ULBIS, CHRISTINE MARIE HONG (SEAT #36)

3BIOLOGY-6

LEVEL OF STRUCTURE IN NUCLEIC ACIDS

Primary Structure order of bases in
polynucleotide sequence
Secondary Structure it is the threedimensional conformation of the backbone
Tertiary Structure the supercoiling of the
molecule

Two Principal Types of Nucleic Acids:

Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
THE
COVALENT
STRUCTURE
OF
POLYNUCLEOTIDES
Nucleotides monomers of nucleic acids and
consists of three parts:
Nitrogenous Bases nitrogen-containing
aromatic compounds that make up the coding
portion of nucleic acids
o Pyramidine

nitrogen-containing
aromatic compounds that contain a sixmembered ring
Cytosine found in both RNA and
DNA
Thymine substitutes uracil in DNA
Uracil occurs only in RNA
o Purine nitrogen-containing aromatic
compounds that contain a six-membered
ring fused to a five-membered ring
Adenine
Guanine
Adenine
Sugar
Phosphoric Acid Residue
Nucleoside a purine or pyramidine base bonded
to a sugar (ribose or deoxyribose); differs from a
nucleotide by lacking a phosphate group and a base
o Ribonucleoside - a compound formed when
a nucleobase forms a glycosidic bond with Dribose
o Deoxyribonucleoside compound formed
when a nucleobase and B-D-deoxyribose form
glycosidic bond
The glycosidic linkage is from the C-1
carbon of the sugar to the N-1 nitrogen of
pyramidines or to the N-9 nitrogen of
purines.
When phosphoric acid is esterified to one of the
hydroxyl groups of the sugar portion of a
nucleoside, a nucleotide is formed.
A nucleotide is named for the parent nucleoside,
with the suffix monophosphate added.
The position of the phosphate ester is
specified by the number of the carbon atom
at the hydroxyl group to which it is esterified.
Example: adenosine 3-monophosphate
Deoxycytidine 5-monophosphate

The linkage between monomers in nucleic acids

involves formation of two ester bonds by
phosphoric acid.
The hydroxyl groups to which the phosphoric acid
is esterified are those bonded to the 3 and 5
carbons on adjacent residues. The resulting
repeated linkage is a 3, 5-phosphodiester bond.
The nucleotide residues of nucleic acids are
numbered from the 5 end, which normally
carries a phosphate group, to the 3 end, which
normally has a free hydroxyl group.
3, 5-phosphodiester bond a covalent
linkage in which phosphoric acid is
esterified to the 3 hydroxyl of one
nucleoside and the 5 hydroxyl of another
nucleoside; forms the backbone of nucleic
acids

THE STRUCTURE OF DNA

Double Helix two polynucleotide chains wrapped
around each other; it is the fundamental structural
motif of DNA
DNA consists of two polynucleotide chains
wrapped around each other to form a helix.
Hydrogen bonds between bases on
opposite chains determine the alignment of
the helix, with the paired bases lying in
planes perpendicular to the helix axis.
Sugar-phosphate backbone is outer part of
helix.
The chains run in anti-parallel directions,
one 3 to 5 and the other 5 to 3.
Base pairing is complementary meaning that
adenine pairs with thymine and that guanine
pairs with cytosine.
Because complementary base pairing
occurs along the entire double-helix, the
two chains are also referred to as
complementary strands.
The outside diameter of the helix is 20 A (2
nm). The length of one complete turn of the
helix along its axis is 34 A (3.4 nm) and
contains 10 base pairs.
The atoms that make up the two polynucleotide
chains of the double helix do not completely fill
an imaginary cylinder; instead, they leave
empty spaces known as grooves at which drugs
or polypeptides bind to DNA.
Major Groove the larger of the two
empty spaces in an imaginary cylinder
that encloses the DNA double helix
Minor Groove the smaller of the two
empty spaces in an imaginary cylinder
that encloses the DNA double helix
At neural, physiological pH, each phosphate
group of the backbone carries a negative
charge.
Positively charged ions, such as Na+ and
Mg2+, and polypeptides with positively
charged side chains must be associated
with DNA in order to neutralize the
negative charges.

