Citric Acid Cycle

[Quark E]

http://en.wikipedia.org/wiki/Citric_acid_cycle

The citric acid cycle � also known as the tricarboxylic acid cycle
(TCA cycle), the Krebs cycle, or the Szent-Gy�rgyi�Krebs cycle[1][2] �
is a series of chemical reactions used by all aerobic organisms to
generate energy

Its central importance to many biochemical pathways suggests that it
was one of the earliest established components of cellular metabolism
and may have originated abiogenically

The name of this metabolic pathway is derived from citric acid (a type
of tricarboxylic acid) that is first consumed and then regenerated by
this sequence of reactions to complete the cycle. In addition, the
cycle consumes acetate (in the form of acetyl-CoA) and water, reduces
NAD+ to NADH, and produces carbon dioxide. The NADH generated by the
TCA cycle is fed into the oxidative phosphorylation pathway. The net
result of these two closely linked pathways is the oxidation of
nutrients to produce usable energy in the form of ATP.

The citric acid cycle is a key component of the metabolic pathway by
which all aerobic organisms generate energy. Through catabolism of
sugars, fats, and proteins, a two carbon organic product acetate in
the form of acetyl-CoA is produced. Acetyl-CoA along with two
equivalents of water (H2O) are consumed by the citric acid cycle
producing two equivalents of carbon dioxide (CO2) and one equivalent
of HS-CoA.

The NADH and QH2 generated by the citric acid cycle are in turn used
by the oxidative phosphorylation pathway to generate energy-rich
adenosine triphosphate (ATP).

One of the primary sources of acetyl-CoA is sugars that are broken
down by glycolysis to produce pyruvate that in turn is decarboxylated
by the enzyme pyruvate dehydrogenase generating acetyl-CoA


The product of this reaction, acetyl-CoA, is the starting point for
the citric acid cycle


The citric acid cycle begins with the transfer of a two-carbon acetyl
group from acetyl-CoA to the four-carbon acceptor compound
(oxaloacetate) to form a six-carbon compound (citrate).
The citrate then goes through a series of chemical transformations,
losing two carboxyl groups as CO2. The carbons lost as CO2 originate
from what was oxaloacetate, not directly from acetyl-CoA. The carbons
donated by acetyl-CoA become part of the oxaloacetate carbon backbone
after the first turn of the citric acid cycle. Loss of the acetyl-CoA-
donated carbons as CO2 requires several turns of the citric acid
cycle. However, because of the role of the citric acid cycle in
anabolism, they may not be lost, since many TCA cycle intermediates
are also used as precursors for the biosynthesis of other molecules.
[9]
Most of the energy made available by the oxidative steps of the cycle
is transferred as energy-rich electrons to NAD+, forming NADH. For
each acetyl group that enters the citric acid cycle, three molecules
of NADH are produced.
Electrons are also transferred to the electron acceptor Q, forming
QH2.
At the end of each cycle, the four-carbon oxaloacetate has been
regenerated, and the cycle continues

[Inez]

On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:
> http://en.wikipedia.org/wiki/Citric_acid_cycle

We all know how to search wikipedia. Did you have a point?

[Quark E]

Here is the first enzyme from step 1:

http://en.wikipedia.org/wiki/Citrate_synthase

Oxaloacetate is the first substrate to bind to the enzyme. This
induces the enzyme to change its conformation, and creates a binding
site for the acetyl-CoA. Only when this citroyl-CoA has formed will
another conformational change cause thioester hydrolysis and release
coenzyme A. This ensures that the energy released from the thioester
bond cleavage will drive the condensation.

Between these two subunits, a single cleft exists containing the
active site. Two binding sites can be found therein: one reserved for
citrate or oxaloacetate and the other for Coenzyme A. The active site
contains three key residues: His274, His320, and Asp375 that are
highly selective in their interactions with substrates

Citrate Synthase has three key amino acids in its active site which
catalyze the conversion of acetyl-CoA (H3CCO-SCoA) and oxaloacetate
(COO-CH2COCOO-) into citrate (COO-CH2COHCOOCH2COO-) and H-SCoA in an
aldol condensation reaction. This conversion begins with the
negatively charged oxygen in Asp375�s R-group deprotonating acetyl
CoA�s alpha carbon. This pushes the e- to form a double-bond with the
carbonyl carbon, which in turn forces the C=O up to pick up a proton
for the oxygen from one of the nitrogens in the R-group of His274.
This neutralizes the R-group (by forming a lone pair on the nitrogen)
and completes the formation of an enol intermediate (CH2COH-SCoA). At
this point, His274�s amino lone pair formed in the last step attacks
the proton that was added to the oxygen in the last step. The oxygen
then reforms the carbonyl bond, which frees half of the C=C to
initiate a nucleophilic attack to oxaloacetate�s carbonyl carbon (COO-
CH2COCOO-). This frees half of the carbonyl bond to deprotonate one of
His320�s amino groups, which neutralizes one of the nitrogens in its R-
group. This nucleophilic addition results in the formation of citroyl-
CoA (COOCH2CHCOOCH2COHSCoA2-). At this point, a water molecule is
brought in and is deprotonated by His320�s amino group and Hydrolysis
is initiated. One of the oxygen�s lone pairs nucleophilically attacks
the carbonyl carbon of citroyl-CoA. This forms a tetrahedral
intermediate and results in the ejection of �SCoA as the carbonyl
reforms. The �SCoA is protonated to form HSCoA. Finally, the hydroxyl
added to the carbonyl in the previous step is deprotonated and citrate
(-COOCH2COHCOO-CH2COO-) is formed

[chris thompson]

On Feb 7, 3:06�pm, Quark E <quarke...@gmail.com> wrote:
> On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:
>

snip

>
> Here is the first enzyme from step 1:
>
> http://en.wikipedia.org/wiki/Citrate_synthase
>

snip

Along with a couple hundred other sufferers, I memorized all this in
my first semester of General Zoology.

What's your point?

Chris

[Roger Shrubber]

On Feb 8, 6:00�am, Quark E <quarke...@gmail.com> wrote:
> http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> The citric acid cycle � also known as the tricarboxylic acid cycle
> (TCA cycle), the Krebs cycle, or the Szent-Gy�rgyi�Krebs cycle[1][2] �
> is a series of chemical reactions used by all aerobic organisms to
> generate energy
>
> Its central importance to many biochemical pathways suggests that it
> was one of the earliest established components of cellular metabolism
> and may have originated abiogenically

Stop. It is not a commonly accepted belief that the TCA cycle arose
abiogenically, even if some seem to be fond of the idea. There isn't
even a good logical argument for it having done so. Fermentation
processes almost certainly came first. And before that the very
basics of the proton gradient. There are many other ways to create
the proton gradient than hydrolysis of glucose.

[I am not a chemist]

I am showing the audience out there the foundational pieces for
looking at what enzymes do.

[I am not a chemist]

On Feb 7, 12:25�pm, chris thompson <chris.linthomp...@gmail.com>
wrote:

> On Feb 7, 3:06�pm, Quark E <quarke...@gmail.com> wrote:
>
> > On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:
>
> snip
>
>
>
> > Here is the first enzyme from step 1:
>
> >http://en.wikipedia.org/wiki/Citrate_synthase
>
> snip

Showing what enzymes do.

[I am not a chemist]

On Feb 7, 1:02�pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:
> On Feb 8, 6:00�am, Quark E <quarke...@gmail.com> wrote:
>
> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> > The citric acid cycle � also known as the tricarboxylic acid cycle
> > (TCA cycle), the Krebs cycle, or the Szent-Gy�rgyi�Krebs cycle[1][2] �
> > is a series of chemical reactions used by all aerobic organisms to
> > generate energy
>
> > Its central importance to many biochemical pathways suggests that it
> > was one of the earliest established components of cellular metabolism
> > and may have originated abiogenically
>
> Stop. It is not a commonly accepted belief that the TCA cycle arose
> abiogenically, even if some seem to be fond of the idea.

Take it up with wiki.
Next time I will leave out disputed items.

[I am not a chemist]

On Feb 7, 12:06�pm, Quark E <quarke...@gmail.com> wrote:
> On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:
>
>
>

<snip>

enzyme step 2:

http://en.wikipedia.org/wiki/Aconitase

Aconitase (aconitate hydratase; EC 4.2.1.3) is an enzyme that
catalyses the stereo-specific isomerization of citrate to isocitrate
via cis-aconitate

In contrast with the majority of iron-sulfur proteins that function as
electron carriers, the iron-sulfur cluster of aconitase reacts
directly with an enzyme substrate. Aconitase has an active [Fe4S4]2+
cluster, which may convert to an inactive [Fe3S4]+ form. Three
cysteine (Cys) residues have been shown to be ligands of the [Fe4S4]
centre. In the active state, the labile iron ion of the [Fe4S4]
cluster is not coordinated by Cys but by water molecules.

Aconitase, displayed in the structures in the right margin of this
page, has two slightly different structures, depending on whether it
is activated or inactivated.[7][8] In the inactive form, its structure
is divided into four domains.[7] Counting from the N-terminus, only
the first three of these domains are involved in close interactions
with the [3Fe-4S] cluster, but the active site consists of residues
from all four domains, including the larger C-terminal domain.[7] The
Fe-S cluster and a SO42- anion also reside in the active site.[7] When
the enzyme is activated, it gains an additional iron atom, creating a
[4Fe-4S] cluster.[8][9] However, the structure of the rest of the
enzyme is nearly unchanged; the conserved atoms between the two forms
are in essentially the same positions, up to a difference of 0.1
angstroms

Aconitase employs a dehydration-hydration mechanism.[10] The catalytic
residues involved are His-101 and Ser-642.[10] His-101 protonates the
hydroxyl group on C3 of citrate, allowing it to leave as water, and
Ser-642 concurrently abstracts the proton on C2, forming a double bond
between C2 and C3, forming a cis-aconitate intermediate.[10][13] At
this point, the intermediate is rotated 180�.[10] This rotation is
referred to as a "flip."[11] Because of this flip, the intermediate is
said to move from a "citrate mode" to a "isocitrate mode."[14]

How exactly this flip occurs is debatable. One theory is that, in the
rate-limiting step of the mechanism, the cis-aconitate is released
from the enzyme, then reattached in the isocitrate mode to complete
the reaction.[14] This rate-liming step ensures that the right
stereochemistry, specifically (2R,3S), is formed in the final product.
[14][15] Another hypothesis is that cis-aconitate stays bound to the
enzyme while it flips from the citrate to the isocitrate mode.[10]

In either case, flipping cis-aconitate allows the dehydration and
hydration steps to occur on opposite faces of the intermediate.[10]
Aconitase catalyzes trans elimination/addition of water, and the flip
guarantees that the correct stereochemistry is formed in the product.
[10][11] To complete the reaction, the serine and histidine residues
reverse their original catalytic actions: the histidine, now basic,
abstracts a proton from water, priming it as a nucleophile to attack
at C2, and the protonated serine is deprotonated by the cis-aconitate
double bond to complete the hydration, producing isocitrate

[Roger Shrubber]

On Feb 8, 7:59�am, I am not a chemist <t2judgm...@gmail.com> wrote:
> On Feb 7, 1:02 pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:

>
> > On Feb 8, 6:00 am, Quark E <quarke...@gmail.com> wrote:
>
> > >http://en.wikipedia.org/wiki/Citric_acid_cycle
>

> > > The citric acid cycle also known as the tricarboxylic acid cycle
> > > (TCA cycle), the Krebs cycle, or the Szent-Gy rgyi Krebs cycle[1][2]

> > > is a series of chemical reactions used by all aerobic organisms to
> > > generate energy
>
> > > Its central importance to many biochemical pathways suggests that it
> > > was one of the earliest established components of cellular metabolism
> > > and may have originated abiogenically
>
> > Stop. It is not a commonly accepted belief that the TCA cycle arose
> > abiogenically, even if some seem to be fond of the idea.
>
> Take it up with wiki.
> Next time I will leave out disputed items.

