Weeks 1-4

Question 1

What are the three phases of polymerization for cytoskeleton?

What is dynamic instability?

How do kinesin and dynein play a role?

Name a disease associated with cytoskeleton.

Answer 1

• 3 phases of polymerization
  
  • Nucleation: assembly of monomers
  • Elongation: rapid growth at (+) end
  • Steady-state: equal rate of polymerization and de-polymerization
• Dynamic instability: rapid de-polymerization to cause separation of mitotic spindle.
• Polymerization and de-polymerization occurs at (+) end and nucleation occurs at (-) end
  
  • Kinesin moves things to (+) end {cell surface is +}
  • Dynesin walks things back to (-) end {centrosome is -}
• Disease: Hereditary Spherocytosis

Question 2

Where do clathrin coats, COP I coats, and COP II coats transport to and from?

Answer 2

Clathrin

• Transport: PM to early endosomes and Golgi to lysosomes

COP I

• Transport: Golgi to PM and Golgi to ER

COP II:

• Transport: From ER to Golgi

Question 3

What is the assembly process of clathrin coats?

Answer 3

• Arf-GEF recruits Arf-ADP → Arf-ATP → inserts into membrane → fatty acid tail exposure → clathrin recruitment → dynamin pinches off vesicle using accessory proteins and PIP2
• Phorsphorylation of PIPs to PIP2s are also involved in recruitment

Question 4

What is the disassembly process of clathrin coats?

Answer 4

• Heat shock protein (Hsp70) is an ATPase stimulated by Auxilin → ATP hydrolyzes into ADP → Hsp70 uses energy from ATP hydrolysis to peel off coat
• PIP2s are dephosphorylated to PIPs weakening coat-membrane interactions

Question 5

What is the COP I assembly process?

Answer 5

• Arf-GEF recruits Arf-ADP → Arf-ATP → inserts into membrane → fatty acid tail exposure → COPI recruitment → dynamin pinches off vesicle using accessory proteins and PIP2
• Phorsphorylation of PIPs to PIP2s are also involved in recruitment

Question 6

What is the COP I disassembly process?

Answer 6

• Heat shock protein (Hsp70) is an ATPase stimulated by Auxilin → ATP hydrolyzes into ADP → Hsp70 uses energy from ATP hydrolysis to peel off coat
• PIP2s are dephosphorylated to PIPs weakening coat-membrane interactions

Question 7

What is the COP II assembly process?

Answer 7

• Sar1-GEF recruits Sar1-GDP → Sar1-GTP → inserts into membrane → fatty acid tail exposure → COPII recruitment → dynamin pinches off vesicle using accessory proteins and PIP2

Question 8

What is the COP II dissassebly process?

Answer 8

• Heat shock protein (Hsp70) is an ATPase stimulated by Auxilin →ATP hydrolyzes into ADP →Hsp70 uses energy from ATP hydrolysis to peel off coat
• PIP2s are dephosphorylated to PIPs weakening coat-membrane interactions

Question 9

What is the function, structure of SNARE proteins, and the fusion process?

Answer 9

• Function: acts as tethers to bring membranes together for fusion; this is a Ca++ dependent process
• Structure
  
  • V-SNARE (transport vesicle made up of one polypeptide chain)
  • T-SNARE (target membrane made up of three polypeptide chains)
• Fusion Process
  
  • T-SNARE traps V-SNARE
  • Energy from four helix bundle drives membrane fusion

Question 10

What is the disassembly process of SNAREs?

Answer 10

• NSF (i.e. NEM sensitive factor) and accessory proteins react with two cysteine residue to block activity
  
  • Hydrolyzes ATP to destabilize four-helix bundle

Question 11

What is the process of RAB GTPases?

Answer 11

• Rab-GEF (could be a SNARE or tether) recruits Rab-GDP on donor membrane → Rab-GTP → Rab-GTP inserts into donor membrane → transport vesicle/budding forms/occurs → Rab effector binds Rab-GTP → fusion → Rab-GDP

Question 12

What is the transport mechanism for lysosomal hydrolase?

Answer 12

• Acid hydrolases are only active at low pH
  
  • Vacuole ATPase pumps H+ against gradient into lysosome
• M6P is used to tag lysosomal hydrolase precursors from ER in the Golgi
• M6P binds to M6P receptor in Golgi → early endosome → lysosome through Clathrin
• Addition of GlcNAc-P to M6P in the early endosome to release hydrolase precursor
• M6P receptor is recycled back to Golgi

Question 13

What are the properties of amino acids and what are the amino acids under each property?

Answer 13

Non-Polar AAs

• GAVLIMP WF – “GAVin LIMPed with Warm Fingers”
  
  • Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Tryptophan, Phenylalanine

Polar

• STCYNQ – “SomeTimes Cats Yell Not Quietly”
  
  • Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

Charged

• DEKRH – “Dumb Evil Kings Rule Hell”
  
  • Aspartate, Glutamate, Lysine, Arginine, Histidine

Question 14

What effect do increases and decreases in pH, DPG, and temperature have on oxygen binding curves?

Answer 14

Question 15

What is a competitive inhibitor and how does the lineweaver-burk plot look like?

Answer 15

• Competitive
  
  • Competes with substrate at active site to bind enzyme
  • Inhibitors have structures similar to the substrate or product

Question 16

What is non-competitive inhibition and what is the lineweaver burk plot for it?

Answer 16

• Inhibitors bind to free E and ES at same affinity
• Can also be called a “mixed” inhibitor as it is both a competitive and non-competitive inhibitor

Question 17

What is uncompetitive inhibition and what is the lineweaver burk plot for it?

Answer 17

• Uncompetitive
  
  • Inhibitors bind only to the ES complex and block product formation
  • Increase substrate affinity

Question 22

Describe how amyloid fibrils form in protein folding diseases. What are the two types that were discussed?

Answer 22

• The amyloid itself is toxic where ever it accumulates.
• In AL, the many different light chains of an AB are misfolded and aggregate together to form amyloid fibrils.
• Familial transthyretin amyloidosis is caused by misfolded transthyretin monomers that denature and aggregate into amyloid.
• Mechanistically, the growth of the amyloid fibril can break cell membranes and kill cells due to its rigid “cross-bridge structure”.

Question 23

What is the preganglionic receptor and its transmitter in the sympathetic nervous system?

