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Metabolism Flashcards

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Organic Chemistry 101 flashcards
1
Q

Metabolism

A

The overall process through which living systems acquire and utilise the free energy they need to carry out their various function

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2
Q

Exergonic energy producing process

A

-DG for reaction nd +ve for ATP formation, Free energy still decreases

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3
Q

Endergonic energy requiring process

A

-DG for phosphoryl transfer by ATP and +DG for endergonic reaction, but free energy still decreases

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4
Q

Why is ATP not stable thermodynamically?

A

The free energy change for hydrolysis is negative under biological conditions, so ATP hydrolysis can occur spontaneously. But it is stable kinetically - slow hydrolysis at pH7 and half life of days.

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5
Q

Catabolism or degradation

A

Constituents are broken down exergonically to simple intermediates (concomitant ATP generation. This is to break down molecules so that they are small enough to be absorbed into cells.

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6
Q

Anabolism or biosynthesis

A

Biological molecules are synthesised endergonically from simpler components (concomitant ATP utilisation)

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7
Q

Starch hydrolysis

A

Starch => maltose (di) + glucose uses amylase (breaks 1-4 glycosidic bonds) ad isomaltase (breaks alpha 1-6 at branch points)
Maltose => glucose by maltase
Intracellular mobilisation of starch reserves uses phosphorylase to generate G-1-P

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8
Q

How are dietary lipids hydrolysed?

A

In the gut to fatty acids and monacylglycerols by lipase

In mammals, fat droplets solubilised by bile salts into micelles

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9
Q

How are proteins digested?

A

Extracellular digestion by proteases => AAs

Oligopeptides taken into the cell -> intracellular peptidases => turnover system

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10
Q

Glycolysis

A

In nearly all living organisms
Glucose is oxidised to pyruvate with concomitant reduction of NAD+ to NADH, generating energy in the form of net ATP production

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11
Q

Lactose intolerance

A

Defects in galactose metabolism in humans - low levels of lactase. Many mammals become lactose intolerant after weaning

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12
Q

Galactosaemia

A

Defect in galactose metabolism caused by the absence of an enzyme converting galactose to glucose
Galactose enerters at G-6-P

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13
Q

What is glycogen and how is it broken down and fed into glycolytic pathway?

A

Intracellular starch storage. Glucose can be broken off easily by glycogen phosphorylase (works with a debranching enzyme) and added to the glycolytic pathway via g-1-p. Has non-reducing one so glucose can be added rapidly.
G-1-P -> Glucose-6-phosphate by phosphoglucomutase

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14
Q

What is glycerol and how is it broken down and fed into the glycolytic pathway?

A

From hydrolysis of lipids and fats. Converted to dihydroxyacetone phosphate.

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15
Q

Stage one of glycolysis

A

2 molecules ATP consumed, due to addition of polar hydrophilic phosphate groups preventing metabolites diffusing out the cell.

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16
Q

Stage two of glycolysis

A

6-carbon sugar splits into 2-3 carbon sugars

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17
Q

Stage three of glycolysis

A

Oxidation of sugars, coupled to NAD+ -> NADH

x2 as 2 molecules G-3-P per F-1,6-BP

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18
Q

Glucose => Glucose-6-phosphate

A

Hexokinase -> induced fit, uses MG2+/ATP complex as substrate
ATP -> ADP
Large -DG and traps glucose inside, as G-6-P cannot be transported out of the cell

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19
Q

Glucose-6-phosphate -> Fructose-6-phosphate

A

Phosphoglucose isomerase
Aldose sugar -> ketose sugar
Reversible

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20
Q

Fructose-6-phosphate => Fructose-1,6-bisphosphate

A

Phosphofructokinsase - activated by fructose-2,6,-bisphosphate which is produced by PFK2/F-2,6-bisphosphatase
ATP -> ADP
Large -DG

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21
Q

Fructose-1,6-bisphoshate -> Glyceraldehde 3-phosphate and dihydroxyacetone phosphate

A

Aldolase
Freely reversible
Both have phosphate groups
DHP interconverted with G-3-P by triode phosphate isomerase (one of the most catabolicallu active enzymes) from a ketose to aldose sugar

