Unit 3 Questions MEGATHREAD :)

[davidle_10]

Strong acid/base refers to the ability to accept or donate protons. While concentrated refers to having more amount of mol in a solution.

[Andiio]

When referring to the phosphate group in a section of a DNA molecule, is writing phosphate GROUP acceptable? Or will we be marked wrong if we don't write it? Do we have to write phosphate ION?

[davidle_10]

I would think both phosphate or phosphate group would be acceptable, but i don't think you can call it as a phosphate ion

[Andiio]

I would think both phosphate or phosphate group would be acceptable, but i don't think you can call it as a phosphate ion

Haha I wrote phosphate group, according to NEAP it's a phosphate ion.

[davidle_10]

First time I've heard of a phosphate ion. but either way you should still be correct saying that it is a phosphate group.

[Mao]

Since zwitterions are said to have a neutral charge, and if Z/side chain groups are affected, what would you draw if you had to draw say, the aspartic acid zwitterion in a pH of 7?

Obviously the normal NH2 and COOH groups would become protonated/de-protonated, but if you deprotonated the COOH in the Z-group, wouldn't the aspartic acid 'zwitterion' retain a negative charge? :\

That depends on the isoelectric point, which you are not required to know.

However, they could word it like "draw aspartic acid at pH=12", in which case the environment is too basic, and all groups deprotonate (net -2 charge).

[In reality, the side group of aspartic acid deprotonates at pH>2.77]

So wait, in acidic/basic conditions the Z group is affected, yet as a zwitterion it isn't?

aah chemistry is just getting worse by the minute

Not sure what you mean. the zwitterion is also affected by the acid/base conditions. I do need to make a correction though, the side group of aspartic acid ionizes at pH>4 (roughly).

Here is a more detailed explanation:

We must consider the amino acid to be in some kind of equilibrium with its surroundings (unit 4 VCE + first year university). However, there are a few things we can know without learning all of that:

-Typically, acids and bases ionize over a pH range of 2. Acids and bases all have an 'acidic constant' Ka (unit 4 VCE), which corresponds to some pKa value. This can be considered to be the 'activation' point of the acid.
--When pH=pKa, the concentration of acid and its conjugate are equal.
--When pH=pKa-1 (i.e. environment is more acidic than the activation of the acid), the protonated form is 10x the concentration of the deprotonated form.
--When pH=pKa+1, the deprotonated form is 10x more concentrated than the protonated form. This transition is smooth.

-Consider the 2-amino acid group.
--The acid group typically have a pKa of ~2. Thus at pH of 3 or greater, it is always deprotonated. (at pH of 2 or slightly below it, a mixture of both deprotonated and protonated form exist)
--The amine group typically have a pKa of ~10. Thus at pH of 9 or less, it is always protonated.
--Combining the above, the zwitterion is dominant in the pH range of 3 to 9.

Consider aspartic acid, with a side group pKa of 3.6

pH=1: NH3+, COOH, Z-group COOH
pH=3: NH3+, COO-, Z-group COOH
pH=5: NH3+, COO-, Z-group COO-
pH=11: NH2, COO-, Z-group COO-

[Lols123]

20mL of a 0.0030M solution of a weak monobasic base is mixed with exactly 20.0 mL of a 0.0030M solution of a strong monoprotic acid.
What colour would the resulting mixture be in the presence of phenol red and thymol blue?
I dont get why it would be yellow for thymol blue :S wouldnt the resulting solution be slightly acidic, turning it red?

[thatricksta]

I would think both phosphate or phosphate group would be acceptable, but i don't think you can call it as a phosphate ion

Haha I wrote phosphate group, according to NEAP it's a phosphate ion.

I wrote phosphate group on that exam, I wouldn't be stressed over that. I would be more concerned about naming the phosodiester xD

[luken93]

Ok, so for the sake of Unit 3 VCE Chemistry.

If an amino acid had the NH2 and COOH group off the 2-C, as well as an NH2 in the Z chain

At pH 2, NH3+, COOH, NH3+
At pH 7, NH3+, COO-, NH3+
At pH 12, NH2, COO-, NH2

And vice versa if it had a COOH group rather than an NH2

That's all I want to know

[thushan]

You mean NH2 COO- NH2 for pH 12 in general luken.

Put it this way; in low pH there is a lot of H3O+ flying around, and H3O+ loves shoving protons into other things. So the NH2 and the COO- would have protons shoved in to form NH3+ and COOH.

In high pH there is a lot of OH- flying around, and OH- loves ripping protons off other things. So the amino group would have its extra proton taken to form -NH2 (from -NH3+) and carboxyl would have its proton ripped off to form COO- (from COOH).

[luken93]

You mean NH2 COO- NH2 for pH 12 in general luken.

Put it this way; in low pH there is a lot of H3O+ flying around, and H3O+ loves shoving protons into other things. So the NH2 and the COO- would have protons shoved in to form NH3+ and COOH.

In high pH there is a lot of OH- flying around, and OH- loves ripping protons off other things. So the amino group would have its extra proton taken to form -NH2 (from -NH3+) and carboxyl would have its proton ripped off to form COO- (from COOH).

Haha I really should proof read my stuff

How're you feeling about today?

[thushan]

I think I should be okay, but I feel queasy...

[nacho]

Since zwitterions are said to have a neutral charge, and if Z/side chain groups are affected, what would you draw if you had to draw say, the aspartic acid zwitterion in a pH of 7?