What are the agonists and antagonists?

Answer 23

• Nicotinic (ACh) [N_N]
• Agonist: nicotine
• Antagonist: curare

Question 24

What is the agonist and antagonist to muscarinic receptors?

Answer 24

• Agonist: muscarine
• Antagonist: atropine

Question 25

What are the agonists and antagonists to adernergic receptors?

Answer 25

• Agonists: NE, EPI
• Antagonists: Proponolol (B1/B2 nonspecific blocker)

Question 26

What are the 3 types of Phase I biotransformation reactions and what do they do?

Answer 26

• Oxidation: CYP P450 are important oxidative enzymes occurring in the ER of liver cells; susceptible to induction and inhibition
  
  • RH (active drug) + O2 + NADPH + H+ → ROH (polar drug metabolite) + H2O + NADP+
• Reduction: favors certain chemical groups (ex: nitro group); carried out by CYP enzymes
• Hydrolysis: uses water to break the parent drug into smaller pieces; carried out by CYP enzymes (ex: esterases)

Question 27

What are the two main types of Phase II reactions and how do they work? What are the other four kinds of reactions possible?

Answer 27

• Glucuronidation: many side-groups (i.e. hydroxyl group) can be glucuronidated by UDPGA (uridine diphosphate glucuronic acid) to become more polar
• Glutathione Conjugation: glutathione readies drugs for excretion by binding to an intermediate (when glutathione is used up, necrosis of liver occurs)
• Sulfation
• Acetylation
• Methylation
• Glycine conjugation

Question 28

What are the factors (6) that impact hepatic clearance and the significance of those factors on drug elimination.

Answer 28

• First pass effect: only fraction of drug reaches bloodstream after oral intake (bioavailability)
• Hepatic blood flow: increased blood flow increases clearance
• Free drug: binding of drug to plasma proteins (ex: albumin) → less free drug to be excreted
• Enzyme inhibitors/inducers: P450 inducers can increase excretion
• Enterohepatic Recirculation: estrogen is often glucuronidated in liver → bile duct → sugar is cleaved by gut bacteria in GI → estrogen is re-circulated in body
• Extraction Ratio: value close to 1 suggests efficient clearance by an organ; value close to 0 suggests inefficient clearance
  
  • E = (Ca – Cv) / Ca

Question 29

What is * glomerular filtration * tubular secretion * tubular reabsorption and how do they impact renal elimination of drugs?

Answer 29

* Glomerular filtration: free drug passively diffused into renal tube * Limited by size * Creatinine is used as measure of renal function (not reabsorbed or secreted) * Tubular reabsorption: lipid-soluble drugs renter bloodstream (can be passive/active) * Acidifying urine (aka: vitamin C) causes acidic drugs to be reabsorbed and vice-versa for basic drugs * Tubular secretion: active transport (or secretion) from blood to tubules after glomerulus with saturation kinetics * Para-aminohippuric acid (PAH) is used as measure since it is completely filtered and secreted

Question 30

What is the difference in Area Under the Curve (AUC) between PO and IV in the context of bioavailability.

Answer 30

PO has less AUC compared to IV because IV is injected directly into blood, therefore having less bioavailability

Question 31

Apply pharmacokinetic principles to make predictions about: * how dose affects duration of action * how changes to clearance * or volume of distribution affect half-life, etc.

Answer 31

* Lower dose → lower drug concentration → low duration of action * Increasing Vd → increases half-life because greater [drug] in body requires elimination (50% of present drug is eliminated each half-life) * Increasing Clearance → lowers half-life because less [drug] in body requiring elimination (50% of present drug is eliminated each half-life)

Question 32

Apply knowledge from ADME lectures to describe elements that can alter a drug’s pharmacokinetic properties. ADME: Absorption, Distribution, Metabolism, Elimination

Answer 32

* Absorption * Increased absorption → increased Vd → increased half-life * Distribution * Increased tagging → increased reservoirs → decreased [drug plasma] → increased Vd → increased half-life * Metabolism (biotransformation) * Increased hepatic blood flow → increased biotransformation → Increased polarity → increased plasma solubility → increased elimination * Elimination (clearance) * Increased renal blood flow → increased secretion → increased elimination

Question 33

Define/describe potency.

Answer 33

* A comparative term to compare drugs that work through the same mechanism (same maximal effect, shape of curve, and slope) * A more potent drug has lower KD

Question 34

Define/describe tachyphylaxis.

Answer 34

Unexpected physiological response due to desensitization (in presence of agonists).

Question 35

Describe pharmacodynamic changes that occur with aging.

Answer 35

* Changes in * [Drug at receptor] * Receptor numbers * Receptor affinity * Post-receptor alterations * Increased “sensitivity” to drugs (especially anti-cholinergics and CNS drugs)

Question 36

What are the different lines/bands of the sarcomere?

Answer 36

* Z-line – anchor of actin * Separate sarcomeres in series * A-band – length of myosin and includes overlap of actin * Does not change length * I-band – actin only * Shrinks during contraction * H-band – area where myosin filaments are not overlapped with actin filaments * Shrinks during contraction * M-line – anchor of myosin

Question 37

Define the steps in excitation-contraction coupling in skeletal muscle.

Answer 37

1. Action Potential Travels into T-tubules 2. L-Type Ca++ Channels Open 3. Direct Coupling Between L-Type Channel and RyR causes Ca++ release from SR 4. Ca++ stimulates contraction – most of the Ca++ that actually stimulates contraction is from the SR (as opposed to the Ca++ coming in through the L-Type Ca++ channels)

Question 38

How is calcium-induced calcium release different than mechanical-induced calcium release?

Answer 38

* Calcium Induced Calcium Release – in cardiac myocytes, RyRs are **ligand-gated**, requiring calcium to bind in order to release calcium * Mechanical Induced Calcium Release – in skeletal muscle, RyRs are **voltage-gated**, sensing conformational change in L-type calcium channel due to depolarization, releasing calcium

Question 39

What are the steps in the myosin ATPase cycle?

Answer 39

ATP binds → myosin head detaches from actin → ATP hydrolyzes on myosin head into ADP + Pi → myosin head goes back to cocked position (“recovery stroke”) → myosin cross-bridges with actin → phosphate group is released → power stroke (“working stroke”) causes filaments to slide past each other → ADP released (rate-limiting step) → ATP binds

Question 40

How are intracellular calcium levels maintained by the SERCA pump and plasma membrane pumps?

