Metabolism Flashcards
What element is central to energy intensive steps in metabolism?
Carbon.
What three reasons mean that decarboxylation has a very negative delta G?
- Very stable.
- Escapes the reaction site as a gas.
- Increases entropy.
Name one example of a decarboxylation reaction and the enzyme that catalyses it.
Pyruvate + CO2 – Oxaloacetate
Pyruvate carboxylase.
Does decarboxylation require energy?
Yes.
What are three sources of hydrogen?
H20, NH3, NH4+.
What are two sources of oxygen?
H20, CO2.
Name an example of a biosynthetic reaction that uses molecular oxygen.
Synthesis of tyrosine from phenylanaline. The oxidation part of the reaction is favourable while the addition of oxygen is unfavourable.
Oxygen is a stable gas. What does this mean in terms of energetics?
That the addition of oxygenic unfavourable and requires energy.
Do biosynthetic reactions use NADPH or NADH?
NADPH.
What ‘high energy bond’ does acetyl coA contain?
Thioester.
Name three occasions in nature where sulphur plays a key role.
- Iron sulphur clusters.
- Protein folding.
- An energy store in some microorganisms.
When will disulphide bonds not be stable?
In reducing conditions.
S-S are strong covalent bonds that can add a large amount of stability to structures. How do they differ from C-C bonds?
They allow some flexibility as they require less energy to make and break.
Why can sulphur coordinate iron?
Has extra orbitals to coordinate metals.
What is acetyl coA a carrier for?
C2.
Why can acetyl coA be a carrier for C2?
It has a thioester bond which are high energy and have less resonance stability than oxygen esters. When this bond is broken it provides enough energy for ne bonds to be made.
What do the evolution theories say H2S used to be and subsequently produce ?
An early reducing molecule producing pyrites (FeS2) on the surface of volcanic rocks.
Where is sulphur thought to have come from for it to be found in biological compounds such as enzymes?
Through the use of H2S as a reducing molecule.
In regards to sulphur why are higher organisms completely dependant on lower organisms?
As only lower organisms can fix sulphur.
How do higher organisms obtain sulphur?
Through their diet.
How can lower organisms turn sulphur into a organic metabolite?
Serine is activated by acetyl coA and captures S from H2S to produce cysteine.
What enzymes allows for the production of cysteine from serine via the use of H2S?
Cysteine synthase.
Where do biosynthetic precursors often come from?
Central catabolic pathways.
What compound in glycolysis produces serine ?
3PGA.
Why is nitrogen very important in biological compounds?
Found in hydrogen bounds.
What entry enzyme is involved in nitrogen fixation?
Nitrogenase.
Why does nitrogenase require lots of ATP?
Fixation of nitrogen requires lots of ATP as it is a very stable gas.
Some lower organisms can fix nitrogen. How do higher organisms obtain nitrogen?
Through amino acid consumption and through inorganic ions such as NH3 and NH4+.
What entry enzyme is used to fix NH3 and NH4+?
Glutamate dehydrogenase.
Are the ammonium ions stable?
Yes, quite.
What is special about glutamate dehydrogenase?
It can use both NADPH and NADH in biosynthetic reactions.
What overall reaction is catalysed by glutamate dehydrogenase to allow nitrogen to enter biosynthetic pathways?
a-ketoglutarate + NH4+ –> glutamate.
What two enzymes can be classed as threshold enzymes as they control the amount of nitrogen that enters the organic world from the inorganic world?
Cysteine synthase, glutamate dehydrogenase.
What sort of affinity do threshold enzymes have to their substrates?
Very high.
Explain how threshold enzymes are expressed.
They are not constitutively expressed. They are controlled at a genetic level and through signalling as they control costly reactions.
What does phosphorus become phosphate naturally?
Because of the high amount of oxygen in the atmosphere.
Name one example were phosphate can be used directly in the cell.
In glycolysis.
Why is phosphorus not as stable in ATP?
As it is in different resonate form- means that ATP is disfavoured to ADP.
What sort of functions do primary pathways have?
Housekeeping functions as they generally have basic roles.
