Mary K.

Campbell
Shawn O. Farrell
[Link]/

Chapter Nine
Nucleic Acids: How Structure
Conveys Information

Paul D. Adams • University of Arkansas

1

Information Transfer in Cells

•Central dogma of biology –
DNA goes to RNA goes to
protein

•Information encoded in the

nucleotide sequence of DNA is
transcribed through RNA
synthesis and RNA is then
translated to protein

•Protein sequence is dictated by

the DNA sequence via the RNA
sequence

•In this chapter we will look at the

composition and structure of
nucleic acids – DNA and RNA

2
 Nucleic Acids
• Levels of structure Similar to proteins
• 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
• 3°structure: supercoiling
• 4°structure: interaction between DNA and proteins

• Nucleic acid: a biopolymer containing three types of monomer units

• a nucleobase derived from purine or pyrimidine a monosaccharide (pentose
sugar), either D-ribose or 2-deoxy-D-ribose
• phosphoric acid Note the numbering of the
• RNA (Ribonucleic Acid, sugar D-ribose ) carbons on the sugar unit
having the superscript ’
• DNA (Deoxyribonucleic Acid,
sugar 2-deoxy-D-ribose)
Polymerization through
phosphate on 5’C and OH
on 3’C

Pyrimidine/Purine Bases
• The structures of pyrimidine and purine are shown here for comparison

Note that the numbering

of the atoms in the
nitrogenous bases
include the nitrogens and
always start with a
nitrogen. You need to
know the numbering.

PUGA2

Remember PUrines are

Guanine and Adenine
and they have 2 rings

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Nucleosides
• Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose
covalently bonded to a nucleobase by a -N-glycosidic bond

Purine bases always

Pyrimidine bases
linked through N9.
always linked through
N1.

No phosphate No phosphate
group at C5’. group at C5’.

-N-glycosidic -N-glycosidic
bond. bond.

Ribonucleoside Deoxyribonucleoside
has OH group at has no OH group at
C2’ of sugar unit. C2’ of sugar unit.

Names of nitrogenous bases and nucleosides

Structure nitrogenous base Name nitrogenous base Name Nucleoside

Pyrimidine
Cytosine Cytidine

Pyrimidine Thymine Thymidine

(in DNA and
some RNA)

Pyrimidine
Uracil Uridine
(only in RNA)

Purine
Adenine Adenosine

Purine
Guanine Guanosine
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
• Polymerization leads to nucleic acids. Linkage is repeated (3’,5’-
phosphodiester bond)

Ribonucleotide Deoxyribonucleotide

Name based on parent Deoxyribonucleotides

nucleoside (cytidine) with have the prefix
a suffix “monophosphate” “deoxy” added.

Watson and Crick, April 1953

James Watson and Francis Crick
published their proposal for the 1°& 2°
structure of DNA in the journal Nature in
April 1953. The model which they built
from wire was based on the X-ray
diffraction data of Franklin and Wilkins,
which was published in the same issue
of Nature. See the copies of the two
articles on BB.
 DNA - 1° Structure
• Deoxyribonucleic acids, DNA: a
biopolymer that consists of a backbone of
alternating units of 2-deoxy-D-ribose and
-N-glycosidic bonds
phosphate between 2’-deoxyribose
and each base
• 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 DNA  2’-deoxyribose
and not ribose
and T)
• Writing a DNA strand 3’-5’-Phosphodiester
bonds
• abbreviated notations
• p – phosphate; d – deoxy
• pdTpdGpdCpdA or pdTGCA or d(TGCA)
• Or simply TGCA
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DNA - 2° Structure
| ≈ 20 Å (2 nm) diameter |
• Secondary structure: the ordered Inside diameter
arrangement of nucleic acid strands ≈ 11 Å; (1.1 nm)

• the double helix model of DNA

2°structure was proposed by Note base-pairing
James Watson and Francis Crick in Largeduplex groove in
A with T
G with C
1953 (≈ 22 Å; 2.2 nm)

• Double helix: a type of 2° structure ≈ 34 Å; 3.4 nm

of DNA molecules in which two Length of one
complete turn
antiparallel polynucleotide strands Minor groove in (ten base pairs)
are coiled in a right-handed manner (≈ 12duplexÅ; 1.2 nm)
about the same axis
• structure based on X-Ray Note bases are always
perpendicular to the
crystallography axis of the helix Minus signs
represent
• The DNA of which Watson and Crick negatively charged
described the structure was called Two strands phosphate groups.
B-DNA. It is the principle form that have opposite
direction (anti-
occurs in nature parallel)

Make sure that you watch the Remember

animation video describing 10 Å = 1 nm
the structure of DNA

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 Summary – secondary structure of DNA

1. DNA forms a regular

right-hand helix, making a
complete turn every 3.4
nm with a diameter of 2
nm giving 10 nucleotides
per turn.

2. The helix contains 2 anti-

parallel polynucleotide
chains – bases facing
inwards, with a purine
always opposite a
pyrimidine.

3. Proportion of G always
the same as the
proportion of C and the
proportion of T the same
as A.

This was already known when Watson and Crick solved Chargaff's Law: A=T, G=C
the structure of DNA – they used this knowledge.

