The Periodic Table - 2016-10-01 (page 1 of 2)

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1:33 AM

!!img/1,3,5-tribromo-2,4,6-trichloro-1,3,5,2,4,6-triazatriborinane

No result found.

user image

How would people synthesize this?

5 hours later…

6:27 AM

@Shadock one can make the trichloro borazine quite easily, but I am not sure how one can install the N-Br bonds. It's probably possible, I suppose.

1 hour later…

7:43 AM

Endoproteinase Lys-C

Endoproteinase Lys-C is a protease that cleaves proteins on the C-terminal side of lysine residues. This enzyme is naturally found in the bacterium Lysobacter enzymogenes and is commonly used in protein sequencing. Lys-C activity is optimal in the pH range 7.0 - 9.0. == See also == Trypsin == References... ==

Does it have other names? Can I write "Lys-C protease"?

Should "Endoproteinase" always stand in front?

Maybe you should ask on Bio chat

They'd know better than everyone how the conventions of treating enzyme names are.

okay!

It's "lysine protease" in Russian

Lysyl endopeptidase

Lysyl endopeptidase (EC 3.4.21.50, Achromobacter proteinase I, Achromobacter lyticus alkaline proteinase I, protease I, achromopeptidase, lysyl bond specific proteinase) is an enzyme. This enzyme catalyses the following chemical reaction Preferential cleavage: Lys-, including -Lys-Pro- This enzyme is isolated from Achromobacter lyticus. == References == == External links == Lysyl endopeptidase at the US National Library of Medicine Medical Subject Headings (MeSH)...

Are they the same thing?

In my context, this "protease" is used for peptide mapping.

I mean, it's used to digest the protein into small peptides

@CowperKettle By my minuscule knowledge in Biochem, whatever comes before -ase is what's being catalyzed and stuff. So peptidase is for peptides, but protease is for proteins. I guess it differs in some places.

You can only be sure if you know what the two do, exactly.

But usually the same enzymes don't have different names.

Even in different languages.

Why is it "endo" peptidase?

I know for sure that Russian "glutamate protease" is English "glutamyl endopeptidase"

There is some difference in naming

@CowperKettle This might be because the Russian version uses an older accepted name

7:53 AM

Because in my document there was a product code after "glutamate protease". I checked with the producer's website, and voila! "glutamyl endopeptidase"

@CowperKettle 'cause it's inside something? Dunno

@Rubisco Inside the overall protein, maybe

I asked on a translator forum, but I never can trust them. They sometimes give answers that come God knows whence.

BBL

@CowperKettle Teehee

2 hours later…

10:14 AM

@orthocresol then how would one compare them?

p- vs m-diiminocyclohexane

10:42 AM

Mew @Wild

@DHMO What about these two?

Also I think it's diamino-, not diimino.

I can't imagine what diiminocyclohexane looks like.

!!img/cyclohexane-1,2-diimine

user image

Oh, like that

@Cowper, endo means that it can cleave peptide bonds within the chain itself.

For example, if you have a polypeptide ABCDEFGHIJ, then an endopeptidase could cut between D and E (for example. Where exactly it cuts will depend on the specificity of the enzyme and its active site).

Whereas an exopeptidase would snip off one amino acid at a time from the ends. So for example it might cut A-B, then B-C...

@Rubisco =^.^=

Meow, you all! :)

10:50 AM

How is you @Wild?

As for the name, I would just go with whatever Wikipedia says. Just do a quick google search to make sure that it is used elsewhere as well.

@Rubisco fine :) you?

@Wildcat couldn't be better

@orthocresol Thank you, Ortho!

1

Q: What is the difference between Endoproteinase Lys-C and Lysyl endopeptidase?

What is the difference between Endoproteinase Lys-C and Lysyl endopeptidase? In the text I'm translating about peptide mapping, "lysine protease" is mentioned (in Russian: лизиновая протеаза). This might be erroneous to translate word for word as "lysine protease". There must be a slight error ...

terminology biotechnology

Dobry den, @Wildcat!

@CowperKettle dobry! :D

11:14 AM

@Rubisco their stability

1 hour later…

12:27 PM

You could always copy mine. — jonsca ♦ 10 hours ago

XD

1:17 PM

No good questions :(

Time to make one myself, then

1 hour later…

2:18 PM

@orthocresol I will be looking forward

Will you also answer your question?

