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SPM > Week 3 > Flashcards

Week 3 Flashcards

1
Q

What is catabolism and provide some examples?

A
  • degradation of complex molecules into small moleculesd
  • release of chemical energy into energy-transferring molecules (i.e. ATP)
  • Example: Breaking down glucose into pyruvate (a three carbon molecule)
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2
Q

What is anabolism and provide an example?

A
  • biosynthesis of complex molecules from simple precursors
  • utilization of chemical energy from energy-transferring molecules
  • Example: Gluconeogenesis
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3
Q

What are the three functions of metabolism (how do they integrate and coordinate biosynthesis/degradation)?

A
  • Obtain chemical energy from the degradation of energy-rich nutrients
  • Convert nutrient molecules into the building-block precursors of macromolecules
  • Assemble the building blocks into proteins, nucleic acids, polysaccharides, lipids, membranes, and other complex components of cells
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4
Q

What are the advantages of multienzyme complexes and why does this occur?

A
  • Speed of reactions are high
  • Fidelity of reactions
  • Why does this occur: The product of reactions become substrates of the next enxymatic reaction. These are close in proximity
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5
Q

Define free energy (ΔG) and how in integrates equlibrium and driving force.

What do negative and positive values of ΔG indicate?

What is the equation?

A
  • The “Free Energy” for a reaction under any conditions is a measure of how far from equilibrium the reaction is.
  • The farther away the reaction is from equilibrium, the greater the driving force is.
  • -ve drives reactions forward
  • +ve drives reactions backward
  • ΔG = ΔH - TΔS
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6
Q

What produces free energy (ΔG) and where is this energy placed?

A
  • Oxidative degradation of fuel molecules liberates a large amount of free energy (ΔG)
  • Much of the free energy derived from these reactions is transferred into high-energy phosphate bonds (e.g. ATP)
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7
Q

How does the transfer of ATP occur (two methods)?

A

This transfer of energy to ATP occurs either:

  • Directly: coupling of reactions to phosphorylation of ADP (substrate level phosphorylation), or
  • Indirectly: via electron carrier molecules (NAD, FAD), which transfer electrons to O2 to synthesize ATP (oxidative phosphorylation)
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8
Q

What type of carrier is NAD+ and what does it accept?

A
  • Coenzyme
  • It accepts 2 electrons and 1 proton
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9
Q

What type of carrier is FAD and what does it accept?

A
  • Prosthetic group
  • accepts two electrons and two protons
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10
Q

What type of carrier is Coenzyme A and what does it accept?

A
  • coenzyme
  • accepts an acyl group
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11
Q

How does ATP transfer energy?

A
  • breaks phosphate bonds
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12
Q

Compare and contrast enzyme-limited reactions and susbtrate-limited reactions.

A
  • Enzyme-limited reactions
    • Have an activation energy that needs to be overcome
    • More enzyme means more reaction while less enzyme would cause less reaction (due to saturation)
    • Steeply -ΔG means that the reaction is driven forward and irreversible meaning that the reaction is enzyme limited
  • Substrate-driven reactions
    • The concentration of the product and reactants drives the reaction.
    • When the ΔG is close to zero, the reaction is usually substrate-driven (i.e. more reactants would cause the reaction to yield more products)
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13
Q

What are the six principles of the pathways by which cells extract and utilize energy?

A
  1. All pathways proceed with a loss of free energy
  2. Pathways are usually reversible although they frequently contain one or more “irreversible” steps
  3. Pathways in opposite directions involve certain different enzymes and/or intermediates (usually to circumvent irreversible steps)
  4. Key pathways may be separated in different subcellular compartments
  5. Compartment boundaries or cell membranes may permit the facilitated transport of key intermediates
  6. Regulation usually occurs at initial committing and/or irreversible steps in pathways
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14
Q

What is an epimer and what are two epimers of glucose?

A
  • Epimer: different configuration of hydroxyl groups around chiral carbon
  • Two epimers of glucose: Manose and Galactose
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15
Q

How does cyclization of glucose work?

A
  • The acetyl group of the sugar attaches to the 5th reducing anomeric carbon
  • This exposes the reducing side chains
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16
Q

What monosaccharides is maltose made of and is it a reducing or nonreducing sugar?

A
  • 2 Glucose molecules (1,4)
  • Reducing sugar (an anomeric carbon is available to make a glycosydic linkage)
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17
Q

What monosaccharides is lactose made of and is it a reducing or nonreducing sugar?

A
  • galactose and glucose (1,4)
  • reducing sugar (one anomeric carbon available)
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18
Q

What monosaccharides is sucrose made of and is it a reducing or nonreducing sugar?

A
  • fructose and glucose (1,2)
  • non-reducing (both anomeric carbons are involved in glycosidic linkage)
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19
Q

What do aldoses and ketoses look like?

A
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20
Q

What is a reducing sugar and a non reducing sugar?