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22
Q

Glyceraldehyde-3-phosphate -> 1,3-bisphosphoglycerate

A 
Glyceralde 3-phopshate dehydrogenase
Pi + NAD+ -> NADH
1,3-BPG has a highly transferable phosphate group
Reversible
x2
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23
Q

1,3-bisphosphoglycerate => 3-phosphoglycerate

A

Phosphoglycerate kinase
ADP-> ATP
Reversible
x2

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24
Q

3-phosphoglycerate => 2-phosphoglycerate -> phosphoenolpyruvate

A

Phosphoglucerate mutase (reversible)
Enolase (-H2O) (reversible)
Phosphophenolpyruvate has a C=C attached to a hydroxyl group (an enol) which means it has a high transfer potential phosphate group
x2

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25
Q

Phosphoenolpyruvate => pyruvate

A

Pyruvate kinase
ADP-> ATP
x2

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26
Q

Where does fructose enter the glycolytic pathway?

A

Fructose-6-phosphate

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27
Q

How does glycerol enter the glycolytic pathway?

A

=> L-glycerol 3-phosphate by glycerol kinase + ATp hydrolysis (reverse = phoshotase +Pi)
=> Dihydrocyacteone in stage 2 by glycerol phosphate dehydrogenase and NAD+ -> NADH + H+

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28
Q

Overall results of glycolytic pathway

And DG value

A

1 molecule glucose oxidised to 2 molecules of pyruvate
2 molecules NAD+ reduced to 2 molecules NADH
2 molecules ATP used
4 molecules ATP produced
Glucose + 2Pi +2ADP + 2NAD+ => 2Pyruvate + 2ATP + 2NADH + 2H+
Dg = -197 kJ/mol

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29
Q

How does anaerobic energy generation reduce pyruvate in mammals and why does it need to do this?

A

To balance out the redox processes - a build up of NADH can no longer be oxidised.
Conversion of pyruvate to lactase in anaerobic muscle (excessive accumulation of lactic acid causes muscle cramp- build up of H+) Glucose + 2Pi + 2ADP => 2lactate + 2ATP
Lactate transported to liver where it is converted back to pyruvate by LHD in the corri cycle. Can then be converted back to glucose in gluconeogenesis.
6ATP = costly

30
Q

How does anaerobic energy generation reduce pyruvate in microorganisms?

A

Conversion to ethanol using NADH
Glucose + 2Pi + 2ADP => 2ethanol + 2CO2 + 2ATP
Carried out by yeasts in brewing and baking

31
Q

Control point in glycolysis

A

Phosphorylation of F-6-P to F-1,6-BP (main)
Supply of pyruvate limits further aerobic energy generation
Formation of G-1-P from starch by phosphorylase
Formation of G-6-P from glucose by hexokinase

32
Q

Hw is PDK activity regulated?

A

Metabolic intermediates. Tetrameric enzyme with allosteric binding sites. Increase in ATP = sigmoidal curve - Vmax equal, but at any conc, less activity. AMP and ADP bind to allosteric site, activating enzyme.
Inhabited by citrate and H+
PFK activates by F-2,6-BP - affinity of the enzyme for the substrate increases with this.
High levels of ATP inhabit enemy at allosteric site and low levels stimulate activity at active site.
Inhibition may partially be blocked by F-2,6-BP as it makes enzyme less sensitive to inhibitory effect and increase enzyme activity.
F-2,6-BP synthesised and degraded by PFK2/F-2,6-BPase, activities switched by phosphorylation and controlled by blood glucose levels in higher annals.
High glucose = F-2,6-BP synthesis, activating PFK
Low glucose = F-2,6-BP degradation, decreasing glycolysis

33
Q

TCA cycle

A

Results in complete oxidation, but generates reduced cofactors, not ADP.
Pyruvate oxidised to activated intermediate, acetyl CoA, which then feeds into the citric acid cycle. Further oxidation loses the remaining carbon to CO2.
Acetyl coA also generated by oxidation of fats.