Where are primary pathways present?
Essentially all cells.
Primary pathways are largely constitutive. Explain how this is possible.
Enzymes are present all the time but the level of the enzyme varies. Sometimes there is one constitutive enzyme set and one that can be varied.
What sort of pathways control specialised functions?
Secondary.
In what cells do secondary pathways occur?
Differentiated.
Secondary pathways are inducible. What triggers these?
External signals.
Name two examples where secondary pathways are used.
- Hormone biosynthesis.
2. Antibiotic production in some bacteria.
Why is knowing weather a primary or secondary pathway is used very important in biotechnology and industry?
As the signals to produce these pathways are very different. You will need to know which pathway to know which signals allow maximum production of the desired product.
Where does glycolysis happen?
The cytosol.
What are the two main functions of glycolysis?
- ATP and NADH production.
2. Intermediates for biosynthesis.
Does glycolysis or the pentose phosphate pathway occur when the body needs energy?
Glycolysis.
Does glycolysis or the pentose phosphate pathway occur when the body needs biosynthesis?
Pentose phosphate pathway.
What is produced from glycolysis?
2 3C pyruvate molecules.
What is produced in the pentose phosphate pathway?
One 5C sugar, such as ribose.
What pathway runs parallel to glycolysis?
Pentose phosphate pathway.
What does the first step of the pentose phosphate pathway generate?
NADPH.
What are the three main functions of the pentose phosphate pathway?
- Genrates 5’ sugars and NADPH for biosynthesis.
- Breakdown route for 5’ sugars.
- Produces intermediates for biosynthesis.
Where does the pentose phosphate pathway occur?
In tissues involved in biosynthesis.
What enzyme makes NADPH in the first step of the pentose phosphate cycle?
Glucose 6 phosphate dehydrogenase.
What type of reaction in the pentose phosphate pathway occurs to make NADPH?
Decarboxylation.
What four carbon sugar involved in the pentose phosphate cycle is needed in aromatic amino acid production?
Ribulose 5-phosphate.
Why can the pyruvate phosphate pathway also result in pyruvate being produced?
As it produces the intermediates Glyceraldehyde 3 phosphate and fructose 6 phosphate, both of which can feed back into glycolysis.
What enzyme is involved in the links reaction?
Pyruvate dehydrogenase.
What is the link reaction a good example of?
A decarboxylation reaction.
What is the overall equation for the link reaction?
Pyruvate- acetyl coA + CO2 + NADH/
What are three functions of the link reaction?
- Processes pyruvate so it can enter Krebs.
- Source of acetyl coA.
- NADH production.
Where does the link reaction occur?
In the mitochondrian.
What is a major source for intermediates for biosynthesis?
The Krebs cycle.
Why is the Krebs cycle an ideal source of intermediates for biosynthesis?
As it is a cycle.
What key experiment carried out by Krebs made him realise that it was a cycle?
When one of the intermediates e.g. succinate was added more CO2 was produced in the muscle preparation.
For every 2C sugar placed into the Krebs cycle how many CO2 molecules are produced?
- The krebs cycle does not increase the amount of intermediates, adding more 2C units just increases the speed of the cycle.
How many molecules of ATP can be produced from krebs/ ETC?
38
What are the main two factions of the Krebs cycle?
- NADH and GTP production.
2. Intermediates produced for biosynthesis.
Where does the Krebs cycle occur?
The mitochondrion.
What three things can intermediates of the Krebs cycle be used to produce?
Amino acids, fatty acids, porphyrins.
What intermediates of the Kreb cycle can lead tot the production of amino acids?
Oxaloactetate and a-ketoglutarate.
What intermediate of the Krebs cycle can produce fatty acids?
Citrate.
What intermediate of the Krebs cycle can produce porphyrins?
Succinyl coA.
What are porphyrins important in the production of?
Haem groups.
What word describes the ‘top up’ mechanisms of the Krebs cycle?
Anaplerotic.
Name one anaplerotic mechanism used to replenish a kerb cycle intermediate.
The production of oxaloacetate from pyruvate via pyruvate carboxylase.