A
  • Reducing sugar: has an anomeric carbon available to make a glycosidic bond
  • Non-reducing sugar: does not have an anomeric carbon available to make a glycosydic bond (both are being used in another glycosydic bond already)
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21
Q

How can you identify an anomeric carbon in a carbohydrate?

A

Find the carbon with two oxygens binded to it.

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22
Q

How is a glycosydic bond formed?

A
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23
Q

What is used for energy storage of glucose?

A
  • Glycogen and starch (formed from many, many glucose molecules)
  • Many, many non-reducing ends where enzymes add or remove residues
  • only ONE reducing end
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24
Q

How are sugars digested and absorbed? What molecule do they need to be catabolized to?

A
  • All sugars are reduced to monosaccharides
  • This allows for transport across a membrane (dissaccharides cannot be transported)
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25
Q

How does the SGLT1 channel function? Where is it located?

A
  • The Na+-glucose symporter (SGLT1) functions exclusively in the intestinal epithelial cells to draw glucose in from the gut lumen and pass it into the blood
    • Uses the concentration gradient of sodium to provide energy
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26
Q

Explain what happens when someone with lactose intolerance ingests a dairy product?

A

Lactase is defective → lactose is not digested → bacterial action builds up lactic acid → lactic acid pulls water into lumen → watery diarrhea and malabsorption of fats, proteins, and drugs

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27
Q

What is the function of GLUT1 and where is it located?

A
  • GLUT1 glucose transporter mediates passive diffusion of

glucose into cells. This is a fully reversible process present in most cells.

  • It is located on plasma membranes to facilitate the diffusion of glucose into cells.
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28
Q

Where is glycolysis located?

How many ATPs are used?

How many ATPs are produced?

A
  • Cytosol
  • 2 ATPs are used
  • 4 ATPs are produce
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29
Q

What are the irreversible steps in glycolysis?

A
  • Glucose → Glucose-6-Phopshate
  • Fructose-6-Phosphate → Fructose 1,6 bisphosphate
  • Phosphoenolpyruvate → pyruvate

All of these have steep -ΔG values.

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30
Q

Compare and contrast hexokinase and glucokinase.

A

Hexokinase

  • Used in all tissues (including liver)
  • Nonspecific (can reduce any molecules)
  • Low Km (if satrurated, reaction cannot continue)
  • Inhibited by product (G6P

Glucokinase

  • Liver only
  • Only works on glucose
  • High Km (everything is phosphorylated as soon as glucose enters)
  • No inhibition
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31
Q
  • \What is step 1 in glycolysis (susbtrate: glucose)?
    • Enzyme
    • Consider if the reaction:
      • is rate-limiting?
      • produces or uses ATP?
      • uses FAD or NAD+?
A
  • Glucose + ATP → Glucose-6-Phosphate + ADP
  • Enzyme: Hexokinase
  • This IS a rate-limiting step.
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32
Q

What is the importance in function of phosphorylated intermediates?

A
  1. Trapping (prevents efflux of glucose)
  2. Energy conservation (phosphate donated to ADP)
  3. Substrate recognition (all intermediates for glycolysis are “tagged”)
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33
Q

What is step 2 in glycolysis (susbtrate: glucose-6-phosphate)?

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?
A

Glucose-6-Phosphate → Fructose-6-Phosphate

  • Enzyme: Phosphohexose Isomerase
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34
Q

What is step 3 in glycolysis (susbtrate: fructose-6-phosphate)?

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?

​

A

Fructose-6-Phosphate + ATP → Fructose 1,6, Bisphosphate + ADP

  • Enzyme: Phosphofructokinase-1
    • Attaches another phosphate molecule
  • It IS a rate-limiting step.
    • This is the investment step and can be highly regulated.
    • ATP and citrate inhibit the enzyme
    • AMP/ADP and fructose 2,6-bisphosphate increase the rate of the enzyme
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35
Q

What is step 4 in glycolysis (susbtrate: fructose 1,6-bisphosphate)?

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?

​

A

Fructose 1,6-bisphosphate → Dihydroxyacetone phosphate AND glyceraldehyde 3-phosphate

  • Enzyme: aldolase
    • Cleaves into two 3 carbon molecules. DAP must be converted to G3P to continue
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36
Q

What is step 5 in glycolysis (susbtrate: dihydroxyacetone phosphate)

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?

​

A

Dihydroxyacetone phosphate → Glyceraldehyde 3-Phosphate

  • Enzyme: triose phosphate isomerase
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37
Q

What is step 6 in glycolysis (susbtrate: 2units of glyceraledhyde 3-phosphate + an inorganic phosphate)

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?

