🚀 go-pugleaf

On 16 Oct 2006 10:19:14 -0700, yubbers9@yahoo.com wrote:

>Hi all,
>
>I'm taking an introductory biology course, and I've been told
>that enzymes always have only one active site.
>
>I'm not sure about this however, because it seems to me
>that there must be some enzyme that has 2 or more,
>after all it's just a lumpy 3-dimensional tangle of protein,
>so why wouldn't there be more than 1 active site?
>For every shape on an enzyme there must be
>some chemical that fits in there, right?
>
>Can anyone please explain why an enzyme is only
>expected to have one active site?
>

It is not easy for evolution to figure out a way of making a chain of
specific amino acids in a specified sequence produce a complex
three-dimensional object that actually does something.  And then
evolution has to figure out how to make it do that thing very well,
indeed.  It really is asking too much to have it do two things at the
same time!

Ordinarily, enzymes catalyze one specific reaction (or category of
reactions) using one specific precursor (or category of precursors).
This bind at one specific active site to make things happen.  That
doesn't mean that the enzyme doesn't also have all sorts of other
binding sites where other things can bind and influence the reaction
that occurs at the "real" active site.  In fact it is quite common for
binding of ligands at a second site, or the phosphorylation of an
amino acid at a second site, to have very large consequences on the
function of the enzyme.  It is just that the enzyme really only
catalyzes one reaction.

Note:  just because a ligand happens to "fit into" and even "bind" to
a second site doesn't necessarily mean that anything will happen as a
result.  Hence it isn't really a site at all, just an accidental and
incidental binding.

> It is not easy for evolution to figure out a way of making a chain of
> specific amino acids in a specified sequence produce a complex
> three-dimensional object that actually does something.  And then
> evolution has to figure out how to make it do that thing very well,
> indeed.  It really is asking too much to have it do two things at the
> same time!

Ah, but what I'm getting at is that the behavior of complex molecules
is technically independent of evolution, so although organisms may
make use of a given active site, there may be others that either
are used, or not.

Anyway I googled for "multiple active sites" and enzyme, and
quite a few references appeared to enzymes that have them,
but I will have to look over the webpages to see if it's just
semantics or really multiple active sites.

For example:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.figgrp.594

yubbe...@yahoo.com wrote:
> > It is not easy for evolution to figure out a way of making a chain of
> > specific amino acids in a specified sequence produce a complex
> > three-dimensional object that actually does something.  And then
> > evolution has to figure out how to make it do that thing very well,
> > indeed.  It really is asking too much to have it do two things at the
> > same time!
>
> Ah, but what I'm getting at is that the behavior of complex molecules
> is technically independent of evolution, so although organisms may
> make use of a given active site, there may be others that either
> are used, or not.

Why is the behaviour of complex molecules independent of evolution?

Chris

>
> Anyway I googled for "multiple active sites" and enzyme, and
> quite a few references appeared to enzymes that have them,
> but I will have to look over the webpages to see if it's just
> semantics or really multiple active sites.
>
> For example:
> http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.figgrp.594

In article <1161019154.389534.46130@m73g2000cwd.googlegroups.com>,
 <yubbers9@yahoo.com> wrote:
>
>Can anyone please explain why an enzyme is only
>expected to have one active site?

Are you sure you understood the answer, or your insstructor understood the 
question?  

Check out leukotriene A4 hydrolase, among other counterexamples.

Ian 

-- 
    Ian York   (iayork@panix.com)  <http://www.panix.com/~iayork/>
    "-but as he was a York, I am rather inclined to suppose him a
     very respectable Man." -Jane Austen, The History of England

chris.linthompson@gmail.com wrote:

> Why is the behaviour of complex molecules independent of evolution?

Evolution is not a thinking mechanism that exerts
conscious control, but is a problem-solving mechanism.

Ian A. York wrote:

> Are you sure you understood the answer, or your insstructor understood the
> question?

I think she just didn't want the students to get confused.

> Check out leukotriene A4 hydrolase, among other counterexamples.

Fascinating.

Here's info for anyone who's curious:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8357975&dopt=Abstract

<yubbers9@yahoo.com> wrote in message 
news:1161028256.974864.264800@e3g2000cwe.googlegroups.com...
>
> chris.linthompson@gmail.com wrote:
>
>> Why is the behaviour of complex molecules independent of evolution?
>
> Evolution is not a thinking mechanism that exerts
> conscious control, but is a problem-solving mechanism.
>

Yes but is the behaviour of complex molecules independent of evolution ? Is 
it not that the structure and fucntion of complex biological molecules are 
actual products of evolution or do you have some other explaination ?

