primary, secondary & tertiary structure of DNA

[olly_s15]

As superflya says, isn't primary structure the ordering of nitrogenous bases?

I believe so. And this ordering is enabled due to covalent bonds.

[shinny]

I wasn't aware there's a 'formalised' primary/secondary/tertiary system for DNA as there is for proteins, so I don't think you should get too hung up on the terminology. It's more important to just know the different sorts of bonds at each level.

[olly_s15]

I wasn't aware there's a 'formalised' primary/secondary/tertiary system for DNA as there is for proteins, so I don't think you should get too hung up on the terminology. It's more important to just know the different sorts of bonds at each level.

which is essentially why i started this thread

[stonecold]

Okay, maybe just say:

The order of nitrogenous bases covelently bonded onto the deoxyribose molecules along the sugar phosphate backbone.

Edit: Thought it could sound a little nicer...

[olly_s15]

Okay, maybe just say:

The order of nitrogenous bases covelently bonded onto the deoxyrobse sugar groups.

sounds good to me.

to further conclude:

the secondary structure involves hydrogen bonding interactions between complementary nitrogenous base pairs

anddd...

tertiary structure refers to the ionic interactions between the negatively charged DNA fragments (caused by the phosphate groups) and positively charged proteins called histones, to result in a tightly packed coil

[stonecold]

yeah, just for secondary, i would probably throw in 'double helix' to be extra consise.

[olly_s15]

yeah, just for secondary, i would probably throw in 'double helix' to be extra consise.

excellent

feeling confident stonecold?

[stonecold]

^ I dunno.  Some days I am switched on, and I do quite well.  Other days, mistakes and clouded thinking destroy me.  My best prac exam paper was NEAP 09, where I lost just the 1 mark.  On another 5 or so exams I've lost roughly 3-4 marks.  But then I have done really poorly on a few, getting low 80%'s.

I shouldn't have done VCAA 2009 when I did it (late at night), and when I hadn't fully revised instrumentation (particularly AAS calculations), and practically screwed up that bit, and then one or two calculating mistakes on top of that cost me dearly...

Waste of an exam.  I feel that I am much better than what I got on that paper.  I'm doing VCAA 08 in the coming days, hoping to smash it haha...

How do you think you're doing...?

[olly_s15]

Similar to you - cloudy at times but becoming more confident.

Best scores have been 96-97% with lowest at around the 80 mark.

Saturday and Sunday will be crucial study wise..

[Slumdawg]

Hey this is a good topic. I've noticed they change it heaps too. Like some say covalent bonding in primary and others say peptide. What do you guys reckon would be best to say if the question came up? Also with tertiary I have written down, hydrogen, ionic, disulfide bridges, dipole-dipole... Once again, which would you guys put down.. Thanks.

[Martoman]

Hey this is a good topic. I've noticed they change it heaps too. Like some say covalent bonding in primary and others say peptide. What do you guys reckon would be best to say if the question came up? Also with tertiary I have written down, hydrogen, ionic, disulfide bridges, dipole-dipole... Once again, which would you guys put down.. Thanks.

Buzz words.

Proteins primary: Covalent, peptide links, amino acids.

Secondary: Hydrogen bonding of the C (double bond) O and the N-H, coiling, pleating.

Tertiary: Overall 3d shape, determines activity (in case of enzymes), disulfide links make it harder to denature coz its strong covalent bonding, ionic attractions, hydrogen bonding, dispersion forces.

Note: Heat and changes in pH can denature a protein to its primary structure. This is because the bonds responsible for the tertiary structure are broken when heated or pH changes. As the tertiary structure is responsible for biological activity (such a active sites on enzymes) this makes sense.

A good question is to ask: which part of a protein (taken from the small intestine) is affected when it is heated with a strong acid?

A) Primary
B) Secondary
C) Tertiary
D) all of the above.


DNA -> Primary: ORDER of nitrogen bases as they are covalently bonded to the deoxy's. IT IS NOT involved in peptide links

Secondary -> Double helix, hydrogen bonding CG = 3, AT = 2, nitrogen bases ordered complementary.

Tertiary -> bonded with histones which have a +ve charge, DNA = -ve charge, SUPERCOILING.

[stonecold]

I'll say B secondary, because that would cause protonation/deprotonation, which would lead to broken H-bonds.

Unless the acid can hydrolyse the amide bonds, which I then guess would make the answer D.

[Martoman]

Yeah it goes the full monty D.

I thought this particularly nasty *witch cackle*

[kate26]

primary structure : sequence of nucleotides i.e one strand of DNA. Covalent bonds form between the phosphate group of one nucleotide and the deoxyribose sugar of another nucleotide. Forming a chain of nucleotides is a condensation reaction (condensation polymerisation)

secondary structure : double helix - hydrogen bonding occurs between nitrogenous bases (C and G is 3 bonds, A and T is 2 bonds)

tertiary structure : supercoiling around histones*

*not sure if you need to know anything about histones but they are proteins that contain high proportions of lysine and arginine, and the variable groups of these amino acids are positively charged at the pH of human cells.

[Studyinghard]

Tertiary structure can be anything. ionic bonding, disulfide links, hydrogen bonding, dispersion forces.