Nucleic Acids: How
Structure Conveys
Information
Chapter 9
Levels of structure in Nucleic Acids
Primary – Order of bases in polynucleotide
sequence
 Secondary – Three-dimensional conformation
of the backbone
 Tertiary – Supercoiling of molecule
 Quaternary - Interaction between DNA and
proteins

What are nucleotides?
Monomers of Nucleic acids – Nucleotides
 Consists of nitrogenous base, sugar and
phosphoric acid residue
 Covalently bonded


RNA (Ribonucleic Acid)

DNA (Deoxyribonucleic Acid)
Pyrimidine and Purine Bases
Other Bases

Less common
bases/Unusual
bases

Principally but not
exclusively, in
transfer RNAs
What are Nucleosides?


Nucleoside: a compound that consists of D-ribose or
2-deoxy-D-ribose covalently bonded to a nucleobase
by a β-N-glycosidic bond
Lacks phosphate group
Nucleotides


A nucleoside in which a
molecule of phosphoric
acid is esterified with an OH of the
monosaccharide, most
commonly either the 3’OH or the 5’-OH
Polymerization leads to
nucleic acids. Linkage is
repeated (3’,5’phosphodiester bond)
DNA - 1° Structure

Deoxyribonucleic acids : a biopolymer that
consists of a backbone of alternating units of
2-deoxy-D-ribose and phosphate
the 3’-OH of one 2-deoxy-D-ribose is joined
to the 5’-OH of the next 2-deoxy-D-ribose
by a phosphodiester bond
DNA - 1° Structure


“d” used to designate
“deoxy”
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
 A,G,C, and T
Secondary structure of DNA

Double helix: a type of
2° structure of DNA
molecules in which two
antiparallel
polynucleotide strands
are coiled in a righthanded manner about
the same axis
How is the base pairing of DNA
complementary?

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
How is the base pairing of DNA
complementary?

G-C base pair
comprised of 3
hydrogen bonds
Are there other possible conformations
of double helix DNA?

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
Are there other possible conformations
of double helix DNA?

B-DNA
 considered the
physiological form
a
right-handed helix
 10
base pairs per turn
(34Å) of the helix
Are there other possible conformations
of double helix DNA?

Z-DNA
• a left-handed double
helix
• may play a role in
gene expression
• Alternating purine and
pyrimidine sequences
Z-form is derivative of B-form

Produced by
flipping one side of
the backbone 180˚
without disturbing
the backbone
covalent bonds or
hydrogen bonds
Differences between three forms
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
Tertiary structure of DNA
Tertiary structure: the three-dimensional
arrangement of all atoms of a nucleic acid;
commonly referred to as supercoiling
 Circular DNA: a type of double-stranded
DNA in which the 5’ and 3’ ends of each stand
are joined by phosphodiester bonds
 Supercoiling- Further coiling and twisting of
DNA helix

What are Topoisomerases?

Enzymes that can change supercoiled state of
DNA – TopoIsomerases

Class I and Class II

DNA gyrase
How does prokaryotic DNA
supercoil into its tertiary structure?
 Class
I: cut the phosphodiester backbone of
one strand, pass the end through, and reseal
 Class II: cut both strands, pass some of the
remaining DNA helix between the cut strands,
and reseal
 DNA gyrase introduces negative supercoils
into DNA
Super DNA Coiled Topology
Double helix can be considered to a 2stranded, right handed coiled rope
 Can undergo positive/negative supercoiling

How does eukaryotic DNA supercoil
into its tertiary structure?

Histone: a protein, particularly rich in the basic amino acids
Lys and Arg; found associated with eukaryotic DNA
 five main types: H1, H2A, H2B, H3, H4

Chromatin: DNA molecules wound around particles of
histones in a beadlike structure

Topological changes induced by supercoiling accommodated
by histone-protein component of chromatin.
Chromatin
• Each “Bead” is a
nucleosome
• Nucleosome consists of:
DNA wrapped around
histone core
Denaturation of DNA

Denaturation: disruption of 2° structure
 most commonly by heat denaturation
(melting)
 absorbance at 260 nm
 Hyperchromicity
 midpoint of transition (melting) curve
= Tm
 the higher the % G-C, the higher the
Tm
 renaturation is possible on slow
cooling
Denaturation and Renaturation of DNA
Double helix unwinds when DNA is denatured
 Can be re-formed with slow cooling and
annealing

Principal Kinds of RNA
Six kinds of RNA –
 messenger RNA (mRNA)
 transfer RNA (tRNA)
 ribosomal RNA (rRNA)
 small nuclear RNA (snRNA)
 micro RNA (miRNA)
 small interfering (siRNA)

Structure of RNA

RNA
 nucleotides joined
by phosphodiester bonds
between the 3’-OH of one pentose and the 5’-OH
of the next
 the pentose unit is D-ribose
 the pyrimidine bases are uracil and cytosine
 RNA is single stranded
Central dogma theory
RNA molecules are classified according to their
structure and function
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
Ribosomal RNA- rRNA
 Only
a few types of rRNA exist in cells
 ribosomes
consist of 60 to 65% rRNA and 35 to 40%
protein
 prokaryotes
and eukaryotes - ribosomes consist of two
subunits
 analyzed by
analytical ultracentrifugation - sedimentation
coefficients - expressed in Svedberg units (S)
Messenger RNA - mRNA

A ribonucleic acid that carries coded genetic
information from DNA to ribosomes for the
synthesis of proteins
 Present
in cells in small amounts (5-10 %)
 Very short-lived
Small nuclear RNA (snRNA)

Found in nucleus of eukaryotes

Small (100-200 nucleotides long)

Forms complexes with protein - small nuclear
ribonucleoprotein particles (snRNPs)

snRNPs help with processing of initial mRNA
transcribed from DNA
Small interfering RNA (siRNA)
Used in RNA interference
 Eliminate expression of an undesirable gene




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