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BIOL1008 > The TCA cycle > Flashcards

The TCA cycle Flashcards

1
Q

Explain the steps to the action of a cofactor (coenzyme)?

A
  1. Apoenzyme becomes active by binding of coenzyme/ cofactor to enzyme
  2. Holoenzyme is formed when associated cofactor/coenzyme binds to the enzyme’s active site
  • The coenzyme has to be bound before the substrate
  • Coenzyme is bound relatively tightly so that the particular group to be transferred is properly orientated to allow catalysis to occur.
  • Once bound to a chemical group, the structure of the coenzyme is changed. Therefore, coenzymes can be considered as the second substrate to the enzyme. Hence, they are called co-substrates.
  • Coenzymes need to regenerate in order to participate in the reaction again and again.
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2
Q

Whats the main function of G3P, Glyceraldehyde-3-phosphate dehydrogenase

A
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3
Q

How many steps are there in the reaction of

Glyceraldehyde-3-phosphate –> 1,3-biphosphoglycerate?

A

There are 3 steps

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4
Q

Whats the first step to the G3P –> 1,3-biphosphoglycerate

A
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5
Q

Whats the second step to the G3P –> 1,3-biphosphoglycerate

A
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6
Q

Whats the third step to the G3P –> 1,3-biphosphoglycerate

A
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7
Q

What process is required for the continual supply of NAD+ ?

A

glycolysis

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8
Q

Whats the limiting factor of glycolysis?

A

NAD+

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9
Q

under aerobic conditions, how is the demand of NAD+ met in glycolysis?

A

Under aerobic conditions, this requirement can be met by the oxidation of NADH by the electron transfer chain (located in the inner mitochondrial membrane)

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10
Q

Under aerobic conditions, pyruvate can enter the mitochondria and be consumed in what?

A

The Tricarboxylic acid cycle, TCA cycle (krebs cycle) to generate even more NADH (ATP)

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11
Q

What does the outer membrane of the mitochondria contain and what does this allow?

A

The outer membrane contains porins, proteins that allow small molecules like pyruvate to enter the intermembranous space

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12
Q

What is the name of the transportes for pyruvate in the mitochondrial membrane?

A

MPC and this transports pyruvate across the impermebale inner mitochondrial membrane

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13
Q

Where does the conversion of pyruvate to acetate occur?

A

In the mitochondrial matrix

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14
Q

What membrane in the mitochondria can NADH cross?

A

Only cross the outer membrane, not the inner membrane

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15
Q

Label the structures of the mitochondria and also the name of the substrates which will pass in those specific locations

A
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16
Q

Under anaerobic conditions, what must a cell still generate?

Give an example of a reaction that produces this?

A

It must still generate NAD+ from NADH

Example: Pyruvate –> Lactate

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17
Q

In the reaction of pyruvate –> lactate, how much pyruvate must be converted under anaerobic conditions for ATP synthesis to continue?

A

all of it

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18
Q

Draw the anaerobic respiration of the conversion of glucose –> lactate

Include by products and the structures of all products

A
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19
Q

Whats the lifespan of a mature RBC?

A

120 days

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20
Q

When RBC lack mitochondria, what pathway must they use and what’s the effect of this?

A

RBC that lack mitochondria can only use the lactic acid pathway; therefore, they cannot use oxygen

this spares the oxygen they carry for delivery to other cells

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21
Q

Alcohol fermentation occurs in yeast, draw this reaction, the by products produced, any enzymes used and the structure of the products

A
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22
Q

during alcohol fermentation, in a closed system, whats bad about the alcohol produced?

A

its toxic to the organism

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23
Q

During anaerobic respiration, what are some fermentation products that are produced in industry
Mention any organisms that may have been used to produce these products

A
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24
Q

Under anaerobic conditions, how many ATP’s are produced for every glucose molecule that is converted to lactate or alcohol ?

A

2

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25
Q

Under anaerobic conditions, what happens when NADH is produced?

A

it is recycled and not used to make more ATP

26
Q

Draw the overall reaction of Pyruvate –> Acetyl-CoA

Draw the structures

The enzymes used

The by products produced

A
27
Q

The reaction of Pyruvate –> Acetyl- CoA is a complicated process, tell me about the enzyme thats used that enables it to be able to carry out such a complicated reaction?

A

The enzyme is made up of 60 subunits and there are 3 main enzymes that carry out the reaction; E1, E2 and E3

28
Q

What type of functional group is Coenzyme A and why is this the case?

A

In chemical terms it is a thiol

this is because it can react with carboxylic acids to form thioesters, thus functioning as a acyl group carrier

29
Q

When there is an excess of glucose, what is CoA used for?

A

It is used in the cytosol for the synthesis of fatty acids

30
Q

What type of reactions is CoA involved in?

A

Catabolic and anabolic processes

31
Q

What is CoA made from?

A

Vitamin B5

32
Q

What are the 3 main roles of CoA?

A
  1. regulation e.g. lipid metabolism
  2. Acetyl-CoA (TCA cycle, CO2 + energy)
  3. Acyl group carrier (fatty acid synthesis and oxidation)
33
Q

What does CoA contian a unit of?

A

ADP

34
Q

What are the precursors of CoA?