Answer 40

SERCA pump uses ATP hydrolysis on SR and NCX/NKX (sodium-calcium/sodium-potassium exchange) system on sarcolemma compete for Ca++ reuptake

Question 41

How does calcium activate the actin thin filament with the three different toponin molecules and tropomyosin in skeletal muscle?

Answer 41

* Troponin C – binds calcium, causing conformational change allowing actin to bind to myosin * Troponin I – covers the myosin binding site * Troponin T – binds tropomyosin and TnC * Tropomyosin – string-like protein that binds actin molecules

Question 42

Define the structural, enzymatic, and functional features of the three major categories (fast-glycolytic, fast-oxidative-glycolytic, and slow-oxidative fiber types) of skeletal muscle fiber types.

Answer 42

Question 44

What are the steps in muscle repair?

Answer 44

1. Degeneration Phase: Injured fibers undergo rapid necrosis and degeneration – due to influx of Ca++ and activation of proteolysis 2. Inflammatory Phase: Necrotic fibers activate an inflammatory response – invasion by inflammatory cell populations 3. Regeneration Phase: Satellite cell (muscle stem cell) activation allows for regeneration of fibers – controversial how they are activated to differentiate into a muscle cell 1. Can be altered by sarcopenia – muscle atrophy due to aging 4. Remodeling/Repair Phase: is characterized by a maturation of the regenerated fibers, remodeling of the extracellular matrix, recovery of functional performance of injured muscle.

Question 45

What are the steps of action in gap junction in cardiac myocytes?

Answer 45

1. AP electrically stimulates the first cell – Na+ ions flow into the cell to depolarize 2. Na+ also flows into the adjacent cell – they are attracted by the more negative ions in the adjacent cell as well as the low concentration of Na+ in the adjacent cell (down concentration gradient) 3. The extracellular current is the capacitive current – the positive ions from inside repel the positive ions near the extracellular surface of the cardiac muscle cell – the positive extracellular ions move back toward the original cell (cell A)

Question 46

What are the two phases of contraction.

Answer 46

* Phase 1: Tension Development – build up of passive elastic forces not yet high enough to move the afterload * Phase 2: Muscle Shortening – when tension can overcome afterload → muscle shortens

Question 48

Describe the differences in actomyosin regulation of smooth and skeletal muscle and indicate the structural similarities in their respective contractile units.

Answer 48

* Activity in skeletal muscle is regulated by troponin C uncovering myosin binding sites on actin, whereas smooth muscle regulates MLCK and * Slow tension development – the kinase activity is slower than diffusion of Ca++ to troponin/tropomyosin in skeletal muscle * The smooth muscle system allows for a graded control of muscle tension – the percentage of myosin crossbridges activated is directly proportional to muscle tension * The response is more graded and not all-or-none like skeletal muscle, different amounts of Ca++ produce different levels of muscle tension

Question 49

What is the equation of bioavailability?

Answer 49

Question 50

What are the equations for loading dose?

Answer 50

Question 51

What are the maintenance dose equations?

Answer 51

Question 52

What are the equations for Ke and half life?

Answer 52

Question 53

What is the clearance equation in terms of Vd and half life?

Answer 53

Question 54

What is the Ct equation in terms of C₀?

Answer 54

Question 55

What are the equilibrium concentrations of Na⁺, Ca²⁺, Cl^-, K⁺?

Answer 55

Question 56

Diagram the two intracellular pathways that control contraction and relaxation in smooth muscle.

Answer 56

* Contraction using Myosin Light Chain Kinase (MLCK) * 4 Ca++ ions bind Calmodulin → activates MLCK → MLCK phosphorylates myosin regulatory light chain (RLC) → activating myosin * Is stretch-induced contraction and is not dependent on nerve stimulation * Relaxation via Latch Bridge Mechanism * The latch bridge occurs when there is an intermediate level of phosphorylation (and calcium) of the smooth muscle myosin regulatory light chain. Relaxation will occur when all of the RLC becomes dephosphorylated which will occur when the calcium levels drop to near baseline. * Reducing [Ca++] → inactivates MLCK

Question 57

Distinguish between electromechanical coupling and pharmacomechanical coupling.

Answer 57

* Electromechanical Coupling * Voltage-gated L-type calcium channel can activate RyR by calcium-induced calcium release * Pharmacomechanical Coupling * GCPR can activate IP3, allowing IP3 to bind to SR receptor to release Ca++ from SR without depolarization

Question 58

Hereditary Spherocytosis

Answer 58

* Description: Disease of the cytoskeleton. Type of hemolytic anemia. * Mechanism: Defects in spectrin → loss of membrane stability.

Question 59

Hutchinson Gilford Progeria Syndrome

Answer 59

* Description: Disease of the nucleus. * Mech: Accelerated aging due to lack of synthesis of Lamina A (DNA/RNA synthesis)

Question 60

Lysosomal Storage Disease (Tay-Sachs, Krabbe, Gaucher)

Answer 60

* Description: Seizures, developmental delay, movement disorders * Mech: lack function of one or more lysosomal hydrolase → undigested material accumulates causing swelling → major impact on neuronal cells

Question 61

Lufts Disease

Answer 61

* Description: weakness, excessive perspiration, increased basal metabolic rate, high caloric intake without increase in body weight * Mechanism: Caused by defect in mitochondrial oxygen utilization → uncoupling of oxidative phosphorylation

Question 62

Age Related Degenerative Diseases (Parkinson and Alzheimer)

Answer 62

* Description: Disease of the mitochondria. * Mech: formation of free radicals (superoxides) that cause DNA damage

Question 63

Zellweger Syndrome Spectrum

Answer 63

* Description: Disease of the peroxisome. * Mech: Mutated PEX gene → inability to import proteins → impaired B-oxidation → increase in FAs

Question 64

Dyskinesia (Kartagener’s Syndrome)

Answer 64

* Description: Disease of the cilia/flagella. * Mech: Defect in motility of cilia → infections in mucus lining * Note: May cause infertility in male. Think sperm.

Question 65

Tay-Sachs

Answer 65

* Description: effects mostly nerve cells in the brain and spinal cord. * Mech: The lysosomal hydrolase not present is hexosaminidase A and therefore GM2 ganglioside does not get broken down. GM2 ganglioside is important in nerve cells.

