MBOD Q’s Block IV
1/15/2010 Nickalus Khan
Mitochondrial Inheritance
1. How many strands does mt DNA have?
2. How many BP?
3. How many genes are encoded?
4. Does mtDNA contain introns?
5. What are 3 major fx. Of mitochondria?
6. Does mtDNA code for most of the complexes of the electron transport chain?
7. Which complex has no contributions from mtDNA?
8. What inheritance does mtDNA disorders have?
9. What tissues typically embody mt disorders?
10. Is the nuclear genome required for maintenance of mt DNA?
11. What is the difference between homoplasmy and heteroplasmy?
12. Do all mtDNA mutations express phenotypically?
13. Do mt disorders exhibit reduced penetrance?
14. What provides a selective advantage for mut mtDNA?
15. What causes mtDNA mutations to be distributed differently in different clonal populations?
16. What are some hallmarks of mt inheritance?
17. Can affecteds be either homoplasmic or heteroplasmic? Unaffected?
18. Are most mtDNA mut deletions?
Functions of Secreted Glycoproteins
19. What is a glycoprotein?
20. Are most extracellular proteins glycosylated? What is the major exception?
21. T or F: The sugar chains of glycoproteins are typically numerous in different sugars.
22. What is a 2’ epimer of glucose?
23. What are two sugar building blocks in glycoproteins discussed in lecture?
24. Where are sugars glycosylated?
25. When are sugars glycosylated?
26. What sequence is a signal for glycosylation?
27. What amino acid residue are N-linked glycoproteins attached to?
28. T or F: the preassembled oligosaccharide is always the same in glycoproteins?
29. What provides the energy for glycosylation?
30. Even though all N-linked sugars are the same initially, are the same eventually?
31. How is O-glycosylation different than N-glycosylation?
32. What is a dimer of 2 similar subunits joined by disulfide bond at C terminal that helps hold
extracellular molecules together?
33. What are some fxn. Of glycoproteins?
34. What are glycoproteins targeted to the lysosome tagged with?
Proteoglycans
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35. What are the components of a proteoglycan?
36. How do proteoglycan form a hydrated shell?
37. What AA sequence do GAG chains in PG bind to?
38. What are 3 disease states correlated with the loss of cartilage tissue discussed in lecture?
39. How are GAG chains linked to the core protein?
40. What are GAG’s repeating chains of?
41. Can GAG chains consist of more than one repeating pattern? Can there be different GAG chains
in PG’s?
42. What exists as a free GAG, not bound to a protein?
43. What are 3 GAG’s covalently attached to proteins through serine & a link trisaccharide xyl-galgal?
44. What is the recognition sequence for a serine-link trisaccharide?
45. Is hyaluronate sulfated?
46. After the link trisaccharide are GAG’s a repeating sequence?
47. What is a very large PG that can aggregate with link protein & hyaluronate to form very large
aggregates?
48. How can PG structure give a temporal dimension to fibroblast growth factor?
49. What can PG’s serve as on the cellular surface?
50. What can defects in integral membrane PG recycling lead to?
Role of Collagen in ECM
51. What is the primary structural element of connective tissue?
52. Is collagen highly post translationally processed?
53. What are the types of collagen that are fibrillar?
54. What are the types of collagen that is network associated?
55. What type of collagen is mostly associated with bone,skin,tendon,cornea,etc.?
56. What type of collagen helps form basal lamina sheets?
57. How many protein subunits is a collagen monomer made of?
58. What special repeating sequence of amino acids is required for collagen?
59. Collagen fibrils come together to form what?
60. What disease is caused by a mutation between gly and cys that lowers the strength of
collagenous tissues?
61. Hydroxylysine and hydroxyproline are hydroxylated in collagen via a rxn. Containing what
cofactors/enzymes?
62. What is deficient in scurvy that is necessary for proper collagen formation & crosslinking?
63. Why is the pro-collagen domain cleaved after secretion and not before?
64. What forms the crosslinks in collagen?
65. What disease is due to defects in collagen crosslinks?
66. What disease results from failing to remove procollagen domain?
67. What does degradation of collagen require?
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68. What type of collagen limits growth of type II collagen? It is a fibrillar collagen on the surface of
another collagen fiber.
69. What type of collagen is part of anchoring fibril to hold epithelia to underlying connective
tissue?
Cell Interactions with ECM
70. What extracellular component forms elastic networks ? How do these elastic networks
function?
71. What holds elastin molecules together?
72. Describe the formation of these crosslinks
73. What are these crosslinks called?
74. How many different polypeptides of elastin can become part of the elastic tissue?
75. What structure does elastin have that causes it to exclude water?
76. What other protein helps elastic networks form?
77. What is an extracellular glycoprotein that has affinity for cell attachment and collagen?
78. Does fibronectin have affinity for itself? What else does it have affinity for?
79. What is closely associated with fibronectin?
80. What is the amino acid sequence of the cell binding (integrin binding) region of
fibronectin?
81. What adaptor protein modules the interaction of intracellular actin and fibronectin?
82. What are integrins made of ?
83. Can signals trigger integrin activation?
84. What determines the kinds of integrins expressed by each differentiated cell?
85. What is a specialized connective tissue that typically underlies epithelial cells?
86. What specialized collagen network does basal lamina contain?
87. What serves functions similar to fibronectin in basal lamina?
88. What does the basal lamina separate?
89. In the kidney how does the basal lamina function to filter wastes?
90. Describe the metastasis of cancer as it relates to basal lamina.
Bone
91. What is responsible for calcium homeostasis in vivo?
92. Does bone have the ability to repair itself?
93. What is a cell that deposits bone?
94. What is a cell that resorbs bone?
95. What is the term for uncalcified bone matrix?
96. What is an osteoblast trapped in osteoid called?
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97. What are specific transcription factors for osteoblast differentiation?
98. What protein family are these transcription factors from?
99. Do osteoclasts have multiple nuclei?
100. What are osteocytes formed from?
101. What does parathyroid hormone stimulate?
102. What is the receptor that osteoblasts have which signal osteoclasts?
103. What is the receptor osteoclasts have that interact with osteoblasts?
104. Bone is constantly remodeled in response to?
105. What hormone enhances calcium release into blood?
106. What hormone inhibits calcium release into the blood?
107. What vitamin is essential for calcium aborption? What is the active form of this
vitamin?
108. What signal inhibits osteoclasts?
109. What are some of the disease states discussed in lecure due to imbalance between
formation/resorption of bone?
110. What common drug blocks bone resorption?
111. What disease is associated with local thickening of bone?
112. What is the disease which formstoo much bone due to constitutively active LRP5?
113. What disease is associated with bone forming in skin, muscle, etc.?
114. What does bone form on in endochondral ossification?
115. Can calcification occur in cartilage matrix?
116. What bud off from hypertrophic chondrocytes that allows for calcification?
117. What is the chemical formla of hydroxyapatite?
118. Proteins with modifications of higher densities of negative charges (sulfation,
glycosylation, carboxylation, phosphorylation) function in what?
119. What vitamin is involved in making γ-carboxyglutamate?
120. What is the purpose of negatively charged bone?
121. What type of collagen is highly crosslinked in bone?
122. What is a transcription factor that stimulates the formation of osteoblasts from preosteoblasts?
Blood Coagulation
123. T or F: Blood is a specialized connective tissue
124. EDTA is an example of?
125. T or F: Blood coagulation is a good example of zymogen activation
126. In order to activate chymotrypsin what must occur?
127. Fibrin aggregates to fibrin based on activation by what molecule?
128. What is the structural protein of a clot?
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129. What factor is a transglutamase that makes the fibrin clot stronger?
130. At the site of injury what happens upon initiation of a clot?
131. What does thrombin signal for in the amplification of the coagulation signal?
132. What happens in the propogation step of coagulation?
133. What inhibits TF-VIIa association to prevent clots from over propogation?
134. What keeps clots localized?
135. What limits amplification of a clot?
136. What limits propogation of a clot?
137. What dissolves a clot?
138. What are a class of genetic disorders associated with mutations in synthesis of blood
coagulation factors?
139. What drug can be used as an anticoagulant therapy?
Molecular Embryology
140. What leads to a specific body plan from conceptus?
141. What is a cell that has unlimited developmental potential?
142. What is another tem for a differentiated cell?
143. What is the process by which germ layers are derived?
144. What gene segments are involved in axis specification?
145. What is the term for a signal molecule that directs cells to a specific function?
146. What is the difference between asymmetrical division and symmetrical division
strategies?
