Unit 3 Questions MEGATHREAD :)

[homosapiens]

really noob question but can you please explain the secondary structure of proteins. I know it is due to hydrogen bonds which will cause coiling and folding but I don't know much else.
My book says hydrogen bonds form between C=O and H-N, I don't really get this because isn't this a peptide link which is a covalent bond?

Yep, CONH is the peptide link between two adjacent amino acids, while the hydrogen bonding in a protein's secondary structure is the interaction between amino acids not necessarily directly next to each other in the chain. So for example the first amino acid may have hydrogen bonds with the 100th amino acid in the chain, which results in its secondary structure.

[mickeymouse]

sorry homosapiens not too sure about whether lipids and nucleic acids are okay in GC

the peptide link is covalent and is between the carboxyl group and amine group but that is the primary structure (between 2 amino acids)

the hydrogen bond between the C=O and NH is the secondary structure and can be between different amino acids on a protein CHAIN (many amino acids)... the diagrams of a coiled, foiled, etc polypeptide might help you... hope this made sense

[luken93]

just wanting some clarification: in fractional distillation involving a tower and crude oil those with a higher molecular mass are collected at the bottom (higher temperature) but fractional distillation in general would result in those with a lower molecular mass collected first and so they are at the bottom?

Smaller molecules generally have less/weaker dispersion forces. Since frac dist separates on principal of boiling point, the fractions collected at the top have the lowest boiling point = least intermolecular forces = smaller chain.

Why are the chem shift values for 13C huge in comparison with that of 1H?

Not completely sure, and we don't need to know it, however I assume it's got something to do with the size of the atom and hence the amount of shielding that it places upon neighbouring atoms?

really noob question but can you please explain the secondary structure of proteins. I know it is due to hydrogen bonds which will cause coiling and folding but I don't know much else.
My book says hydrogen bonds form between C=O and H-N, I don't really get this because isn't this a peptide link which is a covalent bond?

The secondary structure involves hydrogen bonding between C=O and N-H on adjacent peptide linkages. This creates a perfect coiling structure - if you look at Q14 of VCAA 2009 you can see that it's a uniform coil that is evenly spaced.

[david10d]

Trying to categorise molecules into HPLC and GC: I know carbohydrates can't be vaporised, what about nucleic acids, lipids and proteins?

apparently proteins decompose upon heating so I don't think they will vaporize either

ok so just to confirm... carbohydrates and amino acids need to go through HPLC and lipids and nucleic acids can go through GC

If the molecular mass is below 300, it can be analysed with GC. Just add it up the molecular mass to make sure.

[lilaznkev1n]

Thanks everyone for the fast replies
I get it now

[n.]

a question about the last question in the neap 2011 exam....


ii. Would you expect group D on the inhibitor drug to be largely polar or non-polar? Explain
your choice

 "The group of atoms marked D on the drug would be largely non-polar. 1 mark
The side chain on isoleucine is non-polar. Only a non-polar or low-polarity group of
atoms will interact appreciably with this non-polar side chain"

so how do you know that isoleucine is non polar?

what does that even mean...? ive always been confused with this non polar and polar stuff....

[DavidSheena]

Just a question about VCAA 2010.

d.ii Draw a grouping of atoms that would give rise to the triplet and doublet.

The answer was the  methyl group and ethyl group joined together. Whereas I seperated the two and labelled correctly. Would that be correct? As in one of the commercial exams a similar question had the answer with the two seperated.

Edit also:

7a.ii The answers say that one mark is awarded for working out the mass of methanol. But I did it slightly differently by converting density to molarity and then working out volume. Does VCAA  accept alternate methods?

[extcar]

for VCAA 2008, question 7d SA,
it goes what fragment must have been lost from the molecular ion to account for the high peak at m/z 45?
I wrote H+ atom,
the assessor's report wrote H or H atom. and then they went on to say C2H5O+ was also accepted. The most common answer was H+. Does that mean H+ is wrong or right?
http://www.vcaa.vic.edu.au/vce/studies/chemistry/assessreports/2008/chemistry_assessrep_june08.pdf

[tony3272]

for VCAA 2008, question 7d SA,
it goes what fragment must have been lost from the molecular ion to account for the high peak at m/z 45?
I wrote H+ atom,
the assessor's report wrote H or H atom. and then they went on to say C2H5O+ was also accepted. The most common answer was H+. Does that mean H+ is wrong or right?
http://www.vcaa.vic.edu.au/vce/studies/chemistry/assessreports/2008/chemistry_assessrep_june08.pdf

I'm pretty sure that when you are talking about what's lost to cause the peak at a particular m/z you don't include the positive charge.

