The nitrogenous bases (cont’d)

pyrimidine bases
- single-ring aromatic compounds
- include cytosine, thymine, and
uracil.
Chapter Nine
Nucleic Acids: How Structure
Conveys Information

purine bases
- two-ring aromatic compounds
- include adenine and guanine.

Paul D. Adams • University of Arkansas

[Link]/chemistry/campbell

Chapter Outline Other Bases

9-1 Levels of Structure in Nucleic Acids

9-2 The Covalent Structure of Polynucleotides

• Less common bases can occur.
9-3 The Structure of DNA
• Principally but not exclusively, in
transfer RNAs
9-4 Denaturation of DNA

9-5 The Principal Kinds of RNA and Their Structures

Nucleic Acids
The sugars
Levels of structure
The sugar component is ribose, which is present in RNA.
• 1o structure: the order of bases on the polynucleotide sequence;
When the hydroxyl group at the 2’ position is not present, you have 2’-deoxyribose,
the order of bases specifies the genetic code which is what you have in DNA.
• 2o structure: the three-dimensional conformation of the polynucleotide backbone
• 3o structure: supercoiling
• 4o structure: interaction between DNA and proteins

Ribose 2-deoxyribose
(in RNA) (in DNA)
Campbell and Farrel, 2009 edition, Biochemistry
Lehninger, 2004 edition, Biochemistry.

Nucleosides
Nucleotide – building unit of nucleic acids A nucleoside is a compound that consists of D-ribose or 2-deoxy-D-ribose
covalently bonded to a nucleobase by a ẞ-N-glycosidic bond.
An individual nucleotide consists of three parts —
nitrogenous base, This beta-N-glycosidic bond forms between the 1’
sugar, and carbon of the ribose (or deoxyribose) and the
phosphoric acid residue nitrogen atom of the nucleobase (N1 in pyrimidines
—and all of them are covalently bonded with one another. and N9 in purines).

A comparison of the structures of a

ribonucleoside and a deoxyribonucleoside.

(A nucleoside does not have a phosphate

group in its structure.)

The nitrogenous bases

Nucleotide – building unit of nucleic acids
The nitrogenous bases (nucleic acid bases, also called nucleobases) are of two types
Nitrogenous base
the pyrimidines and the purines.

In this case, the word base does not refer to an alkaline compound, such as NaOH;
rather, it refers to a nitrogenous aromatic compound.
Sugar
pyrimidine bases - single-ring aromatic compounds
- include cytosine, thymine, and uracil.

All these bases are found in DNA and RNA except for uracil, which occurs only in RNA.
Phosphoric acid residue

Ribose 2-deoxyribose
(in RNA) (in DNA)
Campbell and Farrel, 2009 edition, Biochemistry.
 The Deoxyribonucleotides A portion of a DNA strand A portion of an RNA strand
The structures and names of the four major deoxyribonucleotides (deoxyribonucleoside 5-monophosphates),
which are the structural units of DNAs (all structures are shown in the forms that exist at pH 7). DNA differs from RNA.
The nucleotide units of DNA are usually symbolized as A, G, T, and C, sometimes as dA, dG, dT, and dC.
They are also commonly abbreviated dAMP, dGMP, dTMP, and dCMP. Participating in the bond formation
are the phosphoric acid residue in
the 5’ position of one nucleotide and
the hydroxyl group at the 3’ position
of another nucleotide, and hence,
the resulting repeated linkage is a
3’,5’ phosphodiester bond.

3’, 5’-phosphodiester bridges link nucleotides

together to form polynucleotide chains.
Lehninger, 2004 edition, Biochemistry.

Nucleic Acids - 1° Structure

The Ribonucleotides
The structures and names of the four major ribonucleotides (ribonucleoside 5-monophosphates)
are the structural units of RNAs (all structures are shown in the forms that exist at pH 7). The Primary Structure of nucleic acids is the sequence of bases along the
pentose-phosphodiester backbone of a polynucleotide molecule
These nucleotide units of RNA are usually symbolized as A, G, U, and C.
• base sequence is read from the 5’ end to the 3’ end
They are sometimes abbreviated as AMP, GMP, UMP, and CMP.
• System of notation single letter (A,G,C,U and T)

Lehninger, 2004 edition, Biochemistry.

