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The Dynamic Cell > Metabolism - Block 5 > Flashcards

Metabolism - Block 5 Flashcards

1
Q

Is Glycolysis + Krebs Cycle an anabolic or catabolic process?

A

Catabolic: sugar&raquo_space; CO2

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2
Q

Are protein, fat & polysacchar­ide synthesis anabolic or catabolic processes?

A

Anabolic: building molecules

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3
Q

Is ATP made or used up during catabolism?

A

ATP is made

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4
Q

Is ATP made or used up during anabolism?

A

ATP is used up

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5
Q

Is NAD(P)H made or used up during catabolism?

A

NAD(P)H is made

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6
Q

Is NAD(P)H made or used up during anabolism?

A

NAD(P)H is used up

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7
Q

NADPH is “nature’s favourite” what?

A

Nature’s favourite reducing agent

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8
Q

What is often used as a model for NADPH, and why?

A

DCPIP is used instead of NADPH
This is because:
1. it is stable, unlike NADPH, and
2. it is blue, so the blue&raquo_space;> colourless reaction can be seen, unlike with colourless NADPH

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9
Q

Where in the cell does glycolysis take place?

A

The cytosol

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10
Q

Where in the cell does the Krebs cycle take place?

A

The mitochondrion

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11
Q

What occurs in the first step of glycolysis?

A

Glucose is converted (phosphorylated) to G6P

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12
Q

What happens to G6P in glycolysis (step 2)?

A

G6P is converted to F6P (isomerisation)

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13
Q

Which enzyme converts glucose to G6P?

A

Hexokinase

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14
Q

Which enzyme converts G6P to F6P?

A

Phospho-hexose isomerase

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15
Q

What happens to F6P in glycolysis (step 3)?

A

F6P is converted to F(1,6)BP (isomerisation)

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16
Q

Which enzyme converts F6P to F(1,6)BP?

A

Phosphofructokinase

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17
Q

What happens to F(1,6)BP in glycolysis (step 4)?

A

It is split into GAP and DHAP (3-Carbon molecules)

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18
Q

Which enzyme converts F(1,6)BP to GAP and DHAP?

A

Aldolase

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19
Q

What happens to GAP and DHAP in glycolysis (step 5)?

A

DHAP is converted to GAP, so two GAP are present

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20
Q

What happens to the two GAP in glycolysis?

A

They are oxidised to GBP (a carboxilic acid with two phosphates)

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21
Q

What oxidant is needed to convert GAP to G(1,3)BP?

A

NAD+

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22
Q

What important process occurs when G(1,3)BP is converted to G3P?

A

The formation of (2) ATP (as there are two GBP molecules to begin with)

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23
Q

What happens to G3P in glycolysis?

A

It is isomerised to G2P

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24
Q

Which steps in glycolysis use ATP?

A
  1. The phosphorylation of glucose to G6P

2. The phosphorylation of F6P to F(1,6)BP

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25
Q

Which steps in glycolysis make ATP?

A
  1. The dephosphorylation of G(1,3)BP to G3P (2x ATP made)

2. The conversion of PEP to enolpyruvate (followed by pyruvate) in the final step

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26
Q

Which steps in glycolysis are irreversible?

A

The ones which use ATP (phosphorylations) AND the final step:

  1. Conversion of glucose > G6P (first step)
  2. The phosphorylation of F6P to F(1,6)BP
  3. Conversion of PEP to (first enolpyruvate, then) Pyruvate
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27
Q

What happens to G2P in glycolysis (penultimate step)?

A

A lyase splits out H2O and converts it to PEP (phospho/enol/pyruvate)

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28
Q

What happens to PEP in glycolysis (final step)?

A

It is dephosphorylated by pyruvate kinase (making 2x ATP) into enolpyruvate, which converts by itself to Pyruvate

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29
Q

What is the net production of ATP after glycolysis?

A

+2 ATP

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30
Q

What does coenzyme A act as?

A

A handle for carrying acid groups

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31
Q

What happens to Pyruvate (3C) in the Krebs Cycle (step 1)?

A

Its CO2 group is swapped for CoA, forming Acetyl CoA (C2).

It loses H atoms to NAD+, making NADH + H.

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32
Q

What happens to Acetyl CoA (2C) in the Krebs Cycle (step 2)?

A

It reacts with Oxaloacetate (C4) to form Citrate (C6)

33
Q

What happens to Citrate (C6) in the Krebs Cycle (step 3)?

A

It is converted to Isocitrate (C6) then 2-Oxo-glutarate (5C)
A CO2 is lost,
It also loses H atoms to NAD+, making NADH + H.

34
Q

What happens to 2-Oxo-glutarate (5C) in the Krebs Cycle (step 4)?

