NUCLEIC ACIDS

Nucleic Acids
Levels of structure
1structure: the order of bases on the
polynucleotide sequence; the order of bases
specifies the genetic code
2structure: the three-dimensional conformation
of the polynucleotide backbone
3structure: supercoiling
4structure: interaction between DNA and
proteins
Nucleic Acids
Nucleic acid: a biopolymer consisting of nucleotides which
consist of the following:

a base derived from purine or pyrimidine (nucleobases or

Nitrogen-bases)
a monosaccharide, either D-ribose (RNA) or 2-deoxy-D-
ribose (DNA)
phosphoric acid

RNA (Ribonucleic Acid)

DNA (Deoxyribonucleic Acid)

Pyrimidine/Purine Bases
The structures of pyrimidine and purine are shown here for
comparison
Other Bases
Less common bases can
occur

Principally but not

exclusively, in transfer
RNAs
Nucleosides
Nucleoside: a
compound that
consists of D-
ribose or 2-deoxy-
D-ribose
covalently bonded
to a nucleobase
by a -N-
glycosidic bond
Lacks phosphate
group
Page 40
Nucleotides
Nucleotide: 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
Name based on parent
nucleoside with a suffix
monophosphate
Polymerization leads to
nucleic acids. Linkage is
repeated (3,5-
phosphodiester bond)
Types of Bonds in a Nucleotide Structure
DNA - 1 Structure
Deoxyribonucleic acids, DNA: 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
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,U and T)

View Animation on Nucleic Acid (DNA) 1 Structure

DNA differs from RNA
Sugar is 2-deoxyribose, not
ribose.
Sometimes d used to
designate deoxy
Writing a DNA strand
an abbreviated notation
even more abbreviated
notations
d(GACAT)
pdApdCpdGpdT
pdACGT
Nucleotide subunits are
linked together by
phosphodiester bonds
Shorthand notation of the 1 Structure
(RNA)
Shorthand notation of the 1 Structure
(DNA)
Tautomerization
DNA - 2 Structure
Secondary structure: the
ordered arrangement of
nucleic acid strands
the double helix model of
DNA 2structure was
proposed by James
Watson and Francis
Crick in 1953
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
structure based on X-Ray
crystallography
X-ray Diffraction picture from the data of R. Franklin and M. Wilkins used by J.D.Watson and F.C. Crick in the
elucidation of the structure of the DNA.
James D. Watson Francis C. Crick
The Groups involved in work for the
elucidation of the DNA Structure

View Film on the Double Helix

 1962 Nobel Prize
2003 - 50 years of the DNA
1953 1st year of the DNA
London Science
Museum
Figure 3-7
Figure 3-8
T-A Base Pairing
Base pairing is complimentary

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

G-C Base Pair
G-C base pair comprised of 3 hydrogen bonds
Other Forms of DNA
B-DNA
considered the physiological form
a right-handed helix, 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
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
 Types of
DNA Double
Helix
Types of DNA Double Helix (continued)

Type A: major conformation of RNA, minor

conformation of DNA;
Type B: major conformation of DNA;
Type Z: minor conformation of DNA

5 3 5 3
5 3

3 5
3 5 B 3 Z
A 5
Wide
Narrow Left-handed
Less tight
tight Least tight
 Forces That Stabilize Nucleic Acid Double Helix

There are THREE major forces that contribute

to stability of helix formation
Hydrogen bonding in base-pairing
Hydrophobic interactions in base stacking
Dipole-dipole interactions (responsible for twist)

5 3

Same strand stacking

cross-strand stacking
3 5
Other Features of DNA
Base stacking
bases are hydrophobic and interact by hydrophobic
interactions
in standard B-DNA, each base rotated by 32
compared to the next and, while this is perfect for
maximum base pairing, it is not optimal for maximum
overlap of bases; in addition, bases exposed to the
minor groove come in contact with water
many bases adopt a propeller-twist in which base
pairing distances are less optimal but base stacking is
more optimal and water is eliminated from minor
groove contacts
 Edges of Base-paired Nucleotides
Edges of base pairs have specific relationships to grooves;
Major groove edges are sequence specific thus provide
sequence recognition sites; Many DNA-binding proteins bind
to major grooves of DNA in gene transcription and
regulation;
Small molecules can recognize minor grooves in DNA;
Minor groove is wider in A helix, thus is more important for
RNA recognition.
major groove major groove
H
H H N
O O
7 N H 4 5
N
N 5 6 N3 6
8 H N N H
N N 2
N N 1
N 1 N
9 4 N 2 O N H O
3 H

