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CU: Biochemistry > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

What is proton-motive force?

A

The unequal distribution of protons generating a pH gradient and transmembrane electrical potential.

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2
Q

What is the overall reactions of the respiratory chain and ATP synthase?

A

Respiratiory Chain: (oxidation of fuels)
NADH + 1/2 O2 + H+ –> H2O + NAD+
ATP synthase: (phosphorylation of ADP)
ADP + Pi + H+ –> ATP + H2O
(Coupled by proton gradient- chemiosmotic hypothesis)

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3
Q

What is cellular respiration?

A

The generation of high-transfer-potential electrons by the CAC, their flow through the respiratory chain (ETC), and synthesis of ATP

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4
Q

What are important aspects of the mitochondria?

A

Outer membrane: permeable most small molecules & ions b/c contain mitochondrial porin (voltage-dependent anion channel, VDAC)
Inner membrane: impermeable to nearly all ions and polar molecules. large family of transporters to shuttle metabolites
- Matrix side aka N side (neg) and Cytoplasmic side aka P side (pos)

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5
Q

What potentials are converted between in oxidative phosphorylation?

A

electron-transfer potential (of NADH, FADH2 (Eo)) to phosphoryl-transfer potential (ATP, AG*’)

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6
Q

How is the redox potential of a substance determined?

A

Standard reference half-cell: electrons flow through wire generate voltage, ions flow through agar bridge.
X- + H+ –> X + 1/2 H2
Reduction potential of X:X- = voltage at start
Reduction potential of H+:H2 = 0
If voltage is known then AG’ can be determines
AG*’ = -nFAE’o

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7
Q

What do the charge values of the redox potential mean for their abilities?

A
  • Negative: strong reducer (donate electrons)
  • Positive: Strong oxidizer (accept electrons)
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8
Q

What does high-powered electrons mean?

A

They have a big AG.

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9
Q

What are the four complexes of the respiratory chain?

A

I: NADH-Q oxidoreductase
II: succinate-Q reductase
III: Q-cytochrome c oxidoreductase
IV: cytochrome C oxidase
I, III, IV: supramacromolecule complex “respirasome”

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10
Q

What is another name for coenzyme Q? What is its structure? What does it do?

A

Ubiquinone: hydrophobic quinone diffuses rapidly inner membrane
- quinone-derivative: 5 C isoprene giving hydrophobicity
e- from C I and II to III

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11
Q

What are the oxidation states of CoQ?

A

Fully oxidized: Q
Q + e- & H+ = (QH•) semiquinone
QH• - H+ = (Q•-) semiquinone radical anion
QH•+ e- & H+ = (QH2) ubiquinol

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12
Q

What is a key aspect of CoQ function?

A

electron-transfer reactions are coupled to proton binding and release (important for transmembrane proton transport)

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13
Q

What are the aspects of cytochrome c?

A

Small soluble protein, shuttle e- from III to IV
On cytoplasmic side of inner membrane
(cytochrome: electron-transferring protein containing a heme prosthetic group)
Heme in cyt c is iron-protoporphyrin IX

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14
Q

What are the aspects of an Iron-Sulfur cluster?

A

All have 4 Cys, variations: Fe, 2Fe-2S, 4Fe-4S
- e- shuttle: pick-up/release without moving

*Frataxin: synthesize Fe-S, no frataxin –> ataxia affect nervous, heart, skeletal systems

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15
Q

What goes on in NADH-Q oxidoreductase?

A

Complex I: L shaped horizontal in memb, vertical in matrix
NADH + Q + 5 H+matrix –> NAD+ + QH2 + 4 H+cytoplasm
Electrons:
NADH e- to FMN –> FMNH2 –> Fe-S
Proton Pump: (H+ attaches to/released from amino acids)
Two sets four proton half-channels
- matrix side linked by long horizontal helix (HL)
- cytoplasmic side linked by B-hair-pin-helix (BH)
- half channels open into hydrophilic funnel attached to Q chamber
- Function: Q accepts 2 e- –> Q2- cause conformational change helixes then Q2- take up 2 H+ –> QH2 join Q pool

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16
Q

What is the Q pool?

A

The ubiquinone (Q) and ubiquinol (QH2)

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17
Q

What goes in in succinate-Q reductase?

A

FADH2 does not leave this complex containing succinate dehydrogenase (CAC) and transfers electrons to Fe-S centers and finally to Q forming QH2
- Does not pump protons so FADH2 forms less ATP than NADH

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18
Q

What goes on in Q-cytochrome c oxidoreductase?

A

Receives electrons from QH2 and transfers them to Cytochrome c
- net transport of 2 H+ to intermemb.
- contains Cyt b & c1 (heme group is iron-protoporphyrin IX, Fe2+ (red) & Fe 3+ (ox))
- 4 prosthetic groups: 3 hemes & 2Fe-2S (Rieske center) coordinated to 2 His not 2 Cys

QH2 + 2 Cyt c(ox) + 2 H+ matrix –> Q + 2 Cyt c(red) + 4 H+ cytoplasm

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19
Q

What are the aspects of the cytochromes in Q-cytochrome c oxidoreductase?

A

Cyt b & c1 (heme group is iron-protoporphyrin IX, Fe2+ (red) & Fe 3+ (ox))
- b: two hemes: heme bL (low affinity) heme bH (high affinity) (diff b/c environment L nearer cytoplasmic, H nearer matrix)
- c1: one heme

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20
Q

What is the Q cycle?

A

In complex III because QH2 has 2 e- cyt c can only take 1 e-
1st QH2 bind to Qo (1st binding site): 1 e- –> Rieske cluster –> cyto c1 –> oxidized cyto c (reducing it) allowing it to diffuse
1 e- –> cyto b –> (Qi) Q converting it to Q.-
Q (was QH2) leaves
2nd QH2 repeat but 1 e- –> Q.- and 2 H+ making QH2

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21
Q

What goes on in cytochrome c oxidase?

