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107 Cards in this Set

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200. What happens in stage two of the Calvin Cycle?

Four things...
1. 3-phosphoglycerate is reduced to glyceraldehyde 3-Pi

2. This is where most of the NADPH and ATP made by light reactions is used

3. For every 6 molecules of glyceraldehyde 3-Pi, one goes to make glucose (gluconeogensis)

4. Five molecules of glyceraldehyde 3-Pi are recycled back to ribulose 1,5-bisPi
201. What are the transformations (and the enzymes used) that convert 3-phosphoglycerate to glyceraldehyde 3-Pi?

Two beefy things...
1. Phosphoglycerate kinase/ATP converts 3-phosphoglycerate to 1,3-bisphosphoglycerate

2. Glyceraldehyde 3-Pi dehydrogenase/NADPH converts
1,3-bisphosphoglycerate to glyceraldehyde 3-Pi
202. What is the purpose of stage three in the Calvin Cycle?
To remake ribulose 1,5-bisphosphate from glyceraldehyde 3-Pi
202. What happens in stage three of the Calvin Cycle?
1. Like pentose phosphate pathway

2. Convert glyceraldehyde 3-Pi into pentose phosphates which are converted to ribulose

3. This is the 2nd step that requires ATP
203. What is the stoichiometry of CO2 assimilation in the Calvin Cycle?

Two things...
1. For every 3 CO2 fixed, one mol of glyceraldehyde 3-Pi is produced

2. Consume: 9 ATP and 6 NADPH
204. How do plants make use of the carbon that was fixed?
1. Two polysaccharides are used for energy storage (starch and sucrose)

2. One polysaccharide is used for structural purpose (cellulose)
205. How are starch and sucrose made?
1. Starch is a glucose polymer similar to glycogen (α1-4 linkage) and is made by starch synthase from ADP-glucose

2. Sucrose is made from glucose-ADP and fructose by sucrose synthase
206. How is cellulose made?
Cellulose (β1-4 linkage) is made by cellulose synthase from UDP-gucose
207. What activates the enzymes of carbon fixation (especially RUBISCO)?
The conditions caused by the light reactions
208. How is coordination between the light reactions and carbon fixation seen?

Two ways...
1. pH/Mg2+ changes regulate enzymes of carbon fixation and RUBISCO activase

2. Redox state of the chloroplast removes disulfide bonds from carbon fixation enzymes
209. How does pH and Mg2+ change due to the light reaction?
1. The light reactions generate a proton gradient causing the stroma be more alkaline

2. This promotes the transports of Mg2+ into the stroma (increase [Mg2+])
210. How do pH and Mg2+ regulate?
Several enzymes in carbon fixation are sensitive to changes in pH and [Mg2+]

Many are more active in an alkaline environment and at high [Mg2+]
211. How is RUBISCO activase affected by pH and Mg2+?
RUBISCO activase (a positive regulator of RUBISCO) favors an alkaline environment and high [Mg2+] meaning formation of RUBISCO is faster
212. What other enzyme has a similar regulation to that of RUBISCO?

Fructose 1,6-bisPi (FBP-1)

-Because it's activity increases as the pH and [Mg2+] increase
211. What modification is important for RUBISCO regulation?
A carbamoylated lysine which once again depends upon [Mg2+]
211. What does RUBISCO activase do?
It carbamoylates RUBISCO which in turns activates RUBISCO
213. How is disulfide bond formation and reduction a means of regulation?
Disulfide bonds affect many enzymes in the carbon fixation
214. What happens to the inhibitory disulfide bonds during the light reactions?
The active e- transport w/in the chloroplast reduces the inhibitory disulfide bonds
215. What enzymes are activated when inhibitory disulfide bonds are reduced?

Four enzymes...

2. FBP-1

3. Sedoheptulose 1,7-bisPi

4. Glyceraldehyde 3-Pi dehydrogenase
216. What enzyme is inactivated when disulfide bonds are reduced?
Glucose 6-Pi dehydrogenase
217. What is RUBISCO's competing side reaction?

