Chapter 4, 5, 6, or 7,

1. It was interesting to learn how in organic chemistry stability relate to every why and how
question about the compounds and in biochemistry hydrogen bond become the answer for what
bond is it or what power is holding the structure. For example, as bond connecting the base pair
purines and pyrimidine, aminoacyl-tRNA’s each branch of the cross being bold by the hydrogen
bond are all hydrogen bondind. Especially with structures, it was interesting to see in RNA
molecule that is bent and fold could have done this by forming a hydrogen a hydrogen bond that
are not even the base pair (Adenine and Guanine), which told me that after all biological
molecules are made up of chemical compounds after all and will follow the organic chemistry
rules. I want to talk more about how hydrogen bond plays such a big rule in biochemistry as I
learn more about it.

2. Three thing that I thought is important is the B form of DNA, Nucleic acid sequence CCCOPO
and the CCN in protein. All three of them not only for the form and sequence itself but the
insights that we can evaluate from it, and the chemical operation we can expect. For example, the
why phosphodiester backbone are at the edge and the base pairs are at the center chemically.
Which explains were the DNA is and where other elements bind to chemically and have a deeper
understanding of one of the most important macromolecules. Also the specific sequence not only
allows us to expect chemical operation of binding and hydrophobic or hydrophilic nature of the
molecule, but also enable me to recognize the macromolecules, I noticed this while having a
discussion about the deoxyhemoglobin and oxyhemoglobin discussion.

3. The Substitution matrix was the hardest part for me to understand, because the Blosum-62
graph was to0 big that it took me time to read and look at the text back and forth while reading
the textbook. It took me some time to understand that how to score the substitution .

4. The basic concepts that describe DNA, the base pair, chemical bonding, conformation, why helix
structure is helix because the center is hydrophobic and hydrophilic when the configuration is
explained chemically, etc. This information resonated well with me because DNA was one of the
biggest topics in general biology and the chemical formation was already learned. It was
interesting to see how everything being connected with organic chemistry and explains the
knowledges that was studied in general biology. For example, the phosphate backbone was a
known information but I did not know they their phosphodiester bond, this phosphodiester bond
explains why the sugar phosphate backbone acts that way.

5. I thought it could have been interesting to talk more about how the restriction enzymes and
DNA ligase operates in more details. The restriction enzyme as I know is one of the key elements
of DNA modifying and gene editing which, though lays at the boundary of the ethics, has a great
potential to cure disorders, disease, and even elongating lifespan. Thus, how this restriction cuts
and DNA ligase actually interact with the DNA molecules other than the DNA fragment that they
recognize. The book put it in a way like what they requires and energy source where they cut in
and join are and not much more detailed level for me to imagine the application.