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The Chemical Nature of
DNA
Md. Habibur Rahaman (HbR)
Lecturer
Dept. of Biology & Chemistry
North South University
Characteristics of Genetic Material
The coding instructions of all living organisms are written in the same genetic
language—that of nucleic acids.
The idea that genes are made of nucleic acids was not widely accepted until
after 1950.
Until the structure of DNA was fully elucidated, it wasn’t clear how DNA could
store and transmit genetic information.
Even before nucleic acids were identified as the genetic material, biologists
recognized that, whatever the nature of genetic material, it must possess four
important characteristics.
First
Genetic material must contain complex biological information in
stable form:
•The genetic material must be capable of storing large
amounts of information—instructions for all the traits and
functions of an organism.
•This information must have the capacity to vary, because
different species and even individual members of a species
differ in their genetic makeup.
•At the same time, the genetic material must be stable,
because most alterations to the genetic instructions
(mutations) are likely to be detrimental.
Second
Genetic material must replicate faithfully:
•Genetic material must have the capacity to be copied accurately.
•Every organism begins life as a single cell, which must undergo
billions of cell divisions to produce a complex, multi-cellular creature
like yourself.
•At each cell division, the genetic instructions must be transmitted to
descendent cells with great accuracy.
•When organisms reproduce and pass genes to their progeny, the
coding instructions must be copied with fidelity.
Third
Genetic material must encode phenotype:
•The genetic material (the genotype) must have the capacity to “code
for” (determine) traits (the phenotype).
• The product of a gene is often a protein; so there must be a
mechanism for genetic instructions to be translated into the amino acid
sequence of a protein.
Fourth
Genetic material must be capable of variation:
•This requirement is somewhat contradictory to the first requirement,
which demanded stability of the genetic material.
• There is, in fact, no a priori reason why genetic material should have
built-in provisions for change; one could certainly design a hypothetical
genetic system in which information would be rigidly conserved from
generation to another.
•The dominant theme in the history of life is, however, organic
evolution, and this demands that genetic material be capable of
change, if only infrequently.
The Nature of Genetic Material
Historical Background
• Miescher isolated nuclei from pus (white
blood cells) in 1869
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–
•
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Found a novel phosphorus-bearing substance
and named nuclein
Nuclein is mostly chromatin, a complex of DNA
and chromosomal proteins
End of 19th century – DNA and RNA
separated from proteins
Levene, Jacobs, et al. characterized the
basic composition
Transforming Principle
• Key experiments done by Frederick Griffith
in 1928
• Observed in Streptococcus pneumoniae
• Heat-killed virulent colonies could
transform avirulent colonies of bacteria
Griffith’s Experiment
DNA: The Transforming Material
In 1944 a group used a transformation test
similar to Griffith’s procedure taking care to
define the chemical nature of the
transforming substance
– Techniques used excluded both protein and
RNA as the chemical agent of transformation
– Other treatments verified that DNA is the
chemical agent of transformation of S.
pneumoniae from avirulent to virulent
DNA: The Transforming Material
Avery–MacLeod–McCarty experiment
DNA Confirmation
• In 1940s geneticists doubted use of DNA
as it appeared to be monotonous repeats
of 4 bases
• By 1953 Watson & Crick published the
double-helical model of DNA structure and
Chargaff had shown that the 4 bases were
not present in equal proportions
• Hershey and Chase demonstrated
confirmed that DNA is the genetic material
Hershey-Chase Experiments
The Hershey–Chase
(“blender”) experiment
Summary
• Genes are made of nucleic acid, usually
DNA
• DNA has the hereditary and transforming
activity
Nucleotides
• Nucleotides are the unit structure of
nucleic acids.
• Nucleotides composed of 3
components:
– Nitrogenous base (A, C, G, T or U)
– Pentose sugar
– Phosphate
Nitrogenous bases
• There are 2 types:
– Purines:
• Two ring structure
• Adenine (A) and Guanine (G)
– Pyrimidines:
• Single ring structure
• Cytosine (C) and Thymine (T) or Uracil (U).