147. What type of signaling molecules act directly on cells in close proximity?
148. What are two ways to deveop a gradient of a morphogen?
149. How many genes are in the FGFR family?
150. What do the four FGFR genes code for?
151. What type of extracellular domain do FGFR’s contain that bind to ligands?
152. Does FGF/FGFR have specific binding?
153. What does a highly active FGFR gene result in? (main symptom of achondroplasia)
154. What type of mutation is the mut causing achondroplasia (gain/loss of fx)
155. What is the most common form of dwarfism?
156. What inheritance does this disorder display (majority)?
157. T or F: Most people with achondroplasia inherit the disorder from their parents
158. Is achondroplasia due to germ line mosaicism?
159. T or F: Increasing maternal age increases achondroplasia incidence in offspring
160. Rank the three disorders discussed in lecture regarding FGFR mutations from lowest o
highest in severity
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161. What type of specific amino acid mutation was discussed in increasing the severity of
FGFR disorders?
162. What is the condition resulting in: Premature fusion of cranial plates, especially the
coronal suture
163. What is the inheritance in the condition in the previous question?
164. How is FGFR2 related craniosynostois tested genetically?
Fibroblast Growth Factor (Dr. Pivnick)
165. What binds to FGF that causes it to dimerize?
166. What are three types of mutations discussed n lecture that can affect FGFR?
167. What term defines proximal, middle, and distal in regards to limb segments?
168. What specific domain types does FGFR gene have?
169. Differentiate between achnodroplasia and hypochondroplasia
170. What is the largest cause of death in age group of 25-54 yrs in Achondroplasia?
171. What is the inheritance pattern of achondroplasia?
172. Are most achondroplasia mutations inherited?
173. Describe homozygous achondroplasia mutation expression.
174. What condition has the most mutations in the FGFR3 gene?
175. Which thanotophoric dysplasia is characteristic of a clover leaf skull?
176. What domain is the mutation for thanotophorc dysplasia in?
177. What FGFR is the mutation for crouzon syndrome in?
178. What FGFR is the mutation for Apert syndrome in?
179. What FGFR is the mutation for Pfeiffer tye acocephalosyndactyly syndrome in?
180. What prevents lack of testing for crouzon syndrome most of the time?
PAX Genes & Waardenberg Syndrome
181. What syndrome is involved in the family of PAX regulatory transcription factors?
182. T or F: differentiated cells contain the genetic instructions to form complete organisms
183. What transcription factor regulates the eyeless gene in drosophila?
184. What does combinatorial control mean?
185. What is a spatial signal in development?
186. How do PAX genes keep themselves turned on?
187. What does high concentrations of BMP result in? SHH?
188. What conserved regions does PAX3 have?
189. What motif does PAX regulatory proteins have that helps in its interaction with DNA?
190. Describe the binding of a gene regulatory like protein, such as PAX to DNA.
191. Which transcription factor is important in melanocyte and muscle development?
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192. Which transcription factor is important in eye development?
193. What does a loss of function in pax genes typically result in? gain of fx.?
194. What transcription factor is involved in development of the kidney?
195. What transcription factor is involved in breast cancer?
196. What condition has a white forelock, wide nasal bridge, deafness, and heterochromia
as its main presentation
197. T or F: defects in PAX6 have reduced penetrance
Hox Genes
198. What special axis do bilateral animals have that is under control of the hox genes?
199. In flies, what gene specifically caused a gain of fx. Mutation that helped to discover the
hox genes?
200. What are the advantages and disadvantages for having more than one to control a fx.?
201. In verterbrate how many genes are in the hox cluster?
202. How many gene clusters are present in mammals? How are they labeled?
203. Which Hox class is lost in mammals?
204. What domain do all these genes have in common?
205. What does this code for?
206. What is the purpose of the answer to #204?
207. What are the two classes of hox genes?
208. In centipedes, millipedes, etc. does their multiple segmented body plan result from
hox gene duplications?
209. What does a hoxa1 mutation cause in human?
210. In the layout of a limb, in humans briefly explain how the gradients in temporal
/special regards are expressed.
211. Why do mutations in some hox genes show no phenotypical expression?
212. What forms 6 digits in humans in regards to hox genes?
Development of the Eye
213. What does the optic stalk form from?
214. What forms the lens placode?
215. What invaginates to become the lens vesicle?
216. Where does the lens placode move into definitively?
217. What forms RPE and neural retina?
218. What forms the eyelids?
219. What is the purpose of the eye?
220. Describe the layers of the retina
221. What are the three main cellular layers? Acellular layers?
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222. Where are Mueller cell bodies found?
223. Mutations in what primarily causes vision loss?
224. What is an inherited disease that presents with loss of vision at birth, nystagmus
movements, ERG + for malfunction of vision
225. What does congenital mean?
226. How many causative genes have been described for LCA?
227. Where are these genes localized to?
228. What vitamin is the RPE involved in recycling?
229. What do all proteins in photoreceptors have to flow through in development?
230. What is the purpose of muller cells?
231. What LCA causing gene is involved in vitamin A recycling?
232. What LCA causing gene is involved with a transcription factor?
233. What LCA causing gene is involved in vitamin A recycling (not the answer to #230)
234. What LCA causing gene is involved with converting GTP to cGMP in the
phototransduction cascade?
235. What LCA causing gene is involved in the rate limiting step of de novo guanine
synthesis?
236. What is an LCA gene involved with nuclear transport/ chaperone activity?
237. What LCA gene is involved with connecting cilium (aka protein trafficking)?
238. What are two other genes involved with LCA that localized to the connecting cilum ?
239. What is an LCA gene involved with cell communication?
240. What is an LCA gene whose fx. Is not yet known?
Introduction to Metabolism
241. What is the sum of all chemical reactions that can occur in a living organism?
242. What is the term used for biosynthetic pathways? Energy producing pathways?
243. What is the energy currency of the body?
244. What does ATP derive its energy from?
245. What is another form of energy in vivo? (hint, reducing equivalent)
246. As a rx. Has a more negative gibbs free energy it is?
247. What organelle consumes the most oxygen in vivo?
248. Each rx. In metabolic pathway is ____________
_____ ___
_____________?
249. The product of one rx. In a pathway is the _______ for the next rx. In the same
pathway.
250. T or F: pathways can be reversible
251. What is the slowest step in a pathway called?
252. What is the first irreversible step in a pathway called?
253. What are two ways to control pathways?
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254. As the energy charge increase what also increases?
255. What are the three stages of metabolism?
Inborn Errors of Metabolism
256. Are inborn errors of metabolism individually rare? Cumulatively?
257. In what areas of ethnic groups, areas of medicine, ages, organ/tissues do IEM’s occur?
258. Are there specific ways to test for these disorders?
259. How do DNA mutations effect enzymatic activity in IEM’s?
260. Where are typical IEM’s found?
261. Are IEM’s loss or gain of fx. mutations?
262. What are two loss of fx. mutations IEM’s discussed in lecture?
263. What is an example of a gain of fx. mutation IEM? (Hint: we had an entire lecture on it,
IE FGFR3 mutation)
264. What is allelic heterogeneity?
265. What is locus heterogeneity?
Bioenergetics
266. How many kJ are in 1 kcal?
267. Bioenergetics is concerned with energy differences between what two states?
268. Is bioenergetics concerned with how a reaction occurs?
269. What is the energy content of complete oxidation to water and carbon dioxide
of the following: glucose, fatty acids, proteins, ethanol.
270. What is the 1st law of thermodynamics ?
271. What is the 2nd law of thermodynamics?
272. What is gibbs free energy eqn?
273. What do you measure temperature in gibbs eqn?
274. What is the definition of free energy?
275. What eqn relates free energy to the equilibrium constant?
276. At equilibrium what is dG? dG’?
277. If dG’ is positive what does this mean?
278. If a reaction is extremely favorable, are any products still converted back to reactants?
279. Define equilibrium for a reaction
280. Can you add Keq’s directly to sum multiple reactions? dG’S?
281. Are phosphate esters higher energy bonds?
282. Describe 5 high energy bonds
283. When EC is high what type of pathways are active? When it is low?
284. What enzyme helps equilibrate the three adenine nucleotides?
285. What molecules provide reducing power in metabolic pathways?
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286. What reduces pyruvate to lactate?
287. Is glycolysis aerobic?
288. What organelle provides most of the ATP generation in vivo?
Introduction to Metabolism II
289. What are the two reducing equivalents used most frequently in glycolysis/TCA for
energy production (hint: has adenine as part of structure)
290. What do the molecules in the answer for #288 contribute to across the mitochondrial
membrane?