minor groove minor groove

Propeller Twists
Bases that are exposed to minor groove contact with water
They twist in a propeller twist fashion
Results in:
less optimal base pair distance
More optimal base pair stacking (eliminates presence of water
molecules)
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
DNA can undergo reversible strand separation
 Denaturation AND Renaturation of DNA
When duplex DNA molecules are subjected to
conditions of pH, temperature or ionic strength that
disrupt hydrogen bonds, the strands are no longer held
together. The double helix is denatured.
If the temperature is the denaturing agent, the double
helix is said to melt; ENZYMES DRIVE THIS IN THE
CELL.
The phenomenon that the relative absorbance of the
DNA solution at 260 nm increases as the bases
unstack is called hyperchromic shift;
If one follows the absorbance as a function of
temperature, the midpoint temperature of the
absorbance curve is termed melting temperature, Tm.
 Structural Changes in DNA Melting

Denaturation of DNA
Double helix unwinds when DNA is denatured

Can be re-formed with slow cooling and annealing

Denaturation of DNA
Denaturation: disruption of 2
structure
most commonly by heat
denaturation (melting)
as strands separate, absorbance
at 260 nm increases
increase is called hyperchromicity
midpoint of transition (melting)
curve = Tm
the higher the % G-C, the higher
the Tm
renaturation is possible on slow
cooling
DNA - 3 Structure
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.
Topoisomerases
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: a bacterial topoisomerase
Super DNA Coiled Topology
Double helix can be considered to a 2-stranded,
right handed coiled rope

Can undergo positive/negative supercoiling

Supercoiling in Eukaryotic DNA
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
The structure of chromatin

Each Bead is a
nucleosome

Nucleosome consists of:

DNA wrapped around
histone core
A model for chromatin packing in metaphase chromosomes
Organization
of Chromatin
and
Chromosomes:
The solenoid model of condensed chromatin
Nonhistone proteins provide a structural scaffold for long
chromatin loops

View Packing of
DNA to
Chromosomes
Principal Kinds of RNA
RNA
consist of long, unbranched chains of 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 (it is 2-deoxy-D-ribose
in DNA)
the pyrimidine bases are uracil and cytosine (they are
thymine and cytosine in DNA)
in general, RNA is single stranded (DNA is double
stranded)
Significance of Chemical Difference between
DNA and RNA
DNA contains 2-deoxy group instead of 2-OH;
DNA contains thymine instead of uracil;
Thus DNA is more stable than RNA;
RNA occurs in multiple forms and copies;
Messenger RNA codes template for protein synthesis;
Ribosomal RNA constitute the catalytic core of the
ribosome;
Transfer RNA is the adaptor between nucleic acids and
proteins;
Small nuclear RNA are essential component of
spliceosome;
microRNA regulates gene expression.
Information Transfer in Cells
Information encoded
in the nucleotide
sequence of DNA is
transcribed through
RNA synthesis

Sequence then
dictated by DNA
sequence

Central dogma of
biology
RNA
RNA molecules are classified according to their
structure and function
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
Transfer RNA Structures

TyC Loop

Anticodon
V ariable Stem
D Loop
loop

Anticodon Loop
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 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)
Ribosomal RNA

Secondary Structure Tertiary Structure

Of large ribosomal RNA Of large ribosome subunit

Ban et al., Science 289 (905-920), 2000

mRNA
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
single stranded
biosynthesis is directed by information encoded on
DNA
a complementary strand of mRNA is synthesized
along one strand of an unwound DNA, starting from
the 3 end
snRNA
Small nuclear RNA (snRNA) is a recently
discovered RNA

Found in nucleus of eukaryotes

Small (100-200 nucleotides long)

