BM101: BIOLOGY FOR ENGINEERS

Nucleic Acids

Instructor: Yashveer Singh, PhD

Slides courtesy: Dr. Durba Pal

16 September 2019 1
 Nucleic acids
▪ Living cells have ability to produce exact
replicas of themselves

▪ Molecules responsible for these

properties are nucleic acids- DNA and
RNA

Stoker’s General, Organic, and Biological Chemistry 2

 Nucleic acids

▪ Complete hydrolysis (where no further hydrolysis is possible) of nucleic acids

gives following three molecules: sugar, base, and acid

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 Nucleic acids

▪ If the nucleic acid is RNA, it yields -D-ribose sugar

▪ If the nucleic acid is DNA, it yields -D-2’-deoxyribose sugar

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Nucleic acids
▪ Nucleic acids have two types of
bases: purine (double ring) and
pyrimidine (single ring)

▪ Purine bases adenine (A) and

guanine (G) are present in both DNA
and RNA

▪ Pyrimidine bases cytosine (C) and

thymine (T) are present in DNA,
whereas cytosine (C) and uracil (U)
are present in RNA

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 Nucleic acids

▪ Both DNA and RNA contain same acid- phosphoric acid

Stoker’s General, Organic, and Biological Chemistry 6

 Nucleic acids
▪ Nucleosides are formed
attaching a base to a
sugar

▪ A pyrimidine (N1) or
purine (N9) site is linked
to 1’-C of ribose or 2’-
deoxyribose sugar,
through a N-glycosidic
linkage

Stoker’s General, Organic, and Biological Chemistry 7

Nucleic acids
▪ Nucleotides are 5’-phosphate esterof
a nucleoside

▪ The structure of adenosine-5’-monophosphate

(AMP), a nucleotide, is shown here

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Nucleic acids
▪ Structure of
nucleotides found in
DNA are shown here

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 Nucleic acids

▪ Names of nucleoside and nucleotide are given in the table. Notice the change
in the nomenclature of purine and pyrimidine nucleosides and nucleotides

Stoker’s General, Organic, and Biological Chemistry 10

Primary structure of DNA
▪ Deoxyribonucleic acid/DNA is found within the
cell nucleus (also mitochondria and chloroplast).
Stores and transfer of genetic information, which
is used to control many functions of a living cell

▪ Primary structure of DNA comprises a

polynucleotide chain linked together through 3’-
5’ phosphodiester linkage. Notice the free 5’-
phosphate and 3’-hydroxy terminals

▪ Notice the presence of deoxyribose sugar and

thymine base

Stoker’s General, Organic, and Biological Chemistry 11

Secondary and tertiary structure of DNA
▪ Base composition studies on
DNA has shown that %A = %T
and %G = %C
▪ An explanation to this was
provided by Watson and Crick
(validated later)
▪ DNA is a double helical
structure containing two
polynucleotide chains, which
run antiparallel
▪ Sugar–phosphate backbone
can be thought of as being
the outside banisters of the
spiral staircase

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Secondary and tertiary structure of DNA
▪ The bases (stairs) of each backbone extend inward
toward the bases of the other strand
▪ The double helical structure is stabilized by hydrogen
bonding interactions between bases on the antiparallel
strand
▪ Due to the size restriction, only purine and pyrimidine
pairing was possible and out of all possibilities, the most
preferred pairs were AT and GC (complementary base
pairing)
▪ Each turn of DNA is made up of 10.4 nucleotide pairs (3.4
nm)
▪ Each base pair is 0.34 nm apart
▪ The coiling of the two strands around each other creates
two grooves in the double helix. The wider groove is called
the major groove and the smaller the minor groove
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 Secondary and tertiary structure of DNA

▪ An AT pair will have two hydrogen bonding interactions, whereas GC pair will have three
hydrogen bonding interactions
▪ Bases in a double helix are positioned with the planes of their rings parallel (like a stack of
coins). Stacking interactions between a given base and the parallel bases directly above it
and below it also contribute to the stabilization of the helix
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Types of DNA
▪ B-DNA (right handed) is
most common

▪ A-DNA, a shorter and

wider form is found in
dehydrated samples
(crystallographic studies)

▪ Z-DNA (left-handed) is a
transient form of DNA
existing in response to
certain types of biological
activity
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 Primary structure of RNA
▪ Ribonucleic acid or RNA occurs in all
parts of a cell and are mainly involved
in the synthesis of proteins, the
molecules that carry out essential
cellular functions
▪ Like DNA, RNA too is a
polynucleotide. However, the sugar is
ribose and uracil is present as one of
the base instead of thymine
▪ A structure of tetranucleotide is
given here

Timberlake’s General, Organic, and Biological Chemistry 16

Secondary structure of RNA
▪ RNA are small (75 to few
thousand nucleotides)
▪ RNA comprises single
polynucleotide strand, the
portion of which (due to
complementary base
pairing) may fold upon itself
to give double helical
regions
▪ Different secondary
structures are possible-
hairpin, stem-loop, clover
leaf, etc.

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Tertiary structure of RNA
▪ tRNA molecules adopt a well-defined
three-dimensional structure in solution,
which is necessary for protein synthesis
▪ Larger rRNA molecules may have locally
well defined tertiary structure with more
flexible links in between

Lodish Molecular Cell Biology 18

 Major types of RNA
▪ Messenger RNA (mRNA): RNA that carried instruction for protein synthesis (genetic
information) to the sites for protein synthesis. The molecular mass of messenger RNA
varies with the length of the protein whose synthesis it will direct

▪ Ribosomal RNA (rRNA): RNA that combines with specific proteins to form
ribosomes, the physical sites for protein synthesis. Ribosomes have molecular
masses on the order of 3 million amu. The rRNA present in ribosomes has no
informational function

▪ Transfer RNA (tRNA): RNA that delivers amino acids to the sites for protein
synthesis. Transfer RNAs are the smallest of the RNAs, possessing only 75–90
nucleotide units

▪ RNAs will be discussed in detail during protein synthesis (translation)

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 Milestones
▪ 1865: Gregor Mendel introduced the concept of heredity
▪ 1909: Wilhelm Johannsen: coined the term gene
▪ 1911: Thomas Hunt Morgan discovered that genes are responsible for
inheritance
▪ 1929: Phoebus Levene discovered that DNA is made of nucleotides,
phosphates, sugars, and four bases
▪ 1944: Oswald Avery showed that DNA can transform the property of cells
(not universally accepted)
▪ 1950: Erwin Chargaff showed that A+G = T+C = 50%
▪ 1951: Rosalind Franklin discovered A and B form of DNA (X-ray diffraction)
▪ 1953: James Watson and Francis Crick proposed the double helical model for
DNA

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 Do it yourself
▪ Read section, The Structure of DNA in Chapter 5 – DNA and chromosomes
from the Essential Cell Biology, B. Alberts, D. Bray, K. Hopkin, A. Johnson, J.
Lewis, M. Raff, K. Roberts, and P. Walter, Garland Science, IV Edition, 2014

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