A

2 heme groups 3 copper ions (alternate Cu+ (red) Cu2+ (ox))

cyt c e- –> CuA/CuA –> heme a –> heme a3 –> CuB the other ends at heme a3
reduces both so they can give 1 e- ea. to O2 form peroxide (O2 2-) bridge
two more cyto c release e- –> active center adding an e- and H+ to each O
two more H+ reaction releases it as H2O
CuB & heme a3 creates active center for O2 (reduced to H2O)

4 Cyt c(red) + 8 H+ matrix + O2 –> 4 Cyt c (ox) + 2 H2O + 4 H+ cytoplasm

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22
Q

How does the inner membrane increase efficiency of the respiratory chain?

A

Create a dimer (two respiratory chains) called respirasome

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23
Q

What is the danger of reducing O2? How does the body handle this?

A

Can produce reactive oxygen species (ROS) (superoxide ion (O2.-) peroxide (O2 2-)) associated with aging and diseases
- Superoxide dismutase (Mn mitochondrial version and Cu-Zn cytoplasmic version) (increased by exercise, very fast (near diffusion-limit rate)) takes superoxide radicals convert to O2 and H2O2
- Catalase takes H2O2 to O2 and 2 H2O

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24
Q

What about electron transfer in oxidative phosphorylation?

A

Protons allows for more-efficient electron transfer increasing the rate

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25
Q

How was the chemiosmotic theory tested?

A

(Bacteriorhodopsin) pumps protons when illuminated + ATP synthase.
Light –> pump –> ATP
no light –> no pump –> no ATP

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26
Q

What makes up ATP synthase? How does it associate?

A

Fo: “Stick” in membrane
- 8-14 c subunits
- 1 a subunit
F1: “ball” in matrix
- a3, B3, y, o, e
- a & B: P-loop NTPase family, only B catalytically active
- y & e: central stalk. y breaks F1 symmetry & distinguishes B by interactions
a subunit, 2 b subunits, & o: exterior column

*associates with other ATP synthases forming dimers 4 stabilization & causing curvature of inner mitochondrial membrane

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27
Q

What is the reaction of forming ATP? What is the mechanism?

A

ADP 3- + HPO4 2- + H+ = ATP 4- + H2O
Terminal O of ADP attaches phosphorus of Pi forming pentacovalent intermediate dissociates into ATP and H2O

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28
Q

What is the use of proton motive force in ATP synthase? How was this determined?

A

Proton flow is needed to release ATP from the synthase.
- causes three active sites of B subunits to change roles by moving the c ring and the ye stalk
Determined by 18O-labeled H2O

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29
Q

What are the roles of the B subunits in ATP synthase?

A

1) ADP and Pi binding (loose)
2) ATP synthesis (tight)
3) ATP release (open)

(120* determined by actin filament and fluorescence microscope)

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30
Q

How does the Fo aspect of ATP synthase drive ATP synthesis?

A

Depends on the structure of a and c subunits
- a: hydrophilic half channels positioned to directly interact with one c subunit each
- c: pair of a helices that span the membrane w/ glu or asp residue in the middle
– proton rich environment: H+ enter, bind to residue kink –> rotate
– proton poor environment: H+ leave, bind to residue unkink
- c ring tightly linked to y and e
- exterior column keeps a3B3 from moving

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31
Q

Why are shuttles needed in the mitochondria? What are the shuttles we learned about?

A

The inner mitochondrial membrane is impermeable to polar molecules and NAD+ needs to be regenerated from NADH and ATP needs to get out
- Glycerol 3-phosphate shuttle
- Malate-Aspartate shuttle
- ATP-ADP translocase/ adenine nucleotide translocase (ANT)
- phosphate carrier

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32
Q

What is the glycerol 3-phosphate shuttle?

A

In cytoplasm
1) glycerol 3-phosphate dehydrogenase catalyzes transfer of e- from NADH to DHAP forming glycerol 3-phosphate which goes across outer mitochondrial membrane
In intermembrane space
2) Glycerol 3-phosphate dehydrogenase isozyme on outer inner mitochondrial membrane glycerol 3-phosphate reoxidized to DHAP and e- pair transferred to FAD forming FADH2 which transfers them to Q forming QH2

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33
Q

What is the malate-aspartate shuttle?

A

From cytoplasm:
1) NADH e- –> oxaloacetate forming malate
2) malate enters matrix exchanging for a-Ketoglutarate
3) deoxidized by NAD+ (forming NADH) forming oxaloacetate (via malate dehydrogenase)
4) Glutamate donates amino group to oxaloacetate forming a-ketoglutarate and aspartate
5) aspartate exits in exchange for glutamate
6) in cytoplasm aspartate is deaminated forming oxaloacetate

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34
Q

How does ATP leave the mitochondria?

A

ATP-ADP translocase
ADP3- (cyto) + ATP4- (mat) –> ADP3-(mat) + ATP4- (cyto)
- no Mg2+
(energetically expensive)
In concert with phosphate carrier: Pi in OH- out (ATP synthasome)

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35
Q

How much ATP is produced by complete oxidation of glucose?

A

30 ATP: 26 from OP, 2 CAC, 2 Glycolysis

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36
Q

What regulates the ETC? What else does this regulate?

A

Phosphorylation, electrons will not flow unless ADP is phosphorylated to ATP (respiratory or acceptor control)

Also: CAC. Low ADP means NADH & FADH2 not consumed by ETC means NAD+ & FAD not available for CAC

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37
Q

How is ATP synthase regulated?

A

Inhibitory factor 1 (IF1) inhibits potential hydrolytic activity of F0F1ATP synthase so when no O2 and no PMF ATP not hydrolyzed by reverse reaction

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38
Q

What is uncoupling of ATP synthesis?

