1
Q
What is ATP?
A
a nucleotide - comprised of a base (adenine), a sugar (ribose), and three phosphate groups which are labeled alpha, beta, gamma
2
Q
How does ATP take place in catabolism and anabolism?
A
catabolism (break down nutrients) - use available energy to turn ADP to ATP
anabolism (making nutrients) - ATP donates its energy to endergonic processes that require energy
3
Q
What is the delta G hydrolysis for ATP
A
-50 kJ/mol
4
Q
Where does the energy processing take place in ATP?
A
the phosphates
5
Q
What does hydrolysis do to ATP?
A
releases the electrostatic repulsion among the negative charges
6
Q
What is the formula for delta G0’
A
Free energy of products-Free energy of reactants
7
Q
What are the steps to hydrolysis of ATP?
A
- hydrolysis breaks the phosphoanhydride bond between the gamme and the beta phosphate(s)
- hydrolysis of the alpha beta linkage yields AMP + PPi which releases the last phosphoanhydride bond
8
Q
How does ATP transfer energy to an enzyme?
A
pyrophosphoryl PPi or adenylate moiety
9
Q
What is catabolism vs anabolism?
A
Catabolism: breakdown of large molecules and foodstuffs into simpler products
Anabolism: building up larger and more complex molecules from simple precursors
10
Q
Catabolic pathways ___ anabolic pathways ____
A
Catabolic pathways converge (e.g. most sugars, fats and amino acids are converted to acetyl co a) and Anabolic pathways diverge (e.g. acetyl co a forms large diversity of things)
11
Q
What is a metabolic pathway?
A
series of enzyme catalyzed reactions which converts a precursor into a product through a series of intermediates (metabolites)
12
Q
What is a metabolic inhibitor?
A
things that inhibit the metabolic pathway
13
Q
What is standard reduction potential?
A
the tendency of a chemical reaction to be reduced (E0)
14
Q
What is E0 vs E0’
A
E0 - standard reduction potential
E0’ - standard reduction potential at standard conditions
15
Q
Which way do electrons flow?
A
to the half reaction with the higher reduction potential
16
Q
What value of deltaE0’ is a spontaneous rxn
A
when deltaE0’>0
17
Q
What is the Gibbs free energy formula?
A
deltaG0’ = -nF(deltaE0’)
F = faraday constant = 96.5 x 10^3 J/V mol
18
Q
What is an enzyme cofactor?
A
chemical compounds that help carry out enzyme functions
19
Q
what are two types of enzyme cofactors?
A
inorganic ions
coenzymes (many are derivatives of adenosine)
20
Q
What is co-enzyme A (CoA/CoASH)
A
a cofactor that acts as a carrier of acyl groups RECOGNIZE STRUCTURE
21
Q
What does CoASH form in terms of derivatives?
A
thioester derivatives with organic acids - any coenzyme A thioester derivative is called acyl CoA
22
Q
What is NAD+ and NADP+ and FAS and FMS
A
universal electron carriers, electrons that are removed are transferred onto these cofactors reducing them
23
Q
What is NAD+ and NADP+ derived from?
A
vitamin niacin B3
24
Q
Where do the redox reactions occur in NAD+ and NADP+?
A
in the nicotinamide ring, during oxidation of it, two hydrogen atoms are removed (dehydrogenation), during reduction, they accept a hydride ion to become reduced to NADH or NADPH
25
What is NAD+ used for
used as oxidizing agent
26
What is NADPH used for?
reducing agent
27
What are FAD and FMN derived from?
riboflavin (B2)
28
What is the redox chemistry of flavin nucleotides (FAD and FMN)?
they can accept either one or two electrons in the form of one or two hydrogen atoms
reduced forms (FADH2 and FMNH2)
greater diversity of reactions because they can accept 1 or 2 e
29
What is the redox chemistry of fats?
chemically very reduced - most of the carbon atoms are CH2 so it releases the max free energy when oxidized all the way to CO2
30
What are the three stages to completing the oxidation of FA to CO2 and H2O?
