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Fall 2022 > Biochem Week 4 > Flashcards

Biochem Week 4 Flashcards

1
Q

Substrate level phosphorylation

A

Phosphate group transferred from molecule of higher free energy to molecule of lower free energy (exergonic)

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2
Q

Enzymes that’s catalyze ATP producing steps of glycolysis

A

Phosphoglycerate kinase and pyruvate kinase

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3
Q

Hexokinase

A

Catalyzes phosphorylation of glucose after it enters a cell, traps glucose molecule in the cell. High affinity for glucose, kicks off glycolysis
Inhibited by downstream product glucose 6 phosphate
Irreversible and regulated

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4
Q

Glucokinase

A

Type of hexokinase
Low affinity for glucose (large Km), binds and metabolized glucose at high concentrations. Not inhibited by glucose-6-P
Expressed in pancreatic islet cells and hepatocytes of liver. Influences secretion of insulin, helps pancreatic beta cells know whether more insulin or more glucagon should be released
Large Vmax: quickly remove glucose from circulation thus minimizing hyperglycemia during FED

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5
Q

Phosphofructokinase-1 (PFK1)

A

fructose-6-P to F1, 6BP
Catalyzes committed step, rate limiting step
Irreversible
Has many Allosteric binding sites
ATP (high= sufficient energy) and citrate (TCA intermediate) are strong inhibitors

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6
Q

Phosphofructokinase 2 (PFK2)

A

Converts fructose-6-P to F2, 6BP
Stimulates glycolysis by allosterically activating PFK1
Regulatory pathway: phosphorylation of PFK-2/FBPase-2 complex makes FBPase-2s activity dominant, and dephosphorylation favors PFK-2. with a phosphate favors the activity of the phosphatase.

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7
Q

Glucagon and insulin

A

Glucagon increases levels of cAMP, activates protein kinase A, phosphorylates PFK-2/FBPase-2 complex, decreasing cellular concentration of F2, 6BP
Insulin opposite
Glucagon increases blood glucose, insulin decreases blood glucose

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8
Q

Epinephrine

A

Binds to receptor which causes increase in cAMP, increase in PKA
in heart, PKA phosphorylates different part of PFK-2/FBPase-2 enzyme so PFK-2 is activated.
Leads to increased F2-6BP and increased rate of glycolysis

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9
Q

Pyruvate kinase

A

Step 3
PEP to pyruvate
Final rate limiting step
Glucagon causes Phosphorylation by PKA, causes it to become less active and slow glycolysis. Regulatory

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10
Q

Protein phosphatase

A

Glucagon causes downstream phosphorylation of Glycolytic enzymes: glucagON puts a phosphate ON

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11
Q

Glucagon slowing glycolysis through decreasing activity of PFK1

A

glucagon binds to receptor activating adenylate cyclase. Increases intracellular cAMP, activates PKA, phosphorylates PFK2/FBPase-2 activity. This increases FBPase-2 activity, decreasing levels of F2, 6BP and decreasing Allosteric activation of PFK1

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12
Q

Anaerobic glycolysis

A

Pyruvate metabolized without oxygen
Lactate dehydrogenase (LDH) converts pyruvate to lactate using one NAD + H+
Occurs in cells that lack oxygen or mitochondria or are rapidly proliferating and preferentially using hydrocarbon components for synthesis of new cells parts

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13
Q

NAD+

A

Essential cofactor for glyceraldehyde 3 phosphate dehydrogenase, product of anaerobic metabolism of pyruvate via LDH
Allows glycolysis to continue

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14
Q

Warburg effect

A

Tendency of tumor cells to metabolize glucose to lactate even in the presence of oxygen
One explanation is that tumor cells undergo changes that favor use of glycolytic intermediates for synthesis of components of new cells over ATP production

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15
Q

2,3- BPG on erythrocytes

A

Decreased hemoglobins affinity for oxygen, making oxygen unload to tissues more likely

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16
Q

2,3- BPG in glycolysis

A

Bisphosphoglycerate mutase converts 1,3- bisphosphoglycerate to 2,3-BPG, which is converted to 3-phosphoglycerate by 2,3- BPG phosphatase

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17
Q

Pyruvate kinase deficiency

A

Produce zero net ATP from glycolysis leading to inability to run Na+ - K+- ATPase… intracellular accumulation of sodium causing swelling and rupture…hemolytic anemia
Consequence is build up of hemoglobin and metabolites (bilirubin- usually conjugated and excreted in liver)

