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Semester 2 Flashcards

1
Q

what is the delta G of complete oxidation of glucose?

A

-2834 kJ/mol

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2
Q

In therory how many ATP molecules could be made from a glucose? and why doesn’t this actually happen

A

95 ATP. Alot of energy is used driving the formation of products rather than reaching equilibrium

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3
Q

why isnt the 2834kj/mol released as heat?

A
  1. Biological systems cannot utilise heat as a source of energy;
  2. No single reaction of metabolism requires this amount of energy to be released in one step;
  3. Always need to overcome the activation energy. Enzymes are capable of effecting only small changes when they catalyse biological reactions, releasing the energy in steps.
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4
Q

when glucose is catabolised what form of energy is released?

A

Chemical, with ATP being the carrier

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5
Q

what are the 10 steps to glycolysis.

A
  1. glucose has phosphates added to each end, from 2 ATP molecules. leaving 6 carbon compound
  2. this 6 carbon compound splits into 2 3 carbon carbohydrates. - these are energy investment steps.
  3. now is is energy pay off.
  4. a phosphate is added to each of the 3 carbon compounds. (Phosphate comes from solution)
  5. per 3 carbon molecules NAD is converted to NADH+H+ and 2 ADP are converted to ATP.
  6. this converts it to pyruvate
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6
Q

what is the net total products of glycolysis?

A

2 ATPs (4 formed, but 2 used)
2 pyruvates
2 NADH +2H+

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7
Q

what is the coenzyme involved in phosphate removal, and what is it during oxidation and reduction

A

P: ATP/ADP

O/R: NADH/NAD+

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8
Q

what is the structure of glycerol?

A

3 carbons with OH groups on each

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9
Q

where is glycerol used in glycolysis?

A

metabolised into an intermediate in glycolysis called dihydroxyacetone phosphate, which may be converted into pyruvic acid

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10
Q

what is another use for dihydroxyacetone?

A

used in gluconeogenesis to make, glucose-6-phosphate for glucose to the blood or glycogen

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11
Q

what is the structure of linear glucose?

A

6 carbon compound. Aldehyde on top. hydroxyl groups on same side except carbon 3.

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12
Q

what is step 1 of glycolysis?

A

glucose is onverted into glucose-6-phosphate. by the addition of a phosphate from a ATP molecule (hydrolysis) , using hexokinase and Mg2+. Irreversible.G°´ = -16.7 kJ/mol
G = -33.5 kJ/mol

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13
Q

how does glucose eneter into a cell

A

as it cannot cross a membrane it uses transport proteins (GLUT2) to move from high to low concentration by facilitated diffusion. phosphorylation of glucose to G6P (Step 1) prevents it from crossing back.

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14
Q

what is step 2 of glycolysis?

A

Glucose-6-phosphate is converted to fructose-6-phosphate by phosphoglucose isomerase.

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15
Q

why does step 2 happen?

A

Because it needs to form a phosphorylate the hydroxyl group on the 1 position so that after cleavage (lysis) both 3 carbons are phosphorylated

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16
Q

what is step 3 of glycolysis?

A

fructose-6-phosphate is converted to fructose 1,6-bisphosphate using phosphofructokinase. Phosphate is supplied by ATP (ADP formed. this step is irreversible.

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17
Q

what is step 4 of glycolysis?

A

fructose 1,6-bisphosphate is cleaved into Dihydroxyacetone phosphate (DHAP) and Glyceraldehyde-3-phosphate (GAP) by aldolase. this is reversible.

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18
Q

what is step 5 of hydrolysis?

A

DHAP is converted by triose phosphate isomerase to GAP, as this is required for the remaining steps.

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19
Q

what is step 6 of hydrolysis?

A

Glyceraldehyde-3-phosphate (GAP) is converted to 1,3-bisphosphoglycerate
by GAP dehydrogenase. this is an oxidation step (exogonic) in which aldehyde is converted to carboxylic acid. phosphate comes from solution not ATP. and NAD+ is reduced to NADH+H+

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20
Q

what is step 7 of glycolysis?

A

1,3-bisphosphoglycerate is convetered by phosphoglycerate kinase to 3-phosphoglycerate and a ATP is formed. negative delta G

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21
Q

which molecules have high and low energy bonds releative to -30 of ATP?

A

high: phosphoenolpyruvate, 1,3-biophosglycerate, phosphocreatine.
low: glucose-6-phosphate, glycerol-3-phosphate

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22
Q

what is step 8 of hydrolysis?