N10: )

yubbers9@yahoo.com wrote:
> chris.linthompson@gmail.com wrote:
>
> > Why is the behaviour of complex molecules independent of evolution?
>
> Evolution is not a thinking mechanism that exerts
> conscious control, but is a problem-solving mechanism.

Can you think of any problems that are solved with enzymes?

Chris

N10 wrote:

> Yes but is the behaviour of complex molecules independent of evolution ? Is
> it not that the structure and fucntion of complex biological molecules are
> actual products of evolution or do you have some other explaination ?

I think that if by random mutation a new protein arises,
and it serves as an enzyme and one of its active sites
benefits the organism, then it may be that any additional
active sites and associated functions that it also has may be
unused or underused under normal circumstances.
Evolution doesn't say "one enzyme, one function".
If an enzyme hypothetically has 3 active sites and functions,
and offers has great benefits but the other two are
mildly problematic, then the gene that codes for the enzyme
will be passed on.

On 16 Oct 2006 15:37:32 -0700, "chris.linthompson@gmail.com"
<chris.linthompson@gmail.com> wrote:

>
>yubbers9@yahoo.com wrote:
>> chris.linthompson@gmail.com wrote:
>>
>> > Why is the behaviour of complex molecules independent of evolution?
>>
>> Evolution is not a thinking mechanism that exerts
>> conscious control, but is a problem-solving mechanism.
>
>Can you think of any problems that are solved with enzymes?
>

Where in the world can I find some N-acetyl-5,0-methyl serotonin when
I need some?  Oh, I just realized that I have some
acetylserotonin-N-methyltransferase sitting around.  No problem!

chris.linthompson@gmail.com wrote:

> Can you think of any problems that are solved with enzymes?

Yes, but suppose a new gene mutation codes for a new enzyme has 3
active sites:

Site 1: useful effect that increases chances of gene being passed on
Site 2: unwanted effect that sligthly decreases chances of gene passing
on
Site 3: unused effect lacking some coenzyme

The balance of the 3 sites will be chances for the gene continuing
improve, even though Site 2 *creates* a problem rather
than solving one.

1) Catalytic sites in enzymes are determined by amino acid residues as
well as 3d structure
2) there is usually one catalytic site due to more efficient control
over them
3) multiple catalitic sites do exist with either identical or different
function.
4) Many enzymes have additional catalytic sites that are only unmasked
upon modification of AA residues (eg. Phsophorylation).

yubbers9@yahoo.com wrote:
> chris.linthompson@gmail.com wrote:
>
> > Can you think of any problems that are solved with enzymes?
>
> Yes, but suppose a new gene mutation codes for a new enzyme has 3
> active sites:
>
> Site 1: useful effect that increases chances of gene being passed on
> Site 2: unwanted effect that sligthly decreases chances of gene passing
> on
> Site 3: unused effect lacking some coenzyme
>
> The balance of the 3 sites will be chances for the gene continuing
> improve, even though Site 2 *creates* a problem rather
> than solving one.

Do you realize you've just made a case for complex molecules being
subject to natural selection, and thus, evolution?

Chris

chris.linthompson@gmail.com wrote:

> Do you realize you've just made a case for complex molecules being
> subject to natural selection, and thus, evolution?

The 3rd site wasn't being used so it wasn't
under any evolutionary pressure to improve.

student_A wrote:
> 1) Catalytic sites in enzymes are determined by amino acid residues as
> well as 3d structure
> 2) there is usually one catalytic site due to more efficient control
> over them
> 3) multiple catalitic sites do exist with either identical or different
> function.
> 4) Many enzymes have additional catalytic sites that are only unmasked
> upon modification of AA residues (eg. Phsophorylation).

Excellent, now that's useful info.

DK wrote:

> There are numerous enzymes that have more than one active site.
> Here is one interesting example:
> http://www.ncbi.nlm.nih.gov/entrez/query.
> fcgi?
> db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=11212301&query_hl=3&itool=p
> ubmed_DocSum

Wow, 3 active sites and an interior tunnel. Amazing.

yubbers9@yahoo.com wrote:
> chris.linthompson@gmail.com wrote:
>
> > Do you realize you've just made a case for complex molecules being
> > subject to natural selection, and thus, evolution?
>
> The 3rd site wasn't being used so it wasn't
> under any evolutionary pressure to improve.

