sigma*R*T*detaC ``` sigma= reflection coeff R= gas constant deltaC= difference in solute conc across a membrane ```

Answer 33

osmosis is diffusion of water across a semipermeable membrane

Answer 34

Reflection coefficient of 1: non-permeable Reflection coefficient of 0: same as water A different reflection coefficient complicates matters. A molec that crosses half as easily as water will exert half of the ideal osmotic P of a non-permeating solute. Clinical implications- shock involves having blood go to extremities, and not to brain. You give them an IV of NaCl because it is non-permeable. Clysis- give fluid subcutaneously if you can’t find a vein. Glucose is less permeable, which temporarily sucks water out of cells before it gets into the cells and starts helping them absorb water.

Answer 35

Osmolarity- total conc of solute particles Ex. 1 M soln of CaCl2 gives 3osM soln Molarity- number of moles of solute per L soln Equivalents- number of “combining weights” of an ion per liter, calculated by a 2-step process ex. For each ion, convert to mosM; multiply mosM by the valence of the ion

Answer 36

effect of a soln on a cell; depends on membrane permeability Hypertonic- soln that makes cell shrink Hypotonic- soln that makes cell swell and burst Isotonic- same

Answer 37

1. Cell needs to move big proteins without compromising membrane integrity a. Thus, transport vesicles (contains cargo targeted for specific membrane-bound organelles) 2. Vesicular transport- basic principle of transporting substances from one intracellular compartment to another 3. Incorrect transport frequently results in disease a. Ex. Cystic fibrosis, due to a failure in chloride ion channel-protein transport

Answer 38

1. Membranes don’t automatically merge when they contact e/o; maintain separation a. 2 membranes coated in water molecs i. Need to remove water to fuse the lipids ii. Overcome charge repulsion between lipids in order to allow merging efficiency iii. Membrane fusion specificity- make sure these should be merging to begin with

Answer 39

a. 3 shapes: i. VAMPs: transmembrane domain at one end, with a helical domain in it ii. Syntaxin: transmembrane domain, one helical domain iii. SNAP25: no transmembrane domain, 2 helical domains, fatty acid binding region that more or less acts as a membrane-binding domain 1. Notice different types of each protein, and each only binds to specific counterparts 2. Helical domains of all 3 proteins serve to bind with each other- form an aligned bundle or tetramer with coiled coils 3. All vesicles contain VAMPs. All target plasma membranes contain syntaxin and SNAP25 4. When the vesicle nears the target membrane, the helical domains on the vesicle bind to those on the target membrane a. These effectively press 2 lipid layers together, squeeze out water, overcome charge repulsion, and promote lipid fusion b. Helical binding needs to be extremely strong to do this (and it is)

Answer 40

a. Enzyme that regulates the dissociation of SNARE proteins: NSF protein i. 6 form a turning barrel around the SNARE complex and twists it apart, using ATP hydrolysis ii. Alpha snap is a cofactor; binds with NSF b. After being unwound, SNARE syntaxin becomes unfolded/denatured i. N-Sec1 refolds it properly and primes it for fusion, but also stays bound and inactivates formation of SNARE complex ii. N-Sec1 needs to be removed to activate syntaxin 1. Syntaxin w/ n-sec1 can create that same (but inactive) tetramer core complex on its own (2 SNAP25, 1 VAMP, 1 Syntaxin) 2. Ca removes N-Sec1 efficiently (ex. In neurotransmitters) c. SNARE cycle: VAMP on vesicle, syntaxin and SNAP25 on target membrane, helical binding and lipid fusion, NSF-mediated unwinding, refolding of syntaxin with Sec1

Answer 41

a. Enveloped viruses (ex. HIV, ebola, influenza viruses) also need to go through membrane fusion to infect cells b. Viruses have a fusion machinery similar to SNARE fusion i. Only 1 protein folded over on itself antiparallel ii. Still achieves efficiency and specificity (2 objectives of fusion) iii. (ex. Influenza virus) Achieved by help of special viral fusion protein 1. Protein contains a transmembrane domain at one end (inserted into viral membrane) and a highly hydrophobic fusion domain a. Normally fusion domain is folded/hidden within viral protein b. Upon signaling (influenza- pH change), the fusion domain is exposed and inserted in target cell membrane c. Fusion proteins immediately refold and causes viral and cellular membrane fusion

Answer 42

5. Regulation of viral fusion a. Signaling- like low pH i. Influenza is internalized via endocytosis, and is activated in lysosome with drop in pH b. Binding to CD4- activates HIV c. HIV also has a pocket domain that can be targeted via drugs d. Blocking fusion will block transmission

Answer 43

1. Electric forces are MUCH stronger than osmotic forces | a. so relatively few excess ions are needed to counter large conc differences

Answer 44

1. Electrochemical gradient a. Chemical gradient (conc difference) b. Electrical potential differences (membrane potential from cation/anion imbalance)

Answer 45

1. Equil pot relates the conc grad to the electrical force and is the electrical potential diff across the membrane that must exist if the ion is to be at equilibrium at the given conc a. Specific to ONE ion 2. If membrane and equil potentials are equal, the ion is at electrochemical equilibrium. Vm=Eion. If not: a. Membrane is impermeable to that ion or b. Ion is being pumped across the membrane

Answer 46

1. Membrane pot is a measure of the real difference in voltage between the internal environment of the cell and the ECF 2. Equilibrium pot is what the voltage diff would be IF a given ion was in equilibrium given a particular ICF/ECF ratio

Answer 47

1. Equilibrium pot can be calculated for each individual ion, while the cell will still have only 1 membrane potential a. Comparison of these 2 indicates whether or not a pump must exist for the ion and which direction it’s pumping

Answer 48

1. Look at conc in vs conc out- determine which way the ion would naturally move 2. Look at charge of ion vs membrane potential- determine which way it would naturally move 3. If these are the same direction- must be a pump moving ions across the gradients 4. If these are different directions- must compare the equilibrium pot to the membrane potential: a. If they are equal- there is no pump required b. If they are different- a pump exists i. Direction of pump: consider which way the ion movement would move to make Vm closer to E 1. Pump pushes ions in the opposite direction

Answer 49

1. Ex. In a typical cell w/ RMP of -80mV: for every 100,000 cations, there are approx. 100,001 anions a. This gives an indication of just how strong electric force is

Answer 50

1. Principle of Electrical Neutrality- [+]out= [-]out and in=in. a. Seems contradictory to membrane potentials arising from excess ions b. Electric force is so powerful that excess number of ions is very small compared to total # ions present in cell

Answer 51

1. The specific ions don’t have to be equal inside and out 2. Cell just must follow Donnan rule: products of ion conc inside must equal product of ion concs outside the cell a. Only relevant to counter ions (K+ and Cl-) 3. Nernst equation- at equilibrium when electric and chem gradients are in agreement?

Answer 52

1. Osmotic balance: mosM inside and out will be equal 2. Charge neutrality: can assume equal number of cations and anions inside the cell (and also outside) but not in=out 3. Nernst equation: E (mV)=-60/z * log(conc out/conc in) 4. If in a steady state with no pumps acting on a cell, Vm=E

Answer 53

1. Each cycle: 3 sodium ions are pumped out from ICF to ECF and 2 potassium ions are pumped into the cell ECF to ICF a. Pump action requires ATP

Answer 54

1. Real cells are often in steady state | a. conc’s aren’t changing, but a constant input of E is needed to maintain this (ATP needed to drive Na/K pump)

Answer 55

1. Dynamic environment 2. Depends on RATIO of permeabilities (number of channels) 3. Permeability changes to reach new steady states

Answer 56

1. a cell with more Na channels than K channels (for ex) will have a different membrane potential than vice versa 2. larger cells with more channels are more vulnerable, quicker, to Na/K pump failure than others

Answer 57

1. Driving force= at any instant, the difference between Vm and Eion

Answer 58

1. Membrane pot is already close to E of K+ 2. Loss of EC Na+ (bringing E of Na+ closer to 0) makes the Vm slightly hyperpolarized (closer to -80mV) but no other significant effect 3. Cell is much more permeable to K+ than Na+ 4. Sensitivity to K conc is higher because its starting conc outside the cell is much smaller than Na+, a. So it’s much more sensitive to small changes in conc