291. T or F: A positive dE yields a nonspontaneous reaction
292. What pathway is used to make ethanol via bacteria?
293. What does lack of NADH in glycolysis produce?
294. Does most of our energy come from glycolysis?
295. What is the primary fuel for body metabolism?
296. What is an example of another fuel we use when glucose is not available?
297. What contains most of the energy stores in normal human individuals?
298. Name 4 anabolic pathways discussed in lecture
299. Name 4 catabolic pathways discussed in lecture
300. What is the significance of the pentose phosphate pathway?
301. What happens in the “fed state”?
302. Can RBC’s undergo oxidative phosphorylation?
303. In the liver, what enzyme activates glucose to glucose-6 phosphate?
304. What can form to make ketone bodies?
Introduction to Carbohydrate Metabolism
305. In terms of carbohydrates, what is the major source in the diet?
306. What is a form of glucose storage in mammals?
307. What carbohydrate vitamin is required for hydroxylation of proline/lysine in collagen?
308. What is a non-digestable carbohydrate that has important roles in digestion?
309. List some functions of carbohydrates
310. What two major hormones play a large role in glucose regulation in vivo?
311. What is an OGTT?
312. T or F: after a meal insulin levels go down
313. What are some pathways that increase blood glucose?
314. What are some pathways that use blood glucose?
315. Where is insulin synthesized?
316. What is insulin initially synthesized as? What is cleaved off of this and use as a glucose
indicator in blood?
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317. What are the effects of epineprhine on blood glucose? Cortisol? Growth hormone?
318. What is the normal range of glucose in the blood?
319. Describe conditions of hypoglycemia
320. Does hyperglycemia or hypoglycemia cause an increase in HbA1c?
321. How is impaired glucose tolerance diagnosed?
322. What are 3 ways to measure glucose from blood?
323. What are 2 ways to measure glucose from urine?
324. What is the most used test? Which is the most specific test?
325. Describe the test in #323
326. What is the “Gold standard” test?
327. What are some causes of glycosuria?
Digestion of Carbohydrates
328. To be metabolized all carbohydrates must be hydrolyzed to what?
329. What is starch composed of?
330. What glycosidic bond does lactose have? Sucrose? Trehalose?
331. What does amylase hydrolyze? What does this form?
332. What two complexes hydrolyze maltose in the brush border?
333. Does glucoamalyse cleave at the reducing end of maltose?
334. What does lactase hydrolyze? Trehalase?
335. Is trehalose a main component of our diet?
336. What does lactase form from lactose? Sucrase from sucrose? Trehalase?
337. What does salivary amylase form? Pancreatic?
338. What are symptoms of lactose intolerance?
339. What product do bacteria excrete that can be tested in a brush border enzyme
(carbohydrate) deficiency?
340. What is elevated in pancreatitis, obstruction of pancreatic ducts, and mumps?
341. What are two sugars bacteria breakdown that we cannot breakdown?
342. What is the function of BEANO?
343. What is the function of PRECOSE?
Glucose Transport and phosphorylation
344. For glucose metabolism to occur the sugar must do what first?
345. Can glucose alone diffuse across lipid membranes?
346. How does it get around the answer to #344?
347. How is glucose entry facilitated?
348. What are the two types of transport proteins on epithelial cells that transport glucose?
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349. Describe the structure of a facilitated glucose transporter.
350. What GLUT transporter is expressed on all tissues? Liver and pancreatic eta cells only?
Muscle and fat cells? Small intestine?
351. How does glucose bind its transport protein?
352. What are signs of hypoglycemia?
353. What is the only way glucose gets into brain?
354. What enzyme phosporylates glucose once it enters the cell?
355. What is the function of glycolysis? Pentose phosphate pathway? Glycogen synthesis?
356. Why do we phosphorylate glucose once its taken up?
357. What enzyme removes the phosphate on G6P?
358. What is different about HK IV? Aka glucokinase?
359. Where is glucose 6 phosphatase found? (organs)
360. What cellular compartment is glucose 6 phosphatase found?
Glycolysis
361. What is the universal fuel for cells?
362. What is the principal pathway by which cells generate ATP from glucose?
363. What does oxidation of glucose yield via glycolysis (net?)
364. Does glycolysis occur in both aerobic and anaerobic conditions?
365. Where does glycolysis take place?
366. What are the two phases of glycolysis?
367. Describe the preparatory phase
368. Describe payoff phase.
369. What enzyme phosphorylates glucose in the first rxn of glycolysis?
370. Which step produces NADH?
371. What steps generate ATP ?
372. How many molecules of pyruvate are formed?
373. What is the commited step of glycolysis?
374. What are the three regulated enzymes of glycolysis?
375. During strenuous exercise in anaerobic glycolysis what is produced?
376. Under aerobic conditions what happens to pyruvate?
377. What is the cori cycle?
378. What is the glycerol 3 phosphate shuttle?
379. What is the malate shuttle?
380. Does glucagon activate glycolysis?
381. What are 5 sites of regulation in glycolysis?
382. What inhibits PFK-1? Activates it?
383. What inhibits hexokinase?
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384. Describe the mechanism of F26BP allosteric control of PFK-1.
385. What inhibits pyruvate kinase? Activates?
386. Does muscle pyruvate kinase have these allosteric sites for regulation?
Gluconeogenesis
387. What precursors can be used for gluconeogenesis?
388. Where does gluconeogenesis occur?
389. Why is gluconeogenesis essential?
390. After a meal what is the source of blood glucose?
391. After 2-3 hours fasting what is source of glucose?
392. After prolonged fasting what is the source of glucose?
393. During exercise what is the source of glucose?
394. What cellular locations does gluconeogenesis occur?
395. What glycolytic enzymes does gluconeogenesis bypass
396. What enzymes are used to bypass the glycolytic reactions?
397. What does pyruvate to oxaloacetate reaction require?
398. What activates pyruvate carboxylase?
399. What does PEPCK require to convert oxaloacetate into PEP?
400. The steps between PEP and G3P occurs where? And what is the reaction pathways for
these steps?
401. What are three ways gluconeogenesis is regulated?
402. What activates pyruvate carboxylase?
403. What inhibits PDH?
404. Describe regulation of the amount of pepck?
405. What inhibits pyruvate kinase?
406. What activates F16Bpase?
407. What is the energetic requirement for gluconeogenesis?
Glycogen Metabolism
408. What is the main storage form of glucose?
409. Where are the largest amounts of glycogen found?
410. Does glycogenesis require energy? Glycogenolysis?
411. What is glycogen made of?
412. Where are branches formed?
413. What is attached at the reducing end of each glycogen molecule?
414. Can glycogen be degraded rapidly?
415. What is the purpose of liver glycogen? Skeletal muscle glycogen?
416. Does muscle have G6Pase?
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417. What provides energy for glycogenesis?
418. What is the glucose donor in glycogen synthesis?
419. What enzyme catalyzes synthesis of glycogen in alpha 1,4 linkages? 1,6?
420. What is the regulated step in glycogen degradation?
421. What removes 3 glucosyl residues from glycogen (debranching enzyme)
422. What hydrolyzes alpha 1,6 glycosidic linkages ?
423. T or F: Insulin/glucagon ratio is low glycogen is degraded
424. When you phosphorylate glycogen phosphorylase is it active? What about glycogen
synthase?
425. What removes phosphates from glycogen phosphorylase & glycogen synthase?
426. In fasting is the answer to #423 active?
427. Does AMP activate liver glycogen phosphorylase?
428. Does glucose inhibit glycogen phosphorylase in muscle?
429. Describe GSD Type I
430. Describe GSD Type II
431. Describe GSD Type III
432. Describe GSD Type IV
433. Describe GSD Type V
434. Describe GSD Type VI
435. Describe GSD Type VII
436. Describe GSD Type IX
437. Describe GSD Type X
Fructose Metabolism
438. What is the second most common sugar in our diet?
439. What transporter does fructose enter on? Where is this located (recall from earlier
lecture)
440. Describe, briefly, how fructose enters glycolysis.
441. What is the major fuel source for sperm?
442. What is the presentation of fructosuria?
443. What is the presentation for hereditary fructose intolerance?
444. How does galactose enter glycolysis?
445. What causes classical galactosemia? Nonclassical?
446. What is the presentation of classical galactosemia?
447. What is the presentation of nonclassical galactosemia?
448. What is the purpose of the pentose phosphate pathway?
449. How many NADPH are made per glucose6phosphate oxidized?
450. What stage produces NADPH? Ribose 5 phosphate?
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451. What is the predominant form of aldolase in liver? Muscle?
452. T or F: aldolase B has a higher affinity for Fructose 1 phosphate than it does for G3P
and DHAP.