Indirect bilirubin is Unconjugated, Direct bilirubin is Conjugated (vowel with vowel, consonant with consonant)

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18
Q

GLUT 4

A

Glucose transporter Regulated by insulin

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19
Q

Features of glycolysis

A

6C (glucose)—> 3C(pyruvate)
Oxygen
2 pyruvates, 2 NADH and 2 ATP produced per 6C glucose

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20
Q

Phase 1 glycolysis

A

Preparation phase
6C glucose + 2ATP—> fructose 1,6 BP

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21
Q

Phase 2 glycolysis

A

ATP generating phase
Fructose 1,6 BP—> 2 triose phosphates —> 2 pyruvate
- 2NADH, 2ATP, 2ATP

22
Q

Arsenic poisoning

A

Arsenate structurally similar to phosphate
Arsenate instead of phosphate is incorporated into glyceraldehyde-3- phosphate step six. Arseno analog is unstable and is spontaneously hydrolyzed to 3- phosphoglycerate. Lose the substrate level phosphorylation in step seven. Thus there is no net gain of ATP from glycolysis.
Huge problem for red blood cells because of the lack of mitochondria

23
Q

Fluoride inhibition of enolase

A

Step 9
Prevention of dental cavities: fluoride inhibits enolase. Water fluoridation reduces lactate production by mouth bacteria thus decreasing dental cavities

24
Q

Cori cycle

A

Recycle lactate in anaerobic glycolysis
Skeletal muscles generates lactate during exercise. Lactic acid produced so glycolysis can continue in shortage of oxygen-regenerate NAD+
during recovery, lactate transports to the liver and used to resythesize glucose via gluconeogenesis
RBCs must use this pathway due to lack of mitochondria

25
Q

Lactic acidosis

A

Elevated concentrations of lactate in blood, lowers pH
Possible causes: failed to regenerate NAD+, inability to reoxidized NADH by ETC, excessive NADH production, pyruvate carboxylase deficiency, impaired PDH (pyruvate to acetyl-CoA), impaired respiration or oxygen delivery, excessive exercise

26
Q

Tandem enzyme

A

Or bifunctional enzyme
Single polypeptide has two enzymatic function (from two separate domain)
Phosphofructokinase-2 (PFK-2) synthesizes F-2-BP from fructose-6-P and ATP
Fructose-2,6- bisphosphatase (FBPase-2) hydrolysis F-2,6-BP to fructose-6-P

Dephospho-tandem enzyme synthesizes F-2,6-BP because PFK-2 active (achieved by phosphatase, activated by insulin)
Phospho- tandem enzyme converts F-2,6-BP to F-6-P because FBP-2 active (achieved by PKA, activated by glucagon)

27
Q

Pasteur effect

A

Slowing of glycolysis in presence of sufficient oxygen
More ATP produced under aerobic than under anaerobic, fewer glucose is consumed aerobically
Under anaerobic, conversion of glucose to pyruvate and then to lactate/ethanol is much faster than under aerobic (yeast cells produce more ethanol- fermentation; muscle cells produce lactate)

28
Q

Location of citric acid cycle

A

Mitochondria

29
Q

Fatty acids and TCA

A

Fatty acids undergo metabolism by beta oxidation. End product is acetyl CoA, enters TCA.
Even number of carbons = produce only acetyl CoA
Odd number of carbons= produce acetyl CoA and propionyl- CoA (further metabolized to succinate- CoA)

30
Q

Malate to oxaloacetate in TCA

A

Unfavorable standard free energy
Still occurs due to re-oxidation of NADH in ETC as well as its conversion to citrate, catalyzed by Malate dehydrogenase in net forward rxn despite positive free energy change

31
Q

Succinate dehydrogenase (SDH)

A

TCA enzyme
Bound to inner mitochondrial membrane.
Catalyzes first dehydration forming fumarate, contains flavin adenine dinucleotide (FAD), electron carrier
Also forms complex 2 in ETC

32
Q

TCA part 1 steps

A

1:formation of citrate from oxaloacetate and acetyl CoA via citrate synthesis (irreversible)
2: isomerization of citrate to isocitrate via aconitate hydratase (Fe-S protein)(inhibited by fluoroacetate)
3: isocitrate oxidized by isocitrate dehydrogenase (important for regulating speed), release molecule CO2, leaving behind 5C alpha ketoglutarate (NAD+ reduced to form NADH) (rate limiting step!, irreversible)
4: alpha ketoglutarate oxidized catalyzed by alpha ketoglutarate dehydrogenase, release molecule CO2, NAD+ reduced to form NADH. Remaining 4C molecule picks up coenzyme A, forms succinyl CoA (last step of part 1)