It's bad form to snip out sections of the conversation, especially
without marking them.  It also makes the thread more difficult to
follow. Please leave the threads intact.

Here's your example:

*****
Site 1: useful effect that increases chances of gene being passed on
Site 2: unwanted effect that sligthly decreases chances of gene passing
on
Site 3: unused effect lacking some coenzyme

The balance of the 3 sites will be chances for the gene continuing
improve, even though Site 2 *creates* a problem rather
than solving one.
*****

So even if the third site is totally neutral, there's still selective
pressure on sites 1 and 2. Look up "balanced polymorphism". This isn't
exactly that situation, but it's close.

I  might also add that even if site 3 is totally nonfunctional, the
entire molecule would (might) be under some selective pressure- to at
least save some energy in production of the enzyme by dropping the
unused portion (if possible).

Chris

On Tue, 16 Oct 2006 yubbers9@yahoo.com wrote:

> student_A wrote:
>
>> 1) Catalytic sites in enzymes are determined by amino acid residues as
>> well as 3d structure
>> 2) there is usually one catalytic site due to more efficient control
>> over them
>> 3) multiple catalitic sites do exist with either identical or different
>> function.
>> 4) Many enzymes have additional catalytic sites that are only unmasked
>> upon modification of AA residues (eg. Phsophorylation).
>
> Excellent, now that's useful info.

Is it? Point 1 is true but trivial, 2 is teleological, 3, although 
misspelled, is quite true, and i'm not sure 4 is even that.

tom

-- 
Taking care of business

On Mon, 16 Oct 2006 yubbers9@yahoo.com wrote:

> I'm taking an introductory biology course, and I've been told that 
> enzymes always have only one active site.

You have been lied to.

> I'm not sure about this however, because it seems to me that there must 
> be some enzyme that has 2 or more, after all it's just a lumpy 
> 3-dimensional tangle of protein, so why wouldn't there be more than 1 
> active site?

You're quite right, as others have pointed out. On top of their examples, 
consider:

- the mammalian fatty acid synthase, a homodimer which catalyses no less 
than four reactions [1]

- the F1 ATPase, in which there are not only three active sites, but 
three active sites whose reaction cycles are rigidly interlinked [2]

- erythrocruorin; i don't know if you count haemoglobin as an enzyme (you 
certainly shouldn't, but never mind), but earthworms have a polymeric 
version with no less than 144 oxygen-binding sites [3]

> For every shape on an enzyme there must be some chemical that fits in 
> there, right?

An infinite number, in fact. That doesn't make it a catalyst!

> Can anyone please explain why an enzyme is only expected to have one 
> active site?

Because, having looked at more enzymes than you can shake a 
spectrophotometer at, biochemists have observed that most do only have one 
active site. And why is that? Good question; i'm not aware that there's a 
definitive answer, and not sure that there even could be one.

tom

[1] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16513973

[2] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15139813

[3] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=10860978

-- 
Taking care of business

There ARE bifunctionol enzymes that catalyse two different reactions.
yubbers9@yahoo.com 写道：

> Hi all,
>
> I'm taking an introductory biology course, and I've been told
> that enzymes always have only one active site.
>
> I'm not sure about this however, because it seems to me
> that there must be some enzyme that has 2 or more,
> after all it's just a lumpy 3-dimensional tangle of protein,
> so why wouldn't there be more than 1 active site?
> For every shape on an enzyme there must be
> some chemical that fits in there, right?
>
> Can anyone please explain why an enzyme is only
> expected to have one active site?
> 
> Thanks!

"Tom Anderson" <twic@urchin.earth.li> wrote in message 
news:Pine.LNX.4.62.0610171928500.24308@urchin.earth.li...
>
> - the mammalian fatty acid synthase, a homodimer which catalyses no less 
> than four reactions [1]

Just curious (this is an honest question), are these four reactions 
catalyzed by four different active sites?  I'm not a biochemist, but I 
understand it's not uncommon for a particular active site to catalyze 
multiple different reactions that have similar mechanistic requirements, 
particularly if the binding pocket isn't too tight/selective.


> Because, having looked at more enzymes than you can shake a 
> spectrophotometer at, biochemists have observed that most do only have one 
> active site. And why is that? Good question; i'm not aware that there's a 
> definitive answer, and not sure that there even could be one.