453. What is the rate limiting step for fructose metabolism?
454. What pathway synthesizes fructose?
455. Describe the pathway of fructose synthesis
456. Describe the oxidative step for the PPP.
457. Describe non-oxidative step.
458. What happens in glucose 6 phosphate dehydrogenase deficiency?
Mitochondria
459. What did mt. descend from?
460. Do mt have their own genome?
461. How many mt proteins have been detected?
462. How many proteins does the mt genome encode for?
463. How many membranes does a mt have?
464. What type of bacteria did mt. descend from?
465. What is contained within the mt.intermembrane space?
466. What is contained within mt. matrix?
467. What controls ATP flux in mitochondria?
468. Describe a mt. under active respiration.
469. What protein controls contact of cristae with mt. inner membrane?
470. What are some apoptotic mitochondrial signals?
471. What structure does a porin have? What is the largest wt. molecule that can pass?
472. What is cardiolipin formed from?
473. What portion of cardiolipin associates with mt. inner membrane?
474. If FA is not saturated then what can this cause?
475. Describe a mitochondrial carrier protein
476. What anion can damage almost any intracellular product? What reduces it?
477. What can convert hydrogen peroxide to oxygen and water.
478. What reduces hydroxyradical?
479. How many e- does it take to get from oxygen to water?
TCA
480. What does TCA strip electrons from? What does it produce?
481. How are the electrons in TCA recovered?
482. How many GTP’s are produced in TCA? ATP?
483. What key intermediate feeds into the TCA cycle ? (Hint: comes from PDH complex)
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484. Where does TCA take place in the mitochondria?
485. What enzyme is bound to mitochondrial inner membrane?
486. Name the three enzymatic portions of PDH
487. What cofactor used in PDH complex catalyzes attack on alpha carbon of pyruvate by
delocalizing electrons from a carbanion?
488. What co factor acts as a long tethering arm to move acetelaldehyde?
489. How does E3 capture high energy electrons?
490. What is the starting point for TCA cycle?
491. What is the first rx. of TCA?
492. What enzyme catalyzes cleavage of citrate in the cytosol to produce acetyl coa for fatty
acid synthesis?
493. What are the two different pathways of TCA that are joined together?
494. What enzyme is alpha ketoglutarate very structurally similar to?
495. What enzyme shifts the hydroxyl on citrate
496. Does aconitase have an iron sulfur cluster?
497. Name the steps in TCA that produce reducing equivalents
498. What step produces GTP?
499. Can TCA get started without any intermediates?
500. For each turn of TCA how many carbons enter and leave?
501. What is the only 5 carbon compound in TCA?
502. Does FA synthesis put a drain on TCA?
503. What is the alpha keto acid of pyruvate?
504. IF pyruvate were to be used for biosynthesis what would it be converted to? If it was
going to be used for energy production what would it be converted to?
505. What inhibits PDH?
506. What are the three regulated steps in TCA besides PDH?
507. What is the glyoxylate cycle?
508. What unique enzymes does the gloxylate cycle have?
509. What enzyme is being targeted in the glyoxylate cycle to fight bacterial infections?
Electron Transport
510. What is the ETC?
511. Electrons in NADH and FADH2 are stored at a very ____________ reduction potential.
512. T or F: NADH has a more negative reduction potential than FADH2.
513. What is the name of complex I? what inhibits complex I?
514. What is the substrate for complex I?
515. Describe the mechanism of complex I.
516. Does FMN or Fe-S clusters get the electrons first?
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517. What is the name of complex II? What is it also a part of?
518. Where is complex II located?
519. What is the substrate for complex II?
520. What are four flavoproteins that reduce UQ in the ETC?
521. Does complex II contribute directly to the proton gradient?
522. Where do electrons from the glycerol shunt enter the ETC?
523. Is Q lipid soluble?
524. Describe the structure of complex III
525. What is unique about electron flow in complex III?
526. What happens to the e- that goes to the rieske iron center?
527. What happens to the e- that goes to bL?
528. Describe movement of protons in complex III.
529. What binds at the N side of complex III and inhibits it? P side?
530. Describe Complex IV (Cyt c oxidase)
531. How does complex IV pump protons?
532. Describe the path of electrons through complex IV
533. Why are there two hemes in complex IV?
534. Describe the formation of reduced oxygen (water) from Complex IV
535. Do the protons that reduce oxygen follow the same routes as those pumped ?
Oxidative Phosphorylation
536. How is respiration coupled to ATP synthesis?
537. Where does the energy for ATP synthesis come from?
538. What produces ATP using this gradient?
539. Which part of ATP synthase contains the catalytic subunits?
540. Which part of ATP synthase is bound in the membrane?
541. What are some ways to uncouple the proton gradient?
542. If ATPase cannot make ATP do electrons still flow in ETC to water?
543. Why would some mammals want to uncouple their proton gradient?
544. Describe the structure of ATP synthase.
545. What rotates relative to F1 in ATP synthesis
546. What are Boyer’s three postulates for the binding change mechanism in the synthesis
of ATP?
547. What proof was there for postulate 1?
548. What proof is there for postulate 2?
549. What proof is there for postulate 3?
550. What is the P/O ratio?
551. How many protons are produced in ETC for 2e-?
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552. How many ATP’s are produced per rotation of ATP synthase? How many protons does
it take to revolve ATP synthase? How many protons per ATP?
553. What forms the rotor of the molecular motor?
554. What forms the stator of the molecular motor?
555. How much ATP/NADH does glycolysis yield?
556. How much ATP/NADH does TCA yield?
557. How much ATP is produced per glucose by using glycolysis, TCA, and ETC complete
oxidation and ATP production?
558. If we use the glycerol dehydrogenase shuttle is it still 32 ATP?
559. How many hydrogens are pumped per pair of electrons?
Cytochrome P450
560. Give some examples of functions of CP450’s
561. What two CP450’s are particularly important in drug metabolism?
562. Do rodents and humans have the same CP450 content?
563. How is the name of Cytochrome P450 relevant to its function?
564. Why is the pharmaceutical industry interested in CP450’s?
565. What is the most important function of CP450’s in drug clearance in humans?
566. What protein donates electrons to P450’s in the ER? Mitochondria?
567. What is the difference in structure between ferrodoxin and NADPH reductase?
568. Name a few examples of how P450’s can be induced
569. What is a non-invasive way to measure CP450 induction?
570. What family of Cp450’s are involved in induction via cigarette smoke?
571. What is the largest family of CP450’s in humans?
572. What are some substrates of CYP26?
573. What CYP is induced in alcoholics?
574. What are some substrates of CYP3A?
575. What causes replenishes glutathione in Tylenol overdose?
576. Describe drug interaction
577. Describe using P450’s in cancer treatment
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Answers:
Mitochondrial Inheritance
1. 2
2. 16700
3. 37
4. No
5. Oxphos; production of reactive oxygen species (cell death); apoptosis signaling
6. No, nuclear DNA does but mtDNA does have contributions
7. Complex II
8. Maternal (oocyte has most mt due to sperm only having mt in motile tail)
9. Skeletal muscle, brain, tissues that have high ATP usage
10. Yes
11. Homoplasmy: A cell contains same type of mtDNA, Hetero: A cell contains diff. populations of
mtDNA, NOT mosaicism
12. No they typically must all cross some threshold for expressivity
13. Yes & also variable expressivity & pleiotropy
14. If it has deletions it is smaller& can replicate more quickly
15. Random drift, diff proportion of mt. genome into each daughter cell
16. Both males and females affected, affected mother give offspring who are affected, affected
father gives no affected offspring
17. Both unaffected and affected individuals can be either homo or heteroplasmic (recall threshold
for expression)
