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Nucleic Acids
DNA & RNA
Lecture 8 (Finals)

What do they do ?
Dictate amino-acid sequence
in proteins
Give information to
chromosomes, which is then
passed from parent to
offspring

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What are they ?

The 4th type of

macromolecules
The chemical link between
generations
The source of genetic
information in chromosomes
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Definitions
Nucleic acids are polymers of nucleotides
A complex organic substance present in living cell, whose molecule consist of many
nucleotide (Building block of nucleic acid) linked in a long chain having varietyof
roles in cellular metabolism.
Nucleic acids largest and heaviest biomolecules, Molecular weight 30,000-millions

Nucleotides are carbon ring structures containing nitrogen linked to a

5-carbon sugar (a ribose)
5-carbon sugar is either a ribose or a deoxy-ribose making the
nucleotide either a ribonucleotide or a deoxyribonucleotide

In eukaryotic cells nucleic acids are either:

Deoxyribose nucleic acids (DNA)

Ribose nucleic acids (RNA)
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (tRNA)

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Functions of Nucleic Acids

◗ Nucleic Acid Functions:
◗ Storage of genetic info (DNA)
◗ Transmission of genetic info (mRNA)
◗ Processing of genetic information (ribozymes)
◗ Protein synthesis (tRNA and rRNA)

RNA
Involved in the transcription/translation of genetic material (DNA)

Genetic material of some viruses

DNA fingerprinting is a method used by forensic

experts to determine paternity.
 It is also used for the identification of criminals.
It has also played a major role in studies regarding
biological evolution and genetics.
Required for storage and expression of
genetic information.
They are the energy currency in
metabolic transactions (nucleotides).

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DNA
DNA – Deoxyribonucleic Acid
• DNA controls all living processes including
production of new cells – cell division
• DNA carries the genetic code – stores and
transmits genetic information from one
generation to the next
• Chromosomes are made of DNA
• DNA is located in the nucleus of the cell

Nucleotide Structure
Despite the complexity and diversity of life the structure of DNA is dependent
on only 4 different nucleotides

Diversity is dependent on the nucleotide sequence

All nucleotides are 2 ring structures composed of:

5-carbon sugar : -D-ribose (RNA)
-D-deoxyribose (DNA)

Base Purine
Pyrimidine

Phosphate group A nucleotide WITHOUT a phosphate group is a

NUCLEOSIDE

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Two types of Nucleotides

(depending on the sugar they contain)
1 Ribonucleic acids (RNA)
The pentose sugar is Ribose (has
a hydroxyl group in the 2rd carbon---
OH)
2 Deoxyribonucleic acids ( DN A )
The pentose sugar is
Deoxyribose (has just a hydrogen in
the same place--- H ) D eoxy =
“minus oxygen”

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Pentose Sugars
◗ The sugars have their carbon atoms numbered with
primes to distinguish them from the nitrogen bases

Ribose sugar-
presence of OH at
position 2

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Purine and Pyrimidine

◗ Pyrimidine contains two pyridine-like nitrogens in
a six- membered aromatic ring
◗ Purine has 4 N’s in a fused-ring structure.Three are
basic like pyridine-like and one is like that in
pyrrole

12 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003

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Nitrogenous Base-Purines
 Purines – Contains Adenine (A) and Guanine (G) nitrogen bases
 Heterocyclic aromatic compound
 Pyrimidines ring fused with imidazole ring
 Carbon atoms in purine ring are numbered in anti-clockwise
direction
 But in imidazole ring numbered in clockwise direction.
 C-4 and C-5 common to both rings
 Four nitrogen atoms present at 1st, 3rd, 7th, and 9th position.

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Nitrogenous Base-- Pyrimidines

 Pyrimidines (C4H4N2) – contains Thymine (T),
Cytosine (C) and Uracil (U) nitrogen bases
 Single Aromatic Compound, having six membered
heterocyclic ring system.
 2 nitrogen atoms at 1st and 3rd position
 4 carbon atoms at 2nd, 4th, 5th and 6th position
 In Pyrimidines C-2 is linked to oxygen by double
bond.