Again, not the opinion of a biochemist, but I suspect it's basically a 
probability/entropic argument.  I suspect that the chances of a new function 
arising in a pre-existing enzyme the has some other function without 
destroying that original function is less than the function arising in a new 
protein or than the new function arising in the original enzyme but at the 
same time destroying the original function of that enzyme.  Certainly 
there's a finite probability that a mutation that helps form the second 
active site in a pre-existing enzyme will destroy the function of the 
original active site by changing the tertiary structure in the wrong way. 
Intuition also tells me that it would be a low entropy configuration to have 
two active sites in a single enzyme, as compared to the same two active 
sites in two separate enzymes.  Maintaining this lower-entropy configuration 
costs the organism more free energy, and that's usually not in the best 
interests of the organism, evolutionarily speaking.

These are just the intuitions of a physical organic chemist with a 
smattering of understanding of biochemistry, but I do understand that 
evolution can behave in counter-intuitive ways.

Eric Lucas 

chris.linthompson@gmail.com wrote:
> yubbers9@yahoo.com wrote:
>> chris.linthompson@gmail.com wrote:
>>
>>> Why is the behaviour of complex molecules independent of evolution?
>> Evolution is not a thinking mechanism that exerts
>> conscious control, but is a problem-solving mechanism.
> 
> Can you think of any problems that are solved with enzymes?

Life solves the problem of maximizing the entropy increase
rate, while using part of the released energy for
preventing  the increase of its own entropy (e.g. decomposition).

Evolution is optimization towards solving this problem
therefor all parts of life (where enzyme are some of the
most critical once) are optimized accordingly.

Regards,
Yevgen

Please show more respect to the subject matter you are studying and
then seek answer to your question.Bipin desai
yubbers9@yahoo.com wrote:
> Hi all,
>
> I'm taking an introductory biology course, and I've been told
> that enzymes always have only one active site.
>
> I'm not sure about this however, because it seems to me
> that there must be some enzyme that has 2 or more,
> after all it's just a lumpy 3-dimensional tangle of protein,
> so why wouldn't there be more than 1 active site?
> For every shape on an enzyme there must be
> some chemical that fits in there, right?
>
> Can anyone please explain why an enzyme is only
> expected to have one active site?
> 
> Thanks!

yubbers9@yahoo.com wrote:
> Hi all,
> 
> I'm taking an introductory biology course, and I've been told
> that enzymes always have only one active site.
> 
> I'm not sure about this however, because it seems to me
> that there must be some enzyme that has 2 or more,
> after all it's just a lumpy 3-dimensional tangle of protein,
> so why wouldn't there be more than 1 active site?
> For every shape on an enzyme there must be
> some chemical that fits in there, right?
> 
> Can anyone please explain why an enzyme is only
> expected to have one active site?
> 
> Thanks!
> 

An enzyme is often made up of two or more protein, held 
together by zinc ions.  It is not uncommon to have two 
active sites for the same substrate compound, and the two 
sites can interact, so that what is happening at one site 
affects the other site.

bm wrote:
> Please show more respect to the subject matter you are studying and
> then seek answer to your question.Bipin desai

Are you on medication?

Is this you?
http://www.cs.concordia.ca/htbin/fac_page.cgi?Desai

yubbers9@yahoo.com wrote:

> I'm taking an introductory biology course, and I've been told
> that enzymes always have only one active site.

They have at least one, otherwise they could not work. However, there
may be more than one. 

First of all there are enzymes with more than one substrate, which have
sites for each of them. Of course, depending on definition, one could
claim that all substrate binding sites make up one active site. For
adenylate kinase (AMP + ATP <-> 2 ADP) there is a film available on the
net that shows how that works (don't recall the URL).

There are also enzymes with two different activities (Rubisco is a
famous example), which use partly different sites.

Also, there are enzymes which have duplicated sites, like the multiple
drug resistance transporter Mdr1 (Pgp, ABCB1p) for ATP. Usually such
duplication results in co-operativity (the iron transporter transferrin
is the only example I know with 2 binding sites and no co-operativity).
Mdr1 can transport various +/- hydrophobic substrates from the internal
leaflet of the plasma membrane to the extracellular fluid. It appears
that there are different, but overlapping, sites for different transport
substrates.

Follow up set to bionet.molbio.proteins

There are several examples of enzymes with multiple active sites. A
couple are pyruvate dehydrogenase and the polypeptide encoded for
phosphofructokinase and fructose 2,6 bisphosphatase I believe.