Answer 59

1. Keq= [products]/[reactants]

Answer 60

2. pH is a measure of the acidity or basicity of a soln a. pH=-log[H+] 3. pKa is a measure of the strength of an acid or base by its propensity to donate or accept protons a. pKa= -logKa b. Ka= [H+][A-]/[HA] c. lower pKa= large Ka = more dissociation= stronger acid

Answer 61

weak acid/base pH= pKa + log [A-]/[HA] shows extent of dissociation pH=pKa when something is 50% dissociated pH lower than pKa= protonated; pH greater than pKa= deprotoated

Answer 62

pH = 6.1 + log ([HCO3-] mM / 0.03 * Pco2 mmHg) normal= (24 mM/0.03 x 40 mmHg) normal pH= 7.4

Answer 63

1. Blood pH: Arterial: 7.34-7.44 venous: 7.28-7.42 a. More CO2= dissolved Co2 reacting w/ water to make carbonic acid (carbonate ions and H+s), so more acidic 2. [HCO3-]= 24mM 3. pCO2= 40 mmHg, or 40*0.03= 1.2mM 4. Ratio of HCO3- to CO2 is 20, gives pH of 7.4 in HH 5. Cytosol= slightly acidic; gastric juice- very acidic

Answer 64

1. Effective buffering occurs in the range from [A-]/[HA] = 0.1 to 10, or within one pH unit of either side of the pKa a. Max buffering capacity is around the pH equaling the pKa (pH changes the least when things added) b. Bicarbonate buffer sys is most important regulator of extracellular pH 2. Weak acids and bases interact in a given range to control pH (existing in protonated and deprotonated states) a. Many drugs, AAs, peptides, proteins, and nucleic acids b. Important weak acids= HCO3- and HPO4 2- c. Important weak bases= purines, pyrimidines, amphetamines, procainamide, nortiptylene, local anesthetics d. pH affects drugs’ effectiveness that have ionizable groups- how rapidly it can be taken up

Answer 65

3. alkalosis= body fluid pH above 7.45 | 4. acidosis= body fluid pH below 7.35

Answer 66

Not much breast development, missing periods Uncomfortable discussions with parents; kept it to themselves Different from peers; difficulties socializing

Answer 67

1. Inappropriate inflammatory response to intestinal microbes in a generally susceptible host 2. No diagnostic assay yet a. Idiopathic “inflammatory bowel disease” (IBD) b. Rarely bloody stool/diarrhea (hematochezia) c. Located in ileum d. Discontinuous pattern (skip lesions) e. Present in upper GI tract f. Extra-GI manifestations common g. Fistulas are common h. Transmural inflammation i. Caused by inappropriate inflammatory response to microbes in genetically susceptible host j. Genetic Factors i. nucleotide oligomerization domain 2 (NOD2) ii. interleukin-23–type 17 helper T-cell (Th17) pathway iii. autophagy genes

Answer 68

i. Changes in diet ii. Antibiotic use, iii. Altered intestinal colonization (e.g., the eradication of intestinal helminths) iv. Tobacco- smokers at increased risk for Crohn’s; former and nonsmokers at a greater risk for ulcerative colitis a. Cigarette smoking is a PROTECTIVE FACTOR for ulcerative colitis b. About 25% of IBD patients show extra-intestinal manifestations