Question 66

Neiman Pick

Answer 66

* Description: This disease mostly impacts neuronal cells but also causes enlargement of liver and spleen. * Mech: effects sphingomyelin forming cells, accumulation of sphingomyelin because of lack of sphingomyelinase. The sphingomyelin accumulates in lysosomes and results in cell death.

Question 67

Gaucher

Answer 67

* Description: most prevalent LSD. Not just nerve cells altered (liver, spleen, white blood cells, kidney, bone marrow). * Mech: A deficiency in glucocerebrosidase which results in the accumulation of sphingolipids

Question 68

I-Cell Disease

Answer 68

* Description: Very severe because all lysosomal hydrolases are not localized to the lysosome and instead are secreted outside the cell. Many cell types altered. * Mech: problem with the targeting of lysosomal hydrolases to the lysosome. Tagging with mannose-6-phosphate is disrupted.

Question 69

Von Gierck’s Disease

Answer 69

Description: Severe hypoglycemia and weakness Mechanism: deficiency in glucose-6-phosphatase (type 1a) or G6P transporter (type 1b) so glucose cannot be mobilized from liver Treatment: Manageable through diet

Question 70

Malignant Hyperthermia

Answer 70

Description: Increased temperature due to increased metabolic activity. Mech: Mutated RyR is sensitive to anesthetic, causing extended opening of RyR, leading to increased hydrolysis of ATP Treatment: RyR blocker

Question 71

Pompe’s Disease

Answer 71

Description: heart enlargement leading to cardiac arrest by age 2; autosomal inherited Mechanism: lose alpha(1-4) glucosidase activity in lysosomes leading to increased levels of glycogen accumulation in many tissues Treatment: no treatment

Question 72

Cori’s Disease

Answer 72

Description: hypoglycemia weakness Mechanism: deficiency in debranching enzyme leads to short outer branches with non-reducing ends Treatment: glucose infusion

Question 73

Andersen’s Disease

Answer 73

Description: liver failure and death Mechanism: deficiency in branching enzyme leading to long Treatment: no treatment just death

Question 74

McArdle’s Disease

Answer 74

Description: painful cramps because muscle can not utilize glucose Mechanism: muscle phosphorylase deficiency → cannot degrade glycogen Treatment: liver is unaffected so mild disease

Question 75

Her’s Disease

Answer 75

Description: nothing notable Mechanism: mild liver phosphorylase deficiency → cannot degrade glycogen Treatment: complete liver phosphorylase deficiency is lethal

Question 76

Refsum’s Disease

Answer 76

* Description: build up of long branched FAs which accumulate in the blood and disrupt function of neurons -- attack myelin * Mechanism: lack peroxisomal hydroxylating enzyme and leads to the accumulation of phytanic acid * Treatment: change diet

Question 77

Deficiencies in Acyl -CoA dehydrogenases

Answer 77

* Description: lethargy, edema, cardiac failure. Deficiencies in these enzymes can be fatal. Different enzymes for different length FAs. (VLCAD, LCAD, MCAD, SCAD). Can lead to SIDS when babies sleep at night because cannot metabolize FAs. * Mechanism: lack of the enzyme means those affected can’t metabolize FAs * Treatment: screening for MCAD for neonates

Question 78

How are sugars digested and absorbed? What molecule do they need to be catabolized to?

Answer 78

* All sugars are reduced to monosaccharides * This allows for transport across a membrane (dissaccharides cannot be transported)

Question 79

How does the SGLT1 channel function? Where is it located?

Answer 79

* The Na+-glucose symporter (SGLT1) functions exclusively in the intestinal epithelial cells to draw glucose in from the gut lumen and pass it into the blood * Uses the concentration gradient of sodium to provide energy

Question 81

What are the irreversible steps in glycolysis?

Answer 81

* Glucose → Glucose-6-Phopshate * Fructose-6-Phosphate → Fructose 1,6 bisphosphate * Phosphoenolpyruvate → pyruvate All of these have steep -ΔG values.

Question 82

Compare and contrast hexokinase and glucokinase.

Answer 82

Hexokinase * Used in all tissues (including liver) * Nonspecific (can reduce any molecules) * Low K_m (if satrurated, reaction cannot continue) * Inhibited by product (G6P Glucokinase * Liver only * Only works on glucose * High K_m (everything is phosphorylated as soon as glucose enters) * No inhibition

Question 83

At what step in gluconeogenesis is the pathway regulated?

Answer 83

* Fructose 1,6-bisphosphate converted to fructose 6-phosphate by fructose 1,6-bisphosphatase (FBPase-1) * Inhibited by: AMP, F26BP * PFK-2/FBPase-2 complex creates F26BP * F26BP ensures that PFK-1 and FBPase-1 are not active at the same time.

Question 84

How does the Cori Cycle maintian glucose availability in the blood? How might it be related to muscle cramps?

Answer 84

* Glucose in muscle cells is used for energy and metabolized into lactate * Lactate is transferred by a transporter via bloodstream to the liver and converted back into glucose through gluconeogenesis * Lactate builds up to quickly in the muscle cells → decrease in pH → muscle cramps

Question 85

How is glycogen degraded in the body?

Answer 85

* Glycogen phosphorylase cleaves an alpha 1,4 linkages creating one glucose molecule (G1P) * G1P to G6P by phosphoglucomutase * Debranching Enzyme * Transferase activity: transfers last 3 alpha 1,4 linked molecules from one branch to another * Glucosidase activity: cleaves an alpha 1,6 linkages creating one glucose molecule

Question 86

How is the TCA cycle regulated?

Answer 86

* Inhibiton: ATP and NADH * Activation: Ca++, AMP, ADP

Question 87

How is glycogen synthesized?

Answer 87

* Formation of UDP-glucose catalyzed by UDP-glucose pyrophosphorylase * Addition of a glucose residue to glycogen catalyzed by glycogen synthase

Question 89

Where does insulin originate from and what is its chemical nature?

Answer 89

* Beta-cells of the pancreatic islets * Chemical Nature * Pre-prohormone synthesized on rough ER * “Pre” domain directs molecule into the ER – it is cleaved from pro-insulin * “Pro” domain (C peptide) organizes disulfide bonds * “Pro” domain is cleaved in trans-Golgi, yielding insulin * "Pro" domain is packaged in same vescile for exocytosis

Question 90

Where does glucagon originate from and what is its chemical nature?