18. No, most are point mutations.
Functions of Secreted Glycoproteins
19. Protein with covalently attached sugar. Lower carbohydrate content than proteoglycans.
20. Yes, Albumin is the major exception
21. False, typically very few repeating sugars.
22. Mannose
23. Sialic acid, GlcNac
24. RER
25. As polypeptide is synthesized
26. Asn-X-Ser/Thr
27. Asparigine
28. T
29. Two high energy phosphate bonds attached to dolichol phosphate + preassembled sugar
30. No; depedent on modifying enzymes that trim off & add sugars
31. Happens one sugar at a time, with specific glycosyl transferases using UDP as transfer molecule
to acceptor hydroxylated AA’s , ex. Hydroxylysine & UDP galactose, PG have O-linked sugars
32. Fibronectin; 3 forms made from 1 gene by alternative splicing multifunctional
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33. Recognition; immunity; solubility
34. Mannose (without this tag we get I cell disease)
Proteoglycans
35. Core protein, repeating disaccharide, GAG, N amino sugar, acid sugar
36. Several polyanions surrounded by water and bound sodium causing a swelling pressure
37. X-X-B-B-X-B-X, where B is ARG or LYS and X is any AA
38. Lupus, degenerative joint disease,osteoarthritis
39. O-glycosylation onto serine residues
40. Amino Sugars & Acid Sugars
41. No,Yes
42. Hyaluronate, found in synovial fuid & vitreous humor
43. Chondroitin sulfate, Dermatan Sulfate, Heparin & Heparan Sulfate
44. ASP/GLU-X-Ser-Gly
45. No
46. Yes
47. Aggrecan
48. Can be stored by PG & released upon its degradation making them available when needed
49. Multivalent receptors
50. Mucopoly-saccharidosis, pt. can have GAG in urine [proteins are recycled, GAG chains degraded
in recycling pathway]
Role of Collagen in ECM
51. Collagen
52. Yes
53. I,II,III,V
54. IV,VIII
55. Type I
56. Type IV
57. 3 protein subunits interwound in a triple helix
58. Gly-X-Y; where X and Y are hydroxyproline and proline residues; tiny glycine side chain faces into
core of helix
59. Collagen fibers
60. Osteogenesis imperfect
61. Iron, vitamin C, prolyl/lysyl hydroxylase (necessary in order to O-glycosylate hydroxylysine
residues in collagen)
62. Hydroxyproline/hydroxylysine (deficiency of vit. C); Hydroxyproline deficiency lowers melting
temp. of collagen & causes it to breakdown weakening collagenous tissues
63. Collagen would crosslink/form fibrils in the cell otherwise & make dense collagenous network in
the cell which would disrupt cell interactions
64. Allysine & lysine cross links via lysyl oxidase
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65. bAPN from lathros oderatus (sweet pea) & Ehler’s Danlos Type IX (defect in lysyl oxidase)
66. Ehlers-Danlos VII (defect in N-propeptidase)
67. Procollagenase, matrix metalloproteinases (MMP), inhibitor’s called TIMP’s
68. Type IX collagen, forms kinks on the surface of Type II collagen and limits its growth
69. Type VII
Cell Interactions with ECM
70. Elastin, functions as hydrophobic springs, water is excluded typically, when elastin stretches
more water is against hydrophobic portions of elastin & causes a recoil of elasin back to its more
favorable state (water excluded)
71. Dilysine crosslinks
72. Lysine & aldehyde lysine (allysine) crosslinks form catalyzed by lysyl oxidase
73. Desmosines
74. 4
75. Beta spiral
76. Fibrillin
77. Fibronectin
78. Yes, heparin & heparin sulfate GAG’s, Integrins
79. Intracellular actin
80. RGD
81. Talin, Integrin
82. 2 transmembrane helix’s , the extracelluar portion binds matrix proteins, intracellular binds
cytoskeletal and signaling machinery
83. Yes; local cytokines/signals can alter cell adhesiveness. Integrin binding can also activate
intracellular signaling.
84. Developmental/Transcriptional controls
85. Basal lamina
86. Type IV collagen network
87. Laminin; can bind to many other things ex. Type IV collagen, perlecan, nidogen
88. Cells and ECM
89. It’s type IV collagen network acts as a sieve to filter out larger macromolecules and let smaller
molecules pass
90. Invasive cells must break through basal lamina barrier; must be able to move; must go through
second basal lamina; must be able to survive in new area
Bone
91. Bone resorption/formation
92. Yes
93. Osteoblast
94. Osteoclast
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95. Osteoid
96. Osteocyte
97. BMP’s (bone morphogentic proteins)
98. TGF-beta
99. Yes
100. Fusion of many monocytes, forms a “giant” cell
101. Osteoblast receptor, osteoblasts then signal osteoclast for bone resorption which raises
calcium in the blood
102. RANK-L
103. RANK
104. Demands for calcium and mechanical stresses
105. PTH
106. Calcitonin
107. Vitamin D, 1,25 dihydroxycholecalciferol
108. OPG, binds to RANK L receptors on osteoblasts -> prevents signaling
109. Osteoporosis, paget’s diseae, osteosclerosis, hyperparathyroidism
110. Bisphosphanate
111. Paget’s
112. Osteosclerosis
113. Fibrodysplasia
114. Cartilage scaffold (cartilage become calcified and is replaced by bone matrix), IE. Cartilage type
II, oseocalcin,osteopontin, bone siaialoprotein, highly cross linked type I Collagen replaces
cartilage
115. No
116. Matrix vesicles containing adequate calcium & phosphate for mineralization, reaches
nucleation sites to form crystallized hydroxyapatite
117. Ca10(PO4)6OH2
118. Regulators of bone formation & mineralization
119. Vitamin K, similar to blood coagulation rxn’s (oxtecalcin & matrix Gla protein require it)
120. Serves as sticky substance for bone proteins to adhere to, then to each other & bone cells
121. Type I
122. CBFA1, without CBFA1 osteoblats become adipocytes
Blood Coagulation
123. T
124. Anticoagulator (Chelator)
125. T
126. Cleavage of a disulfide bond (converts chymotrpsinogen zymogen into active chymotrypsin)
127. Thrombin
128. Fibrin/Fibronogen
129. XIIIa (fibrin stapler)
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130. Factor VIIa binds to the tissue factor and activates Xa which in turn cleaves prothrombin to its
active form, thrombin
131. Increased Factor XIa,Va,VIIIa and platelets; increased facor Va accelerates the production of
thrombin and aggregates platelets (amplification)
132. Thrombin activates fibrin from fibrinogen and Factor XIIIa (fibrin stapler) is activated to provide
more strength (Crosslinks)
133. Lipoprotein associated coagulation inhibitor (LACI)
134. Platelet adhesion
135. Antithrombin III/Heparan inactivates Xa and IXa if they are away from the injured site
136. Endothelial cells that express a protein that binds to thrombin and protein C (activated C-S
complex) this complex inactivates amplifiers Va andVIIIa
137. Plasmin (a protease that digests fibrin); activated by protein C & plasminogen activator
138. Hemophilia
139. Warfarin
Molecular Embryology
140. Differential gene expression
141. Totipotent cell
142. Unipotent
143. Gastrulation
144. Hox Genes
145. Morphogen
146. Asymmetrical: Born differently at birth (asymmetrically segregated), Symmetrical: Born the
same at birth but become different as a result of external influences
147. Paracrine signaling molecules
148. Have a gradient of the morphogen itself or have a gradient of an inhibitor which induces a
gradient in the morphogens concentration
149. 4
150. Membrane spanning tyrosine kinase receptors
151. Immunoglobulin like domains
152. No, nonspecific ligand binding occurs which results in non specific dimerization among any two
FGFRs
153. Diminished bone growth (chondrocyte growth inhibition)
154. Gain of function, further negative regulation of bone growth, excessive growth restriction
155. Achondroplasia
156. Autosomal dominant
157. F: over 80% of achondroplasia pt.’s have a new mutation
158. No
159. F: increasing paternal age increases incidence of achondroplasia in offspring
160. Hypochondroplasia, achondrplasi, thantophoric dysplasia
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161. Mutations resulting in cysteine residues; this provides more intermolecular disulfide bonds
which increases severity through permanent dimerization (more likely found in thantophoric
dysplasia)
162. Craniosynostosis
163. Autosomal dominant; a subset of FGFR disorders (missense mutations)
164. Gene scanning
Fibroblast Growth Factor (Dr. Pivnick)
165. heparin
166. ECM domain mutation, transmembrane mutation, kinase domain activation mutation
167. Rhizomelic, mesomelic, acromelic
168. Transmembrane domain, extracellular, Immunoglobulin like domain, tyrosine kinase domains
169. Achondroplasia: short limbs, higher incidence than hypochondroplasia; hypochondroplasia
does not have as short of limbs and 1/12th incidence of achondroplasia
170. Cardiovascular defects
171. Autosomal dominant
172. No, most are mutations
173. N/A; it is lethal
174. Thanatophoric dysplasia (Greek for death bringer)
175. Type II
176. FGFR3 extracellular domain for Type 1; intracellular tyrosine kinase domain for type 2
177. FGFR2; characteristic of shallow orbits, most commonly on IgIII domain of FGFR2
178. FGFR2; mental retardation, severe limb defects, CNS abnormalities
179. FGFR1 or FGFR2; characteristic of having a broad thumb or toe, FGFR2 mutation is more severe
(clover leaf skull)
180. Lack of insurance
PAX Genes & Waardenberg Syndrome
181. Waardenburg syndrome
182. T: as long as there is not a genetic defect the information should remain
183. PAX6
184. Control of a set of genes by a subset of a combination of regulatory proteins
185. Gradient of a morphogen or inducer that causes proteins to be produced based on the gradient
186. Positive feedback control
187. PAX3, PAX6
188. Homeodomain, paired regions
189. Helix-turn-helix
190. Weak interactions , H-bonds, hydrophobic interactions, van der waals, interacts with edges of
DNA through the helix-turn-helix motif
191. PAX3
192. PAX6
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193. Autosomal dominant disorders; various cancers