Answer 69

``` HEMATOCHEZIA- rarely common Loc- ileum rectum pattern- discont. continuous upper GI tract- Yes no Extra-GI common in both FISTULAS- COMMON RARE Inflam. transmural mucosal ```

Answer 70

o Ill appearance, rapid breathing, nausea/vomiting/belly pain, dehydration o Hyperglycemia, Ketones in blood/urine, acidosis (low pH and HCO3-)

Answer 71

o High blood sugar (>200 mg/dL) o Acidosis (low pH and HCO3-) o Potassium may be high or low (typically normal to elevated blood levels early on, but with risk of falling potassium during treatment) o Dehydration

Answer 72

o Glucose enters the beta cells in the pancreas increased ATP/ADP ratio closes a channel to cause rising intracellular potassium increasing intracellular potassium depolarizes the membrane Calcium ions influx leads to insulin exocytosis

Answer 73

o Liver – store glucose (as glycogen) and lipid, stop lipid and glycogen breakdown o Muscle – store glucose, make protein o Adipose – store glucose and triglyceride (incorporated into chains of fats)

Answer 74

o Cerebral edema is the major cause of morbidity and mortality in DKA o May be present even before treatment starts, but some treatment factors can cause/exacerbate it:  Rapid drops in glucose and sodium from too much or too hypotonic IV fluid o Presents with mental status changes, headache, Cushing’s triad, fixed/dilated pupils. o Treatment is to raise the osmolality of the blood.

Answer 75

1. Primary active transporters= use ATP to do work a. Main ex. Na+/K+ pump; Ca2+ pump, and H+ pump on cell membranes b. Also some within organelles 2. Secondary active transporters= use Na+ leak into the cell to do work a. Much more prevalent b. Can reverse direction, depending on membrane potential

Answer 76

1. Cotransport- secondary active transporter that moves different solute species in the same direction 2. Antiport/exchange- secondary active transporter that moves solute in opposite direction

Answer 77

1. several clinical situations that suggest the presence of a sys that exchanges K+ for H+ and vice versa a. ex. Infusing K+ causes acidemia (the K+ is taken up by the cell in exchange for H+) b. ex. Infusing acid causes hyperkalemia (elevated K) in the blood 2. process actually involves several different transporters, perhaps working in pairs or in parallel a. ex. Hyperkalemia causes extra K+ uptake via the Na/K pump i. also depolarize cells (shift EK in positive direction) 1. change in membrane potential can affect the rate of activity of the electrogenic tranporters 2. ex. Tranporter moving three HCO3-‘s and 1 Na+ from ICF to ECF is inhibited by depo a. reduces bicarbonate extrusion, causing acidemia

Answer 78

1. Glucose gets phosphorylated inside cell, which makes it unable to fit into the glucose transporter a. So glucose is mostly unidirectional into the cell 2. Notice glucose transporters are normally sequestered within vesicles in the cell until insulin signals the cell to make those veisicles merge with the cell surface and transport glucose into the cell

Answer 79

Excess of potassium in blood (outside cells, in ECF). This changes the membrane potential of the cell because it alters the concentration gradient on which the electrical gradient of the membrane is based. Effectively, this raises the equilibrium potential of K+, which in turn makes the membrane potential rise substantially (by ~20 mV for a 2% calcium efflux). This is almost universally fatal. The reason it's so dangerous is that messing with membrane potentials is a good way to screw up action potential propagation, particularly in the pacemakers in the heart-- thus can't get heart contraction signals.

Answer 80

Caused by a variety of things: massively lysed cells, kidney failure, severe muscle damage. Treatment: Can stabilize cardiac conduction system by giving Ca2+ Can get cells to take up the K+ by giving insulin and glucose to stimulate Na-K pump. (Insulin gets glucose into the cell, where it activates the pump to work harder). If you give alka-seltzer and alkylyze blood, can stimulate proton pumps to get K+ into cells. Can use cation exchange resins: Effectively, Na+-lined "flypaper" for K+ in the blood, swapping out Na+ for K+. Can use renal dialysis to pherese excess K+ out of blood.

Answer 81

a. 4 membrane spanning domains, each of which contain 6 alpha helices (S1 through S6) i. In Kv channels each domain is a polypeptide ii. In Nav and Cav channels one polypeptide comprises the entire channel

Answer 82

tetramers in which each of the subunits contains a permeation pathway for water molecules i. These are “anti-ion” channels since they exclude all ions including protons ii. Aquaporins are expressed in cells/tissues where rapid movement of water is important, such as the kidney iii. In addition to the four water channels, the assemblage of the four subunits also produces a central pore which may allow ion permeation and be gated between open and closed.

Answer 83

a. Selectivity varies from highly selective (Kv channels) to little selectivity (nicotinic AChRs) b. Determinants: i. Charge: cation vs anion and ionic valence ii. Size: Molecules larger than pore size will be rejected

Answer 84

iii. Dehydration: Water stabilizes ions and gives them a larger effective size and also mask slight differences in ion size 1. Water must be removed, which is energetically unfavorable 2. Energy compensation by ionic interactions in pore iv. Multiple binding sites can increase selectivity

Answer 85

d. Nav have activation and inactivation gates, both on the intracellular side i. Activation gate functions similarly to Kv with positive potential opening the gate and causing an in-flow of sodium ii. Inactivation gate is open at the resting potential because the binding site is inside the channel, and therefore blocked by the activation gate 1. After activation, the inactivation gate closes, causing current to return to gradually return to zero 2. Gate is formed by cytoplasmic loop connecting repeats III and IV

Answer 86

a. S4 helices have positively charged residues (lys or arg) at every third position i. These structures “sense” voltage ii. Their translocation activates the channel iii. Movement of the activation gate is likely a hinge-like opening of S6 about a conserved glycine b. The S5 and S6 helices along with the P loop form the ion conducting pathway i. This pathway creates the selectivity c. Kv has an activation gate on the intracellular side, that rotates around a center pivot point i. The gate opens when the inside of the cell has a positive potential, allowing potassium ions to exit the cell (activation) ii. When the potential inside the cell is negative, the gate closes and current stops (deactivation)

Answer 87

a. Factors that contribute to sidedness: i. Selectivity filter near extracellular side ii. Vestibule nearer to the intracellular side iii. Activation/inactivation gates near intracellular side b. Drugs such as lidocaine and TTX can only access their target from specific sides and when gates are in a certain state

Answer 88

a. NaCl: Na+ picked up by the apical membrane (high permeability of apical membrane for Na+) and is transported into the cell, then is pumped out by the Na/K pump out the basolateral membrane. Cl- passively follows the Na+ to equalize the electrical potential. b. Water follows the influx of NaCl into cells to balance osmolarity. c. Notice all this is passive (no ATP usage) absorption.

Answer 89

a. Epithelium in GI tract: AA, sugars, and glucose are pumped (secondary active transport) through the apical membrane and diffuse out the basolateral side passively into the blood. i. AA and sugars are picked up by their target cells by secondary active transport mechanisms. ii. Glucose, as mentioned before, diffuses into cell along its gradient (but is phosphorylated in the cell to prevent efflux).

Answer 90

a. Tight: more junction proteins, tighter seal between cells. Used particularly in the distal tubules of the kidney. b. Loose: less junction proteins, looser seal between cells. c. Tight: "fine tuning"-- strictly controlled substance transport at lower levels, don't want backflux. d. Loose: quantity over quality (needs lots of transporters, not too picky about equal amounts).

Answer 91

a. Trans-epithelial membrane potential = basolateral membrane potential - apical membrane potential. i. Notice trans-epithelial is abbreviated PD. b. One thing to remember here is that the membrane potentials of the apical and the basolateral membrane will be different (different ion permeabilities, etc). c. The other thing to remember is that membrane potentials are always written in the form of describing the inside of the membrane with respect to the outside-- ie, in a membrane potential is -10 mV, the inside of the cell is 10 mV more negative than the outside.

Answer 92

a. There's a chloride-selective channel in the apical membrane in some epithelial cells, cAMP-gated on the inside of the cell to open and allow the efflux of Cl- back out of the apical membrane (which takes Na+ and water with it). b. This process is driven by receptors on the basolateral side of the epithelial membrane that are triggered by acetylcholine to open those gates. c. The reason the Cl- channels excrete Cl- instead of intaking it is that there's an non-electrogenic pump on the basolateral side that uses Na+ leakage to import Cl- into the cell. d. Effectively you're putting watery/serous substance out into the epithelial secretions (mucus, etc). i. This is the basis for cystic fibrosis: the chloride channel isn't properly implanted in the cell membrane, and thus no dilution of mucus secretions are possible. ii. This is also the basis for cholera: the cholera toxin gets into the cell and opens the Cl- channel without regulation- which leads to a massive efflux of water out the apical membrane into the epithelial system (diarrhea, etc).

Answer 93

(water, O2, CO2, and urea) a. You can open and close aquaporin channels to allow the water to come in or go out, but it always flows along its gradient

Answer 94

a. CO2, unsurprisingly, is excreted in the alveoli of the lungs. b. Urea is excreted in the urine after being picked up out of the blood in the kidneys.

Answer 95