*RUBISCO acts as an oxygenase in photorespiration
218. What two substrates can RUBISCO use?
1. O2

2. CO2
219. What happens when RUBISCO uses O2?
An oxidized product 2-phosphoglycolate (which is useless) is formed through photorespiration

*This is an even bigger problem at higher temperatures
220. What is one way to deal with the prominent and wasteful side reaction of photorespiration?
Detoxify 2-phosphoglycolate with peroxisome (glycolate pathway)
221. What is the glycolate pathway?
Conversion of phosphoglycolate to glycolate to serine and finally to phosphoglycerate

(glycolate to phosphoglycerate)
222. What is the main enzyme in the glycolate pathway?
Glycine decarboxylase complex
223. What does the glycine decarboxylase complex do?
It oxidizes 2 glycines to CO2, NH4, and serine
224. What is another solution to the problem of photorespiration?
The C4 solution where you physically separate RUBISCO activity and carbon fixation
225. What is the initial compound in C4 photosynthesis?
CO2 to initially generate a 4 carbon compound (often oxaloacetate)
226. What two cells are required for C4 metabolism?
1. Mesophyll cells

2. Bundle sheath cells
227. What happens in mesophyll cells?
CO2 is initially fixed in these cells by phosphoenolpyruvate (PEP) carboxylase to make oxaloacetate
228. What happens in bundle sheath cells?
The CO2 released from oxaloacetate by malic enzyme is used to make 3-phosphoglycerate

*raise CO2 concentration
229. What doe bundle sheath cells contain?
230. In short what is C4 photosynthesis?

Three steps...
1. CO2 is first fixed in mesophyll cells into a 4 carbon compound

2. This compound passes to bundle sheath cells and releases CO2 in high concentrations

3. The released CO2 is fixed by RUBISCO and remaining reaction of Calvin Cycle occur as in C3 plants
231. Why does C4 metabolism reduce photorespiration?

Two reasons...
1. PEP carboxylase has a much higher affinity for CO2 than RUBISCO and doesn't use O2 as an alternative substrate

2. Transport of oxaloacetate and release of CO2 in the bundle sheath cells allows the CO2 to become concentrated in these cells relative to O2 allowing RUBISCO to function more effectively
232. What is a final solution to the problem of photorespiration?
CAM plants which separate carbon fixation and RUBISCO temporally
233. What do CAM plants do to avoid the problem of photorespiration?

Two things...
1. At night, the stomata open and CO2 is fixed into oxaloacetate by PEP carboxylase

2. During the day, the stomata close (seal out O2 & minimize water loss) and the CO2 is released from oxaloacetate and RUBISCO does its thang
234. What is a lipid?
An operational definition that refers to the tendency of these molecules to partition when placed into an organic solvent
235. What one feature is shared by all lipids?
They are hydrophobic (or least part of them is)
236. Name five lipids.
1. Triacylglycerols/Fatty Acids

2. Phospholipids & Sphingolipids

3. Steroids

4. Eicosanoids

5. Isoprenoids
237. What is the function of triacylglycerols?

-Energy storage
238. What is the function of phospholipids and sphingolipids?
Structural components of membranes
239. What are the functions of steroids?

Three things...
1. Membranes (cholesterol)

2. Hormones

3. Bile salts
240. What is the function of eicosanoids?
Signaling molecules and inflammatory response
241. What are the functions of isprenoids?
Extremely Varied
1. Vanilla
2. Turpentine
3. Rubber
4. Vitamin cofactors
242. What are the two functions of fatty acids?
1. Energy storage

2. Membrane biosynthesis
243. How are FA's used for energy storage?
FA's are used to make triacylglycerols which are used to store energy fat
244. What are FA's good for energy storage?
Lipids are much more reduced molecules than carbohydrates so they can generate much more energy when oxidized to CO2
245. How are FA's used for membrane biosynthesis?
FA's are used to make phospholipids that are structural components of membranes
246. What is the structure of triacylglycerols?
Glycerol backbone esterified to 3 fatty acids
247. What are lipases?
Enzymes that hydrolyze the ester bonds in the triacylglycerols to release FA's and glycerol

(liberate FA's and glycerol)
248. Where are FA's made?

Three places...
1. Cytoplasm

2. Endoplasmic reticulum

3. Chloroplast
249. Where are FA's degraded?

Two places...
1. Mitochondrial matrix (simple ones here)

2. Peroxisomes (complex ones here)
250. Describe the big picture of fatty acid degradation.
1. Lipases liberate FA's and glycerol from triacylglycerols

2. FA's are attached to CoA to make fatty acyl CoA

3. Fatty acyl CoA is transported across inner mitochondrial membrane by carnitine transporter

4. Repeated β-oxidation breaks fatty acyl CoA into acetyl CoA

5. Acetyl CoA is processed by citric acid cycle and ox/phos
251. Describe step one in breaking down fatty acids.

Three things...
1. Convert FA to fatty acyl-CoA

2. Fatty Acid CoA synthase is enzyme

3. Large ∆G⁰
252. What are the two steps in conversion of FA to fatty acyl CoA?
1. A FA displaces outer two Pi in ATP (group transfer)

2. Thiol group on CoA carriers out nucleophilic attack kicking out Pi group
252. Where is fatty acid CoA synthase found?
It's found in the outer mitochondrial membrane
253. Describe the second step in breaking down fatty acids.