2:31 PM

dunno

@orthocresol Can you ping me when you post the question?

2:43 PM

Hello :D

@Biker !!greet/Biker

Welcome to The Periodic Table Biker! Here are our chat guidelines and it's recommended that you read them. If you want to turn Mathjax on, follow the instructions in this answer. Happy chatting!

Can we ask quick questions here :D?

@Biker yes (I always do that)

Okay so when you put a zn electrode in water

Zn dissolves right?

Why does it dissolve?

So for example if you put it in a distilled water

I would assume it wont dissolve

2:46 PM

> Zinc virtually has no reaction with cold water. Zinc reacts with steam to give zinc oxide and hydrogen gas.

I just mean this simple reaction Zn -) zn+2 + 2e

It must be getting the energy from somewhere right?

because you have another electrode in the water?

Just a half cell

Because a webpage

a half cell does not work alone

explained that if you place Cu or Zn in water it somehows builds a negative charge on the electrode and zn+2 or Cu+2 dissolves in water

and when you connect the two together

Because one losses electrons more readily you will find a voltage

?

2:50 PM

1

A: Is there a better equation than the Nernst equation for low concentrations?

The Nernst equation does not need a replacement for low concentrations. Yes the limit is $\infty$, which essentially means you can't realistically have zero concentration of anything. We may think of absolutely pure water as an idealized situation. Well, as soon as it gets in touch with copper, s...

Maybe this would be helpful

the energy comes from bonding with water? I'm not sure

"Well, as soon as it gets in touch with copper, some Cu2+CuX2+ ions instantly jump into the solution, and from that point on"

Doesn't it imply that it happens on it is owns?

Yes?

@Biker Is there any problem?

Idk this question has been bothering me for a while

ionic solutes bond with water to lower their energy

NaCl (aq) -> Na+ + Cl- is an extremely simplified equation

user image

user image

So this applies to metal too? Energy is released rather than gained?

?

Every time I ask this question on a forum, they simple reply "You seem to have a lack of understanding of chemistry."
and I am like ._., No one actually explained why this occurs

3:00 PM

@Biker I don't know if the reaction is exothermic or endothermic

@Biker You seem to have a lack of understanding of chemistry.

I am just kidding

:c

I mean I get full marks every year ;-;

Okay so another quick question c:?

@Biker yes

are you satisfied with my answer?

I am satisfied with the ionic substance because we studied that in the previous year and how it is an exothermic reaction

@Biker which reaction is exothermic?

You mean you learnt that Cu -> Cu^2+ + 2e- is exothermic?

@Biker what is your second question?

No no nvm, Nacl is endothermic

Just this"the energy comes from bonding with water? I'm not sure"

"Always endothermic (takes energy to strip the e' from the atom) Na(g) -> Na+(g) + 1e- DH = 496 kJ/mol."

3:07 PM

Ionization itself is endothermic

but if the ion can bond with the water

then it can become exothermic

Yea for example, It takes an amount of energy to seprate NaCl then to bond with water it released energy. So if the bonding of water releases more energy that taken to separate NaCl then it becomes exothermic and vice versa

So the same happens with metals

yes

although I am not sure if it is exothermic for copper

Does being exothermic or endothermic implies spontaneity?

no

that is determined by Gibb's free energy

Entropy: Embrace the Chaos! Crash Course Chemistry #20

(Crashcourse!!)

Yea it is in our book but in the next chapter XD

3:11 PM

start from approx 05:00 @Biker

if you want to save time

All righty

Just saying I really appreciate you helping me :D

you are welcome

@Biker I always ask quick questions and I often don't get answered

(sometimes I do)

so I understand how you feel

What is "carbamidation", I wonder

Can "carbamidation" be a modification in mass-spectrometry

Awesome

I will be back later for my question have to go somewhere :c

Cya DHMO

3:34 PM

@Rubisco - what is "carbamidation"?

Is it a good question for the main site?

@CowperKettle What is the context?

@CowperKettle If a carbamide is added to the compound.

@orthocresol Modification of studied protein during or prior to MS/MS

That's how almost all of the -ations work.

