A closer look at the chemistry of the DNA molecule
Deoxyribonucleic acid, most commonly known as DNA, is a molecule found in the
nucleus of most cells. DNA is a polymer composed of nucleotide monomers. A DNA
nucleotide consists of a sugar (deoxyribose), a phosphate group (phosphoric acid), and
one of the four nitrogenous bases (adenine, thymine, cytosine, or guanine).
Deoxyribose has a chemical formula of C5H10O4. The carbons of the deoxyribose are
numbered 1-5 and are called 1’ to 5’ (1 prime to 5 prime) respectively (Figure 1).
The backbone of the DNA molecule consists of alternating monosaccharide sugar
molecules and phosphate groups. In each case, the bond linking each individual sugar
molecule to the neighboring sugar molecule is a 3’, 5’ phosphodiester bond. This means
that a phosphate group links carbon atom 3’ of one sugar to carbon atom 5’ of the
neighboring sugar (Figure 1).
In addition to being complimentary to each other the two strands of a DNA helix are
said to be antiparallel because they always associate in such a way that the 5’ to 3’
direction of one DNA strand is opposite to that of its partner (Figure 2).
Figure 1
Figure 2
Figure 2 also illustrates two reasons why the nitrogenous bases always pair adenine with thymine and cytosine
with guanine. First off, adenine and guanine each contain two rings and are known as purines. Likewise
cytosine and thymine each contain one ring and are known as pyrimidines. Each base pair within DNA
contains one purine and one pyrimidine. The second reason for specific base pairing has to do with hydrogen
bonds found between the two adjoining nitrogenous bases. There are always two hydrogen bonds between
adenine and thymine and there are always three hydrogen bonds between guanine and cytosine. Using these
two simple chemical properties there are seldom errors matching the correct nitrogenous base pairs in DNA.
DNA Replication
DNA is found in the nucleus of most cells. In order for cells to divide and produce new cells each cell must
first copy its DNA, a process known as DNA replication or DNA synthesis. The 5’ to 3’ directionality of DNA
has consequences in DNA synthesis because the enzyme DNA polymerase can only synthesize DNA in one
direction by adding nucleotides to the 3' end of a new DNA strand.
DNA synthesis begins when the original DNA strands unwind from each other in what is known as a replication
bubble. At either end of the replication bubble and moving in opposite directions are replication forks. This
process is completed by a very organized assembly of many different enzymes.
DNA helicase unwinds and separates the strands of a DNA double helix, a process characterized by the
breaking of hydrogen bonds between connected nucleotide bases. Once the hydrogen bonds have been broken
between the complimentary bases they are held apart by single strand binding proteins. DNA primase then
catalyzes the synthesis of a short RNA segment (called a primer) complementary to a DNA template. DNA
primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis
of a DNA strand without an initial primer.
A primer is a strand of nucleic acid (in this case RNA) that serves as a starting point for DNA synthesis. They
are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only
add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3'-end of the primer,
and copies the opposite strand of DNA.
Because DNA polymerase can only synthesize a new DNA strand in a 5' to 3' manner, the process of replication
goes differently for the two strands comprising the DNA double helix.
Leading strand
The leading strand of DNA is replicated continuously. It is the strand that is being continuously polymerized
towards the replication fork. All DNA synthesis occurs 5'-3'. The original DNA strand must be read 3'-5' to
produce a 5'-3' growing strand.
The leading strand is formed as DNA polymerase "reads" the template DNA and continuously adds nucleotides
to the 3' end of the elongating strand.
Lagging strand
The lagging strand grows in the direction opposite to the movement of the growing fork. It grows away from the
replication fork and it is synthesized discontinuously. Because the strand is growing away from the replication
fork, it needs to be replicated in fragments because the primase (that adds the RNA primer) has to wait until the
fork opens to be able to put in the primer. The RNA polymerase reaches the origin of replication and stops
replication until a new RNA primer is placed. These fragments of DNA produced on the lagging strand are
called Okazaki fragments (named after that man that discovered them). The orientation of the original DNA on
the lagging strand prevents continual synthesis. As a result, replication of the lagging strand is more
complicated than replication of the leading strand.
Okazaki fragments are short molecules of single-stranded DNA that are formed on the lagging strand during
DNA replication. Although the diagram above represents them being much shorter they are between 100 to 200
nucleotides long in most cells.
Primer removal is performed by DNA polymerase which removes the RNA nucleotides and replaces them with
DNA nucleotides. Once all the RNA nucleotides have been replaced DNA polymerase proofreads all newly
created DNA for any base pairing errors, repairing any that it finds. Finally another enzyme, DNA ligase, joins
the Okazaki fragments together forming a now completed copy of DNA.
During cell division, enzymes that duplicate DNA cannot continue their duplication all the way to the end of
chromosomes. A telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects
the end of the chromosome from deterioration. The telomere regions deter the degradation of genes near the
ends of chromosomes by allowing for the shortening of chromosome ends, which necessarily occurs during
chromosome replication. Over time, due to each cell division, the telomere ends do become shorter.
If cells divided without telomeres, they would lose the ends of their chromosomes, and the necessary
information they contain. The telomeres are disposable buffers blocking the ends of the chromosomes, and are
consumed during cell division. They are replenished by an enzyme called telomerase.
Telomerase is an enzyme that lengthens telomeres in DNA strands, thereby limiting the chance that actual genes
will be damaged when the last portion of a chromosome does not become replicated.
Topoisomerase is an enzyme that regulates the overwinding or underwinding of DNA. The winding problem of
DNA arises due to the intertwined nature of its double helical structure. For example, during DNA replication,
DNA becomes overwound ahead of a replication fork. If left unabated, this tension would eventually grind
replication to a halt (a similar event happens during transcription.) In order to help overcome these types of
topological problems caused by the double helix, topoisomerases bind the double-stranded DNA and cut the
phosphate backbone of the DNA. This intermediate break allows the DNA to be untangled or unwound, and at
the end of these processes, the DNA backbone is resealed again. Since the overall chemical composition and
connectivity of the DNA does not change, the tangled and untangled DNAs are chemical isomers, differing only
in their global topology, thus their name.
Transcription
Many of the same enzymes that were involved in unwinding and separating DNA during DNA synthesis are
also involved in the transcription of RNA. However, since RNA nucleotides will now be added together during
transcription the primary enzyme used will be RNA polymerase. Similar to the action of DNA polymerase,
RNA polymerase also adjoins new nucleotides to the growing 3' end of nucleic acid molecule.
During DNA replication the complete molecule of DNA must be copied. In comparison, not all DNA is used
during transcription. Some of the DNA is not even transcribed into RNA, and of the RNA that is created
through transcription some of that is spliced out and discarded. An intron is any nucleotide sequence within a
gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron
refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences
that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of
most organisms, and can be located in a wide range of genes, including those that generate proteins, ribosomal
RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA
splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation.
An exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule after portions of
a pre RNA (introns) have been removed by splicing. Depending on the context, exon can refer to the sequence
in the DNA or its RNA transcript.