Stage 1: Beta oxidation - gives rise to acetyl CoA and reduced cofactors
Stage 2: Citric acid cycle
Stage 3: ETC
31
How are FA catabolized?
2 carbons at a time!
32
How are fatty acids prepared for catabolism?
activating them to fatty acyl CoA
Fatty Acid + CoA + ATP -> Fatty Acyl-CoA + AMP + 2Pi
33
Where does Acyl CoA synthetase occur?
outer mitochondrial membrane
34
What are the two steps to fatty acid activation?
1. nucleophillic oxygen of fatty acid attacks the alpha phosphate of ATP forming PPi and acyl adenylate
2. thiolate anion form of coenzyme A, reacts with acyl adenylate, AMP is leaving group and fatty acyl-CoA is formed
KNOW STRUCTRE
35
Where does beta oxidation take place?
mitochondrial matrix
36
How are fatty acids transported into the mitochondrial matrix in preparation for beta oxidation?
acyl-carnitine/carnitine transporter in the form of fatty acyl-carnitine esters
37
What are the four steps to beta oxidation?
1. oxidation
2. hydration
3. oxidation
4. thiolysis
38
What does beta oxidation do after one cycle?
each round produces an acetyl CoA and shortens the fatty acid chain by two carbons, they are repeated until all carbons are released as acetyl CoAs
1 FADH2 is formed at each turn
1 NADH is formed at each turn
39
Explain step 1 of beta oxidation?
oxidation by FAD forms a double bond between the alpha and beta carbons of fatty acyl CoA (alkane to alkene)
40
Explain step 2 of beta oxidation?
Water is added across the double bond to give an alcohol at the beta carbon (hydration of alkene to alcohol)
41
Explain step 3 of beta oxidation?
oxidation of the alcohol by NAD+
42
Explain step 4 of beta oxidation?
lysis of the bond between the alpha and beta carbons (thiolysis) done by thiolase enzyme
43
What are three stages to the oxidation of glucose?
stage 1: glycoysis + pyruvate dehydrogenase
stage 2: TCA cycle
stage 3: ETC
43
How is glucose transported into cells
cannot enter through passive diffusion, transporter proteins called GLUTs catalyze glucose transport.
44
Glucose is the only pathway that can provide energy under __________ conditions
anaerobic conditions
45
Where does glycolysis occur?
cytosol
46
What are the first five reactions called and the last five reactions?
first five - preparatory phase
last five - payoff phase
47
Explain step 1 of glycolysis
phosphorylation of glucose: atp is used to phosphorylate glucose to glucose-6-phosphate and is catalyzed by hezokinase
48
Explain step 2 of glycolysis
phosphohexose isomerisation: glucose 6-phosphate is isomerized by phophohexos isomerase to fructose 6-phosphate
49
What is step 3 of glycolysis
the second phosphorylation: fructose 6-phosphate is phosphorylated to fructose 1,6-bisphosphate using phosphofructokinase 1 (PFK-1)
50
What is step 4 of glycolysis
the six-carbon fructose is split into two 3-carbon units: fructose 1,6-bisphophate is split into dihydroxyacetone phophate (ketone) and glyceraldehyde 3-phosphate (aldehyde) by aldolase
51
What is step 5 of glycolysis
interconversion of the triose phosphates: dihydroxyacetone phosphhate is isomerized to glyceraldehyde 3-phosphate (G3P) by triose phosphate isomerase
52
What is step 6 of glycolysis?
glyceraldehyde 3-phosphate dehydrogenase reaction: G3P plus an inorganic phosphate is oxidized using NAD+ as a cofactor to 1,3-bisphosphoglycerate by G3P dehydrogenase
53
Explain step 7 of glycolysis
Phosphoryl transfer from 1-3-BPS to ADP the first substrate level phosphorylation: 1,3-BPG's phosphate group is transferred into ADP to synthesize ATP and 3-phosphoglycerate using phosphoglycerate kinase
54
Explain step 8 of glycolysis
Conversion of 3-phosphoglycerate to 2-phosphoglycerate: done by a mutase where the phosphate is moved from carbon 3 to carbon 2
55
What is step 9 of glyolysis?