@CowperKettle ionsource.com/Card/carbam/carbam.htm

3:35 PM

Why would you add carbamide (urea) to a prototype antibody?

A simple reason I could think of, is that both lysine and glutamic acid have the same mass.

By modifying lysine, you can distinguish it via MS.

carbamidation is done to lysine usually?

Yeah, because it's the only one with a free -NH2 in the side chain.

Glutamine, I mean.

But if you have HRMS, this shouldn't really be a problem, glutamine is 128.2 and lysine 128.1.

ah, glutamine. But it will be called "carbamidation@C13" or something?

@orthocresol But it says carbamylation

Urea solution is one of the most commonly employed protein denaturants for protease digestion in proteomic studies. However, it has long been recognized that urea solution can cause carbamylation at the N-termini of proteins/peptides and at the side chain amino groups of lysine and arginine residues.

Protein/peptide carbamylation blocks protease digestion and affects protein identification and quantification in mass spectrometry analysis by blocking peptide amino groups from isotopic/isobaric labeling and changing peptide charge states, retention times and masses.

3:39 PM

Is "carbamylation" synonymous with "carbamidation"?

I think so, it seems to be the more common phrase.

researchgate.net/publication/…

Ignore what I said, I think this is more relevant.

@orthocresol This is interesting!

I should ignore it?

Ya

It was just a guess on my part.

Multitran translates "carbamylation" and "carbamidation" differently.

There's no mention of synonymicity.

If they are synonymous, I'll use the one that is used more often

My authors write that they performed in-gel digestion of the protein, then used MS/MS, then used the NCBI protein database to "piece it together" (my guess)

Carbamide refers to urea, H2NC(O)NH2.

A carbamate is any derivative of urea, i.e. the hydrogens replaced with alkyl/aryl groups.

3:43 PM

They set up "C carbamido-amidation" as "default post-translational modification" in their search. I struggle to understand the meaning of this.

In this case, the process converts lysine into a carbamate.

@Loong you there?

ah, hydrogen from the -NH2 end gets replaced with the whole urea group

Mmhmm, which is why I think they are synonymous, and why carbamylation is the more common term.

@orthocresol lysine and several other things, yes? The key feature is that the -NH2 sticks out?

3:45 PM

I am not sure what else this can happen to.

Maybe I should ask whether they are synonymous on main site

So not there. @Ortho could you do me a favor?

Yes?

@orthocresol arginine?

> he N-termini of proteins/peptides and at the side chain amino groups of lysine and arginine residues.

4

A: Let's not close questions as homework except for blatantly obvious cases (at least for a while)

Pre-experiment stats Questions 16,753 questions 8,376 without accepted answers 3,460 with no answers 2,830 with no answers and not closed $\frac{13,923}{16,753} = 83.107\%$ Answers 19,299 answers Closure 1,641 questions closed 1,124 closed as not a duplicate 517 duplicates homework ...

3:46 PM

Arginine isn't exactly a NH2 - it is a bit special. I don't doubt that it could happen, though.

We need 10k stats stats stats

It is a guanidyl group.

I don't know whether it could happen but if you have a source that says it does, then go with it :D

I wonder why my authors wrote "карбамидоамидирование C" (carbamido-amidation C). What they meant by "C"..

I like biochem a lot, but I know very little about it. So don't trust me too much.

@orthocresol Haha, I only learned about this process 10 minutes ago. (0:

3:47 PM

@Rubisco I see. What stats do you need?

@orthocresol Just ones Loong has written there, the post-experiment version.

Ok, I'll get back to you soon

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Asked: 2326
Closed: 772 (33.19%)

Edit them in.

3:53 PM

Closed as HW: 338 (43.78%)

Bit busy rn

I can do it later, if you want.

I'm fine with later

Ok, sure.

I kinda have something to deal with myself.

4:14 PM

@Rubisco, what's your conclusion then? Looking at the numbers I see no difference pre- and post-.

What did you expect by the way?

@Wildcat I don't see a drastic change either. Some people worried that we'd have a spike in unanswered questions. We haven't had.

@Wildcat We just wanted to see how things go. I'm gonna write a new meta post asking if we should continue being this way or go back to smiting everything that smells.

