Bioenergetics

Question 1

Aconitase defect

Answer 1

(TCA cycle deficiency)

Consequences: mitochondrial iron-sulfur protein deficiency in Friedreich ataxia

Question 2

alpha-ketoglutarate dehydrogenase defect

Answer 2

(TCA cycle deficiency)

Consequences: Severe encephalopathy, hypotonia, psychotic behavior, pyramidal symptoms

Question 3

Succinate dehydrogenase defect

Answer 3

(TCA cycle deficiency)

consequences: Leigh-like syndrome, paraganglioma, and pheochromocytoma, early-onset encephalomyopathies

Question 4

Succinyl CoA synthase defect

Answer 4

(TCA cycle deficiency)

Consequences: encephalomyopathy and mtDNA depletion

Question 5

Fumarase defect

Answer 5

(TCA cycle deficiency)

early encephalomyopathy, seizures, dystonia, uterine leiomyomas, papillary renal cell cancer

Question 6

AA that replenish Oxaloacetate

Answer 6

Asparagine –> aspartate

Question 7

AA that replenish Fumarate

Answer 7

phenylalanine, tyrosine, aspartate

Question 8

AA that replenish Succinyl CoA

Answer 8

Threonine, Methionine, Isoleucine, Valine –> Propionyl CoA

Question 9

AA that replenish a-ketoglutarate

Answer 9

Glutamine, Proline, Histidine, Arginine –> Glutamate

Question 10

Complex 1 (NADH dehydrogenase)

Answer 10

• transmembrane protein, e- transfers facilitated by tightly bound FMN and Fe-S clusters
• Accepts 2e- from NADH and donates them to coenzyme Q
• pumps 4 H+ ions from matrix into intermembrane space

Question 11

Complex II (succinate dehydrogenase)

Answer 11

(also TCA cycle enzyme)

• protein bound to matrix side of inner mitochondrial membrane, e- transfers facilitated by tightly bound FAD and Fe-S clusters
• transfers 2e- from FADH2 to coenzyme Q

Question 12

Coenzyme Q (ubiquinone)

Answer 12

structure: lipophilic molecule, aromatic 6-member ring and long hydrophobic side chain. Mobile, moves freely within lipid bilater of inner mt.mem. converted to ubiquinol upon acceptance of 2e-.
* accepts 2e- from either complex 1 or complex 2, transfers them to complex 3

Question 13

Complex 3 (cytochrome-c reductase)

Answer 13

structure: transmembrane protein, e- transfers facilitated by Fe-S clusters and cytocheomes -b and -c1, which harbor iron containing heme-b and -c molecules.
* accepts 22e- from ubiquinol and donates them to cytochrome-c
* pumps 2H+ from matrix into the intermembrane space

Question 14

Cytochrome C

Answer 14

structure: small protein bound to intermembrane space side of inner mt.mem. Mobile, held to membrane via electrostatic forces. e- transfers are facilitated by an iron-containing heme c group.
* Accepts e- from complex 3 and donates them to Complex 4

Question 15

Complex 4 (cytochrome-c oxidase)

Answer 15

structure; transmembrane protein, e- transfers facilitated by Cu centers and cytochromes -a and -a3, harbor iron containing heme-a molecules.

• accepts electrons from cytochrome-c and transfers them to O2 (forming water)
• pumps 4H+ from matrix to intermem.space

Question 16

Complex 5 (ATP synthase)

Answer 16

structure: multisubunit transmembrane protein, proton movement facilitated by its membrane spanning Fo domain, and ATP synthesis is facilitated by its F1 domain, which protrudes into the matrix
* moves protons from the intermem.space into matrix to obtain energy needed to synthesize ATP from ADP and Pi

Question 17

Pyruvate dehydrogenase complex (PDC)

Answer 17

3 enzymes (E1, E2, E3) and 5 coenzymes (TPP, CoA, Lipolic Acid, FAD, NAD+)
catalyzes decarboxylation of pyruvate:
pyruvate –> CO2 + Acetyl CoA + NADH
phospho form is inactive, dephos form is active
-pyruvate dehydrogenase phosphatase activates (+ by Ca2+ and Mg2+)
- pyruvate dehydrogenase kinase inactivates (+ by Acetyl CoA, NADH, ATP, - by pyruvate, CoA, NAD+ ADP)

Question 18

PDC deficiency

Answer 18

PDC is always inactive - neonatal lactic acidosis
glucose converted to lactate instead of acetyl CoA (PDC cannot decarbox pyruvate –> acetyl CoA)
causes lactic acidosis (affecting CNS), ketogenic diet recommended
- gene for E1 is on X chromosome

