Nucleic Acid

Learning objectives:
1. Identify or recognize nucleic acid
2. Components in nucleic acid:
i. monosaccharide,
ii. nucleobases,
iii. phosphoric acid

3. Differentiate:
i.
ii.

between 2 types of nucleic acids, DNA and RNA

between nucleotide and nucleoside

4. Definition: 1. nucleotide, 2. nucleoside, 3. DNA and

RNA

Nucleic acids
1. Nucleic acid: a biopolymer containing three types
of monomer units
i.

A nitrogenous base (nucleobases), either purine

or pyrimidine
ii. A monosaccharide (aldopentose), either D-ribose
or 2-deoxy-D-ribose
iii. A phosphoric acid/phospharyl group

2. Two types of nucleic acid:i.

ii.

RNA (Ribonucleic Acid)

DNA (Deoxyribonucleic Acid)

Nucleic acids

Nonpolar

i. Nitrogenous bases (nucleobases)

Heterocylic compounds containing C, H, N, and O

Purine and pyrimidine
methyl

1 ring
structure

2 ring
structure

ii. Monosachharide/sugar

Polar

Only anomer
present in nucleic
acid

2 type of aldopentoses found:

1. Ribose (RNA)
2. 2-deoxyribose (DNA)

Deoxyribose is a derivative of ribose. It lacks an

oxygen atom at C2

iii. Phosphoric group

Phosphoric group - polar

Nucleotide

Nucleoside

Nucleosides
1. Nucleoside: a compound that consists of D-ribose
or 2-deoxy-D-ribose (monosaccharide) covalently
bonded to a nucleobase by a -N-glycosidic bond
2. Covalent linkage forms between N9 of purines or N1
of pyrimidines to C1 (anomeric carbon of ribose or 2deoxyribose)

Lack phosphate
group

Pyrimidine

Purine

Nucleotides
1. Nucleotide: a nucleoside in
which a molecule of
phosphoric acid/phosphoryl
group is esterified with an OH of the monosaccharide,
at the 5-OH
2. As constituents of cofactors,
Coenzyme A (CoA), flavin
adenine dinucleotide (FAD)
& nicotinamide adenine
dinucleotides (NAD)
Nucleobase, aldopentose sugar and
phosphoryl group
Phosphoric acid - polar

http://www.sciencewithmrmilstid.com/2009/02/03/

5 = attach to
C5 of pentose

Nomenclature of Nucleotide

Based on the nucleoside, plus the

phosphate group

Nucleotide sequence
Gene: Sequence of nucleotides that encodes a
polypeptide, eventually forming a functional protein
Gene: a discrete unit of hereditary information
consisting of a specific nucleotide sequence in DNA
(RNA in some viruses)
The nucleotide sequence is depending on the bases
(nucleobases) present

Nucleic acid
DNA
Nucleoside

1. Bases = ATGC
2. Aldopentose =
Ribose
3. Phosphoryl group

Naming of nucleotide: if
Base adenine Deoxyadenosine 5
monophosphate

Biopolymer,
nucleotide
as monomer

RNA
1. Bases = AUGC
2. Aldopentose =
Deoxyribose
3. Phosphoryl group
Naming of nucleotide: if
Base adenine Adenosine
5monophosphate

Nucleic acid: DNA & RNA

DNA and RNA are polymers whose monomer
units are nucleotides = polynucleotides

DNA
DNA stands for deoxyribonucleic acid.
It is the genetic code molecule for most
organisms.
NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES

RNA
RNA stands for ribonucleic acid.
RNA molecules are involved in converting the
genetic information in DNA into proteins.
In retroviruses, RNA is the genetic material.

NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES

Polynucleotide = DNA
and RNA

DNA

Hydrolysis break bond

Deoxyribonucleic acids,
DNA: a biopolymer that
consists of a backbone of
alternating units of 2-deoxyD-ribose and phosphoryl
group
the 3-OH of one
nucleotide is joined to the
5 P of the next
nucleotide by a
phosphodiester bond

Condensation form bond

3 5 -phosphodiester bond

DNA Structure
Levels of structure
1 structure: the order of bases on the
polynucleotide sequence; the order of bases
specifies the genetic code
2 structure: the three-dimensional conformation
of the polynucleotide backbone = double helix
structure
3 structure: supercoiling
4 structure: interaction between DNA and
proteins

DNA: 1 Structure
Primary Structure: the
sequence of bases along the
pentose-phosphodiester
backbone of a DNA molecule

base sequence is read

from the 5 end to the 3
end
System of notation single
letter (A,G,C and T)
5 G G C A T T G C G C - 3
On the right

