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What molecule provides the most energy when fully oxidized?
the one w/ the most C-H and C-C bonds
How do cells obtain most of their energy?
thru oxidation rxns (not by direct rxn w/ oxygen)
Thermodynamics
how much energy is released as a rxn proceeds towards equilibrium
Does thermodynamics help predict the rate of a reaction?
no
Gibbs free energy (ΔG)
how far a rxn is from equilibrium
-ΔG
exergonic; reactants → products (Keq >1)
+ΔG
endergonic; products → reactants (Keq < 1)
What does it mean if ΔG = 0?
rxn is at equilibrium
ΔG°
change in energy from standard conditions to equilibrium
How do enzymes increase reaction rate?
they lower activation energy, but don’t change Keq
Change in enthalpy (ΔH)
difference in bond energies between reactants and products
-ΔH
exothermic; >stable bonds are formed and heat is released
+ΔH
endothermic; < stable bonds are formed and heat is absorbed
Change in entropy (ΔS)
randomness
If a system’s entropy decreases, what happens to the entropy of its surroundings?
it increases
How does ATP usually provide energy?
thru group transfers (not by direct hydrolysis)
Glycolysis
1 glucose → 2 pyruvate (NADH) and net gain of 2 ATP
Where does glycolysis occur?
in cytosol
What input does the preparatory stage of glycolysis require?
2 ATP
How much ATP does the payoff stage of glycolysis yield (NOT net gain of glycolysis)?
4 ATP
What is the irreversible step of glycolysis?
phosphofructokinase adds a phosphate to fructose-6-P → fructose-1,6-bisP
How does feedback inhibition of phosphofructokinase work?
small molecules bind to non-active site areas → alters conformation of active site
What inhibits phosphofructokinase (and glycolysis)?
ATP, fatty acids, citrate
What stimulates phosphofructokinase (and glycolysis)?
AMP and ADP signal low energy levels
During the set-up glycolysis reaction, what is the 1st byproduct that’s formed?
CO2
Why is the set-up glycolysis reaction not considered an oxidation reaction?
C-C bond of NADH is replaced by a C-H bond (both are reduced bonds)
What enzyme does the set-up glycolysis reaction take place on?
E1
What enzyme does the oxidation glycolysis reaction take place on?
E2
What is the byproduct of the oxidation glycolysis reaction?
acetyl-CoA
Why is glycolysis irreversible and regulated?
to avoid futile cycling (opposing rxns run simultaneously)
Gluconeogenesis
NADH converts to glucose using “bypass” enzymes and reversible glycolysis rxns
Fermentation
anaerobically regenerates NAD+ from NADH to maintain glycolysis; inefficient way to make energy
Type I fermentation
NADH → lactate and NAD+ (for glycolysis)
Type II fermentation
NADH → ethanol and NAD+ (for glycolysis)
What happens to NADH under anaerobic conditions?
fermentation
What happens to NADH under aerobic conditions?
pyruvate dehydrogenase (PDH) converts NADH into acetyl-CoA
Pyruvate dehydrogenase (PDH)
converts NADH into acetyl-CoA
acetyl-CoA
substrate for citric acid cycle
What are key cofactors of PDH?
NAD+, FAD, TPP, and lipoic acid
Thiamine pyrophosphate (TPP)
acts as an anion involved in the rxn
What compound would be elevated in a thiamine deficient person?
NADH
Lipoic acid
acyl and redox (substrate) carrier
Where does the citric acid cycle occur?
mitochondria
What are inputs of the citric acid cycle?
acetate from acetyl-CoA (2C and 4 reduced bonds)
How many reduced bonds does acetate have? In other words, how many reduced cofactors are formed when acetate is fully oxidized in the citric acid cycle?
4
What are outputs of the citric acid cycle?
3 NADH, FADH2, 2CO2, 1 GTP
Why can the E3 subunit be the same in PDH and α-ketoglutarate dehydrogenase?
the substrates for it are the same in both rxns
When the citric acid cycle is running, the concentration of oxaloacetate must be…
quite low relative to L-malate, so that the actual ΔG is negative
What acts as inhibitors of the citric acid cycle?
high levels of metabolites that indicate there’s plenty of energy in the cell
Lipids
include membrane components, hormones, vitamins, etc.