Conformations of Double Helix

o B-DNA most common form of the DNA
double helix
o A-DNA form of DNA double helix
characterized by having fewer residues per
turn and major and minor grooves with
dimensions that are more similar to each
other than those of B-DNA
It has 11 base pairs for each turn of the
helix.
Its base pairs are not perpendicular to
the helix axis but lie at an angle of
about 20o to the perpendicular.
o Z-DNA form of DNA that is left-handed helix,
which occur naturally, most often when there
is a sequence of alternating DNA
It is produced by flipping one side of the
backbone 180o without having to break
either the backbone or the hydrogen
bonding of the complementary bases.
Name is from the zigzag look of
phosphodiester backbone when viewed
from the side.

that

The ring portions of the DNA bases are very

hydrophobic and interact with each other via
hydrophobic
bonding
(can
der
Waals
interactions) of their pi-cloud electrons. This
process is usually referred to as base stacking,
and even single-stranded DNA tends to form
structures in which the bases stack.
Base stacking interactions between bases
are next to each other in a
DNA chain
In standard B-DNA, each base pair is rotated 32o
with respect to the preceding one. This form is
perfect for maximal base pairing, but it is not
optimal for maximal overlap of the bases. In
addition, the edges of the bases that are
exposed to the minor groove must come in
contact with water in this form.
Many of the bases twist in a characteristic way,
called propeller twist. In this form, the basepairing distances are less optimal, but the base
stacking is more optimal, and water is
eliminated from the minor-groove contacts with
the bases.

Prokaryotic DNA Supercoiling

Prokaryotic DNA is circular and this DNA forms
supercoils (extra twistsover and above those of
the double helixin closed circular DNA).
Negative Supercoils circular DNA with
fewer than the normal number of turns of
the helix.
The strands are underwound and
introduces a torsional stress that
favors unwinding of the right-handed
B-DNA double helix.
Positive Supercoils circular DNA with
more than the normal number of turns of
the helix

They consist of overwound strands

and overwinds right-handed B-DNA
double helix
Both form of supercoiling compact the DNA.
Naturally occurring circular DNA is negatively
supercoiled except during replication, when it
becomes positively supercoiled.
Enzymes that are involved in changing the
supercoiled
state
of
DNA
are
called
topoisomerases. They relax supercoiling in
closed circular DNA.
Class I Topoisomerases cut the
phosphodiester backbone of one strand of
DNA, pass the other end through, and then
reseal the backbone.
Class II Topoisomerases cut both strands
of DNA, pass some of the remaining DNA
helix between the cut ends, and then reseal
DNA gyrase is a bacterial topoisomerase that
introduces negative supercoils into closed
circular DNA.

Eukaryotic DNA Supercoiling

Eukaryotic DNA is complexed with a number of
proteins, especially with basic proteins that
have abundant positively charged side chains at
physiological (neutral) pH.
Electrostatic attraction between the negatively
charged phosphate groups on the DNA and the
positively charged groups on the proteins favor
the formation of complexes. The resulting
material is called chromatin. Thus, topological
changes induced by supercoiling must be
accommodated by histone-protein component
of chromatin.
Chromatin a complex of DNA and protein
found
in eukaryotic nuclei
Histones - basic proteins found complexed
to
eukaryotic DNA
Five main types: H1, H2A, H2B, H3,
and H4
All types contain large numbers of
basic amino acid residues such as
lysine and arginine.
The H1 protein is easy to remove
from chromatin, but disassociating
the other histones from the complex
is more difficult.
In
electron
micrographs,
the chromatin
resembles beads on a string.
o Nucleosome the bead on a string; it is
a globular structure in chromatin in which
DNA is wrapped around an aggregate of
histone molecule
The protein core is an octamer,
which includes two molecules of
each histone but H1.
The composition of the octamer is
(H2A)2(H2B)2(H3)2(H4)2.

