brightsky's Chem Thread

[Mao]

Can't find a simple explanation, but I'm sure someone on AN will (I'd put my money on Mao )

You got it

When dealing with acid/base chemistry, don't think of H+ and OH- as species that have 'identity' with a particular molecule. They are constantly exchanged with the solvent (water) around them. For amino-acids solvated in water, it would gain a proton from water, and lose a proton to water. It would be very unlikely for there to be an "internal transfer".

The rate of exchange is so high that, for the not-very-acidic-at-all alkanol groups, the hydrogen only lasts a few milliseconds before being exchanged for another from the solvent. (this is a problem faced in NMR a fair bit, which is the reason why the chemical shift for the hydroxyl proton is all over the place)

The same can be said about more advanced reactions encountered in first/second year organic chemistry. Things such as hydride shifts do not usually involve an actual shift of hydride, but more often an exchange with the solvent.

[brightsky]

When dealing with acid/base chemistry, don't think of H+ and OH- as species that have 'identity' with a particular molecule. They are constantly exchanged with the solvent (water) around them. For amino-acids solvated in water, it would gain a proton from water, and lose a proton to water. It would be very unlikely for there to be an "internal transfer".

But what if the amino acid isn't dissolved in water, and exists in the solid state?

[Mao]

But what if the amino acid isn't dissolved in water, and exists in the solid state?

In the solid state, the crystal structure is such that the amine group is situated next to the carboxyl group, so as the crystal forms, the proton is exchanged between neighbouring molecules.

[brightsky]

This is more a bio question than a chem question, but what exactly do alleles refer to? The textbook defines an allele as an alternative form of a gene, but what does this mean exactly? As far as I know, a gene is a stretch of DNA, which codes for one protein. As such, it is nothing more than a sequence of nucleotides. What I want to know is: are alleles sequences of nucleotides as well? How, then, do alleles differ from genes? My guess is that when we talk of a gene, we talking about a section of DNA located at a very specific position. For example, when we talk about the gene for hair colour, we are talkling about the sequence of, say, 300 nucleotides at, say, position 5 along the DNA molecule on chromosome, say, 10 (I'm just making numbers up here). However, this sequence may differ from individual to individual. Bob's hair colour gene may begin with ATG...and end with ...TTC (a sequence which produces brown hair), while Sam's hair colour gene may begin with TGG...and end with...CCA (a sequence which produces black hair) (again making stuff up here). This variation, I'm presuming, is what the term allele refers to. Is this correct?

[Scooby]

This is more a bio question than a chem question, but what exactly do alleles refer to? The textbook defines an allele as an alternative form of a gene, but what does this mean exactly? As far as I know, a gene is a stretch of DNA, which codes for one protein. As such, it is nothing more than a sequence of nucleotides. What I want to know is: are alleles sequences of nucleotides as well? How, then, do alleles differ from genes? My guess is that when we talk of a gene, we talking about a section of DNA located at a very specific position. For example, when we talk about the gene for hair colour, we are talkling about the sequence of, say, 300 nucleotides at, say, position 5 along the DNA molecule on chromosome, say, 10 (I'm just making numbers up here). However, this sequence may differ from individual to individual. Bob's hair colour gene may begin with ATG...and end with ...TTC (a sequence which produces brown hair), while Sam's hair colour gene may begin with TGG...and end with...CCA (a sequence which produces black hair) (again making stuff up here). This variation, I'm presuming, is what the term allele refers to. Is this correct?

Humans contain two copies of most genes. Each of these copies is referred to individually as an allele. Therefore humans have two alleles for most genes.
A gene can have several different alleles  - what varies between each of the alleles is the base sequence that makes up the gene. An individual might have two of the same allele, in which case they're homozygous for that gene, or they could have two different alleles, in which case they're heterozygous for that gene. Most genes usually have only two different alleles

[brightsky]

Humans contain two copies of most genes. Each of these copies is referred to individually as an allele. Therefore humans have two alleles for most genes.
A gene can have several different alleles  - what varies between each of the alleles is the base sequence that makes up the gene. An individual might have two of the same allele, in which case they're homozygous for that gene, or they could have two different alleles, in which case they're heterozygous for that gene. Most genes usually have only two different alleles