Nucleotide bases
Types of Nucleic acids
There are 2 types of nucleic acids:
Deoxy-ribonucleic acid (DNA)
•
•
Pentose Sugar is deoxyribose (no OH at 2’ position)
Bases are Purines (A, G) and Pyrimidine (C, T).
Ribonucleic acid (RNA)
•
•
Pentose Sugar is Ribose.
Bases are Purines (A, G) and Pyrimidines (C, U).
Linear Polymerization of Nucleotides
• Nucleic acids are formed of
nucleotide polymers.
• Nucleotides polymerize together
by phospho-diester bonds via
condensation reaction.
• The phospho-diester bond is
formed between:
– Hydroxyl (OH) group of the
sugar of one nucleotide.
– Phosphate group of other
nucleotide
Polymerization of Nucleotides
• The formed polynucleotide chain
is formed of:
– Negative (-ve) charged SugarPhosphate backbone.
• Free 5’ phosphate on one end
(5’ end)
• Free 3’ hydroxyl on other end
(3’ end)
– Nitrogenous bases are not in the
backbone
• Attached to the backbone
• Free to pair with nitrogenous
bases of other polynucleotide
chain
Polymerization of Nucleotides
• Nucleic acids are polymers of nucleotides.
• The nucleotides formed of purine or pyrimedine
bases linked to phosphorylated sugars (nucleotide
back bone).
• The bases are linked to the pentose sugar to form
Nucleoside.
• The nucleotides contain one phosphate group linked
to the 5’ carbon of the nucleoside.
Nucleotide = Nucleoside + Phosphate group
Polymerization of Nucleotides
• The polymerization of nucleotides to form
nucleic acids occur by condensation
reaction by making phospho-diester bond
between 5’-phosphate group of one
nucleotide and 3’-hydroxyl group of another
nucleotide.
• Polynucleotide chains are always
synthesized in the 5’ to 3’ direction, with a
free nucleotide being added to the 3’ OH
group of a growing chain.
Complementary base pairing
• It is the most important structural feature of
nucleic acids
• It connects bases of one polynucleotide
chain (nucleotide polymer) with
complementary bases of other chain
• Complementary bases are bonded together
via:
– Double hydrogen bond between A and T (DNA), A
and U (RNA) (A═T or A═U)
– Triple H-bond between G and C in both DNA or
RNA (G≡C)
Base pairing
Significance of complementary
base pairing
• The importance of such complementary base
pairing is that each strand of DNA can act as
template to direct the synthesis of other strand
similar to its complementary one.
• Thus nucleic acids are uniquely capable of
directing their own self replication.
• The diameter of the helix could only be kept
constant at about 2 nm or 20 Å if one purine and
one pyrimidine base made up each stair/rung
Summary
• DNA and RNA are chain-like molecules
composed of subunits called nucleotides
• Nucleotides contain a base linked to the
1’-position of a sugar and a phosphate
group at 5’-position
• The two polynucleotide strands run in
opposite directions—they are antiparallel
DNA Structure
The Double Helix
Rosalind Franklin’s x-ray data suggested that DNA
had a helical shape
The data also indicated a regular, repeating
structure
Watson and Crick proposed a double helix with
sugar-phosphate backbones on the outside and
bases aligned to the interior
DNA Helix
• Structure compared to a
twisted ladder
– Curving sides of the ladder
represent the sugarphosphate backbone
– Ladder rungs are the base
pairs
– There are about 10 base
pairs per turn
• Arrows indicate that the
two strands are
antiparallel
Forms of DNA
1- B-form helix:
It is the most common form of DNA in cells.
• Right-handed helix
• Turn every 3.4 nm.
