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Cells and Molecules Flashcards

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1
Q

Outline the phosphorylation of Glucose

A

Glucose –> 2(glucose-6-phosphate) + H+, catalyzed by hexokinase. This requires 2ATP and is a group transfer reaction

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2
Q

Outline the conversion to Fructose-6-phosphate

A

Glucose-6-phosphate –> fructose-6-phosphate; catalyzed by phosphoglucose isomerase. This is an isomerization reaction

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3
Q

Outline the phosphorylation to Fructose-1,6-bisphosphate

A

Fructose-6-phosphate –> fructose-1,6-biphosphate; catalyzed by phosphofructokinase. This is a group transfer reaction

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4
Q

Outline the 2 step conversion to Glyceraldehyde-3-phosphate

A

Fructose-1,6-biphosphate –> glyceraldehyde-3-phosphate + dihydroxyacetone phosphate; catalyzed by aldolase. Hydrolytic reaction
Dihydroxyacetone phosphate –> glyceraldehyde-3-phosphate; catalyzed by triose phosphate isomerase. Isomerization reaction

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5
Q

Outline the conversion of Glyceraldehyde-3-phosphate

A

Glyceraldehyde-3-phosphate + NAD+ –> 1,3-biphosphoglycerate + NADH; catalyzed by glyceraldehyde-3-phosphate dehydrogenase. Redox and group transfer reactions

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6
Q

Outline the conversion 1,3-bisphosphoglycerate

A

1,3-biphosphoglycerate + ADP –> 3-phosphoglycerate + ATP; catalyzed by phosphoglycerate kinase. Group transfer reaction

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7
Q

Outline the 2 step conversion of 3-phosphoglycerate

A

3-phosphoglycerate –> 2-phosphoglycerate; catalyzed by phosphoglycerate mutase. Isomerization reaction
2-phosphoglycerate –> phosphoenolpyruvate + H2O; catalyzed by enolase. **Group removal reaction* (& dehydration rxn)

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8
Q

Outline the last step, where pyruvate is formed

A

Phosphoenolpyruvate + ADP –> pyruvate + ATP; catalyzed by pyruvate kinase. Group transfer reaction
2 pyruvate produced because glucose –> 2(glucose-6-phosphate)

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9
Q

Explain Alcoholic Fermentation of Pyruvate

A

Pyruvate + H+ –> acetaldehyde + CO2; catalyzed by pyruvate decarboxylase
Acetaldehyde + NADH + H+ –> ethanol + NAD+
Characteristic of yeast

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10
Q

Describe how Lactate is formed from Pyruvate

A

Pyruvate + NADH + H+ ⇌ lactate + NAD+; catalyzed by lactate dehydrogenase
Anaerobic conditions & mammalian muscle

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11
Q

How is Pyruvate involved in the generation of Acetyl Coenzyme A?

A

Pyruvate + HS CoA + NAD+ –> acetyl CoA + NADH + CO2; catalyzed by pyruvate dehydrogenase complex

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12
Q

Why is it essential that NAD+ is regenerated?

A

Needed for dehydrogenation of glyceraldehyde-3-phosphate to produce ATP
Allows glycolysis to occur anaerobically

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13
Q

How much of each product is formed from 1 turn of Kreb’s Cycle?

A

3 NADH
1 FADH2
1 GTP
2 CO2

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14
Q

Explain Transamination with an example

A

Allows production of non-essential amino acids. An amine group is transferred from one amino acid to a keto acid forming a new pair of amino and keto acids.
Alanine + (alpha-)ketoglutamate → pyruvate + glutamate
Amino Acid —(NH4+)→ Keto acid Group Transfer
Pyruvate then enters krebs cycle and glutamate is reconverted into (alpha-)keto glutamate by glutamate dehydrogenase to form the amino group

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15
Q

What is the purpose of the Glycerol Phosphate Shuttle?

