Mendoza, Alliah Cyrelle S.

14/06/2023
BSA-2A Biochemistry

DNA AND RNA

DNA is the molecule that gives an organism with its unique identity. It is made up of monomers, with
nucleotides coming first. It is a three-sectioned molecule. A monosaccharide consisting of either D-ribose or 2-
deoxy-D-ribose and carbons numbered 1’ through 5’. The presence or absence of hydroxyl on carbon 2
determines the difference, and this sugar can only be found in RNA and DNA, respectively. A heterocyclic base
subsequently extends from the anomeric carbon. It’s a heterocycle because the rings contain an element other than
carbon, and it’s a base because of the lone pairs on the N atoms. These bases can be purines or pyrimidines, with
bases abbreviated as A, G, C, and T or Adenine, Guanine, Cytosine, and Thymine. In RNA, however, the Thymine
loses its methyl group and becomes Uracil. The anomeric carbon contains a glycosidic linkage. It is called a
nucleoside when sugar and a base are combined. If the base is adenine, we get adenosine or 2-deoxyadenosine,
and so on. Phosphate esters connect the 3’ hydroxyl of one nucleotide to the 5’ hydroxyl of another in nucleic
acid. It comprises a backbone made up of identical sugars and phosphate groups, with various bases sticking from
the way we include the primary structure of a protein as we include the amino acid sequence. A and T, as well as
G and C, always exist in roughly equal amounts. This is due to DNA is made up of two strands that pair up in a
base-specific manner, making them complementary. Furthermore, the geometry of DNA is enough that one purine
and one pyrimidine will fit nicely between strands, whereas two purines and two pyrimidines would be too wide
and too narrow. Both of these strands are antiparallel, meaning they operate in opposite directions, one from the 5’
end to the 3’ end. In contrast, RNA, which is made up of ribose sugars rather than 2-deoxyribose, is going to be
single-stranded.
The DNA Is stored by coiling around proteins referred to as histones, which is vital to keeping the DNA
inside the cell despite its length. These coils are then used for supercoiling to preserve even more space. A
chromosome is a long-supercoiled DNA molecule that contains all of the histones, and chromatin is all of the
genetic material in a cell’s nucleus.

Transcription and Translation: Copying the Molecule of Life

DNA is a two-stranded polymer of nucleotides, with each strand having an identical sugar and phosphate
backbone. Every cell in our body consists of all of our genetic material, including the 23 pairs of chromosomes.
Aside from female egg cells, there has never been a single cell in our bodies that was there when we were born.
Each new cell obtains all of the genetic material through the process of DNA replication, which takes place when
a cell divides and each resulting cell maintains a copy of all of your chromosomes.
Helicase is an enzyme that unwinds the double helix and disrupts the hydrogen bonds between the bases,
separating DNA into individual straps and forming a replication fork. The unwinding of the helix generates strain
further ahead in the chain, and topoisomerase will then break, untwist, and reconnect the DNA, always ahead of
the replication fork. With the strands separated, it can begin to copy each one, but the enzyme that copies the
strand needs a starting point, so an enzyme called primase will act as an RNA primase at a specific location to
start the replication. This primer is approximately five to ten nucleotides long, after that another enzyme called
DNA polymerase III binds to it and begins producing an entirely new complementary strand, adding nucleotides
to the new chain that the primer started. Nucleotides enter the active site of the enzyme, and polymerase catalyzes
the synthesis of the phosphodiester bond that participates each new nucleotide to the complementary strand.
On the leading strand, DNA replication proceeds with the replication fork, continuously synthesizing the
complementary strand and requiring only the initial primer, whereas on the lagging strand, polymerase must
continue a single section at a time as new template becomes available. These chunks are referred to as Okazaki
fragments. Each of them must have its own primer for polymerase to bind to and copy the new fragment. After
each fragment has been successfully synthesized, DNA polymerase I will go through and replace the RNA
nucleotides from the primer with DNA nucleotides to ensure that the result is all DNA.
Finally, because polymerase is incapable of linking the last nucleotide of one fragment to the first
nucleotide of the after that, a separate enzyme called ligase must travel through and ensure that everything is
connected. Cells must interact with one another in order to respond to stimuli from the environment and collect
specific behavior at different stages of life so that the body can initiate the necessary changes as we grow. The
exchange of information occurs via receptors that lie in the cell membrane and wait for a particular substance to
bind. Many of these receptors are signaling molecules such as hormones and neurotransmitters that, upon binding
to the receptor, initiate the signaling transduction process, which can have a variety of outcomes.