a. GI tract excretes (in feces) largely things you couldn't absorb in the first place. GI tract absorbs pretty much everything it can that comes in to it indiscriminately (thus its small role in excreting waste). i. However, GI tract does excrete dead red blood cells (excreted into the GI tract from the liver), which is significant. b. Kidney concentrates waste very well in the urine- gets rid of approximately 0.5 moles of non-volatile (nongaseous) metabolic waste a day, mainly end-products of nitrogen metabolism (urea) and protons.

Answer 96

a. Get rid of non-volatile metabolic waste i. Mostly urea and protons ii. forms an ultrafiltrate of plasma in the glomerulus, which contains water, salts, sugars, amino acids, and all other beneficial compounds, as well as the non-volatile metabolic waste products iii. as this plasma ultrafiltrate passes along the renal tubules, the epithelial cells lining the tubules reabsorb (pump back into the blood) the things that it wants to keep (glucose, salts, bicarbonate, etc), allowing the wastes to pass on iv. Requires a large amount of ATP to drive reabsorption pumps v. Kidney also regulates ECF composition

Answer 97

a. Describes different treatments for hyperkalemia i. Calcium-relieve cardiac arrhythmias ii. Bicarbonate-encourages cells to take up potassium by increasing alkalinity, reducing plasma concentration iii. Insulin+Glucose-juices up energy supply of Na-K pump, thereby reducing plasma concentration iv. Kayexalate-ion exchanger with high affinity for K that removes it from the body

Answer 98

The take-home message will be simply that the ‘passive’ electrical properties of axons (that is, their properties without the special sodium channels) are pathetically, laughably inadequate to do the job. Without the sodium channels, electrical signals can’t spread more than a few millimeters from the site of the stimulus.

Answer 99

at rest, the activation gate is shut and the inactivation gate is open. When the membrane is depolarized, they reverse states: the activation gate opens and the inactivation gate closes. This is avoided because the activation gate swings faster than the inactivation gate, so that when the axon is first depolarized there is a brief instant when both gates are open and sodium can then rush into the cell.

Answer 100

Electrical forces can be large from few ions, unlike cellular concentrations.

Answer 101

Ultimately the Na+/K+ pump must be called upon to restore proper ances. While the Na/K pump is necessary over the long run, most axons can give long bursts of AP's without requiring pump activity. It's an elegant system: a large reserve of stored energy (the Na+ and K+ 'batteries') can be tapped rapidly and repeatedly, and restored leisurely at a later time.

Answer 102

After producing an action potential, an axon cannot generate another one for a few milliseconds. This is called the refractory period. It can be subdivided into an absolute refractory period, during which time no stimulus, no matter how strong, can evoke another AP, followed by a relative refractory period, during which time a stronger-than-normal stimulus is required to evoke another AP. The refractory period results primarily from the fact that the sodium channel inactivation (h) gates require time to reopen after repolarization. If a stimulus is applied when some h gates are still closed, the sodium channel activation (m) gates may swing open, but no Na+ can flow owing to the closed inactivation gates. Whenever any channel is blocked by a closed inactivation gate, we say that the channel is inactivated. The potassium channels also contribute to refractoriness. After the axon repolarizes, it takes time (several msec) for the K+ channel gates to close again. The higher K+ conductance makes it harder for a stimulus to depolarize the axon.

Answer 103

Accommodation concerns a nerve cell’s loss of excitability to a stimulus that is applied slowly, rather than quickly. If an axon is depolarized quickly, as occurs normally, an action potential is generated at the usual threshold voltage. However, if the depolarization is applied slowly, many neurons do not generate an action potential as effectively (some fail entirely); this is called accommodation of the action potential. Normally, physiological stimuli evoke fast membrane depolarization, so that sodium channel activation gates swing first, and the inactivation gates, being slower to respond to a change in membrane potential, do not snap shut until after the action potential rising phase has been generated. A slow depolarization, however, provides time for the inactivation gates to close first, so that, when activation gates do open, any channel in which the inactivation gate has already closed is useless; it cannot conduct sodium ions. Susceptibility to accommodation varies widely among different neurons. Some fail altogether to give an action potential when depolarized slowly, while others are barely affected Accommodation also manifests itself during hyperkalemia. That is, the steady membrane depolarization produced by elevated plasma potassium ion concentration closes some inactivation gates. Consequently, when a physiological stimulus arrives, producing a rapid depolarization, inactivated channels are incapable of contributing to the action potential. This is the mechanism that underlies the generation of cardiac arrhythmias.

Answer 104

AP threshold is the point at which the incoming current of Na+ equals the outgoing current of K+ (as Na+ comes in, K+ wants to come out more strongly). If the incoming current (Na+) gets just a little higher, the cell will enter the positive-feedback loop of depolarization. A more intuitive way of thinking about it is that the threshold is the point at which just a hair more depolarization will probably make the cell fire an AP and just a hair less depolarization will probably make the cell return to normal polarization levels.

Answer 105

If the inward Na+ current momentarily exceeds the outward K+ current, it will produce a little bit more depolarization, which will open more Na+ channels and the Na+ entry process will become 'explosive', producing an AP. Once threshold is exceeded, a miniature ‘explosion’ occurs. Remember, at threshold, not all sodium channels are conducting yet. But the sodium entering the channels that are conducting will depolarize the membrane further, and that depolarization will cause more sodium channels to start conducting, which will cause more sodium entry, which will cause more channels to open.... This is called ‘positive feedback.’ In a few tens of microseconds, the sodium channels are all open, and Vm is well on its way to ENa.

Answer 106

You simply could not rely on the passive electrical properties of the wire; you would have to construct booster stations at regular intervals along the wire. Each booster station would do two things. First, of course, it would provide an energy boost to the decaying signal. Second, it would have to know when to apply the boost; that is, it would need to detect the incoming signal. As we will see next, the action potential mechanism in axons is exactly analogous to the engineer's booster station; the energy source is the sodium ‘battery’, and the detector is a voltage- sensing gate in the sodium channel.

Answer 107

Because channels along the whole length of the axon need to open one after another, it is not a “bump your neighbor” type of situation.

Answer 108

The multiple layers of myelin membrane form an electrical insulator, reducing the 'leaky' cable properties of the nerve fiber. In other words, the effective resistance between the axoplasm and the ECF is increased by myelin. In addition, the membrane capacitance, Cm, is decreased by myelination. Now, however, Cm between the nodes is reduced by the myelin and Rm is increased, so that little current is lost between the nodes and the next node is depolarized to threshold very quickly. Because of this elegant specialization, the action potential "jumps" from node to node; this is called saltatory conduction (L. saltare, to jump). Myelination greatly increases conduction velocity.

Answer 109

An AP doesn’t reverse direction because, looking backwards (like riding in the last car on a train and looking back), all one sees is refractory axon – the sodium channels are incapable of firing an AP immediately after the active zone passes.

Answer 110

Ca2+ in the ECF normally remains bound to negative charges on the outer surface of the cell. As the outside of the membrane gets more negative in places, the potential difference across the membrane at those places decreases (ie, it depolarizes), thus triggering the m gates to create an AP without normal signaling.

Answer 111

thick membranes = low membrane capacitance = faster AP transmission. Fewer on channels = high membrane resistance = faster AP transmission. Larger-diameter axon = lower internal resistance = faster AP transmission. Myelination effectively decreases the capacitance of the axonal membrane (making a signal go faster, no waiting for the capacitance to build) and increases the membrane resistance (making a signal go farther, no leaking of ions out of the membrane).

Answer 112

Two causes: The causes are mostly due to K+ escaping from cells, combined with a kidney that can’t do its job of keeping [K+]o below about 5 mM. Mechanism of cardiac arrythmias: In brief, there is a master clock in the wall of the right atrium that triggers each beat. The clock comprises a clump of a few thousand cells (the sino-atrial (SA) node) that depolarize spontaneously (and synchronously). When they reach threshold, each fires one action potential. Axon-like processes fan out to all of the muscle fibers, and each AP carries news to the muscle fibers that it’s time to contract. In fact, a kind of backup system exists, because all cells in the cardiac conduction system depolarize spontaneouslcy. It’s just that the ones in the SA node depolarize fastest and so get to threshold first, setting the overall tempo of beats. But the backups make trouble during hyperkalemia.

Answer 113

1. MS symptoms: fatigue, walking impairment, spasticity, cognitive impairment, bladder dysfunction, pain, mood instability, sexual dysfunction 2. Walking impairment/ Gait: ataxic, spastic, paretic, foot drop; muscle weakness, loss of balance, sensory deficit 3. Disabling: significantly impairs quality of life

Answer 114