Pyruvate + CO2 + ATP +H20 –> ADP + oxloacetate.
What does increasing the level of on of the Kreb cycle intermediates ultimately do and why is this useful in biosynthesis?
Increase the level of all the intermediates. This is s useful in biosynthesis as it means there are multiple top up points. This is not the case for straight pathways.
What is the overall purpose of the mitochondrial electron transport chain?
Maintains a redox while generating ATP.
What is the most common molecule used by enzymes to couple unfavourable reactions?
ATP.
What three molecules does the METC use to generate ATP?
NADH, FADH2 and GTP.
Where does the ETC take place?
The mitorchondrial inner membrane.
What are two functions of beta oxidation of fatty acids?
- Extracts energy from lipid stores.
2. Generates two carbon units for biosynthesis.
Where does beta oxidation of fatty acids occur?
Mitochondrion.
What is used to extract energy form the lipid stores in beta oxidation of fatty acids?
NADH and FADH2.
How can acetyl CoA be produced from fatty acids?
Through the removal of subsequent two carbon units.
Is anabolism or catabolism the building up of molecules?
Anabolism.
What two things make anabolism costly?
- Entropy loss.
2. Law of mass action ratio.
Explain ‘the law of mass action ratio’ in terms of anabolic reaction,’
Anabolism often leads to the release of water (while catabolism often involves hydrolysis.) The amount of water is often enormous pushing the equilibrium back.
Name an example of an anabolic reaction that the ‘law of mass action ratio’ occurs on?
The conversion of free sugars into polysaccharides and water.
What process takes pyruvate back to glucose?
Gluconeogenesis.
Gluceoneogenesis and glycolysis use the same enzymes. True r false?
Fasle.
Why does the cell need to tightly control glyconeogenesis?
As some cells need more energy while some cells need to store energy.
What are two examples of cells where gluconeogenesis needs to happen?
Liver (mainly) and kidney cells where glucose is sent to the brain where it is scarce.
Where does gluconeogeneis happen inside a cell?
In the mitrochondion and the cytosol.
Amino acids can be produced from pyruvate and some precursors in the glycolytic pathway. What does this mean in regards to gluconeogeneis?
That some amino acids can essentially be made into glucose.
What sort of control occurs at genetic level?
Course.
Name one way that cause control can be maintained?
Through changing the amount of expression of an enzyme.
Is course or fine control a slow method of control?
Course.
Name 7 examples of fine control.
- Product inhibitor.
- Competitive inhibition.
- Feedback inhibition.
- Allosteric control.
- Covalent modifications.
- Phosphorylation.
- Proteolysis.
Fine control happens at the allosteric site. True or false?
False, can also happen at the active site.
Allosteric control decreases the level of interactions with enzymes. True or false?
False, it can also increase the amount of interactions.
What does distributive control involve?
Controlling branched pathways.
Why are branched pathways essential in biosynthesis?
As a relatively small number of building blocks need to produce a large number of products.
Why does distributive control often happen at the top of branched pathways?
Because otherwise through reducing the production of one product you would get a massive accumulation of the other products that you don’t need.
What is the most common method of control used in distributive control?
Feedback inhibition- fine.
What are the three strategies of distributive control?
- Enzyme multiplicity (isoenzymes.)
- Single enzyme cumulative control.
- Single enzyme concerted control.
Explain an example of enzyme multiplicity/ distributive control that occurs in E.coli.
Lysine, methionine and threonine are all produced from aspartic acid. E.coli has three different aspartokinases which all have a aspartokinase and regulatory domain. One of these enzymes is inhibited by lysine and one is inhibited by threonine however the final enzyme is not inhibited by methinione- this means you can not switch the aspartoklinae pull off altogether.
What domain is the same and what domain is different in all three aspartokinases fond in E.coli.
The aspartokinase domain is the same, the regulatory domain is different.
What sort of regulation happens with aspartokinases found in E.coli?
Allosteric.
The control in the pathway producing lysine, threonine and methionine from aspartic acid is different in different organisms. Why is this useful?