Two points...
1. Transport FA's into the mitochondrial matrix

2. Use the carnitine shuttle

**This is the rate limiting step of FA degradation**
254. What are the steps of the carnitine shuttle?

Five steps...
1. FA destined for mitochondria form fatty acyl-carnitine

2. Carnitine acyltransferase I

3. Passage into intermembrane space through large pores

4. Enter matrix by facilitated diffusion (acyl-carnitine transporter)

5. In matrix, acyl group is transfered to CoA (carnitine acyltransferase II)
255. Why is this carnitine shuttle necessary for the movement of fatty acids from the cytosol to the matrix?
The inner membrane is very specific and hard to get through (if have 14 or more C length chain need assistance)
256. How many steps are in β-oxidation?
Four steps (similar to citric acid cycle)

*It repeats six times to yield a total of 8 molecules of acetyl CoA
257. What happens it the first step of β-oxidation?

Four steps....
1. The α C of fatty acyl-CoA is oxidized
2. Form a trans double bound bwt the β and α carbons
3. Acyl-CoA dehydrogenase is enzyme
4. Form: trans-∆2-enoyl-CoA
258. What happens to the electrons removed?

Three things...
1. Electrons removed from the fatty acyl CoA are transferred to FAD
2. Reduce FAD to FADH2
3. Reduced form of dehydrogenase donates e- to ETF of mitochondrial respiratory chain
259. What enzyme is acyl-CoA dehydrogenase analogous to?
Succinate dehydrogenase
260. What happens in the second step of β-oxidation?

Three things...
1. Add water to double bond

2. Form L-β-hydroxy-acyl-CoA

3. Enoyl-CoA hydratase is enzyme
261. What is the second reaction analogous to?
The fumarase reaction in the citric acid cycle b/c in both water crosses an β-α double bond
259. How are succinate dehydrogenase and acyl-CoA dehydrogenase similar?
1. The enzyme is bound to the inner membrane

2. Form a β-α double bond

3. FAD is e- acceptor

4. Electrons from reaction ultimately enter respiratory chain
262. What happens in the third step of β-oxidation?

Four things...
1. Form β-ketoacyl-CoA
2. β-hydroxyacyl-CoA dehydrogenase is enzyme
3. NAD+ is e- acceptor
4. NADH formed donates e- to NADH dehydrogenase in respiratory chain
263. What reaction catalyzed by β-hydroxyacyl-CoA dehydrogenase analogous to?
Malate dehydrogenase reaction of citric acid cycle
264. What happens in the fourth step of β-oxidation?

Three steps...
1. β-ketoacyl-CoA reacts w/ free molecule of CoA-SH
2. Split off carboxyl-terminal 2 carbon fragment of the original FA as acetyl-CoA
3. Form acetyl-CoA and thioester of the FA shortened by 2 carbon atoms
265. What enzyme catalyzes the fourth step of β-oxidation?
Acyl-CoA acetyltransferase
266. How does the natural configuration of unsaturated FA's present a problem with β-oxidation?

Two problems
1. Unsaturated FA's have cis rather than trans double bond

2. The bonds are not in the correct place
267. How can we solve for the problem of cis rather than trans double bonds?
Use enoyl-CoA isomerase
268. What is enoyl-CoA isomerase able to do?

Two things...
1. Change cis to trans double bonds

2. Move position of double bonds
269. What is another solution to breaking down poly-unsaturated fatty acids?
Remove one or more double bonds using a reductase and then use enoyl-CoA isomerase to change the one double bond left from cis to trans
270. What problem do we face with FA's that have an odd number of carbons?
They cannot be completely converted to acetyl-CoA
271. Why can't odd number FA's be completely oxidized?
After last run through β-oxidation, you're left with propionyl-CoA (3 carbons)
272. What happens with propionyl-CoA?
It gets converted into succinyl-CoA via a methyl-malonyl-CoA intermediate
273. What new cofactor do we have in the conversion of methyl-malonyl-CoA into succinyl-CoA?
Coenzyme B12

(required by methyl-malonyl-CoA mutase)
274. Where do animals favor β-oxidation?