Answer 90

* Alpha-cells of the pancreatic islets * Chemical Nature * Synthesized as pro-glucagon * “Pro” domains have functional properties in GI tract and brain * In intestinal cells, several exons of the glucagon gene are incretins (cause release of insulin)

Question 91

Where does somatostatin originate from and what is its chemical nature?

Answer 91

* Delta-cells of the pancreatic islets * Somatostatin and prosomatostatin are active

Question 92

Where does amylin originate from and what is its chemical nature?

Answer 92

* Beta-cells of the pancreatic islets * Synthesized as a small precursor

Question 93

Function of somatostatin?

Answer 93

Somatostatin slows everything and inhibits glucagon and insulin release

Question 94

Function of amylin?

Answer 94

Amylin complements insulin by sensitizing cells to insulin

Question 95

What is the process that takes place in Complex I of the Electron Transport Chain? * What is Complex I called? * How many H+ pass into the intermembrane space?

Answer 95

Complex I – NADH Dehydrogenase * NADH + H+ → NAD+ * A hydride ion (H-) is donated from NADH to FMN where 2 electrons pass onto a series of Fe-S centers * The preceding 2 electrons at the FMN pushes the electron at each Fe-S center separately via “tunneling” (wave function of quantum mechanics) * The last Fe-S center pushes an electron to the ironsulfur protein N-2 * Electron transfer from N-2 to ubiquinone (Q) forms (QH2) along with 2 H+ * 4H+ pass to intermembrane space (per NADH)

Question 96

What is the process that takes place in Complex II of the Electron Transport Chain? * What is Complex II called? * How many H+ pass into the intermembrane space?

Answer 96

Complex II – Succinate Dehydrogenase * FADH2 → FAD + 2e- + 2H+ * FADH2 is oxidized to FAD, donating 2e- and 2H+ to Fe-S complexes, pushing the electron at each Fe-S center separately via “tunneling” (wave function of quantum mechanics) * Electron transfer from last Fe-S center to ubiquinone (Q) forms (QH2) * FAD has less negative reduction potential than NAD+, therefore FAD’s electrons have lower energy potential

Question 97

Where does Ubiquinol transfer from and to in the electron transport chain? Why does this occur?

Answer 97

Ubiquinol Transfer from Complex I and II to Complex III * Hydrophobic molecule, so it moves through plasma membrane by planar diffusion to complex III

Question 98

What is the process that takes place in Complex III of the Electron Transport Chain? * What is Complex III called? * How many H+ pass into the intermembrane space?

Answer 98

Complex III – Cytochrome Reductase * 2 QH2 molecules donates 2 electrons each to complex III * One electron → Heme_(b) → Heme_(b) → Free Q at Q_N or Q_P → free radical Q * The free radical Q is reduced back to QH2 with second electron following Q_N or Q_P path (and is used again) * One electron → Fe-S center (Rieske Fe-S Protein) → Heme_(c) → Heme_(c) on Cyt C → Cyt C * The second electron following this path forms second Cyt C (which is why we need 2 NADH to form the 4 Cyt C to be used in complex IV) * 4H+ are pumped into intermembrane (per NADH)

Question 99

What is the process that takes place in Complex IV of the Electron Transport Chain? * What is Complex IV called? * How many H+ pass into the intermembrane space?

Answer 99

Complex IV – Cytochrome C Oxidase * This complex requires 2NADH molecules to get the 4e- required to reduce O2 * Four cytochrome c molecules each bring an electron to complex IV * Electron flows to Cu_A → Fe-Cu Center (aka Heme a) → Heme a₃-Cu_B → O2 → 2H2O * 3 protein subunits critical to electron flow * 2H+ are pumped into intermembrane space per NADH (4 to complete process)

Question 100

What is the transport process for fatty acids from the cytosol into the matrix of the mitochondria?

Answer 100

1. Acyl-CoA Synthetase – an outer mitochondrial membrane enzyme – converts FAs into fatty acyl-CoA using ATP 2. Carnitine acyl transferase I (CPTI) transfers the FA via carnitine, forming acylcarnitine (removes CoA) 3. Acylcarnitine is transferred across inner membrane with the translocase enzyme on the inner mitochondrial membrane 4. Carnitine acyl transferase II (CPTII) transfers the FA back to fatty acyl-CoA and carnitine is restored to the intermembrane space

Question 101

What are key inhibitors in the four electron transport chain complexes?

Answer 101

Complex I (**one**) * Roten**one** – causes an increase [NADH] Complex II * Carboxin – causes an increase [QH₂] Complex III * Antimycin A – cause a block in electron flow from heme *b* to Q, binds at Q_N (**An-3-mycin**) * Myxothiazol – cause a block in electron flow from QH₂ to the Rieske iron-sulfur protein, binds at Q_P Complex IV (CO/CN - **4** letters) * Cyanide – binds to heme A₃ preventing transfer of electrons to O₂ * Carbon Monoxide – binds to heme A₃ preventing transfer of electrons to O₂

Question 102

How are the main fatty acids absorbed by the intestine and then transported to the adipocyte?

Answer 102

1. Fats ingested 2. Bile salts emulsify fats, forming micelles 3. Intestinal lipases degrade triacylglycerols into glycerol and free FAs 4. Free FAs taken up by mucosa and converted back into triacylglycerols in intestinal epithelial cells 5. Triacylglycerols, cholesterol, and apolipoproteins form chylomicrons 6. Chylomicrons move through lymphatic system and bloodstream to tissues 7. Lipoprotein lipases is activated by apoC-II in capillaries releases FAs and glycerol 8. FAs enter cells 9. FAs are oxidized as fuel or converted back to triglycerides for storage

Question 104

What is the general reaction sequence of beta oxidation? * How many ATP are generated?

Answer 104

Reaction Sequence 1. Oxidation that creates FADH2 2. Hydration 3. Oxidation that creates NADH 4. Thiolysis → results in FA with 2 less carbons ATP Generated – 2.5 ATP per NADH and 1.5 per FADH2 are created in each step

Question 105

What is the basic mechanism for synthesis of fatty acids?