dehydration of 2-phosphoglycerate: done by an enolase releasing H2O and making phosphoenolpyruvate
56
What is step 10 of glycolysis
transfer of the phosphoryl group from phosphoenolpyruvate to ADP (the second substrate level phosphorylation): using pyruvate kinase phosphoenolpyruvate uses ADP and turns it into ATP to convert to pyruvate (enol) and then transfers it to pyruvate (keto) through tautomerization
57
What are the three routes pyruvate is further metabolized to?
Ethanol production, lactate production (anaerobic) or CO2 and H2O (aerobic)
58
What is the fate of pyruvate under aerobic conditions?
oxidized to acetyl CoA by pyruvate dehydrogenase which is what connects glycolysis and citric acid cycle
KNOW STRUCTURE
59
What is the pyruvate dehydrogenase complex?
When pyruvate is oxidized to CoA
Pyruvate + CoASH -> Acetyl CoA + CO2
using NAD+, FAD, CoA, TPP, Lipoate as cofactors
60
What happens to acetyl CoA after pyruvate dehydrogenase complex?
Enters citric acid cycle
61
How does NADH enter the mitochondria in order to enter the ETC?
shuttles
62
What is the first shuttle used to bring NADH into the mitrochondria?
1. malate-aspartate shuttle
NADH reacts gets oxidized with oxaloacetate and the malate transports the electron across and then NAD+ is reduced back to NADH and malate becomes oxaloacetate again, it becomes aspartate ad it goes back through the inter mitochondrial membrane to start process again
63
What is the second shuttle for transferring NADH into the mitochondria?
2. glycerol 3-phosphate shuttle
oxidizes NADH + H+ to NAD+ by dihydroxyacetone to G3P which gives the 2H+ to FAD which then is reduced to FADH2 which gives H2 to coenzyme Q in the IMM and the cycle repeats
64
What do animals do with pyruvate under anaerobic conditions?
reduce pyruvate to lactate which uses NADH+ H+ and oxidizes it to NAD+
65
What is the cori cycle?
During recovery from exercise, liver converts lactate back to glucose through gluconeogenesis, glucose is then returned to muscles to replenish muscle glycogen stores
66
What does yeast do with pyruvate when its under anaerobic conditions?
converts pyruvate to ethanol and CO2 (fermentation): 2 step rxn intermediate is acetaldehyde
67
What does the TCA cycle do?
Takes acetyl-CoA and oxidizes them to CO2, energy released through thesse oxidations is conserved in the form of reduced cofactors NADH and FADH2
68
What is step 1 of the TCA cycle
condensation fo acetyl CoA with oxaloacetate to form citrate: using citrate synthase, h2o is added to combine acetyle CoA and oxaloacetate and CoASH is a product to form citrate
69
What is step 2 of the TCA cycle?
isomerization of citrate by aconitase: aconitase removes the water from citrate and turns it into cis-aconitate, hydration of cis aconitate by aconitase makes isocitrate where the OH and H's are switched on C2 and C3
70
What is step 3 of TCA cycle
oxidative decarboxylation of isocitrate: alcohol to ketone using isocitrate dehydrogenase, isocitrate leaves two H atoms for NAD+ to be reduced to NADH+H+ and this generates alpha ketoglutarate and CO2
71
What is step 4 of TCA cycle
Oxidative decarboxylation of alpha ketoglutarate: alpha ketoglutarate dehydrogenase converts alpha ketoglutarate into succinyl CoA and reduces NAD+ to NADH + H and turns CoASH to CO2
72
What is step 5 of TCA cycle
Substrate level phosphorylation: high energy thioester bond of succinyl CoA is hydrolyzed in a rxn coupled to either GTP or ATP synthesis, succinyl CoA is turned into succinate by succinyl CoA synthase by phosphorylating GDP and creating CoASH
73
What is step 6 of TCA cycle
Oxidation of succinate to fumarate: FADH is reduced to FADH2 and succinate is oxidized to fumarate by succinate dehydrogenase
74
What is step 7 of TCA cycle
hydration of fumarate to malate: alkene, fumarate is hydrated to the alcohol, malate by H2O and fumarase
75
What is step 8 of TCA cycle
oxidation of malat to oxaloacetate: malate is oxidized to oxoloacetate by malate dehydrogenase, NAD+ is reduced to NADH+H
76
What is the net creating of TCA cycle?