Wikipedia is a horrible resource for some things. It is good for very
simple "what" type questions. It is horrible for anything of a "why"
nature, or anything that involves deeper understanding. Worse yet, it
promotes the very false sense that "knowledge" can be readily captured
in snippets of organized prose. That sort of factual filings, akin to
the old days of myriad notes captured on 3x5 cards, may be on the
pathway
to actual understanding but it completely misses out on that complex
balance of deeper meanings layered in knowing why one example is
better
than another, where the exceptions lay, what is speculative and what
is axiomatic, and even where the trails of common misconception lead.

Wiki is nice for jogging a memory but it's a fraud as a substitute
for one.

[I am not a chemist]

On Feb 7, 2:09 pm, I am not a chemist <t2judgm...@gmail.com> wrote:

<snip>

step 3 and 4:

http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase

Isocitrate dehydrogenase (IDH) (EC 1.1.1.42) and (EC 1.1.1.41) is an
enzyme that catalyzes the oxidative decarboxylation of isocitrate,
producing alpha-ketoglutarate (α-ketoglutarate) and CO2. This is a two-
step process, which involves oxidation of isocitrate (a secondary
alcohol) to oxalosuccinate (a ketone), followed by the decarboxylation
of the carboxyl group beta to the ketone, forming alpha-ketoglutarate.
In humans, IDH exists in three isoforms: IDH3 catalyzes the third step
of the citric acid cycle while converting NAD+ to NADH in the
mitochondria. The isoforms IDH1 and IDH2 catalyze the same reaction
outside the context of the citric acid cycle and use NADP+ as a
cofactor instead of NAD+.

The NAD-IDH is composed of 3 subunits, is allosterically regulated,
and requires an integrated Mg2+ or Mn2+ ion. The closest homologue
that has a known structure is the E. coli NADP-dependent IDH, which
has only 2 subunits and a 13% identity and 29% similarity based on the
amino acid sequences, making it dissimilar to human IDH and not
suitable for close comparison

The IDH step of the citric acid cycle, due to its large negative free
energy change, is one of the irreversible reactions in the citric acid
cycle, and, therefore, must be carefully regulated

The reactants necessary for this enzyme mechanism to work are
isocitrate, NAD+/NADP+, and Mn2+ or Mg2+. The products of the reaction
are alpha-ketoglutarate, carbon dioxide, and NADH + H+/NADPH + H+.[6]
Water molecules are used to help deprotonate the oxygens (O3) of
isocitrate.


The second box is Step 1, which is the oxidation of the alpha-C (C#2).
[5][6] Oxidation is the first step that isocitrate goes through. In
this process,[5] the alcohol group off the alpha-carbon (C#2) is
deprotonated and the electrons flow to the alpha-C forming a ketone
group and removing a hydride off C#2 using NAD+/NADP+ as an electron
accepting cofactor. The oxidation of the alpha-C allows for a position
where electrons (in the next step) will be coming down from the
carboxyl group and pushing the electrons (making the double bonded
oxygen) back up on the oxygen or grabbing a nearby proton off a nearby
Lysine amino acid.

The third box is Step 2, which is the decarboxylation of
oxalosuccinate. In this step,[5][6] the carboxyl group oxygen is
deprotonated by a nearby Tyrosine amino acid and those electrons flow
down to carbon 2. Carbon dioxide leaves the beta carbon of isocitrate
as a leaving group with the electrons flowing to the ketone oxygen off
the alpha-C placing a negative charge on the oxygen of the alpha-C and
forming an alpha-beta unsaturated double bond between carbons 2 and 3.
The lone pair on the alpha-C oxygen picks up a proton from a nearby
Lysine amino acid.

The fourth box is Step 3, which is the saturation of the alpha-beta
unsaturated double bond between carbons 2 and 3. In this step of the
reaction,[5][6] Lysine deprotonates the oxygen off the alpha carbon
and the lone pair of electrons on the oxygen of the alpha carbon comes
down reforming the ketone double bond and pushing the lone pair
(forming the double bond between the alpha and beta carbon) off,
picking up a proton from the nearby Tyrosine amino acid.[9] This
reaction results in the formation of alpha-ketoglutarate, NADH + H+/
NADPH + H+, and CO2.

Two aspartate amino acid residues (below left) are interacting with
two adjacent water molecules (w6 and w8) in the Mn2+ isocitrate
porcine IDH complex to deprotonate the alcohol off the alpha-carbon
atom. The oxidation of the alpha-C also takes place in this picture
where NAD+ accepts a hydride resulting in oxalosuccinate. Along with
the sp3 to sp2 stereochemical change around the alpha-C, there is a
ketone group that is formed form the alcohol group. The formation of
this ketone double bond allows for resonance to take place as
electrons coming down from the leaving carboxylate group move towards
the ketone.

The decarboxylation of oxalosuccinate (below center) is a key step in
the formation of alpha-ketoglutarate. In this reaction, the lone pair
on the adjacent Tyrosine oxygen pulls off the proton of the carboxyl
group.[9] This carboxyl group is also referred to as the beta subunit
of isocitrate. The deprotonation of the carboxyl proton causes the
lone pair of electrons to move down making carbon dioxide and
separating from oxalosuccinate. The electrons continue to move towards
the alpha carbon pushing the double bond electrons (making the ketone)
up to pull a proton off an adjacent Lysine residue. An alpha-beta
unsaturated double bond results between carbon 2 and three. As you can
see in the picture, the green ion represents either Mg2+ or Mn2+,
which is a cofactor necessary for this reaction to occur. The metal-
ion forms a little complex through ionic interactions with the oxygen
atoms on the fourth and fifth carbons (also known as the gamma subunit
of isocitrate).

After carbon dioxide is split from the oxalosuccinate in the
decarboxylation step (below right), the enol will retautomerize to the
keto from. The reformation of the ketone double bond is started by the
deprotonation of that oxygen off the alpha carbon (C#2) by the same
Lysine that protonated the oxygen in the first place.[9] The lone pair
of electrons moves down kicking off the lone pairs that were making
the double bond. This lone pair of electrons pulls a proton off the
Tyrosine that deprotonated the carboxyl group in the decarboxylation
step. The reason that we can say that the Lys and Tyr residues will be
the same from the previous step because they are helping in holding
the isocitrate molecule in the active site of the enzyme. These two
residues will be able to hydrogen bond back and forth as long as they
are close enough to the substrate

The isocitrate dehydrogenase enzyme as stated above produces alpha-
ketoglutarate, carbon dioxide, and NADH + H+/NADPH + H+. There are
three changes that occurred throughout the reaction. The oxidation of
Carbon 2, the decarboxylation (loss of carbon dioxide) off Carbon 3,
and the formation of a ketone group with a stereochemical change from
sp3 to sp2

1.Isocitrate binds within the active site to a conserved sequence of
about eight amino acids through hydrogen bonds. These acids include
(may vary in residue but with similar properties) tyrosine, serine,
asparagine, arginine, arginine, arginine, tyrosine, and lysine. Their
positions on the backbone vary but they are all within a close range
(i.e. Arg131 DpIDH and Arg133 PcIDH, Tyr138 DpIDH and Tyr140 PcIDH).
[9]
2.The metal ion (Mg2+, Mn2+) binds to three conserved amino acids
through hydrogen bonds. These amino acids include three Aspartate
residues.[9]
3.NAD+ and NADP+ bind within the active site within four regions

[I am not a chemist]

On Feb 7, 2:14�pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:
> On Feb 8, 7:59�am, I am not a chemist <t2judgm...@gmail.com> wrote:
>
>
>
>
>
> > On Feb 7, 1:02 pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:
>
> > > On Feb 8, 6:00 am, Quark E <quarke...@gmail.com> wrote:
>
> > > >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> > > > The citric acid cycle also known as the tricarboxylic acid cycle
> > > > (TCA cycle), the Krebs cycle, or the Szent-Gy rgyi Krebs cycle[1][2]
> > > > is a series of chemical reactions used by all aerobic organisms to
> > > > generate energy
>
> > > > Its central importance to many biochemical pathways suggests that it
> > > > was one of the earliest established components of cellular metabolism
> > > > and may have originated abiogenically
>
> > > Stop. It is not a commonly accepted belief that the TCA cycle arose
> > > abiogenically, even if some seem to be fond of the idea.
>
> > Take it up with wiki.
> > Next time I will leave out disputed items.
>
> Wikipedia is a horrible resource for some things.

Attack the source.

[Roger Shrubber]

>> Wikipedia is a horrible resource for some things. It is good for very
>> simple "what" type questions. It is horrible for anything of a "why"
>> nature, or anything that involves deeper understanding. Worse yet, it
>> promotes the very false sense that "knowledge" can be readily captured
>> in snippets of organized prose. That sort of factual filings, akin to
>> the old days of myriad notes captured on 3x5 cards, may be on the pathway
>> to actual understanding but it completely misses out on that complex
>> balance of deeper meanings layered in knowing why one example is better
>> than another, where the exceptions lay, what is speculative and what
>> is axiomatic, and even where the trails of common misconception lead.

>> Wiki is nice for jogging a memory but it's a fraud as a substitute
>> for one.

> Attack the source.

Indeed I did, with reasons. That part may have escaped you.
When the source is unreliable, and after you said "take it
up with wiki", I explained. This of course was after I took
issue with an earlier point and explained it. Your retort seemed
to be to defer to the source (wiki) rather than to defend
the point yourself. This makes sense as all you've done so
far is cut and paste some things that you don't appear to
understand.

This whole biochemistry thing doesn't appear to be your
bailiwick, nor communication on usenet.

Perhaps you would be more interested in a nice shrubbery?

[Glenn]

"Roger Shrubber" <rog.sh...@gmail.com> wrote in message news:3b09f180-937a-4dc1...@w7g2000yqo.googlegroups.com...

So there is only one?

[I am not a chemist]

On Feb 7, 2:22 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> On Feb 7, 2:09 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> <snip>
>

Next enzyme:

http://en.wikipedia.org/wiki/Alpha-ketoglutarate_dehydrogenase

The reaction catalyzed by this enzyme in the citric acid cycle is:

α-ketoglutarate + NAD+ + CoA → Succinyl CoA + CO2 + NADH


This reaction proceeds in three steps:

decarboxylation of α-ketoglutarate,
reduction of NAD+ to NADH,
and subsequent transfer to CoA, which forms the end product, succinyl
CoA.
ΔG°' for this reaction is -7.2 kcal mol-1. The energy needed for this
oxidation is conserved in the formation of a thioester bond of
succinyl CoA.