Answer 105

1. Acetyl-CoA goes to Malonyl-CoA via acetyl-CoA carboxylase (key regulation prior to fatty acid synthase) 2. Malonyl-CoA goes to Palmitate via Fatty Acid Synthase (adds two carbons at a time via NADPH reactions)

Question 106

What are the control points in fatty acid synthesis?

Answer 106

Control Points by Acting on Acetyl-CoA Carboxylase * FA synthesis turned on/degradation turned off by: * Citrate, insulin, thyroid hormone, high carbohydrate diet, prolonged increased insulin levels

Question 107

What are the control points for fatty acid degradation?

Answer 107

Control Points by Acting on Acetyl-CoA Carboxylase * FA degradation turned on/synthesis turned off by: * Epinephrine, glucagon, palmitoyl-CoA, fasting, high fat diet

Question 108

What is the rate limiting step for cholesterol synthesis?

Answer 108

HMG-CoA Reductase Is Rate-Limiting Step of Cholesterol Synthesis

Question 109

How is HMGCoA reductase regulated? Inhibition of enzyme? Stimulation?

Answer 109

* Inhibited by: high cholesterol, phosphorylation of AMP dependent-kinase (senses high [AMP], glucagon, epinephrine, statin * Stimulated by: insulin

Question 110

What are the other products of intermediates (isopreniod precursors) of the cholesterol pathway? (4)

Answer 110

* coenzyme Q – used in ubiquinone synthesis (ETC) – can lead to muscle soreness * Isoprenyl – used in tRNA synthesis * Farnesyl * Geranyl

Question 111

What are 3 products of synthesis pathways involving cyt. P450s and cholesterol?

Answer 111

Vitamin D BIle Acids Steriod hormones

Question 112

What is LCAT in relation to HDL?

Answer 112

Catalyzes esterification of 2/3 of plasma cholesterol * Nascent HDL → Mature HDL

Question 113

Fuction of ApoE and on what lipoproteins?

Answer 113

Function: Mediates remnant uptake. (**E**verything **E**xcept LDL) LP: Chylomicron, Chlyomicron remnants, VLDL, IDL, HDL

Question 114

Fuction of ApoA-1 and on what lipoproteins? What would a mutation to this cause?

Answer 114

Function: Apo**A**-1 **A**ctivates LCAT LP: Chylomicron, HDL Mutation: Poor HDL function ApoA1 R173C mutation: patients have reduced HDL levels, however, patients are protected from heart attacks. HDL increase their rate of clearance due to low numbers.

Question 115

Fuction of ApoC-II and on what lipoproteins?

Answer 115

Function: Lipoprteins lipase (**C**ofactor that **C**atayzes **C**leavage) LP: Chylomicron, VLDL, HDL

Question 116

Fuction of ApoB-48 and on what lipoproteins?

Answer 116

Function: Mediates chylomicron secretion into lymphatics LP: Chylomicron,Chylomicron remnants

Question 117

Fuction of ApoB-100 and on what lipoproteins?

Answer 117

Function: Binds LDL receptor LP: VLDL, IDL, LDL

Question 118

Identify the source of the fatty acid precursor for eicosanoid synthesis

Answer 118

Most eicosanoids are synthesized from arachidonic acid, which has 20 carbons

Question 119

Describe the role of cyclooxygenase in the synthesis of prostaglandins

Answer 119

Two separate reactions on same enzyme. First cyclooxygenase reaction to make PGG2, then peroxidase reaction to make PGH2, which is substrate for further reactions PGH2 is the precursor to all the prostaglandins in the body

Question 120

How do inhibitors of COX1 and COX2 work?

Answer 120

* Inhibitors of COX1&2: aspirin and NSAIDs (most pain drugs like ibuprofen) * Aspirin: Acetylation of the serine results in the irreversible inactivation of PGH synthase. * NSAIDs inhibit PGH synthase by interacting with the hydrophobic active site thereby blocking its reaction with substrate. * Tylenol (acetaminophen) not an NSAID. Blocks COX enzymes but not inflammation. Acts in CNS.

Question 121

Describe leukotriene chemistry and pharmacology

Answer 121

* Leukotrienes are characterized by the presence of 3 conjugated double bonds. * Longer half-life than other eicosanoids. * Cause contraction of vascular, respiratory, and intestinal smooth muscle. * Leukotrienes can activate CysLT1 receptors on airway smooth muscle cells (SMC) and postcapillary venule endothelial cells to cause bronchoconstriction and edema. * Singulair and Accolate block this binding step.

Question 122

Describe the maintenance of the pools of amino acids required for protein synthesis. (in terms of K_M)

Answer 122

* K_M of aminoacyltransferases is low and therefore prefers to charge tRNA to attract AAs * Degradation has high K_M, or low affinity * tRNA formation has low K_M, or high affinity, favoring protein synthesis

Question 123

Describe why some AAs are essential while others are nonessential.

Answer 123

* Essential AAs cannot be synthesized or the body cannot make them in sufficient quantities * R MLK had HIV WTF * Nonessential are synthesized in appropriate quantities by the body

Question 124

What is the relationship of most nonessential AAs to common intermediary metabolites.

Answer 124

* **The carbon skeletons of the nonessential amino acids are largely related to common intermediates of metabolism** [consider alanine and pyruvate. The reason that the essential amino acids are essential is that we cannot make their carbon skeletons]

Question 125

What is the general equation for creating different metabolites from AAs? What is the cofactor? Name some specific examples?

Answer 125

* General: AA1 + alpha-keto acid2 = alpha-keto acid1 + AA2 (PLP or vitamin B6 as cofactor) * The Keq of reactions using aminotransferases is ~1, meaning the reaction is dependent on concentrations * Alpha-ketoglutarate + aspartate = glutamate + oxaloacetate (using aspartate aminotransferase and PLP as cofactor) * Alpha-ketoglutarate + alanine = glutamate + pyruvate (using alanine aminotransferase and PLP as cofactor)

Question 126

How is PLP affected by certian TB treatments?

Answer 126

Isoniazid – used to treat TB – competitively binds to PLP, inducing a B6 deficiency

Question 127

Describe Kwashiorkor?

Answer 127

* Inadequate protein intake * “the disease of the deposed baby when the next baby is born” so no nutrients through breast milk * Characterized by retention of water in the stomach, failure to thrive, composition of gut bacteria

Question 128

Describe Marasmus?