• Each turn contain 10 base pairs (the distance between each 2
successive bases is 0.34 nm)
Minor groove
Contain 2 grooves;
•
•
Major groove (wide): provide easy access to bases
Minor groove (narrow): provide poor access.
Minor groove
Major groove
2- A-form DNA:
– Less common form of DNA , more common in
RNA
• Right handed helix
• Each turn contain 11 bp/turn
• Contain 2 different grooves:
– Major groove: very deep and narrow
– Minor groove: very shallow and wide (binding site for RNA)
Minor groove
3- Z-form DNA:

Radical change of B-form
 Left handed helix, very extended
 It is GC rich DNA regions.
 The sugar base backbone form Zig-Zag shape
 The B to Z transition of DNA molecule may play a role in
gene regulation.
Minor groove
Major groove
Major and Minor Grooves (Side view)
The major groove occurs where the backbones are far apart, the minor
groove occurs where they are close together.
The major and minor grooves are opposite each other, and each runs continuously
along the entire length of the DNA molecule.
Major and Minor Grooves
(other view)
obtuse angle
acute angle
Significance of Major and Minor Grooves
• Most sequence specific DNA-binding proteins (regulatory
proteins) bind DNA via major groove
• Major grooves primarily help in transcription (serve as
recognition sites for transcription initiation factors,
promote DNA strand separation)
• Minor grooves are thought to accommodate smaller
molecules, intercalators (e.g., anti-cancer drugs, nonprotein ligands) to stop DNA replication (non-sequence
specific binding, so has a global effect as expected)
RNA as Genetic Material
Fraenkal-Conrat and Singer’s experiment
Physical Chemistry of Nucleic
Acids
DNA and RNA molecules can appear in
several different structural variants
– Changes in relative humidity will cause
variation in DNA molecular structure
– The twist of the DNA molecule is normally
shown to be right-handed, but left-handed
DNA was identified in 1979
Variation in DNA between
Organisms
• Ratios of G to C and A to
T are fixed in any specific
organism
• The total percentage of G
+ C varies over a range
to 22 to 73%
• Such differences are
reflected by differences in
physical properties
• Higher GC content
correlates with increased
thermo-tolerance
DNA Melting
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•
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With heating, non-covalent forces holding DNA strands together weaken
and break
When the forces break, the two strands come apart in denaturation or
melting
Temperature at which DNA strands are ½ denatured is the melting
temperature or Tm
GC content of DNA has a significant effect on Tm with higher GC content
meaning higher Tm
Melted DNA absorbs more UV light than double-helical DNA
Summary
• GC content of a natural DNA can vary from less
than 25% to almost 75%
• GC content has a strong effect on physical
properties that increase linearly with GC content
– Melting temperature, the temperature at which the
two strands are half-dissociated or denatured
– Density
– Low ionic strength, high pH and organic solvents also
promote DNA denaturation
DNA Renaturation
• After two DNA strands separate, under proper
conditions the strands can come back together
• Process is called annealing or renaturation
• Three most important factors:
– Temperature – best at about 25C below Tm
– DNA Concentration – within limits higher
concentration better likelihood that 2 complementary
will find each other
– Renaturation Time – as increase time, more
annealing will occur
Polynucleotide Chain
Hybridization
Hybridization is a process of
putting together a
combination of two different
nucleic acids
– Strands could be 1 DNA and
1 RNA
– Also could be 2 DNA with
complementary or nearly
complementary sequences
DNA Sizes
DNA size is expressed in 3 different ways:
– Number of base pairs
– Molecular weight – 660 g/mol/base pair
– Length – 33.2 Å per helical turn of 10.4 base
pairs
Measure DNA size either using electron
microscopy or gel electrophoresis
DNAs of Various Sizes and
Shapes
• Phage DNA is typically circular
• Some DNA will be linear
• Supercoiled DNA coils or wraps around itself like
a twisted rubber band
Summary
• Natural DNAs come in sizes ranging from
several kilobases to thousands of
megabases
• The size of a small DNA can be estimated
by electron microscopy
• This technique can also reveal whether a
DNA is circular or linear and whether it is
supercoiled
DNA Size VS Genetic Capacity
How does one know how many genes are in
a particular piece of DNA?