Where do plants favor β-oxidation?
ANIMALS favor in mitochondria

PLANTS favor in peroxisome/glyoxysome
275. How does the peroxisome/glyoxysome system differ from the mitochondrial system?

Two ways
1. P/G system's first oxidative step passes e- directly to O2 generating water

2. NADH formed in P/G system's second oxidative step cannot be reoxidized in the peroxisome or glyoxysome (reducing equivalents eventually enter mitochondria)
276. What FA degradation do peroxisomes specialize in?

Two things...
1. Very long chain FA's

2. Certain branched FA's (i.e. pytol from chlorophyll)
277. What is Zellweger syndrome?
Disease in which peroxisomes are not made leading to an accumulation of FA's

(fatal in humans)
278. Since we can't make acetyl-CoA into glucose what do we do with it?
We convert 2 molecules of acetyl-CoA into ketone bodies

*Made in liver and transported to organs that need energy
279. What happens when we are hungry and glucose isn't available?
Cells take up ketone bodies and convert them back to acetyl-CoA to be used for energy production
280. Is more ATP made with glucose or palmitoyl-CoA?
Make 10 more ATP with palmitoyl-CoA
281. What is the big picture of fatty acid biosynthesis?

Four things...
1. Malonyl-CoA (product of acetyl-CoA carboxylase) is starting material

2. FA's are made in cytoplasm w/ fatty acid synthase

3. Synthesis occurs through sequential condensation of 8 malonyl-CoA

4. Final product is palmitate
282. What is palmitate?

Two things...
1. A 16 carbon FA

2. Longer or unsaturated FA's are processed from palmitate
283. What is malonyl-CoA?

Three things...
1. The main precursor

2. Serves as an activated form of acetyl-CoA

3. Has a COO- which is a good leaving group
284. What is the first committed step, or key regulatory step, in FA biosynthesis?
Making malonyl-CoA using acetyl-CoA carboxylase, which has three functional regions
285. What are the three functional regions of acetyl-CoA carboxylase?
1. Biotin protein carrier

2. Biotin carboxylase

3. Transcarboxylase
286. What does the biotin carboxylase do?
Activates CO2 by attaching it a nitrogen in the biotin ring (ATP-dependent reaction)
287. What does transcarboxylase do?
Transfers activated CO2 from biotin to acetyl-CoA producing malonyl-CoA
288.Describe fatty acid synthase.

Three points...
1. Seven enzymes in one!

2. Does seven reactions

3. Example of substrate channeling
289. What holds the reaction intermediate in the fatty acid synthase?
The acyl carrier protein (ACP)
290. What is the ACP?

Four things
1. High-energy handle identical to CoA except that a protein replaces the adenine nucleotide

2. It's at the center of the fatty acid synthase

3. It covalently holds the reaction intermediate(s)

4. It's -SH group is the site of entry of the malonyl group during FA synthesis
291. How many substrates binding sites does fatty acid synthase have?

What are their purposes?
It has 2 substrate binding sites

-One is for the growing chain and the other is for binding acetyl-CoA
292. What is the first step in FA synthesis?
Charge the fatty acid synthase enzyme with acetyl-CoA
293. What is the reaction sequence of FA synthesis?

Five steps...
1. Condensation

2. First reduction

3. Dehydration

4. Second reduction

5. Chain transfer

*repeat sequence lots of times to increase length of FA chain
294. What's important about condensation in FA synthesis?
Form a molecule of CO2

*carbon in CO2 is the same carbon originally introduced into the malonyl-CoA
295. What's important about reduction in FA synthesis?

Two things...
1. Reduction is at C3

2. Electron donor is NADPH
296. What is important about dehydration in FA synthesis?
Form double bond bwt C2 and C3 by removing water molecule
297. What is important about the second reduction in FA synthesis?
Trans double bond is reduced and NADPH is e- donor again
298. What is important about chain transfer in FA synthesis?
Move growing chain from one site to another (cys on ACP)
299. What are two complications with FA synthesis?
1. Adding double bonds

2. Making FA's longer than 16 carbons
300. Where do we make FA's longer than 16 carbons?
In the endoplasmic reticulum by a FA elongation system that works very similar to fatty acid synthase
301. What is the precursor of longer, saturated FA's and monounsaturated as well?