Answer 128

* Inadequate energy intake * Characterized by failure to thrive and delayed mental development

Question 129

Describe Marasmic Kwashiorkor?

Answer 129

Inadequate energy and protein intake

Question 130

What is the urea cycle? Explian the cycle. (Intermedates and major enzymes)

Answer 130

Question 132

Describe the glucose-alanine cycle and its roles.

Answer 132

Question 133

Describe the role of glutamine in movement of nitrogen.

Answer 133

* Glutamate + NH₃ + ATP = Glutamine + ADP+ P_i via Glutamine Synthetase in periphery * Glutamine + H₂O → glutamate + NH₃ via Glutaminase in liver and kidney tissue * Therefore, glutamate acts as a shuttle carrier for NH₃

Question 135

Describe the degradation and use of AAs as energy sources.

Answer 135

* Glucogenic: pyruvate or oxaloacetate create a net gain of glucose * Ketogenic: acetyl-CoA and acetoacetyl-CoA enter into citric acid cycle with no net gain of glucose

Question 136

What is the source of NO and pathway?

Answer 136

Source: arginine Arginine + O2 + NADPH → citrulline + nitric oxide + NADP+

Question 137

What are the five metabolites that trypotphan breaks down into?

Answer 137

1. seretonin 2. melatonin 3. xanthuenote 4. NAD+ 5. acetoacetyl CoA

Question 138

What is the importance of Vitamin K? What does deficiency lead to?

Answer 138

* Vitamin K is a cofactor for post-translational modification of glutamate to Gla * Vitamin is oxidized, and in order to be used as a cofactor again, it must be reduced through 2 enzymatic steps * Gla is used in clotting and in osteocalcin (Ca++ binding protein in bone) * VKDB (Vitamin K Deficiency Bleeding): internal bleeding due to lack of blood clotting (can be mistaken for child abuse)

Question 139

What are Vitamin K inhibitors?

Answer 139

Dicumerol Warfarin

Question 141

How tryptophan broken down?

Answer 141

* Tryptophan is broken down into alanine (glucogenic) and acetoacetyl CoA (ketogenic) * Degradation: * Urine color via xanthurenate * Feces odor * Halitosis (bad breath)

Question 142

How does Sumatriptan work?

Answer 142

5-HT1 agonist. Treatment for migraines.

Question 143

What is the pathway of catecholamines?

Answer 143

* Tyrosine → L-Dopa → Dopamine → Norepinephrine → Epinephrine * 1^st Step: tyrosine hydroxylase uses BH₄ as cofactor * Negative feedback by all catecholamines * 3^rd Step: vitamin C is a cofactor * 4^th Step: SAM methylates norepinephrine * Lack of dopamine causes Parkinson’s, which can be treated with L-Dopa because it can cross the blood brain barrier

Question 144

How does Prozac work?

Answer 144

serotonin specific reuptake inhibitor

Question 145

Describe the relationship of phenylalanine and tyrosine?

Answer 145

* Phenylalanine (essential) synthesizes tyrosine (non-essential as long as there is enough F) * F → Y via phenylalanine hydroxylase and BH₄ oxidation * BH₂ must be reduced back to BH₄ in order to act as a cofactor in future reactions

Question 146

PKU causes?

Answer 146

* Phenylketonuria * Malignant: mutation in the dihydrobiopterine reductase (BH₂ to BH₄) * Mutation in phenylalanine hydroxylase, so there is an accumulation of its alpha-ketoacid, phenylpyruvate

Question 148

Pathway for melanin?

Answer 148

Tyrosine → → → Melanin using tyrosinase by adding 2O2

Question 149

How are thryroid hormones created?

Answer 149

* Derived from post-translationally modified tyrosines * Thyroglobulin degrades into T₄

Question 150

Describe the symptoms and basis of oculocutaneous albinism.

Answer 150

* Deficiency in tyrosinase * Symptoms * Sensitivity to sunlight * Decreased visual acuity

Question 151

Describe the synthesis of pyrimidine bases and nucleotides

Answer 151

Question 152

Describe the synthesis of purine nucleotides

Answer 152

Question 153

How are catecholamines inactivated?

Answer 153

* Monoamine oxidase inhibitors (MAOIs) * Catecholamines must be degraded to become inactive * MAO and COMT AND COMT and MAO act together to inactivate these compounds * MAOIs are used to treat depression * May interfere with metabolism of monoamines

Question 154

Describe thymidine (as TMP) synthesis

Answer 154

Question 155

Describe how tetrahydrofolate (THF) carries C1 units at (3) different oxidation levels.

Answer 155

* C1 level at methanol * C1 unit is passed from N5-methyl-THF to another cofactor, S-adenosylmethionine (SAM) * B₁₂ deficiency creates a “folate trap” that prevents 5-methyl-THF from making dTMP and methionine * C1 level at formaldehyde * Glycine/serine interconversion * C1 level at formate * Two reactions in purine biosynthesis

Question 156

Describe why sulfanilamide inhibits bacterial folic acid synthesis
.

Answer 156

* Bacteria treated with sulfanilamide mis-incorporate this compound in place of PABA during synthesis of folic acid * Humans do not have this enzyme to synthesize folic acid, so unaffected

Question 157

Describe the critical role of vitamin B12.

Answer 157

* Used as a cofactor in only two reactions in the body * Homocysteine methionine (for DNA synthesis) * L-methylmalonyl-CoA → succinyl-CoA (oxidation of some AAs or beta-oxidation of odd-numbered fatty acids) * B₁₂ deficiency leads to build up of methylmalonyl-CoA, which can go on to degrade myelin sheaths

Question 160

Formation of deoxyribonucleotides by ribonucleotide reductase

Answer 160

* Ribonucleotide reductase converts NDPs (ribose) to dNDPs (deoxyribose) * 3 different classes of RNRs * Reaction proceeds via free radical mechanism of action

Question 161

How are purines catabolized in the body?

Answer 161

Question 163

Describe the salvage pathway for purines.

Answer 163

Question 164

Describe the salvage pathway for pyrimidines.

Answer 164

Question 165

How does Trimethoprim work and what does in inhibit?