A

3-phosphoglycerate is converted by phosphoglycerate mutase to 2-phosphoglycerate. The phosphoester is not sufficiently exogonic to produce ATP from ADP but this rearrangement allows, in the next step, for such a compound to be formed.

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23
Q

what is step 9 of glycolysis?

A

2-phosphoglycerate is converted to Phosphoenolpyruvate by enolase. there is also removal of water. The removal of this phosphate is now highly exergonic as the phosphoryl group traps the molecule in an unstable enol form.

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24
Q

what is step 10 of glycolysis?

A

Phosphoenolpyruvate is converted to pyruvate by pyruvate kinase. ATP is formed. this step is irreversible. Donation of the phosphate group allows the enol to convert into the mores stable ketone (pyruvate).

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25
what is the energy balance of hydrolyss
2 ATPs used to prime glycolysis 4 ATPs produced from the glycolytic pathway as a result of substrate level phosphorylation 2 NADHs generated (equivalent to 3 ATPs/NADH oxidised by there electron transport chain) 8 ATPs net gained from the conversion of glucose to pyruvate and the re-oxidation of the 2 NADHs produced
26
what is the action of cofactors
apoenzyme becomes active by binding of coenzyme (cofactor) the the enzyme. holoenzyme is formed when associated cofactor or coenzyme binds to the enzymes active site
27
what are features of the action of coenzymes
1. coenzymes has to be bound before substrate. 2. bound relativly tightly so the group being transferred is properly orientated for catalysis to occur. 3. once bound to a chemical group the structure of coenzyme is changed - considered a second substrate (co-substrate) 4. need to regerate to participate in reaction again.
28
what are the three steps in glyceraldehyde-3-phosphate dehydrogenase being converted into 1,3-bisphosphoglycerate?
1. formation of covalent thioether bond between substate (G3P) and enzyme. 2. oxidation of thioether bond to form thioester bond using NAD+ to perform oxidation. hydrolysis of thioesterbond is exergonic. 3. cleavage of thioester bond - supplies energy to drive endergonic phosphorylation. product 1,3-biphosphoglycerate is relased from enzyme.
29
what is the fate of glycolysis under aerobic conditions?
continuous supply of NAD+, under lots of oxygen this is met by oxidation of NADH by electron transfer chain (inner mitochondrial membrane). Pyruvate enters mitochondria and is consumed in tricarboxylic acid (TCA) cycle (krebs cycle) to generate more NADH (atp)
30
what is the fate of glycolysis under anaerobic conditions?
NAD+ must still be generated from NADH.. pyruvate is converted to lactate, all pyruvate has to be converted for ATP sysnthesis to occur.
31
what is the structure of pyruvate and lactate?
P: carboxylate-carbonyl-methyl L: Carboxylate-Hydroxyl-Methyl
32
why can red blood cells only use the lactic acid pathway
they lack mitochondria, and therefore cannot use oxygen. this spares the oxygen they carry for delivery to other cells.
33
what is another form of anaerobic respiration? give the process
leading to alcohol: 1. glucose to pyruvate with production of 2ATP and 2 NADH. 2. pyruvate decarboxylase removes a CO2 group from each pyruvate leaving 2 acetyladehyde molecules which alcohol dehydrogenase converts to ethanol using NADH (NAD+ formed) .
34
what is fermentation
anaerobic respiration using substrate level phosphorylation
35
what are some example where anaerobic glycolysis is used?
pyruvate decarboxylase in brewers and bakers yeast. prodcues CO2 by pyruvate decarboxylation this gives champagne its carbonation. ethanol fermentation in beer.
36
what is the output of glycolysis under anaerobic respiration?
only 2 ATP are produced per glucose that is converted to lactate or alcohol. NADH is recycled and not used to make more ATP
37
what happens to pyruvate after glycolysis?
leaves cytoplasm for the mitochondria and its complete oxidation by the reactions of the tricarboxylic acid (TCA) cycle (kerbs cycle)
38
what is the differences in location between prokaryotic vs eukaryotic glycolysis?
P: glycolysis-cytoplasm, TCA-cytoplasm, ETC (electron chain transport)-cell membrane, fermentation-cytoplasm E: glycolysis-cytoplasm, TCA-mitochondria, ETC-mitochondrial membrane, Fermentation-cytoplasm.
39
how does pyruvate get into the matrix for Krebs cycle
