Nucleic acids are macromolecules responsible for storing genetic

information and translating that genetic information into proteins. The

nucleic acid monomer consists of a sugar, a phosphate group, and one of

four bases. There are two distinct types of nucleic acid (DNA and RNA) that

differ in the identity of the sugar and one of the four bases. In most

organisms it is DNA that actually stores the genetic information while RNA

is directly responsible for the synthesis of a particular protein. As is

often the case, function is directly related to structure and, as a result,

it is important to have a clear understanding of the possible structures of

nucleic acids. They have primary structure (the sequence of bases),

secondary structure (the double helix and occasionally a triple helix in

DNA and cruciforms, hairpins, and the single-strand helix in RNA), and

tertiary structure (supercoils). I found it very interesting that UV/vis

spectrophotometry (a technique we are very familiar with from inorganic

lab) can be used to monitor the melting of DNA and to identify the

different nucleotides. Also, I did not realize that there are several

different forms of double helix (A, B, and Z) and that DNA sometimes forms

a triple helix. What I found most confusing in this chapter was the

explanation of supercoiling using the equation L = W + T. I had trouble

getting a clear mental picture of what was being described.

I found the simplified base pair notation for DNA a little confusing,

especally the pApCpGpTpT and ApCpGpTpTp and how the two are

different. I was also confused by the section about supercoiling and

the various forms and shapes of it. Although I did find it

interesting to learn that there are several different ways in which

the helix can coil, and I was unaware that It could coil in more

than one way. I also found the gained stability of the B form in

water environments. I also really liked how the book tied in the

entrohpy and enthalpy into the stability of various molecules,

connecting biochem with pchem. I don't think I got a clear answere

from the text as to why RNA is an A helix, is the environment in the

cytoplasm somehow different from the nucleus so that this form is

more favorable, or did I miss read and is it only an A-helix in

prokaryotes? Does that make the environment different?

Chapter 4:

The main theme in this chapeter was that of nucleic acids. We learned

about the various different types of compositions of DNA and RNA and the

differences between their compositions. We heard about the discovery that

Watson and Crick made regarding the A-T and C-G pairing. This reminded me

a lot of High School Biology class (which was the last time I had any

course that really talked about genetics) and I quckly recalled many of

the names of various components related to nucelic acid structures. We

also read about how RNA and DNA is formed and the different structures (as

in tertiary and secondary) that are formed. Much of the reasoning behind

why the DNA and RNA form in various shapes reminded me of Organic

Chem. and all the structural ideas we went through there.

This chapter regarding DNA and RNA was very interesting and

cleared up some questions I had, especially recently with the genome

project in the news. The sections I found really interesting were

regarding the secondary and tertiary structures of DNA. I never

thought about DNA having any more complex structure than a perfect,

orderly double helix. It was great learning chemistry favoring a

dissociation of this double helix structure, such as electrostatic

repulsion between the two chains and entropy. Also, I've never

thought about ATP energy being used to obtain superhelix coiling. We

learned about X-Ray diffraction last semester in inorganic, it was

interesting to see its applications to the secondary and tertiary

structures. This chapter was a slow read for me, I found myself

analyzing diagrams and rereading paragraphs. I haven't had biology

since AP Bio junior year of HS. It is amazing how much I forgot

regarding simple concepts such as DNA replication. It is wonderful

to see the chemistry behind these biological processes.

Ok...first of all, I am feeling a little overwhelmed with the length of

time it took me to get through the chapter. I think the combination of the

organic-ish chemistry stuff (organic wasn't exactly my forte) with my rusty

biology memory, made for a bit of a slow-go on the material. I think that

the "entirely new language" point you made in the syllabus is true for me,

and with a little time I will get more used to it. I find the stuff so

interesting so I hope the material becomes a little easier to iron out as

I am reading. I had a little trouble making sense of the pictures and

diagrams, although I really want to understand those better because they

seem to be really helpful aids in terms of being able to visualize what is

happening with nucleic acids. Main points....DNA and RNA are two basic

forms of nuleic acids which differ in terms of their sugar bases (ribose or

deoxyribose) and also in terms of uracril and thymine, biological

conditions influence whether certain reactions are favored or not favored,

DNA holds genetic information encoded in the sequence of its bases, which

is transcribed into RNA which codes for proteins. Huge strands of DNA are

compacted by more interactions which cause supercoiling.

Questions: the mechanisms of some of the reactions are a little confusing

to me (ex. synthesis of polynucleotides). Also...left handed v. right

handed is a little hazy.

Hopefully after the lecture and a second (third, fourth?) reading I will

have a good handle on this stuff.

i think that it is interesting that DNA and RNA are so acidic. i felt

that it would be more logical for the nucleic acids to be more neutral and

it was when the phosphate is ionized and the nucleotide is protonated, the

pH values to be close to neutrality. with this change of pH, it is

interesting to see that DNA is so stable. how polynucleotides that are

thermodynamically unstable in vivo, have a slow hydrolysis without a

catalyst? from previous exposures to chemicals that are thermodynamically

unstable, it usually reacts immediately and swiftly. i think its amazing

that the understanding of DNA took so long now that the information is

laid out in front of me! its also ironic that the synthesis of a

polynucleotide, although is a complex process, it has a simple

reaction. i honestly believe that people like to make things harder than

it is.

As a biology major, most of this chapter is a review for me, yet it is

wonderful introduction to biochem. Biology is a division of chemistry-

life exists due to chemistry. One could say that the very first life was

merely a strand of nucleic acid capable of catalyzing itself for

duplication.It is no wonder that we started the course with this

chapter. The fact that the nucleic acids absorb in the UV spectrum means

that the first life must have existed not only in an environment void of

free oxygen, but also sunlight. I found the most interesting part of this

unit the process of formation of the phosphodiester linkage. I now

understand why hydrolysis is the more thermodynamically favored reaction

between the monophosphate molecule and polynucleotide strand. Previously,

I thought the polynucleotide + triphosphate molecule appeared to be the

thermodynamically unfavorable linkage method because of the energy

required to build the triphosphate molecule. I did not know that there was

such a DNA molecule that is a triple-helical structure; I also do not

quite understand the mechanism of the formation of H-DNA in order to be

composed of three semi-stable backbones, stable enough to determine its

existence. My conclusion after reading this chapter is that I could not

imagine earning a degree in Biology without understanding the chemistry

involved in the essence of biology- the evolution of life.