The DNA double helix

The predominant secondary structure of DNA is the

double helix.
When these nucleotides
This double helix was proposed by James Watson and
(ribonucleotides or deoxyribonucleotides)
Francis Crick in 1953.
are linked as monomers, the resulting
polymer is a nucleic acid. Two DNA strands wrap around each other to form the
DNA double helix.
The two strands run in antiparallel directions.
One strand is 5’ to 3’, while the other is 3’ to 5’.
This Photo by Unknown Author is licensed under CC BY-NC-ND
The two strands are held together by hydrogen bonds.

What links the nucleotides in a nucleic acid? The DNA double helix (cont.)

The Phosphodiester Bond Also, the two strands are said to be complementary
- links nucleotides together to one another because complementary base pairing
to form polynucleotides or occurs along the entire double helix.
nucleic acids
This means that:
The adenine always pairs with thymine, and
The guanine always pairs with cytosine.
3’,5’- Phosphodiester bond
The A–T base pair is held by two hydrogen bonds.
The G–C base pair is held by three hydrogen bonds.

A significant factor stabilizing the double helix is the

base pairing by hydrogen bonding between A-T and
between G-C.

5’-Terminus
By convention, the nucleotide One complete turn of the helix
residues of nucleic acids are spans 10 base pairs (bp)
covers a distance of 34 Å (3.4 nm)
written in abbreviated structure,
Inside diameter is 11 Å (1.1 nm)
with the 5' end, which normally
carries a phosphate group at the Outside diameter is 20 Å (2.0 nm)
left, to the 3' end, which normally Within the cylindrical outline, there
are empty spaces known as grooves:
has a free hydroxyl group at the
major groove
right, or in the 5’ to 3’ direction. 3’,5’- phosphodiester bond
minor groove both are large
enough to
accommodate
The 5’-ends of the chains are at the top; polypeptide chains
the 3’-ends are at the bottom.
Minus signs alongside the strands
represent the negatively charged
phosphate groups along the entire
length of each strand.
3’-Terminus
5’-Terminus 3’-Terminus
Campbell and Farrel, 2009 edition, Biochemistry.
The DNA double helix (cont.) Individual work assignment:
Also, in this imaginary cylinder of the double helix,
there are empty spaces known as grooves.
Essay (700 -1000 words) on a whole sheet of paper
There are large major grooves and smaller minor
written by hand.
grooves.

And these grooves can be the sites at which drugs

or proteins bind to DNA.

In this essay, you should explain what nucleic

acids are, describe their structure and functions,
and discuss why understanding them is crucial in
daily life and in advancing scientific literacy. Try to
connect your insights to SDG 4: Quality
Education, emphasizing how learning about
nucleic acids contributes to promoting
At neutral, physiological pH, ea
phosphate group carries a
negative charge.
knowledge, innovation, and responsible use of
Positively-charged ions science in society. Critical thinking, clarity of
(Na+ or Mg2+)
Polypeptides with +ly charged
side chains explanation, and reflection on real-life relevance
are encouraged.
Need to be associated
with DNA to neutralize
the + charges

Example:
Eukaryotic DNA is complexed
with histones, which are +ly
charged proteins, in the cell
Next meeting: November 15, 2025
nucleus.

Second Lecture Exam

Submission of essay work.

Other Forms of DNA
• B-DNA
• considered the physiological form
• a right-handed helix, diameter 11Å
• 10 base pairs per turn (34Å) of the helix
• A-DNA
• a right-handed helix, but thicker than B-DNA
• 11 base pairs per turn of the helix
• has not been found in vivo
• Z-DNA
• a left-handed double helix
• may play a role in gene expression

Comparison of A,B, and Z forms of DNA

• Both A and B-DNA are

right-handed helices
• Z-DNA is left handed
• Z-DNA occurs in nature,
usually consists of
alternating purine-
pyrimidine bases
• Methylated cytosine
found also in Z-DNA

Triple–helical DNA à observed in 1957

Synthetic oligonucleotides (~15 nucleotides) will bind
to naturally occurring DNA double-helix.
Reactive sites can be important to genetic engineering