A

To carry electrons across the matrix

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16
Q

Explain how the Glycerol Phosphate Shuttle works

A

Cytosolic glycerol-3-phosphate dehydrogenase transfers electrons from NADH to dihydroxyacetone phosphate (DHAP) → Glycerol-3-Phosphate
The membrane-bound form of the same enzyme transfers electrons to FAD to get passed to CoQ

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17
Q

Outline the processes in the Malate - Aspartate Shuttle

A

Redox and transamination reactions occur to transfer electrons from NADH in the cytoplasm to NADH in the mitochondria.
Aspartate + alpha-keto glutarate -> oxaloacetate + glutamate. Catalyzed by aspartate transaminase
Oxaloacetate + NADH -> malate + NAD+. Catalyzed by malate dehydrogenase.
Malate enters the matrix of the mitochondria through antiporters where the reverse reactions occur; where the end product is aspartate which travels to the cytoplasm through antiporters to be used again.

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18
Q

Explain how 38 ATP molecules are formed

A 
Glycolysis → 2 ATP + 2 NADH → 8 ATP
Pyruvate Conversion → 2 NADH → 6 ATP
6 NADH → 18 ATP
2 FADH2 → 4 ATP
2 GTP → 2 ATP
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19
Q

Explain how the Electron Transport Chain works

A

Complexes I, II, IV accept electrons and a proton (H+) from the aqueous solution. As electrons pass through each complex, a proton is pumped into the intermembrane space.
Succinate dehydrogenase uses FAD as a cofactor and can communicate directly with Coenzyme Q. As electrons are passed from FADH2 to Coenzyme Q, it also picks up a pair of protons, regenerating FAD and generating QH2.
Cytochrome C moves between Complexes II and IV, moving electrons from II to IV

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20
Q

What is the Warburg Effect?

A

Mutations in genes of Fumarase dehydrogenase, Succinate dehydrogenase, and Isocitrate Dehydrogenase decrease Kreb’s Cycle activity which enhances aerobic glycolysis; preferential generation of lactate from glucose even in increased O2 availability

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21
Q

Why does re-oxidation of FADH2 mean that less ATP is produced?

A

Just using FADH2 bypasses complex I (since it requires NADH), therefore fewer protons are pumped into the intermembrane space and less ATP is produced.

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22
Q

What does it mean if a redox couple has a negative redox potential?

A

Redox couple has a tendency to donate electrons, so it has more of a reducing power than hydrogen

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23
Q

What is a redox couple?

A

A substrate that can exist in both oxidized and reduced forms (e.g. NAD+/NADH; FAD/FADH2; etc.).

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24
Q

What is redox potential?