That still makes little sense to me. A gene is a stretch of DNA, that is, a sequence of nucleotides. What exactly do you mean when you say 'humans contain two copies of the same gene'? Where are these stretches of DNA located? I appreciate that human chromosomes come in pairs, and that we inherit one set of chromosomes from each parent. I assume this is what you're talking about: that upon analysis of a random pair of chromosomes, one would inevitably find a stretch of DNA that is common to both? You mention that 'a gene can have several different alleles', yet you define an 'allele' as 'a copy of a gene', which confuses me because surely if an allele is a copy of a gene, and there are only two copies of each gene, then it follows that a gene can only ever have two alleles. Sorry if this sounds a bit stupid; I'm a newb at bio. :p

[SocialRhubarb]

A gene is a stretch of DNA which codes for one protein.

You have two chromosomes each with a copy of a gene, coding for the same protein. When we say the 'same protein', what we mean is not that the proteins produced are exactly identical, but that the two proteins both perform the same function.

An allele is one such version of a gene. In a diploid individual, that is, one with two copies of each chromosome, it is true that everyone can only have a maximum of two alleles of a gene. However, that may be two alleles out of six or seven, so it is possible for there to be more than one allele for a gene, although they may not all be present in a single person.

Different alleles do have different nucleotide sequences and hence produce slightly different proteins. But these are still quite similar and usually still perform the same function, and often result in genetic disorders when they don't perform the same function. But in general, two different alleles for a gene produce slightly different proteins, however both perform the same function. For example, genes for hair colour would have several different alleles corresponding to different colours, but all the genes still produce proteins which are pigments for hair, and as such perform the same function.

[brightsky]

Ah thanks, SocialRhubarb, that clears things up a bit!

I have another question, related to thermodynamics. Is chemical energy the same as internal energy. The textbook says that "the chemical energy of a substance is the sum of its potential energy and kinetic energy". I was always under the impression that this was the definition of internal energy. In fact, I've never really heard of the term 'chemical energy' being used in a technical way. Does 'chemical energy' have a formal definition?

Thanks!

[brightsky]

Why does an increase in the temperature result in a decrease in Ka value for an exothermic reaction? Or rather, how do you explain the effects of temperature on Ka value using common sense? Currently, I have to recourse to a whole bunch of fancy formulas, the derivations of which I do not yet understand. Can anyone provide an intuitive explanation of the phenomena outlined above?

And I'll seize this opportunity to bump the question above.

[scribble]

yeah, the internal energy is the sum or its potential energy and kinetic energy. i have no clue what chemical energy is. o.O i imagine its just a word used to describe energy that comes from chemical reactions. for example the combustion of gas, or digestion of food. as opposed to like, mechanical energy or something.

if you find le chatlier intuitive, he says that if you increase the temperature for an exothermic reaction, the system shifts to decrease the temp by favoring the back reaction which is endothermic. since the reactants in the new equlibrium are of a higher concentration, denominator is larger, K is smaller.
another explanation can be given with entropy, though since entropy isn't covered in VCE, i doubt it'd be very intuitive

[psyxwar]

The only way I can think of explaining it seems pretty circular in terms of the reasoning, but oh well, I'll post anyways:

We know that Le Chatellier's principle applies to temperature, but temperature isn't actually part of the equilibrium expression. Thus, the only way for the equilibrium position to shift is if the value of K itself shifts, which makes sense considering that K is temperature dependent. So an increase in temp for an exothermic reaction will mean that the equilibrium position shifts to the left and in order for this to happen the K value must have decreased.

It says in my notes that "it's been shown experimentally that logK = (-deltaH)/(2.302RT) + C, where C is a constant value", which does explain this but doesn't seem very intuitive of an explanation.

Edit: ninja'd

[scribble]

mhm, that definition involves ~*~*entropy*~*~ which is all sorts of fun (but not really at all).
if you really want to understand, pick up a book on physical chem or something. it's a bit too complex to just explain in a forum post.
otherwise, just stick with le chatlier until next year (if you want to continue to study chemistry). he's a cool guy.

[brightsky]

The only way I can think of explaining it seems pretty circular in terms of the reasoning, but oh well, I'll post anyways:

We know that Le Chatellier's principle applies to temperature, but temperature isn't actually part of the equilibrium expression. Thus, the only way for the equilibrium position to shift is if the value of K itself shifts, which makes sense considering that K is temperature dependent. So an increase in temp for an exothermic reaction will mean that the equilibrium position shifts to the left and in order for this to happen the K value must have decreased.