ADP and calcium ions are allosteric activators of the enzyme

[I am not a chemist]

Because you are a troll.
What you did is known as a fallacy.
Trolls are known by their tactics, fallacies are an earmark of a troll.

[I am not a chemist]

On Feb 7, 2:45 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> On Feb 7, 2:22 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> > On Feb 7, 2:09 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> > <snip>
>
> Next enzyme:
>

http://en.wikipedia.org/wiki/Succinyl_coenzyme_A_synthetase

Succinyl coenzyme A synthetase (SCS, also known as succinyl-CoA
synthetase or succinate thiokinase or succinate-CoA ligase) is an
enzyme that catalyzes the reversible reaction of succinyl-CoA to
succinate.[3] The enzyme facilitates the coupling of this reaction to
the formation of a nucleoside triphosphate molecule (either GTP or
ATP) from an inorganic phosphate molecule and a nucleoside diphosphate
molecule (either GDP or ADP). It plays a key role as one of the
catalysts involved in the citric acid cycle, a central pathway in
cellular metabolism

Succinyl CoA synthetase catalyzes the following reversible reaction:

Succinyl CoA + Pi + NDP ↔ Succinate + CoA + NTP
Where Pi denotes inorganic phosphate, NDP denotes nucleoside
diphosphate (either GDP or ADP), and NTP denotes nucleoside
triphosphate (either GTP or ATP). As mentioned, the enzyme facilitates
coupling of the conversion of succinyl CoA to succinate with the
formation of NTP from NDP and Pi. The reaction has a biochemical
standard state free energy change of -3.4 kJ/mol.[4] The reaction
takes place by a three-step mechanism[3] which is depicted in the
image below. The first step involves displacement of CoA from succinyl
CoA by a nucleophilic inorganic phosphate molecule to form succinyl
phosphate. The enzyme then utilizes a histidine residue to remove the
phosphate group from succinyl CoA and generate succinate. Finally, the
phosphorylated histidine transfers the phosphate group to a nucleoside
diphosphate, which generates the high-energy carrying nucleoside
triphosphate

[Quark E]

On Feb 7, 2:52�pm, I am not a chemist <t2judgm...@gmail.com> wrote:

<snip>

next enzyme:

http://en.wikipedia.org/wiki/Succinate_dehydrogenase

It is the only enzyme that participates in both the citric acid cycle
and the electron transport chain

[Richard Norman]

Actually Wikipedia, properly read, is a pretty good source for
starting provided you use it as a basis to then check the citations it
provides and verify all the details with valid primary and secondary
sources. However it does give you a foundation to do those
verifications for an area you are not familiar with.

[Richard Norman]

On Thu, 7 Feb 2013 14:58:42 -0800 (PST), Quark E <quar...@gmail.com>
wrote:

Eventually you might even get to a question or a point to be made.

Many of us who are not technically professional biochemists are
nevertheless quite proficient in biochemistry. we know that you are
just doing a cut-and-paste job of pretty standard stuff (except for
some important details as Shrubber indicates) while simultaneously
demonstrating absolutely no understanding of what you are copying.

[Quark E]

On Feb 7, 3:26�pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Thu, 7 Feb 2013 14:58:42 -0800 (PST), Quark E <quarke...@gmail.com>

> wrote:
>
> >On Feb 7, 2:52 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> ><snip>
>
> >next enzyme:
>
> >http://en.wikipedia.org/wiki/Succinate_dehydrogenase
>
> >It is the only enzyme that participates in both the citric acid cycle
> >and the electron transport chain
>
> Eventually you might even get to a question or a point to be made.

You must be keeping up.
Coincidentally that is where I am at now.

[Dana Tweedy]

On 2/7/13 4:23 PM, Richard Norman wrote:
> On Thu, 7 Feb 2013 14:14:33 -0800 (PST), Roger Shrubber

snip

>> Wiki is nice for jogging a memory but it's a fraud as a substitute
>> for one.
>
> Actually Wikipedia, properly read, is a pretty good source for
> starting provided you use it as a basis to then check the citations it
> provides and verify all the details with valid primary and secondary
> sources. However it does give you a foundation to do those
> verifications for an area you are not familiar with.
>

When I was young, my family had an old set of encyclopedias at home and
I used it to read up on things I wanted to find out about. If I wanted
more information, a more recent, or deeper understanding of the subject,
I'd consult a library, and do further research. This is the way I treat
Wikipedia today.

It's fine for general information, but not something you want to rely
on for a deeper understanding. I sometimes think it's a shame my Dad
died before the internet was readily available. He would have loved
having all this knowledge at his fingertips.

DJT

[Roger Shrubber]

On Feb 8, 9:23�am, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Thu, 7 Feb 2013 14:14:33 -0800 (PST), Roger Shrubber
>
>
>
>
>
>
>
>
>

Time to put back on your curmudgeon hat.

Wiki has become the first and often only source for many.
To know how to use wiki, I do believe you need to know how
to do research without wiki, which in a practical sense, might
mean doing so first, in which case we're in trouble.

But wiki of course suffers from the same disadvantages of any
encyclopedia. It's a distillation. It's artfully written to be
accessible.
It's reviewed by people with deeper understanding, and from
the point of that deeper understanding, the words are technically
correct, but the understanding is not forthcoming. There are
many such things that make sense after you understand them
but until you do, things like wiki give a false sense of
understanding. That is the chief danger.

[Paul J Gans]

Quark E <quar...@gmail.com> wrote:

>http://en.wikipedia.org/wiki/Citric_acid_cycle

>The citric acid cycle ? also known as the tricarboxylic acid cycle
>(TCA cycle), the Krebs cycle, or the Szent-Gy?rgyi?Krebs cycle[1][2] ?

You copy material fairly well. Have you read it?

--
--- Paul J. Gans

[Paul J Gans]

chris thompson <chris.li...@gmail.com> wrote:
>On Feb 7, 3:06?pm, Quark E <quarke...@gmail.com> wrote:

>> On Feb 7, 12:00?pm, Quark E <quarke...@gmail.com> wrote:
>>

>snip

>>
>> Here is the first enzyme from step 1:
>>
>> http://en.wikipedia.org/wiki/Citrate_synthase
>>

>snip

>Along with a couple hundred other sufferers, I memorized all this in
>my first semester of General Zoology.

>What's your point?

He doesn't have one. He's just gibbering for attention.

[Paul J Gans]

I am not a chemist <t2jud...@gmail.com> wrote:

>On Feb 7, 12:05?pm, Inez <savagemouse...@hotmail.com> wrote:
>> On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>>
>> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>>

>> We all know how to search wikipedia. ?Did you have a point?

>I am showing the audience out there the foundational pieces for
>looking at what enzymes do.

Will you pick one nym and stick to it?

[Paul J Gans]

Richard Norman <r_s_n...@comcast.net> wrote:
>On Thu, 7 Feb 2013 14:14:33 -0800 (PST), Roger Shrubber
><rog.sh...@gmail.com> wrote:

Well, yes. I use it a lot to do quick checks on stuff I mostly
already know. I've found some excellent material and some
terrible stuff. I've warned students against it, to no particular
avail.

[chris thompson]

Most of us around here already know what enzymes do and how they do
it- and what you wrote about enzymes is at least partially
incorrect.

Chris

[I am not a chemist]

On Feb 7, 5:04�pm, Paul J Gans <gan...@panix.com> wrote:

> I am not a chemist <t2judgm...@gmail.com> wrote:
>
> >On Feb 7, 12:05?pm, Inez <savagemouse...@hotmail.com> wrote:
> >> On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> >> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> >> We all know how to search wikipedia. ?Did you have a point?
> >I am showing the audience out there the foundational pieces for
> >looking at what enzymes do.
>
> Will you pick one nym and stick to it?

Take it up with google limits.
I will continue to use my two emails.

[I am not a chemist]

On Feb 7, 6:38 pm, chris thompson <chris.linthomp...@gmail.com> wrote:
> On Feb 7, 4:58 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
>
>
>
>
> > On Feb 7, 12:25 pm, chris thompson <chris.linthomp...@gmail.com>
> > wrote:
>
> > > On Feb 7, 3:06 pm, Quark E <quarke...@gmail.com> wrote:
>
> > > > On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> > > snip
>
> > > > Here is the first enzyme from step 1:
>
> > > >http://en.wikipedia.org/wiki/Citrate_synthase
>
> > > snip
>
> > Showing what enzymes do.
>
> Most of us around here already know what enzymes do

I doubt it, unless you are chemists.

>and how they do
> it

Not even biochemists have complete understanding of many of the
enzymes.

> and what you wrote about enzymes is at least partially
> incorrect.

Anything stopping you from correcting your alleged errors in my
understanding?

[Glenn]

"I am not a chemist" <t2jud...@gmail.com> wrote in message news:12cf15ef-992f-4387...@14g2000vbr.googlegroups.com...

Sorry, there is no way to tell whether you are telling the truth
about the impact google limits has on your posting habits.
And posting to other groups is not the concern of talk.origins.
When here, you need to obey the rules.
There is also no way to tell whether your nymshifting is
designed to avoid killfiles, or attract as many viewers as
possible. You could be using google limit as a "convenient" excuse.
In addition, unless you identify your nyms to others, they
may not immediately recognize one as being the same person
as the other, so may not know to killfile. Also, you could add
a nym or ten with the same excuse, so it is really not kosher
to continue to maintain even two nyms simultaneously for an extended
period of time.

[I am not a chemist]

On Feb 8, 11:18�am, "Glenn" <glennshel...@invalid.invalid> wrote:
> "I am not a chemist" <t2judgm...@gmail.com> wrote in messagenews:12cf15ef-992f-4387...@14g2000vbr.googlegroups.com...

>
>
>
> > On Feb 7, 5:04 pm, Paul J Gans <gan...@panix.com> wrote:
> > > I am not a chemist <t2judgm...@gmail.com> wrote:
>
> > > >On Feb 7, 12:05?pm, Inez <savagemouse...@hotmail.com> wrote:
> > > >> On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> > > >> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> > > >> We all know how to search wikipedia. ?Did you have a point?
> > > >I am showing the audience out there the foundational pieces for
> > > >looking at what enzymes do.
>
> > > Will you pick one nym and stick to it?
>
> > Take it up with google limits.
> > I will continue to use my two emails.
>
> Sorry, there is no way to tell whether you are telling the truth
> about the impact google limits has

Severe.

[Glenn]

"I am not a chemist" <t2jud...@gmail.com> wrote in message news:0b035b86-b6fb-41ad...@x15g2000vbj.googlegroups.com...

Not talk.origins problem. It may be that googlegroups restricts you
because of your history of posting in the thousands per month.
You seem to be off to a good start to flooding this group as well
with crap not much more worthy than spam, if any.
Here you are supposed to use one identity at a time only.

[Quark E]

On Feb 8, 11:59 am, "Glenn" <glennshel...@invalid.invalid> wrote:
> "I am not a chemist" <t2judgm...@gmail.com> wrote in messagenews:0b035b86-b6fb-41ad...@x15g2000vbj.googlegroups.com...

