Nucleic Acids

BIOCHEMISTRY
NUCLEIC ACIDS
NUCLEIC ACIDS
Nucleic Acids: chain of nucleotides which store genetic information

in biological systems.
STRUCTURE OF NUCLEOTIDES
❖The monomer of nucleic acids

❖They consist of three parts which are covalently bonded
together
1. Nitrogenous base – purine or pyrimidine

2. Sugar – ribose or deoxyribose
3. Phosphoryl Group
NITROGENOUS BASES
❖ Purines and pyrimidines are nitrogen-containing heterocycles

❖ Their planar character allows close association or stacking,
which helps stabilize DNA.
Purine – includes adenine and guanine

Pyrimidine – includes cytosine, thymine and uracil
NITROGENOUS BASES
Structures of the common nitrogenous bases

SUGARS
❖D-ribose – sugar in RNA

❖D-2’-deoxyribose – sugar in DNA
❖Numerals with a prime distinguish sugar carbons from those of
the nitrogenous base
❖The sugars in nucleic acids are linked through a β-N-glycosidic
bond through N-1 of pyrimidine or N-9 of purine.
SUGARS
NUCLEOSIDE
Nucleoside – nitrogenous base + sugar

Base Ribonucleoside Deoxyribonucleoside
Adenine Adenosine Deoxyadenosine
Guanine Guanosine Deoxyguanosine
Cytosine Cytidine Deoxycytidine
Thymine Deoxythymidine
Uracil Uridine
PHOSPHORYL GROUP
❖Phosphoryl groups are esterified

to the hydroxyl group of a sugar,
mostly at the 5’ position.
Additional phosphoryl groups
can be attached to the
phosphate using acid anhydride
bonds.
❖Nucleotides – nitrogenous +
sugar + phosphoryl residues
NUCLEOTIDES
10
NUCLEOTIDES
Base Ribonucleotide Deoxyribonucleotide
Adenine Adenylate Deoxyadenylate

Guanine Guanylate Deoxyguanylate
Cytosine Cytidylate Deoxycytidylate
Thymine Deoxythymidylate
Uracil Uridylate
PHOSPHODIESTER BONDS
Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids

❖The successive nucleotides of
both DNA and RNA are
covalently linked through
phosphate-group “bridges,” in
which the 5’-phosphate group of
one nucleotide unit is joined to
the 3’-hydroxyl group of the next
nucleotide, creating a
phosphodiester linkage.
❖The convention in writing down
the bases of polynucleotides is
from 5’ to 3’
NUCLEIC ACIDS
A fragment of an RNA chain

NUCLEIC ACIDS
A portion of a DNA chain

DEOXYRIBONUCLEIC ACID (DNA)
❖ Function of DNA
1. store genetic information that
can be accessed by the organism
and used to build proteins
2. Pass down genetic information
to offspring
❖ Functions of RNA
1. Transcribe the information
stored in DNA into a form that can
be understood and read by the cell
2. Assist in the protein synthesis
process
❖Levels of Structures in DNA
1. Primary structure – the order of bases on the polynucleotide

sequence.
2. Secondary structure– three-dimensional conformation of the

polynucleotide backbone
3. Tertiary structure – supercoiling

PRIMARY STRUCTURE
DNA RNA
SECONDARY STRUCTURE
❖ Double helix – proposed by James Watson and Francis Crick

– a type of secondary structure of DNA molecules in
which two antiparallel polynucleotide strands are
coiled in a right-handed manner about the same axis
❖ The two strands of DNA are antiparallel. One runs in the 5’ to 3’
direction, and the other runs in the 3’ to 5’ direction.
❖ There is a large major groove and a smaller minor groove in the
double helix; both can be sites at which drugs or polypeptides bind to
DNA.
❖ The bases in double stranded DNA are paired and follows Chargaff’s
rules: [A]=[T]; [C]=[G]; [pyrimidines]=[purines].
❖The two strands are held together

by hydrogen bonds between A and
T; between G and C.
❖There are 3 hydrogen bonds
between G and C.
❖There are 2 hydrogen bonds
between A and T or A and U.
EXERCISE: What is the complete base composition of a double-stranded

eukaryotic DNA that contains 22% guanine?
Forms of DNA
TERTIARY STRUCTURE
▪ In the tertiary level, the association of DNA to

basic proteins known as histones through non-
covalent interactions between the R groups of
the amino acids of the histones and the
components of the DNA forms the chromatin in
eukaryotes.
▪ In chromatin, the DNA molecule makes a
double turn forming a DNA superhelix at
regular intervals on a core of eight histone units
or nucleosomes.
▪ In contrast, bacteria, plasmids, mitochondria,
and chloroplasts have circular DNA that may
undergo supercoiling – the result of extra
twisting in the linear duplex form just before
covalent joining of the two double strands to
form the circular DNA.
QUATERNARY STRUCTURE
▪ The quaternary structure of DNA consists