pyruvate enters mitochondria through porins, then mitochondrial pyruvate carrier transport it to the matrix. conversion of pyruvate to acetate, occurs for TCA cycle to occur.
40
why are there two pools of NADH
because it cannot move across inner membrane (highly impermeable) porins can get into intermembranes space though.
41
how is pyruvate converted to Acetyl-CoA?
oxidative decarboxylation reaction. pyruvate dehydrogenase complex (E1,2,3 enzymes) removes carboxylate group and attaches CoA-SH. Nad+ is converted to NADH
42
what is CoA?
Derived from vitamin B5. An acetyl carrying group to active sites. in chemical terms, a thiol, it can react with carboxylic acids to form thioesters, thus functioning as an acyl group carrier. In excess glucose, coenzyme A is used in the cytosol for synthesis of fatty acids. Hence involved in catabolic and anabolic processes. Like NAD+ and FAD, CoA contains a unit of ADP.
43
what is an example of an multi enzyme complex?
DNA polymerase- composed of multiple catalytic activities. RNA polymerase and ribosomes, fatty acid synthase, proteosome.
44
what are the oxidation steps of pyruvate?
1. A carboxyl group is removed from pyruvate releasing CO2. leaving 2 carbon molecule acetate 2. acetate is oxidised and NAD+ is reduced to NADH 3. An acetyl group is transferred to coenzyme A, resulting in acetyl CoA ( called a carrier molecule)
45
what is the net movement of molecules in the oxidation of pyruvate?
Two molecules of pyruvate are converted into two molecules of acetyl CoA. Two carbons are released as carbon dioxide—out of the six originally present in glucose. 2 NADH are generated from NAD+.
46
Why do eukaryotic cells physically separate glycolysis and TCA while in prokaryotes it all takes place in the cytoplasm?
Prokaryotic cells are approx. 1000-fold smaller than eukaryotic cells. Thus, prokaryotic cells can rely on diffusion. The greater size and complexity of eukaryotic means the cells cannot reply on diffusion only hence compartmentalisation.
47
what are the similarities between between bacteria and mitochondria?
Size and shape – bacillus rod shaped, ranging between 1 and 10 microns in length. Both bacteria and mitochondria replicate by fission. Type of DNA – both contain circular DNA plasmids Ribosome and protein synthesis - mitochondria carry their own ribosomes to make the proteins they need and they appears more similar to bacterial ribosomes than to ribosomes of eukaryotic cells. Membranes – both inner and outer membranes with the outer membrane containing similar proteins such as porins.
48
why does anaerobic respiration occur?
? So that the NAD+/NADH cycle can be maintained in order to keep making ATP via glycolysis.
49
what is the role of the cristae
gives a huge increase in surface area
50
what are the three steps involved in the link reaction between glycolysis and TCA cycle?
1. oxidation/reduction 2. decarboxylation. 3. transfer of an acetyl group to CoA
51
what are the three enzymes used in the multi-enzyme complex? pyruvate dehydrogenase
E1: Pyruvate dehydrogenase which uses thiamine pyrophosphate (TPP) as its prosthetic group. E2: Dihydrolipoyl transacetylase which uses lipoamide and coenzyme A (also known as CoA-SH) as its prosthetic groups. E3: Dihydrolipoyl dehydrogenase which uses flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NAD+) as its cofactors.
52
what is a prosthetic group? give example
molecules that are tightly bound non-polypeptide units required for enzymatic activity or protein e.g., the porphyrin ring in haemoglobin.
53
what are the prosthetic groups for pyruvate dehydrogense?
TTP – thiamine pyrophosphate – required for pyruvate decarboxylation. Lipoate – required for the transfer of the acetyl group to coenzyme A. FAD – flavin adenine dinucleotide – required for the regeneration of the oxidised form of lipoate.
54
why do enzyme complex exist?
speed up reaction - as products of one reaction can be passed directly to the next enzyme without newly formed substrate having to diffuse to the next enzyme. also this stops unfavourable side reactions.
55
what is step 1 of the TCA cycle?
Acetyl-CoA and Oxaloacetate react in presence of citrate synthase to produce Citrate. Condensation reaction. Also a synthase reaction as ATP is made but not used. delta G =-32.2 so highly exergonic
56
what is step 2 of the TCA cycle?
citrate (tertiary alcohol) is transformed to isocitrate (secondary alcohol) using aconitase. isomerisation reaction with 2 steps, intermediate is cis-aconitase. uses Fe-S complex cofactor
57
