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UCSD BIBC 102 - Midterm Review

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Pyruvate dehydrogenase*Location: mito matrix*Function: pyruvate  acetyl-CoA, which enters Krebs Cycle*Overall Reaction Catalyzed: pyruvate + CoA-SH +NAD+  acetyl-CoA + CO2 + NADH*5 cofactors used:1. coenzyme A: its business end, the –SH, forms thioester bonds with pyruvate2. TPP: decarboxylize pyruvate3. lipoic acid4. FAD/FADH25. NAD+*_______acetyl CoA____ is the product of PDH and is fed into the TCA cycle. NADH is a useful byproduct and enters ETCKrebs Cycle*Location: mito matrix*Products: 3 NADH, 2 CO2, 1 FADH2, 1 GTP which ones enter ETC to make ATP? NADH and FADH2*The 2 CO2 released from the cycle are not from the acetyl-CoA that entered. The carbons from acetyl-CoA get used up in the second turn of the cycle.*regulation: essentially, the cycle is inhibited by energy-rich compounds and enhanced by energy-poor compounds1. ATP and NADH inhibit citrate synthase and isocitrate DH. Completely shuts down cycle when ATP synthesis is not needed and NADH accumulates2. citrate stimulates FA synthesis and inhibits glycolysis via PFK. Ensures proper acetyl coa level3. oxaloacetate inhibits its own synthesis by blocking succinate DH.Glyoxylate cycle*overall reaction: : 2 acetyl-CoA + 2 H20 + NAD+  succinate + 2 CoA + NADH+H+*performed by: plants, fungi, some microorg (yeast and ecoli) and some vertebrate*in plants, the cycle takes place in _glyoxysome____________*function: allow using fat for carb synthesis; cycle lets the org synthesize glu from lipid via the acetyl-CoA generated from FA oxidation-oxaloacetate and malate: can be converted into PEP  gluconeogenesis. -succinate: enter TCA to eventually form oxaloacetate*this cycle bypasses the CO2-releasing steps of Krebs Cycle. It enables 2 acetyle-CoA to produce a succinate.*vertebrates (e.g. humans) cannot run this cycle and turn fat into carb because of two missing enzymes: __isocitrate lyase_ and ___malate synthase__. It would have been a lot easier to lose weight if our body used this cycle to turn fat into easily-spent carbs  Electron Transport Chain and Oxidative Phosphorylation*net equation: NADH + 11H+(matrix) + 0.5O2  NAD+ + 10H+(IMS) + H2O*final electron acceptor: O2*complexes:1. complex I-name: NADH DH-function: extracts the electrons off NADH and pass it to ubiquinone. Uses a FMN-containing protein2. complex II-name: succinate DH-function: catalyze e- transfer from succinate to Q-this is the membrane-bound succinate DH from TCA cycle. Uses iron-sulfur centers. Has heme group.3. complex III-name: Ubiquinol-Cyt C reductase-function: carries e- from reduced Q (QH2) to Cyt C4. complex IV-name: Cyt C oxidase-function: transfers e- from Cyt C to O2. uses heme groups to transfer e-.5. complex V-name: H+-ATPase (or ATP synthase)-function: F0 is H+ channel. As H+ flows through, F1 makes ATP*define “proton motive force.” What are the two forces the proton gradient contributes?The energy stored in the gradient: both chemical and electrical potential energy.Photosynthesis: Light Reaction*chloroplast: the organelle in which photosynthesis takes place chloroplast has two membranes (outer + inner). The inner membrane encloses the stroma, which contains sacs called thylakoids. Thylakoids are usually arranged in stacks called grana. photosynthetic light reaction takes place in the thylakoid MEMBRANE (i.e. lamelle) so chloroplast has three membranes (outer, inner, and thylakoid) and 3 spatial compartments (intermembrane space, stroma, and thylakoid lumen) pigments (e.g. chlorophyll, lutein, etc) gather light energy and are located in LHC (light harvesting complexes) that surround the reaction centers.*the light reaction-location: thylakoid membrane-overall reaction: 2 H2O + 2 NADP+ + 8 photons  O2 + 2NADPH + 2 H+PS II*excitation of this reaction center drives electron flow through __Cyt b6f complex, whichpumps H+ into thylakoid lumen to create proton gradient. This gradient flows through ATP synthase to create ATP in _stroma_. The ATP is used to power the dark reactions.*_H2O_ is the source of electrons, while light provides energy of excitationPS I* excitation of this center eventually passes electron to NADP+ to produce NADPH in thrstroma.*each electron extracted from H2O requires two photons to be donated to NADP+*cyclic photosynthesis: generates only ATP (no NADPH is created). Takes place only at PS I. It gets returned to Cyt bf complex before it reaches NADP+. It allows plants to regulate the NADPH to ATP ratio.Photosynthesis: the dark reactions/Calvin Cycle*location: stroma*fixes CO2 in 3 stages:1. CO2 + ribulose 1,5 BP  2 3PG-the enzyme rubisco is important. Its cofactor Mg2+ helps to orient the substrates.It fixes CO2 with R15BP2. 3 PG reduced to a bunch of triose phosphates-NADPH is used to reduce 1,3 BPG instead of NADH3. 5 triose phosphates  3 ribulose 1,5-BP (regeneration of intermediate); BUT the sixth triose phosphate, GA3P, is created and leaves the cycle. GA3P synthesis is the goal of dark reactions.-The shuffling of carbon skeletons here resembles the non-oxidative path of Pentose Phosphate Shunt. -transaldolases (transfers 3C) and transketolases (transfers 2C and has cofactor TPP) are used to shuffle the carbon fragments in an anabolic process. RegeneratesR15BP to continue the cycle.*overall reaction: 3 CO2 + 9 ATP + 6 NADPH  GA3P + 9 ADP + 6 NADP+ + 8 Pi*summary: this part of photosynthesis is anabolic. Takes 3 CO2 and creates 1 GA3P. the purposeis to use the ATP and NADPH from light reactions to synthesize sugars. 2 GA3Ps can be combined into a larger


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UCSD BIBC 102 - Midterm Review

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