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Biochemistry > Regulation of Metabolic Pathways > Flashcards

Regulation of Metabolic Pathways Flashcards

1
Q

What is intermediary metabolism?

A

It refers to the combines activities of all pathways that interconvert precursors and molecules of low molecular weight.

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2
Q

Where do metabolic processes obtain their energy from?

Name the three main processes categorised into metabolism.

A

They obtain their energy from energy rich nutrient molecules or from solar energy.
Polymerisation, anabolism and catabolism are processes used in metabolism.

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3
Q

Describe the Isoleucine feedback inhibition process

A

Hydroxyethyl-TPP is used to produce Isoleucine through one pathway and Valine, Leucine through another. When Isoleucine builds up it feeds back and inhibits Threonine deaminase which produces α-ketobutyrate, needed for Isoleucine production. This means more valine and Leucine can be produced, when valine levels rise high enough it activates Threonine deaminase and Isoleucine production continues.

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4
Q

What is concerted inhibition, describe according to the Glutamine synthetase?

A

Glutamine sythetase has a central role in the reaction of glutamate and reduced nitrogen to form Glutamine. This can then form 6 end products. Cumulative regulation of the products occurs through their concentrations, their build up of end products serve as negative feedback modulators of the synthetase enzyme.

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5
Q

Conversion of inosinate to adenylate (AMP) requires an amino group derived from what amino acid? Also what is the source of the high energy phosphate in synthesising adenylosuccinate?

A

Aspartate is the source of the amino group,

GTP is the source of the high energy phosphate group.

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6
Q

To convert inosinate to xanthylate what is required?

What amino acid donates an amino group to xanthylate to convert it to guanylate?

A

Inosinate is oxidised by NAD+ using IMP dehydrogenase.

Glutamine donates an amino group.

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7
Q

De novo synthesis of purines is regulated by what inhibition?
What enzyme catalyses the addition of an amino group to PRPP?
What end products inhibit the above enzyme?

A

Feedback inhibition
Glutamine-PRPP-amidotransferase
Inhibited by: IMP (inosinate), GMP (guanylate) and AMP (adenylate)

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8
Q

What end products of the de novo synthesis of purines act synergistically to inhibit Glutamine-PRPP-amidotransferase?

A

AMP adenylate and GMP guanylate

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9
Q

Feedback inhibition occurs in the de novo biosynthesis of pyrimidines, with what inhibiting what?

A

CTP (cytidine-5-triphosphate) inhibits aspartate transcarboxylase

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10
Q

Aspartate transcarboxylase catalyses the first reaction in the de novo synthesis of pyrimidines, what reacts with aspartate?
The molecule above is derived from what, unlike its counterpart in the urea cycle?

A

Carbamoyl phosphate

Derived from the cytosol.

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11
Q

Deoxyribonucleotides are derived from what?
What is replaced by what to convert the preliminary molecule to a deoxyribonucleotide?
What are the substrates and what is the reductant?

A

Deoxyribonucleotides are derived from ribonucleotides.
The 2’OH is replaced with H.
The substrates are rNDP or rNTP and the reductant is NADPH.

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12
Q

Why do many cancer drugs target enzymes in the nucelotide biosynthesis pathways?

A

Because cancer cells have a greater need for nucleotides as precursors for DNA and RNA.

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13
Q

How many moles of ATP are produced during anaerobic glycolysis than aerobic respiration, per mole of glucose?

A

2 mol ATP through anaerobic glycolysis

36 mol ATP through aerobic respiration.

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14
Q

What is the Warburg effect?

A

Cancerous cells carry out glycolysis at a much higher rate than healthy cells, even if oxygen is available. Approximately 4 mol ATP is produced by cancerous cells, even if oxygen is available.

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15
Q

What is metabolism, what is it the sum of?

A

It is the entire set of enzyme catalysed transformations of organic molecules in living things; the sum of anabolism and catabolism.

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16
Q

What can be used to detect tumours, what is the radioactive tracer used?
What is given off by the tracer and after annihilation what is released to be detected?