of nucleic acid sequences that are rich in
G allowing formation of a 4-stranded
structure.
▪ Four G bases can associate through H-
bonding interactions to form a square
planar structure, a guanine tetrad that is
also known as G-quadruplexes or G-
tetrads or G4-DNA. Two or more G-
tetrads can stack on top of each other to
form a G-quadruplex.
▪ RNA molecules that are rich in G are also
known to be involved G-quadruplex
formation.
RIBONUCLEIC ACID
▪ RNA, unlike DNA, is usually

single-stranded. It has a single
chain instead of two. A
mononucleotide in an RNA
chain just like in the primary
level of structure of a DNA will
contain a pentose (ribose
instead of deoxyribose), one of
the four nitrogenous bases (A,
C, G, or U instead of T), and a
phosphate group.
RIBONUCLEIC ACID
▪ In the 2° level the RNA strand rather than folding into a uniform, periodic pattern
as in DNA loops back onto itself containing several structural elements.
Hairpin turns – loops that bring together
complementary stretches forming a double
helix structure
Right-handed double helix – result of
intrastrand folding, triggered by a hairpin
turn with CG, AU complementary pairing
Internal loops and bulges – common in
RNA molecules that lead to disruption of
the formation of continuous double helix
regions
RIBONUCLEIC ACID
There is practically no 3° or 4° structure observed in RNA molecules.

Additionally, the RNA is short: one gene long at most; whereas the DNA is
long, containing many genes.
Let us take a look at four major types of RNA that exist in cells: messenger
RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and regulatory
RNAs.
▪ The mRNA which transmit genetic information from the cell nucleus to
the cytoplasm is an intermediate between a protein-coding gene and its
protein product. If a cell needs to make a particular protein, the gene
encoding the protein will be turned “on,” meaning an RNA-polymerizing
enzyme will catalyze the synthesis of an RNA copy, or transcript, of the
gene’s DNA sequence.
RIBONUCLEIC ACID
▪ A major component of ribosomes, the rRNA is involved in amino acid

assembling during protein synthesis, where it helps mRNA bind in the
right spot so its sequence information can be read out. In the human cell,
the rRNA has a large (60S) and a minor particle (40S). Some rRNAs also act
as enzymes or catalyze chemical reactions specifically the formation of
peptide bonds between amino acids to form a protein. rRNAs that act as
enzymes are known as ribozymes.
RIBONUCLEIC ACID
▪ Molecules of tRNA are also involved in protein synthesis serving as carriers

of amino acids to the ribosome, ensuring that the amino acid added to the
chain is the one specified by the mRNA. They consist of a single strand of
RNA, but this strand has complementary segments that stick together to
make double-stranded regions. This base-pairing creates a complex 3D
structure resembling a cloverleaf that is known to be crucial to the
function of the molecule.
▪ Some types of non-coding RNAs (RNAs that do not encode proteins) help
regulate the expression of other genes. Such RNAs may be called
regulatory RNAs. MicroRNAs (miRNAs) and small interfering RNAs (siRNAs)
are small regulatory RNA molecules about 22 nucleotides long. They bind
to specific mRNA molecules (with partly or fully complementary
sequences) and reduce their stability or interfere with their translation,
providing a way for the cell to decrease or fine-tune levels of these mRNAs.
END

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BIOCHEMISTRY

Nucleic Acids: chain of nucleotides which store genetic information

❖The monomer of nucleic acids

1. Nitrogenous base – purine or pyrimidine

❖ Purines and pyrimidines are nitrogen-containing heterocycles

Purine – includes adenine and guanine

Structures of the common nitrogenous bases

❖D-ribose – sugar in RNA

Nucleoside – nitrogenous base + sugar

❖Phosphoryl groups are esterified

Base Ribonucleotide Deoxyribonucleotide

Adenine Adenylate Deoxyadenylate

Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids

A fragment of an RNA chain

A portion of a DNA chain

❖Levels of Structures in DNA

1. Primary structure – the order of bases on the polynucleotide

2. Secondary structure– three-dimensional conformation of the

3. Tertiary structure – supercoiling

❖ Double helix – proposed by James Watson and Francis Crick

❖The two strands are held together

EXERCISE: What is the complete base composition of a double-stranded

▪ In the tertiary level, the association of DNA to

▪ The quaternary structure of DNA consists

▪ RNA, unlike DNA, is usually

There is practically no 3° or 4° structure observed in RNA molecules.

▪ A major component of ribosomes, the rRNA is involved in amino acid

▪ Molecules of tRNA are also involved in protein synthesis serving as carriers

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