Biochemistry 2

Question 1

dynamic steady state

Answer 1

= homeostasis = not in equilibrium with surroundings

Question 2

Gibbs free energy

Answer 2

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)

Question 3

ΔG vs Q vs Keq

Answer 3

ΔG = ΔG°’ + RTlnQ

ΔG°’ = -RTlnKeq

*** at equilirium:

• Q = Keq
• ΔG = 0
• ΔG° ≠ 0, ΔG° = 0 only if Keq = 1

if Keq = 1 → ΔG = ΔG°

Question 4

ΔG vs spontaneity

Answer 4

+ ΔG = endergonic = nonspontaneous

• ΔG = exergonic = spontaneous

Question 5

protein folding

Answer 5

ΔS = negative

ΔH formation = negative and large in native conformation

→ spontaneous

Question 6

ATP

Answer 6

ΔG°’ for ATP hydrolysis <<< 0

sequential loss of one phosphate group: ATP → ADP → AMP : have - ΔG

AMP → cAMP during cyclization : + ΔG

Question 7

substrate level phosphorylation

Answer 7

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

Question 8

oxidative phosphorylation

Answer 8

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

Question 9

consumption of ATP

Answer 9

• 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

Question 10

redox reactions

Answer 10

redox = NADH/NAD+, NADPH/NADP+, FADH2/FAD, FMNH2/FMN, semiquinone (FMNH radical), ubiquinone, cytochrome

Question 11

aerobic respiration

Answer 11

oxygen serves as final e- acceptor

citric acid cycle and electron transport chain

Question 12

anaerobic respiration

Answer 12

molecule other than oxygen serves as final e- acceptor

fermentation, glycolysis in absense of oxygen, lactic acid cycle in muscles

Question 13

glycolysis

Answer 13

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:

1. glucose → glucose-6-phosphate (via hexokinase)
2. fructose-6-phosphate → fructose-1,6-biphosphate (via phosphofructokinase)
3. phosphoenolpyruvate → pyruvate (via pyruvate kinase)

ATP required:

1. glucose → glucose-6-phosphate
2. fructose-6-phosphate → fructose-1,6-bisphosphate

ATP generated:

1. 1,3-bisphosphoglycerate → 3-phosphoglycerate (via phosphoglycerate kinase)
2. phosphoenolpyruvate → pyruvate

NADH generated:

1. glyceraldehyde-3-phosphate → 1,3-bisphosphoglycerate (via glyceraldehyde-3-phosphate dehydrogenase)

Question 14

feeder pathways for glycolysis

Answer 14

glycogenolysis:

1. glycogen phosphorylase removes glucose residues from reducing ends of glycogen polymers → glucose-1-phosphate
2. phosphoglucomutase converts glucose-1-phosphate → glucose-6-phosphate

fructose metabolism: primary sugar in many fruits, product of sucrose hydrolysis

1. muscle + kidneys: hexokinase converts fructose → fructose-6-phosphate
2. 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:

1. galactose → glucose-1-phosphate, converted over many steps, UDP = coenzyme
2. phosphoglucomutase converts glucose-1-phosphate → glucose-6-phosphate

Question 15

ethanol fermentation

Answer 15

primarily yeast, some bacteria

ethanol is produced and is the final e- acceptor, unique compared to lactic acid fermentation because carbon skeleton changes

Question 16

lactic acid fermentation

Answer 16

lactate produced and is the final e- acceptor

*** important because it produces NAD+ so that glycolysis can continue (necessary in times of oxygen deprivation)

Question 17

gluconeogenesis

Answer 17

location: cytosol of liver cells

*** occurs during fasting, used to increase blood sugar

enzymes to reverse the irreversible steps of glycolysis:

1. pyruvate carboxylase
2. phosphenolpyruvate carboxylase
3. fructose-1,6-bisphosphatase
4. 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

Question 18

pentose phosphate pathway

Answer 18

1. NADPH synthesis → important reducing agent, used during reduction biosynthesis (synthesizing fatty acids / sterols), necessary for production of glutathione (important antioxidant)
2. 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

Question 19

PDH complex

Answer 19

pyruvate → acetyl Co-A

linkage between glycolysis and citric acid cycle

pyruvate = 3 destinations

1. PDH complex → acetyl-CoA (uses 3 different enzymes)
2. lactate dehydrogenase → lactate
3. pyruvate carboxylate → oxaloacetate

Question 20

citric acid cycle / tricarboxylic acid cycle (TCA) / Krebs cycle

Answer 20

acetyl-CoA: first substrate of cycle, 3 origins

1. carbohydrate: glycolysis → pyruvate → PDH complex → acetyl-CoA
2. lipid: B-oxidation → acetyl-CoA
3. protein: amino acid metabolism → acetyl-CoA (among other products)

NADH produced:

1. isocitrate → alpha-ketoglutarate
2. alpha-ketoglutarate → succinyl CoA
3. malate → oxaloacetate

CO2 produced:

1. isocitrate → alpha-ketoglutarate
2. alpha-ketoglutarate → succinyl CoA

GTP produced:

1. succinyl CoA → succinate

FADH2 produced:

1. succinate → fumarate

*** each glucose → 2 acetyl-CoA → 2 cycles per 1 glucose molecule

Question 21

electron transport chain

Answer 21

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

Question 22

glycolysis + citric acid cycle products

Answer 22

Question 23

malate aspartate shuttle

Answer 23

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:

1. NADH donates 2 e- to oxaloacetateconverting it to malate
2. malate passes through inner mitochondrial membrane via malate-alpha-ketoglutarate antiporter
3. malate converted back into oxaloacetate when in mitochondrial matrix → regenerating NADH
4. oxaloacetate converted into aspartate so it can be pumped back into cytosol via glutamate aspartate shuttle

Question 24

glycerol-3-phosphate shuttle

Answer 24

problem: NADH can’t pass through inner mitochondrial membrane to participate in electron transport chain
solution: minor contributor

1. NADH donates two e- to dihydroxyacetone phosphate to form glycerol-3-phosphate
2. glycerol-3-phosphate converted back into dihydroxyacetone phosphate by mitochondrial glycerol-3-phosphate dehydrogenase (an enzyme bound to cytosolic surface of inner mitochondrial membrane)
3. enzyme passes the two e- to FAD to form FADH2

Question 25

carnitine shuttle

Answer 25

problem: fatty acids cannot pass through the inner mitochondrial membrane, where they undergo B-oxidation to generate acetyl-CoA solution: 1. enzyme carnitine acyltransferase attaches the fatty acyl group from an acyl-CoA to the hydroxyl group of carnitine 2. translocase enzyme on inner mitochondrial membrane moves one acyl-carnitine into the matrix and one carnitine back out

Question 26

citrate-acetyl-CoA shuttle

Answer 26

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: 1. acetyl-CoA is combined with oxaloacetate to form citrate 2. citrate is able to pass through inner mitochondrial membrane 3. citrate converted back into oxaloacetate and acetyl-CoA in the cytosol

Question 27

glucocorticoids

Answer 27

* 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

Question 28

catecholamines

Answer 28

* 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

Question 29

thyroid hormones

Answer 29

T3 and T4 increase basal metabolic rate in response to secretion of TSH from anterior pituitary

Question 30

glycolysis regulation

Answer 30

* 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)

Question 31

gluconeogenesis regulation

Answer 31

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

Question 32

glycogenolysis regulation

Answer 32

breakdown of glycogen into glucose-6-phosphate, via glucose-1-phosphate * stimulated by protein kinase A