A

Positron emission topography scans (PET scans) can be used to erect tumours and radio-tagged glucose can be used.
Positrons are given of by the 18F tagged glucose which annihilate and give of gamma photons.

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17
Q

What prevents the radioactive tracer 2-Fluoro-2-deoxyglucose from leaving the cells?

A

2-Fluoro-2-deoxyglucose is phosphorylated by hexokinase to 6-phospho-2-Fluoro-2-deoxyglucose, preventing it from leaving the cell.

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18
Q

The increase in glycolysis in tumour cells is caused by an increase in what?

A

An increase in glycolytic enzymes and an increase in plasma membrane transporters, such as GLUT1 and GLUT3.

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19
Q

What does HIF1-α stand for?

How does HIF1-α aid tumour growth?

A

HIF1-α stands for hypoxia inducible transcription factor.
It is a protein that acts on a mRNA level to stimulate the production of at least eight glycolytic enzymes and GLUT1 and GLUT3 when oxygen supply is limited. This allows tumour cells to survive even though blood vessels haven’t caught up with tumour growth.

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20
Q

HIF1-α stimulates transcription/translation of the VEGF protein. What does VEGF stand for and what does it stimulate?

A

Stands for vascular endothelial growth factor and stimulates angiogenesis

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21
Q

How can HIF1-α levels be regulated?

A

By hydroxylation by oxygen which opens up the binding site on PVHL (von-hippel-lindau tumour suppressor protein) which then leads to degradation.

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22
Q

During hypoxia what happens to HIF1-α and what effects does it have on a cellular level?

A

HIF1-α is not hydroxylated but instead sent to the nucleus where it binds to hypoxia related elements and up-regulates certain genes: those that control angiogenesis, GLUT1 and GLUT3 and those that express lactate dehydrogenase.

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23
Q

Outline the Randle cycle

A

Elevated levels of glucose stimulates insulin secretion which suppresses non-esterified fatty acid (NEFA) release from adipose tissue deposits. This removes substrate competition of utilisation by skeletal muscle. High plasma NEFA concentrations when glucose levels are low results in NEFA being used as fuel.

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24
Q

What are the residues in chymotrypsin’s active site that allow for its proteolytic activity?

A

Serine and histidine residues.

25
Q

What do cofactors do?

What are enzymes that need cofactors described as before and after cofactor binding?

A

Cofactors bind to the enzyme and cause a conformational change that allows the enzyme to catalyse reactions. Apoenzymes are enzymes missing their cofactor and are not functional. Holoenzymes are enzymes with their cofactor and are functional.

26
Q

Give three examples of organic cofactors, inorganic cofactors and cofactors that fit both descriptions.

A

Organic- thiamine pyrophosphate, lipoic acid, nicotinamide adenine dinucleotide, flavin adenine dinucleotide, biotin, panthothenic acid.
Inorganic- 4Fe4S clusters, zinc, copper, iron, molybdenum.
Both- heme, chlorophyll, cyanocobalamin

27
Q

Name the specialised ring in thiamine pyrophosphate (TPP) and what the ring acts as.

A

Possesses a thiazolium ring which acts as an electron sink because it is electron deficient.

28
Q

What enzyme does TPP work with in the first reaction of the Pentose phosphate pathway, and what does this enzyme do in the reaction?

A

TPP is the cofactor for transketolase in the reaction. It transfers a 2 carbon group from a ketose donor to an aldehyde acceptor.

29
Q

Name processes that TPP is used in other than as the cofactor for transketolase?

A

It is the cofactor for pyruvate decarboxylase in alcohol fermentation,
It is used in the decarboxylation of α-keto acids,
Acts as a cofactor for α-ketoglutarate dehydrogenase in the Krebs cycle.

30
Q

Transketolase and transaldolase are used in the non-oxidative reactions of the Pentose phosphate pathway. What molecule is converted to what in these reactions? What does this process allow in the Pentose phosphate pathway?

A

They are used to convert ribose-5-phosphate to glucose-6-phosphate.
This process converts Pentose phosphates to hexose phosphates, allowing the oxidative reactions to occur.