A

To generate heat.
- Uncoupling protein (UCP-1) or thermogenin: transports protons from cytoplasm to matrix using fatty acids (short circuit)
- UCP-2 and UCP-3: Very similar to UCP-1

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39
Q

Where and by what is oxidative phosphorylation inhibited?

A

ETC:
- Complex I: rotenone and amytal
- Complex III: antimycin A
- Complex IV: blocked by CN-, N3-, and CO
ATP Synthase:
- Oligomycin
Uncoupling e- transport from ATP synthase: 2,4-dinitrophenol (DNP)
ATP export: atractyloside or bongkrekic acid

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40
Q

Mitochondrial diseases?

A

Complex I most often affected
Severity depends on number of mitochondria effected
Affect especially nervous system, retina, heart

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41
Q

Mitochondria and apoptosis?

A

regulated programmed cell death by becoming highly permeable (MOMP) instigated by Bcl family proteins
- cyt C
- apoptotic peptidase-activating factor 1
- apoptosome
- caspase 9
- caspase cascade

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42
Q

What is the purpose of the pentose phosphate pathway? What are the phases?

A

To generate NADPH (phase 1) and ribose (phase 2)
Protect against oxidative stress (ROS)

Phase 1: oxidative generation of NADPH
Phase 2: nonoxidative interconversion of sugars (to create F 6P and GAP to make glucose to make more NADPH)

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43
Q

What is the use of NADPH?

A

It is the reducing/oxidizing power in the rest of the cell

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44
Q

What are the intermediates in the pentose phosphate pathway?

A

Glucose 6-phosphate (P)
Ribulose 5-P
Ribose 5-P (C5) + Xylulose 5-P (C5)
C5+ C5 = GAP (C3) + Sedoheptulose 7-P (C&)
C3+C7 = Fructose 6-P (C6) + Erythrose 4-P (C5)
C5 (Ery) + C5 (Xyl) = Fructose 6-P (C6) + GAP (C3)

(Occurs in cytoplasm)

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45
Q

What is the reaction of the first phase of the pentose phosphate pathway?

A

G 6P + 2 NADP+ + H2O –> ribulose 5-P + 2 NADPH + 2 H+ + CO2

1) Dehydrogenation by G 6P dehydrogenase to 6-phosphogluco-delta-lactone (intramolecular ester b/w C-1 & C-5)
2) Hydrolysis by lactonase to 6-phosphogluconate
3) Oxidative decarboxylation by 6-phosphogluconate dehydrogenase

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46
Q

What is the reaction of the second phase of the pentose phosphate pathway?

A

Isomerization by phosphopentose isomerase to Ribose 5-phosphate (C5)
OR
Epimerization by phosphopentose epimerase to Xylulose 5-phosphate (C5)

Transketolase takes 2-C unit from Xylulose 5P to make GAP (C3) and Sedoheptulose 7P (C7)

Transaldolase takes 3-C unit from Sedo to make Fructose 6P (C6) and Erythose 4P (C4)

Transketolase takes 2-C unit from Xylulose 5P + Erythrose to make F 6P and GAP

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47
Q

What is the mechanism of transketolase?

A

1) C-2 of bound TPP ionizes = carbanion
2) carbanion attacks ketose substrate carbonyl
3) C-C cleavage frees aldose product = activated glycolaldehyde joint to TPP
4) aldose acceptor carbonyl group condenses with glycolaldehyde forming new ketose
5) ketose released

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48
Q

What is the mechanism of transaldolase?

A

1) Schiff base forms bw transaldolase Lys and ketose substrate
2) Protonation of Schiff base, C-3 - C-4 bond split
3) Deprotonation releases aldose, 3-C fragment attached to Lys
4) Aldose binds
5) Protonation: formation of C-C bond
6) Deprotonation
4) Hydrolysis Schiff base release ketose

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49
Q

What is a schiff base?

A

An imine: N=C

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50
Q

What is the general concept of transketose/aldoses?

A

Pop off pieces and add to others:
Where break: oxidize
Where add on: reduce

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51
Q

What controls the fate of glucose?

A

The cytoplasmic concentration of NADPH:
- 4 modes (fates)
1) More ribose 5P than NADPH: bypass phase 1 of PPP start at bottom with F 6P and GAP (from glycolysis) go backwards to make ribose 5P w/o creating NADPH
2) Both ribose and NADPH: PPP
3) More NADPH than ribose 5P: PPP phase 1 then phase 2 turn ribulose to F6P and GAP bring to gluconeogenesis to make G6P and restart
4) NADPH and ATP: PPP phase 1 then ribulose to F6P and GAP into glycolysis to make pyruvate and ATP

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52
Q

How does NADPH influence ROS?

A
  • Glutathione peroxidase reduces ROS with reduced glutathione (GSH) making oxidized glutathione (GSSG)
  • Glutathione reductase uses NADPH to reduce GSSG to GSH

deficiency of G 6P dehydrogenase lead to drug-induced hemolytic anemia because there is a lack of NADPH especially felt in cells, such as RBC, that have no other reducing power
also
deficiency of G 6P dehydrogenase protects against falciparum malaria, a parasite that requires NADPH

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53
Q

Why is glycogen metabolism necessary?

A

To store glucose as a non-osmotically active polymer “glycogen” to prevent cell hypertrophy

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54
Q

What is the structure of glycogen?

A

Glycogenin protein core, ~12 layers, ~55,000 glucose residues, mostly a-1,4-glycosidic linkages with a-1,6-glycosidic linkages about every 12 residues (for faster metabolism)

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55
Q

What is the use of glycogen?

A

Not primary storage, but maintain BGL and supply quick energy

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56
Q

What is the breakdown of glycogen?