1. Neuronal damage 2. Slower conduction and smaller effective distance of action potentials 3. Proliferation of sodium channels along the axon

Answer 115

Sodium Channel blockers phenytoin and flecainide preserve axons in the animal model of MS. K+ channel blockade: Enhances conduction of action potentials in demyelinated axons through inhibition of K+ channels

Answer 116

a. Pore complex: network of large nuclear membrane-spanning structures that control entry to and exit from the nucleus. i. The nuclear membrane is double-layered; the pore complex penetrates both. 1. Inner layer: binding sites for chromatin and the nuclear lamina (structural supports consisting of intermediate filaments). 2. Outer layer: continuous with the ER membrane. a. Because this is the case, proteins that are translated into the ER membrane (through the translocon) are only one membrane layer (the inner nuclear membrane layer) away from the inside of the nucleus. 3. Note that the inner and outer nuclear membrane layers are continuous at the pores of the pore complex. ii. 4 structural building blocks of a pore: 1. Column subunits (pore wall) 2. Annular subunits ("spokes" extending in toward the pore's center) 3. Lumenal subunits (transmembrane, hold membrane open and anchor pore to membrane) 4. Ring subunits (cytosolic and nuclear faces of the complex; on the outer and inner surfaces of the nuclear membrane) iii. Very large structures: ~125 million daltons (30X larger than ribosome). iv. Roughly 3000-4000 pores per mammalian cell nucleus v. 9 nm diameter channel, but can expand to accommodate larger transports.

Answer 117

i. The binding receptors are part of the karyopherin family. They directly interact with the FG Nups or with the cargo itself. Are importins or transportins. Interacts with the nuclear pore complex. You need the receptor to recognize specific cargo molecules for their entry into the nucleus if it isn’t something that always should be transported inside. Helps regulate nuclear entry. Requires Ran binding.

Answer 118

i. There is an energy cost for establishing the gradient. ii. RanGTP is required for export and for separating the cargo from the receptor upon import 1. Perhaps high concentrations of RanGTP affect the volume of import/export

Answer 119

1. Molecules less than 5000 daltons can freely diffuse through the pore complex; everything else has to be gated in by a specific receptor protein. 2. Nucleoporin proteins (lots of hydrophobic repeats) line the central pore transporter channel to interact with import/export receptors. 6. Nuclear Localization Signals (NLS): sequences in proteins that allow those proteins to be picked up by a nuclear import/export receptor. Notice the sequence doesn't have to be contiguous.

Answer 120

a. Soluble, cytosolic proteins; bind to both NLS on transported protein and to nucleoporins in the pore channel. b. Exportins export; importins import. Two things: one, they need to be on the right side of the membrane to work, and two, this does take energy (GTP); selective placement of GTPases and GDP phosphorylases on different sides of the nuclear membrane allows a concentration gradient to occur, which helps the proteins to get back to the side that they work on.

Answer 121

3. Common imports: histones, DNA/RNA polymerases, gene regulatory proteins, and RNA-processing proteins 4. Common exports: tRNAs and processed mRNAs a. Export of mRNA: part of mRNA processing is to attach a whole bunch of proteins to it (among others, mRNA exporter proteins). Without all these proteins, it won't exit the nucleus. Note that a lot of the nuclear-exit-signal proteins fall off to be recycled as it leaves the nucleus. 5. Ribosomal proteins: imported into nucleus to be assembled with rRNAs, then exported.

Answer 122

1. NP fusions occur in cancer. a. Acute myeloid leukemia: 2 NPCs fuse and interact with hox proteins, which can turn on transcription and inappropriately activate some genes 2. Specific nucleoporins play lots of roles in other diseases a. Also involved in diseases of a ging 3. Post mitotic cells can become prone to oxidative damage and pores can become leaky 4. The wrong proteins can accumulate in the nucleus

Answer 123

1. Gated transport between the cytosol and the nucleus (nuclear transport) a. Requires specific receptor protein to carry a folded protein through the pore complex 2. Transmembrane transport across a membrane from the cytosol into an organelle through translocators (protein synthesis and mitochondrial import) a. Requires a translocator protein or protein complex (like translocon) 3. Vesicular transport in which membrane bound transport intermediates move protein and lipids from one compartment to another a. Requires adaptor and coat proteins

Answer 124

1. Synthesis of lipids- phospholipid, ceramide, cholesterol 2. Control of cholesterol homeostasis- cholesterol sensor and synthesis 3. Ca2+ storage (rapid uptake and release) 4. Synthesis of proteins on membrane bound ribosomes a. Co-translational folding of proteins and early post-translational modifications b. Post-translational insertion into the membrane 5. Quality control proper protein folding, protein degradation, and turnover

Answer 125

protein-conducting aqueous channel that spans the rough ER membrane

Answer 126

most proteins are “tagged” with a region (primary sequence or tertiary structure) that forms a “recognition patch”: this tells the cell how to package the protein and where to send it a. Notice that there's a specific 5' sequence that signals that the transcript is going to be pulled into the ER; if it's absent, the protein remains soluble in the cytosol. b. The 5' sequence that signals ER translocations causes the ribosome translating that protein to attach to the membrane of the ER (thus causing rough ER vs smooth ER).

Answer 127

: as mRNA is translated, it's moved through the translocon into the ER lumen to be cleaved by signal peptidases and folded. 4. The 5' signal sequence binds to the SRP (signal receptor particle) in the ER membrane; this opens the translocon and the nascent polypeptide is threaded through the translocon into the lumen as it's translated (the 5' signal sequence is cleaved off almost immediately so that it doesn't make up a part of the final protein). a. SRPs: have a multi-methionine "pocket" that binds to a wide variety of 5' signal sequences. b. 5' signal sequences: variable; often mainly nonpolar. 5. Notice that the translocon is regulated on the luminal surface as well by binding protein BiP: it can expel proteins as well as admit them. 6. If the nascent protein is meant to be a membrane protein, the protein contains another region (aside from the 5' signal sequence) that interacts with the translocon: a "stop-transfer sequence" which stops the transfer of the protein into the lumen-- thus the protein remains "stuck" with a transmembrane domain in the ER membrane, one end of the protein in the lumen, and the other end of the protein in the cytosol. The "stuck" protein then translocates out of the translocon for further packaging. 7. Notice that these transmembrane proteins can span (traverse) the membrane many times, depending on the number and location of start- and stop-transfer domains 9. As a protein is being transcribed by the ribosome, a signal sequence is translated that direct the protein to associate with the ER 10. The signal receptor particle binds to this area, stops translation of the protein until the srp binds to the srp receptor in the ER, then it can continue 11. Ribosome can get attached to the translocon, which opens 12. The protein is threaded through the translocon channel and ends up properly folded in the ER

Answer 128

1. Synthesis of complex sphingolipids from the ceramide backbone 2. Additional post-translational modifications of proteins and lipids a. Ex. Proteolytic processing 3. Sorting of proteins and lipids for post-golgi compartments 4. Proteolytic processing (protein cleavage) 5. Morphology: notice that the Golgi complex can be bigger or smaller (more or less cisternae) depending on how much packaging and modification needs to happen in that cell 6. How the Golgi apparatus transports protein/lipids through itself: a. Depends on the type of things transported. Sometimes it's by moving them from cisterna to cisterna with small vesicles; sometimes it's by actually moving or modifying the entire cisterna that contains the material ("cisternal progression"). b. Which one used depends on the nature of the material-- if it won't fit inside a vesicle, tend to use cisternal progression. 7. Notice that N-linked glycosylation is finished in the Golgi: this, again, is a signal to move the protein to a new location 8. "Proproteins": proteins that undergo proteolytic cleavage late in processing (Golgi). 9. One package sorting mechanism: by thickness of the package's membrane (thicker -> plasma membrane; thinner stays in the ER membrane, that sort of thing).

Answer 129

1. Clathrin, COPI, COPII a. Coats are assembled at sites of vesicle formation from soluble cytoplasmic components and sort the molecs (proteins and lipids) to be moved forward or backward b. Coat formation assists in physical deformation of the planar membrane 2. Clathrin coats: highly structured and symmetrical, transport from outside of the cell to inside (endocytosis) or lysosomal transport to/from the Golgi 3. COPI coats: traffic from Golgi to ER 4. COPII coats: traffic from ER to Golgi

Answer 130

a. Severe, rapidly fatal watery diarrhea b. Low-grade fevers and drowsiness c. Fatigue d. Decreased urination (renal failure) and dehydration e. Low K+, Ca2+, low HCO3- f. ileus g. Metabolic/lactic acidosis h. Hypoglycemia i. coma j. Skin tenting without lesions k. Tachycardia l. Muscle cramps, pain, spasms m. Abdominal pain n. Nausea, vomiting o. Hypovolemic shock p. asymptomatic

Answer 131

a. Oral rehydration therapy or IV rehydration b. Rehydrate, maintain hydration, feed early to make sure nutrition doesn’t get too poor c. Overall- replace fluids and electrolytes until the body can eliminate the foreign microorganism i. Can use antibiotics (azithromycin) to quicken this

Answer 132