On Wed, 18 Oct 2006, Yom wrote:

> bm wrote:
>
>> yubbers9@yahoo.com wrote:
>>
>>> I'm taking an introductory biology course, and I've been told that 
>>> enzymes always have only one active site.
>>>
>>> I'm not sure about this however, because it seems to me that there 
>>> must be some enzyme that has 2 or more, after all it's just a lumpy 
>>> 3-dimensional tangle of protein, so why wouldn't there be more than 1 
>>> active site? For every shape on an enzyme there must be some chemical 
>>> that fits in there, right?
>>
>> Please show more respect to the subject matter you are studying and
>> then seek answer to your question.
>
> Are you on medication?

I reckon he's a structural biologist - describing an enzyme as "just a 
lumpy 3-dimensional tangle of protein" is basically guaranteed to get 
those guys in a furious rage.

tom

-- 
packaheomg sogma's

On Wed, 18 Oct 2006, Marvin wrote:

> yubbers9@yahoo.com wrote:
>
>> I'm taking an introductory biology course, and I've been told that 
>> enzymes always have only one active site.
>
> An enzyme is often made up of two or more protein, held together by zinc 
> ions.

Er, or by other things, principally the hydrophobic effect. Any particular 
reason why you mention zinc?

> It is not uncommon to have two active sites for the same substrate 
> compound, and the two sites can interact, so that what is happening at 
> one site affects the other site.

Very true - this is known as 'cooperativity', and is a key concept in 
enzymology.

tom

-- 
packaheomg sogma's

On Wed, 18 Oct 2006 lucasea@sbcglobal.net wrote:

> "Tom Anderson" <twic@urchin.earth.li> wrote in message
> news:Pine.LNX.4.62.0610171928500.24308@urchin.earth.li...
>
>> - the mammalian fatty acid synthase, a homodimer which catalyses no less
>> than four reactions [1]
>
> Just curious (this is an honest question), are these four reactions
> catalyzed by four different active sites?

Yep - as Bob mentioned, they are (and it's six, not four - sorry!). See 
here:

http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fasynthesis.htm#fasyn
http://www.ethlife.ethz.ch/e/articles/sciencelife/banFAShumfung.html

>> Because, having looked at more enzymes than you can shake a 
>> spectrophotometer at, biochemists have observed that most do only have 
>> one active site. And why is that? Good question; i'm not aware that 
>> there's a definitive answer, and not sure that there even could be one.
>
> Again, not the opinion of a biochemist, but I suspect it's basically a 
> probability/entropic argument.  I suspect that the chances of a new 
> function arising in a pre-existing enzyme the has some other function 
> without destroying that original function is less than the function 
> arising in a new protein

A what?

> or than the new function arising in the original enzyme but at the same 
> time destroying the original function of that enzyme.

I'd certainly agree with that - provided that the new activity is pretty 
similar to the old one. If it's wildly different, then i don't see how the 
old active site would be any more likely to lead to the new one than some 
other random cleft on the molecule.

Not that i have a better explanation. There must be work on the evolution 
of new active sites, though - time to hit pubmed ...

> Intuition also tells me that it would be a low entropy configuration to 
> have two active sites in a single enzyme, as compared to the same two 
> active sites in two separate enzymes.  Maintaining this lower-entropy 
> configuration costs the organism more free energy, and that's usually 
> not in the best interests of the organism, evolutionarily speaking.

Hmm. In terms of literal free energy, i don't think that works - it's not 
as if the parts of an enzyme other than its active site are random! 
There's still a specific sequence and fold, it's just not catalytically 
active. Modulo the costs of the actual amino acids involved, making an 
active site and a chunk of inert protein cost the same amount of energy 
(not that i'm saying the rest of the enzyme is inert - the bit that's not 
the active site is where crucial regulatory and structural interactions 
happen).

If you're talking in a slightly more metaphorical sense, about the 
constraints having two active sites would impose on the configuration 
space explored by evolution, then yes, that's an interesting idea. Loading 
more function into a protein means it's more vulnerable to mutations, and 
so less robust over the generations.

My theory is, as student_A suggested, and i rather rudely dismissed, that 
it allows finer control over activities - with each activity on a separate 
protein, the cell can control the level of each individually, making just 
as much as it needs. Where this falls down is where you have enzymes which 
are needed with fixed stoichiometry, such as where they form a pathway 
with no branches. But then this is exactly the sort of situation where we 
*do* see multi-activity enzymes, like fatty acid synthase.

So, er, yes, i don't know.

tom

-- 
packaheomg sogma's