34
Q

Pyruvate dehydrogenase

A

Catalyses pyruvate oxidation. Contains 3 enzymes and 5 coenzymes. Acetyl group from pyruvate attached to CoA to generate A coA. Pyruvate + CoA + NAD+ => ACoA + Co2 + NAD + H+
Mechanism:
1. Thiamine pyrophosphate (TPP) formed
2. Lipoid acid formed
3. FAD formed (flavin Adenine Dinucleotide)
Regulated by reversible phosphorylation - promoted by high levels for ATP, feedback inhibition of PD by energy change, inhabited by high levels of pyruvate - substrate activation of PD.
A coA and NADH also cause feedback inhibition to allow enzyme to spare glucose when FA generation is active.

35
Q

Beriberi

A

Vitamin B1 (thiamine) deficiency disorder. Required for production of TPP. Prevents pyruvate being covered to AcoA. Therefore, build up of pyruvate in blood and NS becomes damaged due to failure to generate sufficient ATP of anabolic metabolism.

36
Q

Other major source of A coA

A

Catabolism of fatty acids.
Intracellular hydrolysis of triacylglycerols is carried out y lipase regulated by hormones via signal transduction system. FA oxidation takes place in mitochondria and generated reduced cofactors.
End product A coA. Oxidation process initiated by Formation of CoA - FA conjugate in an ATP-driven reaction catalysed by acyl coA syntheses.

37
Q

Citrate => Isocitrate

A

Aconitase

38
Q

Isocitrate => alpha ketoglutarate

A

Isocitrate dehydrogenase
Nad+ -> NADH + H+
+ CO2

39
Q

Alpha ketoglutarate => succinyl CoA

A

Alpha-keotoglutarate dehydrogenase complex

NAD+ + CoA => NADH + H+ + CO2

40
Q

Succinyl CoA => Succinate

A

Succinyl CoA synthase

GDP + Pi => GTP

41
Q

Succinate => Fumarate

A

Succinate dehydrogenase

FAD -> FADH2

42
Q

Fumarate => Malate

A

Fumarate

+H2O

43
Q

Malate => oxaloacetate

A

Malate dehydrogenase

NAD+ => NADH + H+

44
Q

Oxaloacetate => citrate

A

Citrate synthase

+ H2O + HC3C=O-

45
Q

Are reactions in TCA ir/reversible?

A

Small DG values (except malate dehydrogenase) so reversible

46
Q

Overall TCA

A

A CoA + 3NAD+ + FAD + GDP + Pi + 2H2O => 2CO2 + 3NADH + FADH2 + GTP + 2H+ + CoA
Glucose has been completely oxidised to CO2, generating a small amount of ATP and a large amount of reduced cofactors

47
Q

Porins

A

Proteins on outer membrane of mitochondria which give access to molecules with Mr 10,000
(inner = limited permeability)

48
Q

Where do the reactions of respiration take place?

A

Glycolysis - cytoplasm: stage 2 and 3 in cytoplasmic compartment of aerobic prokaryotes and mitochondria in eukaryotes
CA cycle and FA oxidation - matrix
Oxidative phosphorylation - inner mitochondrial membrane

49
Q

Proton-motive force

A

Immediate energy sources powering ATP formation by oxidative phosphorylation are proton gradient and electrical potential across the membrane. Generated by step-wise movements if electrons by electron carriers that lead to pumping electrons out of the mitochondrial matrix. Oxidation of NADH and phosphorylation of ADP coupled by generation of a proton gradient.

50
Q

Electron transport chain

A

ATP production maximised by releasing energy in small increments in ETC. Transfer of electrons down this chain is driven by redox potentials - electrons are transmitted from one half reaction to another through protein conductors.

51
Q

NADH affinity for e-

A

Relatively low

52
Q

Complex I

A

Flavin mononucleotide (FMN) and iron-sulphur

53
Q

Complex II

A

Flavin adenosine dinucleotide and Fe-S

54
Q

Complex III

A

Fe-S and cytochrome b

55
Q

Complex IV

A

Copper and cyt a
Cyt c transfers e- to Cu(a), then n to haem a, then finally to a binuclear centre consisting of Cu(b) and haem a(3) - occurs where final transfer to O2 occurs. 4 reduced molecules of cyt c are required to reduced one O2 mol

56
Q

Experiment to demonstrate that ET to oxygen is coupled to proton transfer across the mitochondrial membrane

A

If a suspension of mitochondria is depleted of O2 and NADH is added, no oxidation takes place. On addition of small mounts of O2, protons are pumped out of the mitochondria into the surrounding medium, decreasing its pH. As O2 is depleted, protons move back into the mitochondrion powering ATP synth as pH in medium returns to initial.