Obviously the normal NH2 and COOH groups would become protonated/de-protonated, but if you deprotonated the COOH in the Z-group, wouldn't the aspartic acid 'zwitterion' retain a negative charge? :\

That depends on the isoelectric point, which you are not required to know.

However, they could word it like "draw aspartic acid at pH=12", in which case the environment is too basic, and all groups deprotonate (net -2 charge).

[In reality, the side group of aspartic acid deprotonates at pH>2.77]

So wait, in acidic/basic conditions the Z group is affected, yet as a zwitterion it isn't?

aah chemistry is just getting worse by the minute

Not sure what you mean. the zwitterion is also affected by the acid/base conditions. I do need to make a correction though, the side group of aspartic acid ionizes at pH>4 (roughly).

Here is a more detailed explanation:

We must consider the amino acid to be in some kind of equilibrium with its surroundings (unit 4 VCE + first year university). However, there are a few things we can know without learning all of that:

-Typically, acids and bases ionize over a pH range of 2. Acids and bases all have an 'acidic constant' Ka (unit 4 VCE), which corresponds to some pKa value. This can be considered to be the 'activation' point of the acid.
--When pH=pKa, the concentration of acid and its conjugate are equal.
--When pH=pKa-1 (i.e. environment is more acidic than the activation of the acid), the protonated form is 10x the concentration of the deprotonated form.
--When pH=pKa+1, the deprotonated form is 10x more concentrated than the protonated form. This transition is smooth.

-Consider the 2-amino acid group.
--The acid group typically have a pKa of ~2. Thus at pH of 3 or greater, it is always deprotonated. (at pH of 2 or slightly below it, a mixture of both deprotonated and protonated form exist)
--The amine group typically have a pKa of ~10. Thus at pH of 9 or less, it is always protonated.
--Combining the above, the zwitterion is dominant in the pH range of 3 to 9.

Consider aspartic acid, with a side group pKa of 3.6

pH=1: NH3+, COOH, Z-group COOH
pH=3: NH3+, COO-, Z-group COOH
pH=5: NH3+, COO-, Z-group COO-
pH=11: NH2, COO-, Z-group COO-

Wait, at a pH of 3, why would the COOH group in the main chain donate it's proton? Shouldn't it just be the NH2 accepting protons to form NH3+?

Here's what i think, please correct where incorrect:

in very acid conditions (x< 3 ) the side group, which happens to have NH2 will be effected and receive a proton
in very basic conditions, (x>9) the side group, which happens to have a COOH will be effected and donate its proton

at zwitterion, the sidegroups are not effected?
If the side group contains 1 NH2 and 1 COOH group, will the zwitterion affect the side groups? as if it does, a neutral charge is still maintained in the molecule..

Is that correct, or?

Unnecessarily complicated things, lol


FURTHERMORE
a monoprotic acid will react with a base in a 1:1 ratio, correct?

TSSM 2008 seems to say that for 1 mol of acid in a monoprotic, you need 2 mol of base...

[Mao]

Wait, at a pH of 3, why would the COOH group in the main chain donate it's proton? Shouldn't it just be the NH2 accepting protons to form NH3+?

Here's what i think, please correct where incorrect:

in very acid conditions (x< 3 ) the side group, which happens to have NH2 will be effected and receive a proton
in very basic conditions, (x>9) the side group, which happens to have a COOH will be effected and donate its proton

at zwitterion, the sidegroups are not effected?
If the side group contains 1 NH2 and 1 COOH group, will the zwitterion affect the side groups? as if it does, a neutral charge is still maintained in the molecule..

For aspartic acid, the COOH on its side group does not have the same reactivity as the COOH in its main chain group. The main chain is usually a bit more reactive. This is why at pH~3, the main chain COOH is deprotonated, and the side group is protonated.

You can think of weak acids (-COOH) and weak bases (-NH2) as 'buffers', i.e. they would like to maintain a certain pH range (i.e. pKa +/- 1). e.g. for main group -COOH, it has pKa~2. This means if pH>2, -COOH will deprotonate to lower pH. If pH<2, -COO(-) will protonate to increase pH.

I'm not too sure what you mean by 'at zwitterion, side groups are not affected'. All groups are similarly affected by their surrounding environment (see above, also thushan's post), the difference is that the groups have different 'turning points'. main chain COOH has pKa~2, main chain amine has pKa~9.

The reason why I'm throwing pKa everywhere is because it is a useful tool for working out what has protonated and deprotonated. Given the surrounding environment, we simply need to compare the pKa of the groups to see what form it is. I'll dig out the pKa for all the acidic and basic amino acids, you can use these to practice.


There are only two basic amino acids: lysine (side chain pKa = 10.3) and arginine (side chain pKa=13.2). There are only two acidic amino acids: aspartic acid (side chain pKa=3.6) and glutamic acid (side chain pKa=4.3).

Note that having an N does not make a side group basic (glutamine, asparagine and tryptophan are not basic, they do not protonate). Proline is a special case, the cyclic structure makes the main group amine more basic (pKa=10.6). Tyrosine is also a special case, the aromatic alkanol can deprotonate at high pH (pKa=10.1).

[scocliffe09]

Would anyone be able to explain the concept of n-1 in sulfide links?

I understand that if we have eg. 500 links, then we'd multiply that by the molar mass, and then minus 499 from M of Water, but i'm wondering if that's all.

If you have 500 links then you have 500 water molecules... one water is given off for every peptide bond formed.
Also, they tested on last year's exam, the idea that if you have two chains with a total of 500 peptides, there will be only 498 links, and therefore only 498 molecules of water.