A

The ability of a redox couple to accept or donate electrons

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25
Why is the transfer of electrons from one complex to another, more energetically favorable?
Electrons lose energy as they progress along the chain, so less energy is required to transport them
26
What are the two parts of ATP Synthase called?
F0 is the part bound to the membrane | F1 is the part suspended in the matrix
27
How does ATP Synthase allow the production of ATP?
F0 rotates, converting the mechanical energy into kinetic energy This allows the transportation of H+ from the intermembrane space to the matrix Which synthesizes ATP
28
Why does ATP production vary in the ATP Synthase?
Rotation of the enzyme drives the transitional states with altering affinities for ATP and ADP The flow of Protons through ATP Synthase decides whether ATP synthesis or hydrolysis occurs If there is a higher concentration of H+ in intermembrane space and a lower concentration of ATP in the matrix, then the conditions are more favorable towards ATP Synthesis
29
How can we use the Oxygen Electrode to measure changes in ETC?
By placing suspension of mitochondria into a chamber, we can see the effects of various substrates and inhibitors on ETC through changes in [O2]
30
How do CN- and N3- act as metabolic poisons?
They bind with high affinity to Fe3+ form of haem group in cytochrome oxidase complex, blocking final step of ETC
31
How does Malonate act as a metabolic poison?
Resembles succinate and acts as a competitive inhibitor of succinate dehydrogenase by slowing the flow of electrons from succinate to ubiquinone by inhibiting the oxidation of succinate to fumarate
32
How does Oligomycin act as a metabolic poison?
It is an antibiotic produced by streptomyces that inhibits oxidative phosphorylation by binding to **F1 of ATP Synthase** and blocking the flow of H+ through the enzyme
33
What are metabolic poisons?
Molecules that interfere with the movement of electrons in the ETC or the flow of protons through ATP synthase and therefore interrupt ATP synthesis.
34
What are the metabolic poisons in respiration?
``` Cyanide (CN-), Azide (N3-) Malonate Rotenone Oligomycin Dinitrophenol (DNP) ```
35
How does Rotenone act as a metabolic poison?
It inhibits the transfer of electrons from complex I to coenzyme Q
36
How does dinitrophenol (DNP) act as a metabolic poison?
It can shuttle protons across the inner mitochondrial membrane
37
What are the 5 main classes of lipids?
``` Free fatty acids Triacylglycerols Phospholipids Glycolipids Steroids ```
38
What is the difference between an unsaturated and a saturated fatty acid?
Unsaturated fatty acids have at least one C=C (monounsaturated vs polyunsaturated) while Saturated fatty acids only have C-Cs.
39
What does a triacylglycerol molecule consist of?
3 fatty acid chains attached to a glycerol molecule.
40
What type of bond in triacylglycerols helps to neutralize carboxylic acid groups and hence keep pH in cells within a normal range?
Ester Linkages
41
Where is the majority of cellular ATP made?
Mitochondria
42
Where are lipids derived from?
1. Diet 2. De novo biosynthesis (liver) 3. Storage deposits in adipose tissue
43
Where are bile salts generated and where are they stored?
Generated in liver | Stored in the gall bladder
44
What are bile salts generated from?
Cholesterol
45
Where do bile salts pass through and where do they end up?
Pass from the bile duct into the intestine
46
What happens when there is a lack of bile salts?
Majority of fat passing through the gut undigested (steatorrhea (fatty stool).
47
What is orlistat (tetrahydrolipstatin)?
A potent inhibitor of gastric and pancreatic lipases | obesity treatment to render fats indigestible
48
What are the main side effects of orlistat?
abdominal pain, urgency to defecate, steatorrhea
49
Why is it difficult to transport fats through the plasma?
Because plasma is an aqueous solution, however, the fats have hydrophobic qualities
50
What do lipoproteins do?
Transport lipids in the plasma
51
What is the function of High-Density Lipoproteins (HDLs)?
Reverse cholesterol transport - They transport cholesterol from the peripheral tissues back to the liver for use/disposal
52
What is the function of Low-Density Lipoproteins (LDLs)?
Transport cholesterol synthesized in the liver to peripheral tissues and regulate de novo synthesis at these sites
53
What happens at elevated levels of LDL?
Atherosclerosis - hardening of arteries, increases the risk of myocardial infarctions
54
How are fatty acids and glycerol uptaken by the epithelial cells via the chylomicrons and what happens to chylomicrons after?
Chylomicrons transported around the body via lacteals and collect apoproteins from HDL Chylomicrons have apoproteins lining the hydrophilic area of the chylomicrons The apoproteins bind to lipoprotein lipases along the epithelial cell membrane The triglycerides in the chylomicrons are broken down into fatty acids and glycerol to be taken in by the epithelial cells of the adipose and peripheral tissue Chylomicrons transfer remaining apoproteins to HDL and are uptaken by the liver to be reprocessed into LDLs
55
What happens to the chylomicron remnants and how do they initiate the lipoprotein transport pathways?
They are uptaken by the liver at remnant receptors. VLDLs then transport free fatty acids to adipose and peripheral tissue to become IDLs and LDLs. IDLs taken in by the liver at IDL receptors and LDLs transport cholesterol to peripheral tissue via LDL receptors HDL then takes the cholesterol transported to peripheral tissue by VLDL and LDL back to the liver via HDL receptors
56
How is over half of the body's energy needs including the liver but not the brain generated?
Fatty Acid oxidation
57
What is the purpose of Beta-Oxidation and where does it occur?
To produce Acetyl CoA | Mitochondria
58
Outline the reaction converting Fatty Acids into Acyl CoA
Occurs outside of the mitochondrial membrane Fatty Acid + ATP + HS-CoA → Acyl CoA + AMP + PPi Catalysed by Acyl CoA Synthase
59
Why is AMP produced?
It is a high energy-consuming reaction, so 2 high energy bonds are broken to synthesize the Acyl CoA
60
What is the purpose of the Carnitine Shuttle?
To transport the Acyl CoA species into the matrix
61
Outline the reactions in the Carnitine Shuttle
Acyl from Acyl CoA added to the Carnitine to form Acyl Carnitine and CoA, catalyzed by Carnitine acyltransferase I Acyl Carnitine is transported into the matrix via Translocase and Carnitine is exported into the cytoplasm via Translocase Acyl Carnitine in the matrix loses its Acyl group to CoA to form Acyl CoA in matrix and Carnitine

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