​

A

2 units of Glyceraldehyde 3-Phosphate + 2 Pi + 2NAD+ → 2 units of 1,3-Biphosphoglycerate + 2NADH

  • Enzyme: Glyceraldehyde 3-phosphate dehydrogenase
    • produces a high enegy acyl phosphate
  • Only oxidation reaction in glycolysis
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38
Q

What is step 7 in glycolysis (susbtrate: 2 units of 1,3 biphosphoglyerate)

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?​
A

2 units of 1,3 biphosphoglyerate + 2ADP → 2 units of 3 phosphoglycerate + 2ATP

  • Enzyme: phophoglycerate kinase
    • phosphorylates ADP to ATP
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39
Q

What is step 8 in glycolysis (susbtrate: 2 units of 3-phosphoglycerate)

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?

​

A

2 units of 3-phosphoglycerate → 2 units of 2-phosphogylcerate

  • Enzyme: phosphoglycerate mutase
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40
Q

What is step 9 in glycolysis (susbtrate: 2 units of 2-phosphoglycerate)

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?​
A

2 units of 2-phosphoglycerate → 2 units of phosphoenolpyruvate + 2H2O

  • Enzyme: enolase
    • Produces a high energy enol phosphate
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41
Q

What is step 10 in glycolysis (susbtrate: 2 units of phosphoenolpyruvate)

  • Enzyme
  • Consider if the reaction:
    • is rate-limiting?
    • produces or uses ATP?
    • uses FAD or NAD+?​
A

2 units of Phosphoenolpyruvate + 2ADP → 2 units of Pyruvate + 2ATP

  • Enzyme: Pyruvate kinase
  • Pyruvate remains in the more stable keto form.
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42
Q

What is the net reaction of glycolysis?

A

glucose + 2Pi + 2ADP + 2NAD+

→ 2 pyruvate + 2ATP + 2NADH + 2H+ + 2H2O

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43
Q

How is NAD+ replenished in the glycolysis cycle without oxidative phosphorylation?

A

Pyruvate is converted to Lactate using NADH, which is converted NAD+.

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44
Q

Why is it important to maintian blood glucose levels in terms of tissue function tissue function?

A

Glucose uses its concentration gradient to drive glucose into cells. Since glucose is the main source of energy creation, it must maintain steady levels so that it can enter into cells when intracellular glucose is low.

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45
Q

Where does gluconeogenesis occur?

A
  • Primarily in the liver and kidney
  • Also occurs in skeletal muscle, but without G6Pase
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46
Q

What are the steps in gluconeogenesis?

A
  1. Pyruvate is shuttled from the cytosol to the mitochondrial matrix
  2. Pyruvate carboxylase converts pyruvate to oxaloacetate using ATP (only happens in mitochondria)
  3. Oxaloacetate is converted to malate to be shuttled out of the mitochondria. Malate is then converted back to oxaloacetate in the cytosol.
  4. Oxaloacetate is converted to PEP by hydrolyzing GTP to GTP
  5. PEP to Fructose 1,6-bisphosphate is glycolysis in reverse
  6. Fructose 1,6-bisphosphate converted to fructose 6-phosphate by fructose 1,6-bisphosphatase
  7. Fructose 6-phosphate to G6P is glycolysis in reverse
  8. G6P converted to glucose by glucose 6-phosphatase (in the ER)
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47
Q

How is oxaloacetate converted in gluconeogenesis?

Explain the (2) pathways.

A
  1. Starting with pyruvate: uses Malate shuttle to transfer oxaloacetate and NADH out of the mitochondria to the cytosol
  2. Starting with lactate: oxaloacetate is converted to PEP in the mitochondria and then diffuses out of the cytosol (in liver)
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48
Q

At what step in gluconeogenesis is the pathway regulated?

A
  • Fructose 1,6-bisphosphate converted to fructose 6-phosphate by fructose 1,6-bisphosphatase (FBPase-1)
    • Inhibited by: AMP, F26BP
      • PFK-2/FBPase-2 complex creates F26BP
      • F26BP ensures that PFK-1 and FBPase-1 are not active at the same time.
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49
Q

What is the ATP net use and gain in gluconeogenesis?

A

6 molecules of ATP to convert (2) molecules of pyruvates into one molecule of glucose

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50
Q

How does the Cori Cycle maintian glucose availability in the blood?

How might it be related to muscle cramps?

A
  • Glucose in muscle cells is used for energy and metabolized into lactate
  • Lactate is transferred by a transporter via bloodstream to the liver and converted back into glucose through gluconeogenesis
  • Lactate builds up to quickly in the muscle cells → decrease in pH → muscle cramps
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51
Q

What is the glycogen structure?

A
  • Linear linkages: alpha 1,4 linkages
  • Branching linkages: alpha 1,6 linkages
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52
Q

How is glycogen degraded in the body?

A
  • Glycogen phosphorylase cleaves an alpha 1,4 linkages creating one glucose molecule (G1P)
    • G1P to G6P by phosphoglucomutase
  • Debranching Enzyme
    • Transferase activity: transfers last 3 alpha 1,4 linked molecules from one branch to another
    • Glucosidase activity: cleaves an alpha 1,6 linkages creating one glucose molecule
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53
Q

How is glycogen synthesized?