1. Recall: bacteria isn’t the problem- it’s the toxin that the bacteria secrete 2. A subunit: active site 3. B subunit: transport/binding molecule; binds to the GM1 ganglioside receptor on enterocyte surface 4. A subunit cleaved off and endocytosed: a. Binds to the Gs proteins, inactivating their GTPase activity (so always turned on)- stimulates cAMP production b. cAMP activates CFTR (CF transport regulator) chloride channel in apical membrane i. notice that the Na-K pump on the basolateral side may also be shut down c. perpetual CFTR activation leads to massive chloride efflux d. the efflux of chloride draws water with it, causing diarrhea e. since the tight junctions in apical enteric cells are relatively loose, you can lose a whole lot of water and sodium very quickly paracellularly as they follow the chloride

Answer 133

1. Effectively ORS is just water, sugar, and salt (plus potassium and citrate in WHO formula) a. Homemade= 8 teaspoons sugar, 1 tsp salt in 1 L water 2. Small amounts can be reabsorbed quickly; small sips can rehydrate patients even when emesis follows 3. Glucose helps Na+ uptake (and therefore water retention) in enteric system, also provides nutrition a. Notice can replace glucose w/ rice powder, which may reduce severity of diarrhea by adding amino acids to improve sodium uptake in enterocytes (counteract Cl- and water efflux)

Answer 134

Diarrhea- non-inflammatory (watery) (small bowel) and inflammatory (colon)

Answer 135

1. VIBRIO CHOLERAE- Gram-negative motile rod (flagellin) 2. From brackish water (estuaries: river-ocean) 3. Only infects humans 4. Acute, massive watery diarrhea; lose whole body fluid in 1 day >20L 5. Explosive epidemics 6. Pandemics 7. Pathogenesis of cholera diarrhea: a. Inoculum molec to get past the acid b. Cholera is resistant to pH c. To help swim- flagella d. TCP- toxin-coregulated pilus e. Diarrhea itself- CT cholera toxin

Answer 136

1. Greater than 200 serogroups (different O-specific polysaccharides cause different strains)- inflammation 2. Also necessary to function: a. Pili- supports colonization (binding) b. Toxin – secretory diarrhea; made of 1 A (active) and 5 B (binding) subunit toxins

Answer 137

1. Having the CFTR mutation- heterozygotes have less intense form of cholera (homozygous mutants have cystic fibrosis) 2. Cholera toxin works via Cl- channel; less fluid loss via abnormal channels or no channels 3. Heterozygote advantage

Answer 138

1. Oral Cholera Whole cell rB subunit vaccine a. Killed: i. 60-80% protection x 6-60 months with45% protection in year 1 ii. Dukoral- Killed V. cholera 01 x2 + CtxB iii. Shanchol- Killed V. cholera 01 and 0139 b. Live attenuated: (safe; no CT; efficacy?) i. CVD 103-HgR ii. Peru 15 2. Mechanism of protection: a. V. cholerae 01 and 0139 have no cross protection i. CT is identical ii. OPS is different b. Antibody to CT increases after infection but is short-lived protection by WC is comparable to WC-rBS c. Thus, antibodies to OPS of LPS are the primary mechanism of protection i. Vibriocidal titers

Answer 139

3. Clathrin-coated vesicles: use SNARE proteins on vesicles to merge lipid surface of vesicles with plasma membrane a. Effectively there’s a string of lowered-pH steps in the cell to take endocytosed stuff to the lysosome to be degraded into its component parts. i. Drugs can either be active once degraded by the lysosome or be picked up by their targets somewhere in the process b. Coat forms, get pinched off by dynamin, and then gets uncoated to show the vesicle 4. Caveolae: cholesterol-rich vesicles budding from membrane- evidently having signal functions. a. Survace of the cell has lots of small invaginations called caveolae; they look like little caves i. 3 major coat proteins called caveolins (1,2,3) 1. These proteins form around the invaginations; help form the cave like structure of the membrane 2. Also associate with other proteins that dictate what can come inside; also pinched off by dynamin

Answer 140

a. Provide optimized oxidizing environment for folding and oligomeric assembly b. Folding enzymes c. Molecular chaperones- ATPases d. Folding sensors/quality control

Answer 141

1. Chaperone protein example: heat shock proteins (Hsp’s) 2. Hsp70 family: can bind to exposed hydrophobic domains to reform and prevent aggregation as its being made 3. Hsp60 family: form large barrels which envelope misfolded proteins to refold them without aggregation

Answer 142

a. Protein degradation misfolded proteins need to be trashed; proteins don’t live forever; organelles get damaged and turn over; both good and bad endocytosed materials need to be degraded b. Proteasome: degrade proteins; dispersed throughout the cytosol and nucleus. Also monitors the ER (proteins detected to be misfolded are retrotranslocated back into the cytosol for degradation). It is a big protein- proteases live in the central cylinder. Powered by atp c. When you ubiquitinate a protein, it is destined to be destroyed by a proteasome. Put ubiquitin on, activate it i. Can also be used as regulatory signals (ubiquitination of histones and transcription factors can regulate transcription)

Answer 143

1. Degrades all cellular components in an acidic environment (pH 5- due to proton pump) 2. Targeted via the endocytic pathway 3. Mono-ubiquitinated transmembrane proteins are targeted for endocytosis and are transferred via the late endosome/multivesicular body to the lysosome for degradation 4. Regulated at the Multivesicular Body- prelysosomal compartment; vesicles containing proteins slated for destruction bud into the lumen; when the multivesicular body fuses w/ the lysosome, these vesicles are delivered into the lysosome for degradation. Lysosomal membrane proteins (proton pump and transporters) need to be protected from degradation. They reach the lysosome by vesicles that bud from the Golgi and fuse with the lysosome. Defects in enzymes or membrane proteins can cause lysosomal storage diseases (Gaucher disease). Central and peripheral Nervous Systems are especially susceptible to lysosomal storage diseases

Answer 144

a. Macroautophagy: best studied i. Formation of double-membraned vesicle (autophagosome) that fuses with a lysosome to deliver organelles, proteins, etc. where hydrolases degrade contents of autophagosome. b. Chaperon-mediated autophagy; recognition of specific proteins that contain a specific recognition sequence (based on AA sequence KFERQ). Direct binding and delivery to lysosome

Answer 145

Activate a P13K complex that allowx nucleation of a membrane that will eventually form autophagosome. Regulation of protein conjugation events to extend membrane. Randomly capture, or specifically deliver cargo to the extending autophagosome, then join the membranes to close the vesicle. Fuse with lysosome. Recycle AAs and other macromolecular precursors

Answer 146

a. Aggregate-prone proteins (those with expanded stretches of glutamine residues in diseases like Huntington’s disease) will cause neuronal cell death. Autophagy degrades the aggregate-prone proteins (perhaps after they have started to form small aggregates). No toxic stimulus, no neuronal cell death

Answer 147

a. Many proteins (Bcl-2) that regulate apoptosis/cell death, also control autophagy- remember this could create problems in interpreting results of therapeutic interventions designed to target these proteins. Apoptotic proteases (caspases) can cleave essential autophagy regulators inactivating them and therefore blocking the process of autophagy. In some cases (when starvation-induced cell death) it is easy to see why autophagy would protect; it provides essential nutrients at least in the short term; in others (stress-induced cell death from chemotherapy) it’s less clear why autophagy would be less protective

Answer 148

a. Plasma membrane i. Vigorous, boiling action (zeiosis) ii. Cell tears itself apart, leading to apoptotic bodies 1. Some contain chromatin iii. Normally phosphatidyserine is confined to only the interior leaflet of the plasma memberane 1. After apoptosis begins, approximately half of the PS is on the outer leaflet a. Via scramblase b. Antigenic and detected by receptors on phagocytic cells c. Macrophage engulfs apoptotic cell i. Not activated and therefore not inflammatory ii. Anti-inflammatory by releasing the cytokine TGFβ iii. Physiologically silent

Answer 149

i. Cells lose about a third of their volume in a few seconds 1. In culture, make cells appear to have pulled away from neighbors ii. Cytoskeletal changes accompany shrinkage

Answer 150

i. Nucleus collapses ii. Chromatin becomes supercondensed 1. Appears as crescents around nuclear membrane 2. Eventually becomes spherical featureless beads iii. Correlates to fragmentation of DNA into a length of one or several nucleosomes iv. Degradation by endonuclease in poorly protected region between histones 1. Leads to approximately 300,000 breaks/chromosome

Answer 151

i. Occurs in tissue with severe and sudden trauma 1. E.g. ischemia ii. First, mitochondria begin to swell 1. At the point of “high-amplitude swelling”, the mitochondria can no longer maintain ion gradients and therefore cannot produce ATP through oxidative phosphorylation iii. Lack of ATP causes plasma membrane ion pumps to fail, leading to an influx of water and the cell bursting iv. Intracellular contents of cell comes into contact with the extracellular area, leading to inflammation v. Attracts white blood cells 1. Leads to debris removal, injury resolution, and sometimes scarring vi. More pathogenic than apoptosis vii. Inflammatory

Answer 152

i. Cell is still viable early in apoptosis ii. Ideally, apoptotic cells are taken up by healthy cells before releasing proinflammatory contents into body iii. Seen in cells where death is normal and predictable iv. Death due to relatively minor injury v. More physiological than necrosis vi. Anti-inflammatory

Answer 153

a. Most i. Morphogenetic death 1. In limbs, cells between digits to yield fingers and toes ii. Nervous system 1. Overproduction of cells 2. The cells that make the correct connections are preserved iii. Immune system 1. 95-99% of lymphocytes undergo apoptosis in thymus 2. Are not selected to become mature T-cells b. Least

Answer 154

i. Perturbation of mitochondrial outer membrane function, spontaneously, through withdrawal of growth factors, or some other signal 1. Normally membrane is guarded by anti-apoptotic factors a. Bcl-2 and Bcl-XL 2. In apoptosis, those factors are replaced by pro-apoptotic factors a. Bim and PUMA 3. Lets proteins like Bax and to act on membrane and make it permeable, thereby releasing cytochrome C 4. Cytochrome C activates Apaf-1, which activates Caspase 9 (signal), which activates Caspase 3 (executioner)