3 5 -phosphodiester bond

Segment of DNA Chain

O
5-end C N
N

C N
C
H2N
N
-2
O3PO CH2
O
H
H
H
H
H
O

CH

N
C

guanine
O
C

O
N
O P O CH2
O
O
H
H
H
H
H
O

3-5
link

CH3

C
CH

thymine

NH2
C
N
CH
C
CH
O
N
O P O CH2
O
O
H
H
H
H
OH H

3-end

5 end
phosphate group
is free
3end 3 OH
in deoxyribose is
free

cytosine

DNA: 2 Structure

Secondary structure: the

ordered arrangement of nucleic
acid strands
Double helix: a type of 2
structure of DNA molecules in
which two antiparallel
polynucleotide strands are coiled
in a right-handed manner about
the same axis
The chains run antiparallel and
are held together by hydrogen
bonding between complementary
base pairs: A=T, G=C.
DNA double helix

DNA Structural Elements

2 right-handed, helical,
polynucleotide chains,
coiled around a common
axis to form a double helix
2 characteristic: Major
groove and minor groove
binding site for drug or
polypeptide
2 strands run in opposite
direction (antiparallel)-3,5phosphodiester bridges run
in opposite direction

OH

DNA Structural Elements

1 base (purine) from single strand

link to 1 base (pyrimidine) from
other stand (complimentary)
Bases are perpendicular to helix
axis
Polarity and non-polarity regions
Aqueous environment polar,
charged, covalent backbone
deoxyribose and phosphate
groups outside of the helix
Hydrophobic purine and
pyrimidine bases avoid water by
turning towards the inside of the
structure.

OH

Complementary Base Pairing

Base pairing is complementary: A=T, GC
A major factor stabilizing the double helix is base pairing by
hydrogen bonding between T-A and between C-G
T-A base pair comprised of 2 hydrogen bonds

Complementary base
pairing

Complementary Base airing

G-C base pair comprised of 3 hydrogen bonds

Forms of DNA

B-DNA

considered the physiological form

a right-handed helix, inside diameter 11
10 base pairs per turn (34) 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
Z-DNA occurs in nature, usually consists of alternating purine-

pyrimidine bases
Methylated cytosine found also in Z-DNA

Structural features of A-, B-, and Z- DNA

Type
A-DNA
B-DNA
Z-DNA
Helical senses right handed
right handed
left handed
Diameter ()
~26
~20
~18
Base pairs/turn
11
10
12
Major groove
narrow/deep
wide/deep
Flat
Minor groove wide/shallow
narrow/deep
narrow/deep
Pg 294, Concepts
in Biochemistry.
3/e 2006 John
Wiley & Sons

20

DNA: 3 Structure
Tertiary structure:
the three-dimensional
arrangement of all
atoms of a nucleic
acid; commonly
referred to as
supercoiling
SupercoilingFurther coiling and
twisting of DNA helix.

DNA: 3 Structure
DNA can forms tertiary structure by twist into
complex arrangement supercoil
Circular DNA: a type of double-stranded DNA in
which the 5 and 3 ends of each strand (2
polynucleotide chains) are joined by
phosphodiester bonds
Can be found in microorganisms
(bacteriophages, bacteria)
Circular twisted into supercoiled
DNA - 3 Structure
Supercoil - results of extra
twisting in the linear duplex form

DNA: 3 Structure
Circular DNA: In microorganisms
(bacteriophages, bacteria)
Circular twisted into supercoiled
DNA - 3 Structure
In eukaryotes, the 3 structure
involves histone (protein)Chromatin: DNA molecules
wound around particles of
histones in a beadlike structure

Properties of Supercoil
1. Supercoiled is less stable than the
relaxed form
2. Compact hence it more easily stored in
the cell
3. Play a regulatory role in DNA replication

Bacteriophage :

DNA threadlike
structure

Super DNA Coiled Analogy

Double helix can be considered to a 2-stranded, right
handed coiled rope
Can undergo positive/negative supercoiling

DNA: 4 Structure
Four stranded form of DNA (quadruplex DNA)
Role in regulating and stabilizing telomeres and in
regulation of gene expression
Small molecules such as porphyrins and anthraquinones
present, to stabilize the structure

G-quadruplex

Next: Nucleic acid (2)

Central Dogma of Molecular Biology

DNA replication
(DNA DNA)

DNA Polymerase
DNA
Reverse Transcriptase
Reverse Transcription
(RNA DNA)

Transcription
(DNA RNA)

RNA replication
(RNA RNA)

RNA Polymerase
(+) Sense RNA
Translation
(RNA Protein)

Ribosomes
Protein

(-) Anti-Sense RNA

RNA-Dependent
RNA Polymerase

Learning Objectives
1.
2.
3.
4.