As it provides more opportunities in biotechnology to exploit the pathway.
Two of the aspartokinases found in E.coli contain a further domain which an unclear function. Which two are these?
- Threonine sensitive aspartokinase.
2. Unsensitive aspartokinase.
What type of control is being described here:
An enzyme produces two products, A and B. Either by itself at its require level in the cell has no effect on inhibiting the enzyme. When both products are present at the required level the enzyme will be inhibited.
Concerted allosteric control.
What type of control is being described here:
An enzyme produces two products, A and B. Both A and B have a small amount if inhibitory activity when they have reached their required level within the cell. Together their effect is much more potent and the enzyme may stop altogether.
Cumulative.
Glutamine synthetase is a very large enzyme whose products inhibit it in an additive fashion. how many products is this?
> 10.
Glutamine synthetase produces a large amount of products all of which have an additive inhibitory effect. Are sites available for all these products?
Yes.
What does the term ‘restrictive flux’ relate too?
The slowest step in the pathway or the ‘rate determining step’. Was originally thought that an enzyme at the start of the process which was regulated by end products would determine the rate of the whole process- this is now known not to be the case.
What was the first experiment that showed that the theory of ‘the rate determining step’ was not true?
The level of PFK (phosphofructokinase) was increased 3.5 times by GM. A fairly be increase through glycolysis was expected but in reality there was only a small change in the flux.
What was the second experiment that showed that the theory of ‘the rate determining step’ was not true?
PFK was replaced by a non allosteric version of the enzyme. This also had little effect on flux.
What was originally thought to be the reason why the first rate determining step experiment not producing an increased flux?
Feedback inhibition.
What theory replaced the rate determining step theory?
Distributive control theory.
What is the distributive control hypothesis?
The flux through a pathway is a system property rather than simply a proper of individual enzymes.
What does this describe?
All enzymes in the pathway and the whole system control the amount of product. You can not control the outcome of the pathway via one enzyme through flux.
Distributive control hypothesis.
What is the definition of flux?
The number of molecules being transferred per unit time.
How can you increase the flux of a system?
By increasing the amount of several enzymes- not just one.
Give one example where flux is increased in a biology system by increasing the amount of several enzymes.
The trp operon- all 5 genes can be simultaneously increased 23 fold increasing the flux of tryptophan 9 fold.
This is an example of course control.
What two things do you need to do to measure metabolic flux?
- Identify the enzymes involved in the pathway and know their activity.
- Map the levels of as many intermediates as possible.
What is the definition of the metabolome?
The quantitive complement of all the low molecular weight molecules present in the cell under a given set of conditions.
What two things can be used to investigate the effect of increasing/ decreasing the amount of a specific enzyme in a system allowing you to work out that enzymes effect on the flux?
GM and inhibitors.
Does the flux coefficient (C) apply to a whole pathway or to one enzyme within the pathway?
One enzyme within the pathway.
What does a large C value equate to?
A large effect on the flux.
What is the equation for the flux coefficient (C)?
(change in steady state flux/steady state flux) / (change in enzyme concentration/ enzyme concentration.)
Do early or late enzymes have a high C value so a bigger effect on flux?
Late, this contradicts the original view of allosteric control.
Is distributive control or allosteric control more repaid in vitro?
Allosteric.
What is the biggest implication of the distributive control hypothesis?
Biotechnolosists need to be able to decide which enzymes to increase/ improve to have the greatest effect on the yield.
How can you measure the rate of incorporation in a pathway?
Through the use of metabolic levels such as C13 and P31.
What can P13 accumulation be shown in when measuring flux?
Phosphatidyl chloine.
Why is it easier to see phosphorus accumulation rathe than carbon when measuring flux?
As less compounds contain phosphorus.
What is an advantage of using NMR over mass spec to look at metabolic labels?
It can be done on live cells.
What allows for primary control?
End product feedback.
Why is it important that the cellular level of products is determined by a balance of synthesis and degradation?
Otherwise the process would be wasteful and you would get very hot.
What is the main carrier for C1 groups?
Tetrahydrofolate.
What is the main carrier for C1 methyl groups?