A
  • Formation of UDP-glucose catalyzed by UDP-glucose pyrophosphorylase
  • Addition of a glucose residue to glycogen catalyzed by glycogen synthase
54
Q

How is the metabolism of glycogen regulated?

A
  • Epinephrine uses G protein pathway
    • Activates Phosphorylase a: degradation
    • Deactivates glycogen synthase: synthesis
55
Q

Compare the energetic efficiency of the TCA cycle and glycolysis?

A
  • In anaerobic glycolysis, there is 197kJ/mol of free energy that yields 2 ATP
  • In the aerobic pathway (glycolysis + CAC), there is 2870kJ/mol of free energy yielding 36 ATP
    • So it conserves a higher percentage of energy
  • Glycolysis is almost as efficient as aerobic pathways, but does not produce enough ATP as fast as the CAC
56
Q

Explain the general mechanism of the PDH cycle?

A

PDH cycle: pyruvate is converted to acetyl-CoA via PDH complex

  1. Pyruvate is decarboxylated
  2. Hydroxyethyl binding and oxidation to acetyl
  3. Acetyl transfer
  4. Oxidation of lipoamide
  5. Oxidation of FADH2
57
Q

TCA cycle: Step 1

Oxaloacetate + Acetyl-CoA →

A

Oxaloacetate + Acetyl-CoA → Citrate

Catalyzed: Citrate Synthase

58
Q

TCA cycle: Step 2

Citrate →

A

Citrate → [Cis-Aconitate] → Isocitrate

Catalyzed: Aconitase

59
Q

TCA cycle: Step 3

Isocitrate + _____ →

A

Isocitrate + NAD+ → Alpha-Ketoglutarate + CO2 + NADH

Catalyzed: Isocitrate Dehydrogenase

60
Q

TCA cycle: Step 4

Alpha-ketoglutarate + _____ →

A

Alpha-ketoglutarate + NAD+ → Succinyl-CoA + CO2 + NADH

Catalyzed by: Alpha-Ketoglutarate Dehydrogenase Complex

61
Q

TCA cycle: Step 5

Succinyl-CoA + ______ →

A

Succinyl-CoA + GDP → Succinate + GTP

Catalyzed by: Succinyl-CoA Synthetase

Substrate level phosphorylation

62
Q

TCA cycle: Step 6

Succinate + ____ →

A

Succinate + FAD → Fumarate + FADH2

Catalyzed by: Succinate Dehydrogenase

Electrons on FAD passed directly into the ETC

63
Q

TCA cycle: Step 7

Fumurate →

A

Fumurate → Malate

Catalyzed by: Fumarase

64
Q

TCA Cycle: Step 8

Malate + _____ →

A

Malate + NAD+ → Oxaloacetate + NADH

Catalzyed by: Malate Dehydrogenase

Reaction proceeds in the forward direction because [oxaloacetate] is so low, it pulls reaction to form products

65
Q

How is the TCA cycle regulated?

A
  • Inhibiton: ATP and NADH
  • Activation: Ca++, AMP, ADP
66
Q

How is the TCA cycle an amphibolic cycle?

What are anaplerotic reactions and provide an example?

A
  • Amphibolic Cycle = Catabolic + Anabolic processes occur
  • Anaplerotic – different macromolecules in our body form/replenish intermediates in the CAC
  • Major Example of Anaplerotic Reactions in the CAC
    • High levels of acetyl-CoA stimulate Pyruvate Carboxylase to convert pyruvate into oxaloacetate
    • High levels of acetyl-CoA inactivate Pyruvate Dehydrogenase complex to ensure acetyl-CoA levels match oxaloacetate
67
Q

What is the Oxidative phase of the Pentose Phosphate Pathway?

A

Oxidation Phase

  1. G6P + (2) NADP+ → → ribulose-5-phosphate + (2) NADPH +CO2
    * Main function: to produce NADPH (reductive biosynthesis)
68
Q

What is the non-oxidative phase of the pentose phosphate pathway?

A

Non-oxidative Phase

  1. ribulose-5-phosphate → ribose-5-phosphate via isomerase
  2. R5P → → fructose-6-phosphate OR Glyceraldehyde 3-phosphate
  • Main function: to shuffle carbons to synthesize desired sugars to enter glycolysis/gluconeogenesis
  • R5P can be used for nucleotide synthesis
69
Q

Where does insulin originate from and what is its chemical nature?

A
  • Beta-cells of the pancreatic islets
  • Chemical Nature
    • Pre-prohormone synthesized on rough ER
    • “Pre” domain directs molecule into the ER – it is cleaved from pro-insulin
    • “Pro” domain (C peptide) organizes disulfide bonds
    • “Pro” domain is cleaved in trans-Golgi, yielding insulin
    • “Pro” domain is packaged in same vescile for exocytosis
70
Q

Where does glucagon originate from and what is its chemical nature?