– Can’t determine from DNA size alone
– Factors include:
• How DNA is devoted to genes?
• What is the space between genes?
– Can estimate the upper limit of number genes
a piece of DNA can hold
DNA Size and Genetic Capacity
How many genes are in a piece of DNA?
– Start with basic assumptions
• Gene encodes protein
• Protein is abut 40,000 Da
– How many amino acids does this represent?
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Average mass of an amino acid is about 110 Da
Average protein – 40,000 / 110 = 364 amino acids
Each amino acid = 1 codon= 3 DNA base pairs
364 amino acids requires 1092 base pairs
I Da = 1 g/mol
DNA size and Genetic Capacity
How large is an average piece of DNA?
– E. coli chromosome
• 4.6 x 106 bp
• ~4200 proteins
– Phage l (infects E. coli)
• 4.85 x 104 bp
• ~44 proteins
– Phage x174 (one of smallest)
• 5375 bp
• ~5 proteins
C-Value Paradox
• C-value is the DNA content per haploid cell
• We would expect that, the more complex the
organism, the more DNA is needed to “run it” (larger
C-value)
• Therefore, we would expect a linear relationship
between genome size and organism complexity
• Bacteria have smaller genomes than eukaryotes,
and viruses have smaller genomes than bacteria
• In larger organisms, relationship breaks down
• Yet the frog has 7 times more DNA per cell than
humans
C-Value Paradox
• The observation that more complex
organisms will not always need more
genes than simple organisms is called the
C-value paradox
• Most likely explanation for the paradox is
that organisms have DNA apparently in
excess of what is needed; repetitive
sequences, “junk DNA”
Summary
• There is a rough correlation between DNA
content and number of genes in a cell or
virus
• This correlation breaks down in several
cases of closely related organisms where
the DNA content per haploid cell (C-value)
varies widely
• C-value paradox is probably explained not
by extra genes, but by extra noncoding
DNA in some organisms
The Tertiary Structure of DNA
Packing DNA into Small Spaces
E. coli, a single molecule of DNA with approximately 4.64 million base pairs
Stretched out straight
1,000 times of the cell
Human cells contain 6 billion base pairs of DNA, 1.8 meters
stretched end to end
The human body collectively contain perhaps 25 billion kilometers of DNA
(the distance from the earth to the sun is only 58 million kilometers).
This much DNA weights only about 200 grams, or less than half a pound,
underscoring how incredibly thin it is.
The Tertiary Structure of DNA
Packing DNA into Small Spaces
DNA can be considered at three hierarchical levels:
Primary structure: the nucleotide sequence
Secondary structure: the double-stranded
helix
Tertiary structure: refers to higher-order
folding that allows DNA to be packed into the
confined space of a cell
Histones Package DNA in Eukaryotes
Histones Package DNA in Eukaryotes
beads on a strig
Histones Package DNA in Eukaryotes
https://www.youtube.com/watch?v=gbSIBhFwQ4s
Palindromic sequence and
Significance
5’–ATCGAT–3’
3’–TAGCTA–5’
ROTATOR
ATOYOTA
DNA methylation and Significance
• In bacteria, adenine and cytosine are commonly methylated,
whereas, in eukaryotes, cytosine is the most commonly
methylated base.
• Bacterial DNA is frequently methylated to distinguish it from
foreign, un-methylated DNA that may be introduced by viruses;
bacteria use proteins called restriction enzymes to cut up any
un-methylated viral DNA (Host-controlled restriction and
modification system).
• In eukaryotic cells, Sequences that are methylated typically
show low levels of transcription while sequences lacking
methylation are actively being transcribed.
Thank You!