194. PAX2 (loss of fx.)
195. PAX2 (gain of fx.)
196. Waardenburg
197. F: complete penetrance but variable expressivity
Hox Genes
198. Anterior/Posterior axis
199. Antennapedia
200. If you lose one you can still fx. , allows for specialization of certain genes, disadvantage: genes
can be more easily lost (ex. Mammals have gained and lost some genes in comparison to
insects)
201. 14, (10-14 don’t have orthologs in flies), appears that seven of them come from an ancient
common ancestor (ex. Zen gene)
202. 4, A,B,C,D
203. 14
204. Homeodomain
205. Helix-Turn-Helix motif in proteins (two alphahelixes and AA loop between them; w/ c-terminal
that fits in major groove of DNA)
206. The proteins made from homeodomain (HTH motif) regulate other genes in the expression of
recognition sequence control in development
207. Clustered (like we just talked about in above q. and sporadic dispered, IE PAX genes)
208. No, it results in hox gene changes in regulation
209. Loss of carotid arteries…ouch
210. In a 3D array, allows for intricate specialization in many different dimensions for a complex
product
211. Because there is redundancy, loss of one gene can be filled in by the gene product of another
hox gene
212. Hox13 knockout, expresses polyalanine repeat that causes synpolydactyly
Development of the Eye
213. Extension of brain (diencephalon)
214. Contact of optic cup and surface ectoderm
215. Lens placode
216. Optic cup
217. Optic cup
218. Surface ectoderm
219. Bend incoming light through refraction (snells law) onto the retina to excite the chromophore
(opsin)
220. RPEouter nuclearlayerouter plexiform layerinner nuclear layerinner plexiform
layerganglion cell layer optic nerve fibers
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221. outer nuclear, inner nuclear, ganglion (I think RPE isn’t really containing the CB only the
extensions of rods /cones) acellular: plexiform inner, plexiform outer, RPE
222. inner nuclear layer
223. many retina and RPE expressed genes (vague, but from the slides)
224. lebers congenital amaurosis
225. unusual condition found at birth
226. 11
227. Outer retina: RPE, photoreceptors, muller cells
228. Vitamin A
229. Cilum
230. Support photoreceptor cells, forms adherens jx.with photoreceptor cells at outer limiting
membrane (remember this membrane isn’t actually a membrane just a histological artifact)
231. RPE65; critical for production of 11-cis-retinol via isomerohydrolase
232. CRX (cone rod homeobox, necessary for cone and rod structure)
233. RDH12
234. GUCY2D
235. IMPDH1
236. AIPL1
237. CEP290
238. RPGRIP1 (photoreceptor assembly); LCA5 (unknown fx.)
239. CRB
240. LCA9
Introduction to Metabolism
241. Metabolism
242. Anabolic, Catabolic
243. ATP
244. Phosphoanhydride bonds (resonance, repulsion, entropy)
245. NADH, FADH2
246. More favorable
247. Mitochondria
248. Catalyzed by an enzyme
249. Substrate
250. F, but some individual step may be
251. Rate limiting step
252. Committed step
253. Regulate enzymatic activity, or amount of enzyme, or both
254. ATP utilizing pathways
255. Breakdown of macromolecules to monomers; oxidation of monomers to acetylCoa with limited
ATP formation; complete aerobic oxidation of Acetyl-CoA to carbon dioxide and water (he
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means glycolysis here followed by TCA, in turn with pyruvate DH complex catalyzation followed
by ETC in the end for oxphos)
Inborn Errors of Metabolism
256. Yes, No
257. All
258. Yes; for selected disorders (ex. PKU)
259. Alter activity of enzyme or amount of enzyme produced
260. Mediterranean regions
261. Both
262. PKU, Beta-thalessemia
263. Achondroplasia (loss of inhibition of regulation of bone growth…)
264. Two alleles at one locus (Ex. PKU)
265. Mutations at more than one locus resulting in similar phenotypes
Bioenergetics
266. 4.18
267. Initial and final states (reactants/products)
268. No, only the beginning and ending points (independent of path)
269. 4,9,4,7 kcal/g, respectively
270. Energy cannot be created or destroyed, only interconverted
271. Spontaneous process results increased entropy
272. dG=dH-TdS
273. Kelvin , also use 2 cal/mol/K as R
274. The amount of useful chemical energy that may be obtained from a chemical reaction.
275. dG=dG’+2.3RTlog[products/reactants]
276. 0, -2.3RTlog[products/reactants]
277. Rxn. Is unfavorable, more reactants than products exist at equilibrium
278. Yes, due to thermal bombardments
279. Number of reactants converted to products each second is exactly equal to number of products
converted to reactants each second (no net change on ratio of products/reactants)
280. No, Yes
281. No, they are low energy bonds
282. Anhydrides, mixed anhydride, thiolester, enolphosphate, phophagen (EX. In order : ATP, 1,3
BPG, acylCoa, PEP, phosphocreatine)
283. Biosynthetic, energy generating pathways
284. AMP Kinase (converts 2 ADP to 1 ATP and 1 AMP)
285. NADH, FADH2
286. NADH
287. No, anoxic conditions
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288. ETC in mitochondria
Introduction to Metabolism II
289. NADH, FADH2
290. Electrochemical gradient
291. F, Recall: dG=-nJE
292. Fermentation, via alcohol dehydrogenase, etc.
293. Lactic acid
294. No, from TCA/ETC
295. Glucose
296. Ketone bodies
297. Fat, followed by protein, glycogen, and then glucose
298. Gluconeogenesis, glycogenesis, protein synthesis, lipogenesis
299. Glycolysis, TCA/ETC, proteolysis, lipolysi, glycogenolysis, pentose phosphate pathway
300. Produces pentoses needed for nucleotides and reducing equivalents to counter
oxidative damage (NADPH)
301. Storage, synthesis, oxidation
302. No, they have no mitochondria
303. Hexokinase IV
304. Acetyl coa + acetate beta-hydroxybutyrate
Introduction to Carbohydrate Metabolism
305. Starch
306. Glycogen
307. Vitamin C
308. Fiber
309. Cofactors, DNA/RNA nucleotide sugar phosphate backbone, glycoproteins, glycolipids,
proteoglycans, bacterial walls (NAG/NAM), cellulose, receptors, adhesion molecules,
etc.
310. Glucagon, insulin
311. Oral glucose tolerance test, glucose levels measured after a meal to diagnose diabetes
312. F: they go up in response to increased blood glucose levels
313. Digestion, glycogenolysis, gluconeogenesis
314. Glycolysis, glycogenesis, pentose phosphate pathway
315. Beta cells of pancreas
316. Preproinsulin, C peptide
317. Stimulates glycogenolysis/lipolysisincreases blood glucose; increases blood glucose
long term; increases hepatic glucose production and reduces glucose use
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318. 70-100 mg/dL
319. Shaky, nervous, hungry, sweaty, headache, mood change, confusion, tachycardia, loss
of consciousness (in order from least severe to most)
320. Hyperglycemia
321. Basis of OGTT, blood glucose values between normal and diabetic
322. Reduction methods, glucose oxidase assay, hexokinase assay
323. Reduction methods, glucose oxidase dipstick
324. Glucose oxidase assay; Glucose oxidase assay
325. Catalyzes conversion of glucose to gluconic acid via oxygen and forms peroxide which
reacts with a chromogen to form a colored product
326. Hexokinase assay, specific and accurate test that uses G6P DH to catalyze oxidation of
G6P and reduce NADP+ to NADH which can be measured at 340 nm on a
spectrophotometer
327. Decreased renal tubular reabsorption, pregnancy, etc. dipsticks can be used to
measure glucose in urine (some use glucose oxidase test)
Digestion of Carbohydrates
328. Monosaccharides
329. Amylase (alpha 1-4), amylopectin (alpha 1-4 and some alpha 1-6)
330. Beta 1,4; alpha 1,2; alpha 1-1
331. Alpha 1-4 linkages; maltose, isomaltose and alpha limit dextrins
332. Sucrose-isomaltase; glucoamylase (sucroisomaltase is the major one, glucoamylase
catches leftovers)
333. No, the nonreducing end
334. Beta 1,4 linkages; alpha 1-1 , respectively
335. No
336. Galactose and glucose, fructose and glucose, glucose and glucose
337. Linear and branched oligosaccharides; maltose, maltotriose, alpha limit dextrins
338. Abdominal symptoms, discomfort, distention, flatulence
339. Hydrogen ion
340. Serum and urine amylase
341. Cellulose, raffinose
342. Hydrolyze carbohydrates we can’t break down
343. Slow the breakdown of starch
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Glucose Transport and phosphorylation
344. Enter a cell
345. No, its polar
346. Bound to proteins
347. Facilitated transport via glut transporters (I-5)
348. Sodium dependent, facilitative glucose transporters
349. 12 transmembrane helices, the amino and carboxy terminals are cytoplasmic, family of
five glucose transporters
350. 1 and 3, 2, 4, 5
351. Via interaction with the transport proteins hydroxyl groups