Denaturation of DNA
Identification/recognizing RNA
Differentiate between DNA and RNA
Differentiate between mRNA, tRNA and
rRNA
5. Codons

Denaturation of DNA
DNA can be distrupted by:
1. Heat
2. Bases
3. Acids
4. Organic solvents

Denaturation of DNA = Double helix denatured

= Unwinding of the DNA double helix

Denaturation of DNA
In nature, the
unwinding of the
DNA double helix
is the important
step in DNA
replication
Involves the nitrogenous bases

Denaturation of DNA
Denaturation: Disruption of 2 structure of
DNA
Occurs most commonly by heat denaturation
(melting- the heat denaturation of DNA)

As strands of DNA separate:

Absorbance at 260 nm increases
Increase is called hyperchromicity the wavelength of absorption does
not change but the amount of
light absorbed increases
Midpoint of transition (melting)
curve = Tm
The higher the % G-C, the higher
the Tm
Renaturation/annealing is possible
on slow cooling
This process has principal use in PCR

At the nitrogenous bases

Denaturation of DNA
Double helix unwinds when DNA is denatured
Can be re-formed with slow cooling and annealing

RNA:

Consist of long, unbranched chains of nucleotides joined by

phosphodiester bonds between the 3-OH of one pentose and
the 5-P of the next nucleotide
The pentose: unit is -D-ribose (it is 2-deoxy-D-ribose in DNA)
- the extra OH present in RNA makes this nucleotide more
susceptible to hydrolysis than DNA

The pyrimidine bases: are uracil and cytosine (they are

thymine and cytosine in DNA)
RNA is single stranded | DNA is double stranded

The bases sequences of all types of RNA

are determined by that of DNA

RNA
RNA molecules are classified according to their
structure and function

RNA Structure
Levels of structure
1 structure: the order of bases on the
polynucleotide sequence; complementary to the
DNA template
2 structure: no specific 2 arrangements, but RNA
is not completely lacking of regular structure
3 structure: interaction between DNA and
proteins

RNA 1 Structure
Polymer of nucleotide
Involves single polynucleotide strand

RNA - 2 Structure
Loop back onto themselves to fold into
conformation containing several
different structural elements:
1-hairpin turns
2-right-handed double helixes
3-internal loops

All classes of RNA synthesized as

single-stranded molecules
3OH

5P

 Hairpin turn
- Loops in the single chain

Right-handed double helixes

- Result of intrastrand folding
- Trigger by hairpin turn
- Antiparallel & stabilized in the same
direction as in DNA
- Hold by H bond & stacking interaction

Internal loops
- Common in RNA
- Structural features that disrupt the
formation of continuous double helix
regions

tRNA
Transfer RNA, tRNA:
the smallest kind of the three
RNAs
a single-stranded
polynucleotide chain between
73-94 nucleotide residues
carries an amino acid at its 3
end
intramolecular hydrogen
bonding occurs in tRNA

Function: Involves in
synthesis of polypeptide, to
carry amino acid to site of
protein synthesis

tRNA Structure
Smallest types of RNA
Highly structured
All tRNAs contain between 74 and 93 nucleotides in a
single chain
Structural features: hairpin turns, regions of double
helix and loops (non-hydrogen bonded portions)
Carriers of specific amino acids used for protein
synthesis
Reads the codon message on mRNA and incorporates
amino acid into the protein being synthesized
20 amino acid 20 tRNA

tRNA

o
3

structure

To produce tertiary structure, tRNA folds into an Lshaped conformation

The 3D structure of yeast tRNA

for phenylalanine

rRNA
Ribosomal RNA, rRNA: a ribonucleic acid found in
ribosomes, the site of protein synthesis
Only a few types of rRNA exist in cells
Ribosomes (protein-synthesizing organelles) consist
of 60 to 65% rRNA and 35 to 40% protein
In both prokaryotes and eukaryotes, ribosomes
consist of two subunits, one larger than the other
Analyzed by analytical ultracentrifugation
Particles characterized by sedimentation coefficients,
expressed in Svedberg units (S)
Sequencing of 16S RNA (small subunit of bacteria
rRNA) - identification of bacteria

rRNA Structure
Secondary & tertiary structures of rRNA display
same elements as tRNAs

Secondary structure for

E. coli 16S rRNA.

mRNA

Structure: Linear
polynucleotide
strand

Messenger RNA, mRNA:

a ribonucleic acid that carries coded genetic
information from DNA to ribosomes for the synthesis
of proteins

present in cells in relatively small amounts and very

short-lived (less abundant form of RNA)
single stranded
biosynthesis is directed by information encoded on
DNA
Synthesize from DNA, the nucleotide sequence in
mRNA is similar with the 5-3 strand of DNA, with the
exception of U replacing T

5-3 DNA sequence is the same with RNA sequence (complementary to

3-5DNA) sequence

mRNA Structure
Serves as a template for protein synthesis
(Carries the transient message for protein
synthesis from nuclear DNA to the ribosomes)
Move the information contained in DNA to the
translation machinery
Each molecule carries the instruction for each
gene (codes for one type of polypeptide product)

5 G G C A U U G C G C - 3

Codon
A codon is a sequence of three nucleotides
which codes for a specific amino acid.

Codons
Initiation codon
- Codes for the 1st amino acid in all polypeptide sequences
(AUG)
- N-formyl methionine in prokaryotes and methionine in
eukaryotes

Termination codon
- UAA, UAG & UGA
- Do not code for an amino acid & thus signal the end of
protein synthesis
- Also called stop codon or nonsense codon

http://wwwclass.unl.edu/biochem/gp2/m_biology/animation/ge
ne/gene_a1.html

- End of Chapter: Nucleic acids -