Biochemistry 2 Flashcards
dynamic steady state
= homeostasis = not in equilibrium with surroundings
Gibbs free energy
ΔG = free energy change at some present, non-standard set of conditions
ΔG° = free energy change at standard conditions (25 °C, [1 M])
ΔG°’ = free energy change at standard physiological conditions (pH = 7)
ΔG vs Q vs Keq
ΔG = ΔG°’ + RTlnQ
ΔG°’ = -RTlnKeq
*** at equilirium:
- Q = Keq
- ΔG = 0
- ΔG° ≠ 0, ΔG° = 0 only if Keq = 1
if Keq = 1 → ΔG = ΔG°
ΔG vs spontaneity
+ ΔG = endergonic = nonspontaneous
- ΔG = exergonic = spontaneous
protein folding
ΔS = negative
ΔH formation = negative and large in native conformation
→ spontaneous
ATP
ΔG°’ for ATP hydrolysis <<< 0
sequential loss of one phosphate group: ATP → ADP → AMP : have - ΔG
AMP → cAMP during cyclization : + ΔG
substrate level phosphorylation
formation of ATP from ADP → process must be coupled to an exergonic reaction
occurs primarily in cytosol → glycolysis
occurs in mitochondrial matrix → formation of GTP during citric acid cycle
oxidative phosphorylation
formation of ATP from ADP and Pi by using energy from proton gradient across inner mitochondrial membrane
proton gradient created by coupling oxidation of NADH and FADH2 to pumping of protons
location: only mitochondrial matrix → ATP formed from ATP synthase complex
consumption of ATP
- hydrolysis: ATP + H2O → ADP + Pi + energy, usually coupled to another reaction so energy can be used to drive another reaction / do work → ex = cocking myosin head
- phosphoryl group transfers: ATP → ADP + energy, phosphate transferred onto another molecule → ex = glycolysis: glucose + ATP → glucose-6-phosphate + ADP
- phosphorylation using ATP = major human body regulatory mechanism, phosphorylation: protein kinases + ATP, dephosphorylation: phosphatases and produces Pi → ex = glycogen phosphorylase A (enzyme that catalyzes breakdown of glycogen to glucose): GPA (inactive) + 2 ATP → GPA-PP (active) + 2 ADP
redox reactions
redox = NADH/NAD+, NADPH/NADP+, FADH2/FAD, FMNH2/FMN, semiquinone (FMNH radical), ubiquinone, cytochrome
aerobic respiration
oxygen serves as final e- acceptor
citric acid cycle and electron transport chain
anaerobic respiration
molecule other than oxygen serves as final e- acceptor
fermentation, glycolysis in absense of oxygen, lactic acid cycle in muscles
glycolysis
location: cytoplasm
input: glucose, 2 ATP, 2 ADP, 2 NAD+
output: 2 pyruvate, 4 ATP, 2 NADH, 2 H2O
net gain: 2 ATP, 2 NADH, 2 pyruvate, 2 H2O
irreversible steps:
- glucose → glucose-6-phosphate (via hexokinase)
- fructose-6-phosphate → fructose-1,6-biphosphate (via phosphofructokinase)
- phosphoenolpyruvate → pyruvate (via pyruvate kinase)
ATP required:
- glucose → glucose-6-phosphate
- fructose-6-phosphate → fructose-1,6-bisphosphate
ATP generated:
- 1,3-bisphosphoglycerate → 3-phosphoglycerate (via phosphoglycerate kinase)
- phosphoenolpyruvate → pyruvate
NADH generated:
- glyceraldehyde-3-phosphate → 1,3-bisphosphoglycerate (via glyceraldehyde-3-phosphate dehydrogenase)
feeder pathways for glycolysis
glycogenolysis:
- glycogen phosphorylase removes glucose residues from reducing ends of glycogen polymers → glucose-1-phosphate
- phosphoglucomutase converts glucose-1-phosphate → glucose-6-phosphate
fructose metabolism: primary sugar in many fruits, product of sucrose hydrolysis
- muscle + kidneys: hexokinase converts fructose → fructose-6-phosphate
- liver: fructokinase converts fructose → fructose-1-phosphate, fructose-1-phosphate aldolase converts fructose-1-phosphate → glyceraldehyde-3-phosphate + dihydroxyacetone phosphate, triose phosphate isomerase converts dihydroxyacetone phosphate → glyceraldehyde-3-phosphate
galactose metabolism:
- galactose → glucose-1-phosphate, converted over many steps, UDP = coenzyme
- phosphoglucomutase converts glucose-1-phosphate → glucose-6-phosphate
ethanol fermentation
primarily yeast, some bacteria
ethanol is produced and is the final e- acceptor, unique compared to lactic acid fermentation because carbon skeleton changes
lactic acid fermentation
lactate produced and is the final e- acceptor
*** important because it produces NAD+ so that glycolysis can continue (necessary in times of oxygen deprivation)
gluconeogenesis
location: cytosol of liver cells
*** occurs during fasting, used to increase blood sugar
enzymes to reverse the irreversible steps of glycolysis:
- pyruvate carboxylase
- phosphenolpyruvate carboxylase
- fructose-1,6-bisphosphatase
- glucose-6-phosphatase
input: 2 pyruvate, 4 ATP, 2 GTP, 4 H2O, 2 NADH
output: 4 ADP, 2 GDP, 2 CO2, 2 NAD +, 4 Pi, glucose
net output: 4 ADP, 2 GDP, 2 CO2, 2 NAD +, 4 Pi, glucose
pentose phosphate pathway
- NADPH synthesis → important reducing agent, used during reduction biosynthesis (synthesizing fatty acids / sterols), necessary for production of glutathione (important antioxidant)
- ribose-5-phosphate → used to synthesize nucleotides
oxadative phase:
- glucose-6-phosphate → 6-phosphogluconate → ribulose-5-phosphate
- both steps coupled to conversion of NADP+ → NADPH