Question 19

Arsenite and lipolic acid

Answer 19

lipolic acid subunit modified by arsenite - arsenite links to lipolic acid suflydryl groups irreversibly and limits the available lipolid acid
many enzymes use LA as a coenzyme, these are all limited. slow poison

Question 20

each turn of TCA produces

Answer 20

1 OAA, 2 CO2, 3NADH, 1 FADH2, 1 GTP

Question 21

TCA irreversible rxns by

Answer 21

citrate synthase, isocitrate dehydrogenase, alpha ketoglutarate dehydrogenase

Question 22

TCA step 1 &2

Answer 22

Condensentation and isomerization
Acetyl acid + OAA (enz citrate synthase) –> Citrate –> (enz aconitase) isocitrate
*Citrate synthase catalyzes irreversible rxn

Question 23

TCA step 3&4

Answer 23

oxidations and decarboxylations –> NADH, CO2, Succinyl CoA
**Rate limiting step is catalyzed by isocitrate dehycrogenase
isocitrate –(oxidized &decarbox by isocitrate dehydrogenase)–> alpha ketoglutarate –> succinyl CoA
*a-ketoglut dehyrd. requires same 5 coenzymes as PDC

Question 24

TCA step 5

Answer 24

cleavage of succinyl coA to generate succinate and GTP

- catalyzed by succinyl thiokinase (succinyl coA synthetase)

Question 25

TCA steps 6-8

Answer 25

REVERSIBLE oxidations to produce FADH2, NADH, and OAA

• succinate oxidized to fumarate, produce FADH2 (enz succinate dehydrogenase)
• Fumarate –> Malate (enz fumarase)
• Malate –> OAA (produces NADH, enz malate dehydrogenase)

Question 26

Succinyl CoA in heme synthesis

Answer 26

condensation of succinyl coa and glycine –> aminolevulinic acid
- first step of heme biosynthesis and catalyzed by ALA synthase (rate limiting enzyme of heme biosynthesis), uses it B6 as cofactor

Question 27

Fluroacetate

Answer 27

(rat poison) inhibits TCA cycle. Fluoroacetate +CoA –> fluoroacetyl coA, condenses w OAA –> fluorocitrate.
Fluorocitrate competitively hinhibits aconitase, leads to buildup of citrate, which inhibits citrate synthase. Also allosterically inhibits PFK1 so glycolysis inhibited

Question 28

OxPhos location

Answer 28

mitochondria

• matrix has higher pH (basic) than intermembrane space, site of B oxidation of fatty acids, PDC, TCA cycle, etc
• inner mit.mem w large surface area, only permeable to ammonia, O2, CO2. Location of all protein complexes and carriers for oxphos
• inter.mem.space - high conc of proteins essential for ox phos

Question 29

Cytochrome C + Apoptosis

Answer 29

cyt c is a mobile carrier of electrons between C3 and C4 of ETC. When apoptosis is initiated, stimuli trigger michondrial permeability transition pore complex, causing release of cytochrome C. Induces cascade of rxns and release of caspases.

Question 30

Uncouplers

Answer 30

• generate heat due to energy from flow of protons into the matrix
• ex) Adenosine diphosphate, Cytosine arabinoside (AraC), Azidothymadine (AZT), DNP 2,3 dinitrophenol (DNP), FADH2, NADH, aspirin, thermogenin (UCP-1)
• either damage the membrane, carry protons via lipid soluble across membrane, or create channels

Question 31

Blockage of e- transfer to complexes

Answer 31

• inhibition of complex 1 by: amobarbital (amytal), rotehone, myxothiazol, piericidin A
• inhibit complex 2 by: malonate
• inhibit complex 3 by antimycin A
• inhibit complex 4 by carbon monoxide, cyanide, hydrogen sulfide

Question 32

Synthesis of ATP

Answer 32

catalyzed by Complex V
use energy from pmf –> passes protons down gradient and into matrix, ATP synthase obtains power to form ATP. 1 mol ATP req 3 protons to be passed

Question 33

malate-aspartate and glycerophosphate shuttles

Answer 33

• glycolysis produces NADH, cannot pass into mt. matrix for ETC.
  1. malate-aspartate shuttle (heart, liver, kidneys) - generates NADH in mt matrix, NADH enters ETC @ complex 1
  2. glycerophosphate shuttle (skeletal muscle and brain) - gen FADH2 in mt.memb. –> FADH donates e- at coenzyme Q
• NADH gen 3mol ATP, FADH2 gen 2mol ATP
• via antiporters