what is step 3 of the TCA cycle?
Isocitrate converted by isocitrate dehydrogenase to oxalosuccinate intermediate (oxidative step so cofactor NADH+H+ is formed) the isocitrate dehydrogenase decarboxylates oxalosuccinate to alpha-ketoglutarate. 6C to 5C. oxidative decarboxylation reaction.
58
what is step 4 the TCA cycle?
alpha-ketoglutarate undergoes oxidative decarboxylation using alpha ketoglutarate dehydrogenase. second carbon loss to 4 carbon structure called Succinyl-CoA. NAD+ is reduced to NADH+H+ and CO 2 is formed.
59
what is step 5 of the TCA cycle
succinyl-CoA in converted by Succinyl-CoA synthetase to Succinate. cofactor GDP gains phosphate group to form GTP, energy of this bond formation comes from energy released when thioester bond is hydrolysed. this is substrate level phosphorylation. delta G =-2.9
60
what are the three steps in substrate level phosphorylation?
Succinyl CoA + Pi + Enz = Enz-succinyl phosphate + CoA-SH Enz-succinyl phosphate = Enz-phosphate + succinate Enz-phosphate + GDP = Enz + GTP
61
what is step 6 of the TCA cycle?
succinate is converted to fumarate by succinate dehydrogenase during a oxidative dehydrogenation reaction. cofactor FAD is reduced to FADH2. this is the only enzyme within the inner mitochondrial membrane
62
what is step 7 of the TCA cycle?
fumarate is converted to L-Malate using fumarase and the addition of water. Reaction type. catalyses a stereospecific trans addition of a hydrogen atom and a hydroxyl group
63
what is step 8 of the TCA cycle?
L-malate is converted by oxidative dehydrogenation using malate dehydrogenase to oxaloacetate. cofactor NAD+ is reduced to NADH + H+. delta G' = 29.7. Oxaloacetate is rapidly depleted so reaction is driven forward
64
what is the energy balance for complete catabolism of pyruvate?
``` 1 NADH for the conversion of acetyl-CoA 3 NADHs from one turn of the TCA cycle 1 FADH2 from TCA 1 GTP (ATP) directly from the TCA cycle Total = 4 NADH, 1 FADH2, 1 ATP = 12 ATP + 2 ATP + 1 ATP = 15 ATP x 2 for the 2 pyruvate ```
65
what is the balance for the complete oxidation of glucose
glycolysis generates 8ATP. TCA cycle generate 30 ATP (2 pyruvates) total is 38 net ATP
66
what is the difference of NADH levels in the matrix and the cytoplasm and why?
NADH levels are higher in the matrix, so if there was a transporter (there isn't) it would cause NADH to leave down concentration gradient
67
what is the malate aspartate shuttle?
2 transporters that result in electrons and protons from the cytoplasmic NADH being transferred to the NAD+ in the mitochondrial matric.
68
how many molecules of ATP are form per NADH is they are made using the malate-aspartate shuttle?
3
69
where does the malate-aspartate shuttle occur?
tissues where energy requirements are relatively low e.g. the liver.
70
what is the process of using glycerol to enter glycolysis?
1. glycerol + ATP (kinase) = l-Glycerol 3-phosphate. 2. this gets oxidised by glycerol 3-phosphate dehydrogenase (NADH is reduced) to make dihydroxyacetone phosphate. 3. triose phosphate isomerase converts this to D-Glyceraldehyde 3-phosphate glycolysis can then occur.
71
what is the glycerol -phosphate shuttle?
used in metaboliclly active tissue. There are two glycerol-3-P dehydrogenase enzymes (cytosolic and the other mitochondrial bound with the active site on the intermembraneous side). The glycerol-3-phosphate is produced in the cytoplasm and can easily move into the intermembraneous space of the mitochondria. The DHAP can pass back into the cytoplasm and be used in glycolysis. The one less ATP ensures that this reaction is not able to reverse as it decouples the matrix NADH from the cytoplasmic NADH. This oxidation/reduction cycle produced FADH2 hence using this glycerol-phosphate shuttle produces a total of 2 ATP per NADH.
72
why is the glycerol-phosphate shuttle used in place of the malate-aspartate shuttle?
in highly active cells, high conc of cytoplasmic NADH and oxaloacetate will reverse the cycle is M-A shuttle is there and this is bad.
73
what is the difference in net gain of ATP between the malate-aspartate v glycerol-phosphate shuttle?
G-P: 6 ATPs so 36 from glycolysis | M-A: 8 ATPs so 38 from glycolysis.
74
where does all the ATP come from?
it is the oxidation of the NADH/FADH2 to regenerate NAD+/FAD that produces ATP by the phosphorylation of ADP.
75
where is the major sources of NADH/FADH2
glycolysis, the TCA cycle and β-oxidation of fatty acids.

Biochem (2 decks)

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