57
Q

What is the reduction in redox potential energy linked to ?

A

Protons being pumped out of the matrix into the inter membrane space (H+ pumped out by each complex)

58
Q

What kind of proteins are complexes in the ETC?

A

Transmembrane proteins - CoQ/ubiquinone is a lipid in the inner membrane and reduced complex III. Cyt c is a small proem associated with the outer side of the inner membrane, only 1 haem group. Causes apoptosis by triggering release of cyt c when outer membrane is damaged.

59
Q

Problem of cyt c release when outer membrane is damaged

A

Oxidation of CoQ leads to release of 2e- to pass down chain but cyt c can only accept 1e-.

60
Q

Q cycle

A

The mechanism by which single molecules of cyt c can be reduced which also leads to additional protons being pumped across the mitochondria membrane.

61
Q

Cytochromes

A

Covalently linked to haem. ET occurs by ox/red of the Fe atom in the centre

62
Q

Superoxide dismutase SOD

A

Scavenges superoxide to form hydrogen peroxide that is scavenged by catalase (reactive oxygen species that elapse from reduction of O2)

63
Q

F0

A

A transmembrane complex containing amphipathic helical subunits (c) and a transmembrane subunit bound to the outside of the ring, which contains the proton channel (a) and 2 stalk subunits, projecting into the matrix.
Anchors static part of complex to membrane.

64
Q

F1

A

A water-soluble globular complex in the matrix, containing 3 pairs of subunits with similarity to other NTPases, and a central stalk containing a 3-sided axle subunit. The attachment subunits assist in holding the 2 complexes together.
Gamma axle, driven by the c subunit assembly of F0, rotates

65
Q

Beta subunits of alpha3beta3 hexagmic assembly of F1

A

Carry out catalysis.
Rotation of the gamma subunit relative to the 3 beta subunits changes their conformation => intxeconversion of ADP and ATP. Open, loose or right conformation.

66
Q

Rotation anti/clockwise

A 
Anti = synthesise ATP
Clockwise = hydrolyses ATP
67
Q

H+ half channels

A

When H+ enters, it protonates an aspartic acs on a c subunit.
An Aspartic acid on the next c subunit is released to metric via 2nd half channel. Electrostatic charge forces movement of c ring with respect to subunit. This is repeated, casing c ring to rotate wrt c 0 thereby forcing gamma to rotate wrt the ab hexamer

68
Q

Toxins blocking oxidative phosphorylation

A

Interference of electron flow, proton slow and misc compounds

69
Q

Malate/aspartate shuttle and glycerol phosphate shuttle

A

Needed for oxidation of cytosolic NADH. The inter membrane is impermeable to NADH. Shuttles enable the transfer of reducing equivalents from cytosol to mitochondria. NADH generated in oxidation of G3P is needed to regenerated NAD+ or glycolysis will stop. Anaerobic alternative pyruvate -> lactate by lactate dehydrogenase, regenerates NAD+

70
Q

Glycerol phosphate shuttle

A

Glycerol phosphate shuttle especially active in striated muscle and enables high rates of oxidative phosphorylation. e- form cytosolic NADH are transported to FADH2, losing some energy but continuing to work where there is already a high conc in mitochondria.

71
Q

Malate/aspartate shuttle

A

Mostly in heart and liver. Reversible and also helps to shuttle metabolic intermediates between mitochondria and cytosol.

72
Q

Brown fat

A

Specialised to produce heat - newborns. Thermogenin protein UCP-1 is a proton transporter not connected to ATP synthesis. Adrenaline acting on beta-adrenergic receptors causes lipolysis and free FAs activate UCP-1 mediated proton entry, so energy released by NADH oxidation is converted to hear. Similar uncoupling of OP seen in plants.

Molecules and cells (6 decks)

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