Triglyceride
type of lipid used for energy storage
Detergent
emulsifies (breaks down) triglycerides
Lipase
responsible for hydrolysis of triglycerides to fatty acids, which can be transported across the plasma membrane
High levels of fatty acids are toxic, so they’re…
continuously being disassembled to cross tissues and reassembled so they don’t reach toxic levels
Once inside the cell, fatty acids are…
activated by acyl-CoA synthetases on the outer membrane of the mitochondria
Why do fatty acids bond w/ carnitine prior to β-oxidation?
fatty-acyl-carnitine can be transported across inner mitochondrial membrane; fatty-acyl-CoA can’t
What happens to fatty acids in the mitochondria?
they’re destined for breakdown (β-oxidation)
What happens to fatty acids in cytosol?
fatty acid (and triglyceride) synthesis occurs when there’s excess carbs
β-oxidation
conversion of fatty acid into 8 acetyl-CoA units in mitochondria
How many acetyl-CoAs are formed from (n - 1) β-oxidations?
n acetyl-CoAs
What type of enzyme typically catalyzes redox rxns?
dehydrogenases
Why is NAD+, FAD, and CoA involved in these rxns?
they have 1 end to carry electrons or chemical units, and another to base-pair at the active site of a ribozyme (RNA enzyme w/ a catalytic binding pocket)
High levels of acetyl-CoA ___ PDH and ___ the citric acid cycle.
inhibits; has no effect on the rate of
What was concluded from the Knoop experiment?
fatty acids are oxidized 2-C units at a time
Urea cycle
transforms toxic ammonia byproduct into urea, which is eliminated thru mammal urine
Ammonia
toxic b/c it crosses the blood/brain barrier and converts to glutamine, which can alter osmotic balance → swelling and coma
Glutamine synthetase
detoxifies ammonia generated by non-liver tissues by converting NH4+ and glutamate to glutamine
Glutamine
won’t diffuse across blood/brain barrier; disassembled to release ammonia
Where does the urea cycle occur?
mitochondria and cytosol
Where is urea produced?
liver
What are the N donors into the urea cycle to produce urea?
glutamate and glutamine
Alanine
carries N from muscle cells to the liver, where it’s converted to glutamate before entering the mitochondria
Carbamoyl phosphate
captures ammonia from glutamine and glutamate
When glutamate donates an amino group to oxaloacetate, what is formed?
aspartate
How does aspartate contribute the 2nd N of the urea cycle?
it combines w/ citrulline → argininosuccinate
How is urea formed?
2 former amino groups are added to CO2
Transamination
generates keto acids for the citric acid cycle and glutamate/aspartate for urea formation in liver
Aminotransferase
catalyzes transamination; always involves glutamate and α-ketoglutarate
If C atoms from breakdown of certain amino acids end up in acetyl-CoA, the amino acids are ___
ketogenic
If C atoms from breakdown of certain amino acids end up as part of citric acid cycle intermediates (NADH, oxaloacetate, α-ketoglutarate, etc.), the amino acids are ___
glucogenic
Oxidative phosphorylation
NADH and FADH2 are oxidized for ATP production (phosphorylation of ADP)
Electron transport chain
transports electrons from NADH and FADH2 to O2 and energy stored in ATP
ΔE
difference in reduction potentials that can describe the energy in a redox rxn
Standard reduction potential (E°)
measures a molecule’s affinity for electrons
used to predict direction of a rxn (ΔE and Keq) between any pair
The half-rxn w/ the higher E° value will proceed as…
reduction and accepts electrons
The half-rxn w/ the lower E° value will proceed as…
reverse rxn (oxidation) and donates electrons
Complex I
takes electrons from NADH and transfers them to ubiquinone (carrier)
Ubiquinone (Q)
carrier which takes electrons to complex III
Complex I oxidizes ___ and reduces ___
NADH; Q
Complex III
moves electrons to cytochrome C
Cytochrome C
protein that shuttles electrons between complexes III and IV
Complex III oxidizes ___ and reduces ___
QH2; cytochrome C
Complex IV
gives total of 4 electrons to O2 → H2O
Complex IV oxidizes ___ and reduces ___
cytochrome C; O2
Complex II
takes electrons from FADH2, but otherwise follows the same pathway as complex I
the only membrane-inserted enzyme of the citric cycle
Complex II oxidizes ___ and reduces ___
succinate (FADH2 as bound cofactor); Q
Which complexes pump protons from inside the inner membrane to outside it?
I, III, IV
Overall, electrons flow from…
high energy to low energy (some energy is captured in a proton gradient)
For every 1 NADH molecule oxidized at complex I, how many TOTAL protons are pumped across all complexes from the mitochondrial matrix to the inner membrane space?
10
How many protons are pumped at complex I?
4