DNA and RNA Only in RNA DNA and Traces in

tRNA

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Names of Nucleosides and Nucleotides

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Nucleosides and Nucleotides

◗ A nucleoside consists of a nitrogen base linked by a
glycosidic bond to C 1’ of a ribose or deoxyribose
◗ Nucleosides are named by changing the the nitrogen
base ending to -osine for purines and –idine for
pyrimidines

◗ A nucleotide is a nucleoside that forms a phosphate ester

with the C 5’ O H group of ribose or deoxyribose
◗ Nucleotides are named using the name of the
nucleoside followed by 5’-monophosphate

Nucleotide
Nucleoside Sugar +
Sugar + Nitrogenous Nitrogenous base
base + Phosphate
group
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AMP, ADP and ATP

◗ Additional phosphate groups can be added to the nucleoside
5’- monophosphates to form diphosphates and
triphosphates
◗ AT P is the major energy source for cellular activity

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Conformation around N-Glycosidic Bond

◗ Relatively free rotation can occur around the N-glycosidic

bond in free nucleotides
◗ The torsion angle about the N-glycosidic bond (N-C1') is
denoted by the symbol 
◗ The sequence of atoms chosen to define this angle is O4'- C1'-
N9-C4 for purine,
and O4'-C1'-N1-C2 for pyrimidine derivatives
◗ Angle near 0corresponds to syn conformation
◗ Angle near 180 corresponds to anti conformation
◗ Anti conformation is found in normal B-DNA

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Nucleotide Function

Building blocks for DNA and RNA

Intracellular source of energy - Adenosine triphosphate (ATP)
Second messengers - Involved in intracellular signaling
(e.g. cyclic adenosine monophosphate [cAMP])
Intracellular signaling switches (e.g. G-proteins)
Signal transduction (cAMP)

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How the nucleotides are linked together !!

Phosphodiester bond: (3’-5’)
 The nucleotide of DNA and RNA are linked together by
phosphate “bridges”.
 The 5-phosphate group of one nucleotide unit is linked to the 3-hydroxyl
group of the next nucleotide, creating a phosphodiester linkage/bond.

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How the nucleotides are linked together !!

Phosphodiester bond:
The backbone of both RNA and DNA are hydrophilic. The phosphate group gives
negative charge.

5’ 3’

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Sanger dideoxy sequencing incorporates dideoxy

nucleotides, preventing further synthesis of the DNA
strand

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Formation of Polynucleotides:
Polynucleotide chains do not form through dehydration,
since this reaction is thermodynamically unfavored.

The metastability of DNA and RNA allow for controlled

-H2O turnover and reorganization via base
catalysis (e.g.
Go’=25 kJ/mol nucleases). More to come on this…
+H2O
cat. -OH
2 Go’PPio-PO4=-19 kJ/mol

Metastable

How do polynucleotides form? Coupled reactions!

Breaking high energy phosphate bonds (NTP to
NMP+PPi, and PPi to orthophosphate) provides a
favorable thermodynamic driving
force to yield polynucleotides

Go’NTPNMP=-31 kJ/mol

NTP + H2O NMP + PPi

Go’=-31 kJ/mol
DNAN+NMP DNA(N+1)+H2O
Go’=25 kJ/mol
PPi + H2O 2 HPO42-
Go’=-19 kJ/mol
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DNAN+NTP DNA(N+1)+2HPO42- Go’=-25 Go’Polynucleotide=25 kJ/mol
kJ/mol
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D N A stands for deoxyribose nucleic

acid
This chemical substance is present in the
nucleus of all cells in all living organisms
DNA controls all the chemical changes
which take place in cells
The kind of cell which is formed, (muscle,
blood, nerve etc) is controlled by DNA

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Hydrogen Bonding Interactions

◗ Two bases can hydrogen bond to
form a base pair
◗ For monomers, large number of
base pairs is possible
◗ In polynucleotide, only few
possibilities exist
◗ Watson-Crick base pairs
predominate in double-
stranded DNA
◗ A pairs with T
◗ G pairs with C
◗ Purine pairs with
pyrimidine

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The Difference in the Strands

◗ The strands of D N A are
complementary because of H-
bonding
◗ Whenever a G occurs in one strand, a
C occurs opposite it in the other
strand
◗ W hen an A occurs in one strand,
a T occurs in the other

Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003
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Base Pairing in DNA: The Watson–Crick

Base Pairing
◗ In 1953 W atson and C rick noted that D N A
consists of two polynucleotide strands, running in
opposite directions and coiled around each
other in a double helix
◗ Strands are held together by hydrogen
bonds between specific pairs of bases
◗ Adenine (A) and thymine (T) form strong
hydrogen bonds to each other
◗ Guanine (G) and cytosine (C ) form strong
hydrogen bonds to each other

Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003

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Primary Structure of Nucleic Acids

◗ The primary structure of a nucleic acid is the nucleotide sequence
◗ The nucleotides in nucleic acids are joined by phosphodiester
bonds
◗ The 3’-OH group of the sugar in one nucleotide forms an ester bond
to the phosphate group on the 5’-carbon of the sugar of the next
nucleotide

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Generalized Structure of DNA

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Reading Primary Structure

◗ A nucleic acid polymer has a

free 5’-phosphate group at
one end and a free 3’-OH
group at the other end
◗ The sequence is read from the
free 5’-end using the letters of
the bases
◗ This example reads
5’—A—C—G—T—3’

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Nucleic Acid Structure Polymerization

5’ 3’
Sugar Phosphate
“backbone”

T A G C A C
Bases
5’ 3’
TAGCA
C
P P P P P P
N N
C C
S Phosphodiesterase S
P
+ P P
C
N

P P (PPi) S
N
P
C
S
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Example of DNA Primary Structure

◗ In D N A, A, C , G, and T are linked by 3’-5’ ester bonds
between deoxyribose and phosphate

Nitrogen bases
Sugar
Phosphate
“backbone”

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Properties of a DNA
double helix

The strands of D N A are

antiparallel The strands are

complimentary There are

Hydrogen bond forces There

are base stacking interactions

There are 10 base pairs per turn

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The Double Helix (DNA)

Structural model:
◗ Model proposed by Watson & Crick, 1953
◗ Two sugar-phosphate strands, next to each
other, but running in opposite directions.
◗ Specific Hydrogen bonds occur among bases
from one chain to the other:
A---T , C---G
Due to this specificity, a certain base on one
strand indicates a certain base in the other.
◗ The 2 strands intertwine, forming a double-
helix that winds around a central axis

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• The sides of the ladder are:

Untwisted it
P = phosphate
looks like this:
S = sugar molecule
• The steps of the ladder are C, G, T, A
=
nitrogenous bases
(Nitrogenous means containing the
element nitrogen.)
A = Adenine (Apples are Tasty)
T = Thymine
A always pairs with T in DNA

C = Cytosine (Cookies are Good)

G = Guanine
Nucleotide C always pairs with G in
DNA
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Secondary Structure: DNA Double Helix

◗ In D N A there are two strands of nucleotides that
wind together in a double helix
- the strands run in opposite directions
- the bases are are arranged in step-like pairs
- the base pairs are held together by hydrogen
bonding
◗ The pairing of the bases from the two strands is very
specific
◗ The complimentary base pairs are A-T and G-C
- two hydrogen bonds form between A and T
- three hydrogen bonds form between G and C
◗ Each pair consists of a purine and a pyrimidine, so they are
the same width, keeping the two strands at equal distances
from each other
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Nucleic Acid Structure

“Base Pairing”
DNA base-pairing is antiparallel
i.e. 5’ - 3’ (l-r) on top : 5’ - 3’ (r-l) on

5’ 3’

T A G C A C

A T C G T G
3’ 5’

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Discovering the structure of D N A

Erwin Chargaff – (1905-2002)

• C olumbia University, N Y
• Investigated the composition of D N A
• His findings by 1950
strongly suggested the
base-pairings of A-T &
G-C
• Met with W atson and Crick
in 1952 and shared his
findings
• “Chargaff’s rule” A = T &
C =G

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Erwin Chargaff (1950)

 Chargaff’s base equivalence rule.
 Purines = Pyrimidines, [A+G] = [T+C], [A+G]/[T+C]=1

 Molar concentration of Adenine always equal to thymine, Similarly,

molar conc. of guanine is equal to cytosine
 Sugar and phosphate occur in equimolar proportions
 A-T base pairs are rarely equal to C-G base pairs
 The ratio of [A+T]/[G+C] is variable but constant for a species. It can
used to identify the source of DNA. The ratio is low in primitive
organisms and higher in advanced ones.

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Nucleic Acid Structure

The double helix
First determined by Watson & Crick in 1953

Most energy favorable conformation for double stranded DNA to

form
Shape and size is uniform for all life (i.e. DNA is identical)

Without anti-parallel base pairing this conformation could not

exist
Structure consists of “major” grooves and “minor” grooves

Major grooves are critical for binding proteins that regulate DNA
function

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The paired strands are coiled into a spiral

called

A DOUBLE HELIX

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PO4
PO4 The strands
separate PO 4
PO4

PO4 PO4

PO4 PO4

PO4
PO4

PO4
PO4

PO4
PO4

PO4
PO4

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Nucleic Acid Structure

The double helix

Minor
Groove

Major
Groove

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Watson and Crick model

• Is their any worth of these major and minor grooves!!