A

Glycogen
- a-1,4: to G 1P by glycogen phosphorylase using Pi and producing glycogen minus one residue
- a-1,6: transferase moves 3 glycosyls to make straight chain and a-1,6-glucosidase hydrolyses last glycosyl to glucose
G 1P to G 6P by phosphoglucomutase
Glucose to freedom or to G6P by hexokinase
G6P in Liver to glucose by glucose 6-phosphatase hydrolysis

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57
Q

What are the aspects of phosphorylase?

A

It is a dimer of 2 identical subunits
- each subunit has an amino-terminal domain which contains a glycogen binding site and a carboxyl-terminal domain
- the active site it buried to exclude water
- large gap between binding and catalytic sites allow phosphorylation of many residue without disassociation

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58
Q

What is the coenzyme of phosphorylase?

A

Pyridoxal phosphate (PLP)
- a pyridoxin (vitamin B6) derivative
- “al” indicates aldehyde that forms a Schiff base with the enzyme’s Lys
- possesses phosphate to hold Pi in active site

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59
Q

What is the mechanism of phosphorylase?

A

PLP protonates Pi as it protonates OR
HOR leaves and PI binds to glucosyl residue making G 1P

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60
Q

What are the aspects of a-1,6-glucosidase?

A

It uses H2O to add OH to glycosyl residue making glucose and H to remaining glycogen

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61
Q

What are the aspects of phosphoglucomutase?

A

contains a phosphorylated Ser to give a P to G1P making G16BP then takes a P to make G6P

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62
Q

What are the aspects of glucose 6-phosphatase?

A

Resides in luminal side of smooth ER

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63
Q

What are the aspects of phosphorylase which are integral to its regulation?

A

Two forms:
- a: favors active relaxed (R) state
- b: favors inactive tense (T) state
Inactivity due to active site blocking

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64
Q

What are the aspects of phosphorylase regulation in the Liver?

A

(BGL regulation)
Default to phosphorylase a
- deactivation by glucose binding to convert R to T state
(sufficient glucose, stop degrading glycogen)

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65
Q

What are the aspects of phosphorylase regulation in the muscle?

A

(ATP for work)
Default to phosphorylase b
- activation: AMP binding to nucleoside binding site convert T to R state
- deactivation: ATP binding to nucleoside binding site converts R to T

Type I (endurance) Fatty acids
Type IIb (quick bursts) glycogen
Type IIa trainable

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66
Q

What are the aspects of phosphorylase kinase? (structure, action, regulation)

A
  • Structure: subunit (aByo)4, y: active site, o: calcium binding protein (calmodulin), partial activation, initiated by Ca 2+ binding a & B: targets PKA, full activation
  • Action: phosphorylation of serine of phosphorylase b activating it
  • Regulation: glucagon (liver) and epinephrine (muscle)
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67
Q

How is glycogen breakdown initiation?

A

Cyclic AMP signal transduction cascade
1. Signal molecules bind to 7-transmembrane (7TM) receptors activating Gs protein. Epi: B-adrenergic, Glucagon: glucagon receptor
2. GTP-bound subunit of Gs activates adenylate cyclase catalyzing formation of second messenger cAMP from ATP
3. cAMP activates PKA
4. PKA phosphorylates phosphorylase kinase B than a activating glycogen phosphorylase
Liver: epinephrine bind to a-adrenergic receptor as well initiating phosphoinositide cascade releasing Ca2+ from ER

68
Q

How is glycogen breakdown inhibited?

A

Stopped when hormone no longer secreted
GTPase converts GTP to GDP
Phosphodiesterases: cAMP converted to AMP
Protein phosphatase 1 (PP1): deactivates by dephosphorylation phosphorylase kinase & phosphorylase (to b)

69
Q

What are the aspects of glycogen synthesis?

A

Glucose 1-Phosphate to UDP-glucose by UDP-glucose pyrophosphorylase
- UTP in PPi out then hydrolyzed to 2 Pi (makes it irreversible)
to glycogen (a-1,4) by glycogen synthase

70
Q

What are the role/aspects of glycogen synthase?

A

Role: key regulatory enzyme
- only a-1,4-glycosidic linkages
- two isozymes: liver and muscle
- two forms: a - active (dephosphorylated), b - inactive (phosphorylated)

71
Q

What is the regulation of glycogen synthase?

A

Allosterically of b by G6P stabilizing R
Covalent modification (fine tuning): many phosphorylations, many kinases
- Glycogen synthase kinase (GSK) controlled by insulin and PKA
*Phosphorylation: opposite effect of glycogen synthase and phosphorylates

72
Q

What is the cost of glycogen synthesis? (What’s the enzyme?)

A

One ATP used to phosphorylate UDP to UTP by nucleoside diphosphokinase

73
Q

What is the purpose of reciprocal regulation of the breakdown and synthesis of glycogen? What are the methods?

A

Purpose: processes do not occur simultaneously
Methods: PP1, glycogen phosphorylase, Insulin, Blood Glucose Level

74
Q

What are the aspects (structure/action) of PP1?

A

Protein phosphatase 1
- Structure: subunits (Gm, GL) scaffolds bringing together phosphatase & substrates
- Action: reverses effects of cAMP signal transduction cascade & dephosphorylates and activates glycogen synthase (b–>a)
- Regulation: activity reduced by PKA
1) Gm phosphorylated releasing catalytic subunit OR
2) Small proteins bind to catalytic subunit and inhibit

75
Q

What are the effects of insulin on the regulation of glycogen metabolism?

A

1) bind to receptor
2) phosphorylates insulin-receptor substrates (IRS)
3) trigger signal-transduction pathway, activate protein kinases
4) Inactivate glycogen synthase kinase
5) pp1 dephosphorylates glycogen synthase

76
Q

What are the effects of blood glucose level on glycogen metabolism?