>
>
>
> > On Feb 8, 11:18 am, "Glenn" <glennshel...@invalid.invalid> wrote:
> > > "I am not a chemist" <t2judgm...@gmail.com> wrote in messagenews:12cf15ef-992f-4387...@14g2000vbr.googlegroups.com...
>
> > > > On Feb 7, 5:04 pm, Paul J Gans <gan...@panix.com> wrote:
> > > > > I am not a chemist <t2judgm...@gmail.com> wrote:
>
> > > > > >On Feb 7, 12:05?pm, Inez <savagemouse...@hotmail.com> wrote:
> > > > > >> On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> > > > > >> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> > > > > >> We all know how to search wikipedia. ?Did you have a point?
> > > > > >I am showing the audience out there the foundational pieces for
> > > > > >looking at what enzymes do.
>
> > > > > Will you pick one nym and stick to it?
>
> > > > Take it up with google limits.
> > > > I will continue to use my two emails.
>
> > > Sorry, there is no way to tell whether you are telling the truth
> > > about the impact google limits has
>
> > Severe.
>
> Not talk.origins problem. It may be that googlegroups restricts you

It is general google policy.

> because of your history of posting in the thousands per month.

I have never made thousands of posts in a month.

[eridanus]

El jueves, 7 de febrero de 2013 22:09:29 UTC, I am not a chemist escribió:

> On Feb 7, 12:06 pm, Quark E <quarke...@gmail.com> wrote:
>
> > On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> >
>
> >
>
> >
>
>
>

> <snip>
>
>
>
> enzyme step 2:
>
>
>
> http://en.wikipedia.org/wiki/Aconitase
>
>
>
> Aconitase (aconitate hydratase; EC 4.2.1.3) is an enzyme that
>
> catalyses the stereo-specific isomerization of citrate to isocitrate
>
> via cis-aconitate
>
>
>
> In contrast with the majority of iron-sulfur proteins that function as
>
> electron carriers, the iron-sulfur cluster of aconitase reacts
>
> directly with an enzyme substrate. Aconitase has an active [Fe4S4]2+
>
> cluster, which may convert to an inactive [Fe3S4]+ form. Three
>
> cysteine (Cys) residues have been shown to be ligands of the [Fe4S4]
>
> centre. In the active state, the labile iron ion of the [Fe4S4]
>
> cluster is not coordinated by Cys but by water molecules.
>
>
>
> Aconitase, displayed in the structures in the right margin of this
>
> page, has two slightly different structures, depending on whether it
>
> is activated or inactivated.[7][8] In the inactive form, its structure
>
> is divided into four domains.[7] Counting from the N-terminus, only
>
> the first three of these domains are involved in close interactions
>
> with the [3Fe-4S] cluster, but the active site consists of residues
>
> from all four domains, including the larger C-terminal domain.[7] The
>
> Fe-S cluster and a SO42- anion also reside in the active site.[7] When
>
> the enzyme is activated, it gains an additional iron atom, creating a
>
> [4Fe-4S] cluster.[8][9] However, the structure of the rest of the
>
> enzyme is nearly unchanged; the conserved atoms between the two forms
>
> are in essentially the same positions, up to a difference of 0.1
>
> angstroms
>
>
>
> Aconitase employs a dehydration-hydration mechanism.[10] The catalytic
>
> residues involved are His-101 and Ser-642.[10] His-101 protonates the
>
> hydroxyl group on C3 of citrate, allowing it to leave as water, and
>
> Ser-642 concurrently abstracts the proton on C2, forming a double bond
>
> between C2 and C3, forming a cis-aconitate intermediate.[10][13] At
>
> this point, the intermediate is rotated 180°.[10] This rotation is
>
> referred to as a "flip."[11] Because of this flip, the intermediate is
>
> said to move from a "citrate mode" to a "isocitrate mode."[14]
>
>
>
> How exactly this flip occurs is debatable. One theory is that, in the
>
> rate-limiting step of the mechanism, the cis-aconitate is released
>
> from the enzyme, then reattached in the isocitrate mode to complete
>
> the reaction.[14] This rate-liming step ensures that the right
>
> stereochemistry, specifically (2R,3S), is formed in the final product.
>
> [14][15] Another hypothesis is that cis-aconitate stays bound to the
>
> enzyme while it flips from the citrate to the isocitrate mode.[10]
>
>
>
> In either case, flipping cis-aconitate allows the dehydration and
>
> hydration steps to occur on opposite faces of the intermediate.[10]
>
> Aconitase catalyzes trans elimination/addition of water, and the flip
>
> guarantees that the correct stereochemistry is formed in the product.
>
> [10][11] To complete the reaction, the serine and histidine residues
>
> reverse their original catalytic actions: the histidine, now basic,
>
> abstracts a proton from water, priming it as a nucleophile to attack
>
> at C2, and the protonated serine is deprotonated by the cis-aconitate
>
> double bond to complete the hydration, producing isocitrate

what are you trying to prove telling us this?
That you know how to copy and past from some source?

Eridanus

[Quark E]

Trying to have people out there read and learn foundational pieces so
they can follow the discussion.

[Glenn]

"Quark E" <quar...@gmail.com> wrote in message news:056aefa3-a00d-44fd...@z9g2000vbx.googlegroups.com...

Yes, a general policy that is determined by poster's habits. They don't have a set policy of a certain
number of posts in a specific period of time for all posters. You probably kick off warning bells.
Again, not the problem of talk.origins readers.

>
> > because of your history of posting in the thousands per month.
>
> I have never made thousands of posts in a month.
>

Yes, either you have or others combined have from your ip address.

[Dexter]

"I am not a chemist" <t2jud...@gmail.com> wrote in message

news:4185b431-356e-4780...@hl5g2000vbb.googlegroups.com...

__________________________________________________

Anything stopping you from elucidating what you think /are/
his errors in your understanding?

[eridanus]

El jueves, 7 de febrero de 2013 22:22:44 UTC, I am not a chemist escribi�:
> On Feb 7, 2:14�pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:

>
> > On Feb 8, 7:59�am, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > > On Feb 7, 1:02 pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:
>
> >
>

> > > > On Feb 8, 6:00 am, Quark E <quarke...@gmail.com> wrote:
>
> >
>
> > > > >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> >
>

> > > > > The citric acid cycle also known as the tricarboxylic acid cycle
>
> > > > > (TCA cycle), the Krebs cycle, or the Szent-Gy rgyi Krebs cycle[1][2]
>
> > > > > is a series of chemical reactions used by all aerobic organisms to
>
> > > > > generate energy
>
> >
>
> > > > > Its central importance to many biochemical pathways suggests that it
>
> > > > > was one of the earliest established components of cellular metabolism
>
> > > > > and may have originated abiogenically
>
> >
>
> > > > Stop. It is not a commonly accepted belief that the TCA cycle arose
>
> > > > abiogenically, even if some seem to be fond of the idea.
>
> >
>
> > > Take it up with wiki.
>
> > > Next time I will leave out disputed items.
>
> >
>
> > Wikipedia is a horrible resource for some things.
>
>
>

> Attack the source.

it is not a question of attack the source, it is a question of
understanding a very complex question. If you do not have a very
good understanding of this matter, the only you can do is to
impress your readers with your apparent erudition.

It would take an expert in this matter to corral you with questions
to determine that you have not the faintest idea of this matter.

Eridanus

[eridanus]

El viernes, 8 de febrero de 2013 20:28:11 UTC, Quark E escribi�ｿｽ:
> On Feb 8, 12:19�ｿｽpm, eridanus <leopoldo.perd...@gmail.com> wrote:
>
> > El jueves, 7 de febrero de 2013 22:09:29 UTC, I am not a chemist �ｿｽescribi�ｿｽ:
>
> >
>
> >
>
> >
>
> >
>
> >
>
> > > On Feb 7, 12:06�ｿｽpm, Quark E <quarke...@gmail.com> wrote:

> > > this point, the intermediate is rotated 180�ｿｽ.[10] This rotation is

>
> >
>
> > > referred to as a "flip."[11] Because of this flip, the intermediate is
>
> >
>
> > > said to move from a "citrate mode" to a "isocitrate mode."[14]
>
> >
>
> > > How exactly this flip occurs is debatable. One theory is that, in the
>
> >
>
> > > rate-limiting step of the mechanism, the cis-aconitate is released
>
> >
>
> > > from the enzyme, then reattached in the isocitrate mode to complete
>
> >
>
> > > the reaction.[14] This rate-liming step ensures that the right
>
> >
>
> > > stereochemistry, specifically (2R,3S), is formed in the final product.
>
> >
>
> > > [14][15] Another hypothesis is that cis-aconitate stays bound to the
>
> >
>
> > > enzyme while it flips from the citrate to the isocitrate mode.[10]
>
> >
>
> > > In either case, flipping cis-aconitate allows the dehydration and
>
> >
>
> > > hydration steps to occur on opposite faces of the intermediate.[10]
>
> >
>
> > > Aconitase catalyzes trans elimination/addition of water, and the flip
>
> >
>
> > > guarantees that the correct stereochemistry is formed in the product.
>
> >
>
> > > [10][11] To complete the reaction, the serine and histidine residues
>
> >
>
> > > reverse their original catalytic actions: the histidine, now basic,
>
> >
>
> > > abstracts a proton from water, priming it as a nucleophile to attack
>
> >
>
> > > at C2, and the protonated serine is deprotonated by the cis-aconitate
>
> >
>
> > > double bond to complete the hydration, producing isocitrate
>
> >
>
> > what are you trying to prove telling us this?
>
>
>
> Trying to have people out there read and learn foundational pieces so
>
> they can follow the discussion.

Do you pretend that this matter is at the reach of anyone to go there
and understand the whole shit?

If I were prone to bet, I would bet you do not understand anything of
this matter. And that you are only pretending to show off a feigned
knowledge.

Eridanus

[Richard Norman]

On Fri, 8 Feb 2013 12:28:11 -0800 (PST), Quark E <quar...@gmail.com>
wrote:

>On Feb 8, 12:19�pm, eridanus <leopoldo.perd...@gmail.com> wrote:

>> El jueves, 7 de febrero de 2013 22:09:29 UTC, I am not a chemist �escribi�:

>>
>>
>>
>>
>>
>> > On Feb 7, 12:06�pm, Quark E <quarke...@gmail.com> wrote:
>>
>> > > On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:
>>
>> > <snip>
>>
>> > enzyme step 2:
>>
>> >http://en.wikipedia.org/wiki/Aconitase
>>

<snip Wikipedia cut/paste>

>>
>> > double bond to complete the hydration, producing isocitrate
>>
>> what are you trying to prove telling us this?
>
>Trying to have people out there read and learn foundational pieces so
>they can follow the discussion.

There is no discussion. We understand biochemistry whether you think
so or not. What is your question? What is your point? Do you
think/know/suspect something is wrong with the way biochemistry says
things work? If so tell us what it is.

[I am not a chemist]

On Feb 8, 12:28�pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "Quark E" <quarke...@gmail.com> wrote in messagenews:056aefa3-a00d-44fd...@z9g2000vbx.googlegroups.com...