A

It is converted to Succinyl-CoA (4C)
A CO2 is lost,
It also loses H atoms to NAD+, making NADH + H.

35
Q

What happens to Succinyl-CoA (4C) in the Krebs Cycle (step 5, beginning of 4C home straight)?

A

CoA is removed to convert it to Succinate (C4) and the free energy associated with the reaction makes GTP

36
Q

What happens to Succinate (4C) in the Krebs Cycle?

A

It is dehydrogenated to Fumarate (4C),
Hydrogens taken up by FAD to make FADH2,
This results in an unsaturated bond forming.

37
Q

What happens to Fumarate (4C) in the Krebs Cycle?

A

It undergoes a lyase reaction,
Unsaturated bond replaced by an OH and a H,
It forms Malate as a result.

38
Q

What happens to Malate (4C) in the Krebs Cycle?

A

It is oxidised to Oxaloacetate (C4),

It also loses H atoms to NAD+, making NADH + H.

39
Q

What does NAD+ stand for?

A

Nicotinamide adenine dinucleotide

40
Q

What two nucleotides are present in NAD+?

A

Adenine and nicotinamide (Vit B3)

41
Q

Where does the extra P join onto NAD+ to make it NADP?

A

Onto the ribose of the adenine

42
Q

Where is the the + charge on the NAD+ molecule?

A

The sugar-base bond N on the nicotinamide base

43
Q

What source might provide H atoms for reduction of NAD+ to NAD(P)H?

A

A secondary alcohol CHOH group

44
Q

What kind of pathways are NAD+ and NADH usually involved in?

A

Catabolic pathways (making ATP)

45
Q

What kind of pathways are NADP+ and NADPH usually involved in?

A

Anabolic pathways (biosynthesis)

46
Q

How can you distinguish experimentally between NAD(P)+ and NAD(P)H?

A

UV Spectrophotometry
The oxidised forms, NAD(P)+, do NOT absorb UV
The reduced forms, NAD(P)H, DO absorb UV

47
Q

What kind of enzyme usually creates NADH?

A

Dehydrogenases (in glycolysis and KC)

48
Q

What is the exception to the idea of dehydrogenases creating NADH?

A 
Succinate dehydrogenase (succinate >>> fumarate) creates FADH2 instead of NADH,
This is because succinate is too weak of a reducing agent to make NADH.
49
Q

How many molecules of NADH are made per glucose in glycolysis + KC?

A

10 NADH per glucose

50
Q

How many molecules of FADH2 are made per glucose in glycolysis + KC?

A

2 FAD2 per glucose

51
Q

What process is the source of NADPH?

A

The oxidative pentose phosphate shunt

52
Q

What is the yield of the oxidative pentose phosphate shunt?

A

2x NADPH

1x Ribose-5-phosphate

53
Q

What happens to excess Ribose-5-phosphate (5C) from the oxidative pentose phosphate shunt?

A

It is converted into F6P (6C) and G3P (3C) and used in the glycolysis pathway.

54
Q

What happens to excess NADPH from the oxidative pentose phosphate shunt?

A

F6P and G3P molecules will be drawn from the glycolysis pathway and into the complex sugar interconversion pathway, and Ribose-5-phosphate is produced.

55
Q

Where in the cell doesthe oxidative pentose phosphate shunt take place?

A

In the cytosol (like glycolysis)

56
Q

What cation is ATP normally complexed with?

A

Mg^(2+)

57
Q

How can ATP be replaced?

A
  1. Substrate-level phosphorylations (glycolysis and KC)

2. Oxidative phosphorylation - buildup of NAH+ forms pH gradient and drives ATP production

58
Q

Where does oxidative phosphorylation take place?

A

The cristae of the mitochondrion

59
Q

Which produces more ATP: oxidation of 1x NAHD or oxidation of 1x FADH2?

A

NADH oxidation produces more ATP
> about 2.5 ATP
> about 1.5 ATP is produced by FADH2 oxidation

60
Q

What important group is present on a CoA molecule?

A

An SH (thiol, sulfhydryl) group

61
Q

How does CoA “carry” acids?

A

Acids join to the S atom via a thioester bond

62
Q

How can starch be used as fuel for catabolism EXTRACELLULARLY?

A

Since starch is a polymer of glucose, it can by hydrolysed by hydrolytic enzymes to the monosaccharide.

63
Q

How can starch be used as fuel for catabolism INTRACELLULARLY?

A

Since starch is a polymer of glucose, phosphorylase enzyme attacks the polymer forming glucose-1-phosphate.

64
Q

Why is it more benificial to use a phosphorylase enzyme (intracellular) than a hydrolytic enzymes (extracellular) when catabolising starch?