A
  • Alpha-cells of the pancreatic islets
  • Chemical Nature
    • Synthesized as pro-glucagon
    • “Pro” domains have functional properties in GI tract and brain
    • In intestinal cells, several exons of the glucagon gene are incretins (cause release of insulin)
71
Q

Where does somatostatin originate from and what is its chemical nature?

A
  • Delta-cells of the pancreatic islets
  • Somatostatin and prosomatostatin are active
72
Q

Where does amylin originate from and what is its chemical nature?

A
  • Beta-cells of the pancreatic islets
  • Synthesized as a small precursor
73
Q

What is the time course for the onset and duration for the biological actions of insulin and glucagon?

How is the time course affected in pre-diabetic individuals?

A
  • Early transient increase in glucagon due to nerve impulses of the gut
  • Will be an immediate drop in blood glucagon due to glucose and insulin inhibition of alpha-cells
  • Insulin rises in tandem with glucose level
  • As glucose approaches baseline, glucagon levels rise again, further inhibiting insulin release

In Diabetes

  • There are two phases to insulin release – first (early) phase disappears in pre-diabetic patients
    • First Phase releases insulin vesicles that are close to the PM
    • Second Phase releases larger vesicles of insulin that are far from PM
74
Q

Explain insulin release?

A

Increase in blood glucose → increased intracellular glucose → increased glucose metabolism → increase in ATP → KATP channel closes → less K+ leaves the cell → depolarization → voltage-gated Ca++ enters cell → Ca++ triggered exocytosis → insulin secreted

75
Q

Explain insulin regulation?

A
  • Glucose, GLP1, arginine, leucine, sulfonylureas stimulate release
  • Norepi, somatostatin, diazoxide, exercise, and insulin inhibit release
76
Q

Explain glucagon release?

A

Glucagon released primarily targets liver → binds to GCPR → GS activates adenyl cyclase → increases cAMP → PKA phosphorylates enzymes → stimulates glycogen breakdown, stimulates gluconeogenesis, inhibits glycolysis

77
Q

Explain glucagon regulation?

A
  • Low blood [glucose], epi, arginine, alanine stimulate release
  • High blood [glucose], vagal (parasympathetic) stimulation, somatostatin inhibit release
78
Q

Function of somatostatin?

A

Somatostatin slows everything and inhibits glucagon and insulin release

79
Q

Function of amylin?

A

Amylin complements insulin by sensitizing cells to insulin

80
Q

How can general oxidation and reduction occur respectively?

A
  • Oxidation reactions remove electrons, add oxygens, remove hydrogens, and oxidized form can act as an electron acceptor
  • Reduction reactions add electrons, remove oxygens, add hydrogens, and the reduced form can act as an electron donor
81
Q

What is the Nernst Equation is used for in terms of redox reactions?

A
  • Change in standard free energy can be calculated using the equation
  • The redox potential difference is used to calculate the free energy change associated with electron transfer
82
Q

What is the process that takes place in Complex I of the Electron Transport Chain?

  • What is Complex I called?
  • How many H+ pass into the intermembrane space?
A

Complex I – NADH Dehydrogenase

  • NADH + H+ → NAD+
  • A hydride ion (H-) is donated from NADH to FMN where 2 electrons pass onto a series of Fe-S centers
  • The preceding 2 electrons at the FMN pushes the electron at each Fe-S center separately via “tunneling” (wave function of quantum mechanics)
  • The last Fe-S center pushes an electron to the ironsulfur protein N-2
  • Electron transfer from N-2 to ubiquinone (Q) forms (QH2) along with 2 H+
  • 4H+ pass to intermembrane space (per NADH)
83
Q

What is the process that takes place in Complex II of the Electron Transport Chain?

  • What is Complex II called?
  • How many H+ pass into the intermembrane space?
A

Complex II – Succinate Dehydrogenase

  • FADH2 → FAD + 2e- + 2H+
  • FADH2 is oxidized to FAD, donating 2e- and 2H+ to Fe-S complexes, pushing the electron at each Fe-S center separately via “tunneling” (wave function of quantum mechanics)
  • Electron transfer from last Fe-S center to ubiquinone (Q) forms (QH2)
  • FAD has less negative reduction potential than NAD+, therefore FAD’s electrons have lower energy potential
84
Q

Where does Ubiquinol transfer from and to in the electron transport chain? Why does this occur?

A

Ubiquinol Transfer from Complex I and II to Complex III

  • Hydrophobic molecule, so it moves through plasma membrane by planar diffusion to complex III
85
Q

What is the process that takes place in Complex III of the Electron Transport Chain?