31
Q

What syndrome is caused by a thiamine deficiency? What other disease is caused by a thiamine deficiency? What are the symptoms of these two ailments.

A

Werner-korsakoff syndrome- memory loss, confusion, partial paralysis
Beri-Beri disease- anorexia, subsequent weight loss, odema, cardiac enlargement, neuromuscular symptoms.

32
Q

Werner-korsakoff syndrome is caused by what?

A

Alcohol absorption interferes with thiamine absorption in the intestine.
Condition exacerbated via mutation in transketolase.

33
Q

TPP plays an important role in the decarboxylation of pyruvate to form acetyl-coA. Explain how it does this.

A

The C2 carbon on the thiazolium ring ionises and becomes a cation which attacks the carbonyl group of pyruvate. Decarboxylation is facilitated by electron delocalisation into the thiazolium ring of TPP. Protonation generates hydroxyethyl-TPP and elimination of the thiazolium cation yields acetaldehyde.

34
Q

Along with TPP what other cofactor is needed for pyruvate dehydrogenase?
What characterises this cofactor and what is it able to do?

A

The other cofactor is lipoate (lipoic acid). Lipoate has two thiol groups and is able to undergo reversible oxidation to a disulfide bond.

35
Q

Not all cofactors bind to their enzymes and cause conformational changes that activate them. How else can cofactors interact with some enzymes? Name three example enzyme groups that use this interactions.

A

Some cofactors act as a second substrate, binding to the enzyme as well as the actual substrate. They are both then converted into products and leave the active sites of the enzyme.
Examples: transferases, oxidoreductases and ligases.

36
Q

Detail what oxidoreductases, transferases and ligases do.

A

Oxidoreductases- otherwise known as dehydrogenases, these catalyse redox reactions in which one substrate is reduced at the expense of another which is oxidised.
Transferases- these catalyse reactions where one chemical group is transferred from one substrate to another.
Ligases- these catalyse the joining of two molecules at the expense of ATP.

37
Q

The reduction of NAD+ to NADH can occur to different ways, what two ways are these?

A

The hydride ion can be transferred to either the front or back of the ring. The front is known as the A-side and the back is known as the B-side.

38
Q

What is the conserved motif called that dehydrogenases use to bind to NAD+ or NADP+? What is the motif made up of?

A

It is the rossmann fold and it is made up of six parallel β-sheets and four associated α-helices

39
Q

What is the difference between NAD+ and NADP+?

A

There is a phosphate group bound to the molecule instead of a hydroxyl group.

40
Q

The pyridine rings of NAD+ and NADP+ are synthesised from what? Which is derived from what amino acid?
A deficiency in this amino acid leads to what condition? What are its symptoms?

A

They are synthesised from vitamin niacin which is derived from tryptophan.
A tryptophan deficiency can lead to pellagra, symptoms include dermatitis, diarrhoea and dementia.

41
Q

Outline how NAD+/NADH is used in fermentation and how it is used in alcohol detoxification in mammals.

A

2NAD+ is used to oxidise glucose to form 2 pyruvate molecules, with 2NADH being used to reduce 2 acetaldehyde molecules to form ethanol.
NAD+ is used with ethanol dehydrogenase to oxidise ethanol to ethanal, and then again with acetaldehyde dehydrogenase to oxidise ethanal to ethanoic acid.

42
Q

Lactate dehydrogenase is needed for the conversion of what substrate to what product?
Both alcohol and pyruvate dehydrogenases fit into what category of dehydrogenases?

A

LDH is needed to convert pyruvate to lactate.

Both those enzymes are A-dehydrogenases because they place the hydride ion at the front of the nicotinamide ring.

43
Q

What are the two mechanisms for enzymes that bind two substrates, one being the cofactor?

A

There is the random mechanism in which either one can bind first followed by the other which initiates catalysis.
The second mechanism is the ordered mechanism in which the cofactor must bind first followed by the substrate which leads to catalysis.

44
Q

What type of purification method can be used for LDH and what molecule can be used to purify it and why?