Forms complexes with protein and form small

nuclear ribonucleoprotein particles (snRNPs)

snRNPs help with processing of initial mRNA

transcribed from DNA
RNA as an Enzyme

Self-splicing introns
Large introns (> 200 nucleotides) that are able to splice-out themselves

In bacteria as well as eukaryotes (e.g. pre-RNA of protozoan

Tetrahymena, primary transcripts of the mitochondrial genes of yeast and
plants)

View splicing
 In 1989, Nobel Prize in chemistry has been awarded to Sidney Altman
and Thomas Cech for their discovery that RNA in living cells is not only a
molecule of heredity but also can function as a biocatalyst

S. Altman T. Cech

View RNA folding by Thomas Cech

Addendum: History of DNA

1. Swiss biologist, Friedrich Miescher, isolated DNA from salmon sperm in 1868.
2. In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty showed that
DNA from pathogenic strains of bacterium pneumococcus couls be
transferred into nonpathogenic strains, making them (and any succeeding
generations) pathogenic.
3. Erwin Chargaff reported in 1947 that the quantities of adenine and thymine in
DNA were very close to the same value. Similarly, he observed that cytosine
and guanine were also very close to equal in quantity.
4. In 1952, Alfred Hershey and Martha Chase showed T2 bacteriophage inject
only DNA into cells and this is sufficient to make more T2 bacteriophage.
5. James Watson and Francis Crick proposed the model of the double helix of
DNA in 1953
6. Matthew Meselson and Franklin Stahl demonstrated in 1958 that DNA
replication occurred by a semiconservative mechanism
7. In 1965, Marshall Nirenburg, Philip Leder and others identified the genetic
code.
8. In 1979, an MIT team headed by Alexander Rich reported finding a left-
handed, zig-zagging DNA strand that they named Z-DNA.
Chemical Nature of the Gene: The Watson and Crick Proposal

1. There are 2 chains of nucleotides per molecule.

2. The 2 chains spiral around each other to form a pair of rt-handed helices.
3. The 2 chains composing one double helix run in opposite directions; they
are antiparallel (one is 5->3 and the other 3->5)
4. The sugar-phosphate backbone is located on the outside of the moelcule
with the 2 sets of bases projecting toward the center. The phosphate
groups give the molecule a (-) charge.
5. The bases occupy planes that are approximately perpendicular to the
long axis of the molecule and are stacked one on top of another like a
pile of plates. Hydrophobic interactions and van der Waals forces
between the stacked planar bases provide the stability for the entire DNA
molecule. Together, the helical turns and planar base pairs cause the
molecule to resemble a spiral stair case.
6. The two strands are held together by H-bonds between each base of one
strand and an associated base on the other strand. The H-bonds can be
broken and can become separated during various activities.
Chemical Nature of the Gene: The Watson and Crick Proposal (cont)

7. The distance from the P atom of the backbone to the center of the axis = 1nm,
therefore the width is 2nm.
8. A pyrimidine in one chain is always paired with a purine on the other chain
because of this arrangement, molecule is 2nm wide along its entire length.
9. N are NH2 rather than =NH; O are C=O rather than =C-OH because of these
structural restrictions, A possibel pair only is T and C is G. In Chargaffs rule:
A=T and G C.
10. The spaces between adjacent turns of the helix form 2 grooves; the wider major
groove and the narrow minor groove. Protein binding to DNA often fit these
grooves.
11. A double helix makes one complete turn every 10 residues (3.4nm). Therefore
the distance between base pairs is 0.34nm.
12. The 2 chains are complementary.
The Importance of the Watson and Crick Proposal

Storage of genetic information

As the genetic material, DNA must contain a stored record of
instructions that determine all the heritable characteristics that an
organism exhibits
DNA must contain the information for the specific order of amino acids
in all the proteins that are synthesized by an organism
Self-duplication and inheritance
DNA must contain the information for its own replication
DNA replication allows genetic instructions to be transmitted from one
cell to its daughter cells and from one individual to its offsprings
Expression of genetic message
DNA is more than a storage center but also a director of cellular activity
The information encoded in the DNA has to be expressed in some form
that can take part in events that are taking place within the cell
The information in DNA must be used to direct the order by which
specific amino acids are incorporated into a polypeptide chain