@Wildcat See how peaceful and rigorously objective meta has become.

No complaints. No rants. No hard feelings. No ragequits.

You want my controversial opinion?

Sure

I think the rose bengal question that triggered this whole thing should still have been closed.

At this stage I'm not sure what counts as controversial.

@orthocresol we might find a reason to close it in the future. And it didn't really spark it, it just helped it happen.

4:18 PM

I definitely missed something...

What's your overall rating of the experiment?

@Wildcat Why?

Was there a drama with the question being closed?

@Rubisco I have no idea what "the rose bengal question" is.

@Wildcat Nah, Marko came to meta and complained that a lot of questions are being closed.

5

Q: The policy of excessively closing questions

Nowadays I find more and more of my questions being closed and I don't understand why. I've got the impression that acquiring knowledge isn't the priority here anymore, but rather following some established policies and forms. I think that the homework question policies should be changed. I guess...

discussion homework

5

Q: Generation of singlet oxygen by irradiation

What is the mechanism involved in the generation of singlet oxygen when ground state triplet oxygen is irradiated in the presence of rose bengal?

physical-chemistry photochemistry

I gave him the benefit of the doubt, since he was right at that time.

We did close a lot of things we weren't exactly sure were homework.

We just smited them because of lack of effort.

@orthocresol Consider this though. This turned out to be a fairly well-received question. Is that not what the site is for?

4:21 PM

Aha!

Interesting... I missed that drama.

We should be avoiding circumstances that lead to bad UX and advocate and improve ones that lead to good UX.

@Wildcat It wasn't drama, really.

@Rubisco because I missed it! :D

If everyone goes home happy, closure would mean nothing but . . . being consistent.

And we close things for a bigger reason than just consistency.

It is very hard (if possible at all) to achieve consistency wrt homework questions.

In my opinion all this boils down to two things.

@Wildcat Nah, we just need a bright and fresh mind to think of some guidelines or rules that covers anything that's necessary.

4:25 PM

1) What do want this site to be? Primarily Q&A for specific problems or primarily database of all the chemical knowledge?

Someone to get to the bottom, or the top, of philosophy of closure.

@Wildcat You can't get people to agree on an answer to this.

And sometimes, agreeing to something means sacrificing something you don't wanna give up.

It would have been a well-received question, if from the beginning, he had included more information.

2) SE privileges system is completely broken. Everyone could vote to close a question on every topic. On SO this already lead to a disaster.

If a 1-rep user had done the same thing, it would have been closed without any second thoughts.

@Wildcat Well, we're not that big a site to contain sub-communities in moderation.

@orthocresol This one yeah. That's kinda a red-carpet treatment.

4:28 PM

There is a hw policy for a reason. If we want to change it, that is fine, but we have to decide when we allow these kind of questions thru.

I think we need to rephrase the homework closure completely.

Not enough research effort.

Is it when the asker has a good history on SE? Is it when the question is "high-level" enough?

@orthocresol He, and when we get out of the context of SE, some other people, consider extra info on a clear question with a clear answer as clutter.

Is it homework (in any sense) or not is completely irrelevant.

That is true.

4:29 PM

What matters is did OP try to solve it or not.

Then should we require effort in all of our questions?

@Rubisco yes

Well, good luck getting people to agree with you on that.

Since they won't.

And it's a bit too much.

And it again depend on what do we want this site to be...

pentavalentcarbon

@Rubisco You can't have your cake and eat it too.

The cat is correct.

4:33 PM

@pentavalentcarbon I just want us to avoid going the way that I can predict the outcome of.

I don't want meta to lose focus.

@pentavalentcarbon hi CH5!

pentavalentcarbon

@DHMO o/

or should i call you methanium

@Wildcat I know what I want this site to be. I don't want it to be a homework ghetto. I don't want it to be a clique of only the most elite either. I want those two to coexist without hurting one another.

@Rubisco that is impossible.

Either, or.

4:35 PM

No it's not. Proof chemistry.stackexchange.com/questions

pentavalentcarbon

Part of the problem is that the cognoscenti seem too unwilling to take a definite stance. Waffling hurts both groups.

@Rubisco we're simply not there yet.

@pentavalentcarbon It's the middle ground, not a vague stance.