A

Liver senses (using phosphorylase a) changes in BGL
- when glucose is infused phosphorylase a decreases lag then glycogen synthase a increases
- in the R phosphorylase a becomes a substrate for PP1: glucose binding releases PP1 activating it to activate glycogen synthase as it converts phosphorylase a to b
- the lag period comes from the ratio of 10 phosphorylase a per PP1 synthesis activity only increases after most phosphorylase is converted to b

Three key elements:
1) Allosteric glucose and Ser phosphate
2) PP1 inactivate phosphorylase & activate glycogen synthase
3) bind phosphatase to phosphorylase a

77
Q

What are the drug and disease applications of the glycogen metabolism?

A

Drug: disrupt phosphorylase w/ G2 for Type 2 Diabetes
Disease: G6 Phosphatase missing so glucose cannot be formed from G6P
- others: lack a-1,4-glucosidase, abnormal glycogen structure no a-1,6- glucosidase, OR muscle phosphorylase activity absent

78
Q

What is the use of fatty acids and what property instils them with this purpose?

A

Best energy source because triacylglycerols (TAG) are reduced and anhydrous (not hydrated)

79
Q

What are the roles of fatty acids?

A

1) Fuel molecules
2) Building blocks: phospholipids and glycolipids
3) Covalently modify proteins
4) Hormones & intracellular molecules

80
Q

What is the structure of fatty acids?

A

long hydrocarbon chain and terminal carboxylate group. Coalesce in a lipid droplet surrounded by phospholipids and proteins

81
Q

How are fatty acids stored?

A

In adipocytes specialized for synthesis, storage, and mobilization of TAGs

82
Q

What is the process of storing TAGs from our diet?

A

TAG move as an emulsion into the intestinal epithelium.
Gallbladder secretes bile acids
Pancreas secretes colipase and lipases
fa and MAG made and move as micelles through the plasma membrane into the cell
TAG made and form chylomicrons to move into the lymph system and then the blood to membrane-bound lipases (mostly in adipose and muscle tissue)
fa and MAG are made and transported into the tissue
TAG reformed
- adipose: storage
- muscle: oxidation for energy

83
Q

What are emulsions and chylomicrons?

A

Emulsion: particles of TAG surrounded by cholesterol and cholesterol esters
Chylomicrons: TAG and apoliprotein B-48

84
Q

What are the functions of bile acids, colipase, and lipases?

A

Bile acids: move esters to surface
Colipase: bind to lipase enabling degradation
Lipases: use H2O to remove one fatty acid

85
Q

How do we get stored fatty acids into a useful form? (three general steps)

A

1) Mobilization (degradation)
2) Activation (to transport into mitochondria
3) Breakdown (step-by-step into acetyl CoA)

86
Q

How are fatty acids mobilized?

A

In adipose tissue
glucagon and epinephrine activates 7TM receptors activating adenylate cyclase which converts ATP to cAMP that activated PKA which phosphorylated perilipin and hormone-sensitive lipase
Perilipin
1) restructures fat droplet to increase TAG accessibility
2) trigger adipose triglyceride lipase (ATGL)
ATGL binds to cofactor to turn TAG to fa and DAG
Hormone-sensitive lipase turns DAG to MAG and fa
MAG lipase turns MAG into fa and glycerol

87
Q

What does fatty acids do once they are mobilized?

A

Enter blood bound to albumin to disassociate at a cell membrane and be transported across using transport proteins and shuttled in the cell by fatty acid-binding proteins (FABP)

88
Q

What does glycerol do once it is mobilized?

A

In the liver
glycerol to L-glycerol 3P by glycerol kinase using ATP (produce ADP)
to DHAP by glycerol phosphate dehydrogenase by NAD+ (produce NADH, H+)
to D-GAP by triose phosphate isomerase

89
Q

How are fatty acids activated?

A

On the outer mitochondrial membrane
acyl CoA synthetase
1) fa and ATP to acyl adenylate (AMP) and PPi (hydrolyzed to 1 Pi)
2) CoA sulfhydryl attacks acyl adenylate forming acyl CoA and AMP

90
Q

How are activated fatty acids brought into the mitochondria that they might be broken down?

A

In the inner membrane space: acyl CoA is bound to carnitine by carnitine acyl transferase I
translocase in inner mitochondrial membrane exchanges acyl carnitine (in) for carnitine (out)
In the matrix: carnitine acyl transferase II converts acyl carnitine to acyl CoA

carnitine acyl transferase aka carnitine palmitoyl transferases

91
Q

What is carnitine and how is it converted to acyl carnitine?

A

carnitine: alcohol zwitterion
- acyl transferred from CoA S to carnitine OH

92
Q

How is acyl CoA broken down to acetyl CoA in the mitochondria?

A

Four recurring steps at the B-Carbon atom: B-oxidation pathway
Oxidation, Hydration, Oxidation, Cleavage
(of saturated even-chained fatty acids)

93
Q

What is the first oxidation step of the B-oxidation pathway?

A
  • Produces a trans C-2 C-3 double bond:
    Acyl CoA to trans-A2-Enoyl CoA by acyl CoA dehydrogenase
    Reduces: FAD because AG not enough to reduce NAD+
  • e- transport: FADH2 –> ETF-FADH2–> Fe-S to QH2

ETF: electron-transferring flavoprotein
Fe-S: ubiquinone reductase

94
Q

What is the hydration step of the B-oxidation pathway?

A
  • hydration of C-2 C-3 double bond:
    trans-A2-Enoyl CoA to L-3-Hydroxyacyl CoA by enoyl CoA hydratase
  • stereospecific: trans –> L, cis –> D
95
Q

What is the second oxidation step of the B-oxidation pathway?

A
  • converting C-3 hydroxyl group to keto group:
    L-3-hydroxylacyl CoA to 3-ketoacyl CoA by L-3-hydroxyacyl CoA dehydrogenase
  • uses NAD+
  • enzyme is stereospecific
96
Q

What is the cleavage step of the B-oxidation pathway?