Answer 155

i. Cytotoxic T cells (CTLs) provide surveillance of the surface of body cells, thereby detecting infected or mutated cells ii. A CTL upregulates expression of surface molecule called Fas (CD95) ligand iii. FasL engages and cross links a corresponding molecule (Fas or CD45) on abnormal cell’s surface iv. CD95 transduces a signal to the cell interior, which recruits an adapter molecule FADD to CD95, which activates caspase 8 v. Caspase 8 activates caspase 3 vi. Mutations in Fas or FasL causes autoimmune lymphoproliferative syndrome (ALPS), where cells fail to die vii. A protein called FLIP is proteolytically inactive and elated to caspase-8, which competitively inhibits its binding to FADD 1. Notice viruses such as the herpes viruses (e.g. HHV-8/Kaposi’s sarcoma) have viral FLIPs to avoid apoptosis 2. E. coli can glycosylates FADD to prevent apoptosis viii. CTLs also can secrete enzymes (granzymes) and pore making protein (perforin) that deliver apoptosis-inducing molecules

Answer 156

a. Mutations normally do not progress and di via apoptosis | b. Cancer can result with too much growth and normal apoptosis or normal growth and too little apoptosis

Answer 157

a. Set of intracellular structures that orders the inside of a cell as well as organizing it in the extracellular environment. b. Specifically: provides cell shape, mechanical strength, locomotive structures, plasma membrane support, spatial organization of organelles, and intracellular transport "roads".

Answer 158

all cytoskeletal elets: polyprotein structures c. Microtubules: hollow tubular structure, very flexible, don't stretch. Primarily provide the scaffold for spatial organization and movement of organelles, and also the movements of cilia and flagella. Outer diameter 25 nm. Often clustered near the nucleus (used during mitosis).

Answer 159

d. Intermediate filaments: ropelike structure (more details below), very strong, primarily provide mechanical strength to the cell. Distributed primarily throughout the plasma membrane.

Answer 160

a. Certain drugs interact with microtubule structure and, due to microtubules' role in mitosis, block cell division (thus are compounds of interest in cancer treatment). b. Colchicine and vinblastine (toxic plant extracts) interfere with tubulin polymerization at the plus end. c. Paclitaxel ("Taxol") binds to and stabilizes the microtubule. The net effect of this is to cause aggregations of microtubules, which shuts down effective function during mitosis.

Answer 161

a. "Motor proteins": dyneins and kinesins. Associated with microtubules; use them as tracks to drag cargo to target organelles. b. These proteins convert ATP into mechanical energy by conformational changes. i. Kinesins: 2 head domains and a tail. The heads contain ATPase: effectively the enzyme "walks" its heads down the microtubule and pulls the tail (and cargo) behind it. By hydrolyzing ATP, the enzyme shifts conformation to swing the trailing head group around to attach in front of the leading head group. 1. Notice that the kinesins only ever travel from minus to plus ends of the microtubules. 2. Notice also that the dyneins effectively travel the same way but only ever go from plus to minus ends of the microtubules. ii. Tail domains bind cargo.

Answer 162

Three types of microtubules in the mitotic spindle: astral microtubules radiating from centrosomes (place centrosomes in center of daughter cell, help pull two centrosome halves apart), kinetochore microtubules connecting chromosomes (plus ends bind to specific site of centromere in chromosomes), and overlap microtubules (plus ends bind to each other on opposites ends from each side of the dividing centrosome). i. Kinetochore action is driven by "minus-directing motors": the chromosomes are pulled in the minus direction (away from the middle), and the plus ends depolymerize between them as the centromere separates (thus no remnants left over). ii. Bare-bones: Astral and overlap microtubules pull centrosomes apart (plus-directed motors, kinesins); kinetochores separate chromosomes during this process (minus-directed motors, dyneins).

Answer 163

a. Epidermolysis bullosa simplex: Keratin mutation that affects intermediate filament stability. IFs can't provide mechanical strength: thus a very slight impact on the skin produces skin lesions and dermal bleeding. Effectively the epidermis is ripped away from the underlying subcutaneous tissue with extreme ease due to abnormal intermediate filament connectivity. b. Charcot-Marie-Tooth syndrome: Neurofilament mutation causes peripheral neuropathy. These mutations are also associated with Lou Gehrig's disease. c. Kartagener syndrome: wide variety of symptoms (respiratory disease, male infertility, left/right symmetry mismatch, etc) i. Turns out to be a monocilium (cilia/flagella) defect- sperm can't swim, lungs can't clear mucus, cilial direction that establishes left/right symmetry in early gastrulation is disturbed, etc. Problems in outer dyneins of monocilium. d. Dyneins (minus-end directed motors, can transport into centrosome) often shuttle viruses (which can attach to them) into the nucleus or along peripheral nerves into dorsal root ganglia.

Answer 164

The two key steps are nucleation and extension/retraction of the filament. In the presence of divalent cations and ATP, G-actin assembles to form two- stranded, helical filaments (F-actin). Most of these filaments contain additional actin-binding proteins. Some 60 accessory proteins - a huge number - participate in the regulation of polymerization and disassembly. These include proteins that bind G-actin, others that stabilize, 1crosslink, sever or cap F-actin, and proteins that enable F-actin branching to form MF networks. Nucleation concentration is much higher than monomeric concentration in the cell.

Answer 165

Actin plays a key role in polarization of epithelial cells. One of the most important functions of actin is anchoring proteins that are involved in Tight junction (TJ) and Adherens junction (AJ) formation. Decreased association of AJ proteins (cadherins and catenins) with actin leads to internalization of cadherins and loss of cell-cell adhesion, the step that is a prerequisite for epithelial-to-mesenchymal (EMT) transition and cancer formation. In addition, actin plays a key role in apical microvilli formation. An unusual type of actin anchoring is observed in brush border microvilli: A tight MF bundle forms the core of these microvilli. All actin plus-ends are anchored in the apical protein cap of the microvillus. Actin bundles are held together by the cross-linking proteins villin and fimbrin, and bundles are linked laterally to the plasma membrane by myosin-I. Loss of microvilli is observed in microvilli inclusion disease.

Answer 166

Like MTs, MFs support mechanical activity through the use of motor proteins. Actin-binding motor proteins belong to the myosin family. Myosins (heavy chain) are structurally related to the kinesins and, thus, consist of a head region, containing ATPase activity and actin binding sites, and a tail region. The ATPase is actin-activated and moves to the plus-end of the MF (see figure in Cytoskeleton I and Muscle). The tail region is involved in binding to other molecules. Myosin II, characteristic of striated muscle (see there), forms hetero-oligomers involving two heavy chains and two copies of each of two light chains. The coiled tails of myosin II bundle with the tails of other myosin molecules to form large bipolar assemblies (several hundred myosins), the "thick filaments" in muscle (see there). The ATP-driven walk of myosin heads along actin filaments results in the sliding-filament mechanism responsible for muscle contraction. Other non-conventional myosins, such as I and V, are associated with membranes and, thus, are involved in the F-actin-mediated movement of organelles. Myosin V forms dimers to transport cargo within the cell.

Answer 167

During locomotion, amoeboid cells go through repeated cycles of protrusion (of lamellipodia, filopodia), attachment (of these protrusions), traction (to pull the cell forward), and detachment (of adhesion toward the rear). In other words, tight coordination between actin cytoskeleton dynamics and cell adhesion is a prerequisite for migration

Answer 168

Lissencephaly: This describes a severe defect of brain development resulting in a smooth cortical surface, i.e., the absence gyri. Neuronal migration is a critical process for establishing the normal, complex cytoarchitecture of the brain. Loss-of-function of n-cofilin, an actin filament depolymerizing factor, results in lissencephaly and the associated severe mental retardation. Metastasis: Most of the terminal cancers are characterized by the spread of the tumors from the primary site, the process known as metastasis. The migration of cancer cells from the primary tumor to the blood stream and setting up secondary tumors at the other tissues is at the core of metastasis. Multiple drugs are being developed and used to either prevent or at least slow-down cell movement as a means of preventing spread of tumors.

Answer 169

Actin also plays a key role during last stages of cell division, known as cytokinesis. The formation and contraction of actomyosin ring drives the formation of the cleavage furrow and separation of the daughter cells. The site of actomyosin ring formation and the timing of its contraction are highly regulated events that determine the symmetry of cell division

Answer 170

Examples of asymmetric cell division: Red blood cells (no nucleus!). Generation of platelets. Spermatogonia.

Answer 171