A

Affinity chromatography can be used to purify LDH. Oxamate can be used because it binds to LDH’s active site, so it can be immobilised to the column matrix.

45
Q

Where are the enzymes for fatty acid oxidation found?
What size do they have to be to enter this organelle without help?
What route must they take if larger than this minimum size?

A

They are found in the mitochondria. If smaller than 14 carbon atoms in size they can pass through the membrane unhindered.
If larger they must use the carnitine shuttle.

46
Q

The carnitine shuttle involves three steps, what are they?

A

Esterification of the fatty acid to coA,
Trans-Esterification to carnitine followed by transport,
Trans-Esterification back to coA.

47
Q

What is the method by which fatty acids are broken down?

How does it break the fatty acid down and what is required in the process?

A

β-Oxidation

It removed two carbons from the fatty acid chain in each cycle and requires: FAD, H2O and NAD+

48
Q

Each cycle of β-oxidation produces what molecule?

A

Acetyl-coA

49
Q

Fatty acid biosynthesis takes place where? What cofactor is used?
What 3-carbon intermediate is needed for the reaction?

A

Biosynthesis takes place in the cytosol. It requires NADP as a cofactor. The intermediate needed is Malonyl-coA.

50
Q

Biotin is a cofactor needed for the proper functioning of what enzymes?
What is another name for biotin?

A 
Enzymes that need biotin include: acetyl-coA carboxylase,
Methylcrotonyl-coA carboxylase,
Propionyl-coA carboxylase,
Pyruvate carboxylase.
Another name is vitamin H
51
Q

Explain why a deficiency in biotin is rare?

How can a biotin dependency be caused and how is this diagnosed?

A

It is rare because it’s requirement is low and it is present in many foodstuffs plus the gut bacteria synthesise it.
A mutation for biotinidase can cause a biotin dependency. This can be diagnosed by urinary excretion of certain organic acids.

52
Q

Once synthesised a fatty acid has two pathways open to it. What are these and does the path taken depend on?
What is the first intermediate in the biosynthesis of fatty acids, what is this molecule a substrate for?

A

It can be degraded through mitochondrial β-oxidation or it can be converted into phospholipids. The path taken depends on the rate of transfer of long-chain fatty acyl coA into the mitochondria through the carnitine shuttle.
Malonyl-coA is the first intermediate, it’s a substrate for fatty acid synthase.

53
Q

Increased expression of what is a phenotype common to most human carcinomas?

A

Fatty acid synthase

54
Q

Acetyl-coA carboxylase catalyses which irreversible process?
How many subunits/domains does the enzyme have?
What organisms have the enzyme structure with subunits?
What organisms have the enzyme structure with domains?
What organisms have both the enzyme structures?

A 
The conversion of Malonyl-coA to acetyl-coA. 
It has three subunits/domains.
In bacteria the enzyme has subunits,
In animals the enzyme has domains,
Plants contain both types of enzyme
55
Q

In all forms of acetyl-coA carboxylase what is covalently bonded via what type of linkage to what in one of the domains of the enzyme?

A

In all forms a prosthetic biotin group is covalently bonded through an amide linkage to the ɛ-amino group of a lys residue in one of the three domains of the enzyme.

56
Q

In all organisms the long chain of carbon atoms that form fatty acids is assembled by a system known as what?
How many carbons is the chain extended by with each cycle?
What are the two enzyme variants called and in what organisms are they found?

A

The system is fatty acid synthase.
The chains are extended by two carbons after each cycle.
The two variants are FASI, found in all vertebrates and fungi, and FASII, found in plants and bacteria.

57
Q

Each Malonyl group and acetyl group are activated by what which links the groups to what?

A

They are activated by a thioester which links the groups to fatty acid synthase.

58
Q

Fatty acid synthase is comprised of how many subunits which come together to form the structure?
What moves the intermediates between the different active sites of the protein?

A

It’s comprised of seven subunits.

An acyl carrier protein moves the intermediates between the active sites.

Biochemistry (5 decks)

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