A
35
Q

What type of enzyme is DNA polymerase?

A

A multi-enzyme complex possessed of multiple catalytic acitivites

36
Q

Give other examples of Multi-enzyme complexes

A
  • RNA polymerase
  • Ribosomes
  • Fatty acid synthase
  • Proteasome
37
Q

Tell me the steps to pyruvate oxidation?

A
  1. A carboxyl group is snipped off of pyruvate and released as a molecule of carbon dioxide, leaving behind a two-carbon molecule (acetate).
  2. The two-carbon molecule from step 1 is oxidized, and the electrons lost in the oxidation are picked up by NAD+ to form NADH.
  3. The oxidized two-carbon molecule—an acetyl group, highlighted in green—is attached to Coenzyme A (CoA), an organic molecule derived from vitamin B5, to form acetyl CoA. Acetyl CoA is sometimes called a carrier molecule, and its job here is to carry the acetyl group to the citric acid cycle.
38
Q

Summarise pyruvate oxidation by the products?

A

If we consider the two pyruvates that enter from glycolysis (for each glucose molecule), we can summarize pyruvate oxidation as follows:

  • 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+
39
Q

Is pyruvate dehydrogenase a multi-subunit complex?

A

yes

40
Q

How many times does the reaction of pyruvate –> Acetyl- CoA occur for every 1 glucose molecule?

Where does the reaction occur?

A

It happens twice for every 1 glucose molecule

It occurs in the mitochondrial matrix

41
Q

Whats the metabolic wave?

A
  • As part of metabolic flux, substrates are passed through a series of enzymatic reactions.
  • The enzymes alter the substrate to produce a product but they themselves are not altered.
  • You are the enzymes holding the substrate in both hands like a ball.
  • As you stand up and push the substrate in the air you are overcoming the activation energy
42
Q

Why do eukaryotic cells physically separate glycolysis and TCA while in prokaryotes it all takes place in the cytoplasm?

A
  • Prokaryotic cells are approx. 1000-fold smaller than eukaryotic cells.
  • Thus, prokaryotic cells can reply on diffusion.
  • The greater size and complexity of eukaryotic means the cells cannot reply on diffusion only hence compartmentalisation
43
Q

Why are mitochondria believed to have been derived from symbiotic bacteria?

A

The features that are similar between bacteria and mitochondria include:

  • 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 appear 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
44
Q

What are the 3 main reaction types that occur when pyruvate is converted to Acetyl-CoA?

A
  1. Redox
  2. decarboxylation
  3. Transfer of an acetyl group to CoA
45
Q

The oxidation of pyruvate occurs in the mitochondria. pyruvate dehydrogenase is a multi-enzyme complex that uses three main enzymes.

What are these enzymes?

What does each enzyme use as they cofactor?

A

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.

46
Q

What is a prosthetic group?

A

Molecules which are tightly bound to an enzyme or protein e.g. the porphyrin ring in haemoglobin . if removed and put back you won’t get the correct function of the enzyme

47
Q

What are the 3 main prosthetic groups that are required for pyruvate dehydrogenase ?

What are each of the prosthetic groups required for?

A

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.

Thiamine (vitamin B1) – in thiamine deficiency pyruvate metabolism is compromised (beriberi)

48
Q

Why do enzyme complexes exist?

A
  • speed up reactions

because the products of one reaction can be passed directly to the next enzyme without the newly formed substrate having to diffuse to the next enzyme.

The product of a reaction may be highly reactive and take part in other unfavourable ‘side’ reactions if it is not transferred directly to the next enzyme

49
Q

Draw the overall reaction of the Citric acid cycle/ TCA cycle/ Krebs cycle?

And the by products produced ?

A
50
Q

How many steps are there to the citric acid cycle?

A

8

51
Q

Draw step 1 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

A
52
Q

Draw step 2 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

The cofactor used

A
53
Q

Draw step 3 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

A
54
Q

Draw step 4 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

A
55
Q

Draw step 5 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

A
56
Q

How is step 5 of the citric acid cycle, substrate level phosphorylation?

A

The enzyme involves an enzyme-succinyl phosphate intermediate

Succinyl CoA + Pi + Enz –> Enz-succinyl phosphate + CoA-SH

Enz-succinyl phosphate –> Enz-phosphate + succinate

Enz-phosphate + GDP –> Enz + GTP

A histidine is phosphorylated during the reaction. Bacterial use phosphohistidine in a similar way as eukaryotes do phosphoserine, phosphothreonine and phosphotyrosine.

57
Q

Draw step 6 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

A
58
Q

Draw step 7 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

A
59
Q

Draw step 8 of the citric acid cycle:

The structure of the products

By products produced

Enzymes used

What type of reaction it is

A
60
Q

Whats the energy balance sheet for the complete catabolism of pyruvate ?

A
  • 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 pyruvates

61
Q

Whats the energy balance sheet for the complete oxidation of glucose ?

A
  • Glycolysis generates 8 ATP (under aerobic conditions). Only 2 under anaerobic conditions
  • TCA cycle generates 30 ATP for 2 pyruvates entering the TCA cycle
  • Total 38 net ATPs
62
Q

The following diagram shows where each step of the TCA cycle occurs in the cell

A

BIOL1008 (8 decks)

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