It says in my notes that "it's been shown experimentally that logK = (-deltaH)/(2.302RT) + C, where C is a constant value", which does explain this but doesn't seem very intuitive of an explanation.

Edit: ninja'd

yeah although le chatelier isn't really an explanation - merely a rule of thumb. similarly, 'like dissolves like' doesn't really explain why most polar substances dissolve in water; the 'principle' is just a rule of thumb. and yeah, my friend showed me a formula that bears strong resemblances to the one you provided in your post (btw, did you get that from a textbook, or a personal set of notes...i've been scavanging for books related to this sort of stuff). i tried to look up the derivation of the formula, and apparently people derived it by equating two different mathematical expressions for the standard gibbs free energy of the reaction.

scribble, can you briefly explain to me what exactly entropy is? gibbs free energy seems straightforward enough, but it's the entropy part of it which confuses me. it's well-known that entropy refers to the disorder of a system. but what exactly does 'disorder' mean? and how do you even quantitatively measure 'disorder'? my room is in complete disorder; does this mean that my room has high entropy?

thanks!

[zvezda]

Why does an increase in the temperature result in a decrease in Ka value for an exothermic reaction? Or rather, how do you explain the effects of temperature on Ka value using common sense? Currently, I have to recourse to a whole bunch of fancy formulas, the derivations of which I do not yet understand. Can anyone provide an intuitive explanation of the phenomena outlined above?

And I'll seize this opportunity to bump the question above.

I assume that, if you increase the temperature of the equilibrium mixture, the increased level of energy now in the environment will push the backwards reaction (endothermic) as its activation energy has been reached. Therefore, the forward reaction rate will start to increase (as there are more molecules if reactants that are now going to collide, meaning more frequent successful collisions) until it again equals the rate the backwards reaction, so in the end, there has been a net backwards reaction, thus increasing the concentration of reactants and decreasing the concentration of products. This in the end decreases the K value (im assuming this is basically the same as the Ka, just not dealing with acids, although this may have the potential to be of no help at all)

Ive wrote this whole thing then realised a potential flaw in the first sentence. Now I too am looking for an explanation lol. Ill leave what i wrote in case it does help in some way to reach a conclusion

[psyxwar]

yeah although le chatelier isn't really an explanation - merely a rule of thumb. similarly, 'like dissolves like' doesn't really explain why most polar substances dissolve in water; the 'principle' is just a rule of thumb. and yeah, my friend showed me a formula that bears strong resemblances to the one you provided in your post (btw, did you get that from a textbook, or a personal set of notes...i've been scavanging for books related to this sort of stuff). i tried to look up the derivation of the formula, and apparently people derived it by equating two different mathematical expressions for the standard gibbs free energy of the reaction.

Yeah I know. It was in the lecture notes I got from an olympiad training program

mhm, that definition involves ~*~*entropy*~*~ which is all sorts of fun (but not really at all).
if you really want to understand, pick up a book on physical chem or something. it's a bit too complex to just explain in a forum post.
otherwise, just stick with le chatlier until next year (if you want to continue to study chemistry). he's a cool guy.

lol so I read up a bit on entropy, and what I've gathered so far is that:

Entropy = measure of molecular disorder, by second law of thermodynamics it is always increasing (because it is more probably to be in a state of disorder than a state of order)

Change in entropy of universe = change in entropy of system + change of entropy in surroundings

For a reaction to be spontaneous, its change in entropy for the universe must be a positive value. Change in entropy caused by heat energy varies inversely with temperature; ie. something like 50J of energy will cause a greater change in entropy in the surroundings if it is at 200K than at 300K.

Therefore, change in entropy of surroundings can be modelled by (-deltaH)/T.

Therefore, an exothermic reaction will have an equilibrium position more to the right and a greater K value at lower temperatures because:
- change in entropy in surroundings is positive, as deltaH of system is negative
- inverse relationship with temperature means that a lower temperature, the change in entropy is greater
- greater entropy change of the surroundings = greater (positive) entropy change of universe (assuming it has reached a point where  magnitude of change in entropy of surroundings > magnitude of change in entropy of system)
- thus, the reaction would be "more" spontaneous (not sure if this is a legitimate way of phrasing...) and thus the equilibrium constant would be higher

Is that right?