Nucleic Acids- Primary and Secondary Structure of DNA

What is DNA? Why is it called DNA? Explain parts.

DNA is short for deoxyribonucleic acid. The "deoxyribo-" part comes from name of the sugar in nucleotides of DNA- deoxyribose. Deoxyribose is essentially a ribose sugar but with one of the -OH groups converted to -H, hence "de-oxy." DNA is made up of two strands, each of which is a polymer (i.e. a long chain made up of smaller subunits) of nucleotides. (I have explained the structure of nucleotides in my previous post about purines and pyrimidines.) The two strands run antiparallel (i.e. parallel but in opposite directions) and have hydrogen bonds between their bases. The outer "backbones" of DNA are made up of alternating sugar and phosphate units.

Why is the backbone hydrophilic?

The backbone of DNA is hydrophilic due to the presence of negatively-charged phosphate groups in the backbone.

What is meant by the secondary structure of DNA?

The secondary structure of the DNA is its coiling into a helical structure with two antiparallel strands. I'm not entirely sure what causes the DNA to coil up into a helix, but I think that it has something to do with the stacking of the nitrogenous bases and that it is energetically favourable for base-water contact to be minimised.

How has chemical analyses and physical measurements helped in understanding DNA structure?

X-ray diffraction analyses of DNA were performed, which helped in taking measurements of the diameter, density and so on, which in turn were analysed further to provide the DNA structure. I don't know the full details unfortunately... perhaps this is something that I need to brush up on.

How would you write a DNA sequence?

You would write a DNA sequence by writing the order of the bases, using only the first letter of each base. For example, adenine-thymine-cytosine-guanine would be abbreviated as ATCG.

Why do we usually only write the base?

We usually only write the base because that is the only part that differs between the four nucleotides present in DNA.

What is meant by the primary structure of DNA?

The primary structure of DNA is the order of the bases in the DNA. A bit like how the primary structure of a protein is simply the order of the amino acids.

What evidence shows DNA is the carrier of genetic info?

In 1928, an experiment was done with mice and two strains of streptococcus bacteria: R (rough) and S (smooth). The S strain is lethal to mice, whereas the R strain is not. However, when dead S-strain cells were mixed with live R-strain cells and injected into a mouse, the mouse still died, and live S-strain cells could be recovered.

Later on, in 1944, another group of scientists did another experiment to find out which part of the S-strain was responsible for the propagation of new S-strain cells. They removed various parts of the cell (i.e. proteins, lipids etc.) one at a time, in order to see what would happen. In all of these cases, the mice still died and live S-strain cells could be recovered, except when DNA was removed. This suggested that DNA carried genetic information that could be passed along, creating new live, virulent S-strain cells.

Explain what is meant by base pairing and explain why only certain combinations of base pairs are possible.

Base pairing is the matching up of bases from opposite strands of the double helix. Single-ringed pyrimidines always pair with single-ringed purines. Adenine always pairs with thymine (in DNA) and uracil (in RNA), whereas cytosine always pairs with guanine. This is partly because bases can form hydrogen bonds between various side groups on their rings. Incorrect base pairs cannot form as many hydrogen bonds as correct pairs and thus incorrect base pairing is less stable than correct base pairing. Another reason why only certain combinations of base pairs are possible is because if two purines or two pyrimidines were to pair with each other, they'd be either too close or too far apart to "fit in" with the overall helix structure.

What are the fundamental features of the DNA double helix?

It is right-handed as I'll explain in a bit. It also has major (wide) and minor (narrow) grooves at the side where other binding proteins can "slot in."

What is a right handed helix?

A right-handed helix is a helix that turns clockwise. (A left-handed helix turns anticlockwise.)