12

Base Pairing - the key to the double helix

• The major factor stabilizing the double helix is base pairing by hydrogen
bonding between T-A and between G-C
• Base pairing is complimentary
• T-A base pair comprised of 2 hydrogen bonds
• G-C base pair comprised of 3 hydrogen bonds

Adenine Thymine Guanine Cytosine

(two hydrogen bonds) (three hydrogen bonds)

≈ 11 Å; (1.1 nm) The inside

diameter of the double helix
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 Other Forms of DNA
• B-DNA
• considered the physiological form
• a right-handed helix
• 10 base pairs per turn (34Å) 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 B-DNA & A-DNA are right handed helixes
Z-DNA is a left handed helix
With thumb up the fingers of
• may play a role in gene expression With thumb up the fingers of right hand left hand curl in direction of
curl in direction of the helix. the helix.
• Z-DNA occurs in nature, usually
consists of alternating purine-pyrimidine
bases
• Methylated cytosine found in Z-DNA

15

Other Features of DNA

• Base stacking and Propeller-Twist
• bases are hydrophobic and interact by hydrophobic bonding of their
pi-electrons referred to as base stacking
• in standard B-DNA, each base is 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

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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
• Prokaryotic DNA and DNA of many viruses are circular
• 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

We will revisit
topoisomerases and DNA
gyrase in the next chapter
when we look at replication.

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Bacterial DNA

• Prokaryotic DNA is circular.

• The chromosome of E. coli contains
≈ 4.6 million base pairs bacterial
cell
• If stretched out it is 1.57 mm long –
which is 1000 x longer than a cell
• Bacteria also often contain plasmids
– small pieces of extrachromosomal
DNA which are also circular
• All this DNA can only fit into the
bacterial cell, because it is
supercoiled.

Electron micrograph showing chromosomal DNA

and plasmid DNA (indicated by arrows) released
from a bacterial cell.
Super DNA Coiled Topology
• Prokaryotic DNA is circular. It can form supercoils.
• Double helix can be thought of as a 2-stranded, right handed coiled rope
• Can undergo positive/negative supercoiling

If at all possible make sure

that you watch the video on
supercoiling and
topoisomerases.

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Chromatin
Supercoiling in Eukaryotic DNA
•Eukaryotic DNA is linear Make sure that you
watch the animation
•In humans there are 46 pieces called video describing the
chromosomes (23 pairs) consisting of in total packaging of eukaryotic
DNA
3.3 billion base pairs.
Nucleosome
•The total length of human DNA is 2 m
•In order to fit into a cell eukaryotic DNA is Core of eight histone
molecules wrapped
packaged as chromatin with two turns of DNA
forms a bead
•Chromatin consist of DNA molecules wound
around particles of histones in a beadlike
DNA
structure
Single histone
•Histones are proteins, particularly rich in the molecule holds
basic amino acids Lys and Arg found DNA to core

associated with eukaryotic DNA

• five main types: H1, H2A, H2B, H3, H4
•Nucleosomes are the beadlike structures Recent research has
shown that structure and
in chromatin and consist of DNA spacing of nucleosomes
wrapped around histone cores is important in chromatin
function 23
Denaturation of DNA
• Double helix unwinds when DNA is denatured
• Can be re-formed with slow cooling and annealing
When DNA is cooled
hydrogen bonding is
restored and
Heat disrupts hydrogen amazingly correct
bonding between base base pairing is also
pairs. restored.

25

Denaturation of DNA
• Denaturation: disruption of 2° structure Denatured DNA

• most commonly by heat denaturation

Absorbance

(melting)
• DNA absorbs UV light with a peak
at 260 nm Native DNA

• as strands separate, absorbance at

260
260 nm increases Wavelength (nm)

• increase is called hyperchromicity Absorption spectrum of

DNA – change in
absorbance measured
• midpoint of transition in melting with change in
wavelength
curve = Tm
• the higher the % G-C, the higher the Tm,
because there are three hydrogen bonds
between GC pairs and only two between
AT pairs
• renaturation is possible on slow cooling
Melting curve of DNA – change
in absorbance at 260 nm
measured with change in
temperature 26
 27

RNA
• RNA like DNA 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
• In RNA the pentose unit is -D- -N-glycosidic
bonds between
ribose (it is 2-deoxy-D-ribose in ribose and
each base
DNA)
• In RNA the pyrimidine bases are
uracil and cytosine (they are
thymine and cytosine in DNA)
RNA – sugar is ribose
• In general, RNA is single stranded not 2’-deoxyribose as
in DNA
(DNA is double stranded)
3’-5’-Phosphodiester
• The 2’ OH in RNA causes stability bonds
differences and is reason RNA is Uracil in RNA
replaces
usually not double stranded. thymine in DNA

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 Principal kinds of RNA
• RNA molecules are classified according to their structure and function

30

Transfer RNA - tRNA

• tRNA is the smallest kind of the
Amino acid addition sit
three RNAs
• It consists of a single-stranded
polynucleotide chain between
Interacts with the
73-94 nucleotide residues ribosome

• It carries an amino acid at

its 3’ end to the ribosome
• Intramolecular hydrogen
bonding occurs in tRNA
• Less common bases occur
principally, but not exclusively,
in transfer RNAs

If at all possible make sure

that you watch the animation
video describing the structure
of tRNA.
Anticodon region - base
pairs with the codon in the
mRNA transcript.
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 Ribosomal RNA - rRNA
• rRNA is 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)
Prokaryotic rRNA Eukaryotic rRNA

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Structure of the Prokaryotic Ribosome

Dissociation by
lowering Mg2+ to 10–4
M; elevating Mg2+ to
10–2 M is sufficient to
reverse this step

Note that 30S + 50S DOES NOT

equal 80S.
Sedimentation coefficients are not
additive, because they also depend
on shape of particles.

34
 Messenger RNA - mRNA
• mRNA is a ribonucleic acid
that carries coded genetic
information from DNA to
ribosomes for the synthesis
of proteins
• It is present in cells in
relatively small amounts and
very short-lived
• It is single stranded
• Biosynthesis of rRNA 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

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Small nuclear RNA - 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

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