S-methyladenosine (SAM).
What is the main carrier for CA carboxyl groups?
Biotin.
What is the main carrier for C2 groups?
Acetyl coA.
What is the main carrier for c3 group?
PEP.
What is the main carrier for C5 groups?
Isopentenyl pyrophosphate (IPP).
What is the main carrier for amino groups?
PEP.
What is the main carrier for sulphur?
Cysteine.
Why is biotin a good carrier of carboxyl groups?
As the COO- group next to the carbonyl is not an ideal conformation as the ability for these groups to move is limited due to the fact that they are attached to an aromatic ring. COO- is hence a good leaving group.
What does biotin often bind to?
Lysine.
What is the soluble form of CO2?
Bicarbonate.
How does the carboxylate load onto biotin?
ATP and bicarbonate react to make carboxyphosphate. Carboxyphosphate breaks down to form a phosphate when it hits biotin as it is very reactive. ADP produced. COO becomes attached.
Name an example in which biotin acts as a carrier.
For the anapldrotic reaction off pyruvate being made into oxaloacetate.
What is structurally significant about tetrahydrofolate (FH4) to stop it leaving the cell?
It has a polyglutamate tail which keeps it in the cell due to its negative charge.
What group (s) can be transferred by FH4?
CH and CH2.
Where do the carrier groups attach to FH4.
N5 or N10.
Why does FH4 only rarely cary CH3?
As it is not an energetically good enough donor to carry out this reaction.
What biosynthetic reaction is the FH4 carrier involved in?
Conversion of DUNP to dTMP.
How is dTMP different to DUNP?
It contains a methyl group.
What is the source of CH3 in the conversion of DUNP to dTMP?
Serine.
The main source of CH3 in the conversion of DUNP to dTMP is serine. How does this work?
Serine is converted to glycine and hydrolysed to produce methylene FH4. This is also the main source of glycine.
Why is FH4 a good donor for CH2?
As it is unstable compared to dihydrofolate due to its poor ring system. Dihydrofolate has a much better resonance structure.
What energy source allows FH$4 to act as a donor in the conversion of DUMP to dTMP?
NADPH.
What activates SAM?
A +ve sullphur.
What does the activation of SAM require?
ATP.
What is the source of CH3 carried on SAM?
Serine via FH4.
What is formed when S-adenosylmethionine donates a CH3 group and how does this reform SAM?
S-adenosylhomocysteine. This hydrolyses to become adenosine and homocysteine. Homosycysteine can build a new molecule of SAM through reactivation of methionine using ATP.
Where does a thioester bond occur between?
A thioester and a sulphur.
Name an example of a self contained carrier and donor.
C3 carrier phosphoenylpyruvate,
How is the C3 carrier phosphoenylpyruvate able to be self contained?
It is high energy, and by removing its phosphate it can attach itself onto a growing substrate.
The C3 carrier phosphoenylpyruvate is self contained as it is high energy. Does it still need enzymes?
Yes.
Why is phosphoenolpyruvate high energy?
As the phosphate is attached to the middle carbon meaning it is very close to the negative charge on the carboxylate.
IPP is the main carrier of C5. Why does this work as a carrier?
It is an unstable compound meaning it is favourable to loose the pyrophosphate and add the isopentenyl group to something else.
What is the main c2 carrier?
coenzyme A.
Where in nature is coA being a C2 carrier often found?
In fatty acid biosynthesis.
How can C5 be formed?
Carbon compounds form mevalonate (originally made from 2 acetyl coA groups. One carbon is then lost as a hydrocarbonate ion.
where does the energy come from to allow C5 to be a carrier?
Through decarboxylation and ATP.
How many molecules of ATP needed to allow IPP to be a C5 carrier?
3.
How many IPP units is cholesterol made from?
4.
What is the most common NH2 donor in biosynthesis?
Glutamate.
What forms once glutamate donates a NH2 group?
Glutamine.
What is needed for glutamate to donate NH2?
ATP hydrolysis.
How are pyrimidines formed?
Ring assembled then ribose attached.