352. 18-54mg/dL blood sugar, lightheadedness, dizziness, coma
353. Transport proteins
354. Hexokinase I-IV depending on location, forms glc-6-phosphate which is a branch point
for many pathways
355. Source of ATP; NADPH and ribose precursors; storage of glucose
356. Activates glucose for metabolism; keeps glc within cell can’t be transported back out;
determines direction of glc metabolism
357. Glucose 6 phosphatase (irreversible rxn. ; found in liver and kidney not in muscle)
358. Higher Km, therefore lower affinity, therefore takes higher conc. Of glucose to alter its
activity (reaction velocity)  better regulatory control of glucose in liver
359. Liver and kidney, NOT MUSCLE
360. ER
Glycolysis
361. Glucose (which makes ATP later)
362. Glycolysis (literall: sugar breakdown)
363. 2 ATP, 2 NADH
364. Yes
365. Cytosol, located in all tissues
366. Preparatory, payoff (energy required in preparatory, energy made in payoff)
367. Glucose broken down into Glyceraldehyde 3 phosphate and DHAP, uses 2 ATP (net
negative 2 ATP in this phase)
368. G3P converted to pyruvate, 4 ATP made, 2 NADH made
369. Hexokinase (remember from earlier we have 4 different isozymes depending on tissue)
370. The reaction of G3P to 1,3 BPG via G3P dehydrogenase
371. Pyruvate kinase step, and phosphoglycerate kinase step
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372. Two (remember we had two 3 carbon products of prepatory phase which each go into
a phase of payoff to generate ATP,NADH)
373. PFK-1
374. Hexokinase, PFK-1, pyruvate kinase
375. Lactic acid via lactate dehydrogenase (reduces pyruvate to lactate and replenishes
depleted stores of NAD+ in tissues rapidly performing glycolysis)
376. Completely oxideized via TCA and ETC to carbon dioxide and water
377. Lactate secreted into blood is taken up by liver and oxidized back to pyruvate, pyruvate
goes back to liver for gluconeogenesis
378. Cytosolic G3P DH takes electrons from NADH and makes G3P from DHAP, G3P enters
mitochondria and transfers electrons to FADH2 for transport to ETC via CoQ
379. NADH gives electrons to oxaloacetate to produce malate which can be transferred to
mitochondria, in mitochondria malate is transferred back to oxaloacetate regenerating
mitochondrial NADH, in the mitochondria oxaloacetate is converted to aspartate and
alphaketoglutarate by a transaminase that takes amino groups off glutamate and forms alpha
ketoglutarate and aspartate Aspartate freely moves into cytosol via glutamate/aspartate
transporter Aspartate is then deaminated again in the cytosol to convert back to oxaloacetate
380. Yes (means we need glucose)
381. HK, PFK1, Pyruvate kinase, PDH complex, glucose entry
382. Inhibits: ATP,citrate Activates: F-2,6-BP, AMP
383. G6P
384. F26bisphosphate is usually formed from F16bisphosphate (same substrate for PFK-1 rxn) by a separate
enzyme, PFK-2. This lets PFK1 know that there is still plenty of F16bisphosphate around and we should
continue glycolysis. When blood sugars are low glucagon causes cAMP mediated cascade that results in
phosphorylation of PFK2 and inactivation of its kinase domain that produces F26bisphosphate. Therefore
we have no more F26bisphosphate around and PFK1 is no longer activated. Furthermore, the glucagon
mediated cascade activates a separate domain on PFK2 that acts as F16bisphosphatase in
gluconeogenesis (therefore increasing glucose in response to glucagon signal).
385. ATP and F26BP/AMP , respectively
386. No, not involved in glycolysis regulation, only wants to break down glycogen to give
glucose to skeletal tissue that needs it
Gluconeogenesis
387. Lactate, pyruvate, glycerol, amino acids, etc.
388. Primarily in liver
389. Because brain and RBC’s require glucose and cannot synthesize it on their own
390. Digested food
391. Glycogenolysis
392. Gluconeogenesis
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393. Glycogenolysis and gluconeogenesis
394. Pyruvate carboxylase in mitochondria, PEPCK in between mitochondria and cytosol,
rest is in cytosol except for G6Pase which is in ER
395. Glucokinase, PFK1, pyruvate kinase
396. Pyruvate carboxylase, PEPCK, F-1,6-bipshosphatase, G6Pase
397. Pyruvate carboxylase, Biotin, active in both fed and fasting state
398. Acetyl Coa (means TCA is backed up and we should synthesize glucose)
399. GTP
400. Cytosol, reverse of glycolysis
401. Amount of substrate, amount of enzyme, activity of enzyme
402. Acetyl CoA
403. Acetyl Coa
404. Glucagon /epinephrine signal adenylate cyclasecAMPPKAtranscription factors
more PEPCK
405. cAMP and PKA (opposite to PEPCK since this is a glycolytic vs. gluconeogenitic enzyme)
406. low F-2,6 BP
407. 4 ATP, 2 GTP, and 2 NADH
Glycogen Metabolism
408. Glycogen
409. Liver and skeletal muscle
410. Yes, no
411. Alpha 1-4 and alpha 1-6 glycosidic linkages
412. At alpha-1,6-bonds
413. Glycogenin
414. Yes, enzymes are present and can work on several chains simultaneously
415. Glucose for blood; glucose for ATP use in muscle contraction
416. No, it doesn’t need it, only uses glucose for ATP, does not have gluconeogenesis
417. UTP
418. UDP-glucose
419. Glycogen synthase, amylo 4-6 transferase
420. Glycogen phosporylase
421. Transferase
422. A-1,6-glucosidase
423. True
424. Yes, no
425. Hepatic protein phosphatase 1
MBOD Q’s Block IV
1/15/2010 Nickalus Khan
426. no (leaves P on glycogen synthase making it inactive and P on glycogen phosphorylase
making it active glycogen breakdown and no glycogen synthesis)
427. No, only muscle!
428. No, only liver!
429. Glucose 6 phosphatase deficiency (Von Gierke’s); hepatomegaly, normal glycogen
structure
430. Alpha 1,4 glucosidase deficiency (Pompe’s); cardiomegaly, debranching enzyme
deficiency
431. Debranching deficiency (Cori’s disease), hepatomegaly, dx. By excessive branched
glycogen in urine
432. Branching deficiency; dx. By glycogen that has no branches in urine
433. Muscle phosphorylase deficiency (McArdles); accumulation of glycogen in muscle,
reduced ability to degrade muscle glycogen, lactate not produced in exercise, dx. By
measuring lactate deficiency
434. Liver phosphorylase deficiency
435. Muscle PFK-1 deficiency (elevated F26BP and G6P)
436. Liver phosphorylase kinase defect
437. PKA, cAMP dependent defect
Fructose Metabolism
438. Fructose
439. GLUTV, small intestine
440. FructoseF1P via frucokinase  aldolase B produces G3P and DHAP which enters via
triose phosphate isomerase
441. Fructose (sertoli cells)
442. Pretty benign, fructose appears in urine
443. Toxic deficiency of aldolase B, f1P is toxic in the liver, vomiting, hypoglycemia, etc. uses
up ATP stores and inhibits gluconeogenesis and glycogenolysis
444. Galactosegalactose 1 phosphate via galactokinase glucose 1 phosphate via
galactose 1 phosphate uridilyl transferase (Leloir pathway) via UDP glucose/galactose
exchange
445. Deficiency of galactose-1-phosphate uridyl transferase; defeiciency of galactokinase
446. Accumulation of Galactose1P, vomiting, hypoglycemia, lots of other symptoms,
galactose in blood and tissues
447. Galactose in blood and tissues, galactitol accumulates in lens which can lead to
cataracts, must avoid galactose in diet completely
448. Produce reducing equivalents, ribose phosphates for nucleotide biosynthesis,
449. 2
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450. Oxidative, non oxidative stages respectively
451. B, A, respectively: B is used for glycolytic reasons, A is used for gluconeogenic reasons
452. T
453. Aldolase B cleavage to G3P and DHAP
454. Glucose-polyol pathway
455. Glucosesoribitol/polyol via aldolase reductasefructose via sorbitol DH
456. Glucose 6 phosphateto 6 phosphoglucono-delta-lactone with generation of NADPH via
glucose 6 DH (NADPH inhibits this step)6 phosphogluconolactone to 6
phosphogluconate via glucolactonase reduced to ribulose 5 phosphate via 6
phosphoglucnate DH (therefore generate 2 NADPH and 1 mol ribulose 5 phosphate)
457. Transketolase takes 2 C fragment from xyulose 5 phosphate (which epiremized from
ribose 5 phosphat) and puts it on another ribose 5 phosphate which forms
sedoheptulose 7 phosphate and G3P, Sedoheptulose 7P and G3P then form erythrose 4
phosphate and F6P via a transaldolase, eryhthrose 4P then gains another2C fragment
from another xyulose 5 phosphate to form F6P and G3P (basically forming 3 glycolytic
intermediates)
458. Less NADPHOxidative damage, loss of reducing power to eliminate
radicalsprecipitation of Hb in RBC’s cause Heinz bodies and hemolytic anemia
Mitochondria
459. Protobacteria
460. Yes
461. 670
462. 13
463. 2
464. Alphaprotobacteria
465. Cyt-c
466. TCA enzymes, PDH complex, beta ox enzymes, DNA, RNA, ribosomes, ATP,ADP,Pi, ions,
etc.