Transcription and Translation: From DNA to Protein

Transcription and translation refer to the process by which enzymes read the genetic code in order to
generate all of the proteins within an organism. A chromosome is an extremely long molecule made up of many
millions of base pairs that mostly do nothing, but certain sections of the chromosome are special. The parts that
code for various things are referred to as genes.
The Initial phase would be transcription, whereby an enzyme uses one of the strands of DNA within a
gene as a template to generate messenger RNA (mRNA). RNA polymerase, with the assistance of proteins known
as transcription factors, binds to a specific sequence within the gene known as a promoter and pulls two strands
apart. One template or antisense strand, which will be used to generate mRNA, and one non template or sense
strand. RNA does not require a primer, it merely starts mRNA synthesis at the start codon, and then moves
downstream along the gene in a process called elongation, synthesizing the mRNA as it moves, reading the
antisense strand from 3’ to 5’ and generating the mRNA from the 5’ end, attaching nucleotides to the 3' end,
similar to how the DNA polymerase synthesizes DNA only being different as it uses Uracil instead of thymine and
the deoxyribose. RNA polymerase zips DNA back up as it goes until it reaches the end. Finally, termination
occurs, the enzyme detaches, and DNA returns to its original state while producing mRNA.
mRNA acts as a code for a specific protein during translation. A codon will encode for a specific
anticodon carried by a transfer RNA or tRNA covalently linked to an amino acid. The reading frame is the
arrangement of nucleotides into codons. There is a redundancy in the table of all the mRNA and the amino acids
they code for, with multiple codons resulting in the same amino acids but with an inconsistency. The start codon
initiates translation, and the stop codons terminate it. This process would begin before the next codon enters the
ribosome. It will transport an amino acid that has been covalently bound by the initiator tRNA. The tRNA shifting
will make room for the next one. The new amino acid connects to the first two, which continues until the mRNA,
at which point a polypeptide is formed. DNA is converted into mRNA, that is subsequently transformed into a
molecule of protein.

Mechanisms of DNA Damage and Repair

Our DNA is always under threat of mutation, which means that changes in the genetic information in the
cell could occur due to a variety of factors. In large-scale mutations, an entire chromosome is lost, relocated, or
rearranged, as opposed to point mutations, which are caused by a single nucleotide or the base pair in DNA. In
sickle cell anemia, there’s a difference in a single nucleotide in the gene that codes for one of the subunits of
hemoglobin in the DNA carrier when compared to a non-carrier. In the template strand, there is an A where a T
should be, coding for a U rather than an A in the corresponding mRNA. This altered codon will code for valine
rather than glutamic acid. The hydrophobic side chain on valine differs enough to cause a conformational change.
In low oxygen conditions, this causes hemoglobin to aggregate, resulting in hemoglobin fibers. As a result,
hemoglobin displays a sickle shape. A nucleotide pair substitution is one possibility when there is a point
mutation. Silent mutation occurs when a change in the template strands results in a new mRNA codon that
translates for the same amino acid. A missense mutation occurs when a change in the mRNA codon results in the
translation of a new, different amino acid.
Finally, a substrate of this type may cause the corresponding mRNA codon to no longer code for an amino
acid, but rather to become a stop codon, a phenomenon known as nonsense mutation. Instead of substitution,
insertion or deletion may occur. This is the process by which one base pair is added or deleted from the DNA
sequence. Every single codon will be altered after insertion or deletion, resulting in a large number of missense
mutations and, most likely, an eventual premature stop codon. Because the entire reading frame of the genetic
code is shifted, these are referred to as frameshift mutations.
The first source of mutation Is known as spontaneous mutation. This occurs when the cellular machinery
makes an error on its own, but it is then repaired in a process known as DNA mismatch repair. Mutation can also
be caused by external factors, which are known as mutagens. Radiation is a good example. A repair enzyme can
recognize this distortion or lesion and initiate nucleotide excision repair. Other mutations could be introduced by
alkylating agents, which would be recognized by glycosylase enzymes, which would initiate a base excision
repair snipping the glycosidic bond, explaining why the enzyme is called glycosylase.

Cell Communication
Signaling is classified into three types: autocrine, paracrine, and endocrine. The prefix auto means “self,”
so autocrine signaling is when cells secrete signaling molecules that then bind to receptors on that same cell. The
prefix “para” means “beside or nearby,” so paracrine signaling is a type of local signaling in which a compound
like growth hormone is secreted by a cell that then interacts with nearby cells. Synaptic signaling is another
example of local signaling; this is the way messages travel by means of the nervous system. Finally, long-distance
signaling occurs in our bodies via endocrine signaling. When a gland releases a hormone, it is carried via the
bloodstream to reach its destination.
Several signaling molecules are classified into three structural groups: polypeptides like oxytocin,
steroids, and amines. Adrenaline is another name for epinephrine. When molecules enter liver cells, they bind to a
membrane receptor. This results in the enzyme protein kinase A to be activated. This enzyme encourages glycogen
breakdown while preventing glycogen synthesis. This causes the cell to halt storing glucose in the form of
glycogen and instead ruptures down glycogen to generate more glucose molecules, which are then available for
cellular respiration. It essentially increases energy production so that the organism can escape the predator. Lipid-
soluble hormones, on the other hand, must attach to transport proteins in order to be soluble in the bloodstream,
and receptors that interact with these hormones are usually already inside the cell. Nuclear receptors, on the other
hand, are transcription factors that when activated, trigger the expression of a particular gene in a cell.