 As a consequence (of these grooves), the atoms on the edges of each

base

within these grooves are accessible from outside the helix, forming two

types of binding surfaces.

 DNA-binding proteins can “read” the sequence of bases in duplex DNA by

contacting atoms in either the major or the minor grooves.

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Why did DNA, rather than RNA, evolve to be the carrier of genetic information in
cells?
 The hydrogen at the 2′ position in the deoxyribose of DNA makes it a far more stable
molecule than RNA, which instead has a hydroxyl group at the 2′ position of ribose
 The 2′-hydroxyl groups in RNA participate in the slow, OH− catalyzed hydrolysis of
phosphodiester bonds at neutral pH

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Why the DNA is twisted !!

 The twisting of DNA is the result of both hydrophilic and hydrophobic
interactions between the molecules that comprise DNA and water in a cell.
 DNA is coiled into chromosomes and tightly packed in the nucleus of
our cells. The twisting aspect of DNA is a result of interactions
between the molecules that make up DNA and water.
 The nitrogenous bases are hydrophobic, Since the cell cytoplasm and
cytosol contain water-based liquids, the nitrogenous bases want to avoid
contact with cell fluids. Hydrophilic

 DNA is arranged such that the phosphate and the sugar backbone are on
the
outside and in contact with fluid, while the nitrogenous bases are in
the inner
portion of the molecule. To further prevent the nitrogenous bases from Hydrophobic

coming into contact with cell fluid, the molecule twists to reduce
space between the nitrogenous bases and the phosphate and sugar
strands.

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Structure of DNA

DNA strand separation

DNA double helic can be
disrupted/separated because of
1. Change in PH
2. Change in Temperature

What is melting temperature?

The temperature at which one half of the
helical structure is lost, is defined as melting
temperature.
What is Denaturation?
Complete loss of helical structure in DNA is
called Denaturation.

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Factors Affecting DNA Denaturation

◗ The midpoint of melting (Tm) depends on base

composition
◗ high CG increases Tm

◗ Tm depends on DNA length

◗ Longer DNA has higher Tm
◗ Important for short DNA

◗ Tm depends on pH and ionic strength

◗ High salt increases Tm

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Different forms of DNA

There are six known different morphological forms of DNA double helix.
These have been
named as A, B, C, D, E and Z DNA.
Out of these six forms only B-DNA and Z-DNA are found to occur as cellular
DNA.
 In the number of base pairs present per turn in them
 angle between the base pairs
 Diameter of DNA molecule
 Hardness of coiling of double helix

(1) A-DNA (2) B-DNA

• Discovered by Rosalind • Named by Rosalind Franklin
Franklin
• Right-Handed helix
• Majority of the DNA in a cell is in B-
• Form by the dehydration of B- DNA conformation.
DNA. • Right-Handed helix
• Bp per helix= 11bp • Bp per helix = 10-10.4
• Major Grooves= Narrow and • Major grooves = wide and deep
deep • Minor Grooves = Narrow and deep
• Minor Grooves = wide and
deep

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(3) Z-DNA (4) C-DNA, 5) D-DNA and E-DNA

• Discovered by Andres Wang and They do not occur under normal / natural
condition.
Alexander Rich.
• Left-handed helix.
• It is one of the biologically active forms
of DNA found in vivo in the cells.
• The exact biological function of Z-DNA
is not clear.
• Bp per helix = 12bp
• Major Grooves = flat major Grooves
• Minor Grooves = Narrow and deep

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Ribonucleic Acid (RNA)

◗ RN A is much more abundant than D N A
◗ There are several important differences between RNA
and DNA:
- the pentose sugar in RNA is ribose, in D N A it’s
deoxyribose
- in RNA, uracil replaces the base thymine (U pairs with
A)
- RN A is single stranded while D N A is double
stranded
- RNA molecules are much smaller than D N A molecules
◗ There are three main types of RN A:
- ribosomal (rRNA), messenger (mRNA) and transfer
(tRNA)

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Types of RNA

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Messenger RNA (mRNA)