A

> Hydrolytic enzymes converts starch to glucose, where it can enter the glycolysis pathway.

> Phosphorylase converts starch to glucose-1-phosphate (G1P), an isomer of G6P. With the help of a mutase, this means the first step of glycolysis can be bypassed and one fewer ATP is spent.

65
Q

How can inulin be catabolised?

A

> As a fructose polymer, it can be hydrolysed to fructose.

> A fructokinase can convert this to F6P (with the help of ATP) where it can fit into the glycolysis pathway.

66
Q

How can pectin (dietary fibre) be catabolised?

A

> As a polysaccharide, it can be hydrolysed to many sugars, one of which is L-Arabinose (5C).

> With an isomerase, a kinase and an epimerase (and one ATP) L-Arabinose can be converted to D-Xylulose, which can be ustilised in the Pentose Phosphate Shunt.

67
Q

How can benzene be catabolised?

A

> Benzene is first oxidised (Both O addition and H removal) so it loses aromaticity.

> Some isomerisations then occur,

> The intermediate is condensed with CoA,

> This intermediate is hydrolysed into two products: Acetyl-CoA (C2) and succinate (C4).

68
Q

How can excess amino acids be catabolised?

A
  1. The amino group is removed by transamination with an oxo-acid (usually 2-oxoglutarate from KC).
  2. The amino acid is converted to a new oxo-acid, and the 2-oxoglutarate is converted into glutamate.
  3. The glutamate is dehydrogenated back into 2-oxoglutarate, which is used in another transamination or in the KC. NH3 is also produced here, and is excreted.
  4. The new oxo-acid is reacted with a series of enzymes similar to those at the final steps of KC, cleaved with CoA, and then finally converted into Succinyl-CoA and Acetyl-CoA.
69
Q

How can fats be catabolised?

A
  1. The three ester bonds of the fat are hydrolysed by esterases, forming glycerol and 3x fatty acids.
  2. Glycerol is phosphorylated by ATP, and then oxidised, forming NADH + H, to finally produce DHAP.
  3. The fatty acids are reacted with CoA as acids are wont to do, with ATP being converted to AMP in the process.

4a. The fatty-CoA undergoes a C-C to C=C reaction (producing FADH2), similar to a Succtinate to Fumarate conversion.
4b. The new intermediate undergoes a hydration, similar to a Fumarate to Malate conversion.
4c. The new new intermediate undergoes a dehydrogenation (producing NADH + H), similar to a Malate to Oxaloacetate conversion.
4d. This intermediate is cleaved with CoA, similar to AA catabolism (thiolytic cleavage) and forms Acetyl-CoA plus a shorter fatty-CoA

  1. The shorter fatty-CoA (1C shorter) goes back to the beginning of step 4 to be shortened all over again (( β-Oxidation Spiral )).
70
Q

What are two alternative ways to make ATP?

A

> Oxidative phosphorylation

> Photophopsphorylation

71
Q

What happens to G3P in photosynthesis?

What are the three differences between photosynthesis and glycolysis with respect to this?

A

> G3P is phosphorylated to 1,3-BPG, using ATP
The 1,3-BPG is then converted to GAP

> This is the opposite direction to glycolysis
ATP is used instead of made
NADPH is the carrier instead of NADH

72
Q

What does anabolism require?

A

> ATP

> NADPH

73
Q

What is the plant equivalent of the mitochondrial matrix?

A

The stroma of the chloroplast.

74
Q

What does the Reductive Pentose Phosphate Pathway produce from the 6x G3P?

A

> A Profit of 1x G3P is made and used for anabolism

> 3x ATP are produced to go back into the pathway (which uses x6 ATP to make G3P)

75
Q

Outline how a metabolic pathway could be traced with radiolabelling.

A

> Label a certain substance with a radioisotope, e.g. [C14] Ascorbate, and feed it into the cells.

> Kill the cells at a set time.

> Analyse the cells with chromatography or electrophoresis.

> Detect, quantify & ID the radioactive spots.

76
Q

What are some ways you could kill cells quickly at a set time to investigate a snapshot of their metabolism?

A

> Ethanol

> Liquid N2

> Formic acid

77
Q

How can the radioactive spots be detected?

A

Autoradiography?

78
Q

How can the radioactive spots be quantified?

A

A Geiger or scintillation counter.

79
Q

What are the two methods of radioactive labelling?

A
  1. Pulse-chase - The radioactive precursor is quickly used up, and is traced directly.
  2. Continuous - The supply of added radioactive substance is inexhaustible, and radioactivities of all components reach a plateau (except the final product, which is exponential).

The Dynamic Cell (8 decks)

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