respond to water-soluble signaling. Generally work by activating signal transduction inside the cell. 3 main types: i. Ion channel receptors: 1. Gated channels-- usually closed until ligand binds, at which point gates open and particular ions travel through. 2. Ion channel receptors largely regulate channels for Ca2+. a. Notice that one main type of Ca2+ channel takes up calcium into the endoplasmic reticulum (see "Signaling: Calcium" for details). ii. G-protein coupled receptors: 1. Cytosolic side binds to ligand; intracellular side binds to a G protein complex (heterotrimeric G proteins, which bind GTP; more on this under "Signaling: Receptors"). 2. This protein complex is normally bound to GDP at its alpha subunit; when the ligand binds, the alpha complex binds GTP instead of GDP and dissociates from beta and gamma subunits. a. Both the alpha and beta-gamma subunits can serve as signaling agents inside the cell. 3. Notice this allows a variety of responses (different trimeric proteins) to one ligand in a variety of tissues. iii. Receptor kinases: 1. Often growth factor and insulin receptors. 2. Cytosolic side binds to ligand; intracellular side has a kinase domain on it (tyrosine kinase)-- it will PO4 other proteins with particular tyrosine residues. a. Most receptor kinases act as dimers: once they're both bound to ligand, they will phosphorylate each other, turning on their signaling: once that PO4 is added, it creates a binding site for a set of adaptor proteins, which bind to the receptor kinase dimers and set off a signaling cascade. b. Lots of variety in receptor action here as well: can PO4 other proteins, can have a lot of different potential adaptor proteins to bind to the binding site, etc.

Answer 172

respond to lipid-soluble signaling. i. Generally work by activating transcription of specific genes. It does this largely by activating proteins which activate promoters upstream of transcription start sites. ii. These proteins are also referred to as transcription factors. iii. Steroids: bind to receptor proteins, inducing a conformational change which allows the receptor protein to release its inhibitor protein and bind its activator protein (entire complex: receptor-ligand-activating protein); this complex can interact with promoter regions to activate transcription.

Answer 173

a. Second messengers: small molecules released within the cell in response to the binding of the first ligand; can bind to other intracellular signaling molecules. i. Calcium: first ligand opens ion channel to admit Ca2+; calcium then binds a variety of other things inside the cell. ii. cAMP (cyclic adenosine monophosphate): generated by adenylate cyclase iii. IP3 (inositol triphosphate) iv. DAG (diacylglycerol): generated by phospholipase C (PLC) v. NO (nitric oxide): generated by nitric oxide synthase (NOS) vi. (notice that, for example, calcium can trigger the production of NOS, which triggers NO, which triggers.. etc, etc. Thus can have second messengers activating third messengers activating fourth messengers, and so on, though the third and fourth messengers can also act as second messengers. The cell has no idea that it's screwing up all the cool categories we invent for it. Again: develop a healthy distrust of simple signaling pathways.) b. Other signaling steps: i. Protein modification (PO4ation, ubiquitinylation, etc) ii. Protein-protein binding/targeting iii. GTP/GDP exchange (G-proteins coupled to receptors, small GTPases like ras) 1. Note that GTP does not seem to act as a second messenger: I think it's the fact that GTP changes the configuration of proteins which then act on other proteins that makes the difference. That is, GTP itself is acting as more of a helper than an agent in the signaling. 2. G-proteins: see "Signaling: Receptors." 3. Ras proteins: see "Receptor Tyrosine Kinases."

Answer 174

a. Uptake, breakdown, or diffusion of original signaling molecules b. Desensitization of receptor c. Termination initiated by another signal (phosphorylation, dephosphorylation, etc) d. Termination-dedicated enzymes: ie phosphodiesterases (PDEs) which break down the second messengers cAMP/cGMP. e. Some kind of feedback inhibition: ie, the bound ligand or receptor acts in such a way as to undermine its ability to stay bound or stay active (G-proteins gradually lose their GTP-bound active state).

Answer 175

a. Amplification depends on signaling cascades: one signaling molecule can create a large number of signals, which in turn can create an ever larger number of second signals, etc. b. Positive feedback mechanism (ie. calcium-induced calcium release): very quick but very dangerous signaling pathway (can get out of control rapidly). Usually coupled with a negative feedback mechanism past a certain threshold to keep it under control.

Answer 176

a. Nodes: points in a network that receive multiple inputs and/or multiple outputs. Calcium is evidently the most extensive node in signaling. b. Modules: groups of components that function together, often physically assembled to form complexes. Ie: G-protein heterotrimeric complex would presumably form a signaling module, as would negative feedback mechanisms.

Answer 177

ligand binding drives dimerization, which activates the activity of the kinase resulting in Tyrosine autophosphorylation at specific sites

Answer 178

tyrosine phosphorylation of receptor causes binding by SH2-domain-containing proteins incl the adaptor protein Grb2, which binds a Ras GEF called Sos. Proximity of Sos with membrane-bound Ras results in guanine nucleotide exchange

Answer 179

primary role of antibodies is to block ligand binding to the receptor. TKIs inhibit catalytic activity (usually) by binding in substrate-binding site of the kinase

Answer 180

response to EGFR TKI correlated with receptor mutations that may "activate" the receptor, EGFR amplification, or overexpression as determined by FISH or immunohistochemistry

Answer 181

acquired resistance- second site mutations in EGFR arising or selected in patients who initially benefit from therapy but then acquire resistance and disease progression. these mutations block inhibitior binding to the kinase active site. may be able to design new inhibitors to avoid this problem. activation of other receptors like Met or Erb82. Combine inhibitors or make dual specificty inhibitors? primary resistance- if the tumor has a Ras mutation inhibiting the receptor further up the pathway will not be effective

Answer 182

Basically you've got a 7-unit barrel-shaped receptor protein with a ligand binding domain on the outside of the membrane, then a heterotrimeric G protein complex binding domain on the inside of the membrane, bound to the heterotrimer plus GDP. The G protein complex is made up of three subunits, alpha, beta, and gamma. The beta-gamma subunits are pretty much always stuck together, and in their GDP-bound state they're also stuck to the alpha subunit. Agonist binds in middle pocket

Answer 183

When a ligand binds, GDP dissociates from the Alpha-Beta-GTP complex, which allows GTP to bind to form the active form of the G protein. This step is unfavorable without an agonist, which is why the inactive form is prevalent. When this occurs, the alpha and beta subunit which were previously closely associated, are able to float away to create an effect in the cell. Alpha subunit is a GTPase which will eventually hydrolyze GTP to GDP and return the complex to its original inactive state. The cycle can repeat if agonist remains

Answer 184

PLC is cleaved to make IP3 and DAG. IP3 exerts effects by binding its receptor in the ER, which releases calcium. DAG binds with PKC to stimulate Ca influx into the cell. cAMP is also produced by active alpha and the AC complex. It activates protein kinase A, which eventually leads to an influx of calcium, which leads to increased heart rate and contraction

Answer 185

At the same time that you activate the signaling pathway, another pathway is activated that favors desensitisation of the receptor. Beta activated GRK kinase which phosphorylates the receptor, which attracts Beta arrestin (which prevents association of another g protein), and it interacts with clathrin and causes the receptor to be endocytosed. Internalized receptors can be re-sensitized and recycled, or they can be taken to the lysosome to be chopped up by acid.

Answer 186

• Beta blockers: Prevent activation of a pathway (antagonists) and decreases heart rate. Phosphodiesterase: degrades cAMP and turns it into AMP, which does not activate PKA

Answer 187

e. Phosphate is added to the hydroxyl group of Serine, threonine, and tyrosine. The OH group nucleophilically attacks the gamma phosphate from an ATP molecule. Phosphorylation regulates the activity of a given protein. Phosphorylation is a nucleophilic attack of the hydroxyl group of the AA to the gamma-P of ATP

Answer 188

a. Adenine (double loop), ribose, triphosphate. b. Bonds between phosphates are high-energy- alpha, beta, and gamma phosphates via phosphoanhydride bonds c. Contains E rich bonds; it is an energy equivalent, phosphate donor, nucleotide, conversion to second messenger (cAMP), neuromodulator

Answer 189

a. Based on which residue they phosphorylate (Ser-Thr-Asp) b. Based on their substrate protein c. Based on their activating stimulus d. Based on their phylogenic relationship (certain families of related kinases)

Answer 190

A kinase domain consists of a small and large lobe (green and blue, respectively, regions of PKA that are not conserved among kinases are shown in white). ATP binds in the cleft between the lobes; interaction of the substrate is usually mostly with the large lobe. A “closed conformation” of the glycine rich loop in the small lobe forces the γ-Phosphate of the ATP into the right position for phosphorylation (a fast reaction). An “open conformation” of the glycine rich loop then allow exchange of the generated ADP for a new ATP (a slow reaction). Thus, kinase activity is thought to require alternating open and closed conformations. The active conformation of all kinases is highly conserved. This presents a problem for making specific inhibitors for individual kinases. However, the inactive conformations are not, since there are many ways to distort conformation to prevent activity (an opportunity for specific inhibitors, now also realized by the pharmaceu tical industry). Generally, the ATP binding pocket is somehow distorted in inactive conformations (glycine rich loop; C-helix; activation loop). In many but not all kinases, the activation loop has to be phosphorylated for full activity. Another common regulatory theme is block of the active site by an inhibitory “pseudo-substrate” sequence.

M2M Unit 3 Flashcards

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