> > On Feb 8, 11:59 am, "Glenn" <glennshel...@invalid.invalid> wrote:
> > > "I am not a chemist" <t2judgm...@gmail.com> wrote in messagenews:0b035b86-b6fb-41ad...@x15g2000vbj.googlegroups.com...
>
> > > > On Feb 8, 11:18 am, "Glenn" <glennshel...@invalid.invalid> wrote:
> > > > > "I am not a chemist" <t2judgm...@gmail.com> wrote in messagenews:12cf15ef-992f-4387...@14g2000vbr.googlegroups.com...
>
> > > > > > On Feb 7, 5:04 pm, Paul J Gans <gan...@panix.com> wrote:
> > > > > > > I am not a chemist <t2judgm...@gmail.com> wrote:
>
> > > > > > > >On Feb 7, 12:05?pm, Inez <savagemouse...@hotmail.com> wrote:
> > > > > > > >> On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> > > > > > > >> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> > > > > > > >> We all know how to search wikipedia. ?Did you have a point?
> > > > > > > >I am showing the audience out there the foundational pieces for
> > > > > > > >looking at what enzymes do.
>
> > > > > > > Will you pick one nym and stick to it?
>
> > > > > > Take it up with google limits.
> > > > > > I will continue to use my two emails.
>
> > > > > Sorry, there is no way to tell whether you are telling the truth
> > > > > about the impact google limits has
>
> > > > Severe.
>
> > > Not talk.origins problem. It may be that googlegroups restricts you
>
> > It is general google policy.
>
> Yes, a general policy that is determined by poster's habits. They don't have a set policy of a certain
> number of posts in a specific period of time for all posters.

Yes they do.

> > > because of your history of posting in the thousands per month.
>
> > I have never made thousands of posts in a month.
>

> Yes, either you have or others combined have from your ip address.- Hide quoted text -

Complete nonsense.

[I am not a chemist]

On Feb 8, 1:07�pm, Richard Norman <r_s_nor...@comcast.net> wrote:
> On Fri, 8 Feb 2013 12:28:11 -0800 (PST), Quark E <quarke...@gmail.com>

> wrote:
>
>
>
>
>
> >On Feb 8, 12:19�pm, eridanus <leopoldo.perd...@gmail.com> wrote:
> >> El jueves, 7 de febrero de 2013 22:09:29 UTC, I am not a chemist �escribi�:
>
> >> > On Feb 7, 12:06�pm, Quark E <quarke...@gmail.com> wrote:
>
> >> > > On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:
>
> >> > <snip>
>
> >> > enzyme step 2:
>
> >> >http://en.wikipedia.org/wiki/Aconitase
>
> <snip Wikipedia cut/paste>
>
>
>
> >> > double bond to complete the hydration, producing isocitrate
>
> >> what are you trying to prove telling us this?
>
> >Trying to have people out there read and learn foundational pieces so
> >they can follow the discussion.
>
> There is no discussion.

Claim that no discussion takes place in TO is noted.

[chris thompson]

On Feb 8, 3:41�pm, "Dexter" <N...@home.org> wrote:
> "I am not a chemist" <t2judgm...@gmail.com> wrote in messagenews:4185b431-356e-4780...@hl5g2000vbb.googlegroups.com...

In fact I am happy to mention one. In another thread he described
enzymes as "exact". The clear implication was that any enzyme had an
exact function and catalyzed a single reaction, binding to a single
substrate. It's untrue and a simple-minded view of enzyme function.
Many enzymes are capable of catalyzing a class of reactions. A couple
of examples spring to mind. Phosphorylation is one, but here's
another- carbonic anhydrase catalyzes a reaction that forms carbonic
acid from CO2 (which then forms bicarbonate, an important pH buffer in
blood) and in the lungs also catalyzes the reverse reaction, forming
CO2 that then diffuses out of the lungs to be excreted. (A similar
reaction occurs in the GI tract.) (Richard Norman will certainly
correct me on details and I hope he does).

But those are all functional reactions. A better example might be
ribulose biphosphate carboxylase (rubisco). This enzyme essentially
brings CO2 into the Calvin Cycle, where the carbon will be
incorporated into an organic compound (glyceraldehyde-3-phosphate or
G3P). However, under certain environmental conditions (high
temperatures, for example, when stomata- the openings in leaves
through which CO2 diffuses in and O2 diffuses out) rubisco has no CO2
to work on.

But rubisco has almost as high an affinity for O2 as it does for CO2.
So when the other photosynthetic reactions split water and release O2,
and there's not enough CO2 to fuel the Calvin Cycle, rubisco pumps O2
into the Calvin Cycle instead of CO2. This brings the Calvin Cycle to
a screeching halt in a process called photorespiration. The plant is
no longer producing carbohydrates but stuff that has to be converted
to usable compounds at a real energy cost.

Rubisco is anything but exact, and it takes a real energy cost on the
plant. In fact, some plants have gone to great lengths to avoid this
problem (yah, sounds like teleology but not intended). Some plants
shuttle the carbon into a different part of the leaf, relatively far
away from the O2 that's building up. Other plants sequester the carbon
in organic acids that can later be used.

If the enzyme was _exact_ why would plants need those work-arounds?

Chris

[I am not a chemist]

There is your problem.
Implication.
Your implication to mean something that would indicate me being wrong
is all in your head only and not a fact.

was that any enzyme had an
> exact function and catalyzed a single reaction, binding to a single
> substrate. It's untrue and a simple-minded view of enzyme function.

No wonder you ascribed such a view to me.

> Many enzymes are capable of catalyzing a class of reactions. A couple
> of examples spring to mind. Phosphorylation is one, but here's
> another- carbonic anhydrase catalyzes a reaction that forms carbonic
> acid from CO2 (which then forms bicarbonate, an important pH buffer in
> blood) and in the lungs also catalyzes the reverse reaction, forming
> CO2 that then diffuses out of the lungs to be excreted. (A similar
> reaction occurs in the GI tract.) (Richard Norman will certainly
> correct me on details and I hope he does).

Wow a co2 reversible enzyme.
You have profound information.

>
> But those are all functional reactions. A better example might be
> ribulose biphosphate carboxylase (rubisco). This enzyme essentially
> brings CO2 into the Calvin Cycle, where the carbon will be
> incorporated into an organic compound (glyceraldehyde-3-phosphate or
> G3P). However, under certain environmental conditions (high
> temperatures, for example, when stomata- the openings in leaves
> through which CO2 diffuses in and O2 diffuses out) rubisco has no CO2
> to work on.

You like co2.

>
> But rubisco has almost as high an affinity for O2 as it does for CO2.
> So when the other photosynthetic reactions split water and release O2,
> and there's not enough CO2 to fuel the Calvin Cycle, rubisco pumps O2
> into the Calvin Cycle instead of CO2. This brings the Calvin Cycle to
> a screeching halt in a process called photorespiration. The plant is
> no longer producing carbohydrates but stuff that has to be converted
> to usable compounds at a real energy cost.

What did you do, look up co2 enzymes?

>
> Rubisco is anything but exact, and it takes a real energy cost on the
> plant. In fact, some plants have gone to great lengths to avoid this
> problem (yah, sounds like teleology but not intended). Some plants
> shuttle the carbon into a different part of the leaf, relatively far
> away from the O2 that's building up. Other plants sequester the carbon
> in organic acids that can later be used.
>

Why don't you ask me what i meant by exact?

[Paul J Gans]

I am vastly amused by you trumpeting in here like an elephant
in heat and demanding that we work for you. You could at least
say "please" and "thank you".

[Richard Norman]

The reverse reaction doesn't count as a separate reaction if it is a
true reverse and not a completely separate pathway (as for example in
the phosphorylation/dephosphorylation of glucose to G6P: hexokinase
vs. glucose-6-Phosphatase). But it is true that many enzymes do
catalyse a whole range of similar reactions. Hexokinase, for example,
will phosphorylate a range of hexoses, not just glucose.

Perhaps the best example of a multifunctional enzyme is the Cytochrome
P450 isoform CYP3A4. This enzyme in the liver and intestines is
important in metabolizing all sorts of 'foreign' materials that we
might ingest. Grapefruit contains a compound that inhibits this
enzyme and so tends to increase the effectiveness of many drugs that
would otherwise be broken down by CYP3A4. Hence the prohibition for
eating grapefruit for people taking many of the statins for high
cholesterol. There is a very long list of drugs whose potency in
altered by grapefruit. See, for example
http://en.wikipedia.org/wiki/Grapefruit_drug_interactions


As to carbonic anhydrase -- it is a very important enzyme that is
essential in allowing the blood to transport carbon dioxide. Red
cells have it in abundance. It is also an important enzyme in many
other cells for pH regulation. Also it is an essential step in the
production of stomach acid.

[chris thompson]

Then you should be clearer in that you meant.

>
> �was that any enzyme had an

>
> > exact function and catalyzed a single reaction, binding to a single
> > substrate. It's untrue and a simple-minded view of enzyme function.
>
> No wonder you ascribed such a view to me.

So what did you mean by "exact:?

>
> > Many enzymes are capable of catalyzing a class of reactions. A couple
> > of examples spring to mind. Phosphorylation is one, but here's
> > another- carbonic anhydrase catalyzes a reaction that forms carbonic
> > acid from CO2 (which then forms bicarbonate, an important pH buffer in
> > blood) and in the lungs also catalyzes the reverse reaction, forming
> > CO2 that then diffuses out of the lungs to be excreted. (A similar
> > reaction occurs in the GI tract.) (Richard Norman will certainly
> > correct me on details and I hope he does).
>
> Wow a co2 reversible enzyme.
> You have profound information.

I have basic information, which seems a lot more than you have. Why
don't you post something from your own knowledge, rather than a cut-
and-post from Wikipedia?

>
>
>
> > But those are all functional reactions. A better example might be
> > ribulose biphosphate carboxylase (rubisco). This enzyme essentially
> > brings CO2 into the Calvin Cycle, where the carbon will be
> > incorporated into an organic compound (glyceraldehyde-3-phosphate or
> > G3P). However, under certain environmental conditions (high
> > temperatures, for example, when stomata- the openings in leaves
> > through which CO2 diffuses in and O2 diffuses out) rubisco has no CO2
> > to work on.
>
> You like co2.
>

Yeah, I do, in the right concentration- but I notice you have nothing
of substance to say here.

>
> > But rubisco has almost as high an affinity for O2 as it does for CO2.
> > So when the other photosynthetic reactions split water and release O2,
> > and there's not enough CO2 to fuel the Calvin Cycle, rubisco pumps O2
> > into the Calvin Cycle instead of CO2. This brings the Calvin Cycle to
> > a screeching halt in a process called photorespiration. The plant is
> > no longer producing carbohydrates but stuff that has to be converted
> > to usable compounds at a real energy cost.
>
> What did you do, look up co2 enzymes?

Yeah, I did- about 23 years ago. I teach this stuff. I am not learning
it from your moronic posts.

>
>
>
> > Rubisco is anything but exact, and it takes a real energy cost on the
> > plant. In fact, some plants have gone to great lengths to avoid this
> > problem (yah, sounds like teleology but not intended). Some plants
> > shuttle the carbon into a different part of the leaf, relatively far
> > away from the O2 that's building up. Other plants sequester the carbon
> > in organic acids that can later be used.
>
> Why don't you ask me what i meant by exact?

Because in the English language and biology in particular, "exact" has
meaning. If you want to ascribe a new meaning to "exact" you'd better
specify it ahead of time.