A
  • of 3-ketoacyl CoA by thiol group of second CoA:
    3-ketoacyl CoA to Acyl CoA - 2C & Acetyl CoA by B-ketothiolase
    “thiolysis”
97
Q

How is the energy produced by fatty acid degradation calculated?

A

n-carbon chain makes: n/2 acetyl CoA, (n/2)-1 FADH2 and (n/2)-1 NADH
ATP: 10 per acetyl CoA, 1.5 per FADH2, 2.5 per NADH

98
Q

What is done for monounsaturated fatty acids?

A

They form a cis-A3-enoyl CoA that must be converted to trans-A2-enoyl CoA by cis-A3-enoyl CoA isomerase

99
Q

What is done for polyunsaturated fatty acids?

A

Aside from forming cis-A3-enoyl CoA like monounsaturateds they form
- 2,4-dienoyl intermediates that must be reduces using NADPH to trans-A3-enoyl CoA by 2,4-dienoyl CoA reductase and then to trans-A2-enoyl CoA using the cis-A3-enoyl CoA isomerase monounsaturateds use

100
Q

What is done for odd-chain fatty acids? The intermediates and enzymes?

A

final round produces acetyl CoA and a propionyl CoA (three carbons) which is converted to succinyl CoA

Propionyl CoA to D-Methylmalonyl CoA (carboxylation using propionyl CoA carboxylase and HCO3- + ATP producing ADP +Pi)
to L-Methylmalonyl CoA (racemization)
to succinyl CoA (intramolecular rearrangement by methylmalonyl CoA mutase)

101
Q

What about propionyl CoA carboxylase?

A

biotin enzyme - mechanism like pyruvate carboxylase

102
Q

What about methylmalonyl CoA mutase?

A

Displaces benzimidazole group of cobalamin and bind to Co with His within corrin ring contributing to bond weakness

103
Q

What are the three types of reactions of cobalamin enzyme?

A

1) intramolecular rearrangements
2) methylations
3) reduction of ribonucleotides to deoxynucleotides

104
Q

What is the cobalamin core?

A
  • corrin ring: 4 pyrrole units two directly bonded, two bound by methine bridge
  • central Co: bound to four pyrrole N and dimethylbenzimidazole derivative: in coenzyme B12 also linked with 5’-deoxyadenosyl unit or methyl group
    *essential property of coenzyme B12 is weak Co-C bond
105
Q

What is the reaction catalyzed by coenzyme B12?

A

1) Homolytic cleavage C-Co of 5’-deoxyadenosylcobalamin –> Co2+ form and 5’-deoxyadenosyl radical (-CH2)
2) -CH2 takes H from substrate –> 5’-deoxyadenosine + substrate radical
3) spontaneous rearrangement: carbonyl CoA migrates creating new radical
4) Product radical takes H from -CH3 –> Succinyl CoA + -CH2*

106
Q

What about non-mitochondrial fatty acid oxidation?

A

Peroxisomes shorten long chain fatty acids to 8 C
- the acyl CoA dehydrogenase here uses O2 to receive electrons

107
Q

What about polyunsaturated fatty acids?

A

They are unstable and readily oxidized to saturated and monounsaturated fa forming trans fatty acids which slows B-oxidation

108
Q

What are ketone bodies?

A

acetoacetate, D-3-hydroxybutyrate (majorly produced in the liver)
formed when there is not enough oxaloacetate for the acetyl CoA to enter the citric acid cycle

preferentially used by heart and kidney (brain can adapt)

109
Q

How is acetoacetate formed?

A

1) 2 acetyl CoA to acetoacetyl CoA by thiolase releasing CoA
2) to 3-Hydroxy-3-methyl-glutaryl CoA using another acetyl CoA and H2O releasing CoA (favorable by hydrolyzing a thioester linkage)
3) cleaved to acetoacetate and acetyl CoA

110
Q

How is D-3-Hydroxybutyrate formed?

A

Reducing acetoacetate in the matrix by D-3-hydroxybuterate dehydrogenase
- depending on NADH/NAD+ ratio in the mitochondria

111
Q

How is acetone formed?

A

The slow spontaneous decarboxylation of acetoacetate because it is a B-ketoacid
in starvation conditions can be converted to glucose

112
Q

How are ketone bodies degraded?

A
  • D-3-hydroxybuturate oxidized by NAD+ (producing H+, NADH) to acetoacetate
  • to acetoacetyl CoA by CoA transferase (absent in liver) succinyl CoA to succinate
  • cleaved to 2 acetyl CoA by thiolase and CoA
113
Q

What regulates fatty acid mobilization?

A

Insulin stops fatty acid mobilization

114
Q

What is the use and location of fatty acid synthesis?

A

Use: rare but in embryonic development and lactation
Location: liver and adipose tissue

115
Q

What are the steps of fatty acid synthesis?

A

Condensation: Acetyl ACP + Malonyl ACP to acetoacetyl ACP by B-ketoacyl synthase (releasing ACP and CO2)
Reduction: to D-3-Hydroxbutyryl ACP by B-ketoacyl reductase (NADPH to NADP+)
Dehydration: to crotonyl ACP by 3-hydroxyacyl dehydrase (release H2O)
Reduction: to butyryl ACP by enoyl reductase (NADPH to NADP+)

*Last three steps is the elongation cycle until get to C16-acyl ACP then thioesterase cleaved ACP off

116
Q

How is fatty acid synthesis started?

A

committed step of carboxylation of acetyl CoA to malonyl CoA by acetyl CoA Carboxylase 1 and ATP (produce ADP + Pi)

117
Q

What about acetyl CoA carboxylase 1?

A
  • biotin prosthetic group
  • forms carboxybiotin intermediate (activated CO2 group)
118
Q

What is ACP?

A

acyl carrier protein: links intermediates to sulfhydryl terminal of phosphopantetheine group

119
Q

What is Fatty Acid Synthase?