◗ M essenger RN A carries the
genetic code to the ribosomes
- they are strands of RN A that are
complementary to the D N A of the
gene for the protein to be
synthesized

61 Based on McMurry, Organic Chemistry,

Chapter 28, 6th edition, (c) 2003

61

Ribosomal RNA (rRNA)

◗ Ribosomes are a complex of proteins and rRNA
◗ The synthesis of proteins from amino acids and ATP occurs in
the ribosome
◗ The rRNA provides both structure and catalysis
◗ Ribosomes are the sites of protein synthesis
- they consist of ribosomal D N A (65%) and proteins (35%)
- they have two subunits, a large one and a small one

62 Based on McMurry, Organic

Chemistry, Chapter 28, 6th edition,
(c) 2003

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Transfer RNA (tRNA)

◗ Transports amino acids to the
ribosomes where they are
joined together to make
proteins
◗ There is a specific tRN A for
each amino acid
◗ Recognition of the tRN A at the
anti- codon communicates
which amino acid is attached
63 63 Based on McMurry, Organic
Chemistry, Chapter 28, 6th edition,
(c) 2003

Transfer RNA
◗ Transfer R N A translates the genetic code from the messenger
RNA and brings specific amino acids to the ribosome for protein
synthesis
◗ Each amino acid is recognized by one or more specific tRNA
◗ tRNA has a tertiary structure that is L-shaped
- one end attaches to the amino acid and the other binds to
the mRN A by a 3-base complimentary sequence

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The Parts of Transfer RNA

◗ There are 20 different tRNAs, one for
each of the 61 codons that specifies an
amino acid
◗ tRNA has 70-100 ribonucleotides and is
bonded to a specific amino acid by an
ester linkage through the 3 hydroxyl
on ribose at the 3 end of the tRN A
◗ Each tRN A has a segment called
an anticodon, a sequence of
three ribonucleotides
complementary to the codon
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sequence
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How DNA Works

1DNA stores genetic information in
segments called genes
2The DNA code is in Triplet Codons
(short sequences of 3 nucleotides
each)
3Certain codons are translated by
the cell into certain Amino
acids.
4. Thus, the sequence of
nucleotides in
DNA indicate a sequence of Amino
acids in a protein.
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DNA and Enzymes

The proteins build the cell structures. They also make
enzymes.
The D N A controls which enzymes are made and the
enzymes determine what reactions take place.
The structures and reactions in the cell determine what
sort of a cell it is and what its function is.
So, D N A exerts its control through the enzymes.

A sequence of triplets in the D N A molecule may code for a

complete protein. Such a sequence forms a gene. There may
be a thousand or more bases in one gene.

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The Genetic Code

◗ The genetic code is found in the sequence of nucleotides
in mRN A that is translated from the D N A
◗ A codon is a triplet of bases along the mRNA that codes for
a particular amino acid
◗ Each of the 20 amino acids needed to build a protein has at
least 2 codons
◗ There are also codons that signal the “start” and “end”
of a polypeptide chain
◗ The entire D N A sequence of several organisms, including
humans, have been determined, however,
- only primary structure can be determined this way
- doesn’t give tertiary structure or protein function

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A group of three bases (a triplet) coproduction of a

particular amino acid in the cytoplasm of the cell.

The amino acid sequence of a protein can be

determined by reading the triplets in the D N A
sequence that are complementary to the codons of
the mRN A, or directly from the mRN A sequence

The different amino acids and the order in

which they are joined up determines the
sort of protein being produced

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For example

Cytosine

Adenine Codes for Valine

Thymine

C ytosine
(C ) C odes for A lanine
Guanine
(G)

70 Adenine
(A)
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This is known as the triplet code

Each triplet codes for a specific am ino acid

C GA - C AA - C C A - C C A - GC T - GGG - GAG - C C A -

Ala Val Gly Gly Arg Pro Leu Gly

The amino acids are joined together in the

correct sequence to make part of a protein

Ala Val Gly Gly Arg Pro Leu Gly

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mRNA Codons and Associated Amino Acids

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Reading the Genetic Code

Suppose we want to determine the amino acids coded
for in the following section of a mRN A

5’—CCU —AG C—G GA—CUU —3’

◗ According to the genetic code, the amino acids for

these codons are:

CCU = Proline AGC = Serine

GGA = CUU =
Glycine Leucine
◗ The mRNA section codes for the amino acid sequence
of Pro—Ser—Gly—Leu

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