Chris

[I am not a chemist]

On Feb 8, 8:01�pm, chris thompson <chris.linthomp...@gmail.com> wrote:
> On Feb 8, 7:01�pm, I am not a chemist <t2judgm...@gmail.com> wrote:

> A better example might be
> > > ribulose biphosphate carboxylase (rubisco). This enzyme essentially
> > > brings CO2 into the Calvin Cycle, where the carbon will be
> > > incorporated into an organic compound (glyceraldehyde-3-phosphate or
> > > G3P). However, under certain environmental conditions (high
> > > temperatures, for example, when stomata- the openings in leaves
> > > through which CO2 diffuses in and O2 diffuses out) rubisco has no CO2
> > > to work on.
>
> > You like co2.
>
> Yeah, I do, in the right concentration- but I notice you have nothing
> of substance to say here.

Amazing you noticed the condition here of high temperature being a
factor.
So let us now act like you possess a brain.
In photosynthesis plants, during daylight, it would be warmer.
At night it would be cooler.
Rubisco I think discriminates CO2 4 times as great as O2, although I
may be off on the exact amount.
It is also possible early on that an enzyme complex may be the one
that drags in o2 instead of co2, may need to check on that.
The details on the enzyme itself, where it selects the gas involved,
do you have the details on that?

[Mark Isaak]

On 2/8/13 12:28 PM, Quark E wrote:
> On Feb 8, 12:19 pm, eridanus <leopoldo.perd...@gmail.com> wrote:

>> El jueves, 7 de febrero de 2013 22:09:29 UTC, I am not a chemist escribi�:
>>
>>> [snip cut-and-paste]

>> what are you trying to prove telling us this?
>
> Trying to have people out there read and learn foundational pieces so
> they can follow the discussion.

No, that's not it. What are you trying to prove, really?

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"It is certain, from experience, that the smallest grain of natural
honesty and benevolence has more effect on men's conduct, than the most
pompous views suggested by theological theories and systems." - D. Hume

[I am not a chemist]

On Feb 8, 6:25�pm, Richard Norman <r_s_nor...@comcast.net> wrote:

> �But it is true that many enzymes do

> catalyse a whole range of similar reactions.

Duh.

[I am not a chemist]

On Feb 9, 9:42�am, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> On 2/8/13 12:28 PM, Quark E wrote:
>
> > On Feb 8, 12:19 pm, eridanus <leopoldo.perd...@gmail.com> wrote:
> >> El jueves, 7 de febrero de 2013 22:09:29 UTC, I am not a chemist �escribi�:
>
> >>> [snip cut-and-paste]
> >> what are you trying to prove telling us this?
>
> > Trying to have people out there read and learn foundational pieces so
> > they can follow the discussion.
>
> No, that's not it.

Yes it is.

[Boikat]

On Feb 9, 11:42�am, Mark Isaak <eci...@curioustax.onomy.net> wrote:
> On 2/8/13 12:28 PM, Quark E wrote:
>
> > On Feb 8, 12:19 pm, eridanus <leopoldo.perd...@gmail.com> wrote:
> >> El jueves, 7 de febrero de 2013 22:09:29 UTC, I am not a chemist �escribi�:
>
> >>> [snip cut-and-paste]
> >> what are you trying to prove telling us this?
>
> > Trying to have people out there read and learn foundational pieces so
> > they can follow the discussion.
>
> No, that's not it. �What are you trying to prove, really?

That he's a bigger waste of time than discussing geocentrism with
Pagano, or, "do rocks have free will" with Nando, or, that twit from
India with his smug little "ancient hindu had aircraft tens of
thousands of years ago", or, can cut and paste bigger blocks of text
than UC, or, he's more annoyingly ignorant than spintronic, or,...
Well, you get my drift...


Boikat

[I am not a chemist]

http://en.wikipedia.org/wiki/5-alpha_reductase

5α-reductases, also known as 3-oxo-5α-steroid 4-dehydrogenases, are
enzymes involved in steroid metabolism. They participate in 3
metabolic pathways: bile acid biosynthesis, androgen and estrogen
metabolism, and prostate cancer. There are three isoenzymes of 5-alpha
reductase, which vary in different tissues with age.

5α-reductases catalyze the following chemical reaction:

a 3-oxo-5α-steroid + acceptor a 3-oxo-Δ4-steroid + reduced acceptor
Thus, the two substrates of these enzymes are a 3-oxo-5α-steroid and
acceptor, whereas its two products are 3-oxo-Δ4-steroid and a reduced
acceptor.


Specific substrates include testosterone, progesterone,
androstenedione, epi-testosterone, cortisol, aldosterone, and
deoxycorticosterone

[I am not a chemist]

You mean that I am way better than those.

[I am not a chemist]

On Feb 7, 12:06�pm, Quark E <quarke...@gmail.com> wrote:

> On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:

<snip>

> Here is the first enzyme from step 1:
>
> http://en.wikipedia.org/wiki/Citrate_synthase
>

> Oxaloacetate is the first substrate to bind to the enzyme. This
> induces the enzyme to change its conformation, and creates a binding
> site for the acetyl-CoA. Only when this citroyl-CoA has formed will
> another conformational change cause thioester hydrolysis and release
> coenzyme A. This ensures that the energy released from the thioester
> bond cleavage will drive the condensation.

It appears this enzyme *gasp* is doing more than merely act as a
catalyst.
It appears it is *gasp* actually doing the chemical reaction on the
substrate.


>
> Between these two subunits, a single cleft exists containing the
> active site. Two binding sites can be found therein: one reserved for
> citrate or oxaloacetate and the other for Coenzyme A. The active site
> contains three key residues: His274, His320, and Asp375 that are
> highly selective in their interactions with substrates

Get the picture?

>
> Citrate Synthase has three key amino acids in its active site which
> catalyze the conversion of acetyl-CoA (H3CCO-SCoA) and oxaloacetate
> (COO-CH2COCOO-) into citrate (COO-CH2COHCOOCH2COO-) and H-SCoA in an
> aldol condensation reaction. This conversion begins with the
> negatively charged oxygen in Asp375�s R-group deprotonating acetyl
> CoA�s alpha carbon. This pushes the e- to form a double-bond with the
> carbonyl carbon, which in turn forces the C=O up to pick up a proton
> for the oxygen from one of the nitrogens in the R-group of His274.
> This neutralizes the R-group (by forming a lone pair on the nitrogen)
> and completes the formation of an enol intermediate (CH2COH-SCoA). At
> this point, His274�s amino lone pair formed in the last step attacks
> the proton that was added to the oxygen in the last step. The oxygen
> then reforms the carbonyl bond, which frees half of the C=C to
> initiate a nucleophilic attack to oxaloacetate�s carbonyl carbon (COO-
> CH2COCOO-). This frees half of the carbonyl bond to deprotonate one of
> His320�s amino groups, which neutralizes one of the nitrogens in its R-
> group. This nucleophilic addition results in the formation of citroyl-
> CoA (COOCH2CHCOOCH2COHSCoA2-). At this point, a water molecule is
> brought in and is deprotonated by His320�s amino group and Hydrolysis
> is initiated. One of the oxygen�s lone pairs nucleophilically attacks
> the carbonyl carbon of citroyl-CoA. This forms a tetrahedral
> intermediate and results in the ejection of �SCoA as the carbonyl
> reforms. The �SCoA is protonated to form HSCoA. Finally, the hydroxyl
> added to the carbonyl in the previous step is deprotonated and citrate
> (-COOCH2COHCOO-CH2COO-) is formed- Hide quoted text -
>
> - Show quoted text -

[Quark E]

On Feb 7, 2:09 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> On Feb 7, 12:06 pm, Quark E <quarke...@gmail.com> wrote:

>
> > On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> <snip>
>

> enzyme step 2:
>



>At
> this point, the intermediate is rotated 180�.[10] This rotation is

> referred to as a "flip."[11] Because of this flip, the intermediate is
> said to move from a "citrate mode" to a "isocitrate mode."[14]

Catalyst or actually doing the chemical reaction?

>
> How exactly this flip occurs is debatable. One theory is that, in the
> rate-limiting step of the mechanism, the cis-aconitate is released
> from the enzyme, then reattached in the isocitrate mode to complete
> the reaction.[14] This rate-liming step ensures that the right
> stereochemistry, specifically (2R,3S), is formed in the final product.
> [14][15] Another hypothesis is that cis-aconitate stays bound to the
> enzyme while it flips from the citrate to the isocitrate mode.[10]
>

> In either case...and the flip

> guarantees that the correct stereochemistry is formed in the product.
> [10][11] To complete the reaction, the serine and histidine residues
> reverse their original catalytic actions: the histidine, now basic,
> abstracts a proton from water, priming it as a nucleophile to attack
> at C2, and the protonated serine is deprotonated by the cis-aconitate

[Boikat]

> You mean that I am way better than those.-

If being an poser and an asshole is your goal.

Boikat

[Quark E]

> Boikat- Hide quoted text -

Namecalling.

[Quark E]

On Feb 7, 2:58�pm, Quark E <quarke...@gmail.com> wrote:
> On Feb 7, 2:52�pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> <snip>
>
> next enzyme:
>
> http://en.wikipedia.org/wiki/Succinate_dehydrogenase
>
> It is the only enzyme that participates in both the citric acid cycle
> and the electron transport chain

http://en.wikipedia.org/wiki/File:Succinate_Dehydrogenase_1YQ3_Electron_Carriers_Labeled.png

[Boikat]

> Namecalling.

More like "classifying a bug". That's not the same as "name
calling".

Boikat

[Quark E]

I would imagine someone on the other side of the debate scoring points
would bug you.

[Boikat]

You haven't score any points other than the ones needed to show you
are a waste of time.

Boikat

[Quark E]

LOL.
Delusional you have become.

[David Canzi]

I am not a chemist <t2jud...@gmail.com> wrote:

>On Feb 7, 1:02�pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:

>> On Feb 8, 6:00�am, Quark E <quarke...@gmail.com> wrote:
>>
>> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>>

>> > The citric acid cycle � also known as the tricarboxylic acid cycle
>> > (TCA cycle), the Krebs cycle, or the Szent-Gy�rgyi�Krebs cycle[1][2] �
>> > is a series of chemical reactions used by all aerobic organisms to
>> > generate energy
>>
>> > Its central importance to many biochemical pathways suggests that it
>> > was one of the earliest established components of cellular metabolism
>> > and may have originated abiogenically
>>
>> Stop. It is not a commonly accepted belief that the TCA cycle arose
>> abiogenically, even if some seem to be fond of the idea.
>
>Take it up with wiki.

If you base your argument on an inaccurate premise, your argument
will be incorrect. If the faulty premise was written by somebody
else and not by you, your argument will still be incorrect.