  • What is Complex III called?
  • How many H+ pass into the intermembrane space?
A

Complex III – Cytochrome Reductase

  • 2 QH2 molecules donates 2 electrons each to complex III
    • One electron → Heme(b) → Heme(b) → Free Q at QN or QP → free radical Q
      • The free radical Q is reduced back to QH2 with second electron following QN or QP path (and is used again)
    • One electron → Fe-S center (Rieske Fe-S Protein) → Heme(c) → Heme(c) on Cyt C → Cyt C
      • The second electron following this path forms second Cyt C (which is why we need 2 NADH to form the 4 Cyt C to be used in complex IV)
  • 4H+ are pumped into intermembrane (per NADH)
86
Q

What is the process that takes place in Complex IV of the Electron Transport Chain?

  • What is Complex IV called?
  • How many H+ pass into the intermembrane space?
A

Complex IV – Cytochrome C Oxidase

  • This complex requires 2NADH molecules to get the 4e- required to reduce O2
  • Four cytochrome c molecules each bring an electron to complex IV
  • Electron flows to CuA → Fe-Cu Center (aka Heme a) → Heme a3-CuB → O2 → 2H2O
  • 3 protein subunits critical to electron flow
  • 2H+ are pumped into intermembrane space per NADH (4 to complete process)
87
Q

What are key inhibitors in the four electron transport chain complexes?

A

Complex I (one)

  • Rotenone – causes an increase [NADH]

Complex II

  • Carboxin – causes an increase [QH2]

Complex III

  • Antimycin A – cause a block in electron flow from heme b to Q, binds at QN (An-3-mycin)
  • Myxothiazol – cause a block in electron flow from QH2 to the Rieske iron-sulfur protein, binds at QP

Complex IV (CO/CN - 4 letters)

  • Cyanide – binds to heme A3 preventing transfer of electrons to O2
  • Carbon Monoxide – binds to heme A3 preventing transfer of electrons to O2
88
Q

What is the importance of a functional electron transport chain to an organism?

A
  • If defective, you will not meet ATP needs of body and death
89
Q

What is the chemiosmotic model for oxidative phosphorylation?

A
  • Chemiosmotic Model for Oxidative Phosphorylation – a pH concentration gradient (by H+) is coupled with ATP synthase
  • Uncoupling Drugs – acidic aromatic compounds that act as proton ionophores and have ability to carry H+ across mitochondrial inner membrane
    • DNP was prescribed for weight loss but led to death and now banned by FDA
    • Thermogenin1 – a protein that allows for uncoupling in brown fat of babies to create heat rather than shivering to generate heat
90
Q

What is the mechanism of F0F1 ATP synthase?

A

ATP Synthase

  • 1 NADH causes 10 H+ to be pumped out into intermembrane space à 2.5 ATP produced (4 H+ per ATP)
  • Proton flux into matrix drives F0 (in membrane) to rotate, which causes F1 (in cytosol) to rotate by gamma subunit
  • Trimer of Dimers of F1 (alpha-beta dimer)
    • One dimer has ADP + Pi
    • One dimer has ATP formed
    • One dimer has ATP leaving
91
Q

Why is compartmentalization important in electron transport chain and oxidative phosphorylation?

A
  • The ETC complexes are maximized on the inner membrane of the mitochondria because the mitochondria produces many reducing agents through the Kreb’s Cycle, which initiates the electron transport chain to drive oxidative phosphorylation.
  • It is important for QH2 to be lipophilic and stay in the membrane because it wants to be reduced and can give its electrons away easily.
  • Pushing protons from the matrix to the inner space creates a gradient that can drive ATP synthase
92
Q

What is the origin of the mitochondria? What difference is there between mitochondria DNA and regular DNA?

A
  • Mitochondrias have their own DNA, ribosomes, and tRNA
    • Prokaryotic-like DNA replication. They have lost most of their repair mechanisms, so its DNA is more susceptible to mutation compared to the eukaryotic nucleus.
93
Q

How do most of the mitochondrial diseases occur?

A
  • Inherited or spontaneous mutation in mitochondrial or nuclear DNA which lead to altered functions of proteins or RNA molecules; identical mutations can result in different phenotypes.
  • These are inherited through the mother. Different tissues are affected depending on ATP demand level.
  • List of diseases:
    • Leber’s Hereditary Optic Neuropathy (LHON)
    • Myoclonic epilepsy and ragged red fibers (MERRF)
    • Mitochondrial encephalopathy lactic acidosis and stroke (MELAS)
    • Mutations in cytochrome b
94
Q

What are the important fatty acids in our body?

  • What are their carbon-double bond ratios?
A

Important FAs:

  • Palmitic Acid (16:0)
  • Stearic Acid (18:0)
  • Arachidic Acid (20:0)
95
Q

How are the main fatty acids absorbed by the intestine and then transported to the adipocyte?

A
  1. Fats ingested
  2. Bile salts emulsify fats, forming micelles
  3. Intestinal lipases degrade triacylglycerols into glycerol and free FAs
  4. Free FAs taken up by mucosa and converted back into triacylglycerols in intestinal epithelial cells
  5. Triacylglycerols, cholesterol, and apolipoproteins form chylomicrons
  6. Chylomicrons move through lymphatic system and bloodstream to tissues
  7. Lipoprotein lipases is activated by apoC-II in capillaries releases FAs and glycerol
  8. FAs enter cells
  9. FAs are oxidized as fuel or converted back to triglycerides for storage
96
Q

What is the transport process for fatty acids from the cytosol into the matrix of the mitochondria?