But we reached the bifurcation point!

pentavalentcarbon

Without a better definition the middle ground is a vague stance.

4:37 PM

@Wildcat Not where? If you mean the content that hasn't yet been produced, then go ahead and produce it.

And that is why homework dramas constantly popping up.

@pentavalentcarbon Look dude. Some people lie on the heavy moderation part. Some people lie on the let-it-go-as-long-as-long-as-it-doesn't-hurt part. I'm in the middle. I used to be extreme, but I'm in the middle.

@Wildcat Are they now? They've been silenced for the past month as far as I'm aware.

@Rubisco We didn't yet develop the homework policy.

I'm all up for finding new reasons to close threads that don't result in useful knowledge for future visitors.

@Wildcat We always have something to do. It never ends. That's what developing means.

What I'm not up for, is coming up with a spurious reason such as lack of effort, and thinking that enforcing it will solve all teh thingz.

pentavalentcarbon

@Rubisco Well then, that should be part of the definition. "Does this question or one of its answers result in useful knowledge for future visitors?"

That means effort on someone's part.

4:41 PM

@Rubisco we have 0 development for our homework policy for years now. It is what it is and nobody knows what it is.

@pentavalentcarbon It has always been, and that's the site's mission.

pentavalentcarbon

@Rubisco And yet that doesn't seem to have been transferred to the homework policy.

We're not a site for graduate chem students by definition, and we're not a high school kindergarten either. We're for all chem knowledge.

@pentavalentcarbon That was adapted from Physics, and they themselves just . . . came up with it. What did I say? Spurious reason is spurious.

You need to take into account what the asker has to muster to be able to ask something with the minimum standards.

@Rubisco "for all chem knowledge" is incredibly vague. Could you be more specific?

pentavalentcarbon

@Rubisco I don't understand what any of that means.

4:43 PM

A question with demonstrated effort is a good question, not the minimum IMO.

I get it! It's "Carbamylation (C)". The letter C stands for "carbamylation".

@CowperKettle That non sequitur

I'm a tubelight.

I was thinking of my text, sorry. (0:

pentavalentcarbon

@Rubisco I feel like this reads into people's "labels" a bit too much.

@Wildcat We're not categorizing what we accept or we don't accept. We don't say that if a high school textbook may contain an answer to your question, hidden in some page, you can't ask it here. That's not what we say in the site definition.

4:45 PM

I don't like the high school questions at all, they tend to attract equally lousy answers.

@Rubisco any proof? Where exactly it is said?

But I don't think I have ever VTCed something just because it is too easy

@pentavalentcarbon I mean they just felt the need to come up with something to counter the ~~enemy~~ homework waves. That was what they came up with.

@Wildcat chemistry.stackexchange.com/tour

What I think we need is a too localised close reason again.

This is a site for literally everyone that likes to ask something in chem.

@orthocresol I keep reaching that conclusion nine times a day.

4:46 PM

But I am going off-track, aren't i? ^^

That is not about homework, although I feel like a lot of homework is really too localised.

Oh well...

@Rubisco nothing there

Let me get round to adding the 10k stats!

> Chemistry is a question and answer site for scientists, academics, teachers and students of chemistry.

Aw man, I miss @Mart

Don't get me wrong, @Wild. I'm not saying the HW policy contradicts the site mission.

But I'm saying that thinking about making policies for different courses (university, high school etc.) will become contradictory.

pentavalentcarbon

That wasn't a suggestion.

What wasn't a suggestion?

pentavalentcarbon

4:51 PM

The different policies for different education levels.

It was mentioned.

Shrug

pentavalentcarbon

Why? That isn't very fair to anyone.

The different policies thing?

pentavalentcarbon

Yes.

Back to the main issue at hand, I still think asking for research is a bit too much.

That, or either you have to lower the bar of what constitutes research to something . . . just not useful.

You have to take askers into account. The minimum acceptable question shouldn't be a bar that high.

And then new, interesting questions will pop up, without demonstrated effort but with potentially good answers.

So you either close them and lose some good discussions, or you leave them open and that's unfair to the other questions AND a bit subjective. (What is a good discussion? Where to draw the line?)

And then we have to go through all this again.

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The Periodic Table

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