A

Catalyst for fatty acid synthesis, a complex of enzymes:
- MAT: malonyl/acetyl transferase
- B-KS: B-ketoacyl synthase
- B-KR: B-ketoacyl reductase
- DH: 3-hydroxyacyl dehydrase
- ER: enoyl reductase

120
Q

What about malonyl/acetyl transferase (MAT)?

A

catalyzes acetyl CoA + ACP <=> acetyl ACP + CoA (or propionyl CoA for odd-chain fatty acids)
and malonyl CoA + ACP <=> malonyl ACP + CoA

121
Q

What about the reaction B-ketoacyl synthase catalyzes?

A

Favorable because of a decrease in free energy: ATP used to make malonyl CoA

122
Q

What about the reaction B-ketoacyl reductase catalyzes?

A

differs from degradation by product isomer and reducing agent

123
Q

What is the mechanism of fatty acid synthase?

A

ACP buses intermediates around
1st: acetyl to KS then malonyl to KS reaction
then to HD, ER, and back to KS get new malonyl from MAT

124
Q

What is the reaction of palmitate synthesis?

A

8 acetyl CoA + 7 ATP + 14 NADPH + 6 H+ –> palmitate + 14 NADP+ 8 COA + 6 H2O + 7 ADP + 7Pi

125
Q

What is the problem with the location of fatty acid synthesis?

A

Acetyl CoA is in the mitochondria and fatty acid synthesis is in the cytoplasm and acetyl CoA cannot just diffuse through the membrane

126
Q

How does Acetyl CoA get out of the mitochondria?

A

acetyl CoA condenses with oxaloacetate forming citrate
1) form phospho-enzyme with P from ATP
2) citrate + CoA –> citroyl CoA + P
3) cleave citroyl to CoA and oxaloacetate by ATP-citrate lyase

127
Q

What is the effect of citrate in the cytoplasm?

A

Stimulates acetyl CoA carboxylase
Inhibits phosphofructokinase

128
Q

How does the oxaloacetate formed by citrate get back into the mitochondria?

A
  • Reduction: oxaloacetate to malate by malate dehydrogenase (NADH, H+ –> NAD+)
  • Oxidative decarboxylation: malate to pyruvate by NADP+-linked malate enzyme (NADP+ –> CO2, NADPH)
    *Makes NADPH for fatty acid synthesis, additional NADPH from pentose phosphate pathway
129
Q

How is ATP-citrase lyase stimulated?

A

By insulin to leading to phospholation of the lyase by protein kinase B (PKB)

130
Q

What is the use of amino acids? What is done in their excess?

A

Use: building blocks for protein and nitrogenous compound synthesis
Excess: not excreted, use as metabolic fuel
- carbon skeletons: metabolic intermediates
- amino acids to urea

131
Q

What are the essential amino acids?

A

His, Ile, Leu, Met, Phe, Thr, Trp, Val

132
Q

What happens to dietary proteins?

A

Stomach: denature by acidity and proteolysis by pepsin (active @ pH 2)
Duodenum: plasma membrane proteolytic enzymes + pancreas sodium bicarbonate (neutralize pH) and proteolytic enzymes = free aa & di/tripeptides transported into intestinal cells

transporters specific to different groups of amino acids

133
Q

What is protein turn over?

A

The degradation and resynthesis of proteins

half-lives 11 min to decades

134
Q

What is ubiquitin? What are its linkages and functions?

A

A small protein that marks other proteins for degradation linked by isopeptide bonds and linked to the Lys of proteins

other functions: DNA repair regulation, chromatin remodeling, protein kinase activation, etc

135
Q

What are the enzymes of ubiquitin attachment?

A

E1: ubiquitin-activation enzyme
E2: ubiquitin-conjugating enzyme
E3: ubiquitin-protein ligase

136
Q

What is the mechanism of ubiquitin attachment?

A

E1: adenylated Ub forming acyl adenylate at UB carboxylate C-terminal releasing PPi then transfers Ub to E1 Cys SH releasing AMP
E2: shuttles Ub from E1 SH to E2 SH
E3: transfers Ub from E2 to e-amino group on target protein
- E3 remains on target protein to make UB chain
4+ Ub chain is a strong signal

137
Q

How is ubiquitin attachment determined?

A

By degrons: specific amino acid sequence
- determined by N-terminal amino acid and modifications

Additional degrons
- cyclin destruction boxes
- PEST sequences

138
Q

How does the N-terminal amino acid determine degrons?

A

Half lives are influenced by amino acid
>20 hrs: Ala, Cys, Gly Met Pro Ser Thr Val
2-30 min: Arg His Ile Leu Lys Phe Trp Tyr
3-30 min (post chemical modification): Asn Asp Gln Glu

139
Q

How do modifications determine degrons?

A

Proteolytic cleavages
Post-synthesis addition
Other modifications (acetylation)

140
Q

What is the proteasome? What are the two units?

A

A large 26S protein that degrades Ubiquitin-marked proteins
- 19S: regulatory units (2x)
- 20S: catalytic core

141
Q

What about the 19S regulatory unit of the proteasome?

A
  • ubiquitin receptors (only protein with Ub will be degraded)
  • Isopeptidase (cleaves off Ub)
  • Unfolds protein into 20S
  • 6 ATPases of AAA class: hydrolysis assist unfolding & conformational 20S changes
142
Q

What about the 20S catalytic core of the proteasome?

A
  • barrel of 28 subunits
  • outer 2 rings: a-type subunits
  • inner 2 rings: B-type subunits
    – 3 types of active sites of different specificities all using N-terminal Thr
143
Q

What is the mechanism of the proteasome? (and what happens after)

A
  • Thr OH becomes a nucleophile and attacks peptide bond carbonyl groups
  • forms acyl-enzyme intermediates
  • end: peptides of 7-9 residues
    Then cellular protease degrade these into amino acids
  • intact for biosynthesis
  • degrade to amino groups (N for disposal in urea cycle) & carbon skeletons
144
Q

What processes are regulated by protein degradation?