A
  1. Acyl-CoA Synthetase – an outer mitochondrial membrane enzyme – converts FAs into fatty acyl-CoA using ATP
  2. Carnitine acyl transferase I (CPTI) transfers the FA via carnitine, forming acylcarnitine (removes CoA)
  3. Acylcarnitine is transferred across inner membrane with the translocase enzyme on the inner mitochondrial membrane
  4. Carnitine acyl transferase II (CPTII) transfers the FA back to fatty acyl-CoA and carnitine is restored to the intermembrane space
97
Q

What is the general reaction sequence of beta oxidation?

  • How many ATP are generated?
A

Reaction Sequence

  1. Oxidation that creates FADH2
  2. Hydration
  3. Oxidation that creates NADH
  4. Thiolysis → results in FA with 2 less carbons

ATP Generated – 2.5 ATP per NADH and 1.5 per FADH2 are created in each step

98
Q

What are the modifcations required to beta oxidation for fatty acids with double bonds at even numered carbons?

A
  • Two additional steps
    • Reductase using NADPH
    • Isomerase
99
Q

What are the modifcations required for beta oxidation of fatty acids with double bonds at odd numbered carbons?

A
  • One additional isomerase reaction to make trans
100
Q

What are the modifications necessary for beta oxidation of fatty acids with odd numbered fatty acids?

A
  • Produces final product of proprinoyl-CoA → hydrolysed to proprionic acid and CoA → transported to liver or kidney → formed back into proprinoyl-CoA in mitochondria → converted to succinyl-CoA with coenzyme B12
101
Q

What are the modifcations required for beta oxidation of branched chain fatty acids?

A
  • Alpha-oxidation must be completed first
  • Initial reaction (mixed function oxidase) occurs in perioxisomes
102
Q

What are the differences between synthesis and degradation of fatty acids?

A

Differences

  1. Cellular location
  2. Acyl group carrier
  3. Electron acceptor/donor
  4. Stereochemistry of hydration
  5. Form in which two carbon units are produced/donated
  6. Synthesis uses 159 ATP whereas degradation only gives 129 ATP - more order of entropy requires energy!
103
Q

What is the basic mechanism for synthesis of fatty acids?

A
  1. Acetyl-CoA goes to Malonyl-CoA via acetyl-CoA carboxylase (key regulation prior to fatty acid synthase)
  2. Malonyl-CoA goes to Palmitate via Fatty Acid Synthase (adds two carbons at a time via NADPH reactions)
104
Q

What are the control points in fatty acid synthesis?

A

Control Points by Acting on Acetyl-CoA Carboxylase

  • FA synthesis turned on/degradation turned off by:
    • Citrate, insulin, thyroid hormone, high carbohydrate diet, prolonged increased insulin levels
105
Q

What are the control points for fatty acid degradation?

A

Control Points by Acting on Acetyl-CoA Carboxylase

  • FA degradation turned on/synthesis turned off by:
    • Epinephrine, glucagon, palmitoyl-CoA, fasting, high fat diet
106
Q

How do/Which hormones control fatty acid metabolism and synthesis?

A
  • Mobilization of fatty acid (breakdown) is favored by low glucose levels. Epi and glucagon activated cAMP-dependent kinases activating the lipase in adipose tissue.
  • Insulin decreases cAMP levels, preventing activation of the lipase (decreasing mobilization).
  • Fatty acid oxidation and fatty acid synthesis are reciprocal. Activation of one pathway deactivates the other.
107
Q

What is the rate limiting step for cholesterol synthesis?

A

HMG-CoA Reductase Is Rate-Limiting Step of Cholesterol Synthesis

108
Q

How is HMGCoA reductase regulated?

Inhibition of enzyme?

Stimulation?

A
  • Inhibited by: high cholesterol, phosphorylation of AMP dependent-kinase (senses high [AMP], glucagon, epinephrine, statin
  • Stimulated by: insulin
109
Q

What are the other products of intermediates (isopreniod precursors) of the cholesterol pathway? (4)

A
  • coenzyme Q – used in ubiquinone synthesis (ETC) – can lead to muscle soreness
  • Isoprenyl – used in tRNA synthesis
  • Farnesyl
  • Geranyl
110
Q

What are the general characterisitics of Cyt. P450s?

A

Functions as monooxygenases that adds molecular oxygen (creating H2O in oxidation of compound) using NADPH

111
Q

What are 3 products of synthesis pathways involving cyt. P450s and cholesterol?

A

Vitamin D

BIle Acids

Steriod hormones

112
Q

What are some general features of Vitamin D?