467. Cristae contacts with inner membrane
468. Condensed matrix, expanded intermembrane space, proton pumping into
intermembrane spacecauses water to follow and swells membrane
469. Mitofilin-this is a test question almost 100% sure
470. Bad, Bix, Bax, etc. causes mt. membrane to become leaky and form pores that cause
cyt-c to leak and couple with Apaf-1 which results in a caspase cascade and cell death
471. Beta barrel, 5kDa
472. Glycerol with 2 FA
473. Unsaturated FA
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474. Cardiomyopathy, barth syndrome
475. Can carrier lots of small molecules, has structure with 6 transmembrane helices,
antiporters , alternate conformations based on salt bridgeskinks formed by proline
residues in active site, highly conserved structure
476. Superoxide; superoxide dismutase
477. Catalase
478. Vit C, Vit E
479. 4
TCA
480. Pyruvate, Carbon dioxide, respectively
481. NADH,FADH2
482. 2,0
483. Acetyl Coa
484. Matrix
485. Succinate DH
486. Pyruvate decarboxylase (E1), dihydrolipoyl transacetylase (E2), dihydrolipolyl
dehydrogenase (E3)
487. Thiamine pyrophosphate (TPP)
488. Lipoic acid
489. Takes them off lipoic acid first via FADH2 and then transfers to NADH
490. Acetyl Coa
491. Condensation of OAA with acetyl Coa to form citrate via citrate synthase
492. Citrate lyase
493. 1st takes acetyl Coa plus OAA and makes alpha ketoglutarate, second takes OAA and
makes succinyl coa for heme synthesis, when alpha ketoglutarate DH evolved it made
this a cycle
494. Pyruvate dehydrogenase complex
495. Aconitase
496. Yes
497. Isocitrate DH, alphaketoglutarate DH, succinate DH (FADH), malate DH
498. Succinyl coa synthetase
499. No, has to have a few catalytic precursors
500. 2 carbons enter via acetyl coa, 2 carbons leave via carbon dioxide
501. Alpha ketoglutarate
502. Yes, it pulls citrate out for precursors
503. Oxaloacetate
504. OAA, acetyl coa, respectively
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505. Acetyl Coa, NADH, ATP
506. Isocitrate dh, alphaketogluatate DH, citrate synthase
507. Allows for carbohydrate synthesis via 2 carbon intermediates of TCA, forms acetyl coa
and malate which can be used in gluconeogenesis
508. Isocitrate lyase and malate synthase
509. Isocitrate lyase
Electron Transport
510. A series of four protein complexes that transport electrons to oxygen and pump
protons to create a proton gradient
511. Negative, they want to react and release them to a more positive reduction potential
512. T
513. NADH DH, rotenone
514. NADH
515. Takes 2e- from NADH, moves through iron sulfur clusters & FMN & ultimately pumps 4
protons out, transfers e- to complex III via QH2
516. FMN (required since NADH donates 2e- and ferric iron only accepts 1e- at a time)
517. Succinate DH, TCA cycle
518. Mitochondrial membrane
519. FADH
520. Complex I, Complex II, ETF-QO, sn-glycerophosphate DH
521. No, it only contributes e- to the Q pool
522. Complex II (FADH2)
523. Yes’ that the whole purpose of using it to shuttle electrons through the mitochondrial
membrane
524. Rieske Iron, and two b hemes, Cytochrome c1 on cytosolic side
525. The electron pair from QH2 is split, one travels to the rieske iron center which has a
very positive dE(290mv, recall that dG=-nJdE so very spont. Rxn), another e- travels to
heme bL (low potential heme, -20mv), this happens because iron center can only accept
1 e- at a time
526. Is passed on to cyt c1 and goes onto Complex IV
527. Is passed on to bH, then passed to a fully oxidized UQ at the N side of CIII, forms
semiquinone that is fully reduced upon addition of 1 more e- (next rxn. ) passes QH2
into the Q pool
528. Each time 1 e- is moved through cycle it releases 2H+ via initial binding, and picks up
2H+ from matrix via bL pathway, however since QH2 provides 2 e- each cycle of the Q
cycle in complex III produces a net 4H+ into the cytosol and 2H+ out of the matrix
529. Antimycin, stigmatelin, respectively
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530. Secretes 2H+ into cytosol, binds oxygen in active site and uses it as a terminal electron
acceptor, contains 4 cyt c proteins
531. Takes 4e- to reduce oxygen, 4 cyt c proteins bind e- on interior of protein, in order to
compensate for this thermodynamically unfavorable placement of charge inside a
hydrophobic area we also pump 4H+ into it
532. Cyt cCopper Aheme aheme a3Copper B
533. Charge compensation, you would think that e- would flow directly to heme, however
since we need to compensate for the large charge on the interior we move protons via
one heme and electrons via another
534. Two electrons donated via copper B (one for each metal) and forma peroxide bridge
(Fe-O-O-Cu), following this two protons come in and cleave the oxygen bond; two more
electrons are dumped in to finish the reduction to water
535. No, different pathways
Oxidative Phosphorylation
536. Oxphos
537. Proton gradient
538. ATP synthase (aka complex V, aka F1F0 ATPase)
539. F1
540. F0
541. Leaky membranes, uncoupler proteins (transfer protons across) (aka DNP, FCCP,CCCP)
542. No, the proton gradient is backed up because ATPase can’t use it and the energy
within the gradient just equals the pumping energy therefore no electrons will flow
543. To generate heat (hibernation, etc.) use uncoupler chemical UCP1
544. Membrane (F0) and cytoplasmic (F1) part that are connectec by connecting stalk
545. Gamma subunit
546. 1)Energy of proton gradient is not used to form ATP but to release ATP from its binding
site, 2)three different catalytic sites with different conformations (loose, Tight, open
conformations relative to status with ADP and Pi bound (loose) or ATP (tight), or nothing
(open)), 3) conformation changes are driven by asymmetric gamma subunit relative to
F1
547. O18 incorporated into ATP, ATP with O18 in phosphate bonds not released unless
proton gradient applied
548. Structural studies have supported it
549. Actin attached to F1 and fluorescently labeled to show the rotation of 120 deg.
(triangular shape of gamma subunit) (Noji)
550. ATP produced per atom of oxygen
551. 10 (4 in C1, 4 in CIII, 2 in CIV)
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552. 12 c subunits, 12 protons per subunit, 12 protons per revolution, 3 ATP per revolution,
therefore (12 protons/rev)/ (3ATP/rev) = 4 protons/ATP
553. Epsilon, gamma, and c subunits
554. Alpha, beta, delta subunits
555. 2 ATP, 2NADH
556. 8 NADH, 2 FADH2 and 2 GTP PER GLUCOSE (NOT PER ACETYL COA)
557. 32 ATP/glucose
558. No, that means electrons enter at complex III via NADH and totally skip complex I
559. 10H+
Cytochrome P450
560. Cholesterol synthesis, regulation of blood hemostasis, steroid and arachidonic acid
metabolism, drug metabolism
561. CYP2D6, CYP3A4
562. No, and this is very important in drug testing
563. It’s a cytochrome that contains a heme that absorbs at 450nm
564. To make drugs that are more effective and not binding to them so they can be
metabolized and cleared less quickly
565. Hydroxylation, makes them more soluble for excretion
566. NADPH cytochrome P450 reductase, ferrodoxin
567. NADH reductase is a flavoprotein, ferrodoxin is a iron sulfur cluster
568. Endocrine signals (ACTH), clofibrate (peroxisomal proliferator activated receptor
PPAR), aromatic compounds (CYP1 from cigarette smoking), ethanol
569. Caffeine assay
570. CYP1
571. Family 2, ie. CYP2
572. Antiarrythmics, antidepressants, antipyschotics, beta blockers, analgesis (codeine, etc.)
573. CYP2E1
574. Tylenol, codeine, warfarin, etc.
575. N-acetyl cysteine
576. Drugs given with other drugs that are normally metabolized via the same pathway
(they compete for being metabolized and end up giving overdoses)
577. CYP1A2 can be used via transmitting its gene on a vector and inducing it’s expression in
cancer tissues; this induction results in the P450 hydroxylating the drug and causing it to
be toxic to cancer cells