[jackson1234]

Beta-d-glucose and Galactose differ at carbon 4; in galactose the OH sticks up, in glucose the OH sticks down.

wait i thought it was:

a-glucose, OH sticks down
B-glucose, OH sticks up


and what about alpha-glucose, how does that differ from galactose, if my thoughts are incorrect

the very left carbon, glucose sticks down, galactose sticks up - this is 4-C

The difference between a and b glucose is the very RIGHT carbon atom, a-glucose OH sticks down, b-glucose OH sticks up - this is 1-C

you wont be examined on galactose. Its not even in the data book.

[Greatness]

for VCAA 2008, question 7d SA,
it goes what fragment must have been lost from the molecular ion to account for the high peak at m/z 45?
I wrote H+ atom,
the assessor's report wrote H or H atom. and then they went on to say C2H5O+ was also accepted. The most common answer was H+. Does that mean H+ is wrong or right?
http://www.vcaa.vic.edu.au/vce/studies/chemistry/assessreports/2008/chemistry_assessrep_june08.pdf

I'm pretty sure that when you are talking about what's lost to cause the peak at a particular m/z you don't include the positive charge.

Yep whatever lines you see on the mass spectrum are the components that have lost a group of atoms or an atom - these have a charge. The componenets that are lost dont have a charge.

a question about the last question in the neap 2011 exam....


ii. Would you expect group D on the inhibitor drug to be largely polar or non-polar? Explain
your choice

 "The group of atoms marked D on the drug would be largely non-polar. 1 mark
The side chain on isoleucine is non-polar. Only a non-polar or low-polarity group of
atoms will interact appreciably with this non-polar side chain"

so how do you know that isoleucine is non polar?

what does that even mean...? ive always been confused with this non polar and polar stuff....

ii) Overall isoleucine is polar due to the COOH and NH2, but the z group or side chain is a 4 carbon back bone - which is non-polar. This section of the amino acid is non-polar hence it can interact with the non polar drug. You should know that a carbon back bone is non polar think about butane, pentane etc they are all non-polar.
If something is polar it has an overall charge or the electrons are dragged to one side due to the elctronegativity of one of the atoms.

[luken93]

for VCAA 2008, question 7d SA,
it goes what fragment must have been lost from the molecular ion to account for the high peak at m/z 45?
I wrote H+ atom,
the assessor's report wrote H or H atom. and then they went on to say C2H5O+ was also accepted. The most common answer was H+. Does that mean H+ is wrong or right?
http://www.vcaa.vic.edu.au/vce/studies/chemistry/assessreports/2008/chemistry_assessrep_june08.pdf

Nope, H+ is incorrect.

The reason why is because when a fragment is lost, it is an atom that has been lost, not an ion.

So if I ionise propane for arguments sake, and a C2H5+ fragment occurs, it means that CH3 has been lost, not CH3+.

Think of it this way, if we have a covalent bond between C-C which indicates that is sharing two electrons. I get an axe and put it through that bond, one of the carbons will keep the two electrons, and the other will be left 1 short. Hence, the fragment is the one that has lost an electron and thus has a positive charge, and the fragment lost has gained an electron and is satisfied.
DISCLAIMER: This is not actually how it works, but it's a simplified way of thinking about it.

The reason why they accepted C2H5+ is because they used the word "fragment" - this usually denotes the part of the molecule that has the + charge.

[extcar]

awesome, i get it now.
thanks people

[Water]

When describing HNMR.



Is it possible to say that HNMR allows the identification of the basic backbone of an organic compound?

And can Infrared POSSIBLY be used for quantitative analysis.

[ulbasour]

When describing HNMR.



Is it possible to say that HNMR allows the identification of the basic backbone of an organic compound?

And can Infrared POSSIBLY be used for quantitative analysis.

On your first question, it isn't the best method without supplementary information from MS or IR.

And i don't think so for IR