A

Vitamin D – critical for intestinal absorption of calcium and phosphate

  • DISEASE – Rickets – deficit of vit D in diet and insufficient exposure to sunlight
113
Q

What are some general features of bile acids?

A

Polar derivatives of cholesterol that act as a salt/detergent to break up triacylglycerol aggregates

114
Q

What are lipoproteins?

A

Lipoproteins are composed of varying proportions of cholesterol, TGs, and phosopholipids?

LDL and HDL carry most cholesterol.

115
Q

Why is cholesterol important?

A

needed to maintain cell membrane integrity and synthesize bile acid, steriods, and vitamin D

116
Q

What are Chylmicrons?

A
  • Delivers dietary TGs to peripheral tissues
  • Delivers cholesterol to liver in the form of chylomicron remnants, which are usually depleted of their TGs
  • Secreted by intestinal epithelial cells
117
Q

What are VLDL?

A
  • Delivers hepatic TGs to peripheral tissue
  • Secreted by liver
118
Q

What is IDL?

A
  • Formed in the degradation of VLDL
  • Delivers TGs and cholesterol to liver
119
Q

What is LDL?

where does it deliver?

how is formed?

how is it taken up by cells?

A
  • Delivers hepatic cholesterol to peripheral tissues
  • Formed by hepatic lipase modifications of IDL in the liver and peripheral tissues
  • Taken up by target cells via receptor-mediated endocytosis
120
Q

What is HDL?

Where does it act?

What secretes it?

Effected by alch?

A
  • Mediates reverse cholesterol transport from periphery to liver
  • Acts as a repository for Apoc and ApoE
    • Needed for chylomicron and VLDL metabolism
  • Secreted by liver and intestine
  • Alcohol increase synthesis
121
Q

What is LCAT in relation to HDL?

A

Catalyzes esterification of 2/3 of plasma cholesterol

  • Nascent HDL → Mature HDL
122
Q

Fuction of ApoE and on what lipoproteins?

A

Function: Mediates remnant uptake.

(Everything Except LDL)

LP: Chylomicron, Chlyomicron remnants, VLDL, IDL, HDL

123
Q

Fuction of ApoA-1 and on what lipoproteins?

What would a mutation to this cause?

A

Function: ApoA-1 Activates LCAT

LP: Chylomicron, HDL

Mutation: Poor HDL function

ApoA1 R173C mutation: patients have reduced HDL levels, however, patients are protected from heart attacks. HDL increase their rate of clearance due to low numbers.

124
Q

Fuction of ApoC-II and on what lipoproteins?

A

Function: Lipoprteins lipase (Cofactor that Catayzes Cleavage)

LP: Chylomicron, VLDL, HDL

125
Q

Fuction of ApoB-48 and on what lipoproteins?

A

Function: Mediates chylomicron secretion into lymphatics

LP: Chylomicron,Chylomicron remnants

126
Q

Fuction of ApoB-100 and on what lipoproteins?

A

Function: Binds LDL receptor

LP: VLDL, IDL, LDL

127
Q

What are apoproteins?

A

General: serve as ligands for cell surface receptors, activators of enzymes, or as facilitators for lipid transfer proteins

128
Q

What is the general function of LDL receptors?

A
  • LDLreceptors on liver membrane recognizes B100 allowing it to bind LDL, VLDL, IDL, and chylomicron remnants
  • Binding allows for the LDLcholesterol to be brought back into endosomes of liver cells for destruction. The receptor is recycled back to the plasma membrane.
129
Q

Identify the source of the fatty acid precursor for eicosanoid synthesis

A

Most eicosanoids are synthesized from arachidonic acid, which has 20 carbons

130
Q

Describe the role of cyclooxygenase in the synthesis of prostaglandins

A

Two separate reactions on same enzyme.

First cyclooxygenase reaction to make PGG2, then peroxidase reaction to make PGH2, which is substrate for further reactions

PGH2 is the precursor to all the prostaglandins in the body

131
Q

How do inhibitors of COX1 and COX2 work?

A
  • Inhibitors of COX1&2: aspirin and NSAIDs (most pain drugs like ibuprofen)
    • Aspirin: Acetylation of the serine results in the irreversible inactivation of PGH synthase.
  • NSAIDs inhibit PGH synthase by interacting with the hydrophobic active site thereby blocking its reaction with substrate.
  • Tylenol (acetaminophen) not an NSAID. Blocks COX enzymes but not inflammation. Acts in CNS.
132
Q

Describe leukotriene chemistry and pharmacology

A
  • Leukotrienes are characterized by the presence of 3 conjugated double bonds.
  • Longer half-life than other eicosanoids.
  • Cause contraction of vascular, respiratory, and intestinal smooth muscle.
  • Leukotrienes can activate CysLT1 receptors on airway smooth muscle cells (SMC) and postcapillary venule endothelial cells to cause bronchoconstriction and edema.
    • Singulair and Accolate block this binding step.

SPM (17 decks)

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