--
David Canzi | "Rudeness is the weak man's imitation
| of strength." -- Eric Hoffer

[Richard Norman]

On Sat, 9 Feb 2013 10:15:10 -0800 (PST), I am not a chemist
<t2jud...@gmail.com> wrote:

>On Feb 7, 12:06�pm, Quark E <quarke...@gmail.com> wrote:

>> On Feb 7, 12:00�pm, Quark E <quarke...@gmail.com> wrote:
>
><snip>
>
>> Here is the first enzyme from step 1:
>>
>> http://en.wikipedia.org/wiki/Citrate_synthase
>>
>> Oxaloacetate is the first substrate to bind to the enzyme. This
>> induces the enzyme to change its conformation, and creates a binding
>> site for the acetyl-CoA. Only when this citroyl-CoA has formed will
>> another conformational change cause thioester hydrolysis and release
>> coenzyme A. This ensures that the energy released from the thioester
>> bond cleavage will drive the condensation.
>
>It appears this enzyme *gasp* is doing more than merely act as a
>catalyst.
>It appears it is *gasp* actually doing the chemical reaction on the
>substrate.
>

<snip more details about the action of the enzyme because it is
unnecessary for any argument>

Gee, the enzyme is *gasp* actually *gasp* PARTICIPATING in the
reaction and not just sitting on the sidelines just accelerating it by
shouting "Rah team, go go go!".

I am sure this news will completely overturn everything that real
biochemists hold near and dear, the classic dogma of enzymology that
enzymes are "mere catalysts" and not "actually doing" the reaction.

[Boikat]

Talking like Yoda does not even make you *appear* to be wise.

Boikat

[I am not a chemist]

> enzymes are "mere catalysts" and not "actually doing" the reaction.- Hide quoted text -

>
> - Show quoted text -

http://www.youtube.com/watch?v=3y1dO4nNaKY

[I am not a chemist]

On Feb 9, 11:54�am, "David Canzi" <dmca...@uwaterloo.ca> wrote:

> I am not a chemist �<t2judgm...@gmail.com> wrote:
>
>
>
>
>
> >On Feb 7, 1:02 pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:
> >> On Feb 8, 6:00 am, Quark E <quarke...@gmail.com> wrote:
>
> >> >http://en.wikipedia.org/wiki/Citric_acid_cycle
>
> >> > The citric acid cycle also known as the tricarboxylic acid cycle
> >> > (TCA cycle), the Krebs cycle, or the Szent-Gy rgyi Krebs cycle[1][2]
> >> > is a series of chemical reactions used by all aerobic organisms to
> >> > generate energy
>
> >> > Its central importance to many biochemical pathways suggests that it
> >> > was one of the earliest established components of cellular metabolism
> >> > and may have originated abiogenically
>
> >> Stop. It is not a commonly accepted belief that the TCA cycle arose
> >> abiogenically, even if some seem to be fond of the idea.
>
> >Take it up with wiki.
>
> If you base your argument on an inaccurate premise, your argument
> will be incorrect.

Duh.

>�If the faulty premise was written by somebody

> else and not by you, your argument will still be incorrect.

Since I did not make the argument ....

Are you sensitive on this issue?

Why did you snip out the rest of my explanation?

[Roger Shrubber]

I am not a chemist wrote:
> On Feb 7, 12:06 pm, Quark E <quarke...@gmail.com> wrote:

>> On Feb 7, 12:00 pm, Quark E <quarke...@gmail.com> wrote:
>
> <snip>
>
>> Here is the first enzyme from step 1:
>>
>> http://en.wikipedia.org/wiki/Citrate_synthase
>>
>> Oxaloacetate is the first substrate to bind to the enzyme. This
>> induces the enzyme to change its conformation, and creates a binding
>> site for the acetyl-CoA. Only when this citroyl-CoA has formed will
>> another conformational change cause thioester hydrolysis and release
>> coenzyme A. This ensures that the energy released from the thioester
>> bond cleavage will drive the condensation.
>
> It appears this enzyme *gasp* is doing more than merely act as a
> catalyst.
> It appears it is *gasp* actually doing the chemical reaction on the
> substrate.

Fail.
It's a common failure to think that way but it's still a failure.
It's the general lack of understanding of physical organic
chemistry that's common in molecular biologists that promotes
that sort of deluded teleology.

[Mark Isaak]

If you honestly think that's what you are doing, you are definitely
delusional. Do not take my word for it; print out this thread and show
it to any impartial mental health professional.

[Richard Norman]

That is freshman level introductory biology. What do you have that is
new and interesting?

[Paul J Gans]

Richard Norman <r_s_n...@comcast.net> wrote:
>On Sat, 9 Feb 2013 10:15:10 -0800 (PST), I am not a chemist
><t2jud...@gmail.com> wrote:

>>On Feb 7, 12:06?pm, Quark E <quarke...@gmail.com> wrote:

>>> On Feb 7, 12:00?pm, Quark E <quarke...@gmail.com> wrote:
>>
>><snip>
>>
>>> Here is the first enzyme from step 1:
>>>
>>> http://en.wikipedia.org/wiki/Citrate_synthase
>>>
>>> Oxaloacetate is the first substrate to bind to the enzyme. This
>>> induces the enzyme to change its conformation, and creates a binding
>>> site for the acetyl-CoA. Only when this citroyl-CoA has formed will
>>> another conformational change cause thioester hydrolysis and release
>>> coenzyme A. This ensures that the energy released from the thioester
>>> bond cleavage will drive the condensation.
>>
>>It appears this enzyme *gasp* is doing more than merely act as a
>>catalyst.
>>It appears it is *gasp* actually doing the chemical reaction on the
>>substrate.
>>

><snip more details about the action of the enzyme because it is
>unnecessary for any argument>

>Gee, the enzyme is *gasp* actually *gasp* PARTICIPATING in the
>reaction and not just sitting on the sidelines just accelerating it by
>shouting "Rah team, go go go!".

>I am sure this news will completely overturn everything that real
>biochemists hold near and dear, the classic dogma of enzymology that
>enzymes are "mere catalysts" and not "actually doing" the reaction.

Yup. Catalysts aren't magic. If the reaction takes place without
the catalyst, it is by a different path than with the catalyst.

By the way, chemistry students in their early training, also
have problems with the notion of catalysts.

--
--- Paul J. Gans

[chris thompson]

On Feb 9, 12:38�pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> On Feb 8, 8:01 pm, chris thompson <chris.linthomp...@gmail.com> wrote:
>
> > On Feb 8, 7:01 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> > A better example might be
> > > > ribulose biphosphate carboxylase (rubisco). This enzyme essentially
> > > > brings CO2 into the Calvin Cycle, where the carbon will be
> > > > incorporated into an organic compound (glyceraldehyde-3-phosphate or
> > > > G3P). However, under certain environmental conditions (high
> > > > temperatures, for example, when stomata- the openings in leaves
> > > > through which CO2 diffuses in and O2 diffuses out) rubisco has no CO2
> > > > to work on.
>
> > > You like co2.
>
> > Yeah, I do, in the right concentration- but I notice you have nothing
> > of substance to say here.
>
> Amazing you noticed the condition here of high temperature being a
> factor.

So tell me, what happens at high temperatures that makes it a problem
for plants? I know I hinted at it above but it's not complete.

> So let us now act like you possess a brain.

Rather full of yourself, aren't you?

> In photosynthesis plants, during daylight, it would be warmer.

Brilliant observation!

> At night it would be cooler.

I'm stunned, yes, stunned, at your powers of observation.

> Rubisco I think discriminates CO2 4 times as great as O2, although I
> may be off on the exact amount.

You're way off. It's more like 50-100x. The issue here is not so much
the affinity for O2 as it is the lack of CO2. That's a hint to
answering the question I asked above.

> It is also possible early on that an enzyme complex may be the one
> that drags in o2 instead of co2, may need to check on that.

You do that. Get back to us when you learn something.

> The details on the enzyme itself, where it selects the gas involved,
> do you have the details on that?

Yes, I do, because, as I said elsewhere, I have a basic knowledge of
how enzymes work. Not only biochemists are familiar with enzymes, you
know. Chemists and biologists also know something on the topic.

Chris

[Richard Norman]

Any biologist that has learned about Michaelis-Menten kinetics should
know that the substrate must bind to the enzyme and the reaction
occurs within the bound state. I can't imagine any instructor talking
about this to omit that in the bound state the conformation or
electronic configuration of the substrate is altered so the enzyme
becomes an "active" participant in the process even if the details of
the reaction pathway aren't mentioned.

In any intermediate class (upper division undergrad, for example)
students should learn that the enzyme does not "lower" the activation
energy but rather provides a new pathway for the reaction with a lower
activation energy. "Don't go over that mountain pass to get to the
other side! Take the enzyme tram to the other side of the peak and
you will find an easier route so you don't have to climb that far."

Of course whether students still have problems with the notion is
another problem for education. You can lead a horse to water but...

[John S. Wilkins]

I love listening to grownups talking...
--
John S. Wilkins, Associate, Philosophy, University of Sydney
Honorary Fellow, University of Melbourne
- http://evolvingthoughts.net

[Roger Shrubber]

The confusion stems from people who didn't really understand
the prerequisite knowledge, and frankly, I've met professors
who are confused about enzymatic catalysis.

Partly, it's the trap of language. "Binds" and "attacks" invoke
active imagery. And _active_ is misunderstood. Active in the
sense that there are multiple things that happen can be easily
explained but it is a trap some never escape. Without really
thinking about it, people impart a sort of will to an enzyme.

The second trap is that there is a coordinated dance that
is part of a _successful_ reaction. Bind, conformational
change, formation of covalent intermediate, second
conformational change, hydrolysis of bond, release of
one produce, hydrolysis of enzyme-substrate-product bond,
release of other product. That's quite a coordinated
sequence of events. A surprising number of people don't
grasp that it's often two steps forward, one step back.
There isn't the equivalent of a conveyor belt that that
keeps everything moving _forward_ in the direction that
we write the reaction for didactic purposes.

But those conformational changes: they flutter, at least
sometimes. Each individual subreaction has its own rate
and equilibrium. Is there time to teach this? Many say
no, we're too busy teaching things of more technological
significance. Others say it was supposed to have been
taught elsewhere, being somewhat oblivious to the well
known fact that most people need to get a lesson more
than once to really understand it.

In the end enzymes are NOT active catalysts. They are
complex catalysts that involve more stages. If anyone
disputes that, they will have to explain, in great detail,
what demarcates the transition to active from non-active.
But I'll tell you in advance, if you seek it, you'll
find it isn't there.
..

[jillery]

On Sat, 9 Feb 2013 23:46:56 +0000 (UTC), Paul J Gans
<gan...@panix.com> wrote:

I'm still trying to figure out how trolling T.O. helps solve anybody's
problems.

[Paul J Gans]

So do I. Where are they?

[Paul J Gans]

Interesting. In the chemistry department we deal with
catalysis of various sorts as early as organic chemistry
(a second year course). And more curiously, the
undergraduate biochemistry course is taught in the
chemistry department.

By the time students take it, they've had physical
chemistry, a dose of kinetics, and most importantly,
a good shot of thermodynamics.

No department can teach everything. We are drowning in
knowlege, but that is a topic for a different rant.

[John S. Wilkins]

Paul J Gans <gan...@panix.com> wrote:

> >I love listening to grownups talking...
>
> So do I. Where are they?

I'm sure I saw some around here once upon a time...

Hey! Where's the yacht? It was hear last time I looked.