- 2 NADPH made per 1 glucose-6-phosphate
- 1 glucose-6-phosphate molecule can synthesize 4 glutathione
non-oxidative phase:
- ribulose-5-phosphate → ribose-5-phosphate ⟷ sugar pool ⟷ glucose-6-phosphate
- interconversions between sugars catalyzed by transketolase and transaldolase
PDH complex
pyruvate → acetyl Co-A
linkage between glycolysis and citric acid cycle
pyruvate = 3 destinations
- PDH complex → acetyl-CoA (uses 3 different enzymes)
- lactate dehydrogenase → lactate
- pyruvate carboxylate → oxaloacetate
citric acid cycle / tricarboxylic acid cycle (TCA) / Krebs cycle
acetyl-CoA: first substrate of cycle, 3 origins
- carbohydrate: glycolysis → pyruvate → PDH complex → acetyl-CoA
- lipid: B-oxidation → acetyl-CoA
- protein: amino acid metabolism → acetyl-CoA (among other products)
NADH produced:
- isocitrate → alpha-ketoglutarate
- alpha-ketoglutarate → succinyl CoA
- malate → oxaloacetate
CO2 produced:
- isocitrate → alpha-ketoglutarate
- alpha-ketoglutarate → succinyl CoA
GTP produced:
- succinyl CoA → succinate
FADH2 produced:
- succinate → fumarate
*** each glucose → 2 acetyl-CoA → 2 cycles per 1 glucose molecule
electron transport chain
complex I: pumps 4 protons
complex II: pumps 0 protons (not a transmembrane protein)
complex III: pumps 4 protons
complex IV: pumps 2 protons
*** production of one ATP molecule requires 3 protons
NADH: e- go through complex I, III, IV → 10 protons pumped → 3 ATP
FADH2: e- go through II, III, IV → 6 protons pumped → 2 ATP
glycolysis + citric acid cycle products
malate aspartate shuttle
problem: NADH can’t pass through the inner mitochondrial membrane → NADH generated from glycolysis cannot enter eletron transport chain without help of this shuttle
solution:
- NADH donates 2 e- to oxaloacetateconverting it to malate
- malate passes through inner mitochondrial membrane via malate-alpha-ketoglutarate antiporter
- malate converted back into oxaloacetate when in mitochondrial matrix → regenerating NADH
- oxaloacetate converted into aspartate so it can be pumped back into cytosol via glutamate aspartate shuttle
glycerol-3-phosphate shuttle
problem: NADH can’t pass through inner mitochondrial membrane to participate in electron transport chain
solution: minor contributor
- NADH donates two e- to dihydroxyacetone phosphate to form glycerol-3-phosphate
- glycerol-3-phosphate converted back into dihydroxyacetone phosphate by mitochondrial glycerol-3-phosphate dehydrogenase (an enzyme bound to cytosolic surface of inner mitochondrial membrane)
- enzyme passes the two e- to FAD to form FADH2
carnitine shuttle
problem: fatty acids cannot pass through the inner mitochondrial membrane, where they undergo B-oxidation to generate acetyl-CoA
solution:
- enzyme carnitine acyltransferase attaches the fatty acyl group from an acyl-CoA to the hydroxyl group of carnitine
- translocase enzyme on inner mitochondrial membrane moves one acyl-carnitine into the matrix and one carnitine back out
citrate-acetyl-CoA shuttle
problem: during periods of energy abundance, acetyl-CoA groups in mitochondrial are redirected from the citric acid cycle to fatty acid synthesis, fatty acid synthesis occurs in the cytosol and acetyl-CoA cannot pass through inner mitochondrial membrane
solution:
- acetyl-CoA is combined with oxaloacetate to form citrate
- citrate is able to pass through inner mitochondrial membrane
- citrate converted back into oxaloacetate and acetyl-CoA in the cytosol
glucocorticoids
- cortisol = most significant example → produced by adrenal cortex → in response to ACTH from anterior pituitary
- have “glucagon like” effect on metabolism → stimulate gluconeogenesis, glycogenolysis, fatty acid oxidation
- reduce inflammation
catecholamines
- dopamine, epinephrine, norepinephrine
- dopamine = CNS
- epinephrine, norepinephrine = metabolic hormones
- have “glucagon like” effect → more rapid mobilization of energy stores necessary for fight or flight → fatty acids mobilized for B-oxidation and glycogenolysis is increased
thyroid hormones
T3 and T4 increase basal metabolic rate in response to secretion of TSH from anterior pituitary
glycolysis regulation
- phosphofructokinase: inhibited by high levels of ATP (main source of regulation for glycolysis) → AMP reverse inhibition of ATP, ratio of ATP / AMP is crucial in glycolysis regulation
- hexokinase: inhibited by glucose-6-phosphate (its product) → high levels of glucose-6-phosphate indicate that cell has plenty of energy
- pyruvate kinase: inhibitied by ATP and alanine (pyruvate used as a building block for amino acids, high alanine levels signal that those buliding blocks aren’t needed)
gluconeogenesis regulation
needed when energy levels are high and glucose levels are low
- fructose-1,6-bisphosphate: inhibited by AMP and is stimulated by ATP
- pyruvate carboxylase and phosphenolpyruvate carboxylase are inhibited by ADP
glycogenolysis regulation
breakdown of glycogen into glucose-6-phosphate, via glucose-1-phosphate
- stimulated by protein kinase A