- two carbons of acetyl group of acetyl CoA are oxidized to CO2
- electrons from oxidation reduce 3NAD+ and 1 FAD
- one GTP or ATP is formed
- intermediates ar enot depleted
77
What is the primary goal of the ETC?
oxidation of carbohydrates, lipids and amino acids culminates with oxidative phosphorylation where the energy released from the oxidation of NADH and FADH2 is used to synthesize ATP
78
Where does the ETC take place?
In the mitochondria
79
What are the four complexes that electrons are passed through in the ETC?
NADH
Complex 1: NADH dehydrogenase
Complex 2: Succinate dehydrogenase
Q
Complex 3: Cytochrome C reductase
Cytochrome C
Complex 4: cytochrome oxidase
O2
80
What is coenzyme Q?
Can accept one electron to form semiquinone radical or two electrons to form alcohol ubiquinol, ubiquinol can freely move in the membrane, carrying electrons from one etc complex to the other
81
What is cytochrome C?
soluble protein in the IMM and shuttles electrons from complex 3 to complex 4, carries one electron at a time
82
How do the complexes move electrons?
1. Complex 1 and 2 transfer electrons to Q, reducing it to QH2
2. QH2 passes electorns to cytochrome c through complex 3
3. Complex 4 transfers electrons from reduced cytochrome c to O2
electron flow is accompanied by proton flow
83
What does CoQ collect?
Reducing equilvalents from NADH, succinate dehydrogenase, Acyl CoA dehydrogenase, (FADH2), G3P shuttle
84
What is the proton gradient?
For each pair of electrons transferred frpm NADH to O2:
4 protons are pumped by cmplx 1
4 protons are pumped by complex 3
2 protons are pumped by complex 4
6 protons are pumped for each FADH2 oxidized
all of this creates a proton gradient
85
What is the proton motive force?
The energy stored in the proton gradient
86
Which side has more protons in the proton gradient?
More protons on the intermembrane space and less protons in the matrix
87
What are the two components of proton motives forces
1. chemical potential energy
2. electrical potential energy
88
What is the chemiosmotic theory?
protons flow back into the matrix passively down its concentration gradient through the proton core of the ATP synthase enzyme, the energy of the electrochemical gradient is released and is used for the generation of ATP by the ATP synthase enzyme
89
What inhibits ATP synthesis?
inhibitor of the electron transfer will inhibit both the oxygen consumption and the ATP synthesis, which also blocks the ETC
90
What happens when ATP synthase is blocked?
protons that are pumped remain in the inter membrane space and build up to a very high concentration, energy required to pump protons against this gradient will eventually exceed the energy available from NADH oxidation
91
What does DNP do?
is able to uncouple without damaging the mitochondrial membrane, ATP synthesis ceases, but ETC continues
92
What are the two functional domains of ATP synthase?
F1 peripheral
F0 integral
93
What are the 9 subunits of F1 of ATP synthase?
3 alpha subunits, 3 beta subunits form alpha 3 beta 3 complex, gamma, epsilon, delta at stationary complex
94
What is the composition of F0
ab2C8-17
c10 ring
a subunit resides in the membrane and wraps partially around the c10 ring and contains two half channels for the movement of protons
95
BIOC 2580 - Second Half
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