Answer 165

* Trimethoprim * Antibiotic * Binds to bacterial DHF reductase strongly, inhibiting it in bacteria * Binds weakly to human version * Selectively inhibits bacterial growth

Question 166

How does Hydroxyurea work and what does in inhibit?

Answer 166

* Hydroxyurea * Free radical scavenger * Inhibits ribonucleotide reductase → decreasing dNTP pool (especially in proliferating cells)

Question 167

How does Methotrexate work and what does in inhibit?

Answer 167

* Methotrexate * DHF reductase inhibitor * Competes with DHF for binding DHF reductase * Can't convert to THF * Recovery and reversal by giving high levels of nucleosides and folate * Anti-cancer (inhibits DNA synthesis, stopping cell division)

Question 168

How does 5-fluorouracil work and what does in inhibit?

Answer 168

* 5-fluorouracil * FdUMP a derivative of 5-fluorouracil * “suicide inhibitor” for thymidylate synthase (UMP → TMP)

Question 169

How does 5-azacytidine work and what does in inhibit?

Answer 169

* 5-azacytidine * Prodrug * Pyrimidine biosynthesis inhibitor

Question 170

How does 6-mercaptopurine work and what does in inhibit?

Answer 170

* 6-mercaptopurine * Inhibits purine synthesis at multiple steps * Cells starve of purines and die​

Question 172

Factors effecting presentation of gout? epidemology?

Answer 172

* Presentation * Present at physiological pH as sodium urate * Alcohol consumption – beer has yeast, which produces high levels of purines * Dehydration * High purine diet (meat, seafood, asparagus, spinach) * “Tophi” – monosodium urate tissue aggregates that eat through bone * Sodium urate precipitate in joints and kidney stones * Epidemology * Men \> 30 * Postmenapuasal women

Question 175

Treatments for chronic gout?

Answer 175

Chronic Gout * Xanthine oxidase inhibitor – inhibits purine degradation * Allopurinol * Febuxostat * Uricosuric agent – increase excretion of uric acid in urine * Pegloticase

Question 176

Treatments for acute gout?

Answer 176

Acute Gout * NSAIDs – COX1 & COX2 inhibitor – reduce pain and inflammation * Indomethacin * Colchicine – Reduces gout symptoms * Intra-articular Corticosteroids – Reduce inflammation

Question 177

What is Azanthioprine (AZA)? Whats the mechanism? and effect? How is it affected by Xanthione oxidase inhibitors?

Answer 177

Azathioprine (AZA) * Prodrug * Immunosuppressant * Cyclosporin is often used in conjunction with AZA * Decreases uric acid excretion, leading to higher prevalence of gout in transplant recipients * Xanthine oxidase inhibitors (allopurinol) are used then to decrease uric acid production * Can lead to AZA toxicity because some AZA metabolites use xanthine oxidase

Question 178

What is Cytosine Arabinoside (AraC) and Alanine Arabinose (AraA)? Whats the mechanism? and effect?

Answer 178

Cytosine Arabinoside (AraC) and Alanine Arabinose (AraA) * Arabinose is substituted in place of ribose * Results in cell death in leukemia tumors * Must be phosphorylated to nucleoside triphosphates to be incorporated into DNA

Question 179

What is 2-cholorodeoxyadenosine? Whats the mechanism? and effect?

Answer 179

2-cholorodeoxyadenosine * Used in treatment of hairy cell leukemia * Cytotoxic, especially in inhibition of DNA repair of double-strand breaks * As resists breakdown by adenosine deaminase as a chemotherapeutic drug

Question 180

What is 5-Iodouridine? Whats the mechanism? and effect?

Answer 180

5-Iodouridine * Functional analogue of thymidine (not uridine!) that must be metabolized to a dNTP before it is incorporated into DNA * Pairs with G instead of A due to aberrant hydrogen bonding properties * Mispairs in DNA and RNA * Treats herpesvirus infections

Question 181

What is Acyclovir? Whats the mechanism? and effect?

Answer 181

Acyclovir * Analogue of guanosine that lacks most of ribose ring * Missing 3’-OH group causes chain termination of DNA strand once incorporated * Treats herpesvirus infections * Must be in monophosphorylated form * Only virally-encoded thymidine kinase phosphorylates acyclovir (human thymidine kinase does not)

Question 182

What is Azidothymidine (AZT)? Whats the mechanism? and effect?

Answer 182

Azidothymidine (AZT) * Analogue of thymidine and has no 3’-OH group on ribose ring * DNA elongation is terminated * Treats HIV * Anti-viral because the HIV DNA reverse transcriptase has 100x increase in affinity for AZT triphosphate than normal DNA polymerases

Question 183

What is Hydroxyurea? Whats the mechanism? and effect?

Answer 183

Hydroxyurea * Inhibits ribonucleotide reductase, decreases dNTP pool, especially in proliferating cells * Helps drugs like AZT, which competes with endogenous TTP supply

Question 184

Connect elevated uric acid levels to Lesch-Nyhan Syndrome.

Answer 184

HGPRT deficiency → increased [hypoxanthine] → increased [uric acid]

Question 185

What is receptor-mediated endocytosis and give the process using LDL particles?

Answer 185

* Clathrin mediated * Example: LDL particles * LDL receptors on ECM of PM recognize LDL particle * LDL receptor binds adaptor protein and clathrin coat assembles * Transported to early endosomes then lysosomes * LDL receptor dissociates from LDL particle in early endosome and receptor is recycled back to PM * Free cholesterol enters cytoplasm * Promotes homeostasis by inhibiting LDL receptors and shutting down cholesterol synthesis when [LDL]_cell is high

Question 186

What is transcytosis used for and provide an example of where it would be used?

Answer 186

* Used in polarized epithelial cells to transfer macromolecules from one extracellular space to another (apical to basolateral) * Example: transferring of ABs from mother’s blood to baby’s blood

Question 187

Number of half-lifes or clearance? effect of doubling dose ?

Answer 187

5 double dose only increase time in body by one half-life

Question 188

Vd Numbers?

Answer 188

* 5L - plasma * 15L plasma + insterstitual fluid * 40L plasma + interstitual fluid + intracellular fluid

Question 189

similarities between cardiac and smooth

Answer 189

autonomic gap junctions mecahnical coupling? stretch induced contraction? structure: intercalated disks & desosomes similar to dense bodies types of smooth muscle cont. phasic: GI tonic: blood vessels