How are purines formed?
Ribose formed then ring attached.
How many steps are involved in the pathway for purine biosynthesis?
10.
what is PRPP?
An activated ribose - it has a pyrophosphate attached.
Where does PRPP come from?
The pentose phosphate pathway.
Reactions 2-7 in purine biosynthesis all have the same chemistry. What does this infer?
They gave a common ancestor.
What is require in the reaction 2-7 in purine biosynthesis?
Activation of oxygen via ATP.
PRPP is the activated form of ribose. It comes from the pentose phosphate pathway. What enzyme is responsible for this activation?
Ribose phosphate pyrophosphate kinase.
How is oxygen activated via ATP (3 steps)?
- The lone pair the oxygen is attracted to the partial positive charge on the phosphate resulting in the formation of a CO phosphate.
- Nucleophilic attack of the carbon attached to the oxygen by a lone ammonium group attached to R.
- Phosphate released.
What occurs in the first step of purine synthesis ( including donor and energy source)?
Addition of the first nitrogen onto the purine ring of the ribose phosphate via an animation reaction. NH2 donor glutamate and energy source is the removal of the pyrophosphate from PRPP.
What is the second step in the synthesis of purines?
Glycine donates a CNN group. This requires activation of glycine via oxygen/ATP. The NH2 on the ribose can then attack this group.
What is step 3 in purine synthesis?
Addition of a formyl group from FH4. Energy comes from FH4 which gets its energy from NADPH.
What is step 4 in purine synthesis?
Addition of NH2 from glutamine. This also requires the activation of oxygen via ATP.
What happens in step 5 of purine biosynthesis?
Ring closure via the activation of oxygen.
What complicated step happens in step 6 of purine synthesis?
Addition of CO2 followed by migration- this is different in every species with different carriers being used. In humans this carrier is biotin..
What happens in step 7/8 of purine synthesis?
Addition of NH2 via asparate. This binds to the emerging purine ring using ATP.
What happens in step 9 of purine synthesis?
C1 addition via FH4.
What happens in step 10 of purine synthesis?
Ring closure and loss of water.
What does conversion of ribose to deoxyribose involve?
NADPH to NADP.
What enzyme is needed to convert a ribose to a deoxyribose?
Ribonucleotide reductase.
What overal control mechanism allows for the control of ATP, GTP, purine, pyrimidines, ribs, deoxyribo, NADPH and NADH levels?
Product feedback.
What is throught to decrease the conversion of PRPP to phosphoribosylamine?
IMP, AMP, GMP.
Inosinic acid (IMP) can be converted into AMP and GMP. Howe are these pathways controlled?
Through the co-rectants of the opposite branch. If there is two much ATP it will increase the formation of GMP though ATP hydrolysis and vice versa.
When large amounts of purines are present what happens to ribonucleotide reductase?
The active site changes so it is specific to pyrimidines.
How does ribonucleotide reductase respond deoxyribonucleotide levels?
When dATP is present it decreases the activity and when ATP is present it increases the activity meaning more dexoyribonucleotide is made- this is all dependant on allosteric control.
The enzyme ribonucleotide reductase has two sites allowing it to respond to purine/prymidine levels and deoxyribo/ribo nucleotide levels. What site has the catalytic activity?
Site the binds deoxyribo/ribo nucleotides.
The enzyme ribonucleotide reductase has two sites allowing it to respond to purine/prymidine levels and deoxyribo/ribo nucleotide levels. What site has the substrate specificity?
Purine/pyrimidine site.
What does ribonucleotide reductase use for its reducing activity?
NADPH.
What is ribonucleotide reductase involved in?
Balancing mechanisms.
What establishes the chirality of the carbon atom in amino acids?
The transamination reaction using pyridoxal phosphate.
What does transamination involve?
The exchange of one amino acid with another.
What does amination invole?
The process of getting nitrogen into the body though ammonia or ammonium.
Almost all transaminases are descended from a common ancestor. What enzyme is used in the amination reaction that produces glutamate?
Glutamate dehydrogenase.
Name one example of an amination reaction involving glutamate dehydrogenase.
