CHEM 213 - Nucleic Acids 2
CHEM 213 - Nucleic Acids 2
A nucleotide has a
nitrogenous base, a pentose
sugar (ribose or 2′-
deoxyribose), and one or more
phosphate groups
Parts of a Nucleotide
In both DNA and RNA, a nucleotide consists of three parts:
• Nitrogenous base (base): A nitrogenous base (simply called a “base” in
the context of biochemistry) is an organic molecule that contains nitrogen.
Chemically, it’s a base because of the pair of electrons on the nitrogen
atom.
• Pentose sugar: The sugar is called a “pentose sugar” because it contains
five (pent-) carbon atoms. The carbon atoms are numbered. The sugar in
DNA is 2′-deoxyribose, while the sugar in RNA is ribose. The only
difference between the two sugars is that 2′-deoxyribose has one less
oxygen atom attached to the second carbon.
• Phosphate group: A nucleotide has at least one phosphate (PO43-) group.
One oxygen atom of the phosphate connects to the 5′ carbon in the sugar.
When phosphate groups link together (as in ATP or adenosine
triphosphate), the link looks like O-P-O-P-O-P-O. The nucleotide name
refers to the number of phosphate groups it contains
Nucleotides exist in different forms depending on the number of
phosphate groups:
2. Ribonucleic acid (RNA). The other type of nucleic acid, RNA, is mostly
involved in protein synthesis.
Historical commentary on nucleic acids
• In 1944: Avery, MacLeod & McCarty presented Strong evidence that DNA is
genetic material
• In 1950: Chargaff reported careful analysis of DNA from a wide variety of
organisms. Content of A,T, C & G varied widely according to the organism,
however: A=T and C=G (Chargaff’ Rule)
• In 1953: Watson & Crick - structure of DNA (1962 Nobel Prize with M.
Wilkens, 1962)
DNA Double-Helix Structure
The sugar and phosphate lie on the outside of the helix,
forming the DNA’s backbone. The nitrogenous bases are
stacked in the interior, like a pair of staircase steps.
Hydrogen bonds bind the pairs to each other. Every base
pair in the double helix is separated from the next base pair
by 0.34 nm.
The helix’s two strands run in opposite directions, meaning
that the 5′ carbon end of one strand will face the 3′ carbon
end of its matching strand.
Each cell contains about two meters of DNA. DNA is
“packaged” by coiling around a core of proteins known as
histones. The DNA-histone assembly is called a
nucleosome. Histones are rich is lysine and arginine
residues.
Rules of base pairing
Because of the structure of the bases, A can only
form hydrogen bonds with T, and G can only form
hydrogen bonds with C (remember Chargaff’s
Rules).
• Each strand is therefore said to be
complementary to the other, and so each
strand also contains enough information to act
as a template for the synthesis of the other.
• This complementary redundancy is important
in DNA replication and repair. If the sequence
of one strand is AATTGGCC, the
complementary strand would have the
sequence TTAACCGG.
• During DNA replication, each strand is copied,
resulting in a daughter DNA double helix
containing one parental DNA strand and a
newly synthesized strand.
DNA
20
Reading Primary Structure
Nucleotide
Sugar Phosphate
“backbone”
Describing a Sequence
• Replication: is the process by which DNA is copied with very high fidelity.
• Transcription: process by which the DNA genetic code is read and transferred to
messenger RNA (mRNA). This is an intermediate step in protein expression.
• Translation: The process by which the genetic code is converted to a protein, the
end product of gene expression. The DNA sequence codes for the mRNA
sequence, which codes for the protein sequenc
Enzymes in DNA replication
DNA is replicated by the coordinated efforts of a number of proteins and enzymes. For
replication, DNA must be unknotted, uncoiled and the double helix unwound.
1. Topoisomerase: Enzyme that unknots and uncoils DNA.
2. Helicase: Protein that unwinds the DNA double helix.
3. DNA polymerase: Enzyme that replicates DNA using each strand as a template
for the newly synthesized strand.
4. DNA ligase: enzyme that catalyzes the formation of the phosphodiester bond
between pieces of DNA.
DNA replication is semi-conservative: Each new strand of DNA contains one parental
(old, template) strand and one daughter (newly synthesized) strand
Interesting Links
• https://youtu.be/Qqe4thU-os8?si=6JNOc5W5z5dSSKWN (DNA Replication)