Space Regions string portions and

consist of DNA complexed to some H1
histone and nonhistone proteins
As the DNA coils around the histones in the
nucleosome, about 150 base pairs are in
contact with the proteins; the spacer region is
about 30 to 50 base pairs long.
Histones can be modified by acetylation,
methylation,
phosphorylation,
and
ubiquitinylation.
Ubiquitin is a protein involved in the
degradation of other proteins.
Modifying histones changes their DNA and
protein-binding characteristics, and how these
changes affect transcription and replication is a
subject of active research.
o

However, the stacking of the bases in the

native conformation of DNA contributes
the largest part of the stabilization
energy.
Energy must be added to a sample of
DNA to break the hydrogen bonds and to
disrupt the stacking interactions.
This is usually carried out by heating the
DNA in solution.

Melting heat denaturation of DNA; this can be

monitored
experimentally
by
observing
the
absorption of UV light
The bases absorb light in the 260-nmwavelength region.
Hyperchromicity as the DNA is heated and the
strands separate, the wavelength of absorption does
not change, but the amount of light absorbed
increases
This is based on the fact that the bases,
which are stacked on top of one another in
native DNA, becomes unstacked as the DNA
is denatured.

DENATURATION OF DNA
Hydrogen bonds between the base pairs are an
important factor in holding the double helix
together.
The
amount
of
stabilizing
energy
associated with the hydrogen bonds is not
great, but the hydrogen bonds hold the
two polynucleotide chains in the proper
alignment.
PRINCIPAL KINDS OF RNA AND THEIR
STRUCTURES
A sequence of three bases in mRNA directs the
Various kunds of RNA participate in the
incorporation of a particular amino acid into a
synthesis of protens in a series of reactions
growing protein chain.
ultimately directed by the base sequence of the
In prokaryotes, there is no nuclear
cells DNA.
membrane, so mRNA can direct the
Six kinds of RNA:
synthesis of proteins while it is still
being transcribed
transfer RNA (tRNA)
Eukaryotic mRNA, on the other hand,
ribosomal RNA (rRNA)
undergoes considerable processing. One
messenger RNA (mRNA)
of the most important parts of the
small nuclear RNA (snRNA)
process is splicing out intervening
micro RNA (miRNA)
sequences (introns), so that the parts of
small interfering RNA (siRNA)
the mRNA that will be expressed (exons)
The base sequences of all types of RNA are
are contiguous to each other.
determined by that of DNA.
Small nuclear RNAs are found only in the
The process by which the order of bases is
nucleus of eukaryotic cells, and they are distinct
passed
from
DNA
to
RNA
is
called
from the other RNA types. They are involved in
transcription.
processing of initial mRNA transcription
Ribosomes, in which rRNA is associated with
products to a mature form suitable for export
proteins, are the sites for assembly of the
from the nucleus to the cytoplasm for
growing polypeptide chain in protein synthesis.
translation.
Amino acids are brought to the assembly
Micro RNAs and small interfering RNAs are the
site covalently bonded to tRNA as
most recent discoveries.
aminoacyl-tRNAs.
SiRNAs are the main players in RNA
The order of bases in mRNA specifies the
interference (RNAi), a process that was first
order of amino acids in the growing
discovered in plants and later in mammals,
protein; this process is called translation
including humans.
of the genetic message.
RNA interference (RNAi) process where
Translation the process of protein
short
synthesis in which the amino acid
pieces of RNA affect gene expression
sequence of the protein reflects the
sequence of bases in the gene that
codes for that protein
Roles of Different Kinds of RNA
RNA Type
Size
Function

Transfer RNA

Small

Transports amino acids to site of protein synthesis

Ribosomal RNA

Several kindsvariable in
size

Combines with proteins to form ribosomes, the site of

protein synthesis

Messenger RNA
Small nuclear RNA
Small
RNA

interfering

Micro RNA

Directs amino acid sequence of proteins

Variable
Small

Processes initial mRNA to its mature form in eukaryotes

Small

Affects gene expression; used by scientists to knock out a

gene being studied

Small

Affects gene
development

expression;

important

in

growth

and