A-ketoglutarate (or a-oxo glutarate) + NH3 —–> glutamate.
What is produce from the amination reaction involving glutamate dehydrogenase?
NAD/ NADP.
Where does glutamate dehydrogenase produce glutamate through an animation reaction?
Mitochondrion.
Glutmate synthase and glutamine synthetase carry out very similar reactions. What are their respective reactions?
a-oxo glutarate + glutamine –> glutamate
glutmate + NH3 –> glutamine.
Does glutamate synthase or glutamine synthetase use ATP?
Glutamine synthase.
Does glutamate synthase or glutamine synthetase use NADPH?
Glutamate synthase.
Does the glutamate synthase/ glutamine synthetase reaction cycle product glutamate or glutamine?
Glutmate.
What is a Schiff base?
C=N.
What does a Schiff base do to a structure?
It stops it rotating resulting in fixed planer geometry.
Is the conversion to a Schiff base reversible?
Yes.
What does a schiff base ensure?
Only L isomers are made.
What attacks schiff base to form a L amino acid?
Hydride ion from NADH or NADPH.
What enzyme uses a schiff base in its reaction?
Glutamate dehydrogenase.
How are amino acids classified?
According to their biosynthetic precursor of their carbon skeleton.
What are the 6 metabolic families of the amino acids?
- Oxaloacetate.
- Pyruvate.
- PEP.
- 3-phosphoglycerate.
- Ribulose 5-P
- Ketoglutarate.
What does the synthesis of essential amino acids often involve?
Long series of costly reactions- often aromatic.
What are the three general steps in amino acid synthesis?
- Start with an intermediate of glycolysis, PPP or the TCA cycle.
- Required side chain is assembled on a a-keto acid.
- NH2 group added by transamination.
What does the donor amino acid become in amino acid formation?
Keto acid.
Why does control of amino acid metabolism not happen at the point at they are made?
As the reactions are not far from equilibrium.
What enzymes are involves in the transamination formation of amino acids?
Transaminase/ aminotransferase.
Why can you fully exploit your amino acid pool in amino acid formation?
As any amino acid can be used in a transamination to create another amino acid.
What is normally the limiting factor in amino acid synthesis?
Nitrogen levels.
Does transamination to create new amino acids require much energy?
No.
What amino acid can directly be made from pyruvate?
Analine.
What amino acid can directly be made from oxaloactate?
Aspartate.
What amino acid can be directly made from a-keto glutarate?
Glutamate.
What has to be maintained through the transamination reactions producing amino acids?
Chirality.
Why are transaminases different for different reactions?
They have different side chain specificity.
What coenzyme is used in all transamination reactions?
Pyridoxal phosphate (PLP).
What is the important group found in the coenzyme PLP?
Aldehyde group.
Where is the cofactor PLP derived from?
Vitamin B6.
What are the 5 stages of transamination?
- Binding
- Exchange
- Transfer
- Second substrate reverse reaction
- Schiff base linkage
Explain the 1st step of the transamination reaction in detail.
Binding of the PLP to the enzyme forms a Schiff base.
Explain the 2nd step of the transamination reaction in detail.
Schiff base formed from PLP and the enzyme is exchanged with the donating amino acid. Possible as Schiff base formation is reversible.
Explain the 3rd step of the transamination reaction in detail.
NH2 group transferred to PLP
End with a veto acid and NH@ on the PLP.
Explain the 4th step of the transamination reaction in detail.
Second substrate reverse reaction occurs. Keto acid comes in with a different side chain. This time the N group on the PLP will attack the carbonyl on the incoming keto acid.
Explain the 5th step of the transamination reaction in detail.
Schiff base linkage exchange with enzyme.
Original state of enzyme bound to PLP reformed.
What family of amino acids can serine generate?
Phosphor glycerate including glycine.
What important donor does serine act as?
C1.
What is glycine a precursor of?
Methionine and threonine.
What can the precursor of aromatic amino acid synthesis be (2 things)?
- Phosphoenolpyruvate- C3 donor and a product of glycolysis.