33
Q

FADH2 generation

A

Step 6 of TCA
succinate is oxidized forming fumarate
Two electrons transferred to FAD producing FADH2

34
Q

Final NADH in TCA

A

last step of cycle
Oxaloacetate is regenerated by oxidation of Malate
One molecule of NAD+ is reduced to NADH

35
Q

Alpha ketoglutarate dehydrogenase

A

Similar properties to pyruvate dehydrogenase
Also same cofactors:
Thiamine pyrophosphate
Lipoic acid
Coenzyme A
FAD
NAD+

36
Q

Thiamine deficiency

A

Affects functioning of different vitamin B1- requiring enzymes like alpha ketoglutarate dehydrogenase

37
Q

Pyruvate dehydrogenase complex

A

Member of alpha-keto acid dehydrogenase family
Catalyzes conversion of pyruvate to acetyl CoA
Enzymes: pyruvate decarboxylase (pyruvate dehydrogenase), dihydrolipoyl transacetylase, dihydrolipoyl dehydrogenase
Cofactors: thiamine, lipoic acid, CoA, fad, nad+

38
Q

Hyper ammonia

A

Alpha ketoglutarate gets depleted in hyper ammonia because of its increased use in glutamate formation

39
Q

Succinyl coenzyme A

A

Intermediate of TCA used for heme synthesis

40
Q

Pyruvate dehydrogenase regulation

A

PDH kinase inhibits E1, allosterically activated by ATP, acetyl CoA, and NADH
PDH phosphatase activates E1, also stimulates PDH and energy production after skeletal muscle cells release calcium during contraction
Pyruvate inhibits PDH kinase

41
Q

Pyruvate dehydrogenase deficiency

A

E1deficiency causes congenital lactic acidosis because pyruvate is shunted to lactic acid via LDH
Brain particularly sensitive to lactic acidosis
E1 is X-linked gene, brain classified as X-linked dominant due to sensitivity
No proven treatment

42
Q

Arsenite poisoning

A

Type of arsenic poisoning
Arsenide inhibits enzymes requiring lipoic acid including PDH, alpha ketoglutarate dehydrogenase, branched-chain amino acid alpha-keto acid dehydrogenase
Forms stable complex with thio group of lipoic acid
Affects brain, causes neurological disturbance and death

43
Q

TCA part 2 steps

A

Step 5: cleavage of succinyl CoA. Produces one GTP, converted to ATP by nucleoside diphosphate kinase. Substrate level phosphorylation
Step 6: oxidation of succinate, SUCCINATE DEHYDROGENASE . Produce one FADH2.
Step 7: fumarase, hydration of fumarate (reversible)
Step 8: oxidation or malate (malate dehydrogenase), produces 3rd and final NADH

44
Q

TCA Products

A

12/10 ATP per one molecule acetyl CoA

45
Q

One molecule glucose

A

Produces total of 36-38 ATPS after glycolysis, TCA, and oxidative phosphorylation

46
Q

Regulatory enzymes of TCA

A

citrate synthase, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase

47
Q

TCA cycle intermediates as precursors

A

Citrate- fatty acid, sterols
Alpha ketoglutarate- neurotransmitter in brain, glutamate, other amino acids.
Succinyl CoA- porophyrins, heme, chlorophyll
Malate- gluconeogenesis
Oxaloacetate- aspartate, other amino acids

48
Q

Anaplerotic reaction-1

A

Pathways or reactions that replenish the intermediates of TCA cycle (filling up)
Pyruvate carboxylase - contains biotin and requires ATP and mg2+. Activated by acetyl CoA, also catalyzes first reaction of gluconeogenesis

49
Q

Anaplerotic reaction-2

A

Amino acid degradation

50
Q

Leigh syndrome

A

Subacute necrotizing encephalomyelopathy
Can be cause by mutations in pyruvate dehydrogenase complex deficiency or pyruvate carboxylase deficiency
Lactic acidemia
Respiratory failure

51
Q

Beriberi disease and wernicke- korsakoff syndrome

A

Thiamine (vitamin B1) deficiency
Cofactor of PDH and alpha-ketoglutarate dehydrogenase

Fall 2022 (15 decks)

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