[chris thompson]

On Feb 9, 12:55 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> On Feb 9, 9:47 am, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> > On Feb 8, 6:25 pm, Richard Norman <r_s_nor...@comcast.net> wrote:
>
> > > But it is true that many enzymes do
> > > catalyse a whole range of similar reactions.
>
> > Duh.
>
> http://en.wikipedia.org/wiki/5-alpha_reductase
>
> 5α-reductases, also known as 3-oxo-5α-steroid 4-dehydrogenases, are
> enzymes involved in steroid metabolism. They participate in 3
> metabolic pathways: bile acid biosynthesis, androgen and estrogen
> metabolism, and prostate cancer. There are three isoenzymes of 5-alpha
> reductase, which vary in different tissues with age.
>
> 5α-reductases catalyze the following chemical reaction:
>
> a 3-oxo-5α-steroid + acceptor  a 3-oxo-Δ4-steroid + reduced acceptor
> Thus, the two substrates of these enzymes are a 3-oxo-5α-steroid and
> acceptor, whereas its two products are 3-oxo-Δ4-steroid and a reduced
> acceptor.
>
> Specific substrates include testosterone, progesterone,
> androstenedione, epi-testosterone, cortisol, aldosterone, and
> deoxycorticosterone

You might be interesting (but I dought it) if you did anything other
than copy and paste from Wikipedia. All in all, you bore me.

Chris

[Richard Norman]

That fluttery business is a hard one to get across. And I did
purposely put the word "active" in quotes. The enzyme is definitely a
participant but you are quite right, an 'active' agent takes charge to
direct a result in common opinion. And an 'active' process, in
physiology at least, is one that generally needs an energy input
because it is otherwise "uphill" thermodynamically. Still an awful
lot of biochemistry (dare I say almost all?) is somewhat far from
equilibrium so that the fluttering ends up, given enough molecules
participating, being a headlong rush one way. "Active" be damned,
thermodynamics demands that the conveyor belt run the right way and
the entirety of cellular structure and metabolism is set up to make
sure the thermodynamics stays that way.

I used to teach that cellular metabolism is like traffic patterns.
There is morning rush hour one way and evening rush hour another and a
big game at the stadium still another pattern. If you get in the TV
station traffic helicopter you can see the pattern but if you follow
any one particular car it might well do something entirely different
-- go off against the flow to grandmother's house or something. Look
at the individual participants and they all flutter. Look at the
overall picture and it gives the impression of being totally
organized.

[Boikat]

He's a poser. To paraphrase, "He knows no more about biochemistry
than a tea leaf knows the history of the East India Company".

Boikat

[Glenn]

"chris thompson" <chris.li...@gmail.com> wrote in message news:de53c67f-704e-4dec...@cd3g2000vbb.googlegroups.com...

That is your brain on donughts.

[I am not a chemist]

On Feb 9, 1:59�pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:

> It's the general lack of understanding of physical organic
> chemistry

So now you have taken third year chemistry with the required math have
you?

[I am not a chemist]

Can you tell me or is it a secret?
I would like to see these details.

> Not only biochemists are familiar with enzymes, you
> know. Chemists and biologists also know something on the topic.

Know of any enzymes that are defective?

[Richard Norman]

There are rather a large number of non functional enzymes found in
human blood plasma. Many of these are measured in clinical assays.

There are rather a large number of defective enzymes responsible for
hereditary diseases.

[chris thompson]

On Feb 10, 5:36�pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> On Feb 9, 4:24�pm, chris thompson <chris.linthomp...@gmail.com> wrote:
>
> > On Feb 9, 12:38�pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> �> The details on the enzyme itself, where it selects the gas
> involved,
>
> > > do you have the details on that?
>
> > Yes, I do, because, as I said elsewhere, I have a basic knowledge of
> > how enzymes work
>
> Can you tell me or is it a secret?
> I would like to see these details.

Yes, it's a secret closely guarded by the conspiracy. You can only
learn the answer if you take some biology classes or have access to
Google.

>
> > Not only biochemists are familiar with enzymes, you
> > know. Chemists and biologists also know something on the topic.
>
> Know of any enzymes that are defective?

Hexosaminidase, in people suffering from Tay-Sachs disease.

Chris

[I am not a chemist]

On Feb 10, 3:40�pm, chris thompson <chris.linthomp...@gmail.com>
wrote:

> On Feb 10, 5:36�pm, I am not a chemist <t2judgm...@gmail.com> wrote:

> > > Not only biochemists are familiar with enzymes, you
> > > know. Chemists and biologists also know something on the topic.
>
> > Know of any enzymes that are defective?
>
> Hexosaminidase, in people suffering from Tay-Sachs disease.

http://www.mun.ca/biology/scarr/Round_&_Wrinkled.htm

starch branching enzyme

In fact, the wrinkled trait is due to a disruption in the biochemical
process responsible for making starch in these peas. During
development of normal round peas, sugar is converted into starch,
which is stored by the mature seed until needed for germination.
Wrinkled peas convert much less of their sugar into starch. The sugar
level builds up inside the pea and so they taste sweeter than round
ones.
Having established that the wrinkled trait was due to a disruption in
starch synthesis, scientists at the JIC started looking for the exact
part of the process that is defective in wrinkled peas. They
discovered that wrinkled peas don�t produce one crucial enzyme needed
for normal starch production. They concluded that the loss of this
enzyme, known as starch branching enzyme, explains the block in the
transformation of sugar into starch
So the JIC scientists set about discovering why normal, round peas
have the starch branching enzyme but wrinkled peas do not. They found
that the gene for starch branching enzyme in wrinkled peas contains an
extra piece of DNA that stops the gene from working, so the enzyme
that it encodes is not produced.
But why are the peas wrinkled? This is due to a process known as
osmosis � the natural tendency of water to move from a more dilute to
a more concentrated solution. The high sugar content of wrinkled peas
means that water moves in by osmosis, causing the pea to expand inside
its seed coat. Once it is mature, it loses the water as it dries and
shrivels. But having been stretched, the seed coat then wrinkles as
the pea inside shrinks. As round peas contain less sugar than wrinkled
ones, they take up less water and the seed coat doesn�t stretch. As
round peas dry, the seed coat shrinks to leave a smooth surface.

[I am not a chemist]

On Feb 9, 5:48�pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:

> In the end enzymes are NOT active catalysts. They are
> complex catalysts that involve more stages.

Hint: they are not mere catalysts, more is going on than just
catalysing.

[Glenn]

"chris thompson" <chris.li...@gmail.com> wrote in message news:093fa3e0-d595-4ee8...@hl5g2000vbb.googlegroups.com...

"G6PD deficiency is the most common human enzyme defect"

although this is a deficiency and not itself a defective enzyme,

"When all remaining reduced glutathione is consumed, enzymes and other proteins (including hemoglobin) are subsequently damaged by the oxidants, leading to electrolyte imbalance, cross-bonding and protein deposition in the red cell membranes."

http://en.wikipedia.org/wiki/Glucose-6-phosphate_dehydrogenase_deficiency

How'd I do for a 2 minute google search?

[I am not a chemist]

On Feb 10, 4:11�pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "chris thompson" <chris.linthomp...@gmail.com> wrote in messagenews:093fa3e0-d595-4ee8...@hl5g2000vbb.googlegroups.com...

> > On Feb 10, 5:36 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
> > > On Feb 9, 4:24 pm, chris thompson <chris.linthomp...@gmail.com> wrote:
>
> > > > On Feb 9, 12:38 pm, I am not a chemist <t2judgm...@gmail.com> wrote:
>
> > > > The details on the enzyme itself, where it selects the gas
> > > involved,
>
> > > > > do you have the details on that?
>
> > > > Yes, I do, because, as I said elsewhere, I have a basic knowledge of
> > > > how enzymes work
>
> > > Can you tell me or is it a secret?
> > > I would like to see these details.
>
> > Yes, it's a secret closely guarded by the conspiracy. You can only
> > learn the answer if you take some biology classes or have access to
> > Google.

You claim you have it and know it let us see it then.

[Glenn]

"I am not a chemist" <t2jud...@gmail.com> wrote in message news:af22c73b-3c05-481c...@oz6g2000pbb.googlegroups.com...

So now I am Chris?

[chris thompson]

On Feb 10, 7:11�pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "chris thompson" <chris.linthomp...@gmail.com> wrote in messagenews:093fa3e0-d595-4ee8...@hl5g2000vbb.googlegroups.com...

> http://en.wikipedia.org/wiki/Glucose-6-phosphate_dehydrogenase_defici...

>
> How'd I do for a 2 minute google search?

I doubt it took you 2 minutes to find that- you're pretty proficient,
unlike the non-chemist.

Chris

[Richard Norman]

There are proteins that act as structural entities in addition to
being catalysts. There are proteins that act as sensory transducers
in addition to being catalysts. There are proteins that act as
control agents in addition to being catalysts. There are proteins
involved in membrane transport in addition to being catalysts. There
are proteins that are produce cellular motility in addition to being
catalysts.

So I am still waiting. Tell is either something new or something that
might be wrong with our understanding of cellular biochemistry,
molecular biology, or physiology.

[Roger Shrubber]

For the record, you've said nothing of substance above
yet in doing so have said more than in the bulk of your
posts.

Further for the record, consider yourself on notice that
continuing with your current behavior of posting extended
screeds without discussion is spamming the newsgroup.
Your usage of two different posting IDs is also a violation
of newsgroup policy. Your stated need to use two IDs,
the limitation imposed by google, does not help your cause
when the overwhelming majority of your posts are spam.
To restate, if you didn't spam the group so much, you
would not need two IDs.

The moderator has been cc'd and I expect that you
will be blocked if you continue in your current behavior.

[Paul J Gans]

I am not a chemist <t2jud...@gmail.com> wrote:

What do you think goes on with "catalysing"?

[Paul J Gans]

Richard Norman <r_s_n...@comcast.net> wrote:
>On Sun, 10 Feb 2013 16:10:18 -0800 (PST), I am not a chemist
><t2jud...@gmail.com> wrote:

>>On Feb 9, 5:48?pm, Roger Shrubber <rog.shrub...@gmail.com> wrote:
>>
>>> In the end enzymes are NOT active catalysts. They are
>>> complex catalysts that involve more stages.
>>
>>Hint: they are not mere catalysts, more is going on than just
>>catalysing.

>There are proteins that act as structural entities in addition to
>being catalysts. There are proteins that act as sensory transducers
>in addition to being catalysts. There are proteins that act as
>control agents in addition to being catalysts. There are proteins
>involved in membrane transport in addition to being catalysts. There
>are proteins that are produce cellular motility in addition to being
>catalysts.

>So I am still waiting. Tell is either something new or something that
>might be wrong with our understanding of cellular biochemistry,
>molecular biology, or physiology.

Even in just plain old inorganic chemistry catalysis can be rather
complicated. For instance many reactions take place on surfaces
such as the glass surface of a beaker. The substrate is adsorbed
onto the glass surface where it can be held rigidly, or perhaps
dissociates (bond breaking), or allowed to move on the surface
so that it can interact with similar molecules, or perhaps some
other behavior entirely.

Everybody who has done any chemistry at all knows that the word
"catalysis" covers a multitude of sins that are often glossed
over because what is important is the final product and not
necessarily the mechanism by which it comes about.

[I am not a chemist]

On Feb 10, 4:38�pm, "Glenn" <glennshel...@invalid.invalid> wrote:
> "I am not a chemist" <t2judgm...@gmail.com> wrote in messagenews:af22c73b-3c05-481c...@oz6g2000pbb.googlegroups.com...

> So now I am Chris?- Hide quoted text -

No you are glenn.