- Erythrose 4-phosphate part of the pentose phosphase pathway
How can erythrose 4- phosphate and phosphoenolpyruvate be used in aromatic amino acid synthesis?
They can produce prephenate. Transamination can then occur and tyrosine and penylanaline can be produced.
What are the two equivalent modes of transamination?
Through GDH or thorough glutamine synthetase and glutamate synthase.
Why are there two equivalent modes of transamination?
GDH has a much higher KM than glutamine synthetase meaning it needs higher concentrations of ammonia.
Is glutamate dehydrogenase, glutamate synthase or glutamine synthetase known as a scavenging enzyme?
Glutamine synthetase.
Glutamine synthetase is known as a scavenging enzyme. Why is this not used all the time?
As it requires ATP.
What species often have multiple isoenzymes?
Plants.
How can you control how much Nitrogen enters the body?
through the control of glutamate synthase and glutamine synthetase.
Why is glutamine synthetase an ideal enzyme to control how much nitrogen enters the body?
As it is the first step in many pathways. Products can have an allosteric effect in a cumulative fashion.
How can glutamine synthetase have its activity enhanced?
Through convent modification.
Explain the covalent modification which allows glutamine synthetase to be enhanced.
Glutamine synthetase can be covalently modified via adenylation so it has AMP attached.
Is glutamine synthetase more active when it is adenylated?
No.
Glutamine synthetase is less active when it is adenylated. Why?
It is more sensitive to feedback inhibition when the AMP group is present..
What enzyme is responsible for the adenylation of glutamine synthetase?
Adenylyl transferase (AT).
Adenylyl transferase uses GTP. True or false?
False, it uses ATP.
What is responsible for controlling wether adenyl transferase does the forward or backwards reaction?
The P protein.
How does the P protein change which way AT works?
It changes its specificity.
The P protein controls AT by chaining its specificity. How many forms of the P protein are there?
2, PA adneylating form and PD denadenylating form.
What allows the P protein to convert between its two forms of PA and PD?
Uridyl transferase.
How does uridyl transferase convert between the two froms of the P protein?
Through covalent modification.
Can uridyl transferase or Adenyl transferase not carry out the backwards reaction?
Uridyl transferase.
What can have an inhibitory effect on uridyl transferase?
Glutamine. Its product a-ketoglutarate is a substate to it and can bind.
If there is too much glutamine in the cell how will it respond?
Increase the level of Pa, increase AT adenylation to decrease glutamine synthetase activity.
Branched pathways can also show feedback inhibiton. Name an example of this.
Phenylanaline, tyrosine and tryptophan can inhibit the aldolases used in their synthesis.
What can be a useful anticancer drugs?
Nucleotide biosynthesis inhibitors.
Nucleotide biosyntheses inhibitors can be useful anticancer drugs. What do you want these not to effect in a cell?
RNA production and protein synthesis- Only want them to act as deoxyribose inhibitors.
What does Flurouracil inhibit?
Thymidylate synthase.
What type of inhibitor is the flurouracil inhibitor?
Suicide inhibotr- once it is there the enzyme is permentaly inactive.
What does the body convert flurouracil into to allow it to act as a suicide inhibitor to thymidylate synthase?
Deoxyribose- flurouracil.
Why cant D flurouracil inhibit purine synthesis?
As you start with the ribose and then add the ring whereas with nucleotides you start with the ring.
What does methotrexate inhibit?
Dihydrofolate reductase
What type of inhibitor is methotrexate?
Competitive inhibitor.
What is the inhibition constant for a drug?
Concentration of the drug necessary for half its full activity.
What is the inhibiton constant of methotrexate and what effect does this have?
Below nano molar- need very small amounts of the drug for it to work.
What cancers is methotrexate used to treat?
Leukemia and placental cancer.
Does tetrahydrofolate of methotrexate rapidly kill dividing cells including bone marrow and hair follicles?
Methotrexate,
Name four reasons why amino acids are biologically important?
- In proteins.
- Nucleotide biosynthesis.
- Biosynthesis of porphyrins.
- Main entry point of N in metabolism.