A
  • Gene transcription
  • Cell-cycle progression
  • Organ formation
  • Circadian rhythms
  • Inflammatory response
  • Tumor suppression
  • Cholesterol metabolism
  • Antigen processing
145
Q

What is the first step of amino acid degradation? What are the options?

A

Removal of nitrogen
- a-amino group to a-ketoglutarate forming glutamate then oxidative deamination
- direct deamination of

146
Q

What are the catalyst and prosthetic group for an a-amino group transfer to a-ketoglutarate?

A
  • catalyst: amino transferases (“transaminases”) catalyzes a-amino group from a-amino acids to a-ketoacids
  • prosthetic group: pyridoxal phosphate
    *reversible to form a-amino acids from a-ketoacid
147
Q

What are the aspects of oxidative deamination? (steps of catalyst) (inhibition/simulus)

A

glutamate N to NH4+ (free ammonium ion)
catalyst: glutamate dehydrogenase (uses NAD+ pr NADP+)
- dehydration of C-N forms ketimine intermediate
- hydrolysis releases NH+
- reversible reaction driven by product/reactant concentrations
- Inhibited: GTP promoting abortive complex formation
- Stimulated: ADP destabilize abortive complex formation

148
Q

What is an abortive complex?

A

Product replaced by substrate before reaction completion

149
Q

What are the aspects of direct deamination?

A

No a-ketoglutarate to be converted into NH4+
- Ser & Thr
- catalyst: Ser/Thr dehydratase dehydration then deamination
–PLP prosthetic group

150
Q

What are the aspects of PLP? The mechanism for aminotransferases?

A

Pyridoxal phosphate
- aldehyde: allows Schiff base formation
– binds with enzyme Lys until aa added then bind with aa (external aldimine)
–> quinonoid by a-C aa deprotonation
–> ketimine by reprotonation at aldehyde C
–> a-ketoacid & PMP (pyridoxamine phosphate)
*Then reverse
- a-ketoacid with enzyme (E)-PMP –> aa & E-PLP

151
Q

What are the reactions of PLP? And general principles of PLP?

A

decarboxylations, deaminations, racemizations, aldol cleavages
- protonation makes it an e- sink
- bond being broken (a-carbon of amino acid) must be perpendicular to the pi orbitals of the electron sink (in line with the PLP ring)

152
Q

What is the fate of nitrogen once it has been removed from an amino acid?

A
  • consumed in biosynthesis of N compounds (some)
  • converted to urea (most)
153
Q

What happens when N is produced NOT in the liver?

A
  • Glucose-alanine cycle: glutamate N to pyruvate making alanine –> liver
  • Glutamine: glutamate + NH4+ ATP –> glutamine + ADP + Pi –> Liver (glutamine synthetase)
154
Q

What is the urea cycle?

A

carbamoyl phosphate + ornithine (ornithine transcarbamoylase)
citrulline + aspartate & ATP (AMP, PPi) (argininosuccinate synthetase)
Argininosuccinate (argininosuccinase) –> fumatrate + arginine
Arginine –> ornithine (Arginase: + H2O, produce Urea)

(citrulline out of mitochondria, ornithine into)

155
Q

What is the committed reaction of the urea cycle? (The steps)

A

HCO3- + NH3 –> carbamoyl phosphate by carbamoyl phosphate synthetase 1 (uses 2 ATP: essentially irreversible)
a. phosphorylation HCO3- –> carboxyphosphate
b. + NH3 –> carbamic acid (loose Pi)
c. phosphorylation –> carbamoyl phosphate

156
Q

How is carbamoyl phosphate synthetase regulated?

A
  • allosteric: NAG synthesized by NAG synthase activated by Arg
    – inhibited by acetylation when not a lot of aa making NH4
  • NAD+: stimulate deacetylase to activate (energy poor state)
157
Q

What amino acids become a-ketoglutarate?

A

Arginine, Glutamate, Glutamine, Histidine, Proline

Q H E R P

158
Q

What amino acids become Succinyl CoA?

A

Isoleucine, Methionine, Threonine, Valine
M I T V
(first form proprionyl)

159
Q

What amino acids become fumarate?

A

Aspartate, Phenylalanine, Tyrosine
F Y D

160
Q

What amino acids become oxaloacetate?

A

Asparagine and Aspartate
N D

161
Q

What amino acids become Pyruvate?

A

Alanine, Cysteine, Glycine, Serine, Threonine, Tryptophan

W A G C S T

162
Q

What amino acids become Acetyl CoA?

A

Isoleucine, Leucine, Tryptophan
(Ketogenic)
I W L

163
Q

What amino acids become acetoacetyl CoA?

A

Leucine, Lysine, Phenylalanine, Tryptophan, Tyrosine
(ketogenic)
K L F W Y

164
Q

What are ketogenic amino acids?

A

Amino acids that degrade to acetyl CoA or acetoacetyl CoA
- Leucine and lysine are the only solely ketogenic amino acids
- I, F, W,Y are both ketogenic and glucogenic

165
Q

What are glucogenic amino acids?

A

amino acids that degrade to pyruvate, a-ketoglutarate, succinyl CoA, fumarate, or oxaloacetate

166
Q

What does methionine degradation form? Why is this important?

A

forms succinyl COA by making S-Adenosylmethionine intermediate (SAM)
- important methylating agent

167
Q

How are aromatic amino acids broken down?

A

Uses molecular oxygen by adding the oxygen, deamination, breaking open ring, and cleavage to two groups
- Monooxygenases incorporate one O
- dioxygenases incorporate two O
*Add in oxygens until the ring breaks

CU: Biochemistry (4 decks)

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